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/articles/web_only/FOCUS_Z.html | 42 ++--- .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 107009 -> 107009 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 106095 -> 106098 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 76831 -> 76831 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 37495 -> 37494 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 81750 -> 81751 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 106404 -> 106406 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 89119 -> 89110 bytes docs/articles/web_only/NAFTA_examples.html | 189 ++++++++++----------- .../NAFTA_examples_files/figure-html/p10-1.png | Bin 81540 -> 81542 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 77571 -> 77580 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 79748 -> 79748 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 81186 -> 81186 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 83142 -> 83142 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 102935 -> 102934 bytes docs/articles/web_only/benchmarks.html | 33 +++- docs/articles/web_only/compiled_models.html | 22 +-- docs/articles/web_only/dimethenamid_2018.html | 55 +++--- docs/articles/web_only/multistart.html | 28 +-- .../figure-html/unnamed-chunk-3-1.png | Bin 66934 -> 65359 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 53020 -> 53645 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 22355 -> 22804 bytes docs/articles/web_only/saem_benchmarks.html | 53 +++++- 23 files changed, 242 insertions(+), 180 deletions(-) (limited to 'docs/articles/web_only') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 9602adb5..4cda45e3 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -134,7 +134,7 @@ Ranke

Last change 16 January 2018 -(rebuilt 2023-04-20)

+(rebuilt 2023-05-19) Source: vignettes/web_only/FOCUS_Z.rmd @@ -189,7 +189,7 @@ pathway from parent directly to sink included (default in mkin).

plot_sep(m.Z.2a) 

-summary(m.Z.2a, data = FALSE)$bpar
+summary(m.Z.2a, data = FALSE)$bpar 
##            Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
 ## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
@@ -217,7 +217,7 @@ the model formulation:

 plot_sep(m.Z.2a.ff)

-summary(m.Z.2a.ff, data = FALSE)$bpar
+summary(m.Z.2a.ff, data = FALSE)$bpar 
##            Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
 ## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
@@ -247,7 +247,7 @@ previous fit when adding a further metabolite.

 plot_sep(m.Z.3)

-summary(m.Z.3, data = FALSE)$bpar
+summary(m.Z.3, data = FALSE)$bpar 
##       Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0  97.01488   2.597342  37.352 2.0106e-24 91.67597 102.3538
 ## k_Z0   2.23601   0.146904  15.221 9.1477e-15  1.95354   2.5593
@@ -299,27 +299,27 @@ accelerate the optimization.

 plot_sep(m.Z.FOCUS)

-summary(m.Z.FOCUS, data = FALSE)$bpar
+summary(m.Z.FOCUS, data = FALSE)$bpar 
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
-## Z0_0       96.838822   1.994274 48.5584 4.0280e-42 92.826981 100.850664
-## k_Z0        2.215393   0.118458 18.7019 1.0413e-23  1.989456   2.466989
-## k_Z1        0.478305   0.028258 16.9266 6.2418e-22  0.424708   0.538666
-## k_Z2        0.451627   0.042139 10.7176 1.6314e-14  0.374339   0.544872
-## k_Z3        0.058692   0.015245  3.8499 1.7803e-04  0.034808   0.098965
-## f_Z2_to_Z3  0.471502   0.058351  8.0805 9.6608e-11  0.357769   0.588274
-## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736
+## Z0_0 96.842440 1.994291 48.5598 4.0226e-42 92.830421 100.854459 +## k_Z0 2.215425 0.118457 18.7023 1.0404e-23 1.989490 2.467019 +## k_Z1 0.478307 0.028257 16.9272 6.2332e-22 0.424709 0.538669 +## k_Z2 0.451642 0.042139 10.7178 1.6304e-14 0.374348 0.544894 +## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034804 0.098975 +## f_Z2_to_Z3 0.471483 0.058348 8.0806 9.6585e-11 0.357720 0.588287 +## sigma 3.984431 0.383402 10.3923 4.5576e-14 3.213126 4.755737 
 endpoints(m.Z.FOCUS)
## $ff
 ##   Z2_Z3 Z2_sink 
-##  0.4715  0.5285 
+## 0.47148 0.52852 
 ## 
 ## $distimes
 ##        DT50    DT90
-## Z0  0.31288  1.0394
-## Z1  1.44917  4.8141
-## Z2  1.53478  5.0984
-## Z3 11.80986 39.2315
+## Z0 0.31287 1.0393 +## Z1 1.44917 4.8140 +## Z2 1.53473 5.0983 +## Z3 11.80991 39.2317

This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.

@@ -350,7 +350,7 @@ improved. However, the covariance matrix is not returned.

plot_sep(m.Z.mkin.1) 

-summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
+summary(m.Z.mkin.1, data = FALSE)$cov.unscaled 
## NULL

Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the @@ -442,11 +442,11 @@ obtained.

## ## $SFORB ## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g -## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 +## 2.4471342 0.0075124 0.9519866 0.0800071 0.0000000 0.9347816 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA +## Z0 0.3043 1.1848 0.35666 0.28325 92.267 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA ## Z2 1.6414 5.4526 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png index 33269a34..c1011a35 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png index 6e1877f4..dfd2dd50 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png index 113c1b0b..74173f36 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png index 6b0dbc34..1c5793cc 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png index d080a57a..8c594ec9 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png index 3119be2d..84d473d6 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png index 1938b499..492cdcc8 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 49d1db33..87cef18a 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +33,7 @@ mkin - 1.2.3 + 1.2.4 @@ -135,7 +135,7 @@ to the US EPA SOP for the NAFTA guidance Ranke

26 February 2019 (rebuilt -2023-04-20)

+2023-05-19) Source: vignettes/web_only/NAFTA_examples.rmd @@ -171,7 +171,7 @@ same.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p5a)
+plot(p5a) 

 print(p5a)
@@ -200,7 +200,7 @@ same.

## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.26e-12 5.00e-01 0.0000 Inf +## k2 3.41e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -209,7 +209,7 @@ same.

## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.59e+11 3.07e+11 +## DFOP 55.5 3.70e+11 2.03e+11 ## ## Representative half-life: ## [1] 321.51 @@ -222,7 +222,7 @@ same.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p5b)
+plot(p5b) 

 print(p5b)
@@ -251,7 +251,7 @@ same.

## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 8.63e-12 5.00e-01 0.0000 Inf +## k2 9.07e-12 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -260,7 +260,7 @@ same.

## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.32e+11 8.04e+10 +## DFOP 83.6 1.25e+11 7.64e+10 ## ## Representative half-life: ## [1] 215.87 @@ -273,7 +273,7 @@ same.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p6)
+plot(p6) 

 print(p6)
@@ -302,7 +302,7 @@ same.

## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.22e-11 5.00e-01 0.0000 Inf +## k2 3.84e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -311,7 +311,7 @@ same.

## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 1.01e+10 2.15e+10 +## DFOP 34.1 8.50e+09 1.80e+10 ## ## Representative half-life: ## [1] 53.17 @@ -324,7 +324,7 @@ same.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p7)
+plot(p7) 

 print(p7)
@@ -353,7 +353,7 @@ same.

## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 3.63e-10 5.00e-01 0.0000 Inf +## k2 3.62e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -362,7 +362,7 @@ same.

## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 3.77e+09 1.91e+09 +## DFOP 96.4 3.79e+09 1.92e+09 ## ## Representative half-life: ## [1] 454.55 @@ -383,7 +383,7 @@ lower value for the rate constant is used here.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p8)
+plot(p8) 

 print(p8)
@@ -438,7 +438,7 @@ lower value for the rate constant is used here.

## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-plot(p9a)
+plot(p9a) 

 print(p9a)
@@ -476,7 +476,7 @@ lower value for the rate constant is used here.

## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.69e+11 +## DFOP 10.5 1.38e+12 7.68e+11 ## ## Representative half-life: ## [1] 101.43 @@ -489,17 +489,12 @@ suggest a simple exponential decline.

 p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
-
## Warning in sqrt(diag(covar)): NaNs produced
-
## Warning in sqrt(diag(covar_notrans)): NaNs produced
-
## Warning in sqrt(1/diag(V)): NaNs produced
-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
## The half-life obtained from the IORE model may be used
-
-plot(p9b)
+
+plot(p9b)

-
+
 print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -526,8 +521,8 @@ suggest a simple exponential decline.

 ##          Estimate   Pr(>t)   Lower   Upper
 ## parent_0  94.7123 1.61e-16 93.1355 96.2891
 ## k1         0.0389 1.08e-04  0.0266  0.0569
-## k2         0.0389 2.23e-04  0.0255  0.0592
-## g          0.5256      NaN      NA      NA
+## k2         0.0389 2.24e-04  0.0255  0.0592
+## g          0.5256 5.00e-01  0.0000  1.0000
 ## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
@@ -549,18 +544,15 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from
 

 
Example on page 10
 

-
+
 p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

-
## Warning in sqrt(diag(covar)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

+
## Warning in sqrt(diag(covar_notrans)): NaNs produced

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p10)

+
+plot(p10)

 

-
+
 print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -584,12 +576,12 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from
 ## sigma              4.90 1.77e-04  2.837   6.968
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower    Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1         0.0495 6.58e-03  0.0303   0.0809
-## k2         0.0495 2.60e-03  0.0410   0.0598
-## g          0.4487 5.00e-01      NA       NA
-## sigma      8.0152 2.50e-04  4.5886  11.4418
+##          Estimate   Pr(>t)   Lower   Upper
+## parent_0 101.7315 1.41e-09 91.6534 111.810
+## k1         0.0495 3.04e-03  0.0188   0.131
+## k2         0.0495 4.92e-04  0.0197   0.124
+## g          0.4487      NaN  0.0000   1.000
+## sigma      8.0152 2.50e-04  4.5886  11.442
 ## 
 ## 
 ## DTx values:
@@ -613,14 +605,14 @@ difference in IORE model parameters between PestDF and mkin.

 

 
Example on page 11
 

-
+
 p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p11)

+
+plot(p11)

 

-
+
 print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -659,7 +651,7 @@ difference in IORE model parameters between PestDF and mkin.

 ## DFOP 3.07e+11 1.93e+12 6.98e+11
 ## 
 ## Representative half-life:
-## [1] 41148170

+## [1] 41148169

 
In this case, the DFOP fit reported for PestDF resulted in a negative
 value for the slower rate constant, which is not possible in mkin. The
 other results are in agreement.

@@ -676,21 +668,17 @@ overparameterisation.

 

 
Example on page 12, upper panel
 

-
+
 p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

 
## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix

-
## Warning in sqrt(diag(covar)): NaNs produced

 
## Warning in sqrt(diag(covar_notrans)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p12a)

+
+plot(p12a)

 

-
+
 print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -718,7 +706,7 @@ overparameterisation.

 ## parent_0  100.521 2.74e-10 92.2366 108.805
 ## k1          0.124 2.53e-05  0.0908   0.170
 ## k2          0.124 2.52e-02  0.0456   0.339
-## g           0.793      NaN      NA      NA
+## g           0.793      NaN  0.0000   1.000
 ## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
 ## 
@@ -734,18 +722,21 @@ overparameterisation.

 

 
Example on page 12, lower panel
 

-
+
 p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])

+
## Warning in sqrt(diag(covar)): NaNs produced

 
## Warning in qt(alpha/2, rdf): NaNs produced

 
## Warning in qt(1 - alpha/2, rdf): NaNs produced

-
## Warning in sqrt(diag(covar_notrans)): NaNs produced

 
## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced

+
## Warning in sqrt(1/diag(V)): NaNs produced

+
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
+## is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p12b)

+
+plot(p12b)

 

-
+
 print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -789,14 +780,14 @@ overparameterisation.

 

 
Example on page 13
 

-
+
 p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p13)

+
+plot(p13)

 

-
+
 print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -822,8 +813,8 @@ overparameterisation.

 ## $DFOP
 ##          Estimate Pr(>t)    Lower    Upper
 ## parent_0 92.73500     NA 8.95e+01 95.92118
-## k1        0.00258     NA 4.14e-04  0.01611
-## k2        0.00258     NA 1.74e-03  0.00383
+## k1        0.00258     NA 4.18e-04  0.01592
+## k2        0.00258     NA 1.75e-03  0.00381
 ## g         0.16452     NA 0.00e+00  1.00000
 ## sigma     3.41172     NA 2.02e+00  4.79960
 ## 
@@ -841,7 +832,7 @@ overparameterisation.

 

 
DT50 not observed in the study and DFOP problems in PestDF
 

-
+
 p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

 
## Warning in sqrt(diag(covar)): NaNs produced

 
## Warning in sqrt(1/diag(V)): NaNs produced

@@ -849,10 +840,10 @@ overparameterisation.

 ## is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p14)

+
+plot(p14)

 

-
+
 print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -879,7 +870,7 @@ overparameterisation.

 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
 ## k1       9.53e-03 1.20e-01  0.00638   0.0143
-## k2       6.08e-12 5.00e-01  0.00000      Inf
+## k2       5.21e-12 5.00e-01  0.00000      Inf
 ## g        3.98e-01 2.19e-01  0.30481   0.4998
 ## sigma    1.17e+00 7.68e-06  0.77406   1.5610
 ## 
@@ -888,7 +879,7 @@ overparameterisation.

 ##          DT50     DT90 DT50_rep
 ## SFO  2.48e+02 8.25e+02 2.48e+02
 ## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 3.05e+10 2.95e+11 1.14e+11
+## DFOP 3.55e+10 3.44e+11 1.33e+11
 ## 
 ## Representative half-life:
 ## [1] 6697.44

@@ -899,14 +890,18 @@ same results in mkin and PestDF.

 

 
N is less than 1 and DFOP fraction parameter is below zero
 

-
+
 p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

+
## Warning in sqrt(diag(covar)): NaNs produced

+
## Warning in sqrt(1/diag(V)): NaNs produced

+
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
+## is doubtful

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p15a)

+
+plot(p15a)

 

-
+
 print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
@@ -932,9 +927,9 @@ same results in mkin and PestDF.

 ## $DFOP
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 97.96751 2.85e-13 94.21913 101.7159
-## k1        0.00952 6.28e-02  0.00250   0.0363
-## k2        0.00952 1.27e-04  0.00646   0.0140
-## g         0.21241 5.00e-01  0.00000   1.0000
+## k1        0.00952 6.28e-02  0.00260   0.0349
+## k2        0.00952 1.27e-04  0.00652   0.0139
+## g         0.21241 5.00e-01       NA       NA
 ## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
@@ -946,18 +941,16 @@ same results in mkin and PestDF.

 ## 
 ## Representative half-life:
 ## [1] 41.33

-
+
 p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

-
## Warning in sqrt(diag(covar)): NaNs produced

-
## Warning in sqrt(1/diag(V)): NaNs produced

-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result
-## is doubtful

+
## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
+## matrix

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
-plot(p15b)

+
+plot(p15b)

 

-
+
 print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
@@ -975,18 +968,18 @@ same results in mkin and PestDF.

 ## 
 ## $IORE
 ##                Estimate   Pr(>t)    Lower  Upper
-## parent_0          99.83 1.81e-16 97.51349 102.14
+## parent_0          99.83 1.81e-16 97.51348 102.14
 ## k__iore_parent     0.38 3.22e-01  0.00352  41.05
 ## N_parent           0.00 5.00e-01 -1.07696   1.08
 ## sigma              2.21 2.57e-04  1.23245   3.19
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## parent_0 1.01e+02     NA 9.82e+01 1.04e+02
-## k1       4.86e-03     NA 8.63e-04 2.73e-02
-## k2       4.86e-03     NA 3.21e-03 7.35e-03
-## g        1.88e-01     NA       NA       NA
-## sigma    2.76e+00     NA 1.58e+00 3.94e+00
+##          Estimate Pr(>t) Lower Upper
+## parent_0 1.01e+02     NA    NA    NA
+## k1       4.86e-03     NA    NA    NA
+## k2       4.86e-03     NA    NA    NA
+## g        1.88e-01     NA    NA    NA
+## sigma    2.76e+00     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -1005,16 +998,16 @@ mkin and PestDF.

 

 
The DFOP fraction parameter is greater than 1
 

-
+
 p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The representative half-life of the IORE model is longer than the one corresponding

 
## to the terminal degradation rate found with the DFOP model.

 
## The representative half-life obtained from the DFOP model may be used

-
-plot(p16)

+
+plot(p16)

 

-
+
 print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png
index 566625ea..1d4a25e0 100644
Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png
index b5fd7d91..aa55169e 100644
Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png
index dfbc996f..d17c7aae 100644
Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png
index 6fd175cb..9e38e696 100644
Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png
index 856c6778..e6e3abbe 100644
Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png differ
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png
index b078fb88..7c5d4bab 100644
Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png differ
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 3e73bd12..315ad54e 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -33,7 +33,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -134,7 +134,7 @@
 Ranke
             
             
Last change 17 February 2023
-(rebuilt 2023-04-20)

+(rebuilt 2023-05-19)
       
       Source: vignettes/web_only/benchmarks.rmd
       
@@ -425,6 +425,14 @@ models fitted to two datasets, i.e. eight fits for each test.

 1.406
 1.948
 
+
+Linux
+Ryzen 9 7950X
+4.3.0
+1.2.4
+1.386
+1.960
+
 
 
 

@@ -652,6 +660,15 @@ for each test.

 2.109
 1.178
 
+
+Linux
+Ryzen 9 7950X
+4.3.0
+1.2.4
+0.779
+2.080
+1.106
+
 
 
 

@@ -963,6 +980,18 @@ dataset, i.e. one fit for each test.

 0.743
 0.989
 
+
+Linux
+Ryzen 9 7950X
+4.3.0
+1.2.4
+0.410
+0.526
+0.553
+1.249
+0.712
+0.948
+
 
 
 

diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index a411dad1..3c53b40a 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -33,7 +33,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -134,7 +134,7 @@ definitions in mkin
                         
Johannes
 Ranke

             
-            
2023-04-20

+            
2023-05-19

       
       Source: vignettes/web_only/compiled_models.rmd
       
@@ -213,10 +213,10 @@ solution is also implemented, which is included in the tests below.

   print("R package rbenchmark is not available")
 }

 
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.103
-## 3     deSolve, compiled            1    1.291   0.133
-## 2      Eigenvalue based            1    1.718   0.177
-## 1 deSolve, not compiled            1   22.136   2.280

+## 4            analytical            1    1.000   0.099
+## 3     deSolve, compiled            1    1.303   0.129
+## 2      Eigenvalue based            1    1.697   0.168
+## 1 deSolve, not compiled            1   21.475   2.126

 
We see that using the compiled model is by more than a factor of 10
 faster than using deSolve without compiled code.

 

@@ -247,12 +247,12 @@ compiled code is available.

 }

 
## Temporary DLL for differentials generated and loaded

 
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.171
-## 1 deSolve, not compiled            1   24.199   4.138

-
Here we get a performance benefit of a factor of 24 using the version
+## 2     deSolve, compiled            1    1.000   0.165
+## 1 deSolve, not compiled            1   22.673   3.741

+
Here we get a performance benefit of a factor of 23 using the version
 of the differential equation model compiled from C code!

-
This vignette was built with mkin 1.2.3 on

-
## R version 4.2.3 (2023-03-15)
+
This vignette was built with mkin 1.2.4 on

+
## R version 4.3.0 Patched (2023-05-18 r84448)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 12 (bookworm)

 
## CPU model: AMD Ryzen 9 7950X 16-Core Processor

diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html
index 4575067b..a89631a2 100644
--- a/docs/articles/web_only/dimethenamid_2018.html
+++ b/docs/articles/web_only/dimethenamid_2018.html
@@ -33,7 +33,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -135,7 +135,7 @@ from 2018
 Ranke
             
             
Last change 1 July 2022,
-built on 20 Apr 2023

+built on 19 May 2023
       
       Source: vignettes/web_only/dimethenamid_2018.rmd
       
@@ -222,12 +222,12 @@ least in some datasets the degradation slows down towards later time
 points, and that the scatter of the residuals error is smaller for
 smaller values (panel to the right):

 
-plot(mixed(f_parent_mkin_const["SFO", ]))

+plot(mixed(f_parent_mkin_const["SFO", ]))

 

 
Using biexponential decline (DFOP) results in a slightly more random
 scatter of the residuals:

 
-plot(mixed(f_parent_mkin_const["DFOP", ]))

+plot(mixed(f_parent_mkin_const["DFOP", ]))

 

 
The population curve (bold line) in the above plot results from
 taking the mean of the individual transformed parameters, i.e. of log k1
@@ -239,7 +239,7 @@ dominates the average. This is alleviated if only rate constants that
 pass the t-test for significant difference from zero (on the
 untransformed scale) are considered in the averaging:

 
-plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)

+plot(mixed(f_parent_mkin_const["DFOP", ]), test_log_parms = TRUE)

 

 
While this is visually much more satisfactory, such an average
 procedure could introduce a bias, as not all results from the individual
@@ -251,7 +251,7 @@ degradation model and the error model (see below).

 predicted residues is reduced by using the two-component error
 model:

 
-plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)

+plot(mixed(f_parent_mkin_tc["DFOP", ]), test_log_parms = TRUE)

 

 
However, note that in the case of using this error model, the fits to
 the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by
@@ -341,7 +341,7 @@ effects does not improve the fits.

 
The selected model (DFOP with two-component error) fitted to the data
 assuming no correlations between random effects is shown below.

 
-plot(f_parent_nlme_dfop_tc)

+plot(f_parent_nlme_dfop_tc)

 

 

 

@@ -549,7 +549,7 @@ iterations second phase, 15 chains).

   saemix_is = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so,
     f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC, method = "is")
 )
-kable(AIC_all)

+kable(AIC_all)

 
@@ -614,13 +614,13 @@ satisfactory precision.

-
R version 4.2.3 (2023-03-15)
+
R version 4.3.0 Patched (2023-05-18 r84448)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so
+BLAS:   /home/jranke/svn/R/r-patched/build/lib/libRblas.so 
+LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3;  LAPACK version 3.11.0
 
 locale:
  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
@@ -630,27 +630,30 @@ locale:
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
+time zone: Europe/Berlin
+tzcode source: system (glibc)
+
 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 other attached packages:
-[1] saemix_3.2   npde_3.3     nlme_3.1-162 mkin_1.2.3   knitr_1.42  
+[1] nlme_3.1-162 mkin_1.2.4   knitr_1.42  
 
 loaded via a namespace (and not attached):
- [1] highr_0.10        pillar_1.9.0      bslib_0.4.2       compiler_4.2.3   
- [5] jquerylib_0.1.4   tools_4.2.3       mclust_6.0.0      digest_0.6.31    
- [9] tibble_3.2.1      jsonlite_1.8.4    evaluate_0.20     memoise_2.0.1    
-[13] lifecycle_1.0.3   gtable_0.3.3      lattice_0.21-8    pkgconfig_2.0.3  
-[17] rlang_1.1.0       DBI_1.1.3         cli_3.6.1         yaml_2.3.7       
-[21] parallel_4.2.3    pkgdown_2.0.7     xfun_0.38         fastmap_1.1.1    
-[25] gridExtra_2.3     dplyr_1.1.1       stringr_1.5.0     generics_0.1.3   
-[29] desc_1.4.2        fs_1.6.1          vctrs_0.6.1       sass_0.4.5       
-[33] systemfonts_1.0.4 tidyselect_1.2.0  rprojroot_2.0.3   lmtest_0.9-40    
-[37] grid_4.2.3        glue_1.6.2        R6_2.5.1          textshaping_0.3.6
-[41] fansi_1.0.4       rmarkdown_2.21    purrr_1.0.1       ggplot2_3.4.2    
-[45] magrittr_2.0.3    codetools_0.2-19  scales_1.2.1      htmltools_0.5.5  
-[49] colorspace_2.1-0  ragg_1.2.5        utf8_1.2.3        stringi_1.7.12   
-[53] munsell_0.5.0     cachem_1.0.7      zoo_1.8-12       

+ [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    saemix_3.2       
+ [5] stringi_1.7.12    lattice_0.21-8    digest_0.6.31     magrittr_2.0.3   
+ [9] evaluate_0.21     grid_4.3.0        fastmap_1.1.1     rprojroot_2.0.3  
+[13] jsonlite_1.8.4    DBI_1.1.3         mclust_6.0.0      gridExtra_2.3    
+[17] purrr_1.0.1       fansi_1.0.4       scales_1.2.1      textshaping_0.3.6
+[21] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       munsell_0.5.0    
+[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.0       parallel_4.3.0   
+[29] memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2    
+[33] vctrs_0.6.2       R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3  
+[37] stringr_1.5.0     fs_1.6.2          ragg_1.2.5        pkgconfig_2.0.3  
+[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0     
+[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 xfun_0.39        
+[49] tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0  npde_3.3         
+[53] htmltools_0.5.5   rmarkdown_2.21    compiler_4.3.0   

 
References
diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html
index 04093e82..b9224bb0 100644
--- a/docs/articles/web_only/multistart.html
+++ b/docs/articles/web_only/multistart.html
@@ -33,7 +33,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -134,7 +134,7 @@
 Ranke
Last change 20 April 2023
-(rebuilt 2023-04-20)

+(rebuilt 2023-05-19)Source: vignettes/web_only/multistart.rmd
@@ -175,7 +175,7 @@ assessment using multiple runs with different starting values.

 parameter, so we reduce the parameter distribution model by removing the
 intersoil variability for k2.
-f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
+f_saem_reduced <- stats::update(f_saem_full, no_random_effect = "log_k2")
 illparms(f_saem_reduced)
 f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
 parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2))

@@ -190,18 +190,20 @@ runs:

 
We can use the anova method to compare the models.

 
 anova(f_saem_full, best(f_saem_full_multi),
-  f_saem_reduced, best(f_saem_reduced_multi))

+  f_saem_reduced, best(f_saem_reduced_multi), test = TRUE)
## Data: 155 observations of 1 variable(s) grouped in 6 datasets
 ## 
-##                            npar    AIC    BIC     Lik
-## f_saem_reduced                9 663.73 661.86 -322.86
-## best(f_saem_reduced_multi)    9 663.69 661.82 -322.85
-## f_saem_full                  10 669.77 667.69 -324.89
-## best(f_saem_full_multi)      10 665.56 663.48 -322.78

-
The reduced model gives the lowest information criteria and similar
-likelihoods as the best variant of the full model. The multistart method
-leads to a much lower improvement of the likelihood for the reduced
-model, indicating that it converges faster.

+##                            npar    AIC    BIC     Lik  Chisq Df Pr(>Chisq)
+## f_saem_reduced                9 663.67 661.80 -322.84                     
+## best(f_saem_reduced_multi)    9 663.65 661.78 -322.82 0.0219  0           
+## f_saem_full                  10 670.09 668.01 -325.05 0.0000  1          1
+## best(f_saem_full_multi)      10 665.61 663.52 -322.80 4.4870  0
+
The reduced model results in lower AIC and BIC values, so it is
+clearly preferable. Using multiple starting values gives a large
+improvement in case of the full model, because it is less well-defined,
+which impedes convergence. For the reduced model, using multiple
+starting values only results in a small improvement of the model
+fit.

 
@@ -134,7 +134,7 @@
 Ranke
Last change 17 February 2023
-(rebuilt 2023-04-20)

+(rebuilt 2023-05-19)Source: vignettes/web_only/saem_benchmarks.rmd
@@ -238,22 +238,22 @@ explanation of the following preprocessing.

-
-
-
+
+
+
-
-
+
+
-
-
+
+
@@ -402,6 +402,16 @@ systems. All trademarks belong to their respective owners.

+
+
+
+
+
+
+
+
+
+

 

 Degradation model
 
 
 
 
             
             
       
       
       
 
 
   
 
   
             
             
       
       
       
 

 dfop_tc
 10669.8667.7-324.9670.1668.0-325.0
 

 

 sforb_tc
 10662.8660.7662.9660.8
 -321.4
 

 

 hs_tc
 10667.3665.2667.2665.1
 -323.6
 

 
 
1.926
 2.398
 
Ryzen 9 7950XLinux1.2.43.20.9722.5501.9872.055

 
 

 
Two-component error fits for SFO, DFOP, SFORB and HS.

@@ -477,6 +487,16 @@ systems. All trademarks belong to their respective owners.

 3.253
 3.530
 
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+2.127
+3.587
+3.433
+3.595
+
 
 
 

@@ -542,6 +562,14 @@ systems. All trademarks belong to their respective owners.

 12.841
 292.688
 
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+12.160
+265.934
+
 
 
 

@@ -600,6 +628,13 @@ systems. All trademarks belong to their respective owners.

 3.2
 483.027
 
+
+Ryzen 9 7950X
+Linux
+1.2.4
+3.2
+456.252
+
-- cgit v1.2.1