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-rw-r--r--DESCRIPTION4
-rw-r--r--NEWS.md2
-rw-r--r--build.log2
-rw-r--r--check.log5
-rw-r--r--docs/404.html2
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/news/index.html3
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/index.html2
-rw-r--r--test.log16
12 files changed, 24 insertions, 20 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 5f38d12c..0facf77e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: mkin
Type: Package
Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.50
-Date: 2020-05-07
+Version: 0.9.50.1
+Date: 2020-05-11
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de",
comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index 2512f361..49828447 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
- 'mkinmod': Make 'use_of_ff' = "max" the default
+- Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO
+
# mkin 0.9.49.11 (2020-04-20)
- Increase a test tolerance to make it pass on all CRAN check machines
diff --git a/build.log b/build.log
index b3df3235..4c64021a 100644
--- a/build.log
+++ b/build.log
@@ -5,5 +5,5 @@
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
-* building ‘mkin_0.9.50.tar.gz’
+* building ‘mkin_0.9.50.1.tar.gz’
diff --git a/check.log b/check.log
index 8064f9a6..99cb6f86 100644
--- a/check.log
+++ b/check.log
@@ -1,11 +1,11 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R Under development (unstable) (2020-05-10 r78402)
+* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-tests --as-cran’
* checking for file ‘mkin/DESCRIPTION’ ... OK
* checking extension type ... Package
-* this is package ‘mkin’ version ‘0.9.50’
+* this is package ‘mkin’ version ‘0.9.50.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
@@ -35,6 +35,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
diff --git a/docs/404.html b/docs/404.html
index c6da911d..afb82b3f 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 7091d4c9..5179c1bc 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/authors.html b/docs/authors.html
index bc170e49..5ec134d6 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 5c4a0a9b..37ed972a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 1e13041d..3965df70 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
@@ -145,6 +145,7 @@
<ul>
<li><p>Support SFORB with formation fractions</p></li>
<li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li>
+<li><p>Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO</p></li>
</ul>
</div>
<div id="mkin-0-9-49-11-2020-04-20" class="section level1">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 814bf679..aa796e47 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
NAFTA_examples: web_only/NAFTA_examples.html
benchmarks: web_only/benchmarks.html
compiled_models: web_only/compiled_models.html
-last_built: 2020-05-11T13:00Z
+last_built: 2020-05-11T13:20Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7e7fff29..ed6debdd 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/test.log b/test.log
index f2f9ff85..54f61d9b 100644
--- a/test.log
+++ b/test.log
@@ -4,19 +4,19 @@ Testing mkin
✔ | 2 | Export dataset for reading into CAKE
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ | 7 | Fitting the SFORB model [3.4 s]
-✔ | 4 | Analytical solutions for coupled models [1.7 s]
+✔ | 7 | Fitting the SFORB model [3.2 s]
+✔ | 5 | Analytical solutions for coupled models [3.0 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [1.0 s]
-✔ | 14 | Error model fitting [4.0 s]
+✔ | 14 | Error model fitting [3.8 s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
✔ | 12 | Special cases of mkinfit calls [0.6 s]
✔ | 8 | mkinmod model generation and printing [0.2 s]
-✔ | 3 | Model predictions with mkinpredict [0.4 s]
+✔ | 3 | Model predictions with mkinpredict [0.3 s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4 s]
-✔ | 9 | Nonlinear mixed-effects models [7.6 s]
+✔ | 9 | Nonlinear mixed-effects models [7.5 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
✔ | 3 | Summary
✔ | 14 | Plotting [1.4 s]
@@ -24,13 +24,13 @@ Testing mkin
✔ | 4 | Residuals extracted from mkinfit models
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.4 s]
✔ | 9 | Hypothesis tests [6.5 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 36.4 s
+Duration: 37.3 s
-OK: 158
+OK: 159
Failed: 0
Warnings: 0
Skipped: 0

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