From a01fe8923ff50dcc76c34fb09ad500f5f5433063 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 May 2023 22:35:52 +0200 Subject: Release date, update pkgdown development docs --- NEWS.md | 2 +- docs/dev/articles/FOCUS_D.html | 12 +- docs/dev/articles/FOCUS_L.html | 62 ++--- docs/dev/articles/index.html | 4 +- docs/dev/articles/mkin.html | 12 +- docs/dev/articles/prebuilt/2022_cyan_pathway.html | 263 +++++++++++---------- docs/dev/articles/prebuilt/2022_dmta_parent.html | 140 +++++------ docs/dev/articles/prebuilt/2022_dmta_pathway.html | 51 ++-- docs/dev/articles/twa.html | 4 +- docs/dev/articles/web_only/FOCUS_Z.html | 4 +- docs/dev/articles/web_only/NAFTA_examples.html | 4 +- docs/dev/articles/web_only/benchmarks.html | 82 ++++++- docs/dev/articles/web_only/compiled_models.html | 20 +- docs/dev/articles/web_only/dimethenamid_2018.html | 43 ++-- docs/dev/articles/web_only/multistart.html | 4 +- docs/dev/articles/web_only/saem_benchmarks.html | 96 +++++++- docs/dev/authors.html | 6 +- docs/dev/index.html | 2 +- docs/dev/news/index.html | 13 +- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/AIC.mmkin.html | 2 +- docs/dev/reference/CAKE_export.html | 2 +- docs/dev/reference/D24_2014.html | 4 +- docs/dev/reference/DFOP.solution.html | 2 +- docs/dev/reference/Extract.mmkin.html | 2 +- docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/dev/reference/FOCUS_2006_datasets.html | 2 +- docs/dev/reference/FOMC.solution.html | 2 +- docs/dev/reference/HS.solution.html | 2 +- docs/dev/reference/IORE.solution.html | 2 +- docs/dev/reference/NAFTA_SOP_2015.html | 2 +- docs/dev/reference/NAFTA_SOP_Attachment.html | 2 +- docs/dev/reference/Rplot001.png | Bin 20558 -> 13993 bytes docs/dev/reference/Rplot002.png | Bin 16467 -> 13470 bytes docs/dev/reference/SFO.solution.html | 2 +- docs/dev/reference/SFORB.solution.html | 2 +- docs/dev/reference/add_err.html | 2 +- docs/dev/reference/anova.saem.mmkin.html | 2 +- docs/dev/reference/aw.html | 2 +- docs/dev/reference/confint.mkinfit.html | 6 +- docs/dev/reference/create_deg_func.html | 10 +- docs/dev/reference/dimethenamid_2018.html | 14 +- docs/dev/reference/ds_mixed.html | 2 +- docs/dev/reference/endpoints.html | 2 +- docs/dev/reference/experimental_data_for_UBA.html | 2 +- docs/dev/reference/f_time_norm_focus.html | 2 +- docs/dev/reference/focus_soil_moisture.html | 2 +- docs/dev/reference/get_deg_func.html | 2 +- docs/dev/reference/hierarchical_kinetics.html | 2 +- docs/dev/reference/illparms.html | 2 +- docs/dev/reference/ilr.html | 2 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/intervals.saem.mmkin.html | 2 +- docs/dev/reference/llhist.html | 2 +- docs/dev/reference/loftest.html | 2 +- docs/dev/reference/logLik.mkinfit.html | 2 +- docs/dev/reference/logLik.saem.mmkin.html | 2 +- docs/dev/reference/logistic.solution.html | 2 +- docs/dev/reference/lrtest.mkinfit.html | 2 +- docs/dev/reference/max_twa_parent.html | 2 +- docs/dev/reference/mccall81_245T.html | 2 +- docs/dev/reference/mean_degparms.html | 2 +- docs/dev/reference/mhmkin.html | 2 +- docs/dev/reference/mixed.html | 2 +- docs/dev/reference/mkin_long_to_wide.html | 2 +- docs/dev/reference/mkin_wide_to_long.html | 2 +- docs/dev/reference/mkinds.html | 2 +- docs/dev/reference/mkindsg.html | 2 +- docs/dev/reference/mkinerrmin.html | 2 +- docs/dev/reference/mkinerrplot.html | 2 +- docs/dev/reference/mkinfit.html | 26 +- docs/dev/reference/mkinmod.html | 6 +- docs/dev/reference/mkinparplot.html | 2 +- docs/dev/reference/mkinplot.html | 2 +- docs/dev/reference/mkinpredict.html | 11 +- docs/dev/reference/mkinresplot.html | 2 +- docs/dev/reference/mmkin.html | 6 +- docs/dev/reference/multistart.html | 2 +- docs/dev/reference/nafta.html | 2 +- docs/dev/reference/nlme.html | 2 +- docs/dev/reference/nlme.mmkin.html | 2 +- docs/dev/reference/nobs.mkinfit.html | 2 +- docs/dev/reference/parms.html | 2 +- docs/dev/reference/parplot.html | 2 +- docs/dev/reference/plot.mixed.mmkin.html | 4 +- docs/dev/reference/plot.mkinfit.html | 2 +- docs/dev/reference/plot.mmkin.html | 2 +- docs/dev/reference/plot.nafta.html | 2 +- docs/dev/reference/read_spreadsheet.html | 2 +- docs/dev/reference/reexports.html | 2 +- docs/dev/reference/residuals.mkinfit.html | 2 +- docs/dev/reference/saem.html | 12 +- docs/dev/reference/schaefer07_complex_case.html | 2 +- docs/dev/reference/set_nd_nq.html | 2 +- docs/dev/reference/sigma_twocomp.html | 2 +- docs/dev/reference/status.html | 2 +- docs/dev/reference/summary.mkinfit.html | 10 +- docs/dev/reference/summary.mmkin.html | 4 +- docs/dev/reference/summary.nlme.mmkin.html | 12 +- docs/dev/reference/summary.saem.mmkin.html | 12 +- docs/dev/reference/summary_listing.html | 2 +- .../dev/reference/synthetic_data_for_UBA_2014.html | 12 +- docs/dev/reference/test_data_from_UBA_2014.html | 2 +- docs/dev/reference/transform_odeparms.html | 2 +- docs/dev/reference/update.mkinfit.html | 2 +- vignettes/web_only/mkin_benchmarks.rda | Bin 1922 -> 1980 bytes vignettes/web_only/saem_benchmarks.rda | Bin 855 -> 925 bytes 110 files changed, 630 insertions(+), 487 deletions(-) diff --git a/NEWS.md b/NEWS.md index 054a82e9..aba99664 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ - -# mkin 1.2.4 +# mkin 1.2.4 (2023-05-19) - R/endpoints.R: Fix the calculation of endpoints for user specified covariate values diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index 4a9406de..ddfb268d 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.5 @@ -136,7 +136,7 @@ D Ranke

Last change 31 January 2019 -(rebuilt 2023-04-16)

+(rebuilt 2023-05-19) Source: vignettes/FOCUS_D.rmd @@ -238,10 +238,10 @@ 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:     Sun Apr 16 08:35:12 2023 
-## Date of summary: Sun Apr 16 08:35:12 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:10 2023 
+## Date of summary: Fri May 19 17:34:10 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 853194fb..9500e661 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.3
+        1.2.5
       
     
 
@@ -135,8 +135,8 @@ to L3
                         
Johannes
 Ranke

             
-            
Last change 18 May 2022
-(rebuilt 2023-04-16)

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

       
       Source: vignettes/FOCUS_L.rmd
       
@@ -170,10 +170,10 @@ 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:     Sun Apr 16 08:35:14 2023 
-## Date of summary: Sun Apr 16 08:35:14 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:11 2023 
+## Date of summary: Fri May 19 17:34:11 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -277,10 +277,10 @@ 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:     Sun Apr 16 08:35:14 2023 
-## Date of summary: Sun Apr 16 08:35:14 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:12 2023 
+## Date of summary: Fri May 19 17:34:12 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -428,10 +428,10 @@ 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:     Sun Apr 16 08:35:14 2023 
-## Date of summary: Sun Apr 16 08:35:14 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:12 2023 
+## Date of summary: Fri May 19 17:34:12 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -512,10 +512,10 @@ 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:     Sun Apr 16 08:35:15 2023 
-## Date of summary: Sun Apr 16 08:35:15 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:12 2023 
+## Date of summary: Fri May 19 17:34:12 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -629,10 +629,10 @@ 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:     Sun Apr 16 08:35:15 2023 
-## Date of summary: Sun Apr 16 08:35:15 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:13 2023 
+## Date of summary: Fri May 19 17:34:13 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -756,10 +756,10 @@ 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:     Sun Apr 16 08:35:15 2023 
-## Date of summary: Sun Apr 16 08:35:16 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:13 2023 
+## Date of summary: Fri May 19 17:34:13 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -821,10 +821,10 @@ 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:     Sun Apr 16 08:35:15 2023 
-## Date of summary: Sun Apr 16 08:35:16 2023 
+
## mkin version used for fitting:    1.2.5 
+## R version used for fitting:       4.3.0 
+## Date of fit:     Fri May 19 17:34:13 2023 
+## Date of summary: Fri May 19 17:34:13 2023 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index c9116643..e11f3f16 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -17,7 +17,7 @@
       
       
         mkin
-        1.2.4
+        1.2.5
       
     
 
@@ -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/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index fa3ac11c..e0011a5a 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -5,13 +5,13 @@
 
 
 
-Introduction to mkin • mkin
+Short introduction to mkin • mkin
 
 
 
 
 
-
+