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-rw-r--r--README.md48
1 files changed, 26 insertions, 22 deletions
diff --git a/README.md b/README.md
index 6b128ec3..9d19890e 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
@@ -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

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