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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-11 09:47:46 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-11 09:47:46 +0100
commit349285fccfcb3327eb1f9924db5a880f1e5e1a7d (patch)
treeb551d2f526920c58404056dc81496cd558c7b1b0
parent606ef9ad6cae0ddfae6db6b90deb03f81140e46f (diff)
Add print and plot calls to the saem example code
-rw-r--r--R/saemix.R8
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/Rplot001.pngbin19782 -> 19395 bytes
-rw-r--r--docs/dev/reference/Rplot002.pngbin16877 -> 16843 bytes
-rw-r--r--docs/dev/reference/Rplot003.pngbin28593 -> 28735 bytes
-rw-r--r--docs/dev/reference/Rplot004.pngbin49175 -> 49269 bytes
-rw-r--r--docs/dev/reference/Rplot005.pngbin15024 -> 57095 bytes
-rw-r--r--docs/dev/reference/saem-1.pngbin48512 -> 47315 bytes
-rw-r--r--docs/dev/reference/saem-2.pngbin48630 -> 48720 bytes
-rw-r--r--docs/dev/reference/saem-3.pngbin82018 -> 82102 bytes
-rw-r--r--docs/dev/reference/saem-4.pngbin128571 -> 128231 bytes
-rw-r--r--docs/dev/reference/saem-5.pngbin0 -> 164443 bytes
-rw-r--r--docs/dev/reference/saem.html160
-rw-r--r--man/saem.Rd7
14 files changed, 112 insertions, 65 deletions
diff --git a/R/saemix.R b/R/saemix.R
index 68bbd233..50497423 100644
--- a/R/saemix.R
+++ b/R/saemix.R
@@ -70,10 +70,13 @@
#' # solutions written for mkin this took around four minutes
#' f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#' f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
+#' # We can use print, plot and summary methods to check the results
+#' print(f_saem_dfop_sfo)
+#' plot(f_saem_dfop_sfo)
#' summary(f_saem_dfop_sfo, data = FALSE)
#'
-#' # Using a single core, the following takes about 6 minutes, using 10 cores
-#' # it is slower instead of faster
+#' # Using a single core, the following takes about 6 minutes as we do not have an
+#' # analytical solution. Using 10 cores it is slower instead of faster
#' #f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
#' }
#' @export
@@ -381,7 +384,6 @@ saemix_model <- function(object, cores = 1, verbose = FALSE, ...) {
"Mixed model generated from mmkin object",
transform.par = transform.par,
error.model = error.model,
- error.init = error.init,
verbose = verbose
)
attr(res, "mean_dp_start") <- degparms_optim
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 17d7c266..20533121 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-11-10T04:11Z
+last_built: 2020-11-11T08:36Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index fc26276a..bca41e2c 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
Binary files differ
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index 48e8698c..9b97a634 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
Binary files differ
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index b4581e35..ff6bc722 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
Binary files differ
diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png
index 2a90c6ee..98dd019e 100644
--- a/docs/dev/reference/Rplot004.png
+++ b/docs/dev/reference/Rplot004.png
Binary files differ
diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png
index b9285d56..5e675828 100644
--- a/docs/dev/reference/Rplot005.png
+++ b/docs/dev/reference/Rplot005.png
Binary files differ
diff --git a/docs/dev/reference/saem-1.png b/docs/dev/reference/saem-1.png
index 9c3421bd..2df248bb 100644
--- a/docs/dev/reference/saem-1.png
+++ b/docs/dev/reference/saem-1.png
Binary files differ
diff --git a/docs/dev/reference/saem-2.png b/docs/dev/reference/saem-2.png
index bc975b79..d4a2c1be 100644
--- a/docs/dev/reference/saem-2.png
+++ b/docs/dev/reference/saem-2.png
Binary files differ
diff --git a/docs/dev/reference/saem-3.png b/docs/dev/reference/saem-3.png
index 5744b722..6a32cda1 100644
--- a/docs/dev/reference/saem-3.png
+++ b/docs/dev/reference/saem-3.png
Binary files differ
diff --git a/docs/dev/reference/saem-4.png b/docs/dev/reference/saem-4.png
index b020dbbc..bf24d6b0 100644
--- a/docs/dev/reference/saem-4.png
+++ b/docs/dev/reference/saem-4.png
Binary files differ
diff --git a/docs/dev/reference/saem-5.png b/docs/dev/reference/saem-5.png
new file mode 100644
index 00000000..6e6e0f91
--- /dev/null
+++ b/docs/dev/reference/saem-5.png
Binary files differ
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index f9cdf1c8..bc54e1e1 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -241,53 +241,53 @@ using <a href='mmkin.html'>mmkin</a>.</p>
state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:21 2020"
+#&gt; [1] "Wed Nov 11 09:36:41 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:23 2020"</div><div class='input'>
+#&gt; [1] "Wed Nov 11 09:36:43 2020"</div><div class='input'>
<span class='va'>f_mmkin_parent</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><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='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:24 2020"
+#&gt; [1] "Wed Nov 11 09:36:44 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:26 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 09:36:45 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:26 2020"
+#&gt; [1] "Wed Nov 11 09:36:46 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:28 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 09:36:48 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:29 2020"
+#&gt; [1] "Wed Nov 11 09:36:48 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:32 2020"</div><div class='input'>
+#&gt; [1] "Wed Nov 11 09:36:51 2020"</div><div class='input'>
<span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
<span class='co'># functions from saemix</span>
<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Package saemix, version 3.1.9000</span>
#&gt; <span class='message'> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
-#&gt; 1 624.2428 622.2900
-#&gt; 2 467.7644 465.0305
-#&gt; 3 491.3541 487.8391</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+#&gt; 1 624.2484 622.2956
+#&gt; 2 467.7096 464.9757
+#&gt; 3 495.4373 491.9222</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Plotting convergence plots</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span>
</div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span>
</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Simulating data using nsim = 1000 simulated datasets
#&gt; Computing WRES and npde .
#&gt; Plotting npde</div><div class='img'><img src='saem-3.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; ---------------------------------------------
#&gt; Distribution of npde:
-#&gt; mean= -0.01736 (SE= 0.098 )
-#&gt; variance= 0.8562 (SE= 0.13 )
-#&gt; skewness= 0.513
-#&gt; kurtosis= 1.202
+#&gt; mean= -0.01528 (SE= 0.098 )
+#&gt; variance= 0.862 (SE= 0.13 )
+#&gt; skewness= 0.5016
+#&gt; kurtosis= 1.18
#&gt; ---------------------------------------------
#&gt;
#&gt; Statistical tests
-#&gt; Wilcoxon signed rank test : 0.652
-#&gt; Fisher variance test : 0.338
-#&gt; SW test of normality : 0.0757 .
-#&gt; Global adjusted p-value : 0.227
+#&gt; Wilcoxon signed rank test : 0.679
+#&gt; Fisher variance test : 0.36
+#&gt; SW test of normality : 0.0855 .
+#&gt; Global adjusted p-value : 0.257
#&gt; ---
#&gt; Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
#&gt; ---------------------------------------------</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"vpc"</span><span class='op'>)</span>
@@ -307,13 +307,13 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
<span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:34 2020"
+#&gt; [1] "Wed Nov 11 09:36:54 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:39 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 09:36:59 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt; AIC BIC
-#&gt; 1 467.7644 465.0305
-#&gt; 2 469.4862 466.3617</div><div class='input'>
+#&gt; 1 467.7096 464.9757
+#&gt; 2 469.5208 466.3963</div><div class='input'>
<span class='va'>sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
@@ -330,20 +330,62 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># solutions written for mkin this took around four minutes</span>
<span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:42 2020"
+#&gt; [1] "Wed Nov 11 09:37:01 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:47 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Nov 11 09:37:06 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Tue Nov 10 05:12:48 2020"
+#&gt; [1] "Wed Nov 11 09:37:06 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Tue Nov 10 05:12:57 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
+#&gt; [1] "Wed Nov 11 09:37:15 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
+#&gt; Structural model:
+#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#&gt; * parent
+#&gt; d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
+#&gt; * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
+#&gt; exp(-k2 * time))) * parent - k_A1 * A1
+#&gt;
+#&gt; Data:
+#&gt; 170 observations of 2 variable(s) grouped in 5 datasets
+#&gt;
+#&gt; Likelihood computed by importance sampling
+#&gt;
+#&gt; LL by is "-407.78 (df=13)"
+#&gt; AIC BIC logLik
+#&gt; 841.6 836.5 -407.8
+#&gt;
+#&gt; Fitted parameters:
+#&gt; estimate lower upper
+#&gt; parent_0 93.76647 91.15312 96.3798
+#&gt; log_k_A1 -6.13235 -8.45788 -3.8068
+#&gt; f_parent_qlogis -0.97364 -1.36940 -0.5779
+#&gt; log_k1 -2.53176 -3.80372 -1.2598
+#&gt; log_k2 -3.58667 -5.29524 -1.8781
+#&gt; g_qlogis 0.01238 -1.07968 1.1044
+#&gt; Var.parent_0 7.61106 -3.34955 18.5717
+#&gt; Var.log_k_A1 4.64679 -2.73133 12.0249
+#&gt; Var.f_parent_qlogis 0.19693 -0.05498 0.4488
+#&gt; Var.log_k1 2.01717 -0.51980 4.5542
+#&gt; Var.log_k2 3.63412 -0.92964 8.1979
+#&gt; Var.g_qlogis 0.20045 -0.97425 1.3751
+#&gt; a.1 1.88335 1.66636 2.1004
+#&gt; SD.parent_0 2.75881 0.77234 4.7453
+#&gt; SD.log_k_A1 2.15564 0.44429 3.8670
+#&gt; SD.f_parent_qlogis 0.44377 0.15994 0.7276
+#&gt; SD.log_k1 1.42027 0.52714 2.3134
+#&gt; SD.log_k2 1.90634 0.70934 3.1033
+#&gt; SD.g_qlogis 0.44771 -0.86417 1.7596</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
+</div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt;
+#&gt; LL by is "-407.78 (df=13)"</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
#&gt; mkin version used for pre-fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Tue Nov 10 05:12:58 2020
-#&gt; Date of summary: Tue Nov 10 05:12:58 2020
+#&gt; Date of fit: Wed Nov 11 09:37:16 2020
+#&gt; Date of summary: Wed Nov 11 09:37:16 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -358,7 +400,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 10.382 s using 300, 100 iterations
+#&gt; Fitted in 9.691 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Constant variance
#&gt;
@@ -375,33 +417,33 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Likelihood computed by importance sampling
#&gt; AIC BIC logLik
-#&gt; 841.3 836.2 -407.7
+#&gt; 841.6 836.5 -407.8
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; est. lower upper
-#&gt; parent_0 93.7514328 91.114 96.389
-#&gt; log_k_A1 -6.1262333 -8.432 -3.820
-#&gt; f_parent_qlogis -0.9739852 -1.372 -0.576
-#&gt; log_k1 -2.4818389 -3.747 -1.217
-#&gt; log_k2 -3.6138617 -5.294 -1.934
-#&gt; g_qlogis -0.0004614 -1.063 1.062
+#&gt; est. lower upper
+#&gt; parent_0 93.76647 91.153 96.3798
+#&gt; log_k_A1 -6.13235 -8.458 -3.8068
+#&gt; f_parent_qlogis -0.97364 -1.369 -0.5779
+#&gt; log_k1 -2.53176 -3.804 -1.2598
+#&gt; log_k2 -3.58667 -5.295 -1.8781
+#&gt; g_qlogis 0.01238 -1.080 1.1044
#&gt;
#&gt; Correlation:
#&gt; prnt_0 lg__A1 f_prn_ log_k1 log_k2
#&gt; log_k_A1 -0.013
#&gt; f_parent_qlogis -0.025 0.050
#&gt; log_k1 0.030 0.000 -0.005
-#&gt; log_k2 0.013 0.005 -0.003 0.037
-#&gt; g_qlogis -0.068 -0.016 0.011 -0.181 -0.181
+#&gt; log_k2 0.010 0.005 -0.003 0.032
+#&gt; g_qlogis -0.063 -0.015 0.010 -0.167 -0.177
#&gt;
#&gt; Random effects:
#&gt; est. lower upper
-#&gt; SD.parent_0 2.7857 0.7825 4.7889
-#&gt; SD.log_k_A1 2.1413 0.4425 3.8400
-#&gt; SD.f_parent_qlogis 0.4463 0.1609 0.7317
-#&gt; SD.log_k1 1.4097 0.5241 2.2954
-#&gt; SD.log_k2 1.8739 0.6979 3.0499
-#&gt; SD.g_qlogis 0.4559 -0.8150 1.7268
+#&gt; SD.parent_0 2.7588 0.7723 4.7453
+#&gt; SD.log_k_A1 2.1556 0.4443 3.8670
+#&gt; SD.f_parent_qlogis 0.4438 0.1599 0.7276
+#&gt; SD.log_k1 1.4203 0.5271 2.3134
+#&gt; SD.log_k2 1.9063 0.7093 3.1033
+#&gt; SD.g_qlogis 0.4477 -0.8642 1.7596
#&gt;
#&gt; Variance model:
#&gt; est. lower upper
@@ -409,24 +451,24 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt;
#&gt; Backtransformed parameters with asymmetric confidence intervals:
#&gt; est. lower upper
-#&gt; parent_0 93.751433 9.111e+01 96.38921
-#&gt; k_A1 0.002185 2.177e-04 0.02193
-#&gt; f_parent_to_A1 0.274087 2.023e-01 0.35986
-#&gt; k1 0.083589 2.359e-02 0.29618
-#&gt; k2 0.026948 5.021e-03 0.14463
-#&gt; g 0.499885 2.567e-01 0.74312
+#&gt; parent_0 93.766473 9.115e+01 96.37983
+#&gt; k_A1 0.002171 2.122e-04 0.02222
+#&gt; f_parent_to_A1 0.274156 2.027e-01 0.35942
+#&gt; k1 0.079519 2.229e-02 0.28371
+#&gt; k2 0.027691 5.015e-03 0.15288
+#&gt; g 0.503095 2.536e-01 0.75109
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_A1 0.2741
-#&gt; parent_sink 0.7259
+#&gt; parent_A1 0.2742
+#&gt; parent_sink 0.7258
#&gt;
#&gt; Estimated disappearance times:
#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 13.91 60.89 18.33 8.292 25.72
-#&gt; A1 317.26 1053.91 NA NA NA</div><div class='input'>
-<span class='co'># Using a single core, the following takes about 6 minutes, using 10 cores</span>
-<span class='co'># it is slower instead of faster</span>
+#&gt; parent 14.11 59.53 17.92 8.717 25.03
+#&gt; A1 319.21 1060.38 NA NA NA</div><div class='input'>
+<span class='co'># Using a single core, the following takes about 6 minutes as we do not have an</span>
+<span class='co'># analytical solution. Using 10 cores it is slower instead of faster</span>
<span class='co'>#f_saem_fomc &lt;- saem(f_mmkin["FOMC-SFO", ], cores = 1)</span>
<span class='co'># }</span>
</div></pre>
diff --git a/man/saem.Rd b/man/saem.Rd
index f75470a9..c37fbcfe 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -114,10 +114,13 @@ f_mmkin <- mmkin(list(
# solutions written for mkin this took around four minutes
f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
+# We can use print, plot and summary methods to check the results
+print(f_saem_dfop_sfo)
+plot(f_saem_dfop_sfo)
summary(f_saem_dfop_sfo, data = FALSE)
-# Using a single core, the following takes about 6 minutes, using 10 cores
-# it is slower instead of faster
+# Using a single core, the following takes about 6 minutes as we do not have an
+# analytical solution. Using 10 cores it is slower instead of faster
#f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
}
}

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