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.
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index 11706305..c732be75 100644
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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
 
 
 
 
 
-
+