mason/breeders_toolbox/drone_imagery/drone_imagery_analysis.mas

   1 <%args>
   2 </%args>
   3
   4 <!--button class='btn btn-success' style='margin:3px;float:right' id='drone_imagery_calculate_statistics_link'>Drone Imagery Statistics</button-->
   5
   6 <div class="modal fade" id="drone_imagery_calculate_statistics_dialog" name="drone_imagery_calculate_statistics_dialog" tabindex="-1" role="dialog" aria-labelledby="droneImageryCalculateStatisticsDialog" data-backdrop="static">
   7   <div class="modal-dialog modal-xl" role="document">
   8     <div class="modal-content">
   9       <div class="modal-header">
  10         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
  11         <h4 class="modal-title" id="droneImageryCalculateStatisticsDialog">Calculate statistics on aerial image phenotypes</h4>
  12       </div>
  13       <div class="modal-body">
  14         <div class="container-fluid">
  15
  16             <&| /util/workflow.mas, id=> "drone_imagery_calculate_statistics_workflow" &>
  17                 <&| /util/workflow.mas:step, title=> "Intro" &>
  18                     <& /page/page_title.mas, title=>"Select the type of analysis to perform" &>
  19                     <center>
  20                     <button class="btn btn-default" id="drone_imagery_calculate_statistics_intro_single_trial_select_step">Single Trial Field Analysis</button>
  21                     </center>
  22                     <br/>
  23                     <!--center>
  24                     <button class="btn btn-default" id="drone_imagery_calculate_statistics_intro_single_trial_multiseason_select_step">Single Trial Multi-Season Field Analysis</button>
  25                     </center-->
  26                 </&>
  27                 <&| /util/workflow.mas:step, title=> "Field Trial" &>
  28                     <& /page/page_title.mas, title=>"Select the field trial you are interested in. Select only one." &>
  29                     <br/><br/>
  30                     <form class="form-horizontal">
  31                         <div class="form-group">
  32                             <label class="col-sm-3 control-label">Field Trial(s): </label>
  33                             <div class="col-sm-9" >
  34                                 <div id="drone_imagery_calculate_statistics_trial_select_div"></div>
  35                             </div>
  36                         </div>
  37                     </form>
  38                     <center>
  39                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_field_trial_select_step">Go to Next Step</button>
  40                     </center>
  41                 </&>
  42                 <&| /util/workflow.mas:step, title=> "Trait Selection" &>
  43                     <& /page/page_title.mas, title=>"Select the observation variable(s) you are interested in" &>
  44                     <br/><br/>
  45                     <form class="form-horizontal">
  46                         <div class="form-group">
  47                             <label class="col-sm-3 control-label">Observation Variable Type: </label>
  48                             <div class="col-sm-9" >
  49                                 <select class="form-control" id="drone_imagery_calculate_statistics_select_observation_variable_type">
  50                                     <option value="time_ontology">Time Series</option>
  51                                     <option value="">Single Trait</option>
  52                                 </select>
  53                             </div>
  54                         </div>
  55                         <div class="form-group">
  56                             <label class="col-sm-3 control-label">Observation Variables Phenotyped in the Selected Field Trial: </label>
  57                             <div class="col-sm-9" >
  58                                 <div id="drone_imagery_calculate_statistics_trait_select_div"></div>
  59                             </div>
  60                         </div>
  61                     </form>
  62                     <center>
  63                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_trait_select_step">Go to Next Step</button>
  64                     </center>
  65                 </&>
  66                 <&| /util/workflow.mas:step, title=> "Statistics" &>
  67                     <& /page/page_title.mas, title=>"Select statistics to calculate" &>
  68
  69                     <select class="form-control" id="drone_imagery_calculate_statistics_select_input">
  70                         <option value="">Select A Model</option>
  71                         <!--option value="lmer_germplasmname_replicate">LMER BLUPs y~replicate+1|Germplasm. Univariate genetic effects</option-->
  72
  73                         <option value="sommer_grm_genetic_blups">Sommer GBLUPs Y~replicate+GRM. Multivariate genetic effects using GRM</option>
  74                         <option value="sommer_grm_spatial_genetic_blups">Sommer Spatial GBLUPs Y~replicate+GRM+spatial. Multivariate genetic + 2Dspl spatial effects</option>
  75
  76                         <!--option value="blupf90_grm_random_regression_dap_blups">BLUPf90 GBLUPs Y~replicate+GRM+temporal random regression using days after planting. Multivariate genetic + permanent environment effects</option>
  77                         <option value="blupf90_grm_random_regression_gdd_blups">BLUPf90 GBLUPs Y~replicate+GRM+temporal random regression using growing degree days. Multivariate genetic + permanent environment effects</option-->
  78
  79                         <option value="airemlf90_grm_random_regression_dap_blups">AIREMLf90 GBLUPs Y~replicate+GRM+temporal random regression using days after planting. Multivariate genetic + permanent environment effects</option>
  80                         <option value="airemlf90_grm_random_regression_gdd_blups">AIREMLf90 GBLUPs Y~replicate+GRM+temporal random regression using growing degree days. Multivariate genetic + permanent environment effects</option>
  81
  82                         <!--option value="sommer_grm_temporal_random_regression_dap_genetic_blups">Sommer Temporal Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic + permanent environment effects using days after planting</option>
  83                         <option value="sommer_grm_temporal_random_regression_gdd_genetic_blups">Sommer Temporal Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic + permanent environment effects using growing degree days</option>
  84                         <option value="sommer_grm_genetic_only_random_regression_dap_genetic_blups">Sommer Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic effects using days after planting</option>
  85                         <option value="sommer_grm_genetic_only_random_regression_gdd_genetic_blups">Sommer Random Regression GBLUPs Y~replicate+GRM+LegendrePoly. Multivariate genetic effects using growing degree days</option-->
  86
  87                         <!--option value="marss_germplasmname_block">MARSS prediction for each germplasm</option-->
  88                     </select>
  89
  90                     <div id="drone_imagery_calculate_statistics_relationship_matrix_type_div" style="display:none">
  91                         <hr>
  92                         <div class="form-horizontal">
  93                             <div class="form-group">
  94                                 <label class="col-sm-3 control-label">Relationship Matrix Type: </label>
  95                                 <div class="col-sm-9" >
  96                                     <select class="form-control" id="drone_imagery_calculate_statistics_relationship_matrix_type_select_div">
  97                                         <option value="">Identity</option>
  98                                         <option value="htp_phenotypes">High-throughput Phenotyping Data</option>
  99                                         <option value="genotypes">Genotyping Data</option>
 100                                     </select>
 101                                 </div>
 102                             </div>
 103                         </div>
 104                     </div>
 105
 106                     <div id="drone_imagery_calculate_statistics_genotyping_protocol_div" class="well well-sm" style="display:none">
 107                         <div class="form-horizontal">
 108                             <div class="form-group">
 109                                 <label class="col-sm-3 control-label">Genotyping Protocol To Calculate Genomic Relationship Matrix (optional. If none selected, an identity matrix is used): </label>
 110                                 <div class="col-sm-9" >
 111                                     <div id="drone_imagery_calculate_statistics_genotyping_protocol_select_div"></div>
 112                                 </div>
 113                             </div>
 114                             <div class="form-group">
 115                                 <label class="col-sm-3 control-label">Compute Genotypes From Parents: </label>
 116                                 <div class="col-sm-9" >
 117                                     <select class="form-control" id="drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select">
 118                                         <option value="no">No</option>
 119                                         <option value="yes">Yes</option>
 120                                     </select>
 121                                 </div>
 122                             </div>
 123                             <div class="form-group" id="drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select_div" style="display:none">
 124                                 <label class="col-sm-3 control-label">Use Parental Relationship Matrices: </label>
 125                                 <div class="col-sm-9" >
 126                                     <select class="form-control" id="drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select">
 127                                         <option value="no">No</option>
 128                                         <option value="yes">Yes</option>
 129                                     </select>
 130                                 </div>
 131                             </div>
 132                             <div class="form-group" id="drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select_div" style="display:none">
 133                                 <label class="col-sm-3 control-label">Include Pedigree Info Into Relationship Matrix: </label>
 134                                 <div class="col-sm-9" >
 135                                     <select class="form-control" id="drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select">
 136                                         <option value="no">No</option>
 137                                         <option value="yes">Yes</option>
 138                                     </select>
 139                                 </div>
 140                             </div>
 141                         </div>
 142                     </div>
 143
 144                     <div id="drone_imagery_calculate_statistics_htp_phenotypes_rel_matrix_div" class="well well-sm" style="display:none">
 145                         <div class="form-horizontal">
 146                             <div class="form-group">
 147                                 <label class="col-sm-3 control-label">How to calculate the relationship matrix with high-throughput phenotypes: </label>
 148                                 <div class="col-sm-9" >
 149                                     <select class="form-control" id="drone_image_calculate_statistics_htp_phenotypes_rel_matrix_select">
 150                                         <option value="correlations">Correlations</option>
 151                                         <option value="blues">BLUEs</option>
 152                                     </select>
 153                                 </div>
 154                             </div>
 155                             <div class="form-group">
 156                                 <label class="col-sm-3 control-label">Time Points to Use: </label>
 157                                 <div class="col-sm-9" >
 158                                     <select class="form-control" id="drone_image_calculate_statistics_htp_phenotypes_rel_matrix_times_select">
 159                                         <option value="all">All Available</option>
 160                                         <option value="latest_trait">Up to the latest date selected in traits</option>
 161                                         <option value="vegetative" disabled>Vegetative Growth Stage</option>
 162                                         <option value="reproductive" disabled>Reproductive Growth Stage</option>
 163                                         <option value="mature" disabled>Mature Growth Stage</option>
 164                                     </select>
 165                                 </div>
 166                             </div>
 167                             <div class="form-group" id="drone_image_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select_div" style="display:none">
 168                                 <label class="col-sm-3 control-label">HTP BLUEs Inversion Tolerance: </label>
 169                                 <div class="col-sm-9" >
 170                                     <select class="form-control" id="drone_image_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select">
 171                                         <option value="0.00001">0.00001</option>
 172                                         <option value="0.0001">0.0001</option>
 173                                         <option value="0.001">0.001</option>
 174                                         <option value="0.01">0.01</option>
 175                                         <option value="0.1">0.1</option>
 176                                         <option value="0.5">0.5</option>
 177                                     </select>
 178                                 </div>
 179                             </div>
 180                         </div>
 181                     </div>
 182
 183                     <div id="drone_image_calculate_statistics_use_area_under_curve_select_div" style="display:none">
 184                         <hr>
 185                         <div class="form-horizontal">
 186                             <div class="form-group">
 187                                 <label class="col-sm-3 control-label">Use Cumulative Area-Under-Curve Phenotype in Analysis: </label>
 188                                 <div class="col-sm-9" >
 189                                     <select class="form-control" id="drone_image_calculate_statistics_use_area_under_curve_select">
 190                                         <option value="no">No</option>
 191                                         <option value="yes">Yes</option>
 192                                     </select>
 193                                 </div>
 194                             </div>
 195                         </div>
 196                     </div>
 197
 198                     <div id="drone_image_calculate_statistics_inversion_tolerance_select_div" style="display:none">
 199                         <hr>
 200                         <div class="form-horizontal">
 201                             <div class="form-group">
 202                                 <label class="col-sm-3 control-label">Inversion Tolerance: </label>
 203                                 <div class="col-sm-9" >
 204                                     <select class="form-control" id="drone_image_calculate_statistics_tolparinv_select">
 205                                         <option value="0.000001">0.000001</option>
 206                                         <option value="0.00001">0.00001</option>
 207                                         <option value="0.0001">0.0001</option>
 208                                         <option value="0.001">0.001</option>
 209                                         <option value="0.01">0.01</option>
 210                                         <option value="0.05">0.05</option>
 211                                         <option value="0.08">0.08</option>
 212                                         <option value="0.1">0.1</option>
 213                                         <option value="0.2">0.2</option>
 214                                         <option value="0.5">0.5</option>
 215                                     </select>
 216                                 </div>
 217                             </div>
 218                         </div>
 219                     </div>
 220
 221                     <div id="drone_imagery_calculate_statistics_legendre_polynomial_div" style="display:none">
 222                         <hr>
 223                         <div class="form-horizontal">
 224                             <div class="form-group">
 225                                 <label class="col-sm-3 control-label">Legendre Polynomial Order: </label>
 226                                 <div class="col-sm-9" >
 227                                     <select class="form-control" id="drone_image_calculate_statistics_legendre_order_number_select">
 228                                         <option value="1">1</option>
 229                                         <option value="2">2</option>
 230                                         <option value="3">3</option>
 231                                         <option value="4">4</option>
 232                                         <option value="5">5</option>
 233                                     </select>
 234                                 </div>
 235                             </div>
 236                         </div>
 237                     </div>
 238
 239                     <div id="drone_imagery_calculate_statistics_marss_div" style="display:none">
 240                         $$x_t = Bx_{t-1} + u + w_t\\ w_t \sim MVN(0,Q)\\ y_t = Zx_t + a + v_t\\ v_t \sim MVN(0,R)\\ x_0 \sim MVN(\pi, \Lambda)$$
 241                         <hr>
 242                         <select class="form-control" id="drone_imagery_calculate_statistics_select_marss" name="drone_imagery_calculate_statistics_select_marss">
 243                             <option value="marss_predict_last_time_point">Predict Last Time Point</option>
 244                             <option value="marss_predict_last_two_time_points">Predict Last Two Time Point</option>
 245                         </select>
 246                     </div>
 247
 248                     <div id="drone_imagery_calculate_statistics_permanent_env_structure_div" style="display:none">
 249                         <hr>
 250                         <div class="form-horizontal">
 251                             <div class="form-group">
 252                                 <label class="col-sm-3 control-label">Permanent Environment Structure: </label>
 253                                 <div class="col-sm-9" >
 254                                     <select class="form-control" id="drone_image_calculate_statistics_permanent_env_structure_select">
 255                                         <option value="identity">Identity Matrix</option>
 256                                         <option value="phenotype_correlation">Phenotype Correlation Matrix</option>
 257                                         <option value="euclidean_rows_and_columns">Euclidean Distance From Rows and Columns Matrix</option>
 258                                     </select>
 259                                 </div>
 260                             </div>
 261                         </div>
 262
 263                         <div id="drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_div" style="display:none">
 264                             <div class="form-horizontal">
 265                                 <div class="form-group">
 266                                     <label class="col-sm-3 control-label">Phenotypes For Correlation Matrix: </label>
 267                                     <div class="col-sm-9" >
 268                                         <div id="drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_select_div"></div>
 269                                     </div>
 270                                 </div>
 271                             </div>
 272                         </div>
 273
 274                     </div>
 275
 276                     <br/><br/>
 277                     <center>
 278                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_select_step">Submit</button>
 279                     </center>
 280                 </&>
 281                 <&| /util/workflow.mas:step, title=> "Results" &>
 282                     <& /page/page_title.mas, title=>"Statistics results" &>
 283
 284                     <hr>
 285                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual" style="display:none">Go To Save Analysis Results For Genetic and Environment BLUPS and Residuals</button>
 286                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_analysis_save_blups_genetic" style="display:none">Go To Save Analysis Results For Genetic BLUPS</button>
 287                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_analysis_save_blups_spatial" style="display:none">Go To Save Analysis Results For Spatial BLUPS</button>
 288                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_analysis_save_blups_pe" style="display:none">Go To Save Analysis Results For Permanent Environmental BLUPS</button>
 289                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_analysis_save_residuals" style="display:none">Go To Save Analysis Results For Residuals</button>
 290                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_analysis_save_fitted" style="display:none">Go To Save Analysis Results For Fitted Values</button>
 291                     <hr>
 292
 293                     <div id ="drone_imagery_calculate_statistics_result_div">
 294                     </div>
 295                 </&>
 296             </&>
 297
 298         </div>
 299
 300       </div>
 301       <div class="modal-footer">
 302         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 303       </div>
 304     </div>
 305   </div>
 306 </div>
 307
 308 <div class="modal fade" id="drone_imagery_calculate_statistics_single_trial_multiseason_dialog" name="drone_imagery_calculate_statistics_single_trial_multiseason_dialog" tabindex="-1" role="dialog" aria-labelledby="droneImageryCalculateStatisticsSingleTrialMultiSeasonDialog" data-backdrop="static">
 309   <div class="modal-dialog modal-xl" role="document">
 310     <div class="modal-content">
 311       <div class="modal-header">
 312         <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
 313         <h4 class="modal-title" id="droneImageryCalculateStatisticsSingleTrialMultiSeasonDialog">Calculate statistics on aerial image phenotypes</h4>
 314       </div>
 315       <div class="modal-body">
 316         <div class="container-fluid">
 317
 318             <&| /util/workflow.mas, id=> "drone_imagery_calculate_statistics_single_trial_multiseason_workflow" &>
 319                 <&| /util/workflow.mas:step, title=> "Field Trial" &>
 320                     <& /page/page_title.mas, title=>"Select the field trial you are interested in. Select only one." &>
 321                     <br/><br/>
 322                     <form class="form-horizontal">
 323                         <div class="form-group">
 324                             <label class="col-sm-3 control-label">Field Trial(s): </label>
 325                             <div class="col-sm-9" >
 326                                 <div id="drone_imagery_calculate_statistics_multiseason_trial_select_div"></div>
 327                             </div>
 328                         </div>
 329                     </form>
 330                     <center>
 331                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_multiseason_field_trial_select_step">Go to Next Step</button>
 332                     </center>
 333                 </&>
 334                 <&| /util/workflow.mas:step, title=> "Trait Selection" &>
 335                     <& /page/page_title.mas, title=>"Select the observation variable(s) you are interested in" &>
 336                     <br/><br/>
 337                     <form class="form-horizontal">
 338                         <div class="form-group">
 339                             <label class="col-sm-3 control-label">Observation Variables Phenotyped in the Selected Field Trial: </label>
 340                             <div class="col-sm-9" >
 341                                 <div id="drone_imagery_calculate_statistics_multiseason_trait_select_div"></div>
 342                             </div>
 343                         </div>
 344                     </form>
 345                     <center>
 346                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_multiseason_trait_select_step">Go to Next Step</button>
 347                     </center>
 348                 </&>
 349                 <&| /util/workflow.mas:step, title=> "Statistics" &>
 350                     <& /page/page_title.mas, title=>"Select statistics to calculate" &>
 351
 352                     <select class="form-control" id="drone_imagery_calculate_statistics_multiseason_select_input">
 353                         <option value="">Select A Model</option>
 354
 355                         <option value="sommer_grm_genetic_blups">Sommer GBLUPs Y~replicate+GRM. Multivariate genetic effects using GRM</option>
 356                         <option value="sommer_grm_spatial_genetic_blups">Sommer Spatial GBLUPs Y~replicate+GRM+spatial. Multivariate genetic + 2Dspl spatial effects</option>
 357                     </select>
 358
 359                     <hr>
 360                     <div class="form-horizontal">
 361                         <div class="form-group">
 362                             <label class="col-sm-3 control-label">Relationship Matrix Type: </label>
 363                             <div class="col-sm-9" >
 364                                 <select class="form-control" id="drone_imagery_calculate_statistics_multiseason_relationship_matrix_type_select_div">
 365                                     <option value="">Identity</option>
 366                                     <option value="htp_phenotypes">High-throughput Phenotyping Data</option>
 367                                     <option value="genotypes">Genotyping Data</option>
 368                                 </select>
 369                             </div>
 370                         </div>
 371                     </div>
 372
 373                     <div id="drone_imagery_calculate_statistics_multiseason_genotyping_protocol_div" class="well well-sm" style="display:none">
 374                         <div class="form-horizontal">
 375                             <div class="form-group">
 376                                 <label class="col-sm-3 control-label">Genotyping Protocol To Calculate Genomic Relationship Matrix (optional. If none selected, an identity matrix is used): </label>
 377                                 <div class="col-sm-9" >
 378                                     <div id="drone_imagery_calculate_statistics_multiseason_genotyping_protocol_select_div"></div>
 379                                 </div>
 380                             </div>
 381                             <div class="form-group">
 382                                 <label class="col-sm-3 control-label">Compute Genotypes From Parents: </label>
 383                                 <div class="col-sm-9" >
 384                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_genotyping_protocol_compute_from_parents_select">
 385                                         <option value="no">No</option>
 386                                         <option value="yes">Yes</option>
 387                                     </select>
 388                                 </div>
 389                             </div>
 390                             <div class="form-group" id="drone_image_calculate_statistics_multiseason_genotyping_protocol_use_parental_grms_select_div" style="display:none">
 391                                 <label class="col-sm-3 control-label">Use Parental Relationship Matrices: </label>
 392                                 <div class="col-sm-9" >
 393                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_genotyping_protocol_use_parental_grms_select">
 394                                         <option value="no">No</option>
 395                                         <option value="yes">Yes</option>
 396                                     </select>
 397                                 </div>
 398                             </div>
 399                             <div class="form-group" id="drone_image_calculate_statistics_multiseason_genotyping_protocol_include_pedigree_select_div" style="display:none">
 400                                 <label class="col-sm-3 control-label">Include Pedigree Info Into Relationship Matrix: </label>
 401                                 <div class="col-sm-9" >
 402                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_genotyping_protocol_include_pedigree_select">
 403                                         <option value="no">No</option>
 404                                         <option value="yes">Yes</option>
 405                                     </select>
 406                                 </div>
 407                             </div>
 408                         </div>
 409                     </div>
 410
 411                     <div id="drone_imagery_calculate_statistics_multiseason_htp_phenotypes_rel_matrix_div" class="well well-sm" style="display:none">
 412                         <div class="form-horizontal">
 413                             <div class="form-group">
 414                                 <label class="col-sm-3 control-label">How to calculate the relationship matrix with high-throughput phenotypes: </label>
 415                                 <div class="col-sm-9" >
 416                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_htp_phenotypes_rel_matrix_select">
 417                                         <option value="correlations">Correlations</option>
 418                                         <option value="blues">BLUEs</option>
 419                                     </select>
 420                                 </div>
 421                             </div>
 422                             <div class="form-group">
 423                                 <label class="col-sm-3 control-label">Time Points to Use: </label>
 424                                 <div class="col-sm-9" >
 425                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_htp_phenotypes_rel_matrix_times_select">
 426                                         <option value="all">All Available</option>
 427                                         <option value="latest_trait">Up to the latest date selected in traits</option>
 428                                         <option value="vegetative" disabled>Vegetative Growth Stage</option>
 429                                         <option value="reproductive" disabled>Reproductive Growth Stage</option>
 430                                         <option value="mature" disabled>Mature Growth Stage</option>
 431                                     </select>
 432                                 </div>
 433                             </div>
 434                             <div class="form-group" id="drone_image_calculate_statistics_multiseason_htp_phenotypes_rel_matrix_inversion_select_div" style="display:none">
 435                                 <label class="col-sm-3 control-label">HTP BLUEs Inversion Tolerance: </label>
 436                                 <div class="col-sm-9" >
 437                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_htp_phenotypes_rel_matrix_inversion_select">
 438                                         <option value="0.00001">0.00001</option>
 439                                         <option value="0.0001">0.0001</option>
 440                                         <option value="0.001">0.001</option>
 441                                         <option value="0.01">0.01</option>
 442                                         <option value="0.1">0.1</option>
 443                                         <option value="0.5">0.5</option>
 444                                     </select>
 445                                 </div>
 446                             </div>
 447                         </div>
 448                     </div>
 449
 450                     <hr>
 451                     <div class="form-horizontal">
 452                         <div class="form-group">
 453                             <label class="col-sm-3 control-label">Inversion Tolerance: </label>
 454                             <div class="col-sm-9" >
 455                                 <select class="form-control" id="drone_image_calculate_statistics_multiseason_tolparinv_select">
 456                                     <option value="0.000001">0.000001</option>
 457                                     <option value="0.00001">0.00001</option>
 458                                     <option value="0.0001">0.0001</option>
 459                                     <option value="0.001">0.001</option>
 460                                     <option value="0.01">0.01</option>
 461                                     <option value="0.05">0.05</option>
 462                                     <option value="0.08">0.08</option>
 463                                     <option value="0.1">0.1</option>
 464                                     <option value="0.2">0.2</option>
 465                                     <option value="0.5">0.5</option>
 466                                 </select>
 467                             </div>
 468                         </div>
 469                     </div>
 470
 471                     <div id="drone_imagery_calculate_statistics_multiseason_legendre_polynomial_div" style="display:none">
 472                         <hr>
 473                         <div class="form-horizontal">
 474                             <div class="form-group">
 475                                 <label class="col-sm-3 control-label">Legendre Polynomial Order: </label>
 476                                 <div class="col-sm-9" >
 477                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_legendre_order_number_select">
 478                                         <option value="1">1</option>
 479                                         <option value="2">2</option>
 480                                         <option value="3">3</option>
 481                                         <option value="4">4</option>
 482                                         <option value="5">5</option>
 483                                     </select>
 484                                 </div>
 485                             </div>
 486                         </div>
 487                     </div>
 488
 489                     <div id="drone_imagery_calculate_statistics_multiseason_permanent_env_structure_div" style="display:none">
 490                         <hr>
 491                         <div class="form-horizontal">
 492                             <div class="form-group">
 493                                 <label class="col-sm-3 control-label">Permanent Environment Structure: </label>
 494                                 <div class="col-sm-9" >
 495                                     <select class="form-control" id="drone_image_calculate_statistics_multiseason_permanent_env_structure_select">
 496                                         <option value="identity">Identity Matrix</option>
 497                                         <option value="phenotype_correlation">Phenotype Correlation Matrix</option>
 498                                         <option value="euclidean_rows_and_columns">Euclidean Distance From Rows and Columns Matrix</option>
 499                                     </select>
 500                                 </div>
 501                             </div>
 502                         </div>
 503
 504                         <div id="drone_imagery_calculate_statistics_multiseason_permanent_env_structure_phenotype_correlation_div" style="display:none">
 505                             <div class="form-horizontal">
 506                                 <div class="form-group">
 507                                     <label class="col-sm-3 control-label">Phenotypes For Correlation Matrix: </label>
 508                                     <div class="col-sm-9" >
 509                                         <div id="drone_imagery_calculate_statistics_multiseason_permanent_env_structure_phenotype_correlation_select_div"></div>
 510                                     </div>
 511                                 </div>
 512                             </div>
 513                         </div>
 514
 515                     </div>
 516
 517                     <br/><br/>
 518                     <center>
 519                     <button class="btn btn-primary" id="drone_imagery_calculate_statistics_multiseason_select_step">Submit</button>
 520                     </center>
 521                 </&>
 522                 <&| /util/workflow.mas:step, title=> "Results" &>
 523                     <& /page/page_title.mas, title=>"Statistics results" &>
 524
 525                     <div id ="drone_imagery_calculate_statistics_multiseason_result_div">
 526                     </div>
 527                 </&>
 528             </&>
 529
 530         </div>
 531
 532       </div>
 533       <div class="modal-footer">
 534         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 535       </div>
 536     </div>
 537   </div>
 538 </div>
 539
 540 <script>
 541
 542 jQuery(document).ready(function() {
 543
 544     //
 545     // Calculate statistics
 546     //
 547
 548     var manage_drone_imagery_calculate_statistics_field_trial_id_array = undefined;
 549     var manage_drone_imagery_calculate_statistics_field_trial_id_string = "";
 550     var manage_drone_imagery_calculate_statistics_observation_variable_type;
 551     var manage_drone_imagery_calculate_statistics_trait_ids = [];
 552     var manage_drone_imagery_calculate_statistics_trait_names = [];
 553     var manage_drone_imagery_calculate_statistics_accession_names = [];
 554     var manage_drone_imagery_calculate_statistics_plot_names = [];
 555     var manage_drone_imagery_calculate_statistics_select = '';
 556     var manage_drone_imagery_calculate_statistics_phenotype_training_file;
 557     var manage_drone_imagery_calculate_statistics_grm_training_file;
 558     var manage_drone_imagery_calculate_statistics_response = {};
 559
 560     var manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_array = undefined;
 561     var manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_string = "";
 562     var manage_drone_imagery_calculate_statistics_multiseason_trait_ids = [];
 563     var manage_drone_imagery_calculate_statistics_multiseason_trait_names = [];
 564     var manage_drone_imagery_calculate_statistics_multiseason_accession_names = [];
 565     var manage_drone_imagery_calculate_statistics_multiseason_plot_names = [];
 566     var manage_drone_imagery_calculate_statistics_multiseason_select = '';
 567     var manage_drone_imagery_calculate_statistics_multiseason_phenotype_training_file;
 568     var manage_drone_imagery_calculate_statistics_multiseason_grm_training_file;
 569     var manage_drone_imagery_calculate_statistics_multiseason_response = {};
 570
 571     jQuery('#drone_imagery_calculate_statistics_link').click(function(){
 572         get_select_box('trials', 'drone_imagery_calculate_statistics_trial_select_div', { 'name' : 'drone_imagery_calculate_statistics_field_trial_id', 'id' : 'drone_imagery_calculate_statistics_field_trial_id', 'empty':1, 'multiple':1 });
 573
 574         get_select_box('trials', 'drone_imagery_calculate_statistics_multiseason_trial_select_div', { 'name' : 'drone_imagery_calculate_statistics_multiseason_field_trial_id', 'id' : 'drone_imagery_calculate_statistics_multiseason_field_trial_id', 'empty':1, 'multiple':1 });
 575
 576         jQuery('#drone_imagery_calculate_statistics_dialog').modal('show');
 577     });
 578
 579     jQuery('#drone_imagery_calculate_statistics_intro_single_trial_multiseason_select_step').click(function(){
 580         jQuery('#drone_imagery_calculate_statistics_single_trial_multiseason_dialog').modal('show');
 581     });
 582
 583     jQuery('#drone_imagery_calculate_statistics_intro_single_trial_select_step').click(function(){
 584         Workflow.complete("#drone_imagery_calculate_statistics_intro_single_trial_select_step");
 585         Workflow.focus('#drone_imagery_calculate_statistics_workflow', 1);
 586     });
 587
 588     jQuery('#drone_imagery_calculate_statistics_select_observation_variable_type').change(function(){
 589         manage_drone_imagery_calculate_statistics_observation_variable_type = jQuery('#drone_imagery_calculate_statistics_select_observation_variable_type').val();
 590         if (manage_drone_imagery_calculate_statistics_observation_variable_type == 'time_ontology') {
 591             get_select_box('traits', 'drone_imagery_calculate_statistics_trait_select_div', { 'name' : 'drone_imagery_calculate_statistics_trait_id_select', 'id' : 'drone_imagery_calculate_statistics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_calculate_statistics_observation_variable_type, 'select_format':'component_table_select' });
 592         }
 593         else {
 594             get_select_box('traits', 'drone_imagery_calculate_statistics_trait_select_div', { 'name' : 'drone_imagery_calculate_statistics_trait_id_select', 'id' : 'drone_imagery_calculate_statistics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_calculate_statistics_observation_variable_type });
 595         }
 596     });
 597
 598     jQuery('#drone_imagery_calculate_statistics_field_trial_select_step').click(function(){
 599         manage_drone_imagery_calculate_statistics_field_trial_id_array = undefined;
 600         manage_drone_imagery_calculate_statistics_field_trial_id_string = "";
 601         manage_drone_imagery_calculate_statistics_field_trial_id_array = jQuery('#drone_imagery_calculate_statistics_field_trial_id').val();
 602
 603         if (manage_drone_imagery_calculate_statistics_field_trial_id_array.length > 1) {
 604             alert('Please only select a single field trial for now!');
 605             return false;
 606         }
 607
 608         manage_drone_imagery_calculate_statistics_field_trial_id_string = manage_drone_imagery_calculate_statistics_field_trial_id_array.join(",");
 609         manage_drone_imagery_calculate_statistics_observation_variable_type = jQuery('#drone_imagery_calculate_statistics_select_observation_variable_type').val();
 610         if (manage_drone_imagery_calculate_statistics_field_trial_id_string == '') {
 611             alert('Please select a field trial first!');
 612         } else {
 613             if (manage_drone_imagery_calculate_statistics_observation_variable_type == 'time_ontology') {
 614                 get_select_box('traits', 'drone_imagery_calculate_statistics_trait_select_div', { 'name' : 'drone_imagery_calculate_statistics_trait_id_select', 'id' : 'drone_imagery_calculate_statistics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_calculate_statistics_observation_variable_type, 'select_format':'component_table_select' });
 615             }
 616             else {
 617                 get_select_box('traits', 'drone_imagery_calculate_statistics_trait_select_div', { 'name' : 'drone_imagery_calculate_statistics_trait_id_select', 'id' : 'drone_imagery_calculate_statistics_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':manage_drone_imagery_calculate_statistics_observation_variable_type });
 618             }
 619
 620             get_select_box('traits', 'drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_select_div', { 'name' : 'drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_select', 'id' : 'drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_field_trial_id_string, 'stock_type':'plot' });
 621
 622             Workflow.complete("#drone_imagery_calculate_statistics_field_trial_select_step");
 623             Workflow.focus('#drone_imagery_calculate_statistics_workflow', 2);
 624         }
 625         return false;
 626     });
 627
 628     jQuery('#drone_imagery_calculate_statistics_multiseason_field_trial_select_step').click(function(){
 629         manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_array = undefined;
 630         manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_string = "";
 631         manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_array = jQuery('#drone_imagery_calculate_statistics_multiseason_field_trial_id').val();
 632
 633         if (manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_array.length > 1) {
 634             alert('Please only select a single field trial for now!');
 635             return false;
 636         }
 637
 638         manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_string = manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_array.join(",");
 639
 640         get_select_box('traits', 'drone_imagery_calculate_statistics_multiseason_trait_select_div', { 'name' : 'drone_imagery_calculate_statistics_multiseason_trait_id_select', 'id' : 'drone_imagery_calculate_statistics_multiseason_trait_id_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_string, 'stock_type':'plot', 'contains_composable_cv_type':'time_ontology', 'select_format':'component_table_multiseason_select' });
 641
 642         get_select_box('traits', 'drone_imagery_calculate_statistics_multiseason_permanent_env_structure_phenotype_correlation_select_div', { 'name' : 'drone_imagery_calculate_statistics_multiseason_permanent_env_structure_phenotype_correlation_select', 'id' : 'drone_imagery_calculate_statistics_multiseason_permanent_env_structure_phenotype_correlation_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':manage_drone_imagery_calculate_statistics_multiseason_field_trial_id_string, 'stock_type':'plot' });
 643
 644         Workflow.complete("#drone_imagery_calculate_statistics_multiseason_field_trial_select_step");
 645         Workflow.focus('#drone_imagery_calculate_statistics_single_trial_multiseason_workflow', 2);
 646     });
 647
 648     jQuery('#drone_imagery_calculate_statistics_trait_select_step').click(function(){
 649         get_select_box('genotyping_protocol', 'drone_imagery_calculate_statistics_genotyping_protocol_select_div', { 'name' : 'drone_image_calculate_statistics_genotyping_protocol_select', 'id' : 'drone_image_calculate_statistics_genotyping_protocol_select', 'empty':1 });
 650
 651         manage_drone_imagery_calculate_statistics_trait_ids = [];
 652
 653         if (manage_drone_imagery_calculate_statistics_observation_variable_type == 'time_ontology') {
 654             jQuery('input[name="drone_imagery_calculate_statistics_trait_id_select"]').each(function() {
 655                 if (this.checked){
 656                     manage_drone_imagery_calculate_statistics_trait_ids.push(jQuery(this).val());
 657                 }
 658             });
 659         }
 660         else {
 661             manage_drone_imagery_calculate_statistics_trait_ids = jQuery('#drone_imagery_calculate_statistics_trait_id_select').val();
 662             if (manage_drone_imagery_calculate_statistics_trait_ids == null || manage_drone_imagery_calculate_statistics_trait_ids == undefined) {
 663                 alert('Please select at least one observation variable!');
 664                 return false;
 665             }
 666         }
 667
 668         if (manage_drone_imagery_calculate_statistics_trait_ids.length < 1){
 669             alert('Please select at least one observation variable!');
 670         } else {
 671             Workflow.complete("#drone_imagery_calculate_statistics_trait_select_step");
 672             Workflow.focus('#drone_imagery_calculate_statistics_workflow', 3);
 673         }
 674         return false;
 675     });
 676
 677     jQuery('#drone_imagery_calculate_statistics_select_input').change(function(){
 678         jQuery("#drone_imagery_calculate_statistics_relationship_matrix_type_select_div").val('').change();
 679         jQuery("#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select").val('no').change();
 680
 681         manage_drone_imagery_calculate_statistics_select = jQuery('#drone_imagery_calculate_statistics_select_input').val();
 682         if (manage_drone_imagery_calculate_statistics_select == 'marss_germplasmname_block') {
 683             jQuery('#drone_imagery_calculate_statistics_marss_div').show();
 684             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').hide();
 685             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 686             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 687             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').hide();
 688             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 689             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 690             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 691             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 692             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').hide();
 693             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 694             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').hide();
 695             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').hide();
 696         }
 697         else if (manage_drone_imagery_calculate_statistics_select == 'lmer_germplasmname_replicate') {
 698             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 699             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').hide();
 700             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 701             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 702             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').show();
 703             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 704             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 705             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 706             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 707             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').hide();
 708             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 709             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').hide();
 710             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').hide();
 711         }
 712         else if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 713             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 714             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').show();
 715             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 716             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').show();
 717             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').hide();
 718             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 719             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 720             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 721             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 722             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').hide();
 723             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 724             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').hide();
 725             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').show();
 726         }
 727         else if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups' || manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
 728             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 729             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').show();
 730             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 731             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 732             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').show();
 733             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 734             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').show();
 735             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 736             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 737             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').show();
 738             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 739             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').show();
 740             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').show();
 741         }
 742         else if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_only_random_regression_dap_genetic_blups' || manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_only_random_regression_gdd_genetic_blups') {
 743             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 744             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').show();
 745             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 746             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 747             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').show();
 748             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 749             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 750             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 751             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 752             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').show();
 753             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 754             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').show();
 755             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').show();
 756         }
 757         else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
 758             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 759             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').show();
 760             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 761             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').show();
 762             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').hide();
 763             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 764             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 765             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 766             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 767             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').show();
 768             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').show();
 769             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').show();
 770             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').show();
 771         }
 772         else if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_blups') {
 773             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 774             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').show();
 775             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 776             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 777             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').show();
 778             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 779             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 780             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 781             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 782             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').hide();
 783             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 784             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').hide();
 785             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').show();
 786         }
 787         else {
 788             jQuery('#drone_imagery_calculate_statistics_marss_div').hide();
 789             jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_div').hide();
 790             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 791             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 792             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').hide();
 793             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').hide();
 794             jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').hide();
 795             jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').hide();
 796             jQuery('#drone_imagery_calculate_statistics_analysis_save_fitted').hide();
 797             jQuery('#drone_imagery_calculate_statistics_legendre_polynomial_div').hide();
 798             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_div').hide();
 799             jQuery('#drone_image_calculate_statistics_use_area_under_curve_select_div').hide();
 800             jQuery('#drone_image_calculate_statistics_inversion_tolerance_select_div').hide();
 801         }
 802
 803     });
 804
 805     jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_select_div').change(function(){
 806         if (jQuery(this).val() == 'genotypes') {
 807             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').show();
 808             jQuery('#drone_imagery_calculate_statistics_htp_phenotypes_rel_matrix_div').hide();
 809         }
 810         else if (jQuery(this).val() == 'htp_phenotypes') {
 811             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 812             jQuery('#drone_imagery_calculate_statistics_htp_phenotypes_rel_matrix_div').show();
 813         }
 814         else {
 815             jQuery('#drone_imagery_calculate_statistics_genotyping_protocol_div').hide();
 816             jQuery('#drone_imagery_calculate_statistics_htp_phenotypes_rel_matrix_div').hide();
 817         }
 818     });
 819
 820     jQuery('#drone_image_calculate_statistics_htp_phenotypes_rel_matrix_select').change(function(){
 821         if (jQuery(this).val() == 'blues') {
 822             jQuery('#drone_image_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select_div').show();
 823         }
 824         else {
 825             jQuery('#drone_image_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select_div').hide();
 826         }
 827     });
 828
 829     jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').change(function(){
 830         if (jQuery(this).val() == 'yes') {
 831             jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select_div').show();
 832             jQuery('#drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select_div').show();
 833         }
 834         if (jQuery(this).val() == 'no') {
 835             jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select_div').hide();
 836             jQuery('#drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select_div').hide();
 837             jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select option[value=no]').attr('selected','selected');
 838             jQuery('#drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select option[value=no]').attr('selected','selected');
 839         }
 840     });
 841
 842     jQuery('#drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select').change(function(){
 843         if (jQuery(this).val() == 'yes') {
 844             jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select option[value=no]').attr('selected','selected');
 845             jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select_div').hide();
 846         }
 847         if (jQuery(this).val() == 'no') {
 848             jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select_div').show();
 849         }
 850     });
 851
 852     jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').change(function(){
 853         if (jQuery(this).val() == 'euclidean_rows_and_columns') {
 854             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_div').hide();
 855         }
 856         else if (jQuery(this).val() == 'phenotype_correlation') {
 857             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_div').show();
 858         }
 859         else {
 860             jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_div').hide();
 861         }
 862     });
 863
 864     jQuery('#drone_imagery_calculate_statistics_select_step').click(function(){
 865
 866         manage_drone_imagery_calculate_statistics_select = jQuery('#drone_imagery_calculate_statistics_select_input').val();
 867
 868         if (manage_drone_imagery_calculate_statistics_select == 'marss_germplasmname_block' && manage_drone_imagery_calculate_statistics_observation_variable_type != 'time_ontology') {
 869             alert('The MARSS model fit and prediction only works for Time Series traits! Please go to Trait Selection and select time series traits.');
 870             return false;
 871         }
 872         if (jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select').val() == 'yes' && jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val() != 'yes') {
 873             alert('You can only use pedigree info in the relationship matrix if you will compute the genotypes from the parents!');
 874             return false;
 875         }
 876         if (jQuery('#drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select').val() == 'yes' && jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val() != 'yes') {
 877             alert('You can only use parental relationship matrices if you will compute the genotypes from the parents!');
 878             return false;
 879         }
 880
 881         var manage_drone_imagery_calculate_statistics_rr_structure_phenotype_correlation = [];
 882         if (jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').val() == 'phenotype_correlation') {
 883             manage_drone_imagery_calculate_statistics_rr_structure_phenotype_correlation = jQuery('#drone_imagery_calculate_statistics_permanent_env_structure_phenotype_correlation_select').val();
 884             if (!manage_drone_imagery_calculate_statistics_rr_structure_phenotype_correlation || manage_drone_imagery_calculate_statistics_rr_structure_phenotype_correlation.length < 3) {
 885                 alert('Please select at least three phenotypes to use in random regression phenotype correlation structure!');
 886                 return false;
 887             }
 888         }
 889
 890         jQuery.ajax({
 891             url : '/api/drone_imagery/calculate_statistics',
 892             type : 'POST',
 893             data : {
 894                 'observation_variable_id_list':JSON.stringify(manage_drone_imagery_calculate_statistics_trait_ids),
 895                 'field_trial_id_list':JSON.stringify(manage_drone_imagery_calculate_statistics_field_trial_id_array),
 896                 'statistics_select':manage_drone_imagery_calculate_statistics_select,
 897                 'statistics_select_marss_options':jQuery('#drone_imagery_calculate_statistics_select_marss').val(),
 898                 'relationship_matrix_type':jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_select_div').val(),
 899                 'protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
 900                 'compute_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
 901                 'use_parental_grms_if_compute_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_use_parental_grms_select').val(),
 902                 'include_pedgiree_info_if_compute_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_include_pedigree_select').val(),
 903                 'htp_pheno_rel_matrix_type':jQuery('#drone_image_calculate_statistics_htp_phenotypes_rel_matrix_select').val(),
 904                 'htp_pheno_rel_matrix_time_points':jQuery('#drone_image_calculate_statistics_htp_phenotypes_rel_matrix_times_select').val(),
 905                 'htp_pheno_rel_matrix_blues_inversion':jQuery('#drone_image_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select').val(),
 906                 'tolparinv':jQuery('#drone_image_calculate_statistics_tolparinv_select').val(),
 907                 'legendre_order_number':jQuery('#drone_image_calculate_statistics_legendre_order_number_select').val(),
 908                 'use_area_under_curve':jQuery('#drone_image_calculate_statistics_use_area_under_curve_select').val(),
 909                 'permanent_environment_structure':jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').val(),
 910                 'permanent_environment_structure_phenotype_correlation_traits':JSON.stringify(manage_drone_imagery_calculate_statistics_rr_structure_phenotype_correlation)
 911             },
 912             beforeSend: function() {
 913                 jQuery("#working_modal").modal("show");
 914             },
 915             success: function(response){
 916                 console.log(response);
 917                 jQuery("#working_modal").modal("hide");
 918
 919                 if (response.error) {
 920                     alert(response.error);
 921                 }
 922                 else {
 923                     manage_drone_imagery_calculate_statistics_response = response;
 924
 925                     var html = '';
 926                     if (response.sum_square_residual) {
 927                         html = html + '<h4>Sum square residual: '+response.sum_square_residual+'</h4><hr>';
 928                     }
 929                     if (response.genetic_effects_line_plot) {
 930                         html = html + '<img src="'+response.genetic_effects_line_plot+'"><hr>';
 931                     }
 932                     if (response.env_effects_heatmap_plot) {
 933                         html = html + '<img src="'+response.env_effects_heatmap_plot+'"><hr>';
 934                     }
 935                     if (response.unique_accessions.length > 0 && response.unique_traits.length > 0 && response.result_blup_genetic_data) {
 936                         manage_drone_imagery_calculate_statistics_accession_names = response.unique_accessions;
 937                         manage_drone_imagery_calculate_statistics_trait_names = response.unique_traits;
 938                         manage_drone_imagery_calculate_statistics_phenotype_training_file = response.stats_tempfile;
 939                         manage_drone_imagery_calculate_statistics_grm_training_file = response.grm_file;
 940
 941                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Accessions</th>';
 942                         for (var i=0; i<manage_drone_imagery_calculate_statistics_trait_names.length; i++) {
 943                             html = html + '<th>'+manage_drone_imagery_calculate_statistics_trait_names[i]+'</th>';
 944                         }
 945                         html = html + '</tr></thead><tbody>';
 946                         for (var k=0; k<response.unique_accessions.length; k++) {
 947                             var acc = response.unique_accessions[k];
 948                             html = html + '<tr><td>'+acc+'</td>';
 949                             for (var i=0; i<manage_drone_imagery_calculate_statistics_trait_names.length; i++) {
 950                                 if (response.result_blup_genetic_data[acc] && response.result_blup_genetic_data[acc][manage_drone_imagery_calculate_statistics_trait_names[i]]) {
 951                                     html = html + '<td>'+response.result_blup_genetic_data[acc][manage_drone_imagery_calculate_statistics_trait_names[i]][0]+'</td>';
 952                                 }
 953                                 else {
 954                                     html = html + '<td>NA</td>';
 955                                 }
 956                             }
 957                             html = html + '</tr>';
 958                         }
 959                         html = html + '</tbody></table>';
 960                     }
 961
 962                     if (response.unique_plots.length > 0 && response.unique_traits.length > 0 && response.result_blup_spatial_data) {
 963                         manage_drone_imagery_calculate_statistics_plot_names = response.unique_plots;
 964                         manage_drone_imagery_calculate_statistics_trait_names = response.unique_traits;
 965
 966                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Plots</th>';
 967                         for (var i=0; i<response.unique_traits.length; i++) {
 968                             html = html + '<th>'+response.unique_traits[i]+'</th>';
 969                         }
 970                         html = html + '</tr></thead><tbody>';
 971                         for (var k=0; k<response.unique_plots.length; k++) {
 972                             var plot = response.unique_plots[k];
 973                             html = html + '<tr><td>'+plot+'</td>';
 974                             for (var i=0; i<response.unique_traits.length; i++) {
 975                                 html = html + '<td>'+response.result_blup_spatial_data[plot][response.unique_traits[i]][0]+'</td>';
 976                             }
 977                             html = html + '</tr>';
 978                         }
 979                         html = html + '</tbody></table>';
 980                     }
 981
 982                     if (response.unique_plots.length > 0 && response.unique_traits.length > 0 && response.result_blup_pe_data) {
 983                         manage_drone_imagery_calculate_statistics_plot_names = response.unique_plots;
 984                         manage_drone_imagery_calculate_statistics_trait_names = response.unique_traits;
 985
 986                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Plots</th>';
 987                         for (var i=0; i<response.unique_traits.length; i++) {
 988                             html = html + '<th>'+response.unique_traits[i]+'</th>';
 989                         }
 990                         html = html + '</tr></thead><tbody>';
 991                         for (var k=0; k<response.unique_plots.length; k++) {
 992                             var plot = response.unique_plots[k];
 993                             html = html + '<tr><td>'+plot+'</td>';
 994                             for (var i=0; i<response.unique_traits.length; i++) {
 995                                 if (response.result_blup_pe_data[plot] && response.result_blup_pe_data[plot][response.unique_traits[i]]) {
 996                                     html = html + '<td>'+response.result_blup_pe_data[plot][response.unique_traits[i]][0]+'</td>';
 997                                 }
 998                                 else {
 999                                     html = html + '<td>NA</td>';
1000                                 }
1001                             }
1002                             html = html + '</tr>';
1003                         }
1004                         html = html + '</tbody></table>';
1005                     }
1006
1007                     if (response.results.length > 0) {
1008                         html = '<table class="table table-bordered table-hover"><thead><tr><th>Observation Variable</th><th>Statistics</th><th>Plot</th></tr></thead><tbody>';
1009                         for (var i=0; i<response.results.length; i++) {
1010                             html = html + '<tr><td>'+response.results[i][0]+'</td><td>'+response.results[i][1]+'</td><td><img src="'+response.results[i][2]+'"></td></tr>';
1011                         }
1012                         html = html + '</tbody></table>';
1013                     }
1014
1015                     html = html + '<hr><a href="'+response.stats_out_tempfile_string+'.log" target=_blank>Stats file or log</a>';
1016
1017                     if (jQuery('#drone_imagery_calculate_statistics_relationship_matrix_type_select_div').val() == 'htp_phenotypes') {
1018                         html = html + '<hr><a href="'+response.stats_out_htp_rel_tempfile_out_string+'" target=_blank>HTP Relationship Matrix</a>';
1019                     }
1020
1021                     jQuery('#drone_imagery_calculate_statistics_result_div').html(html);
1022
1023                     Workflow.complete("#drone_imagery_calculate_statistics_select_step");
1024                     Workflow.focus('#drone_imagery_calculate_statistics_workflow', 4);
1025                 }
1026             },
1027             error: function(response){
1028                 jQuery("#working_modal").modal("hide");
1029                 alert('Error calculating statistics!')
1030             }
1031         });
1032     });
1033
1034     jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic_pe_residual').click(function(){
1035         jQuery('#generic_save_analysis_template_dialog').modal('show');
1036     });
1037
1038     jQuery('#generic_save_analysis_template_submit_button').click(function(){
1039         var generic_save_analysis_template_analysis_name = jQuery('#generic_save_analysis_template_analysis_name').val();
1040         var generic_save_analysis_template_analysis_description = jQuery('#generic_save_analysis_template_analysis_description').val();
1041         var generic_save_analysis_template_analysis_year = jQuery('#generic_save_analysis_template_analysis_year').val();
1042         var generic_save_analysis_template_breeding_program_id = jQuery('#generic_save_analysis_template_breeding_program_id').val();
1043
1044         if (generic_save_analysis_template_analysis_name == '') {
1045             alert('Please give an analysis template name');
1046             return false;
1047         }
1048         if (generic_save_analysis_template_analysis_description == '') {
1049             alert('Please give an analysis template description');
1050             return false;
1051         }
1052         if (generic_save_analysis_template_analysis_year == '') {
1053             alert('Please give an analysis template year');
1054             return false;
1055         }
1056
1057         var drone_imagery_stats_parameters = {};
1058         var drone_imagery_stats_protocol = '';
1059         var drone_imagery_stats_auxiliary_files = [];
1060         var drone_imagery_stats_result_summary = {};
1061         var statistical_ontology_term = '';
1062         var drone_imagery_stats_compose_trait_info;
1063
1064         var drone_imagery_stats_tolparinv_param = jQuery('#drone_image_calculate_statistics_tolparinv_select').val();
1065         var drone_imagery_stats_numbers_traits = manage_drone_imagery_calculate_statistics_response.unique_traits.length;
1066         var drone_imagery_legendre_order = jQuery('#drone_image_calculate_statistics_legendre_order_number_select').val();
1067
1068         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
1069
1070             var drone_imagery_stats_mv_traits = [];
1071             for (var i=1; i<drone_imagery_stats_numbers_traits+1; i++) {
1072                 drone_imagery_stats_mv_traits.push('t'+i);
1073             }
1074             var drone_imagery_stats_mv_traits_string = drone_imagery_stats_mv_traits.join();
1075
1076             drone_imagery_stats_protocol = 'mmer('+drone_imagery_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+drone_imagery_stats_numbers_traits+')) +vs(rowNumberFactor, Gtc=diag('+drone_imagery_stats_numbers_traits+')) +vs(colNumberFactor, Gtc=diag('+drone_imagery_stats_numbers_traits+')) +vs(spl2D(rowNumber, colNumber), Gtc=diag('+drone_imagery_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), data=mat, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1077
1078             drone_imagery_stats_parameters = {
1079                 'tolparinv':drone_imagery_stats_tolparinv_param,
1080                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1081                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1082                 'protocol':drone_imagery_stats_protocol
1083             };
1084
1085             drone_imagery_stats_auxiliary_files = [{'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
1086
1087             drone_imagery_stats_compose_trait_info = JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info);
1088
1089             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and row and column spatial effects computed using Sommer R|SGNSTAT:0000001";
1090         }
1091         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_blups') {
1092
1093             var drone_imagery_stats_mv_traits = [];
1094             for (var i=1; i<drone_imagery_stats_numbers_traits+1; i++) {
1095                 drone_imagery_stats_mv_traits.push('t'+i);
1096             }
1097             var drone_imagery_stats_mv_traits_string = drone_imagery_stats_mv_traits.join();
1098
1099             drone_imagery_stats_protocol = 'mmer('+drone_imagery_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), data=mat, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1100
1101             drone_imagery_stats_parameters = {
1102                 'tolparinv':drone_imagery_stats_tolparinv_param,
1103                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1104                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1105                 'protocol':drone_imagery_stats_protocol
1106             };
1107
1108             drone_imagery_stats_auxiliary_files = [{'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_blups_grm_file'}];
1109
1110             drone_imagery_stats_compose_trait_info = JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info);
1111
1112             statistical_ontology_term = "Multivariate genetic BLUPs using genetic relationship matrix computed using Sommer R|SGNSTAT:0000024";
1113         }
1114         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups') {
1115
1116             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1117
1118             drone_imagery_stats_parameters = {
1119                 'tolparinv':drone_imagery_stats_tolparinv_param,
1120                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1121                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1122                 'legendre_polynomial_order':drone_imagery_legendre_order,
1123                 'protocol':drone_imagery_stats_protocol
1124             };
1125
1126             drone_imagery_stats_auxiliary_files = [
1127                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_grm_file'},
1128                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_genetic_coefficients_file'},
1129                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_permanent_environment_coefficients_file'},
1130             ];
1131
1132             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000004";
1133         }
1134         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
1135
1136             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1137
1138             drone_imagery_stats_parameters = {
1139                 'tolparinv':drone_imagery_stats_tolparinv_param,
1140                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1141                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1142                 'legendre_polynomial_order':drone_imagery_legendre_order,
1143                 'protocol':drone_imagery_stats_protocol
1144             };
1145
1146             drone_imagery_stats_auxiliary_files = [
1147                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_grm_file'},
1148                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_genetic_coefficients_file'},
1149                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_permanent_environment_coefficients_file'}
1150             ];
1151
1152             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000006";
1153         }
1154         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_only_random_regression_dap_genetic_blups') {
1155
1156             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1157
1158             drone_imagery_stats_parameters = {
1159                 'tolparinv':drone_imagery_stats_tolparinv_param,
1160                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1161                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1162                 'legendre_polynomial_order':drone_imagery_legendre_order,
1163                 'protocol':drone_imagery_stats_protocol
1164             };
1165
1166             drone_imagery_stats_auxiliary_files = [
1167                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_grm_file'},
1168                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_genetic_coefficients_file'},
1169             ];
1170
1171             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000004";
1172         }
1173         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_only_random_regression_gdd_genetic_blups') {
1174
1175             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1176
1177             drone_imagery_stats_parameters = {
1178                 'tolparinv':drone_imagery_stats_tolparinv_param,
1179                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1180                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1181                 'legendre_polynomial_order':drone_imagery_legendre_order,
1182                 'protocol':drone_imagery_stats_protocol
1183             };
1184
1185             drone_imagery_stats_auxiliary_files = [
1186                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_grm_file'},
1187                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_genetic_coefficients_file'},
1188             ];
1189
1190             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000006";
1191         }
1192
1193         var training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1194
1195         if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups' || manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1196
1197             training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1198             var drone_imagery_permanent_env_structure = jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').val();
1199
1200             if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups' || manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
1201                 drone_imagery_stats_protocol = 'blupf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
1202             }
1203             if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1204                 drone_imagery_stats_protocol = 'airemlf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
1205             }
1206
1207             drone_imagery_stats_parameters = {
1208                 'tolparinv':drone_imagery_stats_tolparinv_param,
1209                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1210                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1211                 'legendre_polynomial_order':drone_imagery_legendre_order,
1212                 'protocol':drone_imagery_stats_protocol,
1213                 'permanent_environment_structure':drone_imagery_permanent_env_structure
1214             };
1215
1216             if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups') {
1217                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using BLUPf90|SGNSTAT:0000010";
1218
1219                 drone_imagery_stats_auxiliary_files = [
1220                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_grm_file'},
1221                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_param_file'},
1222                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_log_file'},
1223                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_genetic_coefficients_file'},
1224                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_permanent_environment_coefficients_file'},
1225                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
1226                 ];
1227                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1228                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1229                 }
1230             }
1231             else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
1232                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using BLUPf90|SGNSTAT:0000008";
1233
1234                 drone_imagery_stats_auxiliary_files = [
1235                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_grm_file'},
1236                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_param_file'},
1237                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_log_file'},
1238                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_genetic_coefficients_file'},
1239                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_permanent_environment_coefficients_file'},
1240                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
1241                 ];
1242                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1243                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1244                 }
1245             }
1246             else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups') {
1247                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using AIREMLf90|SGNSTAT:0000018";
1248
1249                 drone_imagery_stats_auxiliary_files = [
1250                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_grm_file'},
1251                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_param_file'},
1252                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_log_file'},
1253                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_genetic_coefficients_file'},
1254                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_permanent_environment_coefficients_file'},
1255                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
1256                 ];
1257                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1258                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1259                 }
1260             }
1261             else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1262                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using AIREMLf90|SGNSTAT:0000020";
1263
1264                 drone_imagery_stats_auxiliary_files = [
1265                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_grm_file'},
1266                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_param_file'},
1267                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_log_file'},
1268                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_genetic_coefficients_file'},
1269                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_permanent_environment_coefficients_file'},
1270                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
1271                 ];
1272                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1273                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1274                 }
1275             }
1276         }
1277         if (manage_drone_imagery_calculate_statistics_select == 'lmer_germplasmname_replicate') {
1278             drone_imagery_stats_protocol = 'lmer(t1~replicate + 1|germplasmName, data=mat, na.action = na.omit)';
1279             drone_imagery_stats_parameters = {
1280                 'protocol':drone_imagery_stats_protocol
1281             };
1282             statistical_ontology_term = "Univariate linear mixed model genetic BLUPs using germplasmName computed using LMER R|SGNSTAT:0000002";
1283         }
1284
1285         jQuery.ajax({
1286             type: 'POST',
1287             url : '/ajax/analysis/store/json',
1288             data : {
1289                 'analysis_to_save_boolean':'yes',
1290                 'analysis_name':generic_save_analysis_template_analysis_name+'_GBLUPS',
1291                 'analysis_description':generic_save_analysis_template_analysis_description,
1292                 'analysis_year':generic_save_analysis_template_analysis_year,
1293                 'analysis_breeding_program_id':generic_save_analysis_template_breeding_program_id,
1294                 'analysis_protocol':drone_imagery_stats_protocol,
1295                 'analysis_dataset_id':'',
1296                 'analysis_accession_names':JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions),
1297                 'analysis_trait_names':JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_traits),
1298                 'analysis_statistical_ontology_term':statistical_ontology_term,
1299                 'analysis_precomputed_design_optional':'',
1300                 'analysis_result_values':JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_blup_genetic_data),
1301                 'analysis_result_values_type':'analysis_result_values_match_accession_names',
1302                 'analysis_result_summary':JSON.stringify(drone_imagery_stats_result_summary),
1303                 'analysis_result_trait_compose_info':drone_imagery_stats_compose_trait_info,
1304                 'analysis_model_id':'',
1305                 'analysis_model_name':generic_save_analysis_template_analysis_name+'_GBLUPSandPEandResiduals_Model',
1306                 'analysis_model_description':generic_save_analysis_template_analysis_description,
1307                 'analysis_model_is_public':'yes',
1308                 'analysis_model_language':manage_drone_imagery_calculate_statistics_response.analysis_model_language,
1309                 'analysis_model_type':manage_drone_imagery_calculate_statistics_response.analysis_model_type,
1310                 'analysis_model_properties':JSON.stringify(drone_imagery_stats_parameters),
1311                 'analysis_model_application_name':manage_drone_imagery_calculate_statistics_response.application_name,
1312                 'analysis_model_application_version':manage_drone_imagery_calculate_statistics_response.application_version,
1313                 'analysis_model_file':'',
1314                 'analysis_model_file_type':'',
1315                 'analysis_model_training_data_file':training_data_file,
1316                 'analysis_model_training_data_file_type':manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type,
1317                 'analysis_model_auxiliary_files':JSON.stringify(drone_imagery_stats_auxiliary_files)
1318             },
1319             beforeSend: function() {
1320                 jQuery('#working_modal').modal('show');
1321             },
1322             success: function(response){
1323                 console.log(response);
1324                 if (response.error) {
1325                     alert(response.error);
1326                 }
1327                 if (response.success) {
1328                     var html = '<center>';
1329                     if (response.model_id) {
1330                         html = html + '<p>Go to saved <a href="/analyses_model/'+response.model_id+'" target=_blank >model</a></p>';
1331                     }
1332                     if (response.analysis_id) {
1333                         html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >GBLUP analysis</a></p>';
1334                     }
1335                     html = html + '</center>';
1336                     jQuery('#generic_save_analysis_template_response_div').html(html);
1337
1338                     var statistical_ontology_term;
1339                     var drone_imagery_stats_auxiliary_files;
1340                     var drone_imagery_stats_training_data_file;
1341                     var generic_save_analysis_template_name_type = '_PermanentEnvironment';
1342                     var generic_save_analysis_template_env1_result_values = JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_blup_pe_data);
1343
1344                     if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups') {
1345                         drone_imagery_stats_auxiliary_files = [
1346                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_grm_file'},
1347                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_genetic_coefficients_file'},
1348                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_permanent_environment_coefficients_file'}
1349                         ];
1350
1351                         statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000004";
1352
1353                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1354                     }
1355                     if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
1356                         drone_imagery_stats_auxiliary_files = [
1357                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_grm_file'},
1358                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_genetic_coefficients_file'},
1359                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_permanent_environment_coefficients_file'}
1360                         ];
1361
1362                         statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000006";
1363
1364                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1365                     }
1366                     if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups') {
1367                         statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using BLUPf90|SGNSTAT:0000011";
1368
1369                         drone_imagery_stats_auxiliary_files = [
1370                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
1371                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
1372                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
1373                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
1374                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
1375                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
1376                         ];
1377                         if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1378                             drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1379                         }
1380
1381                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1382                     }
1383                     else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
1384                         statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using BLUPf90|SGNSTAT:0000009";
1385
1386                         drone_imagery_stats_auxiliary_files = [
1387                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
1388                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
1389                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
1390                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
1391                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
1392                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
1393                         ];
1394                         if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1395                             drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1396                         }
1397
1398                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1399                     }
1400                     if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1401                         statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using AIREMLf90|SGNSTAT:0000021";
1402
1403                         drone_imagery_stats_auxiliary_files = [
1404                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
1405                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
1406                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
1407                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
1408                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
1409                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
1410                         ];
1411                         if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1412                             drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1413                         }
1414
1415                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1416                     }
1417                     else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups') {
1418                         statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using AIREMLf90|SGNSTAT:0000019";
1419
1420                         drone_imagery_stats_auxiliary_files = [
1421                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
1422                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
1423                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
1424                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
1425                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
1426                             {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
1427                         ];
1428                         if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1429                             drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1430                         }
1431
1432                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1433                     }
1434
1435                     if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
1436                         statistical_ontology_term = "Multivariate linear mixed model 2D spline spatial BLUPs using genetic relationship matrix and row and column spatial effects computed using Sommer R|SGNSTAT:0000003";
1437
1438                         drone_imagery_stats_auxiliary_files = [{'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
1439
1440                         generic_save_analysis_template_name_type = '_Spatial';
1441                         generic_save_analysis_template_env1_result_values = JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_blup_spatial_data);
1442
1443                         drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1444                     }
1445
1446                     jQuery.ajax({
1447                         type: 'POST',
1448                         url : '/ajax/analysis/store/json',
1449                         data : {
1450                             'analysis_to_save_boolean':'yes',
1451                             'analysis_name':generic_save_analysis_template_analysis_name+generic_save_analysis_template_name_type,
1452                             'analysis_description':generic_save_analysis_template_analysis_description,
1453                             'analysis_year':generic_save_analysis_template_analysis_year,
1454                             'analysis_breeding_program_id':generic_save_analysis_template_breeding_program_id,
1455                             'analysis_protocol':drone_imagery_stats_protocol,
1456                             'analysis_dataset_id':'',
1457                             'analysis_accession_names':JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions),
1458                             'analysis_trait_names':JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_traits),
1459                             'analysis_statistical_ontology_term':statistical_ontology_term,
1460                             'analysis_precomputed_design_optional':JSON.stringify(manage_drone_imagery_calculate_statistics_response.field_trial_design),
1461                             'analysis_result_values':generic_save_analysis_template_env1_result_values,
1462                             'analysis_result_values_type':'analysis_result_values_match_precomputed_design',
1463                             'analysis_result_summary':JSON.stringify(drone_imagery_stats_result_summary),
1464                             'analysis_result_trait_compose_info':'',
1465                             'analysis_model_id':response.model_id,
1466                             'analysis_model_name':'',
1467                             'analysis_model_description':'',
1468                             'analysis_model_is_public':'yes',
1469                             'analysis_model_language':manage_drone_imagery_calculate_statistics_response.analysis_model_language,
1470                             'analysis_model_type':manage_drone_imagery_calculate_statistics_response.analysis_model_type,
1471                             'analysis_model_properties':JSON.stringify(drone_imagery_stats_parameters),
1472                             'analysis_model_application_name':manage_drone_imagery_calculate_statistics_response.application_name,
1473                             'analysis_model_application_version':manage_drone_imagery_calculate_statistics_response.application_version,
1474                             'analysis_model_file':'',
1475                             'analysis_model_file_type':'',
1476                             'analysis_model_training_data_file':drone_imagery_stats_training_data_file,
1477                             'analysis_model_training_data_file_type':manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type,
1478                             'analysis_model_auxiliary_files':JSON.stringify(drone_imagery_stats_auxiliary_files)
1479                         },
1480                         success: function(response){
1481                             console.log(response);
1482                             if (response.error) {
1483                                 alert(response.error);
1484                             }
1485                             if (response.success) {
1486                                 html = html + '<center>';
1487                                 if (response.analysis_id) {
1488                                     if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
1489                                         html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >spatial BLUP analysis</a></p>';
1490                                     }
1491                                     else {
1492                                         html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >permanent environment BLUP analysis</a></p>';
1493                                     }
1494                                 }
1495                                 html = html + '</center>';
1496                                 jQuery('#generic_save_analysis_template_response_div').html(html);
1497
1498                                 var drone_imagery_stats_auxiliary_files;
1499                                 var drone_imagery_stats_training_data_file;
1500                                 if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups') {
1501
1502                                     drone_imagery_stats_auxiliary_files = [
1503                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_grm_file'},
1504                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_genetic_coefficients_file'},
1505                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_permanent_environment_coefficients_file'},
1506                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_residual_file'}
1507                                     ];
1508
1509                                     statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000030";
1510
1511                                     drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1512                                 }
1513                                 if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
1514
1515                                     drone_imagery_stats_auxiliary_files = [
1516                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_grm_file'},
1517                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_genetic_coefficients_file'},
1518                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_permanent_environment_coefficients_file'},
1519                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_residual_file'}
1520                                     ];
1521
1522                                     statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000031";
1523
1524                                     drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1525                                 }
1526                                 if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups') {
1527                                     statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using BLUPf90|SGNSTAT:0000029";
1528
1529                                     drone_imagery_stats_auxiliary_files = [
1530                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
1531                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
1532                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
1533                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
1534                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
1535                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'},
1536                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_residual_file'}
1537                                     ];
1538                                     if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1539                                         drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1540                                     }
1541
1542                                     drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1543                                 }
1544                                 else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
1545                                     statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using BLUPf90|SGNSTAT:0000028";
1546
1547                                     drone_imagery_stats_auxiliary_files = [
1548                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
1549                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
1550                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
1551                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
1552                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
1553                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'},
1554                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_residual_file'}
1555                                     ];
1556                                     if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1557                                         drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1558                                     }
1559
1560                                     drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1561                                 }
1562                                 if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1563                                     statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using AIREMLf90|SGNSTAT:0000027";
1564
1565                                     drone_imagery_stats_auxiliary_files = [
1566                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
1567                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
1568                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
1569                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
1570                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
1571                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'},
1572                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_residual_file'}
1573                                     ];
1574                                     if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1575                                         drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1576                                     }
1577
1578                                     drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1579                                 }
1580                                 else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups') {
1581                                     statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using AIREMLf90|SGNSTAT:0000026";
1582
1583                                     drone_imagery_stats_auxiliary_files = [
1584                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
1585                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
1586                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
1587                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
1588                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
1589                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'},
1590                                         {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_residual_file'}
1591                                     ];
1592                                     if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1593                                         drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1594                                     }
1595
1596                                     drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1597                                 }
1598
1599                                 if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
1600                                     jQuery('#working_modal').modal('hide');
1601                                     alert('Analysis and/or model saved!');
1602                                     return false;
1603                                 }
1604
1605                                 jQuery.ajax({
1606                                     type: 'POST',
1607                                     url : '/ajax/analysis/store/json',
1608                                     data : {
1609                                         'analysis_to_save_boolean':'yes',
1610                                         'analysis_name':generic_save_analysis_template_analysis_name+'_Residual',
1611                                         'analysis_description':generic_save_analysis_template_analysis_description,
1612                                         'analysis_year':generic_save_analysis_template_analysis_year,
1613                                         'analysis_breeding_program_id':generic_save_analysis_template_breeding_program_id,
1614                                         'analysis_protocol':drone_imagery_stats_protocol,
1615                                         'analysis_dataset_id':'',
1616                                         'analysis_accession_names':JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions),
1617                                         'analysis_trait_names':JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_residual_traits),
1618                                         'analysis_statistical_ontology_term':statistical_ontology_term,
1619                                         'analysis_precomputed_design_optional':JSON.stringify(manage_drone_imagery_calculate_statistics_response.field_trial_design),
1620                                         'analysis_result_values':JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_residual_data),
1621                                         'analysis_result_values_type':'analysis_result_values_match_precomputed_design',
1622                                         'analysis_result_summary':JSON.stringify(drone_imagery_stats_result_summary),
1623                                         'analysis_result_trait_compose_info':JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info),
1624                                         'analysis_model_id':response.model_id,
1625                                         'analysis_model_name':'',
1626                                         'analysis_model_description':'',
1627                                         'analysis_model_is_public':'yes',
1628                                         'analysis_model_language':manage_drone_imagery_calculate_statistics_response.analysis_model_language,
1629                                         'analysis_model_type':manage_drone_imagery_calculate_statistics_response.analysis_model_type,
1630                                         'analysis_model_properties':JSON.stringify(drone_imagery_stats_parameters),
1631                                         'analysis_model_application_name':manage_drone_imagery_calculate_statistics_response.application_name,
1632                                         'analysis_model_application_version':manage_drone_imagery_calculate_statistics_response.application_version,
1633                                         'analysis_model_file':'',
1634                                         'analysis_model_file_type':'',
1635                                         'analysis_model_training_data_file':drone_imagery_stats_training_data_file,
1636                                         'analysis_model_training_data_file_type':manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type,
1637                                         'analysis_model_auxiliary_files':JSON.stringify(drone_imagery_stats_auxiliary_files)
1638                                     },
1639                                     success: function(response){
1640                                         jQuery('#working_modal').modal('hide');
1641                                         console.log(response);
1642                                         if (response.error) {
1643                                             alert(response.error);
1644                                         }
1645                                         if (response.success) {
1646                                             alert('Analysis and/or model saved!');
1647                                             html = html + '<center>';
1648                                             if (response.analysis_id) {
1649                                                 html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >residuals analysis</a></p>';
1650                                             }
1651                                             html = html + '</center>';
1652                                             jQuery('#generic_save_analysis_template_response_div').html(html);
1653                                         }
1654                                     },
1655                                     error: function(response){
1656                                         alert('Error saving analysis multiple!');
1657                                     }
1658                                 });
1659                             }
1660                         },
1661                         error: function(response){
1662                             alert('Error saving analysis multiple!');
1663                         }
1664                     });
1665                 }
1666             },
1667             error: function(response){
1668                 jQuery('#working_modal').modal('hide');
1669                 alert('Error saving analysis multiple!');
1670             }
1671         });
1672     });
1673
1674     jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_genetic').click(function(){
1675         jQuery('#generic_save_analysis_dialog').modal('show');
1676
1677         var drone_imagery_stats_parameters = {};
1678         var drone_imagery_stats_protocol = '';
1679         var drone_imagery_stats_auxiliary_files = [];
1680         var drone_imagery_stats_result_summary = {};
1681         var statistical_ontology_term = '';
1682
1683         var drone_imagery_stats_tolparinv_param = jQuery('#drone_image_calculate_statistics_tolparinv_select').val();
1684         var drone_imagery_stats_numbers_traits = manage_drone_imagery_calculate_statistics_response.unique_traits.length;
1685         var drone_imagery_legendre_order = jQuery('#drone_image_calculate_statistics_legendre_order_number_select').val();
1686
1687         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
1688
1689             var drone_imagery_stats_mv_traits = [];
1690             for (var i=1; i<drone_imagery_stats_numbers_traits+1; i++) {
1691                 drone_imagery_stats_mv_traits.push('t'+i);
1692             }
1693             var drone_imagery_stats_mv_traits_string = drone_imagery_stats_mv_traits.join();
1694
1695             drone_imagery_stats_protocol = 'mmer('+drone_imagery_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+drone_imagery_stats_numbers_traits+')) +vs(rowNumberFactor, Gtc=diag('+drone_imagery_stats_numbers_traits+')) +vs(colNumberFactor, Gtc=diag('+drone_imagery_stats_numbers_traits+')) +vs(spl2D(rowNumber, colNumber), Gtc=diag('+drone_imagery_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), data=mat, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1696
1697             drone_imagery_stats_parameters = {
1698                 'tolparinv':drone_imagery_stats_tolparinv_param,
1699                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1700                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1701                 'protocol':drone_imagery_stats_protocol
1702             };
1703
1704             drone_imagery_stats_auxiliary_files = [{'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
1705
1706             jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info));
1707
1708             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and row and column spatial effects computed using Sommer R|SGNSTAT:0000001";
1709         }
1710         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_blups') {
1711
1712             var drone_imagery_stats_mv_traits = [];
1713             for (var i=1; i<drone_imagery_stats_numbers_traits+1; i++) {
1714                 drone_imagery_stats_mv_traits.push('t'+i);
1715             }
1716             var drone_imagery_stats_mv_traits_string = drone_imagery_stats_mv_traits.join();
1717
1718             drone_imagery_stats_protocol = 'mmer('+drone_imagery_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), data=mat, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1719
1720             drone_imagery_stats_parameters = {
1721                 'tolparinv':drone_imagery_stats_tolparinv_param,
1722                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1723                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1724                 'protocol':drone_imagery_stats_protocol
1725             };
1726
1727             drone_imagery_stats_auxiliary_files = [{'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_blups_grm_file'}];
1728
1729             jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info));
1730
1731             statistical_ontology_term = "Multivariate genetic BLUPs using genetic relationship matrix computed using Sommer R|SGNSTAT:0000024";
1732         }
1733         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups') {
1734
1735             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1736
1737             drone_imagery_stats_parameters = {
1738                 'tolparinv':drone_imagery_stats_tolparinv_param,
1739                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1740                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1741                 'legendre_polynomial_order':drone_imagery_legendre_order,
1742                 'protocol':drone_imagery_stats_protocol
1743             };
1744
1745             drone_imagery_stats_auxiliary_files = [
1746                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_grm_file'},
1747                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_genetic_coefficients_file'},
1748                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_permanent_environment_coefficients_file'},
1749             ];
1750
1751             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000004";
1752         }
1753         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
1754
1755             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1756
1757             drone_imagery_stats_parameters = {
1758                 'tolparinv':drone_imagery_stats_tolparinv_param,
1759                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1760                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1761                 'legendre_polynomial_order':drone_imagery_legendre_order,
1762                 'protocol':drone_imagery_stats_protocol
1763             };
1764
1765             drone_imagery_stats_auxiliary_files = [
1766                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_grm_file'},
1767                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_genetic_coefficients_file'},
1768                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_permanent_environment_coefficients_file'}
1769             ];
1770
1771             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000006";
1772         }
1773         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_only_random_regression_dap_genetic_blups') {
1774
1775             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1776
1777             drone_imagery_stats_parameters = {
1778                 'tolparinv':drone_imagery_stats_tolparinv_param,
1779                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1780                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1781                 'legendre_polynomial_order':drone_imagery_legendre_order,
1782                 'protocol':drone_imagery_stats_protocol
1783             };
1784
1785             drone_imagery_stats_auxiliary_files = [
1786                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_grm_file'},
1787                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_genetic_coefficients_file'},
1788             ];
1789
1790             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000004";
1791         }
1792         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_genetic_only_random_regression_gdd_genetic_blups') {
1793
1794             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1795
1796             drone_imagery_stats_parameters = {
1797                 'tolparinv':drone_imagery_stats_tolparinv_param,
1798                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1799                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1800                 'legendre_polynomial_order':drone_imagery_legendre_order,
1801                 'protocol':drone_imagery_stats_protocol
1802             };
1803
1804             drone_imagery_stats_auxiliary_files = [
1805                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_grm_file'},
1806                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_genetic_legendre_polynomial_genetic_blups_genetic_coefficients_file'},
1807             ];
1808
1809             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000006";
1810         }
1811
1812         var training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
1813
1814         if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups' || manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1815
1816             training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
1817             var drone_imagery_permanent_env_structure = jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').val();
1818
1819             if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups' || manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
1820                 drone_imagery_stats_protocol = 'blupf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
1821             }
1822             if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups' || manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1823                 drone_imagery_stats_protocol = 'airemlf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
1824             }
1825
1826             drone_imagery_stats_parameters = {
1827                 'tolparinv':drone_imagery_stats_tolparinv_param,
1828                 'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1829                 'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1830                 'legendre_polynomial_order':drone_imagery_legendre_order,
1831                 'protocol':drone_imagery_stats_protocol,
1832                 'permanent_environment_structure':drone_imagery_permanent_env_structure
1833             };
1834
1835             if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups') {
1836                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using BLUPf90|SGNSTAT:0000010";
1837
1838                 drone_imagery_stats_auxiliary_files = [
1839                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_grm_file'},
1840                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_param_file'},
1841                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_log_file'},
1842                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_genetic_coefficients_file'},
1843                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_genetic_blups_permanent_environment_coefficients_file'},
1844                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
1845                 ];
1846                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1847                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1848                 }
1849             }
1850             else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
1851                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using BLUPf90|SGNSTAT:0000008";
1852
1853                 drone_imagery_stats_auxiliary_files = [
1854                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_grm_file'},
1855                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_param_file'},
1856                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_log_file'},
1857                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_genetic_coefficients_file'},
1858                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_genetic_blups_permanent_environment_coefficients_file'},
1859                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
1860                 ];
1861                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1862                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1863                 }
1864             }
1865             else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups') {
1866                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using AIREMLf90|SGNSTAT:0000018";
1867
1868                 drone_imagery_stats_auxiliary_files = [
1869                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_grm_file'},
1870                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_param_file'},
1871                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_log_file'},
1872                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_genetic_coefficients_file'},
1873                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_genetic_blups_permanent_environment_coefficients_file'},
1874                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
1875                 ];
1876                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1877                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
1878                 }
1879             }
1880             else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
1881                 statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using AIREMLf90|SGNSTAT:0000020";
1882
1883                 drone_imagery_stats_auxiliary_files = [
1884                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_grm_file'},
1885                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_param_file'},
1886                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_log_file'},
1887                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_genetic_coefficients_file'},
1888                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_genetic_blups_permanent_environment_coefficients_file'},
1889                     {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
1890                 ];
1891                 if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
1892                     drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
1893                 }
1894             }
1895         }
1896         if (manage_drone_imagery_calculate_statistics_select == 'lmer_germplasmname_replicate') {
1897             drone_imagery_stats_protocol = 'lmer(t1~replicate + 1|germplasmName, data=mat, na.action = na.omit)';
1898             drone_imagery_stats_parameters = {
1899                 'protocol':drone_imagery_stats_protocol
1900             };
1901             statistical_ontology_term = "Univariate linear mixed model genetic BLUPs using germplasmName computed using LMER R|SGNSTAT:0000002";
1902         }
1903
1904         jQuery('#generic_save_analysis_protocol').val(drone_imagery_stats_protocol);
1905         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(drone_imagery_stats_parameters));
1906         //jQuery('#generic_save_analysis_dataset_id').val();
1907         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions));
1908         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_traits));
1909         jQuery('#generic_save_analysis_statistical_ontology_term').val(statistical_ontology_term);
1910         //jQuery('#generic_save_analysis_design').val();
1911         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_blup_genetic_data));
1912         jQuery('#generic_save_analysis_result_values_type').val(manage_drone_imagery_calculate_statistics_response.analysis_result_values_type);
1913         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(drone_imagery_stats_result_summary));
1914         jQuery('#generic_save_analysis_model_language').val(manage_drone_imagery_calculate_statistics_response.analysis_model_language);
1915         jQuery('#generic_save_analysis_model_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_type);
1916         jQuery('#generic_save_analysis_model_application_name').val(manage_drone_imagery_calculate_statistics_response.application_name);
1917         jQuery('#generic_save_analysis_model_application_version').val(manage_drone_imagery_calculate_statistics_response.application_version);
1918         //jQuery('#generic_save_analysis_model_file').val();
1919         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
1920         jQuery('#generic_save_analysis_model_training_data_file').val(training_data_file);
1921         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type);
1922         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(drone_imagery_stats_auxiliary_files));
1923
1924         return false;
1925     });
1926
1927     jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_spatial').click(function(){
1928         if (manage_drone_imagery_calculate_statistics_field_trial_id_array.length>1) {
1929             alert('Saving spatial BLUPs currently only implemented for a single trial, so only select one field trial in your analysis');
1930             return false;
1931         }
1932
1933         jQuery('#generic_save_analysis_dialog').modal('show');
1934
1935         var drone_imagery_stats_result_summary = {};
1936
1937         var drone_imagery_stats_tolparinv_param = jQuery('#drone_image_calculate_statistics_tolparinv_select').val();
1938         var drone_imagery_stats_numbers_traits = manage_drone_imagery_calculate_statistics_response.unique_traits.length;
1939
1940         var drone_imagery_stats_mv_traits = [];
1941         for (var i=1; i<drone_imagery_stats_numbers_traits+1; i++) {
1942             drone_imagery_stats_mv_traits.push('t'+i);
1943         }
1944         var drone_imagery_stats_mv_traits_string = drone_imagery_stats_mv_traits.join();
1945
1946         var drone_imagery_stats_protocol = 'mmer('+drone_imagery_stats_mv_traits_string+'~1, random=~vs(id, Gu=geno_mat, Gtc=unsm('+drone_imagery_stats_numbers_traits+')) +vs(rowNumberFactor, Gtc=diag('+drone_imagery_stats_numbers_traits+')) +vs(colNumberFactor, Gtc=diag('+drone_imagery_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+drone_imagery_stats_numbers_traits+')), data=mat, tolparinv='+drone_imagery_stats_tolparinv_param+');';
1947
1948         var drone_imagery_stats_parameters = {
1949             'tolparinv':drone_imagery_stats_tolparinv_param,
1950             'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
1951             'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
1952             'protocol':drone_imagery_stats_protocol
1953         };
1954
1955         var statistical_ontology_term = "Multivariate linear mixed model 2D spline spatial BLUPs using genetic relationship matrix and row and column spatial effects computed using Sommer R|SGNSTAT:0000003";
1956
1957         jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info));
1958
1959         var drone_imagery_stats_auxiliary_files = [{'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
1960
1961         jQuery('#generic_save_analysis_protocol').val(drone_imagery_stats_protocol);
1962         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(drone_imagery_stats_parameters));
1963         //jQuery('#generic_save_analysis_dataset_id').val();
1964         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions));
1965         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_traits));
1966         jQuery('#generic_save_analysis_statistical_ontology_term').val(statistical_ontology_term);
1967         jQuery('#generic_save_analysis_design').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.field_trial_design));
1968         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_blup_spatial_data));
1969         jQuery('#generic_save_analysis_result_values_type').val('analysis_result_values_match_precomputed_design');
1970         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(drone_imagery_stats_result_summary));
1971         jQuery('#generic_save_analysis_model_language').val(manage_drone_imagery_calculate_statistics_response.analysis_model_language);
1972         jQuery('#generic_save_analysis_model_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_type);
1973         jQuery('#generic_save_analysis_model_application_name').val(manage_drone_imagery_calculate_statistics_response.application_name);
1974         jQuery('#generic_save_analysis_model_application_version').val(manage_drone_imagery_calculate_statistics_response.application_version);
1975         //jQuery('#generic_save_analysis_model_file').val();
1976         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
1977         jQuery('#generic_save_analysis_model_training_data_file').val(manage_drone_imagery_calculate_statistics_response.stats_tempfile);
1978         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type);
1979         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(drone_imagery_stats_auxiliary_files));
1980
1981         return false;
1982     });
1983
1984     jQuery('#drone_imagery_calculate_statistics_analysis_save_blups_pe').click(function(){
1985         if (manage_drone_imagery_calculate_statistics_field_trial_id_array.length>1) {
1986             alert('Saving spatial BLUPs currently only implemented for a single trial, so only select one field trial in your analysis');
1987             return false;
1988         }
1989
1990         jQuery('#generic_save_analysis_dialog').modal('show');
1991
1992         var drone_imagery_stats_result_summary = {};
1993
1994         var drone_imagery_stats_tolparinv_param = jQuery('#drone_image_calculate_statistics_tolparinv_select').val();
1995         var drone_imagery_legendre_order = jQuery('#drone_image_calculate_statistics_legendre_order_number_select').val();
1996         var drone_imagery_permanent_env_structure = jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').val();
1997
1998         var drone_imagery_stats_protocol = '';
1999         var statistical_ontology_term;
2000         var drone_imagery_stats_auxiliary_files;
2001         var drone_imagery_stats_training_data_file;
2002         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups') {
2003
2004             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
2005
2006             drone_imagery_stats_auxiliary_files = [
2007                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_grm_file'},
2008                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_genetic_coefficients_file'},
2009                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_permanent_environment_coefficients_file'}
2010             ];
2011
2012             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000004";
2013
2014             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
2015         }
2016         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
2017
2018             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
2019
2020             drone_imagery_stats_auxiliary_files = [
2021                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_grm_file'},
2022                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_genetic_coefficients_file'},
2023                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_permanent_environment_coefficients_file'}
2024             ];
2025
2026             statistical_ontology_term = "Multivariate linear mixed model genetic BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000006";
2027
2028             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
2029         }
2030         if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups') {
2031             drone_imagery_stats_protocol = 'blupf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2032
2033             statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using BLUPf90|SGNSTAT:0000011";
2034
2035             drone_imagery_stats_auxiliary_files = [
2036                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
2037                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
2038                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
2039                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
2040                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
2041                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
2042             ];
2043             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2044                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
2045             }
2046
2047             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2048         }
2049         else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
2050             drone_imagery_stats_protocol = 'blupf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2051
2052             statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using BLUPf90|SGNSTAT:0000009";
2053
2054             drone_imagery_stats_auxiliary_files = [
2055                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
2056                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
2057                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
2058                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
2059                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
2060                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
2061             ];
2062             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2063                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
2064             }
2065
2066             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2067         }
2068         if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
2069             drone_imagery_stats_protocol = 'airemlf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2070
2071             statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using AIREMLf90|SGNSTAT:0000021";
2072
2073             drone_imagery_stats_auxiliary_files = [
2074                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
2075                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
2076                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
2077                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
2078                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
2079                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'}
2080             ];
2081             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2082                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
2083             }
2084
2085             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2086         }
2087         else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups') {
2088             drone_imagery_stats_protocol = 'airemlf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2089
2090             statistical_ontology_term = "Multivariate linear mixed model permanent environment BLUPs using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using AIREMLf90|SGNSTAT:0000019";
2091
2092             drone_imagery_stats_auxiliary_files = [
2093                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
2094                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
2095                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
2096                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
2097                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
2098                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'}
2099             ];
2100             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2101                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
2102             }
2103
2104             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2105         }
2106
2107         var drone_imagery_stats_parameters = {
2108             'tolparinv':drone_imagery_stats_tolparinv_param,
2109             'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
2110             'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
2111             'legendre_polynomial_order':drone_imagery_legendre_order,
2112             'protocol':drone_imagery_stats_protocol,
2113             'permanent_environment_structure':drone_imagery_permanent_env_structure
2114         };
2115
2116         jQuery('#generic_save_analysis_protocol').val(drone_imagery_stats_protocol);
2117         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(drone_imagery_stats_parameters));
2118         //jQuery('#generic_save_analysis_dataset_id').val();
2119         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions));
2120         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_traits));
2121         jQuery('#generic_save_analysis_statistical_ontology_term').val(statistical_ontology_term);
2122         jQuery('#generic_save_analysis_design').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.field_trial_design));
2123         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_blup_pe_data));
2124         jQuery('#generic_save_analysis_result_values_type').val('analysis_result_values_match_precomputed_design');
2125         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(drone_imagery_stats_result_summary));
2126         jQuery('#generic_save_analysis_model_language').val(manage_drone_imagery_calculate_statistics_response.analysis_model_language);
2127         jQuery('#generic_save_analysis_model_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_type);
2128         jQuery('#generic_save_analysis_model_application_name').val(manage_drone_imagery_calculate_statistics_response.application_name);
2129         jQuery('#generic_save_analysis_model_application_version').val(manage_drone_imagery_calculate_statistics_response.application_version);
2130         //jQuery('#generic_save_analysis_model_file').val();
2131         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
2132         jQuery('#generic_save_analysis_model_training_data_file').val(drone_imagery_stats_training_data_file);
2133         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type);
2134         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(drone_imagery_stats_auxiliary_files));
2135
2136         return false;
2137     });
2138
2139     jQuery('#drone_imagery_calculate_statistics_analysis_save_residuals').click(function(){
2140         jQuery('#generic_save_analysis_dialog').modal('show');
2141
2142         var drone_imagery_stats_result_summary = {};
2143
2144         jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.trait_composing_info));
2145
2146         var drone_imagery_stats_tolparinv_param = jQuery('#drone_image_calculate_statistics_tolparinv_select').val();
2147         var drone_imagery_legendre_order = jQuery('#drone_image_calculate_statistics_legendre_order_number_select').val();
2148         var drone_imagery_permanent_env_structure = jQuery('#drone_image_calculate_statistics_permanent_env_structure_select').val();
2149
2150         var drone_imagery_stats_protocol = '';
2151         var statistical_ontology_term;
2152         var drone_imagery_stats_auxiliary_files;
2153         var drone_imagery_stats_training_data_file;
2154         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_dap_genetic_blups') {
2155
2156             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_DAP, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
2157
2158             drone_imagery_stats_auxiliary_files = [
2159                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_grm_file'},
2160                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_genetic_coefficients_file'},
2161                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_permanent_environment_coefficients_file'},
2162                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_DAP_genetic_blups_residual_file'}
2163             ];
2164
2165             statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using Sommer R|SGNSTAT:0000030";
2166
2167             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
2168         }
2169         if (manage_drone_imagery_calculate_statistics_select == 'sommer_grm_temporal_random_regression_gdd_genetic_blups') {
2170
2171             drone_imagery_stats_protocol = 'mmer(value~1+replicate, random=~vs(id, Gu=geno_mat) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), id) +vs(leg(time_GDD, '+drone_imagery_legendre_order+', intercept=TRUE), plot_id), rcov=~vs(units), data=mat_long_format, tolparinv='+drone_imagery_stats_tolparinv_param+');';
2172
2173             drone_imagery_stats_auxiliary_files = [
2174                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_grm_file'},
2175                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_genetic_coefficients_file'},
2176                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_permanent_environment_coefficients_file'},
2177                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'nicksmixedmodels_v1.01_sommer_grm_temporal_legendre_polynomial_GDD_genetic_blups_residual_file'}
2178             ];
2179
2180             statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using Sommer R|SGNSTAT:0000031";
2181
2182             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.stats_tempfile;
2183         }
2184         if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_gdd_blups') {
2185             drone_imagery_stats_protocol = 'blupf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2186
2187             statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using BLUPf90|SGNSTAT:0000029";
2188
2189             drone_imagery_stats_auxiliary_files = [
2190                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
2191                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
2192                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
2193                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
2194                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
2195                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'},
2196                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_residual_file'}
2197             ];
2198             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2199                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
2200             }
2201
2202             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2203         }
2204         else if (manage_drone_imagery_calculate_statistics_select == 'blupf90_grm_random_regression_dap_blups') {
2205             drone_imagery_stats_protocol = 'blupf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2206
2207             statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using BLUPf90|SGNSTAT:0000028";
2208
2209             drone_imagery_stats_auxiliary_files = [
2210                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
2211                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
2212                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
2213                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
2214                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
2215                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'},
2216                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_residual_file'}
2217             ];
2218             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2219                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'blupf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
2220             }
2221
2222             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2223         }
2224         if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_gdd_blups') {
2225             drone_imagery_stats_protocol = 'airemlf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2226
2227             statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on growing degree days computed using AIREMLf90|SGNSTAT:0000027";
2228
2229             drone_imagery_stats_auxiliary_files = [
2230                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_grm_file'},
2231                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_param_file'},
2232                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_log_file'},
2233                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_genetic_coefficients_file'},
2234                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_permanent_environment_coefficients_file'},
2235                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_solutions_file'},
2236                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_permanent_environment_blups_residual_file'}
2237             ];
2238             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2239                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_GDD_blups_permanent_environment_structure_file'});
2240             }
2241
2242             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2243         }
2244         else if (manage_drone_imagery_calculate_statistics_select == 'airemlf90_grm_random_regression_dap_blups') {
2245             drone_imagery_stats_protocol = 'airemlf90(random regression GRM and Permanent Environment '+drone_imagery_permanent_env_structure+', conv_crit='+drone_imagery_stats_tolparinv_param+');';
2246
2247             statistical_ontology_term = "Multivariate linear mixed model residual using genetic relationship matrix and temporal Legendre polynomial random regression on days after planting computed using AIREMLf90|SGNSTAT:0000026";
2248
2249             drone_imagery_stats_auxiliary_files = [
2250                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_grm_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_grm_file'},
2251                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_param_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_param_file'},
2252                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.stats_out_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_log_file'},
2253                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_genetic_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_genetic_coefficients_file'},
2254                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.rr_pe_coefficients, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_permanent_environment_coefficients_file'},
2255                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_solutions, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_solutions_file'},
2256                 {'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.yhat_residual_tempfile, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_permanent_environment_blups_residual_file'}
2257             ];
2258             if (drone_imagery_permanent_env_structure == 'euclidean_rows_and_columns') {
2259                 drone_imagery_stats_auxiliary_files.push({'auxiliary_model_file':manage_drone_imagery_calculate_statistics_response.blupf90_permanent_environment_structure_file, auxiliary_model_file_archive_type:'airemlf90_grm_temporal_leg_random_regression_DAP_blups_permanent_environment_structure_file'});
2260             }
2261
2262             drone_imagery_stats_training_data_file = manage_drone_imagery_calculate_statistics_response.blupf90_training_file;
2263         }
2264
2265         var drone_imagery_stats_parameters = {
2266             'tolparinv':drone_imagery_stats_tolparinv_param,
2267             'genotyping_protocol_id':jQuery('#drone_image_calculate_statistics_genotyping_protocol_select').val(),
2268             'compute_genotypes_from_parents':jQuery('#drone_image_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
2269             'legendre_polynomial_order':drone_imagery_legendre_order,
2270             'protocol':drone_imagery_stats_protocol,
2271             'permanent_environment_structure':drone_imagery_permanent_env_structure
2272         };
2273
2274         jQuery('#generic_save_analysis_protocol').val(drone_imagery_stats_protocol);
2275         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(drone_imagery_stats_parameters));
2276         //jQuery('#generic_save_analysis_dataset_id').val();
2277         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_accessions));
2278         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.unique_residual_traits));
2279         jQuery('#generic_save_analysis_statistical_ontology_term').val(statistical_ontology_term);
2280         jQuery('#generic_save_analysis_design').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.field_trial_design));
2281         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(manage_drone_imagery_calculate_statistics_response.result_residual_data));
2282         jQuery('#generic_save_analysis_result_values_type').val('analysis_result_values_match_precomputed_design');
2283         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(drone_imagery_stats_result_summary));
2284         jQuery('#generic_save_analysis_model_language').val(manage_drone_imagery_calculate_statistics_response.analysis_model_language);
2285         jQuery('#generic_save_analysis_model_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_type);
2286         jQuery('#generic_save_analysis_model_application_name').val(manage_drone_imagery_calculate_statistics_response.application_name);
2287         jQuery('#generic_save_analysis_model_application_version').val(manage_drone_imagery_calculate_statistics_response.application_version);
2288         //jQuery('#generic_save_analysis_model_file').val();
2289         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
2290         jQuery('#generic_save_analysis_model_training_data_file').val(manage_drone_imagery_calculate_statistics_response.stats_tempfile);
2291         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(manage_drone_imagery_calculate_statistics_response.analysis_model_training_data_file_type);
2292         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(drone_imagery_stats_auxiliary_files));
2293
2294         return false;
2295     });
2296 });
2297
2298 </script>