From 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 May 2022 21:26:17 +0200 Subject: Remove outdated comment in FOCUS L vignette, update docs This also adds the first benchmark results obtained on my laptop system --- docs/articles/web_only/FOCUS_Z.html | 50 ++++++++++++++++++------------------- 1 file changed, 25 insertions(+), 25 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 43508280..0dafb98a 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -105,7 +105,7 @@

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

Last change 16 January 2018 (rebuilt 2022-03-07)

+

Last change 16 January 2018 (rebuilt 2022-05-18)

Source: vignettes/web_only/FOCUS_Z.rmd @@ -234,33 +234,31 @@ quiet = TRUE) 
## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :
 ## Observations with value of zero were removed from the data
-
## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:
-## false convergence (8)
-
+
 plot_sep(m.Z.FOCUS)

 

-
+
 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
+## Z0_0       96.838397   1.994270 48.5583 4.0284e-42 92.826435 100.850359
+## k_Z0        2.215406   0.118459 18.7018 1.0416e-23  1.989466   2.467005
+## k_Z1        0.478300   0.028257 16.9267 6.2409e-22  0.424702   0.538662
+## k_Z2        0.451616   0.042137 10.7178 1.6305e-14  0.374328   0.544863
+## k_Z3        0.058693   0.015245  3.8499 1.7803e-04  0.034805   0.098976
+## f_Z2_to_Z3  0.471509   0.058352  8.0804 9.6622e-11  0.357739   0.588317
 ## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736

-
+
 endpoints(m.Z.FOCUS)

 
## $ff
 ##   Z2_Z3 Z2_sink 
-##  0.4715  0.5285 
+## 0.47151 0.52849 
 ## 
 ## $distimes
 ##        DT50    DT90
 ## Z0  0.31288  1.0394
-## Z1  1.44917  4.8141
-## Z2  1.53478  5.0984
-## Z3 11.80986 39.2315

+## Z1  1.44919  4.8141
+## Z2  1.53481  5.0985
+## Z3 11.80971 39.2310

 
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.

 

 

@@ -268,32 +266,34 @@
 
 
As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.

 
Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the \(\chi^2\) error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.

-
+
 Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO", "Z3"),
                     Z3 = mkinsub("SFORB"))

 
## Temporary DLL for differentials generated and loaded

-
+
 m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
 ## value of zero were removed from the data

-
+
 plot_sep(m.Z.mkin.1)

 

-
+
 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 assumption that the model fit for the parent compound can be improved by using the SFORB model.

-
+
 Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO"))

 
## Temporary DLL for differentials generated and loaded

-
+
 m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
 ## value of zero were removed from the data

+
## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Optimisation did not converge:
+## false convergence (8)

 
 plot_sep(m.Z.mkin.3)

 

@@ -359,11 +359,11 @@
 ## 
 ## $SFORB
 ##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 2.4471322 0.0075125 0.0800069 0.0000000 
+## 2.4471376 0.0075126 0.0800073 0.0000000 
 ## 
 ## $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     92.264         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

@@ -398,7 +398,7 @@
 
 

   

-
Site built with pkgdown 2.0.2.

+
Site built with pkgdown 2.0.3.

 

 
       
-- 
cgit v1.2.1