From d2c1ab854491ff047135fa8377400a68499e72de Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Jul 2014 12:53:30 +0200 Subject: Handle non-convergence and maximum number of iterations For details see NEWS.md --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 833acd8e..fb32b807 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-32 -Date: 2014-07-14 +Date: 2014-07-17 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From a1567638a3ba9f4d62fa199525097a94ddfd7912 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 21 Jul 2014 08:20:44 +0200 Subject: Bugfix, model shorthand, state.ini[[1]] from observed data - The bug occurred when using transform_rates=FALSE for FOMC, DFOP or HS - Make it possible to use mkinfit("SFO", ...) - Take initial mean value at time zero for the variable with the highest value in the observed data - Update of vignette/FOCUS_L - Improve the Makefile to build single vignettes --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index fb32b807..bad72501 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-32 -Date: 2014-07-17 +Date: 2014-07-21 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 4c6f29fe2a3ece5a85160b891c89ce0f55299c11 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 23 Jul 2014 08:34:59 +0200 Subject: Parallel metabolite formation with formation fractions in mkinerrmin --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index bad72501..de9ff203 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-32 -Date: 2014-07-21 +Date: 2014-07-23 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 8be01094ecbc65d4bdf1e7f819ef01b7a252b39d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Jul 2014 09:58:55 +0200 Subject: Avoid artificial zero residual in mkinresplot --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index de9ff203..2da7f1c1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-32 -Date: 2014-07-23 +Date: 2014-07-24 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 9b947f0358d3a1b1fc922bfd0187ca444ce5811d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 24 Jul 2014 14:42:59 +0200 Subject: Bump version, better default for state.ini --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 2da7f1c1..bf0fa09a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data -Version: 0.9-32 +Version: 0.9-33 Date: 2014-07-24 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), -- cgit v1.2.1 From e5c955f82adf6139d76f842a0b85e5d383685793 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Jul 2014 09:36:15 +0200 Subject: Fix internal naming of g for transform_fractions=FALSE --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index bf0fa09a..02480e56 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-33 -Date: 2014-07-24 +Date: 2014-07-25 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 37a252cb44fed78c4f7a00a2f7874f1c47456468 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 19 Aug 2014 17:55:06 +0200 Subject: Improve formatting of differential equations in output Rebuild of FOCUS_Z vignette with improved formatting --- DESCRIPTION | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 02480e56..3898f69a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-33 -Date: 2014-07-25 +Date: 2014-08-19 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), @@ -24,5 +24,6 @@ LazyData: yes Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues -URL: http://kinfit.r-forge.r-project.org, http://cran.r-project.org/package=mkin, +URL: http://cran.r-project.org/package=mkin, + http://kinfit.r-forge.r-project.org/mkin_static, http://github.com/jranke/mkin -- cgit v1.2.1 From 81dc12a8c149e11d57190ebf59f3f7e9c7b99af7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 20 Aug 2014 14:42:20 +0200 Subject: Fix mkinfit for a special situation See NEWS.md: When the parent was not the (only) variable with the highest value out of all variables in the observed data, it could happen that the initial value (state.ini) was not initialised. --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 3898f69a..e8b7195d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-33 -Date: 2014-08-19 +Date: 2014-08-20 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 8ec5b635e104b94a1a5bb1614e97fdc2ce6e6f7b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 11 Oct 2014 09:56:17 +0200 Subject: Updates intended for releasing mkin 0.9-33 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index e8b7195d..86776cb2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data Version: 0.9-33 -Date: 2014-08-20 +Date: 2014-10-11 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 2635402fbc6400b8418a6b4eddaf0c91cc65a102 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 11 Oct 2014 11:19:03 +0200 Subject: Start new development version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 86776cb2..b3d9ca14 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data -Version: 0.9-33 +Version: 0.9-34 Date: 2014-10-11 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), -- cgit v1.2.1 From 14a373d281dea33d26f4fae3c9d804cd7d522b7b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Oct 2014 13:47:39 +0200 Subject: Use title case for the title Tried to adhere to the Chicago Manual of Style, but am not sure about "with". --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index b3d9ca14..6c4545c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: mkin Type: Package -Title: Routines for fitting kinetic models with one or more state - variables to chemical degradation data +Title: Routines for Fitting Kinetic Models with One or More State + Variables to Chemical Degradation Data Version: 0.9-34 Date: 2014-10-11 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), -- cgit v1.2.1 From 4510a609159216041f10a33146534f5a8366ac76 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 14 Oct 2014 22:04:54 +0200 Subject: Further formatting improvement for differential equations --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index 6c4545c4..a984391c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data Version: 0.9-34 -Date: 2014-10-11 +Date: 2014-10-14 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1 From 65d31e345f9e61e9d05584b24df6a01c6c6ed18d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 15 Oct 2014 01:13:48 +0200 Subject: Switch to using the Port algorithm per default --- DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index a984391c..d36c35cc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data Version: 0.9-34 -Date: 2014-10-14 +Date: 2014-10-15 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), @@ -12,9 +12,9 @@ Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical solvers - and a choice of the optimisation methods made available by the FME package - (default is a Levenberg-Marquardt variant). Please note that no warranty is - implied for correctness of results or fitness for a particular purpose. + and a choice of the optimisation methods made available by the FME package. + Please note that no warranty is implied for correctness of results or fitness + for a particular purpose. Depends: minpack.lm, rootSolve Imports: FME, deSolve Suggests: knitr, RUnit -- cgit v1.2.1 From c0803a4e6660a6ad3a3a219476b6269bab528bfe Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 22 Oct 2014 09:18:41 +0200 Subject: Always include 0 on y axis when plotting during the fit --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'DESCRIPTION') diff --git a/DESCRIPTION b/DESCRIPTION index d36c35cc..da7037a6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Routines for Fitting Kinetic Models with One or More State Variables to Chemical Degradation Data Version: 0.9-34 -Date: 2014-10-15 +Date: 2014-10-22 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), -- cgit v1.2.1