From 48c463680b51fa767b4cd7bd62865f192d0354ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 6 Feb 2021 18:30:32 +0100 Subject: Reintroduce interface to saemix Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. --- DESCRIPTION | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index dd57aefa..15871070 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.0.1 +Version: 1.0.1.9000 Date: 2021-02-06 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), @@ -19,9 +19,10 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, particular purpose. Depends: R (>= 2.15.1), parallel Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.17), numDeriv, - lmtest, pkgbuild, nlme (>= 3.1-151), purrr + lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix (>= 3.1.9000) Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, benchmarkme, tibble, stats4 +Remotes: github::saemixdevelopment/saemixextension License: GPL LazyLoad: yes LazyData: yes -- cgit v1.2.1 From c6eb6b2bb598002523c3d34d71b0e4a99671ccd6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 9 Jun 2021 16:53:31 +0200 Subject: Rudimentary support for setting up nlmixr models - All degradation models are specified as ODE models. This appears to be fast enough - Error models are being translated to nlmixr as close to the mkin error model as possible. When using the 'saem' backend, it appears not to be possible to use the same error model for more than one observed variable - No support yet for models with parallel formation of metabolites, where the ilr transformation is used in mkin per default - There is a bug in nlmixr which appears to be triggered if the data are not balanced, see nlmixrdevelopment/nlmixr#530 - There is a print and a plot method, the summary method is not finished --- DESCRIPTION | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 48aaf81f..5b90ef37 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.0.4.9000 -Date: 2021-04-21 +Version: 1.0.5 +Date: 2021-06-03 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", @@ -18,11 +18,10 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, note that no warranty is implied for correctness of results or fitness for a particular purpose. Depends: R (>= 2.15.1), parallel -Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.17), numDeriv, - lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix (>= 3.1.9000) +Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.19), numDeriv, + lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix, nlmixr Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, benchmarkme, tibble, stats4 -Remotes: github::saemixdevelopment/saemixextension License: GPL LazyLoad: yes LazyData: yes -- cgit v1.2.1 From 0c9b2f0e3c8ce65cb790c9e048476784cbbea070 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 11 Jun 2021 11:14:45 +0200 Subject: Finished 'summary.nlmixr.mmkin', checks, docs --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 5b90ef37..e81fcb32 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,7 +19,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, particular purpose. Depends: R (>= 2.15.1), parallel Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.19), numDeriv, - lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix, nlmixr + dplyr, lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix, nlmixr Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, benchmarkme, tibble, stats4 License: GPL -- cgit v1.2.1 From 88cf130615a6cde0c4e65d14db32fed7f6e43085 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 12 Jun 2021 11:05:24 +0200 Subject: Small cosmetics --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index e81fcb32..c6151839 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.0.5 -Date: 2021-06-03 +Date: 2021-06-11 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", -- cgit v1.2.1 From 40b78bed232798ecbeb72759cdf8d400ea35b31f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 23 Jul 2021 13:55:34 +0200 Subject: Some example evaluations of dimethenamid data Evaluations with nlme, saemix and nlmixr are included --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index c6151839..4689cb2a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.0.5 -Date: 2021-06-11 +Version: 1.1.0 +Date: 2021-06-23 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", -- cgit v1.2.1 From 137612045c23198f10d6e8612c32e266c2a6c00e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 29 Jul 2021 12:17:56 +0200 Subject: Go back to 1.0.x version, update docs --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 4689cb2a..2364ee75 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.1.0 -Date: 2021-06-23 +Version: 1.0.5 +Date: 2021-07-29 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", -- cgit v1.2.1 From 1bef803fc9d83989352f1b029d83e66918a0e58a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 29 Jul 2021 12:37:27 +0200 Subject: Add citations to the DESCRIPTION --- DESCRIPTION | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 2364ee75..8f243796 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,9 +14,14 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, 2014). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers. If a C compiler (on windows: 'Rtools') is installed, differential - equation models are solved using automatically generated C functions. Please - note that no warranty is implied for correctness of results or fitness for a - particular purpose. + equation models are solved using automatically generated C functions. + Heteroscedasticity can be taken into account using variance by variable or + two-component error models as described by Ranke and Meinecke (2018) + . Interfaces to several nonlinear + mixed-effects model packages are available, some of which are described by + Ranke et al. (2021) . Please note that no + warranty is implied for correctness of results or fitness for a particular + purpose. Depends: R (>= 2.15.1), parallel Imports: stats, graphics, methods, deSolve, R6, inline (>= 0.3.19), numDeriv, dplyr, lmtest, pkgbuild, nlme (>= 3.1-151), purrr, saemix, nlmixr -- cgit v1.2.1 From 07430d00a8c220b4ac45a680f7ba207bdaaef756 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 1 Oct 2021 13:55:53 +0200 Subject: Bump date to update online dev docs --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 15bbeafa..d216d6fb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 1.1.0 -Date: 2021-09-15 +Date: 2021-10-01 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", -- cgit v1.2.1