From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- docs/dev/articles/index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/dev/articles/index.html') diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 6daa6960..441d49c0 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -71,7 +71,7 @@ mkin - 0.9.50.4 + 1.0.1.9000 -- cgit v1.2.3 From 3dde3b95f1db925c89cd04d19f95c6fc9f68f473 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 12:40:44 +0100 Subject: Update docs --- docs/dev/404.html | 2 +- docs/dev/articles/index.html | 2 +- docs/dev/authors.html | 2 +- docs/dev/index.html | 2 +- docs/dev/news/index.html | 18 ++++++++++---- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/endpoints.html | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/plot.mixed.mmkin.html | 6 ++--- docs/dev/reference/saem.html | 38 +++++++++++++++--------------- docs/dev/reference/summary.saem.mmkin.html | 14 +++++------ 11 files changed, 49 insertions(+), 41 deletions(-) (limited to 'docs/dev/articles/index.html') diff --git a/docs/dev/404.html b/docs/dev/404.html index 5f29faf2..ea547a2a 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 441d49c0..57d0c0eb 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 9641eec0..8ffb9f97 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/index.html b/docs/dev/index.html index 8888633d..ff9b201f 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -38,7 +38,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 998917f2..eab75984 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 @@ -141,9 +141,9 @@ Source: NEWS.md -
-

-mkin 1.0.1.9000 Unreleased +
+

+mkin 1.0.2.9000 Unreleased

  • Switch to a versioning scheme where the fourth version component indicates development versions

    • @@ -151,10 +151,18 @@

  • ‘saemix_model’ and ‘saemix_data’: Helper functions to set up nonlinear mixed-effects models for mmkin row objects

  • ‘saem’: generic function to fit saemix models using ‘saemix_model’ and ‘saemix_data’, with a generator ‘saem.mmkin’, summary and plot methods

+
+
+

+mkin 1.0.2 Unreleased +

+
    +
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
    • +

-mkin 1.0.1 Unreleased +mkin 1.0.1 2021-02-10

  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults

    • diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index f9b16e29..8921a1e4 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: 2021-02-06T17:26Z +last_built: 2021-02-13T11:32Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index a13e11a7..301b454f 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.1.9000 + 1.0.2.9000
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 7e98aa50..b52ecb22 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000

diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 601e1554..ef169074 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.1.9000 + 1.0.2.9000 @@ -283,10 +283,10 @@ corresponding model prediction lines for the different datasets.

f_saem <- saem(f, transformations = "saemix")
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:17 2021" +#> [1] "Sat Feb 13 12:33:07 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:23 2021"
plot(f_saem) +#> [1] "Sat Feb 13 12:33:13 2021"
plot(f_saem)
# We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 4578db2a..02483bec 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -74,7 +74,7 @@ Expectation Maximisation algorithm (SAEM)." /> mkin - 1.0.1.9000 + 1.0.2.9000
@@ -261,27 +261,27 @@ using mmkin.

state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:26 2021" +#> [1] "Sat Feb 13 12:33:16 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:27 2021"
+#> [1] "Sat Feb 13 12:33:18 2021"
f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:28 2021" +#> [1] "Sat Feb 13 12:33:19 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:30 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Sat Feb 13 12:33:20 2021"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:30 2021" +#> [1] "Sat Feb 13 12:33:20 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:32 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Sat Feb 13 12:33:22 2021"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:32 2021" +#> [1] "Sat Feb 13 12:33:23 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:35 2021"
+#> [1] "Sat Feb 13 12:33:25 2021"
# The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -324,10 +324,10 @@ using mmkin.

f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:37 2021" +#> [1] "Sat Feb 13 12:33:28 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:42 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Sat Feb 13 12:33:32 2021"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
#> Error in compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)): 'compare.saemix' requires at least two models.
sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), A1 = mkinsub("SFO")) @@ -346,15 +346,15 @@ using mmkin.

# four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:44 2021" +#> [1] "Sat Feb 13 12:33:35 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:48 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Sat Feb 13 12:33:39 2021"
f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:29:49 2021" +#> [1] "Sat Feb 13 12:33:40 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:29:57 2021"
# We can use print, plot and summary methods to check the results +#> [1] "Sat Feb 13 12:33:48 2021"
# We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo)
#> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -395,10 +395,10 @@ using mmkin.

#> SD.g_qlogis 0.44771 -0.86417 1.7596
plot(f_saem_dfop_sfo)
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:29:57 2021 -#> Date of summary: Sat Feb 6 18:29:58 2021 +#> Date of fit: Sat Feb 13 12:33:48 2021 +#> Date of summary: Sat Feb 13 12:33:48 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -413,7 +413,7 @@ using mmkin.

#> #> Model predictions using solution type analytical #> -#> Fitted in 8.539 s using 300, 100 iterations +#> Fitted in 8.875 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index 93e1365d..81054813 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.0.1.9000 + 1.0.2.9000
@@ -260,15 +260,15 @@ saemix authors for the parts inherited from saemix.

quiet = TRUE, error_model = "tc", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)
#> Running main SAEM algorithm -#> [1] "Sat Feb 6 18:30:00 2021" +#> [1] "Sat Feb 13 12:33:52 2021" #> .... #> Minimisation finished -#> [1] "Sat Feb 6 18:30:11 2021"
summary(f_saem_dfop_sfo, data = TRUE) +#> [1] "Sat Feb 13 12:34:03 2021"
summary(f_saem_dfop_sfo, data = TRUE)
#> saemix version used for fitting: 3.1.9000 -#> mkin version used for pre-fitting: 1.0.1.9000 +#> mkin version used for pre-fitting: 1.0.2.9000 #> R version used for fitting: 4.0.3 -#> Date of fit: Sat Feb 6 18:30:12 2021 -#> Date of summary: Sat Feb 6 18:30:12 2021 +#> Date of fit: Sat Feb 13 12:34:04 2021 +#> Date of summary: Sat Feb 13 12:34:04 2021 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -283,7 +283,7 @@ saemix authors for the parts inherited from saemix.

#> #> Model predictions using solution type analytical #> -#> Fitted in 11.769 s using 300, 100 iterations +#> Fitted in 11.899 s using 300, 100 iterations #> #> Variance model: Two-component variance function #> -- cgit v1.2.3 From b9be19af5e3085216d0cd5af439332f631fa8b92 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 15 Feb 2021 17:36:12 +0100 Subject: Fully rebuild docs, rerun tests and check --- GNUmakefile | 2 +- build.log | 3 +- check.log | 4 +- docs/dev/404.html | 2 +- docs/dev/articles/FOCUS_D.html | 23 +-- .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../articles/FOCUS_D_files/figure-html/plot-1.png | Bin 81432 -> 79176 bytes .../FOCUS_D_files/header-attrs-2.6/header-attrs.js | 12 ++ docs/dev/articles/FOCUS_L.html | 129 ++++++------ .../accessible-code-block-0.0.1/empty-anchor.js | 15 ++ .../figure-html/unnamed-chunk-10-1.png | Bin 43110 -> 42203 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 84605 -> 82006 bytes .../figure-html/unnamed-chunk-13-1.png 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docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js (limited to 'docs/dev/articles/index.html') diff --git a/GNUmakefile b/GNUmakefile index 8604d3b3..d7c68ebf 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -112,7 +112,7 @@ pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" git add -A -pd_release: roxygen +pd_all: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE)" git add -A diff --git a/build.log b/build.log index 293831aa..d50a4860 100644 --- a/build.log +++ b/build.log @@ -6,4 +6,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.0.2.9000.tar.gz’ +* building ‘mkin_1.0.3.9000.tar.gz’ + diff --git a/check.log b/check.log index 2a4d87ad..ac59f6af 100644 --- a/check.log +++ b/check.log @@ -5,12 +5,12 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.0.2.9000’ +* this is package ‘mkin’ version ‘1.0.3.9000’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ -Version contains large components (1.0.2.9000) +Version contains large components (1.0.3.9000) Unknown, possibly mis-spelled, fields in DESCRIPTION: ‘Remotes’ diff --git a/docs/dev/404.html b/docs/dev/404.html index ea547a2a..f9e51aa3 100644 --- a/docs/dev/404.html +++ b/docs/dev/404.html @@ -71,7 +71,7 @@ mkin - 1.0.2.9000 + 1.0.3.9000
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index dd86f677..a35a255a 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -32,7 +32,7 @@ mkin - 0.9.50.4 + 1.0.3.9000 @@ -81,7 +81,7 @@