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 ++++++++++++++++++------------------- 1 file changed, 21 insertions(+), 21 deletions(-) (limited to 'docs/articles/web_only/FOCUS_Z.html') 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 -- cgit v1.2.1