From 9298a503d8de99dad1f61d6eb8bc228dd4acce6b Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 5 Nov 2020 08:31:21 +0100
Subject: Fix link and update docs
---
docs/dev/reference/saemix.html | 35 +++++++++++++++++++----------------
1 file changed, 19 insertions(+), 16 deletions(-)
(limited to 'docs/dev/reference/saemix.html')
diff --git a/docs/dev/reference/saemix.html b/docs/dev/reference/saemix.html
index 2c4fd2d7..c8cf9fab 100644
--- a/docs/dev/reference/saemix.html
+++ b/docs/dev/reference/saemix.html
@@ -153,7 +153,7 @@ list of mkinfit objects that have been obtained by fitting the same model to
a list of datasets.</p>
</div>
- <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>
+ <pre class="usage"><span class='fu'>saemix_model</span><span class='op'>(</span><span class='va'>object</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
<span class='fu'>saemix_data</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
@@ -162,12 +162,15 @@ a list of datasets.</p>
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>object</th>
- <td><p>An mmkin row object containing several fits of the same model to different datasets</p></td>
+ <td><p>An mmkin row object containing several fits of the same model
+to different datasets</p></td>
</tr>
<tr>
<th>cores</th>
- <td><p>The number of cores to be used for multicore processing.
-On Windows machines, cores > 1 is currently not supported.</p></td>
+ <td><p>The number of cores to be used for multicore processing using
+<code><a href='https://rdrr.io/r/parallel/mclapply.html'>parallel::mclapply()</a></code>. Using more than 1 core is experimental and may
+lead to uncontrolled forking, apparently depending on the BLAS version
+used.</p></td>
</tr>
<tr>
<th>...</th>
@@ -237,8 +240,8 @@ variances of the deviations of the parameters from these mean values.</p>
#> res <- unlist(res_list)
#> return(res)
#> }
-#> <bytecode: 0x555555c89340>
-#> <environment: 0x555555c82680>
+#> <bytecode: 0x55555d62aeb8>
+#> <environment: 0x55555e35c170>
#> Nb of parameters: 4
#> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#> distribution:
@@ -271,10 +274,10 @@ variances of the deviations of the parameters from these mean values.</p>
nbiter.saemix <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>200</span>, <span class='fl'>80</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>f_saemix</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix</span>, <span class='va'>d_saemix</span>, <span class='va'>saemix_options</span><span class='op'>)</span>
</div><div class='output co'>#> Running main SAEM algorithm
-#> [1] "Thu Oct 15 14:51:26 2020"
+#> [1] "Thu Nov 5 08:26:39 2020"
#> ..
#> Minimisation finished
-#> [1] "Thu Oct 15 14:53:18 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm
+#> [1] "Thu Nov 5 08:28:33 2020"</div><div class='img'><img src='saemix-1.png' alt='' width='700' height='433' /></div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm
#> -----------------------------------
#> ---- Data ----
#> -----------------------------------
@@ -338,8 +341,8 @@ variances of the deviations of the parameters from these mean values.</p>
#> res <- unlist(res_list)
#> return(res)
#> }
-#> <bytecode: 0x555555c89340>
-#> <environment: 0x555555c82680>
+#> <bytecode: 0x55555d62aeb8>
+#> <environment: 0x55555e35c170>
#> Nb of parameters: 4
#> parameter names: parent_0 log_k_parent log_k_A1 f_parent_ilr_1
#> distribution:
@@ -483,8 +486,8 @@ variances of the deviations of the parameters from these mean values.</p>
#> res <- unlist(res_list)
#> return(res)
#> }
-#> <bytecode: 0x555555c89340>
-#> <environment: 0x55555df58cf8>
+#> <bytecode: 0x55555d62aeb8>
+#> <environment: 0x55555cd8e028>
#> Nb of parameters: 2
#> parameter names: parent_0 log_k_parent
#> distribution:
@@ -510,10 +513,10 @@ variances of the deviations of the parameters from these mean values.</p>
#> Structured data: value ~ time + name | ds
#> X variable for graphs: time () </div><div class='input'><span class='va'>f_saemix_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/saemix.html'>saemix</a></span><span class='op'>(</span><span class='va'>m_saemix_tc</span>, <span class='va'>d_saemix_tc</span>, <span class='va'>saemix_options</span><span class='op'>)</span>
</div><div class='output co'>#> Running main SAEM algorithm
-#> [1] "Thu Oct 15 14:53:35 2020"
+#> [1] "Thu Nov 5 08:28:50 2020"
#> ..
#> Minimisation finished
-#> [1] "Thu Oct 15 14:54:25 2020"</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm
+#> [1] "Thu Nov 5 08:29:41 2020"</div><div class='output co'>#> Nonlinear mixed-effects model fit by the SAEM algorithm
#> -----------------------------------
#> ---- Data ----
#> -----------------------------------
@@ -577,8 +580,8 @@ variances of the deviations of the parameters from these mean values.</p>
#> res <- unlist(res_list)
#> return(res)
#> }
-#> <bytecode: 0x555555c89340>
-#> <environment: 0x55555df58cf8>
+#> <bytecode: 0x55555d62aeb8>
+#> <environment: 0x55555cd8e028>
#> Nb of parameters: 2
#> parameter names: parent_0 log_k_parent
#> distribution:
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