From 7094934f1061563725f6caa8723dc3e23c8ca677 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 16 Nov 2022 11:30:06 +0100 Subject: Update online docs --- vignettes/web_only/saem_benchmarks.rda | Bin 359 -> 359 bytes 1 file changed, 0 insertions(+), 0 deletions(-) (limited to 'vignettes') diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda index e8b139da..55fabf1d 100644 Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ -- cgit v1.2.1 From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- vignettes/web_only/mkin_benchmarks.rda | Bin 1586 -> 1592 bytes vignettes/web_only/saem_benchmarks.rda | Bin 359 -> 353 bytes 2 files changed, 0 insertions(+), 0 deletions(-) (limited to 'vignettes') diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda index 2d3deb26..629b70bd 100644 Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda index 55fabf1d..509b1008 100644 Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ -- cgit v1.2.1 From af7c6de4db9981ac814362c441fbac22c8faa2d7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Nov 2022 09:02:26 +0100 Subject: Start online docs of the development version --- vignettes/web_only/mkin_benchmarks.rda | Bin 1592 -> 1650 bytes vignettes/web_only/saem_benchmarks.rda | Bin 353 -> 466 bytes 2 files changed, 0 insertions(+), 0 deletions(-) (limited to 'vignettes') diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda index 629b70bd..aec48422 100644 Binary files a/vignettes/web_only/mkin_benchmarks.rda and b/vignettes/web_only/mkin_benchmarks.rda differ diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda index 509b1008..6921f78c 100644 Binary files a/vignettes/web_only/saem_benchmarks.rda and b/vignettes/web_only/saem_benchmarks.rda differ -- cgit v1.2.1 From 478c6d5eec4c84b22b43adcbdf36888b302ead00 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 6 Dec 2022 10:33:24 +0100 Subject: Some parplot improvements llquant argument, improved legend text, tests --- vignettes/FOCUS_D.html | 37 +++++++++------------- vignettes/FOCUS_L.html | 83 +++++++++++++++++++++++--------------------------- 2 files changed, 53 insertions(+), 67 deletions(-) (limited to 'vignettes') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 9f768b06..b8a63a7b 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -299,8 +299,8 @@ pre code { border-radius: 4px; } -.tabset-dropdown > .nav-tabs > li.active:before { - content: ""; +.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before { + content: "\e259"; font-family: 'Glyphicons Halflings'; display: inline-block; padding: 10px; @@ -308,16 +308,9 @@ pre code { } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { - content: ""; - border: none; -} - -.tabset-dropdown > .nav-tabs.nav-tabs-open:before { - content: ""; + content: "\e258"; font-family: 'Glyphicons Halflings'; - display: inline-block; - padding: 10px; - border-right: 1px solid #ddd; + border: none; } .tabset-dropdown > .nav-tabs > li.active { @@ -364,7 +357,7 @@ pre code {

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

Last change 31 January 2019 (rebuilt 2022-07-08)

+

Last change 31 January 2019 (rebuilt 2022-12-06)

@@ -438,10 +431,10 @@ print(FOCUS_2006_D)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Fri Jul  8 15:44:37 2022 
-## Date of summary: Fri Jul  8 15:44:38 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:42 2022 
+## Date of summary: Tue Dec  6 09:39:42 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -449,7 +442,7 @@ print(FOCUS_2006_D)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.13 s
+## Fitted using 401 model solutions performed in 0.158 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -492,11 +485,11 @@ print(FOCUS_2006_D)
## ## 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 -1.174e-06 -## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.492e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.220e-07 -## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.307e-06 -## sigma -1.174e-06 -8.492e-07 8.220e-07 1.307e-06 1.000e+00 +## 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 +## 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 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index da6c11fe..b8c9ba0c 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -1373,8 +1373,8 @@ pre code { border-radius: 4px; } -.tabset-dropdown > .nav-tabs > li.active:before { - content: ""; +.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before { + content: "\e259"; font-family: 'Glyphicons Halflings'; display: inline-block; padding: 10px; @@ -1382,16 +1382,9 @@ pre code { } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { - content: ""; - border: none; -} - -.tabset-dropdown > .nav-tabs.nav-tabs-open:before { - content: ""; + content: "\e258"; font-family: 'Glyphicons Halflings'; - display: inline-block; - padding: 10px; - border-right: 1px solid #ddd; + border: none; } .tabset-dropdown > .nav-tabs > li.active { @@ -1517,7 +1510,7 @@ div.tocify {

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

Last change 18 May 2022 (rebuilt 2022-09-14)

+

Last change 18 May 2022 (rebuilt 2022-12-06)

@@ -1536,17 +1529,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:35 2022 
-## Date of summary: Wed Sep 14 22:28:35 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:45 2022 
+## Date of summary: Tue Dec  6 09:39:45 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.032 s
+## Fitted using 133 model solutions performed in 0.033 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1637,10 +1630,10 @@ summary(m.L1.SFO)

 
## 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:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:35 2022 
-## Date of summary: Wed Sep 14 22:28:35 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:45 2022 
+## Date of summary: Tue Dec  6 09:39:45 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -1742,17 +1735,17 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:35 2022 
-## Date of summary: Wed Sep 14 22:28:35 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:45 2022 
+## Date of summary: Tue Dec  6 09:39:45 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.049 s
+## Fitted using 239 model solutions performed in 0.048 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1820,10 +1813,10 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:36 2022 
-## Date of summary: Wed Sep 14 22:28:36 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:46 2022 
+## Date of summary: Tue Dec  6 09:39:46 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1832,7 +1825,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.135 s
+## Fitted using 581 model solutions performed in 0.131 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1920,10 +1913,10 @@ plot(mm.L3)

 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

 
We can extract the summary and plot for e.g. the DFOP fit, 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:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:36 2022 
-## Date of summary: Wed Sep 14 22:28:36 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:46 2022 
+## Date of summary: Tue Dec  6 09:39:46 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1932,7 +1925,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.081 s
+## Fitted using 376 model solutions performed in 0.078 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2028,17 +2021,17 @@ plot(mm.L4)

 

 
The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test 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:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:36 2022 
-## Date of summary: Wed Sep 14 22:28:37 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:47 2022 
+## Date of summary: Tue Dec  6 09:39:47 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.034 s
+## Fitted using 142 model solutions performed in 0.03 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2092,10 +2085,10 @@ plot(mm.L4)

 ##        DT50 DT90
 ## parent  106  352

 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version used for fitting:    1.1.2 
-## R version used for fitting:       4.2.1 
-## Date of fit:     Wed Sep 14 22:28:37 2022 
-## Date of summary: Wed Sep 14 22:28:37 2022 
+
## mkin version used for fitting:    1.2.2 
+## R version used for fitting:       4.2.2 
+## Date of fit:     Tue Dec  6 09:39:47 2022 
+## Date of summary: Tue Dec  6 09:39:47 2022 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
-- 
cgit v1.2.1


From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001
From: Johannes Ranke 
Date: Mon, 9 Jan 2023 06:22:04 +0100
Subject: Prebuilt PDF vignettes, summary_listing

---
 vignettes/FOCUS_D.html                             |  44 +-
 vignettes/FOCUS_L.html                             | 215 ++++++---
 vignettes/dmta_parent_2022_prebuilt.rnw            |   7 +
 vignettes/dmta_pathway_2022_prebuilt.rnw           |   7 +
 vignettes/mkin.html                                | 310 +++++++++---
 vignettes/prebuilt/2022_cyan_pathway.rmd           | 536 +++++++++++++++++++++
 vignettes/prebuilt/2022_dmta_parent.rmd            | 406 ++++++++++++++++
 vignettes/prebuilt/2022_dmta_pathway.rmd           | 426 ++++++++++++++++
 vignettes/prebuilt/references.bib                  | 187 +++++++
 vignettes/references.bib                           |  34 +-
 vignettes/twa.html                                 | 108 +++--
 vignettes/web_only/FOCUS_Z.R                       | 115 +++++
 vignettes/web_only/FOCUS_Z.html                    | 278 +++++++----
 vignettes/web_only/benchmarks.R                    | 114 +++++
 vignettes/web_only/benchmarks.html                 | 193 +++++++-
 vignettes/web_only/compiled_models.R               |  65 +++
 vignettes/web_only/compiled_models.html            | 230 +++++----
 vignettes/web_only/dimethenamid_2018.R             | 152 ++++++
 vignettes/web_only/dimethenamid_2018.html          | 365 ++++++++++----
 .../figure-html/f_parent_mkin_dfop_const-1.png     | Bin 58608 -> 57786 bytes
 .../f_parent_mkin_dfop_const_test-1.png            | Bin 58777 -> 57786 bytes
 .../figure-html/f_parent_mkin_dfop_tc_test-1.png   | Bin 60062 -> 59396 bytes
 .../figure-html/f_parent_mkin_sfo_const-1.png      | Bin 56694 -> 55982 bytes
 .../figure-html/f_parent_saemix_sfo_tc-1.png       | Bin 28655 -> 28538 bytes
 .../figure-html/plot_parent_nlme-1.png             | Bin 59194 -> 59192 bytes
 vignettes/web_only/mkin_benchmarks.rda             | Bin 1650 -> 1722 bytes
 26 files changed, 3293 insertions(+), 499 deletions(-)
 create mode 100644 vignettes/dmta_parent_2022_prebuilt.rnw
 create mode 100644 vignettes/dmta_pathway_2022_prebuilt.rnw
 create mode 100644 vignettes/prebuilt/2022_cyan_pathway.rmd
 create mode 100644 vignettes/prebuilt/2022_dmta_parent.rmd
 create mode 100644 vignettes/prebuilt/2022_dmta_pathway.rmd
 create mode 100644 vignettes/prebuilt/references.bib
 create mode 100644 vignettes/web_only/FOCUS_Z.R
 create mode 100644 vignettes/web_only/benchmarks.R
 create mode 100644 vignettes/web_only/compiled_models.R
 create mode 100644 vignettes/web_only/dimethenamid_2018.R

(limited to 'vignettes')

diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index b8a63a7b..c729e3c2 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -31,7 +31,7 @@ document.addEventListener('DOMContentLoaded', function(e) {
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