Static documentation except articles rebuilt by pkgdown

10 files changed, 15 insertions, 220 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index e18c3fea..9c2ac14a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.46
+Version: 0.9.46.1
 Date: 2017-07-29
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
diff --git a/build.log b/build.log
index 2d06c4dc..a02e93ae 100644
--- a/build.log
+++ b/build.log
@@ -2,9 +2,4 @@
 * preparing ‘mkin’:
 * checking DESCRIPTION meta-information ... OK
 * installing the package to build vignettes
-* creating vignettes ... OK
-* checking for LF line-endings in source and make files
-* checking for empty or unneeded directories
-* looking to see if a ‘data/datalist’ file should be added
-* building ‘mkin_0.9.46.tar.gz’
-
+* creating vignettes ...
\ No newline at end of file
diff --git a/check.log b/check.log
index ab7bef11..5d8f5a1a 100644
--- a/check.log
+++ b/check.log
@@ -1,5 +1,5 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R Under development (unstable) (2017-07-28 r72992)
+* using R version 3.4.1 (2017-06-30)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
@@ -7,8 +7,12 @@
 * checking extension type ... Package
 * this is package ‘mkin’ version ‘0.9.46’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... WARNING
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
+
+Insufficient package version (submitted: 0.9.46, existing: 0.9.46)
+
+The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -64,5 +68,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking PDF version of manual ... OK
 * DONE
 
-Status: OK
+Status: 1 WARNING
+See
+  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
 
diff --git a/docs/index.html b/docs/index.html
index 9898d6f5..dae43514 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -116,7 +116,7 @@
 <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li>
 <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li>
 <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li>
-<li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li>
+<li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight.method = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li>
 <li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li>
 </ul>
 </div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index bf7cd233..1eff1c12 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -102,7 +102,7 @@
     <div class="page-header">
       <h1>
         Reference
-        <small>version&nbsp;0.9.46</small>
+        <small>version&nbsp;0.9.46.1</small>
       </h1>
     </div>
 
diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png
index 87d3351d..48ab5271 100644
--- a/docs/reference/plot.mkinfit-10.png
+++ b/docs/reference/plot.mkinfit-10.png
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png
index 7739e3b0..21af1e7b 100644
--- a/docs/reference/plot.mmkin-2.png
+++ b/docs/reference/plot.mmkin-2.png
diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png
index e2eb3aae..3004f48f 100644
--- a/docs/reference/plot.mmkin-4.png
+++ b/docs/reference/plot.mmkin-4.png
diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png
index 3bbd390a..02ed2ab1 100644
--- a/docs/reference/plot.mmkin-6.png
+++ b/docs/reference/plot.mmkin-6.png
diff --git a/test.log b/test.log
index 195d9e5b..a4a37c44 100644
--- a/test.log
+++ b/test.log
@@ -9,214 +9,6 @@ Testing mkin
 Calculation of FOCUS chi2 error levels: ..
 Results for FOCUS D established in expertise for UBA (Ranke 2014): ......
 The t-test for significant difference from zero: ..
-Fitting the FOMC model with large parameter correlation: Model cost at call  1 :  2154.97 
-Model cost at call  2 :  2154.97 
-Model cost at call  4 :  2154.97 
-Model cost at call  5 :  388.1874 
-Model cost at call  9 :  198.5808 
-Model cost at call  10 :  198.5806 
-Model cost at call  13 :  167.315 
-Model cost at call  15 :  167.315 
-Model cost at call  17 :  122.5165 
-Model cost at call  21 :  110.3697 
-Model cost at call  25 :  99.37279 
-Model cost at call  26 :  99.37279 
-Model cost at call  29 :  85.86611 
-Model cost at call  30 :  85.86609 
-Model cost at call  33 :  83.79827 
-Model cost at call  35 :  83.79825 
-Model cost at call  37 :  77.76253 
-Model cost at call  39 :  77.76252 
-Model cost at call  40 :  77.76252 
-Model cost at call  41 :  74.85232 
-Model cost at call  45 :  71.0713 
-Model cost at call  49 :  69.0689 
-Model cost at call  53 :  65.69063 
-Model cost at call  54 :  65.69063 
-Model cost at call  57 :  63.81175 
-Model cost at call  58 :  63.81174 
-Model cost at call  61 :  61.77925 
-Model cost at call  65 :  60.68903 
-Model cost at call  69 :  58.787 
-Model cost at call  73 :  57.79498 
-Model cost at call  77 :  56.72184 
-Model cost at call  78 :  56.72184 
-Model cost at call  81 :  56.27078 
-Model cost at call  82 :  56.27077 
-Model cost at call  85 :  55.76643 
-Model cost at call  89 :  55.06746 
-Model cost at call  93 :  54.77276 
-Model cost at call  97 :  54.46435 
-Model cost at call  101 :  53.97206 
-Model cost at call  105 :  53.7466 
-Model cost at call  109 :  53.45331 
-Model cost at call  113 :  53.15008 
-Model cost at call  117 :  52.8698 
-Model cost at call  122 :  52.79044 
-Model cost at call  126 :  52.64587 
-Model cost at call  127 :  52.56412 
-Model cost at call  131 :  52.37304 
-Model cost at call  135 :  52.29005 
-Model cost at call  139 :  52.20652 
-Model cost at call  143 :  52.05187 
-Model cost at call  147 :  51.95367 
-Model cost at call  151 :  51.80296 
-Model cost at call  152 :  51.80296 
-Model cost at call  153 :  51.80296 
-Model cost at call  155 :  51.79287 
-Model cost at call  156 :  51.79286 
-Model cost at call  157 :  51.79286 
-Model cost at call  159 :  51.71749 
-Model cost at call  163 :  51.69885 
-Model cost at call  164 :  51.66416 
-Model cost at call  169 :  51.61289 
-Model cost at call  173 :  51.5739 
-Model cost at call  177 :  51.5122 
-Model cost at call  181 :  51.44598 
-Model cost at call  185 :  51.42107 
-Model cost at call  189 :  51.37519 
-Model cost at call  193 :  51.32105 
-Model cost at call  194 :  51.32105 
-Model cost at call  195 :  51.32105 
-Model cost at call  197 :  51.29233 
-Model cost at call  199 :  51.29233 
-Model cost at call  200 :  51.29233 
-Model cost at call  202 :  51.27541 
-Model cost at call  206 :  51.24732 
-Model cost at call  210 :  51.20348 
-Model cost at call  214 :  51.1884 
-Model cost at call  218 :  51.15654 
-Model cost at call  222 :  51.12473 
-Model cost at call  226 :  51.1093 
-Model cost at call  230 :  51.09604 
-Model cost at call  234 :  51.07288 
-Model cost at call  238 :  51.04678 
-Model cost at call  243 :  51.03801 
-Model cost at call  247 :  51.02297 
-Model cost at call  248 :  51.01588 
-Model cost at call  252 :  50.99353 
-Model cost at call  253 :  50.99353 
-Model cost at call  254 :  50.99353 
-Model cost at call  256 :  50.98775 
-Model cost at call  257 :  50.97537 
-Model cost at call  258 :  50.97537 
-Model cost at call  259 :  50.97537 
-Model cost at call  260 :  50.97537 
-Model cost at call  262 :  50.97142 
-Model cost at call  266 :  50.96632 
-Model cost at call  272 :  50.9654 
-Model cost at call  276 :  50.96385 
-Model cost at call  279 :  50.96385 
-Model cost at call  284 :  50.96354 
-Model cost at call  286 :  50.96354 
-Model cost at call  290 :  50.96292 
-Model cost at call  293 :  50.96292 
-Model cost at call  298 :  50.9628 
-Model cost at call  300 :  50.9628 
-Model cost at call  305 :  50.96277 
-Model cost at call  307 :  50.96277 
-Model cost at call  312 :  50.96277 
-Model cost at call  314 :  50.96277 
-Model cost at call  318 :  50.96276 
-Model cost at call  321 :  50.96276 
-Model cost at call  326 :  50.96276 
-Model cost at call  328 :  50.96276 
-Model cost at call  332 :  50.96275 
-Model cost at call  333 :  50.96274 
-Model cost at call  336 :  50.96274 
-Model cost at call  337 :  50.96274 
-Model cost at call  342 :  50.96274 
-Model cost at call  344 :  50.96274 
-Model cost at call  348 :  50.96274 
-Model cost at call  351 :  50.96274 
-Model cost at call  357 :  50.96274 
-Model cost at call  359 :  50.96274 
-Model cost at call  363 :  50.96274 
-Model cost at call  364 :  50.96274 
-Model cost at call  367 :  50.96274 
-Model cost at call  375 :  50.96274 
-Model cost at call  381 :  50.96274 
-Model cost at call  388 :  50.96274 
-Model cost at call  452 :  50.96274 
-.Model cost at call  1 :  2154.97 
-Model cost at call  3 :  2154.97 
-Model cost at call  5 :  2154.97 
-Model cost at call  6 :  716.4083 
-Model cost at call  8 :  716.4082 
-Model cost at call  11 :  136.1354 
-Model cost at call  12 :  136.1354 
-Model cost at call  15 :  64.35183 
-Model cost at call  16 :  64.35183 
-Model cost at call  20 :  61.48715 
-Model cost at call  22 :  61.48715 
-Model cost at call  24 :  59.59792 
-Model cost at call  26 :  59.59792 
-Model cost at call  28 :  57.47603 
-Model cost at call  30 :  57.47603 
-Model cost at call  32 :  57.10469 
-Model cost at call  34 :  57.10468 
-Model cost at call  36 :  54.78942 
-Model cost at call  38 :  54.78942 
-Model cost at call  40 :  54.29399 
-Model cost at call  42 :  54.29399 
-Model cost at call  44 :  53.55295 
-Model cost at call  46 :  53.55294 
-Model cost at call  49 :  53.10239 
-Model cost at call  51 :  53.10239 
-Model cost at call  53 :  52.95095 
-Model cost at call  55 :  52.95095 
-Model cost at call  57 :  52.41198 
-Model cost at call  59 :  52.41198 
-Model cost at call  61 :  52.24816 
-Model cost at call  63 :  52.24816 
-Model cost at call  65 :  51.99669 
-Model cost at call  67 :  51.99669 
-Model cost at call  69 :  51.82092 
-Model cost at call  71 :  51.82092 
-Model cost at call  74 :  51.69389 
-Model cost at call  76 :  51.69389 
-Model cost at call  78 :  51.64468 
-Model cost at call  80 :  51.64468 
-Model cost at call  82 :  51.46367 
-Model cost at call  84 :  51.46366 
-Model cost at call  86 :  51.407 
-Model cost at call  88 :  51.407 
-Model cost at call  90 :  51.30871 
-Model cost at call  92 :  51.30871 
-Model cost at call  94 :  51.23556 
-Model cost at call  96 :  51.23556 
-Model cost at call  98 :  51.17829 
-Model cost at call  100 :  51.17829 
-Model cost at call  103 :  51.13498 
-Model cost at call  105 :  51.13498 
-Model cost at call  107 :  51.11419 
-Model cost at call  109 :  51.11419 
-Model cost at call  111 :  51.05405 
-Model cost at call  113 :  51.05405 
-Model cost at call  115 :  51.0096 
-Model cost at call  117 :  51.0096 
-Model cost at call  119 :  50.97496 
-Model cost at call  121 :  50.97496 
-Model cost at call  125 :  50.96419 
-Model cost at call  126 :  50.96419 
-Model cost at call  129 :  50.96365 
-Model cost at call  131 :  50.96365 
-Model cost at call  134 :  50.96354 
-Model cost at call  136 :  50.96354 
-Model cost at call  138 :  50.96333 
-Model cost at call  140 :  50.96333 
-Model cost at call  142 :  50.9629 
-Model cost at call  144 :  50.9629 
-Model cost at call  147 :  50.96282 
-Model cost at call  149 :  50.96282 
-Model cost at call  152 :  50.9628 
-Model cost at call  156 :  50.96277 
-Model cost at call  161 :  50.96276 
-Model cost at call  165 :  50.96275 
-Model cost at call  170 :  50.96274 
-Model cost at call  175 :  50.96274 
-Optimisation by method Marq successfully terminated.
-.
 Model predictions with mkinpredict: ...
 Fitting of parent only models: .....................
 Complex test case from Schaefer et al. (2007) Piacenza paper: ..