From cf54ccca37d27480dbf8d59eb027300518f7ad75 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 17:08:43 +0200 Subject: Prepare release of v1.2.4 - Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release --- docs/articles/web_only/multistart.html | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) (limited to 'docs/articles/web_only/multistart.html') diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html index 04093e82..b9224bb0 100644 --- a/docs/articles/web_only/multistart.html +++ b/docs/articles/web_only/multistart.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -134,7 +134,7 @@ Ranke

Last change 20 April 2023 -(rebuilt 2023-04-20)

+(rebuilt 2023-05-19) Source: vignettes/web_only/multistart.rmd @@ -175,7 +175,7 @@ assessment using multiple runs with different starting values.

parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.

-f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
+f_saem_reduced <- stats::update(f_saem_full, no_random_effect = "log_k2")
 illparms(f_saem_reduced)
 f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
 parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2))
@@ -190,18 +190,20 @@ runs:

We can use the anova method to compare the models.

 anova(f_saem_full, best(f_saem_full_multi),
-  f_saem_reduced, best(f_saem_reduced_multi))
+ f_saem_reduced, best(f_saem_reduced_multi), test = TRUE) 
## Data: 155 observations of 1 variable(s) grouped in 6 datasets
 ## 
-##                            npar    AIC    BIC     Lik
-## f_saem_reduced                9 663.73 661.86 -322.86
-## best(f_saem_reduced_multi)    9 663.69 661.82 -322.85
-## f_saem_full                  10 669.77 667.69 -324.89
-## best(f_saem_full_multi)      10 665.56 663.48 -322.78
-

The reduced model gives the lowest information criteria and similar -likelihoods as the best variant of the full model. The multistart method -leads to a much lower improvement of the likelihood for the reduced -model, indicating that it converges faster.

+## npar AIC BIC Lik Chisq Df Pr(>Chisq) +## f_saem_reduced 9 663.67 661.80 -322.84 +## best(f_saem_reduced_multi) 9 663.65 661.78 -322.82 0.0219 0 +## f_saem_full 10 670.09 668.01 -325.05 0.0000 1 1 +## best(f_saem_full_multi) 10 665.61 663.52 -322.80 4.4870 0 +

The reduced model results in lower AIC and BIC values, so it is +clearly preferable. Using multiple starting values gives a large +improvement in case of the full model, because it is less well-defined, +which impedes convergence. For the reduced model, using multiple +starting values only results in a small improvement of the model +fit.