fixed intendtation
[PsN.git] / html / directory_docs_test2.php
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4 <title>PsN :: Directory Structure</title>
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129 style="position: absolute; left: 335px; top: 42px; width: 388px; height: 43px; z-index: 1; font-size: x-small; visibility: visible;">
130 <div class="style1" align="right">Directory Structure </div>
131 </div>
132 <div id="Layer2"
133 style="position: absolute; left: 226px; top: 188px; width: 497px; height: 431px; z-index: 2; visibility: visible;">
134 <p align="justify">Here follows an example directory listing. This particular run is from an <strong>scm</strong> with five parameter covariate relations. The files and directories are listed in roughly the order they were created. The blue and green boxes provide an explanatory text for the directory content. </p>
135 <p align="justify"> The names, order or existance of files and directories are not set in stone, but they should give you an idea of what a PsN tool run can produce. Click on the highlighted direcories and files to display a summary of their function. </p>
136 <table width="100%" border="0" cellspacing="0" cellpadding="0">
137 <tr>
138 <td colspan="4"><tt><img src="gfx/folder.open.gif" width="27" height="22" hspace="5" align="absbottom">scm_dir1</tt></td>
139 </tr>
140 <tr>
141 <td width="4%"><tt></tt></td>
142 <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>
143 </tr>
144 <tr>
145 <td><tt></tt></td>
146 <td width="4%"><tt></tt></td>
147 <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>
148 </tr>
149 <tr>
150 <td>&nbsp;</td>
151 <td>&nbsp;</td>
152 <td width="4%">&nbsp;</td>
153 <td width="88%"><dl>
154 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON</code></dt>
155 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON.0</code></dt>
156 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON.1</code></dt>
157 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FCON.orig</code></dt>
158 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FDATA</code></dt>
159 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FREPORT</code></dt>
160 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FSTREAM</code></dt>
161 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FSUBS</code></dt>
162 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">FSUBS.f</code></dt>
163 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">LINK.LNK</code></dt>
164 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">PRDERR</code></dt>
165 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">compilation_output.txt</code></dt>
166 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">data6_multi.dta</code></dt>
167 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">data6_single.dta</code></dt>
168 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">done</code></dt>
169 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">get_sub0.f</code></dt>
170 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">msf5</code></dt>
171 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.lst</code></dt>
172 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.lst.0</code></dt>
173 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.lst.1</code></dt>
174 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">psn.mod</code></dt>
175 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">reader0.f</code></dt>
176 </dl></td>
177 </tr>
178 <tr>
179 <td>&nbsp;</td>
180 <td>&nbsp;</td>
181 <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>
182 </tr>
183 <tr>
184 <td>&nbsp;</td>
185 <td>&nbsp;</td>
186 <td>&nbsp;</td>
187 <td><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">prepared_models.log</code></td>
188 </tr>
189 <tr>
190 <td>&nbsp;</td>
191 <td>&nbsp;</td>
192 <td colspan="2"><dl>
193 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">model_NMrun_translation.txt</code></dt>
194 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">modelfit.log</code></dt>
195 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">resume.file</code></dt>
196 </dl></td>
197 </tr>
198 <tr>
199 <td>&nbsp;</td>
200 <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>
201 </tr>
202 <tr>
203 <td>&nbsp;</td>
204 <td>&nbsp;</td>
205 <td colspan="2"><dl>
206 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAAGE2.mod</code></dt>
207 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAALKO2.mod</code></dt>
208 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASEX2.mod</code></dt>
209 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASMOK2.mod</code></dt>
210 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="1" align="absbottom">BAWT2.mod</code></dt>
211 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAAGE2.lst</code></dt>
212 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAALKO2.lst</code></dt>
213 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASEX2.lst</code></dt>
214 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BASMOK2.lst</code></dt>
215 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">BAWT2.lst</code></dt>
216 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">done</code></dt>
217 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">done.log</code></dt>
218 <dt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">prepared_models.log</code></dt>
219 </dl></td>
220 </tr>
221 <tr>
222 <td>&nbsp;</td>
223 <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>
224 </tr>
225 <tr>
226 <td>&nbsp;</td>
227 <td>&nbsp;</td>
228 <td colspan="2"><p><tt><img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run1<br>
229 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run2<br>
230 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run3<br>
231 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run4<br>
232 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">NM_run5<br>
233 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m1<br>
234 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m2<br>
235 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m3<br>
236 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m4<br>
237 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m5 <br>
238 </tt><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">model_NMrun_translation.txt<br>
239 </code><code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">resume.file</code></p></td>
240 </tr>
241 <tr>
242 <td>&nbsp;</td>
243 <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>
244 </tr>
245 <tr>
246 <td>&nbsp;</td>
247 <td>&nbsp;</td>
248 <td colspan="2"><tt><img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">m1<br>
249 <img src="gfx/folder.gif" width="20" height="22" hspace="5" align="absbottom">modelfit_dir1 <br>
250 <code><img src="gfx/file.gif" width="20" height="21" hspace="5" vspace="2" align="absbottom">modelfit1.log</code></tt></td>
251 </tr>
252 <tr>
253 <td>&nbsp;</td>
254 <td colspan="3"><dl>
255 <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>
256 <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>
257 <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>
258 <dd><code></code></dd>
259 </dl></td>
260 </tr>
261 </table>
262 </div>
263 <div id="origmodelfitdir" style="position:absolute; left:495px; top:328px; width:261px; height:152px; z-index:3; visibility: hidden;">
264 <div align="left">This is the <code>orig_modelfit_dir1</code> which is created for any input model which is not run prior to the PsN tool. The most important files in this directory is <tt>model_NMrun_translation.txt</tt> which lists the names of the original model file names and in which <tt>NM_run</tt> directory they have been run. The <tt>modelfit.log</tt> which lists a brief summary for each NONMEM run, and whether it was successful or not. </div>
265 </div>
266 <div id="nmrun" style="position:absolute; left:495px; top:328px; width:261px; height:309px; z-index:3; visibility: hidden;">
267 <p align="left">This is a typical NONMEM run directory. This is the ordinary output from NONMEM with a few additions. The model that is run is in <tt>psn.mod</tt> and the corresponding output is in <tt>psn.lst</tt>. In this particular run the data set was to wide for NONMEM so it has been split into two <tt>data6_multi.dta</tt> and <tt>data6_single.dta</tt>. To make NONMEM cope with the extra data there is extra fortran code in <tt>reader0.f</tt> and <tt>get_sub0.f</tt>, there may be more files like this, they will be named <tt>reader1.f</tt>, <tt>reader2.f</tt> and so forth.</p>
268 <p align="left">Special for this run is the <tt>FCON.0</tt>,<tt> FCON.1</tt>,<tt> psn.lst.0</tt> and <tt>psn.lst.1</tt>. They come from the reruns that PsN does when NONMEM fails. In the <tt>FCON</tt> files are new intial estimates and in <tt>psn.lst</tt> is the result for each rerun. <tt>FCON.orig</tt> is the original file that <tt>nmtran</tt> created and <tt>FCON</tt> corresponds to the last run. </p>
269 </div>
270 <div id="m11" style="position:absolute; left:495px; top:921px; width:261px; height:152px; z-index:3; visibility: hidden;">
271 <div align="left">The <tt>m1</tt> directory is not very interesting for modelfit directories. Look at the <tt>m1</tt> directory for the <b>scm</b> further down. </div>
272 </div>
273 <div id="m12" style="position:absolute; left:495px; top:1037px; width:261px; height:152px; z-index:3; visibility: hidden;">
274 <div align="left">In the <b>scm</b> the <tt>m1</tt> directories contain what we call prepared models. Before the <b>scm</b> step is run we creat all modelfiles that will be evaluated in this directory. When the execution is finished we place the ouput files here, also ther is the <tt>done</tt> file which is created when the <b>scm</b> step is finished (It is used by PsN in resume mode, to figure out if this step needs to be redone). <tt>done.log</tt> and <tt>prepared_models.log</tt> is for internal PsN use only. You should not rely on them for information. </div>
275 </div>
276 <div id="modelfit" style="position:absolute; left:495px; top:1388px; width:261px; height:152px; z-index:3; visibility: hidden;">
277 <div align="left">This is the modelfit directory for the <b>scm</b>, in here you may find all of the models for this <b>scm</b> step that have been completed. It follows the same structure as <tt>orig_modelfit_dir1</tt> above. The files listed in <tt>model_NMrun_translation.txt</tt> refers to files in the <tt>m1</tt> directory. </div>
278 </div>
279 <div id="logs" style="position:absolute; left:495px; top:1772px; width:261px; height:44px; z-index:3; visibility: hidden;">
280 <div align="left">These are the log files for the outermost tool, the <b>scm</b> in this case. </div>
281 </div>
282 <div id="scm" style="position:absolute; left:495px; top:1681px; width:261px; height:152px; z-index:3; visibility: hidden;">
283 <div align="left">This <b>scm</b> directory contains the files created by the second <b>scm</b> step. It follows the same structure as the current <b>scm</b> directory. When the <b>scm</b> finishes no further <b>scm</b> directories are created. Possibly there is a <tt>scm_dir2</tt> in the top level <b>scm</b> , then in <tt>scm_dir2</tt> is the files created for the backwards step. </div>
284 </div>
285 <table border="0" cellpadding="0" cellspacing="0" width="780">
286 <tbody>
287 <tr>
288 <td height="600" width="780">
289 <table border="0" cellpadding="0" cellspacing="0" width="780">
290 <tbody>
291 <tr>
292 <td colspan="7" height="201" width="780"><img
293 src="images/indexpane1_1_.jpg" name="" alt="" border="0" height="201"
294 width="780"></td>
295 </tr>
296 <tr>
297 <td height="46" width="26"><img
298 src="images/indexpane1_2_.jpg" name="" alt="" border="0" height="46"
299 width="26"></td>
300 <td height="46" width="73"><a href="index.php"
301 onmouseover="changeImages(/*CMP*/ 'object', /*URL*/ 'images/indexhomeov.jpg'); return true;"
302 onmouseout="changeImages(/*CMP*/ 'object', /*URL*/ 'images/indexhome.jpg'); return true;"><img
303 src="images/indexhome.jpg" name="object" alt="Home" border="0"
304 height="46" width="73"></a></td>
305 <td height="46" width="11"><img
306 src="images/indexpane3_2_.jpg" name="" alt="" border="0" height="46"
307 width="11"></td>
308 <td height="46" width="25"><img
309 src="images/indexpane4_2_.jpg" name="" alt="" border="0" height="46"
310 width="25"></td>
311 <td height="46" width="15"><img
312 src="images/indexpane5_2_.jpg" name="" alt="" border="0" height="46"
313 width="15"></td>
314 <td height="46" width="40"><img
315 src="images/indexpane6_2_.jpg" name="" alt="" border="0" height="46"
316 width="40"></td>
317 <td height="46" width="590"><img
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