Date: Fri, 22 Jul 2022 11:43:49 +0200 Subject: Update static docs --- _pkgdown.yml | 3 + docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/articles/web_only/benchmarks.html | 79 ++++++++++----- docs/authors.html | 6 +- docs/index.html | 2 +- docs/news/index.html | 8 +- docs/pkgdown.yml | 2 +- docs/reference/convergence.html | 163 +++++++++++++++++++++++++++++++ docs/reference/illparms.html | 171 ++++++++++++++++++++++++++++++++ docs/reference/index.html | 14 ++- docs/reference/summary.mkinfit.html | 67 +++++++++---- docs/reference/summary.mmkin.html | 173 +++++++++++++++++++++++++++++++++ docs/sitemap.xml | 9 ++ vignettes/web_only/mkin_benchmarks.rda | Bin 1482 -> 1543 bytes 15 files changed, 651 insertions(+), 50 deletions(-) create mode 100644 docs/reference/convergence.html create mode 100644 docs/reference/illparms.html create mode 100644 docs/reference/summary.mmkin.html diff --git a/_pkgdown.yml b/_pkgdown.yml index 77cb0323..787fb371 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -38,6 +38,9 @@ reference: - "`[.mmkin`" - plot.mmkin - AIC.mmkin + - convergence + - illparms + - summary.mmkin - title: Mixed models desc: Create and work with nonlinear mixed effects models contents: diff --git a/docs/404.html b/docs/404.html index 7a6ede72..750f0ae7 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index 9cdfa9de..9a014b09 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 4e0cbba7..0b14fea2 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -33,7 +33,7 @@ @@ -105,7 +105,7 @@

Benchmark timings for mkin

Johannes Ranke

Last change 1 July 2022 (rebuilt 2022-07-12)

Last change 14 July 2022 (rebuilt 2022-07-22)

Source: vignettes/web_only/benchmarks.rmd

benchmarks.rmd

@@ -116,20 +116,32 @@

Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.

Every fit is only performed once, so the accuracy of the benchmarks is limited.

The following wrapper function for mmkin is used because the way the error model is specified was changed in mkin version 0.9.49.1.

+if (packageVersion("mkin") > "0.9.48.1") {
+  mmkin_bench <- function(models, datasets, error_model = "const") {
+    mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
+  }
+} else {
+  mmkin_bench <- function(models, datasets, error_model = NULL) {
+    mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
+  }
+}

Test cases

Parent only:

+ FOCUS_C <- FOCUS_2006_C
 FOCUS_D <- subset(FOCUS_2006_D, value != 0)
 parent_datasets <- list(FOCUS_C, FOCUS_D)
 
+
 t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets))[["elapsed"]]
 t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), parent_datasets,
     error_model = "tc"))[["elapsed"]]
 One metabolite:
-+ SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
@@ -145,7 +157,7 @@
 t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = "obs"))[["elapsed"]]
 Two metabolites, synthetic data:
-+ m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"),
@@ -172,12 +184,6 @@
     error_model = "obs"))[["elapsed"]]
 t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c),
     error_model = "obs"))[["elapsed"]]
--mkin_benchmarks[system_string, paste0("t", 1:11)] <-
-  c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-save(mkin_benchmarks, file = benchmark_path)
-# Hide rownames from kable for results section
-rownames(mkin_benchmarks) <- NULL
 
 
 Results
@@ -322,8 +328,16 @@
 Ryzen 7 1700
 4.2.1
 1.1.1
-1.809
-3.468
+1.770
+3.377
+
+
+Linux
+Ryzen 7 1700
+4.2.1
+1.1.2
+1.962
+3.606
 
 
 
@@ -483,9 +497,18 @@
 Ryzen 7 1700
 4.2.1
 1.1.1
-1.336
-5.820
-2.621
+1.308
+5.758
+2.558
+
+
+Linux
+Ryzen 7 1700
+4.2.1
+1.1.2
+1.465
+6.184
+2.752
 
 
 
@@ -693,12 +716,24 @@
 Ryzen 7 1700
 4.2.1
 1.1.1
-0.707
-1.148
-1.339
-2.812
-1.752
-2.594
+0.696
+1.124
+1.321
+2.786
+1.744
+2.566
+
+
+Linux
+Ryzen 7 1700
+4.2.1
+1.1.2
+0.857
+1.298
+1.504
+3.011
+1.888
+2.756
 
 
 
diff --git a/docs/authors.html b/docs/authors.html
index afa0d11c..9daad578 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       
       
         mkin
-        1.1.1
+        1.1.2
       
     
 
@@ -109,13 +109,13 @@
 
     Ranke J (2022).
 mkin: Kinetic Evaluation of Chemical Degradation Data.
-R package version 1.1.1, https://pkgdown.jrwb.de/mkin/. 
+R package version 1.1.2, https://pkgdown.jrwb.de/mkin/. 
 
     @Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
   year = {2022},
-  note = {R package version 1.1.1},
+  note = {R package version 1.1.2},
   url = {https://pkgdown.jrwb.de/mkin/},
 }
 
diff --git a/docs/index.html b/docs/index.html
index 6e6a90fa..6118572b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -44,7 +44,7 @@
       
       
         mkin
-        1.1.1
+        1.1.2
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index e7a7f571..d5c30552 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       
       
         mkin
-        1.1.1
+        1.1.2

@@ -81,6 +81,12 @@ Source: NEWS.md

+ +

‘R/convergence.R’: New generic to show convergence information with a method for ‘mmin’ objects.
‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’ and ‘mmkin’ objects.
‘R/summary.mmkin.R’: Summary method for mmkin objects.

’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.

Method to get convergence information — convergence • mkin

+ + + +

+ + +

Method to get convergence information

+ +

convergence(object, ...)
+
+# S3 method for mmkin
+convergence(object, ...)
+
+# S3 method for convergence.mmkin
+print(x, ...)

+ +

Arguments

object: The object to investigate
...: For potential future extensions
x: The object to be printed

Value

+ + +

For mkinfit objects, a character vector containing +For mmkin objects, an object of class 'convergence.mmkin' with a +suitable printing method.

+ +

Examples

# \dontrun{
+fits <- mmkin(
+  c("SFO", "FOMC"),
+  list("FOCUS A" = FOCUS_2006_A,
+       "FOCUS B" = FOCUS_2006_C),
+  quiet = TRUE)
+convergence(fits)
+#>       dataset
+#> model  FOCUS A FOCUS B
+#>   SFO  OK      OK     
+#>   FOMC OK      OK     
+#> 
+#> OK: No warnings
+# }
+

+ +

+ + +

Method to get the names of ill-defined parameters — illparms • mkin

+ + + +

+ + +

Method to get the names of ill-defined parameters

+ +

illparms(object, ...)
+
+# S3 method for mkinfit
+illparms(object, conf.level = 0.95, ...)
+
+# S3 method for mmkin
+illparms(object, conf.level = 0.95, ...)
+
+# S3 method for illparms.mmkin
+print(x, ...)

+ +

Arguments

object: The object to investigate
...: For potential future extensions
conf.level: The confidence level for checking p values
x: The object to be printed

Value

+ + +

For mkinfit objects, a character vector of parameter names +For mmkin objects, an object of class 'illparms.mmkin' with a +suitable printing method.

+ +

Examples

fit <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE)
+illparms(fit)
+#> [1] "parent_0" "alpha"    "beta"     "sigma"   
+# \dontrun{
+fits <- mmkin(
+  c("SFO", "FOMC"),
+  list("FOCUS A" = FOCUS_2006_A,
+       "FOCUS C" = FOCUS_2006_C),
+  quiet = TRUE)
+illparms(fits)
+#>       dataset
+#> model  FOCUS A                      FOCUS C
+#>   SFO                                      
+#>   FOMC parent_0, alpha, beta, sigma        
+# }
+

+ +

+ + +

@@ -167,6 +167,18 @@ of an mmkin object

AIC(<mmkin>) BIC(<mmkin>)

Calculate the AIC for a column of an mmkin object

+ +

convergence() print(<convergence.mmkin>)

+ +

Method to get convergence information

+ +

illparms() print(<illparms.mmkin>)

+ +

Method to get the names of ill-defined parameters

+ +

summary(<mmkin>) print(<summary.mmkin>)

+ +

Summary method for class "mmkin"

Mixed models

Create and work with nonlinear mixed effects models

diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 6d816366..17ecdfe4 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."> + + +

+ + + +

+ + +

Shows convergence information on the mkinfit objects contained in the object +and gives an overview of ill-defined parameters calculated by illparms.

+ +

# S3 method for mmkin
+summary(object, conf.level = 0.95, ...)
+
+# S3 method for summary.mmkin
+print(x, digits = max(3, getOption("digits") - 3), ...)

+ +

Arguments

object: an object of class mmkin
conf.level: confidence level for testing parameters
...: optional arguments passed to methods like print.
x: an object of class summary.mmkin.
digits: number of digits to use for printing

+ +

Examples


+fits <- mmkin(
+  c("SFO", "FOMC"),
+  list("FOCUS A" = FOCUS_2006_A,
+       "FOCUS C" = FOCUS_2006_C),
+  quiet = TRUE, cores = 1)
+  summary(fits)
+#> Error model: Constant variance 
+#> Fitted in 0.607 s
+#> 
+#> Convergence:
+#>       dataset
+#> model  FOCUS A FOCUS C
+#>   SFO  OK      OK     
+#>   FOMC OK      OK     
+#> 
+#> OK: No warnings
+#> 
+#> Ill-defined parameters:
+#>       dataset
+#> model  FOCUS A                      FOCUS C
+#>   SFO                                      
+#>   FOMC parent_0, alpha, beta, sigma        
+
+

+ +

+ + +

+ + + + + + + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index f39832fb..ba8f37e6 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -102,6 +102,9 @@ https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html + + https://pkgdown.jrwb.de/mkin/reference/convergence.html + https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html @@ -123,6 +126,9 @@ https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html + + https://pkgdown.jrwb.de/mkin/reference/illparms.html + https://pkgdown.jrwb.de/mkin/reference/ilr.html @@ -261,6 +267,9 @@ https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html + + https://pkgdown.jrwb.de/mkin/reference/summary.mmkin.html + https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda index d507131a..14ae6346 100644 Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ -- cgit v1.2.1

Benchmark timings for mkin

Johannes Ranke

Last change 1 July 2022 (rebuilt 2022-07-12)

Last change 14 July 2022 (rebuilt 2022-07-22)

Test cases

mkin 1.1.2

mkin 1.1.1

Method to get convergence information

Arguments

Value

Examples

Method to get the names of ill-defined parameters

Arguments

Value

Examples

Mixed models

Summary method for class "mmkin"

Arguments

Examples