Update for gmkin 0.6.12v1.0.2

mkinfit: Keep model names stored in mkinmod objects, avoiding their loss in gmkin

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 <jranke@uni-bremen.de>’
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 @@
       </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">1.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
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 @@
       </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">1.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
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 @@
       </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">1.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
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 @@
       </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">1.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
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 @@
       </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">1.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
@@ -141,9 +141,17 @@
       <small>Source: <a href='https://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
+    <div id="mkin-102" class="section level1">
+<h1 class="page-header" data-toc-text="1.0.2">
+<a href="#mkin-102" class="anchor"></a>mkin 1.0.2<small> Unreleased </small>
+</h1>
+<ul>
+<li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li>
+</ul>
+</div>
     <div id="mkin-101" class="section level1">
 <h1 class="page-header" data-toc-text="1.0.1">
-<a href="#mkin-101" class="anchor"></a>mkin 1.0.1<small> Unreleased </small>
+<a href="#mkin-101" class="anchor"></a>mkin 1.0.1<small> 2021-02-10 </small>
 </h1>
 <ul>
 <li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li>
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
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index bb624e64..d24e35b4 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
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." />
       </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">1.0.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
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 @@
       </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">1.0.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png
index 9c46481c..9c9a2211 100644
--- a/docs/reference/plot.mixed.mmkin-1.png
+++ b/docs/reference/plot.mixed.mmkin-1.png
diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png
index e228f764..0f66ff0f 100644
--- a/docs/reference/plot.mixed.mmkin-2.png
+++ b/docs/reference/plot.mixed.mmkin-2.png
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 @@
       </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">1.0.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.2</span>
       </span>
     </div>
 
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 ]