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-rw-r--r--DESCRIPTION2
-rw-r--r--NEWS.md2
-rw-r--r--R/mmkin.R5
-rw-r--r--check.log8
-rw-r--r--docs/news/index.html1
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/Rplot001.pngbin1011 -> 27637 bytes
-rw-r--r--docs/reference/Rplot002.pngbin16524 -> 59394 bytes
-rw-r--r--docs/reference/Rplot003.pngbin15401 -> 33192 bytes
-rw-r--r--docs/reference/Rplot004.pngbin10689 -> 23509 bytes
-rw-r--r--docs/reference/Rplot005.pngbin19483 -> 23509 bytes
-rw-r--r--docs/reference/Rplot006.pngbin24302 -> 22129 bytes
-rw-r--r--docs/reference/mmkin-1.pngbin111569 -> 110844 bytes
-rw-r--r--docs/reference/mmkin-2.pngbin108319 -> 107612 bytes
-rw-r--r--docs/reference/mmkin-3.pngbin96596 -> 96248 bytes
-rw-r--r--docs/reference/mmkin-4.pngbin67345 -> 66653 bytes
-rw-r--r--docs/reference/mmkin-5.pngbin65269 -> 65046 bytes
-rw-r--r--docs/reference/mmkin.html9
-rw-r--r--docs/reference/nlme-1.pngbin70276 -> 70244 bytes
-rw-r--r--docs/reference/plot.mixed.mmkin-1.pngbin85433 -> 84976 bytes
-rw-r--r--man/mmkin.Rd5
-rw-r--r--test.log43
-rw-r--r--tests/figs/plotting/mkinfit-plot-for-focus-c-with-residuals-like-in-gmkin.svg42
-rw-r--r--tests/figs/plotting/mkinfit-plot-for-focus-c-with-sep-true.svg42
-rw-r--r--tests/figs/plotting/plot-res-for-focus-c.svg42
-rw-r--r--tests/figs/plotting/plot-res-for-focus-d.svg98
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",
diff --git a/NEWS.md b/NEWS.md
index 9d03fa3d..88509b66 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -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
diff --git a/R/mmkin.R b/R/mmkin.R
index 030fb27b..fe04129e 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -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")
diff --git a/check.log b/check.log
index 0d04e05e..b848a900 100644
--- a/check.log
+++ b/check.log
@@ -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
index 17a35806..49fb9af1 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
Binary files differ
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index 808f1968..745d583d 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
Binary files differ
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index 97f650e2..eba202e9 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
Binary files differ
diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png
index 21ad6783..a4f878c8 100644
--- a/docs/reference/Rplot004.png
+++ b/docs/reference/Rplot004.png
Binary files differ
diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png
index 4828f5b2..a4f878c8 100644
--- a/docs/reference/Rplot005.png
+++ b/docs/reference/Rplot005.png
Binary files differ
diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png
index 4aed2c87..ff8a5d83 100644
--- a/docs/reference/Rplot006.png
+++ b/docs/reference/Rplot006.png
Binary files differ
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png
index 26586ab9..f6bb2131 100644
--- a/docs/reference/mmkin-1.png
+++ b/docs/reference/mmkin-1.png
Binary files differ
diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png
index dbcdd8ee..50102a3d 100644
--- a/docs/reference/mmkin-2.png
+++ b/docs/reference/mmkin-2.png
Binary files differ
diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png
index 80245fc6..9aa7f0db 100644
--- a/docs/reference/mmkin-3.png
+++ b/docs/reference/mmkin-3.png
Binary files differ
diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png
index 328aa564..f4f413d1 100644
--- a/docs/reference/mmkin-4.png
+++ b/docs/reference/mmkin-4.png
Binary files differ
diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png
index 9ce5e919..48ab2c50 100644
--- a/docs/reference/mmkin-5.png
+++ b/docs/reference/mmkin-5.png
Binary files differ
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 &gt; 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'>#&gt; user system elapsed
-#&gt; 5.387 0.413 1.864 </div><div class='input'><span class='va'>time_1</span>
+#&gt; 4.656 0.403 1.734 </div><div class='input'><span class='va'>time_1</span>
</div><div class='output co'>#&gt; user system elapsed
-#&gt; 5.786 0.008 5.794 </div><div class='input'>
+#&gt; 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'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index cca4ce0a..c41adc27 100644
--- a/docs/reference/nlme-1.png
+++ b/docs/reference/nlme-1.png
Binary files differ
diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png
index 2224d96e..65660abe 100644
--- a/docs/reference/plot.mixed.mmkin-1.png
+++ b/docs/reference/plot.mixed.mmkin-1.png
Binary files differ
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.}
diff --git a/test.log b/test.log
index b49088e5..a8b42364 100644
--- a/test.log
+++ b/test.log
@@ -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>
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