From cff25a78e0e5a9d46db575b1ae3b02ace560aaf6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke 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 @@ mkin - 1.1.1 + 1.1.2 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 @@ mkin - 1.1.1 + 1.1.2 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 @@ mkin - 1.1.1 + 1.1.2 @@ -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 @@ -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
+
+ +
@@ -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        
+
+
+
+
+ +
+ + +
+ +
+

Site built with pkgdown 2.0.5.

+
+ +
+ + + + + + + + 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