From 3532d769c1a3561de37e0d10cffa9801fe9df7c6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 13 Feb 2021 06:54:46 +0100 Subject: Update for gmkin 0.6.12 mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin --- DESCRIPTION | 4 ++-- NEWS.md | 4 ++++ R/mkinfit.R | 11 +++++++++-- build.log | 2 +- check.log | 2 +- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 12 ++++++++++-- docs/pkgdown.yml | 2 +- docs/reference/Rplot001.png | Bin 1011 -> 27554 bytes docs/reference/Rplot002.png | Bin 37427 -> 59342 bytes docs/reference/endpoints.html | 2 +- docs/reference/index.html | 2 +- docs/reference/plot.mixed.mmkin-1.png | Bin 85176 -> 84734 bytes docs/reference/plot.mixed.mmkin-2.png | Bin 173876 -> 173916 bytes docs/reference/plot.mixed.mmkin.html | 2 +- test.log | 16 ++++++++-------- 19 files changed, 43 insertions(+), 24 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index dd57aefa..c28966c1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.0.1 -Date: 2021-02-06 +Version: 1.0.2 +Date: 2021-02-13 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", diff --git a/NEWS.md b/NEWS.md index 124111d6..da3fbc44 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# mkin 1.0.2 + +- 'mkinfit': Keep model names stored in 'mkinmod' objects, avoiding their loss in 'gmkin' + # mkin 1.0.1 - 'confint.mmkin', 'nlme.mmkin', 'transform_odeparms': Fix example code in dontrun sections that failed with current defaults diff --git a/R/mkinfit.R b/R/mkinfit.R index 704e70a9..4da39841 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -261,8 +261,15 @@ mkinfit <- function(mkinmod, observed, summary_warnings <- character() # Derive the name used for the model - if (is.character(mkinmod)) mkinmod_name <- mkinmod - else mkinmod_name <- deparse(substitute(mkinmod)) + if (is.character(mkinmod)) { + mkinmod_name <- mkinmod + } else { + if (is.null(mkinmod$name)) { + mkinmod_name <- deparse(substitute(mkinmod)) + } else { + mkinmod_name <- mkinmod$name + } + } # Check mkinmod and generate a model for the variable whith the highest value # if a suitable string is given diff --git a/build.log b/build.log index 09d94134..328804ad 100644 --- a/build.log +++ b/build.log @@ -6,5 +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_1.0.1.tar.gz’ +* building ‘mkin_1.0.2.tar.gz’ diff --git a/check.log b/check.log index d0aeb08a..2dd7b49d 100644 --- a/check.log +++ b/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.0.1’ +* this is package ‘mkin’ version ‘1.0.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ diff --git a/docs/404.html b/docs/404.html index 45a45f3e..f038fb95 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ mkin - 1.0.1 + 1.0.2 diff --git a/docs/articles/index.html b/docs/articles/index.html index 66393487..52770090 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1 + 1.0.2 diff --git a/docs/authors.html b/docs/authors.html index 0f68e2ce..e80c3930 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -71,7 +71,7 @@ mkin - 1.0.1 + 1.0.2 diff --git a/docs/index.html b/docs/index.html index bcdaa7e4..51571c81 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ mkin - 1.0.1 + 1.0.2 diff --git a/docs/news/index.html b/docs/news/index.html index 5b24742f..766e6549 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1 + 1.0.2 @@ -141,9 +141,17 @@ Source: NEWS.md +
+

+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/pkgdown.yml b/docs/pkgdown.yml index 4100aea3..f1fe0ec9 100644 --- a/docs/pkgdown.yml +++ b/docs/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: 2021-02-06T08:46Z +last_built: 2021-02-13T05:53Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 17a35806..762a3dd4 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index bb624e64..d24e35b4 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 9bfbfdc8..e42ca9fe 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -78,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 1.0.0 + 1.0.2
diff --git a/docs/reference/index.html b/docs/reference/index.html index 0859a152..7b1bc4f1 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -71,7 +71,7 @@ mkin - 1.0.1 + 1.0.2 diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png index 9c46481c..9c9a2211 100644 Binary files a/docs/reference/plot.mixed.mmkin-1.png and b/docs/reference/plot.mixed.mmkin-1.png differ diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png index e228f764..0f66ff0f 100644 Binary files a/docs/reference/plot.mixed.mmkin-2.png and b/docs/reference/plot.mixed.mmkin-2.png differ diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 232d26e7..46303c44 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -72,7 +72,7 @@ mkin - 1.0.0 + 1.0.2 diff --git a/test.log b/test.log index d609022b..18f1a89f 100644 --- a/test.log +++ b/test.log @@ -3,14 +3,14 @@ Loading required package: parallel Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation -✔ | 2 | Export dataset for reading into CAKE +✔ | 2 | Export dataset for reading into CAKE [0.2 s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] ✔ | 7 | Fitting the SFORB model [3.4 s] -✔ | 5 | Analytical solutions for coupled models [3.3 s] +✔ | 5 | Analytical solutions for coupled models [3.1 s] ✔ | 5 | Calculation of Akaike weights -✔ | 12 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [4.2 s] +✔ | 12 | Confidence intervals and p-values [1.1 s] +✔ | 14 | Error model fitting [4.1 s] ✔ | 5 | Time step normalisation ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] @@ -21,17 +21,17 @@ Testing mkin ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.3 s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] -✔ | 9 | Nonlinear mixed-effects models [8.0 s] +✔ | 9 | Nonlinear mixed-effects models [7.9 s] ✔ | 14 | Plotting [1.7 s] ✔ | 4 | Residuals extracted from mkinfit models ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] ✔ | 4 | Summary [0.1 s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] -✔ | 9 | Hypothesis tests [8.1 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.6 s] +✔ | 9 | Hypothesis tests [8.2 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 41.3 s +Duration: 41.0 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 174 ] -- cgit v1.2.1