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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 48 |
1 files changed, 26 insertions, 22 deletions
@@ -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 @@ -34,20 +34,26 @@ 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 - library("mkin") 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) + plot(fit2, show_residuals = TRUE) -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") @@ -58,16 +64,15 @@ 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 @@ -88,8 +93,7 @@ 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) @@ -120,10 +124,9 @@ 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 [documentation page](http://kinfit.r-forge.r-project.org/gmkin_static) +for installation instructions and a manual. ## Credits and historical remarks @@ -153,7 +156,8 @@ 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](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 |