From cf54ccca37d27480dbf8d59eb027300518f7ad75 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 17:08:43 +0200 Subject: Prepare release of v1.2.4 - Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release --- docs/404.html | 2 +- docs/articles/FOCUS_D.html | 20 +- docs/articles/FOCUS_L.html | 150 +- .../figure-html/unnamed-chunk-10-1.png | Bin 42972 -> 42974 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 36606 -> 36579 bytes docs/articles/index.html | 4 +- docs/articles/mkin.html | 12 +- .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 91107 -> 91109 bytes docs/articles/prebuilt/2022_cyan_pathway.html | 3262 +++++++++----------- .../figure-html/unnamed-chunk-13-1.png | Bin 363943 -> 363589 bytes 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deletions(-) (limited to 'docs') diff --git a/docs/404.html b/docs/404.html index 4d888396..b9ab1f25 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ mkin - 1.2.3.1 + 1.2.4 diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 0d2f56f5..19367c68 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -135,7 +135,7 @@ D Ranke

Last change 31 January 2019 -(rebuilt 2023-04-20)

+(rebuilt 2023-05-19) Source: vignettes/FOCUS_D.rmd @@ -237,10 +237,10 @@ the mkinparplot function.

summary method for mkinfit objects.

 summary(fit)
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:14 2023 
-## Date of summary: Thu Apr 20 07:37:14 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:23 2023 
+## Date of summary: Fri May 19 09:20:23 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -248,7 +248,7 @@ the mkinparplot function.

## ## Model predictions using solution type analytical ## -## Fitted using 401 model solutions performed in 0.047 s +## Fitted using 401 model solutions performed in 0.048 s ## ## Error model: Constant variance ## @@ -292,10 +292,10 @@ the mkinparplot function.

## Parameter correlation: ## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma ## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06 -## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07 +## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.479e-07 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.211e-07 ## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06 -## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00 +## sigma -1.172e-06 -8.479e-07 8.211e-07 1.305e-06 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index e47ed9d7..dabb16f2 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -134,8 +134,8 @@ to L3

Johannes Ranke

-

Last change 18 May 2022 -(rebuilt 2023-04-20)

+

Last change 18 May 2023 +(rebuilt 2023-05-19)

Source: vignettes/FOCUS_L.rmd @@ -169,10 +169,10 @@ report.

 m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:15 2023 
-## Date of summary: Thu Apr 20 07:37:15 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:25 2023 
+## Date of summary: Fri May 19 09:20:25 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -276,17 +276,17 @@ objects.

## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
 ## is doubtful
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:16 2023 
-## Date of summary: Thu Apr 20 07:37:16 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:25 2023 
+## Date of summary: Fri May 19 09:20:25 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 369 model solutions performed in 0.025 s
+## Fitted using 342 model solutions performed in 0.021 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -314,22 +314,22 @@ objects.

## ## Results: ## -## AIC BIC logLik -## 95.88781 99.44929 -43.9439 +## AIC BIC logLik +## 95.88782 99.44931 -43.94391 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 92.47 1.2820 89.720 95.220 -## log_alpha 13.78 NaN NaN NaN -## log_beta 16.13 NaN NaN NaN -## sigma 2.78 0.4598 1.794 3.766 +## log_alpha 13.20 NaN NaN NaN +## log_beta 15.54 NaN NaN NaN +## sigma 2.78 0.4607 1.792 3.768 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.0000000 NaN NaN 0.0001671 -## log_alpha NaN 1 NaN NaN -## log_beta NaN NaN 1 NaN -## sigma 0.0001671 NaN NaN 1.0000000 +## parent_0 log_alpha log_beta sigma +## parent_0 1.000000 NaN NaN 0.000603 +## log_alpha NaN 1 NaN NaN +## log_beta NaN NaN 1 NaN +## sigma 0.000603 NaN NaN 1.000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -337,9 +337,9 @@ objects.

## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 9.247e+01 NA NA 89.720 95.220 -## alpha 9.658e+05 NA NA NA NA -## beta 1.010e+07 NA NA NA NA -## sigma 2.780e+00 NA NA 1.794 3.766 +## alpha 5.386e+05 NA NA NA NA +## beta 5.633e+06 NA NA NA NA +## sigma 2.780e+00 NA NA 1.792 3.768 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df @@ -347,8 +347,8 @@ objects.

## parent 3.619 3 6 ## ## Estimated disappearance times: -## DT50 DT90 DT50back -## parent 7.25 24.08 7.25
+## DT50 DT90 DT50back +## parent 7.249 24.08 7.249

We get a warning that the default optimisation algorithm Port did not converge, which is an indication that the model is overparameterised, i.e. contains too many parameters @@ -427,17 +427,17 @@ kinetics.

 summary(m.L2.FOMC, data = FALSE)
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:16 2023 
-## Date of summary: Thu Apr 20 07:37:16 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:25 2023 
+## Date of summary: Fri May 19 09:20:25 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.015 s
+## Fitted using 239 model solutions performed in 0.013 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -472,10 +472,10 @@ kinetics.

## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09 -## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.602e-07 -## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.372e-07 -## sigma -7.828e-09 -1.602e-07 -1.372e-07 1.000e+00 +## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09 +## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07 +## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.386e-07 +## sigma -7.436e-09 -1.617e-07 -1.386e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -511,10 +511,10 @@ the data.

 summary(m.L2.DFOP, data = FALSE)
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:16 2023 
-## Date of summary: Thu Apr 20 07:37:16 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:25 2023 
+## Date of summary: Fri May 19 09:20:25 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -523,7 +523,7 @@ the data.

## ## Model predictions using solution type analytical ## -## Fitted using 581 model solutions performed in 0.04 s +## Fitted using 581 model solutions performed in 0.038 s ## ## Error model: Constant variance ## @@ -554,18 +554,18 @@ the data.

## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.950 9.998e-01 91.5900 96.3100 -## log_k1 3.112 1.842e+03 -4353.0000 4359.0000 +## log_k1 3.113 1.849e+03 -4369.0000 4375.0000 ## log_k2 -1.088 6.285e-02 -1.2370 -0.9394 ## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638 ## sigma 1.414 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_qlogis sigma -## parent_0 1.000e+00 6.783e-07 -3.390e-10 2.665e-01 -2.967e-10 -## log_k1 6.783e-07 1.000e+00 1.116e-04 -2.196e-04 -1.031e-05 -## log_k2 -3.390e-10 1.116e-04 1.000e+00 -7.903e-01 2.917e-09 -## g_qlogis 2.665e-01 -2.196e-04 -7.903e-01 1.000e+00 -4.408e-09 -## sigma -2.967e-10 -1.031e-05 2.917e-09 -4.408e-09 1.000e+00 +## parent_0 1.000e+00 6.763e-07 -8.944e-10 2.665e-01 -1.083e-09 +## log_k1 6.763e-07 1.000e+00 1.112e-04 -2.187e-04 -1.027e-05 +## log_k2 -8.944e-10 1.112e-04 1.000e+00 -7.903e-01 9.464e-09 +## g_qlogis 2.665e-01 -2.187e-04 -7.903e-01 1.000e+00 -1.532e-08 +## sigma -1.083e-09 -1.027e-05 9.464e-09 -1.532e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -573,7 +573,7 @@ the data.

## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 -## k1 22.4800 5.553e-04 4.998e-01 0.0000 Inf +## k1 22.4900 5.533e-04 4.998e-01 0.0000 Inf ## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909 ## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591 ## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960 @@ -585,7 +585,7 @@ the data.

## ## Estimated disappearance times: ## DT50 DT90 DT50back DT50_k1 DT50_k2 -## parent 0.5335 5.311 1.599 0.03084 2.058
+## parent 0.5335 5.311 1.599 0.03083 2.058

Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion.

@@ -628,10 +628,10 @@ using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 summary(mm.L3[["DFOP", 1]])
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:17 2023 
-## Date of summary: Thu Apr 20 07:37:17 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:26 2023 
+## Date of summary: Fri May 19 09:20:26 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -640,7 +640,7 @@ summary and plot functions working on mkinfit objects.

## ## Model predictions using solution type analytical ## -## Fitted using 376 model solutions performed in 0.024 s +## Fitted using 376 model solutions performed in 0.021 s ## ## Error model: Constant variance ## @@ -678,11 +678,11 @@ summary and plot functions working on mkinfit objects.

## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_qlogis sigma -## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.664e-08 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.147e-07 +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.696e-08 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.148e-07 ## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06 -## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.926e-07 -## sigma -9.664e-08 7.147e-07 1.022e-06 -7.926e-07 1.000e+00 +## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.930e-07 +## sigma -9.696e-08 7.148e-07 1.022e-06 -7.930e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -755,17 +755,17 @@ passes is slightly lower for the FOMC model. However, the difference appears negligible.

 summary(mm.L4[["SFO", 1]], data = FALSE)
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:17 2023 
-## Date of summary: Thu Apr 20 07:37:17 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:26 2023 
+## Date of summary: Fri May 19 09:20:26 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.009 s
+## Fitted using 142 model solutions performed in 0.008 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -797,9 +797,9 @@ appears negligible.

## ## Parameter correlation: ## parent_0 log_k_parent sigma -## parent_0 1.000e+00 5.938e-01 3.387e-07 -## log_k_parent 5.938e-01 1.000e+00 5.830e-07 -## sigma 3.387e-07 5.830e-07 1.000e+00 +## parent_0 1.000e+00 5.938e-01 3.430e-07 +## log_k_parent 5.938e-01 1.000e+00 5.885e-07 +## sigma 3.430e-07 5.885e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -820,17 +820,17 @@ appears negligible.

## parent 106 352
 summary(mm.L4[["FOMC", 1]], data = FALSE)
-
## mkin version used for fitting:    1.2.3 
-## R version used for fitting:       4.2.3 
-## Date of fit:     Thu Apr 20 07:37:17 2023 
-## Date of summary: Thu Apr 20 07:37:17 2023 
+
## mkin version used for fitting:    1.2.4 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 09:20:26 2023 
+## Date of summary: Fri May 19 09:20:26 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.014 s
+## Fitted using 224 model solutions performed in 0.012 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -865,10 +865,10 @@ appears negligible.

## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07 -## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.478e-08 -## log_beta -5.543e-01 9.889e-01 1.000e+00 5.211e-08 -## sigma -2.468e-07 2.478e-08 5.211e-08 1.000e+00 +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.447e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.198e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 4.923e-08 +## sigma -2.447e-07 2.198e-08 4.923e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png index 11706305..c732be75 100644 Binary files a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png index c3f55dd6..dfeb7907 100644 Binary files a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index 991f8994..7060b377 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ mkin - 1.2.3.1 + 1.2.4 @@ -111,7 +111,7 @@
Example evaluation of FOCUS Laboratory Data L1 to L3
-
Introduction to mkin
+
Short introduction to mkin
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 88c63bef..6213916b 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -5,13 +5,13 @@ -Introduction to mkin • mkin +Short introduction to mkin • mkin - +