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-rw-r--r--DESCRIPTION2
-rw-r--r--build.log7
-rw-r--r--check.log14
-rw-r--r--docs/index.html2
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/plot.mkinfit-10.pngbin19456 -> 19640 bytes
-rw-r--r--docs/reference/plot.mmkin-2.pngbin11258 -> 11215 bytes
-rw-r--r--docs/reference/plot.mmkin-4.pngbin11349 -> 11308 bytes
-rw-r--r--docs/reference/plot.mmkin-6.pngbin8386 -> 8312 bytes
-rw-r--r--test.log208
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
Binary files differ
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
Binary files differ
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
Binary files differ
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
Binary files differ
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: ..

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