mason/analyses/analysis_calculate_statistics.mas

   1 analysis_calculate_statistics_select<%args>
   2 </%args>
   3
   4 <!--button class='btn btn-primary' style='margin:3px;float:right' id='analysis_calculate_statistics_link'>Single/Multi Trial GEBV Analysis</button-->
   5
   6 <div class="modal fade" id="analysis_calculate_statistics_dialog" name="analysis_calculate_statistics_dialog" tabindex="-1" role="dialog" aria-labelledby="analysisCalculateStatisticsDialog" 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="analysisCalculateStatisticsDialog">Calculate statistics</h4>
  12       </div>
  13       <div class="modal-body">
  14         <div class="container-fluid">
  15
  16             <&| /util/workflow.mas, id=> "analysis_calculate_statistics_workflow" &>
  17                 <&| /util/workflow.mas:step, title=> "Field Trial" &>
  18                     <& /page/page_title.mas, title=>"Select the field trial(s) you are interested in." &>
  19                     <br/><br/>
  20                     <form class="form-horizontal">
  21                         <div class="form-group">
  22                             <label class="col-sm-3 control-label">Field Trial(s): </label>
  23                             <div class="col-sm-9" >
  24                                 <div id="analysis_calculate_statistics_trial_select_div"></div>
  25                             </div>
  26                         </div>
  27                     </form>
  28                     <center>
  29                     <button class="btn btn-primary" id="analysis_calculate_statistics_field_trial_select_step">Go to Next Step</button>
  30                     </center>
  31                 </&>
  32                 <&| /util/workflow.mas:step, title=> "Trait Selection" &>
  33                     <& /page/page_title.mas, title=>"Select the observation variable you are interested in" &>
  34                     <br/><br/>
  35                     <form class="form-horizontal">
  36                         <div class="form-group">
  37                             <label class="col-sm-3 control-label">Observation Variables Phenotyped in the Selected Field Trial(s): </label>
  38                             <div class="col-sm-9" >
  39                                 <div id="analysis_calculate_statistics_trait_select_div"></div>
  40                             </div>
  41                         </div>
  42                     </form>
  43                     <center>
  44                     <button class="btn btn-primary" id="analysis_calculate_statistics_trait_select_step">Go to Next Step</button>
  45                     </center>
  46                 </&>
  47                 <&| /util/workflow.mas:step, title=> "Statistics" &>
  48                     <& /page/page_title.mas, title=>"Select statistics to calculate" &>
  49
  50                     <div id="analysis_calculate_statistics_model_select_div"></div>
  51
  52                     <br/><br/>
  53                     <center>
  54                     <button class="btn btn-default" id="analysis_calculate_statistics_create_new_model_button">My Model is Not Shown, So Create New Model</button>
  55                     </center>
  56
  57                     <div id="analysis_calculate_statistics_create_new_model_div" style="display:none">
  58                         <hr>
  59
  60                         <div class="well well-sm">
  61                             <select class="form-control" id="analysis_calculate_statistics_select_input">
  62                                 <option value="">Select A Model</option>
  63                                 <option value="lmer_germplasmname_replicate">LMER BLUPs y~replicate+location_year+1|Germplasm. Univariate genetic effects across location_years</option>
  64                                 <option value="sommer_grm_genetic_blups">Sommer GBLUPs Y~replicate+location_year+GRM. Multivariate genetic effects using GRM across location_years</option>
  65                                 <option value="sommer_grm_spatial_genetic_blups">Sommer Spatial GBLUPs Y~replicate+location_year+GRM+spatial. Multivariate genetic + 2Dspl spatial effects across location_years</option>
  66                             </select>
  67
  68                             <div id="analysis_calculate_statistics_relationship_matrix_type_div" style="display:none">
  69                                 <hr>
  70                                 <div class="form-horizontal">
  71                                     <div class="form-group">
  72                                         <label class="col-sm-3 control-label">Relationship Matrix Type: </label>
  73                                         <div class="col-sm-9" >
  74                                             <select class="form-control" id="analysis_calculate_statistics_relationship_matrix_type_select_div">
  75                                                 <option value="">Identity</option>
  76                                                 <option value="htp_phenotypes">High-throughput Phenotyping Data</option>
  77                                                 <option value="genotypes">Genotyping Data</option>
  78                                             </select>
  79                                         </div>
  80                                     </div>
  81                                 </div>
  82                             </div>
  83
  84                             <div id="analysis_calculate_statistics_genotyping_protocol_div" style="display:none">
  85                                 <hr>
  86                                 <div class="form-horizontal">
  87                                     <div class="form-group">
  88                                         <label class="col-sm-3 control-label">Genotyping Protocol To Calculate Genomic Relationship Matrix (optional. If none selected, an identity matrix is used): </label>
  89                                         <div class="col-sm-9" >
  90                                             <div id="analysis_calculate_statistics_genotyping_protocol_select_div"></div>
  91                                         </div>
  92                                     </div>
  93                                     <div class="form-group">
  94                                         <label class="col-sm-3 control-label">Compute Genotypes From Parents: </label>
  95                                         <div class="col-sm-9" >
  96                                             <select class="form-control" id="analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select">
  97                                                 <option value="no">No</option>
  98                                                 <option value="yes">Yes</option>
  99                                             </select>
 100                                         </div>
 101                                     </div>
 102                                 </div>
 103                             </div>
 104
 105                             <div id="analysis_calculate_statistics_htp_phenotypes_rel_matrix_div" class="well well-sm" style="display:none">
 106                                 <div class="form-horizontal">
 107                                     <div class="form-group">
 108                                         <label class="col-sm-3 control-label">How to calculate the relationship matrix with high-throughput phenotypes: </label>
 109                                         <div class="col-sm-9" >
 110                                             <select class="form-control" id="analysis_calculate_statistics_htp_phenotypes_rel_matrix_select">
 111                                                 <option value="correlations">Correlations</option>
 112                                                 <option value="blues">BLUEs</option>
 113                                             </select>
 114                                         </div>
 115                                     </div>
 116                                     <div class="form-group">
 117                                         <label class="col-sm-3 control-label">Time Points to Use: </label>
 118                                         <div class="col-sm-9" >
 119                                             <select class="form-control" id="analysis_calculate_statistics_htp_phenotypes_rel_matrix_times_select">
 120                                                 <option value="all">All Available</option>
 121                                                 <option value="latest_trait">Up to latest days after planting selecting in traits</option>
 122                                                 <option value="vegetative" disabled>Vegetative Growth Stage</option>
 123                                                 <option value="reproductive" disabled>Reproductive Growth Stage</option>
 124                                                 <option value="mature" disabled>Mature Growth Stage</option>
 125                                             </select>
 126                                         </div>
 127                                     </div>
 128                                     <div class="form-group" id="analysis_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select_div" style="display:none">
 129                                         <label class="col-sm-3 control-label">HTP BLUEs Inversion Tolerance: </label>
 130                                         <div class="col-sm-9" >
 131                                             <select class="form-control" id="analysis_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select">
 132                                                 <option value="0.00001">0.00001</option>
 133                                                 <option value="0.0001">0.0001</option>
 134                                                 <option value="0.001">0.001</option>
 135                                                 <option value="0.01">0.01</option>
 136                                                 <option value="0.1">0.1</option>
 137                                                 <option value="0.5">0.5</option>
 138                                             </select>
 139                                         </div>
 140                                     </div>
 141                                 </div>
 142                             </div>
 143
 144                             <hr>
 145                             <div class="form-horizontal">
 146                                 <div class="form-group">
 147                                     <label class="col-sm-3 control-label">Inversion Tolerance: </label>
 148                                     <div class="col-sm-9" >
 149                                         <select class="form-control" id="analysis_calculate_statistics_tolparinv_select">
 150                                             <option value="0.000001">0.000001</option>
 151                                             <option value="0.00001">0.00001</option>
 152                                             <option value="0.0001">0.0001</option>
 153                                             <option value="0.001">0.001</option>
 154                                             <option value="0.01">0.01</option>
 155                                             <option value="0.05">0.05</option>
 156                                             <option value="0.08">0.08</option>
 157                                             <option value="0.1">0.1</option>
 158                                             <option value="0.2">0.2</option>
 159                                             <option value="0.5">0.5</option>
 160                                         </select>
 161                                     </div>
 162                                 </div>
 163                             </div>
 164
 165                             <hr>
 166                             <div class="form-horizontal">
 167                                 <div class="form-group">
 168                                     <label class="col-sm-3 control-label">Fixed Effects: </label>
 169                                     <div class="col-sm-9" >
 170                                         <select class="form-control" id="analysis_calculate_statistics_fixed_effect_select_div">
 171                                             <option value="replicate">Replicate</option>
 172                                             <option value="fixed_effect_trait">Select a continuous trait (e.g. soil elevation curvature)</option>
 173                                         </select>
 174                                     </div>
 175                                 </div>
 176                                 <div class="form-group" id="analysis_calculate_statistics_fixed_effect_select_trait_div" style="display:none">
 177                                     <label class="col-sm-3 control-label">Fixed Effect Trait: </label>
 178                                     <div class="col-sm-9" >
 179                                         <div id="analysis_calculate_statistics_fixed_effect_trait_select_div"></div>
 180                                     </div>
 181                                 </div>
 182                                 <div class="form-group" id="analysis_calculate_statistics_fixed_effect_select_quantile_div" style="display:none">
 183                                     <label class="col-sm-3 control-label">Fixed Effect Continuous Trait Quantile Binning: </label>
 184                                     <div class="col-sm-9" >
 185                                         <select class="form-control" id="analysis_calculate_statistics_fixed_effect_select_quantile">
 186                                             <option value="10">10% Quantiles</option>
 187                                             <option value="5">20% Quantiles</option>
 188                                             <option value="4">25% Quantiles</option>
 189                                             <option value="3">33% Quantiles</option>
 190                                             <option value="20">5% Quantiles</option>
 191                                         </select>
 192                                     </div>
 193                                 </div>
 194                             </div>
 195
 196                         </div>
 197
 198                     </div>
 199
 200                     <br/><br/>
 201                     <center>
 202                     <button class="btn btn-primary" id="analysis_calculate_statistics_select_step">Submit</button>
 203                     </center>
 204                 </&>
 205                 <&| /util/workflow.mas:step, title=> "Results" &>
 206                     <& /page/page_title.mas, title=>"Statistics results" &>
 207
 208                     <hr>
 209                     <button class="btn btn-primary" id="analysis_calculate_statistics_analysis_save_blups_genetic_pe_residual" style="display:none">Go To Save Analysis Results For Genetic and Environment BLUPS and Residuals</button>
 210                     <button class="btn btn-primary" id="analysis_calculate_statistics_analysis_save_blups_genetic" style="display:none">Go To Save Analysis Results For Genetic BLUPS</button>
 211                     <button class="btn btn-primary" id="analysis_calculate_statistics_analysis_save_blups_spatial" style="display:none">Go To Save Analysis Results For Spatial BLUPS</button>
 212                     <button class="btn btn-primary" id="analysis_calculate_statistics_analysis_save_residuals" style="display:none">Go To Save Analysis Results For Residuals</button>
 213                     <button class="btn btn-primary" id="analysis_calculate_statistics_analysis_save_fitted" style="display:none">Go To Save Analysis Results For Fitted Values</button>
 214                     <hr>
 215
 216                     <div id ="analysis_calculate_statistics_result_div">
 217                     </div>
 218                 </&>
 219             </&>
 220
 221         </div>
 222
 223       </div>
 224       <div class="modal-footer">
 225         <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
 226       </div>
 227     </div>
 228   </div>
 229 </div>
 230
 231 <script>
 232
 233 jQuery(document).ready(function() {
 234
 235     //
 236     // Calculate statistics
 237     //
 238
 239     var analysis_calculate_statistics_field_trial_id_array = undefined;
 240     var analysis_calculate_statistics_field_trial_id_string = "";
 241     var analysis_calculate_statistics_trait_id = [];
 242     var analysis_calculate_statistics_trait_names = [];
 243     var analysis_calculate_statistics_accession_names = [];
 244     var analysis_calculate_statistics_plot_names = [];
 245     var analysis_calculate_statistics_select = '';
 246     var analysis_calculate_statistics_phenotype_training_file;
 247     var analysis_calculate_statistics_grm_training_file;
 248     var analysis_calculate_statistics_response = {};
 249
 250     jQuery('#analysis_calculate_statistics_link').click(function(){
 251         get_select_box('trials', 'analysis_calculate_statistics_trial_select_div', { 'name' : 'analysis_calculate_statistics_field_trial_id', 'id' : 'analysis_calculate_statistics_field_trial_id', 'empty':1, 'multiple':1, 'include_location_year':1 });
 252
 253         jQuery('#analysis_calculate_statistics_dialog').modal('show');
 254     });
 255
 256     jQuery('#analysis_calculate_statistics_field_trial_select_step').click(function(){
 257         analysis_calculate_statistics_field_trial_id_array = undefined;
 258         analysis_calculate_statistics_field_trial_id_string = "";
 259         analysis_calculate_statistics_field_trial_id_array = jQuery('#analysis_calculate_statistics_field_trial_id').val();
 260
 261         analysis_calculate_statistics_field_trial_id_string = analysis_calculate_statistics_field_trial_id_array.join(",");
 262         if (analysis_calculate_statistics_field_trial_id_string == '') {
 263             alert('Please select a field trial first!');
 264         } else {
 265             get_select_box('traits', 'analysis_calculate_statistics_trait_select_div', { 'name' : 'analysis_calculate_statistics_trait_id_select', 'id' : 'analysis_calculate_statistics_trait_id_select', 'empty':1, 'multiple':0, 'trial_ids':analysis_calculate_statistics_field_trial_id_string, 'stock_type':'plot' });
 266
 267             get_select_box('traits', 'analysis_calculate_statistics_permanent_env_structure_phenotype_correlation_select_div', { 'name' : 'analysis_calculate_statistics_permanent_env_structure_phenotype_correlation_select', 'id' : 'analysis_calculate_statistics_permanent_env_structure_phenotype_correlation_select', 'empty':1, 'multiple':1, 'size': 20, 'trial_ids':analysis_calculate_statistics_field_trial_id_string, 'stock_type':'plot' });
 268
 269             get_select_box('traits', 'analysis_calculate_statistics_permanent_env_structure_phenotype_select_div', { 'name' : 'analysis_calculate_statistics_permanent_env_structure_phenotype_select', 'id' : 'analysis_calculate_statistics_permanent_env_structure_phenotype_select', 'empty':1, 'multiple':1, 'size':20, 'trial_ids':analysis_calculate_statistics_field_trial_id_string, 'stock_type':'plot' });
 270
 271             get_select_box('traits', 'analysis_calculate_statistics_fixed_effect_trait_select_div', { 'name' : 'analysis_calculate_statistics_fixed_effect_trait_select', 'id' : 'analysis_calculate_statistics_fixed_effect_trait_select', 'empty':0, 'multiple':0, 'trial_ids':analysis_calculate_statistics_field_trial_id_string, 'stock_type':'plot' });
 272
 273             get_select_box('genotyping_protocol', 'analysis_calculate_statistics_genotyping_protocol_select_div', { 'name' : 'analysis_calculate_statistics_genotyping_protocol_select', 'id' : 'analysis_calculate_statistics_genotyping_protocol_select', 'empty':1 });
 274
 275             get_select_box('models', 'analysis_calculate_statistics_model_select_div', { 'name' : 'analysis_calculate_statistics_model_select', 'id' : 'analysis_calculate_statistics_model_select', 'empty':0, 'nd_protocol_type':'analysis_model_properties_multi_trial' });
 276
 277             Workflow.complete("#analysis_calculate_statistics_field_trial_select_step");
 278             Workflow.focus('#analysis_calculate_statistics_workflow', 1);
 279         }
 280         return false;
 281     });
 282
 283     jQuery('#analysis_calculate_statistics_trait_select_step').click(function(){
 284         analysis_calculate_statistics_trait_id = undefined;
 285
 286         analysis_calculate_statistics_trait_id = jQuery('#analysis_calculate_statistics_trait_id_select').val();
 287         if (analysis_calculate_statistics_trait_id == null || analysis_calculate_statistics_trait_id == undefined) {
 288             alert('Please select one observation variable!');
 289             return false;
 290         }
 291
 292         Workflow.complete("#analysis_calculate_statistics_trait_select_step");
 293         Workflow.focus('#analysis_calculate_statistics_workflow', 2);
 294         return false;
 295     });
 296
 297     jQuery('#analysis_calculate_statistics_create_new_model_button').click(function(){
 298         jQuery('#analysis_calculate_statistics_create_new_model_div').show();
 299     });
 300
 301     jQuery('#analysis_calculate_statistics_select_input').change(function(){
 302         jQuery("#analysis_calculate_statistics_relationship_matrix_type_select_div").val('').change();
 303         jQuery("#analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select").val('no').change();
 304
 305         analysis_calculate_statistics_select = jQuery('#analysis_calculate_statistics_select_input').val();
 306         if (analysis_calculate_statistics_select == 'lmer_germplasmname_replicate') {
 307             jQuery('#analysis_calculate_statistics_relationship_matrix_type_div').hide();
 308             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').hide();
 309             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 310             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic').show();
 311             jQuery('#analysis_calculate_statistics_analysis_save_blups_spatial').hide();
 312             jQuery('#analysis_calculate_statistics_analysis_save_residuals').hide();
 313             jQuery('#analysis_calculate_statistics_analysis_save_fitted').hide();
 314             jQuery('#analysis_calculate_statistics_random_regression_pe_structure_div').hide();
 315         }
 316         else if (analysis_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 317             jQuery('#analysis_calculate_statistics_relationship_matrix_type_div').show();
 318             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').hide();
 319             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic_pe_residual').show();
 320             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic').hide();
 321             jQuery('#analysis_calculate_statistics_analysis_save_blups_spatial').hide();
 322             jQuery('#analysis_calculate_statistics_analysis_save_residuals').hide();
 323             jQuery('#analysis_calculate_statistics_analysis_save_fitted').hide();
 324             jQuery('#analysis_calculate_statistics_random_regression_pe_structure_div').hide();
 325         }
 326         else if (analysis_calculate_statistics_select == 'sommer_grm_genetic_blups') {
 327             jQuery('#analysis_calculate_statistics_relationship_matrix_type_div').show();
 328             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').hide();
 329             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 330             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic').show();
 331             jQuery('#analysis_calculate_statistics_analysis_save_blups_spatial').hide();
 332             jQuery('#analysis_calculate_statistics_analysis_save_residuals').hide();
 333             jQuery('#analysis_calculate_statistics_analysis_save_fitted').hide();
 334             jQuery('#analysis_calculate_statistics_random_regression_pe_structure_div').hide();
 335         }
 336         else {
 337             jQuery('#analysis_calculate_statistics_relationship_matrix_type_div').hide();
 338             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').hide();
 339             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic_pe_residual').hide();
 340             jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic').hide();
 341             jQuery('#analysis_calculate_statistics_analysis_save_blups_spatial').hide();
 342             jQuery('#analysis_calculate_statistics_analysis_save_residuals').hide();
 343             jQuery('#analysis_calculate_statistics_analysis_save_fitted').hide();
 344             jQuery('#analysis_calculate_statistics_random_regression_pe_structure_div').hide();
 345         }
 346
 347     });
 348
 349     jQuery('#analysis_calculate_statistics_relationship_matrix_type_select_div').change(function(){
 350         if (jQuery(this).val() == 'genotypes') {
 351             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').show();
 352             jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_div').hide();
 353         }
 354         else if (jQuery(this).val() == 'htp_phenotypes') {
 355             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').hide();
 356             jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_div').show();
 357         }
 358         else {
 359             jQuery('#analysis_calculate_statistics_genotyping_protocol_div').hide();
 360             jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_div').hide();
 361         }
 362     });
 363
 364     jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_select').change(function(){
 365         if (jQuery(this).val() == 'blues') {
 366             jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select_div').show();
 367         }
 368         else {
 369             jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select_div').hide();
 370         }
 371     });
 372
 373     jQuery('#analysis_calculate_statistics_fixed_effect_select_div').change(function(){
 374         if (jQuery(this).val() == 'replicate') {
 375             jQuery('#analysis_calculate_statistics_fixed_effect_select_trait_div').hide();
 376             jQuery('#analysis_calculate_statistics_fixed_effect_select_quantile_div').hide();
 377         }
 378         if (jQuery(this).val() == 'fixed_effect_trait') {
 379             jQuery('#analysis_calculate_statistics_fixed_effect_select_trait_div').show();
 380             jQuery('#analysis_calculate_statistics_fixed_effect_select_quantile_div').show();
 381         }
 382     });
 383
 384     jQuery('#analysis_calculate_statistics_select_step').click(function(){
 385
 386         analysis_calculate_statistics_select = jQuery('#analysis_calculate_statistics_select_input').val();
 387
 388         jQuery.ajax({
 389             url : '/api/drone_imagery/calculate_statistics',
 390             type : 'POST',
 391             data : {
 392                 'observation_variable_id_list':analysis_calculate_statistics_trait_id,
 393                 'field_trial_id_list':JSON.stringify(analysis_calculate_statistics_field_trial_id_array),
 394                 'statistics_select':analysis_calculate_statistics_select,
 395                 'relationship_matrix_type':jQuery('#analysis_calculate_statistics_relationship_matrix_type_select_div').val(),
 396                 'protocol_id':jQuery('#analysis_calculate_statistics_genotyping_protocol_select').val(),
 397                 'compute_from_parents':jQuery('#analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select').val(),
 398                 'htp_pheno_rel_matrix_type':jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_select').val(),
 399                 'htp_pheno_rel_matrix_time_points':jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_times_select').val(),
 400                 'htp_pheno_rel_matrix_blues_inversion':jQuery('#analysis_calculate_statistics_htp_phenotypes_rel_matrix_inversion_select').val(),
 401                 'tolparinv':jQuery('#analysis_calculate_statistics_tolparinv_select').val(),
 402                 'legendre_order_number':jQuery('#analysis_calculate_statistics_legendre_order_number_select').val(),
 403                 'fixed_effect_type':jQuery('#analysis_calculate_statistics_fixed_effect_select_div').val(),
 404                 'fixed_effect_trait_id':jQuery('#analysis_calculate_statistics_fixed_effect_trait_select').val(),
 405                 'fixed_effect_quantiles':jQuery('#analysis_calculate_statistics_fixed_effect_select_quantile').val()
 406             },
 407             beforeSend: function() {
 408                 jQuery("#working_modal").modal("show");
 409             },
 410             success: function(response){
 411                 console.log(response);
 412                 jQuery("#working_modal").modal("hide");
 413
 414                 if (response.error) {
 415                     alert(response.error);
 416                 }
 417                 else {
 418                     analysis_calculate_statistics_response = response;
 419
 420                     var html = '';
 421                     if (response.sum_square_residual) {
 422                         html = html + '<h4>Sum square residual: '+response.sum_square_residual+'</h4><hr>';
 423                     }
 424                     if (response.genetic_effects_line_plot) {
 425                         html = html + '<img src="'+response.genetic_effects_line_plot+'"><hr>';
 426                     }
 427                     if (response.env_effects_heatmap_plot) {
 428                         html = html + '<img src="'+response.env_effects_heatmap_plot+'"><hr>';
 429                     }
 430                     if (response.unique_accessions.length > 0 && response.unique_traits.length > 0 && response.result_blup_genetic_data) {
 431                         analysis_calculate_statistics_accession_names = response.unique_accessions;
 432                         analysis_calculate_statistics_trait_names = response.unique_traits;
 433                         analysis_calculate_statistics_phenotype_training_file = response.stats_tempfile;
 434                         analysis_calculate_statistics_grm_training_file = response.grm_file;
 435
 436                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Accessions</th>';
 437                         for (var i=0; i<analysis_calculate_statistics_trait_names.length; i++) {
 438                             html = html + '<th>'+analysis_calculate_statistics_trait_names[i]+'</th>';
 439                         }
 440                         html = html + '</tr></thead><tbody>';
 441                         for (var k=0; k<response.unique_accessions.length; k++) {
 442                             var acc = response.unique_accessions[k];
 443                             html = html + '<tr><td>'+acc+'</td>';
 444                             for (var i=0; i<analysis_calculate_statistics_trait_names.length; i++) {
 445                                 if (response.result_blup_genetic_data[acc] && response.result_blup_genetic_data[acc][analysis_calculate_statistics_trait_names[i]]) {
 446                                     html = html + '<td>'+response.result_blup_genetic_data[acc][analysis_calculate_statistics_trait_names[i]][0]+'</td>';
 447                                 }
 448                                 else {
 449                                     html = html + '<td>NA</td>';
 450                                 }
 451                             }
 452                             html = html + '</tr>';
 453                         }
 454                         html = html + '</tbody></table>';
 455                     }
 456
 457                     if (response.unique_plots.length > 0 && response.unique_traits.length > 0 && response.result_blup_spatial_data) {
 458                         analysis_calculate_statistics_plot_names = response.unique_plots;
 459                         analysis_calculate_statistics_trait_names = response.unique_traits;
 460
 461                         html = html + '<table class="table table-bordered table-hover"><thead><tr><th>Plots</th>';
 462                         for (var i=0; i<response.unique_traits.length; i++) {
 463                             html = html + '<th>'+response.unique_traits[i]+'</th>';
 464                         }
 465                         html = html + '</tr></thead><tbody>';
 466                         for (var k=0; k<response.unique_plots.length; k++) {
 467                             var plot = response.unique_plots[k];
 468                             html = html + '<tr><td>'+plot+'</td>';
 469                             for (var i=0; i<response.unique_traits.length; i++) {
 470                                 html = html + '<td>'+response.result_blup_spatial_data[plot][response.unique_traits[i]][0]+'</td>';
 471                             }
 472                             html = html + '</tr>';
 473                         }
 474                         html = html + '</tbody></table>';
 475                     }
 476
 477                     if (response.results.length > 0) {
 478                         html = '<table class="table table-bordered table-hover"><thead><tr><th>Observation Variable</th><th>Statistics</th><th>Plot</th></tr></thead><tbody>';
 479                         for (var i=0; i<response.results.length; i++) {
 480                             html = html + '<tr><td>'+response.results[i][0]+'</td><td>'+response.results[i][1]+'</td><td><img src="'+response.results[i][2]+'"></td></tr>';
 481                         }
 482                         html = html + '</tbody></table>';
 483                     }
 484
 485                     html = html + '<hr><a href="'+response.stats_out_tempfile_string+'.log" target=_blank>Stats file or log</a>';
 486
 487                     if (jQuery('#analysis_calculate_statistics_relationship_matrix_type_select_div').val() == 'htp_phenotypes') {
 488                         html = html + '<hr><a href="'+response.stats_out_htp_rel_tempfile_out_string+'" target=_blank>HTP Relationship Matrix</a>';
 489                     }
 490
 491                     jQuery('#analysis_calculate_statistics_result_div').html(html);
 492
 493                     Workflow.complete("#analysis_calculate_statistics_select_step");
 494                     Workflow.focus('#analysis_calculate_statistics_workflow', 3);
 495                 }
 496             },
 497             error: function(response){
 498                 jQuery("#working_modal").modal("hide");
 499                 alert('Error calculating statistics!')
 500             }
 501         });
 502     });
 503
 504     jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic_pe_residual').click(function(){
 505         jQuery('#generic_save_analysis_template_dialog').modal('show');
 506     });
 507
 508     jQuery('#generic_save_analysis_template_submit_button').click(function(){
 509         var generic_save_analysis_template_analysis_name = jQuery('#generic_save_analysis_template_analysis_name').val();
 510         var generic_save_analysis_template_analysis_description = jQuery('#generic_save_analysis_template_analysis_description').val();
 511         var generic_save_analysis_template_analysis_year = jQuery('#generic_save_analysis_template_analysis_year').val();
 512         var generic_save_analysis_template_breeding_program_id = jQuery('#generic_save_analysis_template_breeding_program_id').val();
 513
 514         if (generic_save_analysis_template_analysis_name == '') {
 515             alert('Please give an analysis template name');
 516             return false;
 517         }
 518         if (generic_save_analysis_template_analysis_description == '') {
 519             alert('Please give an analysis template description');
 520             return false;
 521         }
 522         if (generic_save_analysis_template_analysis_year == '') {
 523             alert('Please give an analysis template year');
 524             return false;
 525         }
 526
 527         var analysis_stats_parameters = {};
 528         var analysis_stats_protocol = '';
 529         var analysis_stats_auxiliary_files = [];
 530         var analysis_stats_result_summary = {};
 531         var analysis_statistical_ontology_term = '';
 532         var analysis_stats_compose_trait_info;
 533
 534         var analysis_stats_tolparinv_param = jQuery('#analysis_calculate_statistics_tolparinv_select').val();
 535         var analysis_stats_numbers_traits = analysis_calculate_statistics_response.unique_traits.length;
 536         var analysis_legendre_order = jQuery('#analysis_calculate_statistics_legendre_order_number_select').val();
 537         var analysis_genotyping_protocol_id = jQuery('#analysis_calculate_statistics_genotyping_protocol_select').val();
 538         var analysis_compute_genotypes_from_parents = jQuery('#analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select').val();
 539
 540         var analysis_stats_mv_traits = [];
 541         for (var i=1; i<analysis_stats_numbers_traits+1; i++) {
 542             analysis_stats_mv_traits.push('t'+i);
 543         }
 544         var analysis_stats_mv_traits_string = analysis_stats_mv_traits.join();
 545
 546         if (analysis_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 547
 548             analysis_stats_protocol = 'mmer('+analysis_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+analysis_stats_numbers_traits+')) +vs(rowNumberFactor, Gtc=diag('+analysis_stats_numbers_traits+')) +vs(colNumberFactor, Gtc=diag('+analysis_stats_numbers_traits+')) +vs(spl2D(rowNumber, colNumber), Gtc=diag('+analysis_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+analysis_stats_numbers_traits+')), data=mat, tolparinv='+analysis_stats_tolparinv_param+');';
 549
 550             analysis_stats_parameters = {
 551                 'tolparinv':analysis_stats_tolparinv_param,
 552                 'genotyping_protocol_id':analysis_genotyping_protocol_id,
 553                 'compute_genotypes_from_parents':analysis_compute_genotypes_from_parents,
 554                 'protocol':analysis_stats_protocol
 555             };
 556
 557             analysis_stats_auxiliary_files = [{'auxiliary_model_file':analysis_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nickssinglemultitrialgebvanalyses_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
 558
 559             analysis_stats_compose_trait_info = JSON.stringify(analysis_calculate_statistics_response.trait_composing_info);
 560
 561             analysis_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";
 562         }
 563         if (analysis_calculate_statistics_select == 'sommer_grm_genetic_blups') {
 564
 565             analysis_stats_protocol = 'mmer('+analysis_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+analysis_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+analysis_stats_numbers_traits+')), data=mat, tolparinv='+analysis_stats_tolparinv_param+');';
 566
 567             analysis_stats_parameters = {
 568                 'tolparinv':analysis_stats_tolparinv_param,
 569                 'genotyping_protocol_id':analysis_genotyping_protocol_id,
 570                 'compute_genotypes_from_parents':analysis_compute_genotypes_from_parents,
 571                 'protocol':analysis_stats_protocol
 572             };
 573
 574             analysis_stats_auxiliary_files = [{'auxiliary_model_file':analysis_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nickssinglemultitrialgebvanalyses_v1.01_sommer_grm_genetic_blups_grm_file'}];
 575
 576             analysis_stats_compose_trait_info = JSON.stringify(analysis_calculate_statistics_response.trait_composing_info);
 577
 578             analysis_statistical_ontology_term = "Multivariate genetic BLUPs using genetic relationship matrix computed using Sommer R|SGNSTAT:0000024";
 579         }
 580
 581         var training_data_file = analysis_calculate_statistics_response.stats_tempfile;
 582
 583         if (analysis_calculate_statistics_select == 'lmer_germplasmname_replicate') {
 584             analysis_stats_protocol = 'lmer(t1~replicate + 1|germplasmName, data=mat, na.action = na.omit)';
 585             analysis_stats_parameters = {
 586                 'protocol':analysis_stats_protocol
 587             };
 588             analysis_statistical_ontology_term = "Univariate linear mixed model genetic BLUPs using germplasmName computed using LMER R|SGNSTAT:0000002";
 589         }
 590
 591         jQuery.ajax({
 592             type: 'POST',
 593             url : '/ajax/analysis/store/json',
 594             data : {
 595                 'analysis_to_save_boolean':'yes',
 596                 'analysis_name':generic_save_analysis_template_analysis_name+'_GBLUPS',
 597                 'analysis_description':generic_save_analysis_template_analysis_description,
 598                 'analysis_year':generic_save_analysis_template_analysis_year,
 599                 'analysis_breeding_program_id':generic_save_analysis_template_breeding_program_id,
 600                 'analysis_protocol':analysis_stats_protocol,
 601                 'analysis_dataset_id':'',
 602                 'analysis_accession_names':JSON.stringify(analysis_calculate_statistics_response.unique_accessions),
 603                 'analysis_trait_names':JSON.stringify(analysis_calculate_statistics_response.unique_traits),
 604                 'analysis_analysis_statistical_ontology_term':analysis_statistical_ontology_term,
 605                 'analysis_precomputed_design_optional':'',
 606                 'analysis_result_values':JSON.stringify(analysis_calculate_statistics_response.result_blup_genetic_data),
 607                 'analysis_result_values_type':'analysis_result_values_match_accession_names',
 608                 'analysis_result_summary':JSON.stringify(analysis_stats_result_summary),
 609                 'analysis_result_trait_compose_info':analysis_stats_compose_trait_info,
 610                 'analysis_model_id':'',
 611                 'analysis_model_name':generic_save_analysis_template_analysis_name+'_GBLUPSandPEandResiduals_Model',
 612                 'analysis_model_description':generic_save_analysis_template_analysis_description,
 613                 'analysis_model_is_public':'yes',
 614                 'analysis_model_language':analysis_calculate_statistics_response.analysis_model_language,
 615                 'analysis_model_type':analysis_calculate_statistics_response.analysis_model_type,
 616                 'analysis_model_properties':JSON.stringify(analysis_stats_parameters),
 617                 'analysis_model_application_name':analysis_calculate_statistics_response.application_name,
 618                 'analysis_model_application_version':analysis_calculate_statistics_response.application_version,
 619                 'analysis_model_file':'',
 620                 'analysis_model_file_type':'',
 621                 'analysis_model_training_data_file':training_data_file,
 622                 'analysis_model_training_data_file_type':analysis_calculate_statistics_response.analysis_model_training_data_file_type,
 623                 'analysis_model_auxiliary_files':JSON.stringify(analysis_stats_auxiliary_files)
 624             },
 625             beforeSend: function() {
 626                 jQuery('#working_modal').modal('show');
 627             },
 628             success: function(response){
 629                 console.log(response);
 630                 if (response.error) {
 631                     alert(response.error);
 632                 }
 633                 if (response.success) {
 634                     var html = '<center>';
 635                     if (response.model_id) {
 636                         html = html + '<p>Go to saved <a href="/analyses_model/'+response.model_id+'" target=_blank >model</a></p>';
 637                     }
 638                     if (response.analysis_id) {
 639                         html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >GBLUP analysis</a></p>';
 640                     }
 641                     html = html + '</center>';
 642                     jQuery('#generic_save_analysis_template_response_div').html(html);
 643
 644                     var analysis_statistical_ontology_term;
 645                     var analysis_stats_auxiliary_files;
 646                     var analysis_stats_training_data_file;
 647                     var generic_save_analysis_template_name_type = '_Spatial';
 648                     var generic_save_analysis_template_env1_result_values = JSON.stringify(analysis_calculate_statistics_response.result_blup_spatial_data);
 649
 650                     if (analysis_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 651                         analysis_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";
 652
 653                         analysis_stats_auxiliary_files = [{'auxiliary_model_file':analysis_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nickssinglemultitrialgebvanalyses_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
 654
 655                         analysis_stats_training_data_file = analysis_calculate_statistics_response.stats_tempfile;
 656                     }
 657
 658                     jQuery.ajax({
 659                         type: 'POST',
 660                         url : '/ajax/analysis/store/json',
 661                         data : {
 662                             'analysis_to_save_boolean':'yes',
 663                             'analysis_name':generic_save_analysis_template_analysis_name+generic_save_analysis_template_name_type,
 664                             'analysis_description':generic_save_analysis_template_analysis_description,
 665                             'analysis_year':generic_save_analysis_template_analysis_year,
 666                             'analysis_breeding_program_id':generic_save_analysis_template_breeding_program_id,
 667                             'analysis_protocol':analysis_stats_protocol,
 668                             'analysis_dataset_id':'',
 669                             'analysis_accession_names':JSON.stringify(analysis_calculate_statistics_response.unique_accessions),
 670                             'analysis_trait_names':JSON.stringify(analysis_calculate_statistics_response.unique_traits),
 671                             'analysis_analysis_statistical_ontology_term':analysis_statistical_ontology_term,
 672                             'analysis_precomputed_design_optional':JSON.stringify(analysis_calculate_statistics_response.field_trial_design),
 673                             'analysis_result_values':generic_save_analysis_template_env1_result_values,
 674                             'analysis_result_values_type':'analysis_result_values_match_precomputed_design',
 675                             'analysis_result_summary':JSON.stringify(analysis_stats_result_summary),
 676                             'analysis_result_trait_compose_info':'',
 677                             'analysis_model_id':response.model_id,
 678                             'analysis_model_name':'',
 679                             'analysis_model_description':'',
 680                             'analysis_model_is_public':'yes',
 681                             'analysis_model_language':analysis_calculate_statistics_response.analysis_model_language,
 682                             'analysis_model_type':analysis_calculate_statistics_response.analysis_model_type,
 683                             'analysis_model_properties':JSON.stringify(analysis_stats_parameters),
 684                             'analysis_model_application_name':analysis_calculate_statistics_response.application_name,
 685                             'analysis_model_application_version':analysis_calculate_statistics_response.application_version,
 686                             'analysis_model_file':'',
 687                             'analysis_model_file_type':'',
 688                             'analysis_model_training_data_file':analysis_stats_training_data_file,
 689                             'analysis_model_training_data_file_type':analysis_calculate_statistics_response.analysis_model_training_data_file_type,
 690                             'analysis_model_auxiliary_files':JSON.stringify(analysis_stats_auxiliary_files)
 691                         },
 692                         success: function(response){
 693                             console.log(response);
 694                             if (response.error) {
 695                                 alert(response.error);
 696                             }
 697                             if (response.success) {
 698                                 html = html + '<center>';
 699                                 if (response.analysis_id) {
 700                                     if (analysis_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 701                                         html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >spatial BLUP analysis</a></p>';
 702                                     }
 703                                 }
 704                                 html = html + '</center>';
 705                                 jQuery('#generic_save_analysis_template_response_div').html(html);
 706
 707                                 var analysis_stats_auxiliary_files;
 708                                 var analysis_stats_training_data_file;
 709
 710                                 if (analysis_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 711                                     jQuery('#working_modal').modal('hide');
 712                                     alert('Analysis and/or model saved!');
 713                                     return false;
 714                                 }
 715
 716                                 jQuery.ajax({
 717                                     type: 'POST',
 718                                     url : '/ajax/analysis/store/json',
 719                                     data : {
 720                                         'analysis_to_save_boolean':'yes',
 721                                         'analysis_name':generic_save_analysis_template_analysis_name+'_Residual',
 722                                         'analysis_description':generic_save_analysis_template_analysis_description,
 723                                         'analysis_year':generic_save_analysis_template_analysis_year,
 724                                         'analysis_breeding_program_id':generic_save_analysis_template_breeding_program_id,
 725                                         'analysis_protocol':analysis_stats_protocol,
 726                                         'analysis_dataset_id':'',
 727                                         'analysis_accession_names':JSON.stringify(analysis_calculate_statistics_response.unique_accessions),
 728                                         'analysis_trait_names':JSON.stringify(analysis_calculate_statistics_response.unique_residual_traits),
 729                                         'analysis_analysis_statistical_ontology_term':analysis_statistical_ontology_term,
 730                                         'analysis_precomputed_design_optional':JSON.stringify(analysis_calculate_statistics_response.field_trial_design),
 731                                         'analysis_result_values':JSON.stringify(analysis_calculate_statistics_response.result_residual_data),
 732                                         'analysis_result_values_type':'analysis_result_values_match_precomputed_design',
 733                                         'analysis_result_summary':JSON.stringify(analysis_stats_result_summary),
 734                                         'analysis_result_trait_compose_info':JSON.stringify(analysis_calculate_statistics_response.trait_composing_info),
 735                                         'analysis_model_id':response.model_id,
 736                                         'analysis_model_name':'',
 737                                         'analysis_model_description':'',
 738                                         'analysis_model_is_public':'yes',
 739                                         'analysis_model_language':analysis_calculate_statistics_response.analysis_model_language,
 740                                         'analysis_model_type':analysis_calculate_statistics_response.analysis_model_type,
 741                                         'analysis_model_properties':JSON.stringify(analysis_stats_parameters),
 742                                         'analysis_model_application_name':analysis_calculate_statistics_response.application_name,
 743                                         'analysis_model_application_version':analysis_calculate_statistics_response.application_version,
 744                                         'analysis_model_file':'',
 745                                         'analysis_model_file_type':'',
 746                                         'analysis_model_training_data_file':analysis_stats_training_data_file,
 747                                         'analysis_model_training_data_file_type':analysis_calculate_statistics_response.analysis_model_training_data_file_type,
 748                                         'analysis_model_auxiliary_files':JSON.stringify(analysis_stats_auxiliary_files)
 749                                     },
 750                                     success: function(response){
 751                                         jQuery('#working_modal').modal('hide');
 752                                         console.log(response);
 753                                         if (response.error) {
 754                                             alert(response.error);
 755                                         }
 756                                         if (response.success) {
 757                                             alert('Analysis and/or model saved!');
 758                                             html = html + '<center>';
 759                                             if (response.analysis_id) {
 760                                                 html = html + '<p>Go to saved <a href="/analyses/'+response.analysis_id+'" target=_blank >residuals analysis</a></p>';
 761                                             }
 762                                             html = html + '</center>';
 763                                             jQuery('#generic_save_analysis_template_response_div').html(html);
 764                                         }
 765                                     },
 766                                     error: function(response){
 767                                         alert('Error saving analysis multiple!');
 768                                     }
 769                                 });
 770                             }
 771                         },
 772                         error: function(response){
 773                             alert('Error saving analysis multiple!');
 774                         }
 775                     });
 776                 }
 777             },
 778             error: function(response){
 779                 jQuery('#working_modal').modal('hide');
 780                 alert('Error saving analysis multiple!');
 781             }
 782         });
 783     });
 784
 785     jQuery('#analysis_calculate_statistics_analysis_save_blups_genetic').click(function(){
 786         jQuery('#generic_save_analysis_dialog').modal('show');
 787
 788         var analysis_stats_parameters = {};
 789         var analysis_stats_protocol = '';
 790         var analysis_stats_auxiliary_files = [];
 791         var analysis_stats_result_summary = {};
 792         var analysis_statistical_ontology_term = '';
 793
 794         var analysis_stats_tolparinv_param = jQuery('#analysis_calculate_statistics_tolparinv_select').val();
 795         var analysis_stats_numbers_traits = analysis_calculate_statistics_response.unique_traits.length;
 796         var analysis_legendre_order = jQuery('#analysis_calculate_statistics_legendre_order_number_select').val();
 797         var analysis_genotyping_protocol_id = jQuery('#analysis_calculate_statistics_genotyping_protocol_select').val();
 798         var analysis_compute_genotypes_from_parents = jQuery('#analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select').val();
 799
 800         var analysis_stats_mv_traits = [];
 801         for (var i=1; i<analysis_stats_numbers_traits+1; i++) {
 802             analysis_stats_mv_traits.push('t'+i);
 803         }
 804         var analysis_stats_mv_traits_string = analysis_stats_mv_traits.join();
 805
 806         if (analysis_calculate_statistics_select == 'sommer_grm_spatial_genetic_blups') {
 807
 808             analysis_stats_protocol = 'mmer('+analysis_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+analysis_stats_numbers_traits+')) +vs(rowNumberFactor, Gtc=diag('+analysis_stats_numbers_traits+')) +vs(colNumberFactor, Gtc=diag('+analysis_stats_numbers_traits+')) +vs(spl2D(rowNumber, colNumber), Gtc=diag('+analysis_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+analysis_stats_numbers_traits+')), data=mat, tolparinv='+analysis_stats_tolparinv_param+');';
 809
 810             analysis_stats_parameters = {
 811                 'tolparinv':analysis_stats_tolparinv_param,
 812                 'genotyping_protocol_id':analysis_genotyping_protocol_id,
 813                 'compute_genotypes_from_parents':analysis_compute_genotypes_from_parents,
 814                 'protocol':analysis_stats_protocol
 815             };
 816
 817             analysis_stats_auxiliary_files = [{'auxiliary_model_file':analysis_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nickssinglemultitrialgebvanalyses_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
 818
 819             jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(analysis_calculate_statistics_response.trait_composing_info));
 820
 821             analysis_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";
 822         }
 823         if (analysis_calculate_statistics_select == 'sommer_grm_genetic_blups') {
 824
 825             analysis_stats_protocol = 'mmer('+analysis_stats_mv_traits_string+'~1+replicate, random=~vs(id, Gu=geno_mat, Gtc=unsm('+analysis_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+analysis_stats_numbers_traits+')), data=mat, tolparinv='+analysis_stats_tolparinv_param+');';
 826
 827             analysis_stats_parameters = {
 828                 'tolparinv':analysis_stats_tolparinv_param,
 829                 'genotyping_protocol_id':analysis_genotyping_protocol_id,
 830                 'compute_genotypes_from_parents':analysis_compute_genotypes_from_parents,
 831                 'protocol':analysis_stats_protocol
 832             };
 833
 834             analysis_stats_auxiliary_files = [{'auxiliary_model_file':analysis_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nickssinglemultitrialgebvanalyses_v1.01_sommer_grm_genetic_blups_grm_file'}];
 835
 836             jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(analysis_calculate_statistics_response.trait_composing_info));
 837
 838             analysis_statistical_ontology_term = "Multivariate genetic BLUPs using genetic relationship matrix computed using Sommer R|SGNSTAT:0000024";
 839         }
 840
 841         var training_data_file = analysis_calculate_statistics_response.stats_tempfile;
 842
 843         if (analysis_calculate_statistics_select == 'lmer_germplasmname_replicate') {
 844             analysis_stats_protocol = 'lmer(t1~replicate + 1|germplasmName, data=mat, na.action = na.omit)';
 845             analysis_stats_parameters = {
 846                 'protocol':analysis_stats_protocol
 847             };
 848             analysis_statistical_ontology_term = "Univariate linear mixed model genetic BLUPs using germplasmName computed using LMER R|SGNSTAT:0000002";
 849         }
 850
 851         jQuery('#generic_save_analysis_protocol').val(analysis_stats_protocol);
 852         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(analysis_stats_parameters));
 853         //jQuery('#generic_save_analysis_dataset_id').val();
 854         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(analysis_calculate_statistics_response.unique_accessions));
 855         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(analysis_calculate_statistics_response.unique_traits));
 856         jQuery('#generic_save_analysis_analysis_statistical_ontology_term').val(analysis_statistical_ontology_term);
 857         //jQuery('#generic_save_analysis_design').val();
 858         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(analysis_calculate_statistics_response.result_blup_genetic_data));
 859         jQuery('#generic_save_analysis_result_values_type').val(analysis_calculate_statistics_response.analysis_result_values_type);
 860         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(analysis_stats_result_summary));
 861         jQuery('#generic_save_analysis_model_language').val(analysis_calculate_statistics_response.analysis_model_language);
 862         jQuery('#generic_save_analysis_model_type').val(analysis_calculate_statistics_response.analysis_model_type);
 863         jQuery('#generic_save_analysis_model_application_name').val(analysis_calculate_statistics_response.application_name);
 864         jQuery('#generic_save_analysis_model_application_version').val(analysis_calculate_statistics_response.application_version);
 865         //jQuery('#generic_save_analysis_model_file').val();
 866         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
 867         jQuery('#generic_save_analysis_model_training_data_file').val(training_data_file);
 868         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(analysis_calculate_statistics_response.analysis_model_training_data_file_type);
 869         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(analysis_stats_auxiliary_files));
 870
 871         return false;
 872     });
 873
 874     jQuery('#analysis_calculate_statistics_analysis_save_blups_spatial').click(function(){
 875         if (analysis_calculate_statistics_field_trial_id_array.length>1) {
 876             alert('Saving spatial BLUPs currently only implemented for a single trial, so only select one field trial in your analysis');
 877             return false;
 878         }
 879
 880         jQuery('#generic_save_analysis_dialog').modal('show');
 881
 882         var analysis_stats_result_summary = {};
 883
 884         var analysis_stats_tolparinv_param = jQuery('#analysis_calculate_statistics_tolparinv_select').val();
 885         var analysis_stats_numbers_traits = analysis_calculate_statistics_response.unique_traits.length;
 886         var analysis_genotyping_protocol_id = jQuery('#analysis_calculate_statistics_genotyping_protocol_select').val();
 887         var analysis_compute_genotypes_from_parents = jQuery('#analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select').val();
 888
 889         var analysis_stats_mv_traits = [];
 890         for (var i=1; i<analysis_stats_numbers_traits+1; i++) {
 891             analysis_stats_mv_traits.push('t'+i);
 892         }
 893         var analysis_stats_mv_traits_string = analysis_stats_mv_traits.join();
 894
 895         var analysis_stats_protocol = 'mmer('+analysis_stats_mv_traits_string+'~1, random=~vs(id, Gu=geno_mat, Gtc=unsm('+analysis_stats_numbers_traits+')) +vs(rowNumberFactor, Gtc=diag('+analysis_stats_numbers_traits+')) +vs(colNumberFactor, Gtc=diag('+analysis_stats_numbers_traits+')), rcov=~vs(units, Gtc=unsm('+analysis_stats_numbers_traits+')), data=mat, tolparinv='+analysis_stats_tolparinv_param+');';
 896
 897         var analysis_stats_parameters = {
 898             'tolparinv':analysis_stats_tolparinv_param,
 899             'genotyping_protocol_id':analysis_genotyping_protocol_id,
 900             'compute_genotypes_from_parents':analysis_compute_genotypes_from_parents,
 901             'protocol':analysis_stats_protocol
 902         };
 903
 904         var analysis_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";
 905
 906         jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(analysis_calculate_statistics_response.trait_composing_info));
 907
 908         var analysis_stats_auxiliary_files = [{'auxiliary_model_file':analysis_calculate_statistics_response.grm_file, auxiliary_model_file_archive_type:'nickssinglemultitrialgebvanalyses_v1.01_sommer_grm_spatial_genetic_blups_grm_file'}];
 909
 910         jQuery('#generic_save_analysis_protocol').val(analysis_stats_protocol);
 911         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(analysis_stats_parameters));
 912         //jQuery('#generic_save_analysis_dataset_id').val();
 913         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(analysis_calculate_statistics_response.unique_accessions));
 914         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(analysis_calculate_statistics_response.unique_traits));
 915         jQuery('#generic_save_analysis_analysis_statistical_ontology_term').val(analysis_statistical_ontology_term);
 916         jQuery('#generic_save_analysis_design').val(JSON.stringify(analysis_calculate_statistics_response.field_trial_design));
 917         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(analysis_calculate_statistics_response.result_blup_spatial_data));
 918         jQuery('#generic_save_analysis_result_values_type').val('analysis_result_values_match_precomputed_design');
 919         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(analysis_stats_result_summary));
 920         jQuery('#generic_save_analysis_model_language').val(analysis_calculate_statistics_response.analysis_model_language);
 921         jQuery('#generic_save_analysis_model_type').val(analysis_calculate_statistics_response.analysis_model_type);
 922         jQuery('#generic_save_analysis_model_application_name').val(analysis_calculate_statistics_response.application_name);
 923         jQuery('#generic_save_analysis_model_application_version').val(analysis_calculate_statistics_response.application_version);
 924         //jQuery('#generic_save_analysis_model_file').val();
 925         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
 926         jQuery('#generic_save_analysis_model_training_data_file').val(analysis_calculate_statistics_response.stats_tempfile);
 927         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(analysis_calculate_statistics_response.analysis_model_training_data_file_type);
 928         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(analysis_stats_auxiliary_files));
 929
 930         return false;
 931     });
 932
 933     jQuery('#analysis_calculate_statistics_analysis_save_residuals').click(function(){
 934         jQuery('#generic_save_analysis_dialog').modal('show');
 935
 936         var analysis_stats_result_summary = {};
 937
 938         jQuery('#generic_save_analysis_result_compose_trait_info').val(JSON.stringify(analysis_calculate_statistics_response.trait_composing_info));
 939
 940         var analysis_stats_tolparinv_param = jQuery('#analysis_calculate_statistics_tolparinv_select').val();
 941         var analysis_legendre_order = jQuery('#analysis_calculate_statistics_legendre_order_number_select').val();
 942         var analysis_permanent_env_structure = jQuery('#analysis_calculate_statistics_permanent_env_structure_select').val();
 943         var analysis_genotyping_protocol_id = jQuery('#analysis_calculate_statistics_genotyping_protocol_select').val();
 944         var analysis_compute_genotypes_from_parents = jQuery('#analysis_calculate_statistics_genotyping_protocol_compute_from_parents_select').val();
 945
 946         var analysis_stats_protocol = '';
 947         var analysis_statistical_ontology_term;
 948         var analysis_stats_auxiliary_files;
 949         var analysis_stats_training_data_file;
 950
 951         var analysis_stats_parameters = {
 952             'tolparinv':analysis_stats_tolparinv_param,
 953             'genotyping_protocol_id':analysis_genotyping_protocol_id,
 954             'compute_genotypes_from_parents':analysis_compute_genotypes_from_parents,
 955             'legendre_polynomial_order':analysis_legendre_order,
 956             'protocol':analysis_stats_protocol,
 957             'permanent_environment_structure':analysis_permanent_env_structure
 958         };
 959
 960         jQuery('#generic_save_analysis_protocol').val(analysis_stats_protocol);
 961         jQuery('#generic_save_analysis_model_properties').val(JSON.stringify(analysis_stats_parameters));
 962         //jQuery('#generic_save_analysis_dataset_id').val();
 963         jQuery('#generic_save_analysis_accession_names').val(JSON.stringify(analysis_calculate_statistics_response.unique_accessions));
 964         jQuery('#generic_save_analysis_trait_names').val(JSON.stringify(analysis_calculate_statistics_response.unique_residual_traits));
 965         jQuery('#generic_save_analysis_analysis_statistical_ontology_term').val(analysis_statistical_ontology_term);
 966         jQuery('#generic_save_analysis_design').val(JSON.stringify(analysis_calculate_statistics_response.field_trial_design));
 967         jQuery('#generic_save_analysis_result_values').val(JSON.stringify(analysis_calculate_statistics_response.result_residual_data));
 968         jQuery('#generic_save_analysis_result_values_type').val('analysis_result_values_match_precomputed_design');
 969         jQuery('#generic_save_analysis_result_summary_values').val(JSON.stringify(analysis_stats_result_summary));
 970         jQuery('#generic_save_analysis_model_language').val(analysis_calculate_statistics_response.analysis_model_language);
 971         jQuery('#generic_save_analysis_model_type').val(analysis_calculate_statistics_response.analysis_model_type);
 972         jQuery('#generic_save_analysis_model_application_name').val(analysis_calculate_statistics_response.application_name);
 973         jQuery('#generic_save_analysis_model_application_version').val(analysis_calculate_statistics_response.application_version);
 974         //jQuery('#generic_save_analysis_model_file').val();
 975         //jQuery('#generic_save_analysis_model_archived_model_file_type').val();
 976         jQuery('#generic_save_analysis_model_training_data_file').val(analysis_calculate_statistics_response.stats_tempfile);
 977         jQuery('#generic_save_analysis_model_archived_training_data_file_type').val(analysis_calculate_statistics_response.analysis_model_training_data_file_type);
 978         jQuery('#generic_save_analysis_model_auxiliary_files').val(JSON.stringify(analysis_stats_auxiliary_files));
 979
 980         return false;
 981     });
 982 });
 983
 984 </script>