html/directory_docs.php

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 130 <div class="style1" align="right">Directory Structure </div>
 131 </div>
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 134
 135   <p align="justify">Here follows an example directory listing. This
 136 particular run is from an <strong>scm</strong> with five parameter
 137 covariate relations. The files and directories are listed in roughly
 138 the order they were created.</p>
 139   <p align="justify"> The names, order or existance of files and
 140 directories are not set in stone, but they should give you an idea of
 141 what a PsN tool run can produce. Click on the highlighted direcories
 142 and files to display a summary of their function. </p>
 143   <table width="100%"  border="0" cellspacing="0" cellpadding="0">
 144     <tr>
 145       <td colspan="4"><tt><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom">scm_dir1</tt></td>
 146     </tr>
 147     <tr>
 148       <td width="4%"><tt></tt></td>
 149       <td colspan="3"><tt onClick="MM_showHideLayers('origmodelfitdir','','show','nmrun','','hide')"><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom"><a name="origmodelfitdir"></a><a href="#origmodelfitdir" onClick="MM_showHideLayers('origmodelfitdir','','show','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','hide','scm','','hide')">orig_modelfit_dir1</a></tt></td>
 150     </tr>
 151     <tr>
 152       <td><tt></tt></td>
 153       <td width="4%"><tt></tt></td>
 154       <td colspan="2"><tt onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','show')"><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom"><a name="nmrun"></a><a href="#nmrun" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','show','m11','','hide','m12','','hide','modelfit','','hide','logs','','hide','scm','','hide')">NM_run1</a></tt></td>
 155     </tr>
 156     <tr>
 157       <td>&nbsp;</td>
 158       <td>&nbsp;</td>
 159       <td width="4%">&nbsp;</td>
 160       <td width="88%"><dl>
 161           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON</code></dt>
 162           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON.0</code></dt>
 163           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON.1</code></dt>
 164           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON.orig</code></dt>
 165           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FDATA</code></dt>
 166           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FREPORT</code></dt>
 167           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FSTREAM</code></dt>
 168           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FSUBS</code></dt>
 169           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FSUBS.f</code></dt>
 170           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">LINK.LNK</code></dt>
 171           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">PRDERR</code></dt>
 172           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">compilation_output.txt</code></dt>
 173           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">data6_multi.dta</code></dt>
 174           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">data6_single.dta</code></dt>
 175           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">done</code></dt>
 176           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">get_sub0.f</code></dt>
 177           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">msf5</code></dt>
 178           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.lst</code></dt>
 179           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.lst.0</code></dt>
 180           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.lst.1</code></dt>
 181           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.mod</code></dt>
 182           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">reader0.f</code></dt>
 183       </dl></td>
 184     </tr>
 185     <tr>
 186       <td>&nbsp;</td>
 187       <td>&nbsp;</td>
 188       <td colspan="2"><tt><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom"><a name="m11"></a><a href="#m11" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','show','m12','','hide','modelfit','','hide','logs','','hide','scm','','hide')">m1</a></tt></td>
 189     </tr>
 190     <tr>
 191       <td>&nbsp;</td>
 192       <td>&nbsp;</td>
 193       <td>&nbsp;</td>
 194       <td><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">prepared_models.log</code></td>
 195     </tr>
 196     <tr>
 197       <td>&nbsp;</td>
 198       <td>&nbsp;</td>
 199       <td colspan="2"><dl>
 200           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">model_NMrun_translation.txt</code></dt>
 201           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">modelfit.log</code></dt>
 202           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">resume.file</code></dt>
 203       </dl></td>
 204     </tr>
 205     <tr>
 206       <td>&nbsp;</td>
 207       <td colspan="3"><tt onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','show')"><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom"><a name="m12"></a><a href="#m12" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','show','modelfit','','hide','logs','','hide','scm','','hide')">m1</a></tt></td>
 208     </tr>
 209     <tr>
 210       <td>&nbsp;</td>
 211       <td>&nbsp;</td>
 212       <td colspan="2"><dl>
 213           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAAGE2.mod</code></dt>
 214           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAALKO2.mod</code></dt>
 215           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASEX2.mod</code></dt>
 216           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASMOK2.mod</code></dt>
 217           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="1" align="absbottom">BAWT2.mod</code></dt>
 218           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAAGE2.lst</code></dt>
 219           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAALKO2.lst</code></dt>
 220           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASEX2.lst</code></dt>
 221           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASMOK2.lst</code></dt>
 222           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAWT2.lst</code></dt>
 223           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">done</code></dt>
 224           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">done.log</code></dt>
 225           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">prepared_models.log</code></dt>
 226       </dl></td>
 227     </tr>
 228     <tr>
 229       <td>&nbsp;</td>
 230       <td colspan="3"><tt><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom"><a name="modelfit"></a><a href="#modelfit" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','show','logs','','hide','scm','','hide')">modelfit_dir1</a></tt></td>
 231     </tr>
 232     <tr>
 233       <td>&nbsp;</td>
 234       <td>&nbsp;</td>
 235       <td colspan="2"><p><tt><img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run1<br>
 236                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run2<br>
 237                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run3<br>
 238                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run4<br>
 239                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run5<br>
 240                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m1<br>
 241                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m2<br>
 242                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m3<br>
 243                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m4<br>
 244                 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m5 <br>
 245           </tt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">model_NMrun_translation.txt<br>
 246       </code><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">resume.file</code></p></td>
 247     </tr>
 248     <tr>
 249       <td>&nbsp;</td>
 250       <td colspan="3"><tt><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom"><a name="scm"></a><a href="#scm" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','hide','scm','','show')">scm_dir1</a></tt></td>
 251     </tr>
 252     <tr>
 253       <td>&nbsp;</td>
 254       <td>&nbsp;</td>
 255       <td colspan="2"><tt><img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m1<br>
 256             <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">modelfit_dir1 <br>
 257             <code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">modelfit1.log</code></tt></td>
 258     </tr>
 259     <tr>
 260       <td>&nbsp;</td>
 261       <td colspan="3"><dl>
 262           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom"><a name="logs"></a><a href="#logs" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','show','scm','','hide')">modelfit1.log</a></code></dt>
 263           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom"><a href="#logs" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','show','scm','','hide')">psn_results.csv</a></code></dt>
 264           <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom"><a href="#logs" onClick="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','show','scm','','hide')">scmlog_parallel1.txt</a></code></dt>
 265           <dd><code></code></dd>
 266       </dl></td>
 267     </tr>
 268   </table>
 269 </div>
 270 <div id="origmodelfitdir" style="position:absolute; left:495px; top:328px; width:261px; height:152px; z-index:3; visibility: hidden;">
 271
 272   <div align="left">This is the <code>orig_modelfit_dir1</code> which
 273 is created for any input model which is not run prior to the PsN
 274 tool. The most important files in this directory is
 275 <tt>model_NMrun_translation.txt</tt> which lists the names of the
 276 original model file names and in which <tt>NM_run</tt> directory they
 277 have been run. The <tt>modelfit.log</tt> which lists a brief summary
 278 for each NONMEM run, and whether it was successful or not. </div>
 279 </div>
 280
 281 <div id="nmrun" style="position:absolute; left:495px; top:328px; width:261px; height:309px; z-index:3; visibility: hidden;">
 282
 283   <p align="left">This is a typical NONMEM run directory. This is the
 284 ordinary output from NONMEM with a few additions. The model that is
 285 run is in <tt>psn.mod</tt> and the corresponding output is in
 286 <tt>psn.lst</tt>. In this particular run the data set was to wide for
 287 NONMEM so it has been split into two <tt>data6_multi.dta</tt> and
 288 <tt>data6_single.dta</tt>. To make NONMEM cope with the extra data
 289 there is extra fortran code in <tt>reader0.f</tt> and
 290 <tt>get_sub0.f</tt>, there may be more files like this, they will be
 291 named <tt>reader1.f</tt>, <tt>reader2.f</tt> and so forth.</p>
 292
 293   <p align="left">Special for this run is the <tt>FCON.0</tt>,<tt>
 294 FCON.1</tt>,<tt> psn.lst.0</tt> and <tt>psn.lst.1</tt>. They come from
 295 the reruns that PsN does when NONMEM fails. In the <tt>FCON</tt> files
 296 are new intial estimates and in <tt>psn.lst</tt> is the result for
 297 each rerun. <tt>FCON.orig</tt> is the original file that
 298 <tt>nmtran</tt> created and <tt>FCON</tt> corresponds to the last
 299 run. </p>
 300
 301 </div>
 302
 303 <div id="m11" style="position:absolute; left:495px; top:921px; width:261px; height:152px; z-index:3; visibility: hidden;">
 304   <div align="left">The <tt>m1</tt> directory is not very interesting for modelfit directories. Look at the <tt>m1</tt> directory for the scm further down. </div>
 305 </div>
 306 <div id="m12" style="position:absolute; left:495px; top:1037px; width:261px; height:152px; z-index:3; visibility: hidden;">
 307
 308   <div align="left">In the scm the <tt>m1</tt> directories contain
 309 what we call prepared models. Before the scm step is run we creat all
 310 modelfiles that will be evaluated in this directory. When the
 311 execution is finished we place the ouput files here, also ther is the
 312 <tt>done</tt> file which is created when the scm step is finished (It
 313 is used by PsN in resume mode, to figure out if this step needs to be
 314 redone). <tt>done.log</tt> and <tt>prepared_models.log</tt> is for
 315 internal PsN use only. You should not rely on them for information.
 316
 317 </div>
 318 </div>
 319
 320 <div id="modelfit" style="position:absolute; left:495px; top:1388px; width:261px; height:152px; z-index:3; visibility: hidden;">
 321
 322   <div align="left">This is the modelfit directory for the scm, in
 323 here you may find all of the models for this scm step that have been
 324 completed. It follows the same structure as
 325 <tt>orig_modelfit_dir1</tt> above. The files listed in
 326 <tt>model_NMrun_translation.txt</tt> refers to files in the
 327 <tt>m1</tt> directory.
 328
 329 </div>
 330 </div>
 331
 332 <div id="logs" style="position:absolute; left:495px; top:1772px;width:261px; height:44px; z-index:3; visibility: hidden;">
 333
 334   <div align="left">These are the log files for the outermost tool, the scm in this case. </div>
 335
 336 </div>
 337
 338 <div id="scm" style="position:absolute; left:495px; top:1681px; width:261px; height:152px; z-index:3; visibility: hidden;">
 339
 340   <div align="left">This scm directory contains the files created by
 341 the second scm step. It follows the same structure as the current scm
 342 directory. When the scm finishes no further scm directories are
 343 created. Possibly there is a <tt>scm_dir2</tt> in the top level scm ,
 344 then in <tt>scm_dir2</tt> is the files created for the backwards step.
 345
 346 </div>
 347 </div>
 348
 349 <table border="0" cellpadding="0" cellspacing="0" width="780">
 350   <tbody>
 351     <tr>
 352       <td height="600" width="780">
 353       <table border="0" cellpadding="0" cellspacing="0" width="780">
 354         <tbody>
 355           <tr>
 356             <td colspan="7" height="201" width="780"><img
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