From 7a3f2ee22419608a8a634fd4d71d7176303b2f41 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Sep 2022 12:55:00 +0200 Subject: Improve parhist and llhist In particular, adapt the display of parameter boxplots for saem fits using mkin transformations to the way used for saem fits using saemix transformations, i.e. always show parameters on the natural scale, and normalised them by dividing by the median from the multiple runs. --- docs/dev/articles/web_only/multistart.html | 6 +++--- .../figure-html/unnamed-chunk-2-1.png | Bin 52067 -> 61772 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 50142 -> 56540 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 39793 -> 39866 bytes docs/dev/pkgdown.yml | 2 +- docs/dev/reference/parhist.html | 23 ++++++++------------- 6 files changed, 13 insertions(+), 18 deletions(-) (limited to 'docs') diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index b3108120..f9b27a0c 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -109,7 +109,7 @@

Short demo of the multistart method

Johannes Ranke

-

Last change 16 September 2022 (rebuilt 2022-09-16)

+

Last change 19 September 2022 (rebuilt 2022-09-19)

Source: vignettes/web_only/multistart.rmd @@ -135,13 +135,13 @@ f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE) f_saem_full <- saem(f_mmkin) f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -parhist(f_saem_full_multi, lpos = "bottomright") +parhist(f_saem_full_multi)

We see that not all variability parameters are identifiable, most problematic is the variance of k2. So we reduce the parameter distribution model by removing the intersoil variability for this parameter.

 f_saem_reduced <- update(f_saem_full, covariance.model = diag(c(1, 1, 0, 1)))
 f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
-parhist(f_saem_reduced_multi, lpos = "bottomright")
+parhist(f_saem_reduced_multi, lpos = "topright")

We can also analyse the log-likelihoods obtained in the multiple runs:

diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-2-1.png
index e30e56f0..18800fb9 100644
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diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index 3ed0d546..908989e9 100644
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diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index 957c2457..e50177cc 100644
Binary files a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png and b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png differ
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index c9b168a6..144a7f80 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
-last_built: 2022-09-16T19:23Z
+last_built: 2022-09-19T10:47Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/parhist.html b/docs/dev/reference/parhist.html
index a2fd717b..bc230c21 100644
--- a/docs/dev/reference/parhist.html
+++ b/docs/dev/reference/parhist.html
@@ -1,10 +1,6 @@
 
-Plot parameter distributions from multistart objects — parhist • mkinPlot parameter distributions from multistart objects — parhist • mkin
@@ -49,11 +45,14 @@ median, as in the paper by Duchesne et al. (2021).">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models
     
     
  • 
-      Example evaluation of FOCUS Example Dataset Z
+      Short demo of the multistart method
     
    • 
     
  • 
       Performance benefit by using compiled model definitions in mkin
     
    • 
+    
  • 
+      Example evaluation of FOCUS Example Dataset Z
+    
    • 
     
  • 
       Calculation of time weighted average concentrations with mkin
     
    • 
@@ -88,16 +87,12 @@ median, as in the paper by Duchesne et al. (2021).">
 
     
    
-    
    Produces a boxplot with all parameters from the multiple runs, scaled using
-their medians. If parameter transformations were done by mkin (default in
-saem), then the parameters found by saem are on the transformed scale, and
-scaling is simply done by subtracting the median. If parameter
-transformations were done by saemix, scaling is done by dividing by the
-median, as in the paper by Duchesne et al. (2021).
    
+    
    Produces a boxplot with all parameters from the multiple runs, divided by
+using their medians as in the paper by Duchesne et al. (2021).
    
     
    
 
     
    
-    
    parhist(object, lpos = "topleft", main = "", ...)
    
+    
    parhist(object, lpos = "bottomleft", main = "", ...)
    
     
    
 
     
    
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