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 116 <div class="style1" align="right">User
 117 Documentation</div>
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 121 <div align="justify">
 122 <h3 class="heading1">PsN-Utilities Introduction</h3>
 123 <p>
 124 PsN-Utilities is a set of command line programs that gives you the control of the main features of PsN. At present PsN-Utilities
 125 consists of:</p>
 126 <dl>
 127   <dt><b><a href="bootstrap_docs.php">the bootstrap</a></b></dt>
 128   <dd>  Non-parametric bootstrap using the percentile or BCa methods.</dd>
 129   <dt><b><a href="cdd_docs.php">cdd</a></b></dt>
 130   <dd>Case-deletion Diagnostics.</dd>
 131   <dt><b><a href="execute_docs.php">execute</a></b></dt>
 132   <dd>The  NONMEM runs are started using one or
 133 multiple model files.</dd>
 134   <dt><b><a href="jackknife_docs.php">the jackknife</a></b></dt>
 135   <dd>The Jacknife if used to calculate the bias of the parameter estimates.</dd>
 136   <dt><b><a href="llp_docs.php">llp</a></b></dt>
 137   <dd>Log-likelihood Profiling around maximum-likelihood parameter estimates.</dd>
 138   <dt><b><a href="scm_docs.php">scm</a></b></dt>
 139   <dd>Stepwise Covariate Model building.</dd>
 140   <dt><b><a href="sumo_docs.php">sumo</a></b></dt>
 141   <dd>Summarizes the output
 142 files from NONMEM.</dd>
 143   <dt><b><a href="data_stats_docs.php">data_stats</a></b></dt>
 144   <dd>Prints simple statistics for data set columns.</dd>
 145   <dt><b><a href="create_extra_data_model_docs.php">create_extra_data_model</a></b></dt>
 146   <dd>This small utility helps you create a model file with more than one data file per problem.</dd>
 147   <dd><b><a href="create_extra_data_model_docs.php"></a></b></dd>
 148   <dt><b><a href="single_valued_columns_docs.php">single_valued_columns</a></b></dt>
 149   <dd>Identifies data-set columns with values that do not vary within an individual. This is useful for creation of extra data files when the number of columns needed are above 20. </dd>
 150   </dl>
 151 <p>You can click on any of the utilities in the list above for specific documentation.</p>
 152 <p>A utility is run by first typing its
 153 name on the command line and then pressing
 154 enter, e.g.: </p>
 155 <p>
 156   <b><tt>$ execute</tt></b>
 157 </p>
 158 <p>
 159   Depending on you Perl installation under Microsoft Windows the command may have to be:
 160 </p>
 161 <p>
 162   <b>
 163     <tt>$ C:\path to perl\perl execute</tt>
 164   </b>
 165 </p>
 166 <p>
 167   The above command will give you this message:
 168 </p>
 169 <p>
 170   <b>
 171     <tt>At least one model file must be specified. Use 'execute -h' for help.</tt>
 172   </b>
 173 </p>
 174 <p>
 175
 176   To start the NONMEM execution you must give the name of at least one
 177 model file. This is true for all the utilities except for the <tt>'scm'</tt>,
 178 <tt>'sumo'</tt> and <tt>'data_stats'</tt></p>
 179
 180 <p>
 181   <b>
 182     <tt>$ execute file.mod</tt>
 183   </b>
 184 </p>
 185 <p>
 186   This will start the NONMEM execution using the model file <tt>"file.mod"</tt>. It will also create a directory called
 187   <tt>"modelfit_dirX"</tt>, where "X" is the number of the directory starting from one. The  numbers of any additional directories will  be increased by one
 188         for each time you run <tt>"execute"</tt>. This makes it possible  to do multiple runs at
 189         the same time in one directory. After the run you will find the  output from NONMEM in the file named <tt>"file.lst"</tt>, and any table files specified in the model file. </p>
 190 <p>
 191   All utilities accept a set of options which allow you to modify the behaviour of the utility. For example, the bootstrap creates 200 new data sets from the original data by default. However    the number of data sets can be limited to for example 50, by changing the number in the <span class="style2">-sample</span> option in the bootstrap utility.</p>
 192 <p>
 193   <b><tt>$ bootstrap --samples=50 file.mod</tt></b>
 194 </p>
 195 <p>
 196   The <tt>'--samples'</tt> option is unique to the bootstrap utility. However, all options that are valid for the
 197   <tt>execute</tt> tool are also valid for  the <tt>bootstrap</tt>, <tt>cdd</tt>,
 198   <tt>jackknife</tt>, <tt>llp</tt> and <tt>scm</tt>. The <tt>'--threads'</tt> option is an example of a common option:
 199 </p>
 200 <p>
 201   <b><tt>$ bootstrap --samples=50 --threads=6 file.mod</tt></b>
 202 </p>
 203 <p>
 204   In this example the threads option makes the bootstrap utility run six NONMEM runs
 205   in parallel, starting a new run as soon as a previous has terminated.</p>
 206 <p>
 207
 208   If a PsN utility is stopped before it has finished it is possible to
 209   resume it from where it stopped. This is handled in PsN by the
 210   creation of a checkpoint after each NONMEM run. From this checkpoint
 211   a utility can always be resumed. To resume a utility the PsN
 212   directory created by the utility that stopped must be specified. In
 213   addition, the options used in the run that stopped must be
 214   defined. The options and their values are saved in the file
 215   <tt>"command.txt"</tt> under the directory from
 216   which you are resuming. If, for example, a bootstrap run in a
 217   directory named <tt>bootstrap_dir1</tt> stopped before it was
 218   finished it can easily be resumed by:
 219
 220 </p>
 221 <p>
 222   <tt><b>$ bootstrap --samples=50 --threads=6 --directory=bootstrap_dir1</b></tt>
 223 </p>
 224 <p>
 225   In the example above the bootstrap utility will see that a directory already exists and the information in that directory will therefore be used to continue the bootstrap run.
 226 </p>
 227 <h3 class="heading1">More options</h3>
 228 <p>
 229   If you need information on any of the PsN utilities the
 230   <tt>'--h'</tt> option can be used to get a list of valid options. To
 231   get a description of all the options use the <tt>'--help'</tt> option.
 232  </p>
 233 <h3 class="heading1">PsN Directory structure</h3>
 234 <p>
 235   PsN needs to create quite a few files to keep track of its executions as well as to enable resuming. During the execution the tools also create many
 236   NONMEM model-, data- and output files. In order to keep things manageable
 237   we have decided to order all files in a generic directory
 238   structure. You will get the output summaries from the command line tools, but it
 239   may still be useful to orient yourself in the directory structure. You
 240   can, for instance, find individual NONMEM run outputs as well as logs
 241   from PsN. To make it a bit easier we have created <a href="directory_docs.php">The PsN Directory Guide</a>, which is a small guide to the
 242   structure of the directories. <tt><tt>&nbsp;</tt></tt></p>
 243 <p>&nbsp;</p>
 244 </div>
 245 </div>
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