html/bootstrap_docs.php

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 112  style="background-color: rgb(255, 255, 255);">
 113 <!-- The table is not formatted nicely because some browsers cannot join images in table cells if there are any hard carriage returns in a TD. -->
 114 <div id="Layer1"
 115  style="position: absolute; left: 335px; top: 42px; width: 388px; height: 43px; z-index: 1; font-size: x-small;">
 116 <div class="style1" align="right">the Bootstrap</div>
 117 </div>
 118 <div id="Layer2"
 119  style="position: absolute; left: 226px; top: 188px; width: 497px; height: 431px; z-index: 2;">
 120 <div align="justify">
 121 <?php
 122 include("bootstrap_synopsis.php");
 123 include("bootstrap_description.php");
 124 include("bootstrap_options.php");
 125 include("bootstrap_examples.php");
 126 php?>
 127 <!--
 128 <h3 class="heading1">Synopsis</h3>
 129 <p><tt>$                     bootstrap [ -h | -? ] [ --help ]<br>
 130 [ --bca ]<br>
 131 [ --sample_size=integer ]<br>
 132 [ --samples=integer ]<br>
 133 [ --stratify_on='string' ]<br>
 134 [ --abort_on_fail ]<br>
 135 [ --clean ]<br>
 136 [ --compress ]<br>
 137 [ --cpu_time=integer ]<br>
 138 [ --debug=0 ]<br>
 139 [ --debug_package='string' ]<br>
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 144 [ --grid_batch_size=integer ]<br>
 145 [ --missing_data_token='string' ]<br>
 146 [ --nm_directory='string' ]<br>
 147 [ --nm_version='string' ]<br>
 148 [ --outputfile='string' ]<br>
 149 [ --picky ]<br>
 150 [ --remove_temp_files ]<br>
 151 [ --results_file='string' ]<br>
 152 [ --retries=integer ]<br>
 153 [ --run_on_nordugrid ]<br>
 154 [ --seed='string' ]<br>
 155 [ --threads=integer ]<br>
 156 [ --tweak_inits ]</tt>
 157   </p>
 158 <h3 class="heading1">Description</h3>
 159 <p>
 160       The bootstrap can be used to calculate bias, standard errors and
 161       confidence intervals. It does so by resampling with replacement
 162       from the data, see Efron B, An Introduction to the Bootstrap,
 163       Chap. & Hall, London UK, 1993. To compute standard errors for
 164       all parameters of a model using the non-parametric bootstrap
 165       implemented here, roughly 200 model fits are necessary. To asses
 166       95% confidence intervals approximately 2000 runs will suffice.
 167 </p>
 168 <h3 class="heading1">Options</h3>
 169 <p>
 170       The options are given here in their long form. Any option may be
 171       abbreviated to any nonconflicting prefix. The <span class="style2">-threads</span> option
 172       may be abbreviated to <span class="style2">-t</span> (or even <span class="style2">-thr</span>) but <span class="style2">-debug</span> may not be
 173       abbreviated to <span class="style2">-d</span> because it conflicts with <span class="style2">-debug_packages</span> and
 174       <span class="style2">-debug_subroutines</span>.
 175 </p>
 176 <p>
 177       The following options are valid:
 178 </p>
 179       <span class="style2">-model='filename'
 180       </p>
 181       </span>
 182     <p>
 183       The name of the model file. May be specified with or without the
 184       "'".
 185 </p>
 186 <p class="style2">
 187       -samples
 188 </p>
 189 <p>
 190       The number of bootstrap samples.
 191 </p>
 192 <p class="style2">
 193       -sample_size
 194 </p>
 195 <p>
 196       The number of subjects in each bootstrap data set. The default
 197       value is set to the number of individuals in the original data
 198       set.
 199 </p>
 200 <p class="style2">
 201       -bca
 202 </p>
 203 <p>
 204       Using the <span class="style2">-bca </span>option, the bootstrap utility will calculate  the confidence intervals through the BCa method. The
 205       default approach however, is not to use the BCa (see Efron B, An introduction to
 206       the Bootstrap, 1993). The BCa is intended for calculation
 207       of second-order correct confidence intervals.
 208 </p>
 209 <p class="style2">
 210       -stratify_on=integer
 211 </p>
 212 <p>
 213       It may be necessary to use stratification in the resampling
 214       procedure. For example, if the original data consists of two
 215       groups of patients - say 10 patients with full pharmacokinetic
 216       profiles and 90 patients with sparse  concentration
 217       measurements - it may be wise to restrict the resampling
 218       procedure to resample within the two groups, producing bootstrap
 219       data sets that all contain 10 rich + 90 sparse data patients but
 220       with different compositions. The default is not to use
 221       stratification. Set stratify_on to the column that defines the
 222       two groups.
 223 </p>
 224 <p>
 225       See the <a href="execute_docs.php">execute documentation</a> for a description of common options.
 226 </p>
 227 -->
 228 <h3 class="heading1">Output</h3>
 229 <p>
 230   The Boostrap creates a log file and a result file. Both are by default placed in the bootstrap_dirX directory
 231   and are called boostraplog.csv and bootstrap-results.csv.
 232 </p>
 233 <!--
 234 <h3 class="heading1">Example</h3>
 235 <p align="justify" class="style2">$ bootstrap modelfile.mod -samples=200</p>
 236 <p>
 237   This will run a non-parametric bootstrap of 200 samples and give
 238   you good estimates of the standard errors of the parameter
 239   estimates. You will get some estimates for the confidence
 240   intervals too, but they will generally not be of high quality.</p>
 241 <p class="style2">
 242   $ bootstrap modelfile.mod -samples=2000 -bca
 243 </p>
 244 <p> This will run a non-parametric bootstrap using the BCa technique.</p>
 245 <p class="style2">
 246   $ bootstrap modelfile.mod -samples=2000 -bca -stratify_on=5
 247 </p>
 248 <p>
 249   This is the same BCa approach as above but with stratification
 250   on the factors of column five.</p>
 251 -->
 252 </div>
 253 </div>
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 263  width="780"></td>
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 265           <tr>
 266             <td height="46" width="26"><img
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 268  width="26"></td>
 269             <td height="46" width="73"><a href="index.php"
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