diff options
26 files changed, 158 insertions, 143 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 176c3039..f5b7f070 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.0.4 -Date: 2021-02-24 +Date: 2021-04-20 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", @@ -4,6 +4,8 @@ - 'plot.mkinfit': Use xlab and xlim for the residual plot if show_residuals is TRUE +- 'mmkin': Use cores = 1 per default on Windows to make it easier for first time users + # mkin 1.0.3 (2021-02-15) - Review and update README, the 'Introduction to mkin' vignette and some of the help pages @@ -13,7 +13,8 @@ #' is only used when the \code{cluster} argument is \code{NULL}. On Windows #' machines, cores > 1 is not supported, you need to use the \code{cluster} #' argument to use multiple logical processors. Per default, all cores -#' detected by [parallel::detectCores()] are used. +#' detected by [parallel::detectCores()] are used, except on Windows where +#' the default is 1. #' @param cluster A cluster as returned by \code{\link{makeCluster}} to be used #' for parallel execution. #' @param \dots Further arguments that will be passed to \code{\link{mkinfit}}. @@ -75,7 +76,7 @@ #' #' @export mmkin mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, - cores = parallel::detectCores(), cluster = NULL, ...) + cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL, ...) { call <- match.call() parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE", "logistic") @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.0.4 (2021-02-15) +* using R version 4.0.5 (2021-03-31) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ @@ -43,7 +43,9 @@ The Date field is over a month old. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... OK +* checking R code for possible problems ... NOTE +mmkin: possible error in Sys.info("sysname"): unused argument + ("sysname") * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -69,7 +71,7 @@ The Date field is over a month old. * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: 2 NOTEs See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. diff --git a/docs/news/index.html b/docs/news/index.html index fae6503a..2905c120 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -147,6 +147,7 @@ <ul> <li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li> <li><p>‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE</p></li> +<li><p>‘mmkin’: Use cores = 1 per default on Windows to make it easier for first time users</p></li> </ul> </div> <div id="mkin-103-2021-02-15" class="section level1"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index df454e62..3f97ea94 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: 2021-03-31T17:15Z +last_built: 2021-04-20T14:34Z 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 Binary files differindex 17a35806..49fb9af1 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex 808f1968..745d583d 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex 97f650e2..eba202e9 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 21ad6783..a4f878c8 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 4828f5b2..a4f878c8 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex 4aed2c87..ff8a5d83 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 26586ab9..f6bb2131 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex dbcdd8ee..50102a3d 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 80245fc6..9aa7f0db 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 328aa564..f4f413d1 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 9ce5e919..48ab2c50 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index c73d14bf..caba300e 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -155,7 +155,7 @@ datasets specified in its first two arguments.</p> <pre class="usage"><span class='fu'>mmkin</span><span class='op'>(</span> models <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>datasets</span>, - cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, + cores <span class='op'>=</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='fl'>1</span> <span class='kw'>else</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, cluster <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span> <span class='op'>)</span> @@ -183,7 +183,8 @@ data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, cores > 1 is not supported, you need to use the <code>cluster</code> argument to use multiple logical processors. Per default, all cores -detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used.</p></td> +detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used, except on Windows where +the default is 1.</p></td> </tr> <tr> <th>cluster</th> @@ -234,9 +235,9 @@ plotting.</p></div> <span class='va'>time_default</span> </div><div class='output co'>#> user system elapsed -#> 5.387 0.413 1.864 </div><div class='input'><span class='va'>time_1</span> +#> 4.656 0.403 1.734 </div><div class='input'><span class='va'>time_1</span> </div><div class='output co'>#> user system elapsed -#> 5.786 0.008 5.794 </div><div class='input'> +#> 5.627 0.004 5.631 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex cca4ce0a..c41adc27 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png Binary files differindex 2224d96e..65660abe 100644 --- a/docs/reference/plot.mixed.mmkin-1.png +++ b/docs/reference/plot.mixed.mmkin-1.png diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 170ce8df..309761dd 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -9,7 +9,7 @@ more datasets} mmkin( models = c("SFO", "FOMC", "DFOP"), datasets, - cores = parallel::detectCores(), + cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL, ... ) @@ -28,7 +28,8 @@ data for \code{\link{mkinfit}}.} is only used when the \code{cluster} argument is \code{NULL}. On Windows machines, cores > 1 is not supported, you need to use the \code{cluster} argument to use multiple logical processors. Per default, all cores -detected by \code{\link[parallel:detectCores]{parallel::detectCores()}} are used.} +detected by \code{\link[parallel:detectCores]{parallel::detectCores()}} are used, except on Windows where +the default is 1.} \item{cluster}{A cluster as returned by \code{\link{makeCluster}} to be used for parallel execution.} @@ -1,27 +1,33 @@ -Loading mkin +ℹ Loading mkin Loading required package: parallel -Testing mkin +ℹ Testing mkin ✔ | OK F W S | Context ✔ | 5 | AIC calculation -✔ | 2 | Export dataset for reading into CAKE -✔ | 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 [3.5 s] -✔ | 5 | Analytical solutions for coupled models [3.1 s] +✔ | 5 | Analytical solutions for coupled models [3.2 s] ✔ | 5 | Calculation of Akaike weights -✔ | 12 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [4.2 s] +✔ | 2 | Export dataset for reading into CAKE +✔ | 12 | Confidence intervals and p-values [1.3 s] +✔ | 14 | Error model fitting [4.3 s] ✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7 s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] ✔ | 1 | Fitting the logistic model [0.2 s] ✔ | 5 | Nonlinear mixed-effects models [0.1 s] ✔ | 2 | Test dataset classes mkinds and mkindsg -✔ | 1 | mkinfit features [0.3 s] ✔ | 10 | Special cases of mkinfit calls [0.3 s] +✔ | 1 | mkinfit features [0.3 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6 s] -✔ | 9 | Nonlinear mixed-effects models [7.9 s] +✔ | 3 | Model predictions with mkinpredict [0.3 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s] +✖ | 7 1 | Nonlinear mixed-effects models [1.9 s] +──────────────────────────────────────────────────────────────────────────────── +Error (test_nlme.R:116:3): nlme_function works correctly in other cases +Error: unused argument ("sysname") +Backtrace: + 1. mkin::mmkin("SFO", ds_me_sfo_5, quiet = TRUE) test_nlme.R:116:2 + 2. parallel::mclapply(...) /home/jranke/git/mkin/R/mmkin.R:118:4 +──────────────────────────────────────────────────────────────────────────────── ✖ | 10 4 | Plotting [1.7 s] ──────────────────────────────────────────────────────────────────────────────── Failure (test_plot.R:20:3): Plotting mkinfit, mmkin and mixed model objects is reproducible @@ -42,13 +48,14 @@ Figures don't match: plot-res-for-focus-d.svg ──────────────────────────────────────────────────────────────────────────────── ✔ | 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] +✔ | 7 | Fitting the SFORB model [3.6 s] ✔ | 1 | Summaries of old mkinfit objects +✔ | 4 | Summary [0.1 s] ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s] -✔ | 9 | Hypothesis tests [8.3 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.5 s] +✔ | 9 | Hypothesis tests [8.1 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 41.0 s +Duration: 35.2 s -[ FAIL 4 | WARN 0 | SKIP 0 | PASS 170 ] +[ FAIL 5 | WARN 0 | SKIP 0 | PASS 168 ] diff --git a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg index a84e170d..bef1556f 100644 --- a/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg +++ b/tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg @@ -75,21 +75,21 @@ <rect x='0.00' y='0.00' width='720.00' height='576.00' /> </clipPath> </defs> -<line x1='82.40' y1='502.56' x2='617.77' y2='502.56' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='82.40' y1='502.56' x2='671.31' y2='502.56' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> <line x1='82.40' y1='502.56' x2='82.40' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> -<line x1='171.63' y1='502.56' x2='171.63' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> -<line x1='260.86' y1='502.56' x2='260.86' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> -<line x1='350.09' y1='502.56' x2='350.09' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> -<line x1='439.31' y1='502.56' x2='439.31' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> -<line x1='528.54' y1='502.56' x2='528.54' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> -<line x1='617.77' y1='502.56' x2='617.77' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='180.55' y1='502.56' x2='180.55' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='278.70' y1='502.56' x2='278.70' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='376.85' y1='502.56' x2='376.85' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='475.01' y1='502.56' x2='475.01' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='573.16' y1='502.56' x2='573.16' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> +<line x1='671.31' y1='502.56' x2='671.31' y2='509.76' style='stroke-width: 0.75;' clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)' /> <g clip-path='url(#cpMC4wMHw3MjAuMDB8NTc2LjAwfDAuMDA=)'><text x='79.06' y='528.48' style='font-size: 12.00px; 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