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 --- README.md | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'README.md') diff --git a/README.md b/README.md index e171180f..48c667bf 100644 --- a/README.md +++ b/README.md @@ -47,6 +47,11 @@ A very simple usage example would be plot(SFO.fit, show_residuals = TRUE) summary(SFO.fit) +If you have parent only degradation data, you can use a shorthand notation +like `SFO` or `FOMC` for the model without the need to use `mkinmod` + + FOMC.fit <- mkinfit("FOMC", example_data) + A fairly complex usage example using a built-in dataset: data <- mkin_wide_to_long(schaefer07_complex_case, time = "time") -- cgit v1.2.1 From a89ee67280d2e2876b7ef4b6c345bc407ef2e0a9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 21 Jul 2014 09:29:54 +0200 Subject: Simplify usage examples --- README.md | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 48c667bf..d4f290dd 100644 --- a/README.md +++ b/README.md @@ -34,25 +34,25 @@ detailed guidance and helpful tools have been developed as detailed in ## Usage -A very simple usage example would be +The simplest usage example that I can think of, using model shorthand notation +(available since mkin 0.9-32) and a built-in dataset is library("mkin") + fit <- mkinfit("SFO", FOCUS_2006_C) + plot(fit, show_residuals = TRUE) + summary(fit) + +A still very simple usage example including the definition of the same data in R +code would be + example_data = data.frame( name = rep("parent", 9), time = c(0, 1, 3, 7, 14, 28, 63, 91, 119), value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6) ) - SFO <- mkinmod(parent = list(type = "SFO")) - SFO.fit <- mkinfit(SFO, example_data) - plot(SFO.fit, show_residuals = TRUE) - summary(SFO.fit) + fit2 <- mkinfit("FOMC", example_data) -If you have parent only degradation data, you can use a shorthand notation -like `SFO` or `FOMC` for the model without the need to use `mkinmod` - - FOMC.fit <- mkinfit("FOMC", example_data) - -A fairly complex usage example using a built-in dataset: +A fairly complex usage example using another built-in dataset: data <- mkin_wide_to_long(schaefer07_complex_case, time = "time") @@ -63,16 +63,15 @@ A fairly complex usage example using a built-in dataset: C1 = list(type = "SFO"), A2 = list(type = "SFO"), use_of_ff = "max") - fit <- mkinfit(model, data, method.modFit = "Port") + fit3 <- mkinfit(model, data, method.modFit = "Port") - plot(fit, show_residuals = TRUE) - summary(fit) - mkinparplot(fit) + plot(fit3, show_residuals = TRUE) + summary(fit3) + mkinparplot(fit3) For more examples and to see results, have a look at the examples provided in the [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html) -documentation -or the package vignettes referenced from the +documentation or the package vignettes referenced from the [mkin package documentation page](http://kinfit.r-forge.r-project.org/mkin_static/index.html) ## Features -- cgit v1.2.1 From b083911a0e6a99dd4f083d785e044379205c2f0d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 21 Jul 2014 09:39:33 +0200 Subject: Residual plots are important --- README.md | 1 + 1 file changed, 1 insertion(+) (limited to 'README.md') diff --git a/README.md b/README.md index d4f290dd..c1efb808 100644 --- a/README.md +++ b/README.md @@ -51,6 +51,7 @@ code would be value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6) ) fit2 <- mkinfit("FOMC", example_data) + plot(fit2, show_residuals = TRUE) A fairly complex usage example using another built-in dataset: -- cgit v1.2.1 From 5d298a8dcb7fa19d6308cce9fbaa33af392f05be Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 30 Aug 2014 01:42:52 +0200 Subject: Add a link to the KinGUII website --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index c1efb808..e5463e18 100644 --- a/README.md +++ b/README.md @@ -155,7 +155,8 @@ The first `mkin` code was [first CRAN version](http://cran.r-project.org/src/contrib/Archive/mkin) on 18 May 2010. -After this, Bayer has developed an R based successor to KinGUI named KinGUII +After this, Bayer has developed an R based successor to KinGUI named +![KinGUII](http://kinguii.github.io) whose R code is based on `mkin`, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed -- cgit v1.2.1 From fc00890dd8557706a97de4d2eee05dc2c76cafa7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 30 Aug 2014 01:46:00 +0200 Subject: Correct the link to KinGUII --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index e5463e18..bb77fa76 100644 --- a/README.md +++ b/README.md @@ -156,7 +156,7 @@ The first `mkin` code was on 18 May 2010. After this, Bayer has developed an R based successor to KinGUI named -![KinGUII](http://kinguii.github.io) +[KinGUII](http://kinguii.github.io) whose R code is based on `mkin`, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed -- cgit v1.2.1 From db8b6a43fec8d052b853f272e016079d0a9f91b6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 30 Aug 2014 01:46:43 +0200 Subject: Change to https to avoid messages about leaving secured grounds --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index bb77fa76..e8040d55 100644 --- a/README.md +++ b/README.md @@ -156,7 +156,7 @@ The first `mkin` code was on 18 May 2010. After this, Bayer has developed an R based successor to KinGUI named -[KinGUII](http://kinguii.github.io) +[KinGUII](https://kinguii.github.io) whose R code is based on `mkin`, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed -- cgit v1.2.1 From 1e1f36ae89b20b354f9bef039b57b36a39b09aef Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 14 Oct 2014 14:12:41 +0200 Subject: Link the the new gmkin homepage --- README.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index e8040d55..37c0bb1a 100644 --- a/README.md +++ b/README.md @@ -122,10 +122,9 @@ documentation or the package vignettes referenced from the ## GUI -There is a graphical user interface that I consider useful for real work. -It is available from github in the separate package -[gmkin](http://github.com/jranke/gmkin). - +There is a graphical user interface that I consider useful for real work. Please +refer to its homepage of [gmkin](http://kinfit.r-forge.r-project.org/gmkin_static) +for installation instructions and futher information. ## Credits and historical remarks -- cgit v1.2.1 From 8ecaa61db8e264c28561a3af98d524889e6065b2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 14 Oct 2014 14:17:46 +0200 Subject: Some cosmetics --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 37c0bb1a..dfb735f0 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ You can install the latest released version from [CRAN](http://cran.r-project.org/package=mkin) from within R: ```s -install.packages('mkin') +install.packages("mkin") ``` If looking for the latest features, you can install directly from @@ -21,7 +21,7 @@ vignettes, to make installation as fast and painless as possible. ```s require(devtools) -install_github("mkin", "jranke", quick = TRUE) +install_github("jranke/mkin", quick = TRUE) ``` ## Background @@ -37,7 +37,7 @@ detailed guidance and helpful tools have been developed as detailed in The simplest usage example that I can think of, using model shorthand notation (available since mkin 0.9-32) and a built-in dataset is - library("mkin") + library(mkin) fit <- mkinfit("SFO", FOCUS_2006_C) plot(fit, show_residuals = TRUE) summary(fit) @@ -124,7 +124,7 @@ documentation or the package vignettes referenced from the There is a graphical user interface that I consider useful for real work. Please refer to its homepage of [gmkin](http://kinfit.r-forge.r-project.org/gmkin_static) -for installation instructions and futher information. +for installation instructions and further information. ## Credits and historical remarks -- 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 --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index dfb735f0..fba6f851 100644 --- a/README.md +++ b/README.md @@ -93,8 +93,7 @@ documentation or the package vignettes referenced from the * Model optimisation with [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html) internally using the `modFit` function from the `FME` package, - which uses the least-squares Levenberg-Marquardt algorithm from - `minpack.lm` per default. + but using the Port routine `nlminb` per default. * By default, kinetic rate constants and kinetic formation fractions are transformed internally using [`transform_odeparms`](http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html) -- cgit v1.2.1 From daf7487c9ce9b67ba6845da3f2b99c097e1ea73e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 23 Oct 2014 12:22:39 +0200 Subject: Update to README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index fba6f851..87daa0c5 100644 --- a/README.md +++ b/README.md @@ -122,8 +122,8 @@ documentation or the package vignettes referenced from the ## GUI There is a graphical user interface that I consider useful for real work. Please -refer to its homepage of [gmkin](http://kinfit.r-forge.r-project.org/gmkin_static) -for installation instructions and further information. +refer to its [documentation page](http://kinfit.r-forge.r-project.org/gmkin_static) +for installation instructions and a manual. ## Credits and historical remarks -- cgit v1.2.1