From 7b333cff452dd1b36cb994c18b0b19e97facbc72 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 7 Sep 2017 08:32:41 +0200 Subject: Static documentation except articles rebuilt by pkgdown --- DESCRIPTION | 2 +- build.log | 7 +- check.log | 14 ++- docs/index.html | 2 +- docs/reference/index.html | 2 +- docs/reference/plot.mkinfit-10.png | Bin 19456 -> 19640 bytes docs/reference/plot.mmkin-2.png | Bin 11258 -> 11215 bytes docs/reference/plot.mmkin-4.png | Bin 11349 -> 11308 bytes docs/reference/plot.mmkin-6.png | Bin 8386 -> 8312 bytes test.log | 208 ------------------------------------- 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 ’ + +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 ’ * 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 @@
  • The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.
  • Summary and plotting functions. The summary of an mkinfit object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.
  • The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.
    • -
  • Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument reweight = "obs" to your call to mkinfit 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.
    • +
  • Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument reweight.method = "obs" to your call to mkinfit 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.
  • When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.
    • 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 @@

    Reference - version 0.9.46 + version 0.9.46.1

    diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png index 87d3351d..48ab5271 100644 Binary files a/docs/reference/plot.mkinfit-10.png and b/docs/reference/plot.mkinfit-10.png differ diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png index 7739e3b0..21af1e7b 100644 Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png index e2eb3aae..3004f48f 100644 Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png index 3bbd390a..02ed2ab1 100644 Binary files a/docs/reference/plot.mmkin-6.png and b/docs/reference/plot.mmkin-6.png 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: .. -- cgit v1.2.1