# gmkin
The R package [gmkin](http://kinfit.r-forge.r-project.org/gmkin_static)
provides a browser based graphical user interface (GUI) for
fitting kinetic models to chemical degradation data based on R package
[mkin](http://github.com/jranke/mkin). The GUI is based on the
[gWidgetsWWW2](http://github.com/jverzani/gWidgetsWWW2) package developed by
John Verzani. The GUI elements are created by the JavaScript library
ExtJS which is bundled with gWidgetsWWW2.
## System requirements
For running gmkin you need a system running a recent version of R (version
3.1.0 or later), the gWidgesWWW2 package, the gmkin package and a web browser
(Firefox/Iceweasel and Chrome work for me) with JavaScript enabled.
It should be possible to run gmkin on most laptop or desktop computers running
Linux, Mac OS X, Windows XP or Windows 7. It is frequently checked under Linux and
Windows 7.
To view the complete set of widgets in the browser window without resizing
anything, it needs a screen space of 1366x740 pixels.
### Installing R
Please refer to [CRAN](http://cran.r-project.org) for installation instructions
and binary packages. If you are on Windows, please consult the
[FAQ for Windows](http://cran.r-project.org/bin/windows/base/rw-FAQ.html), especially
the entries
"[How do I install R for Windows?](http://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-install-R-for-Windows_003f)",
"[How do I run it?](http://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-run-it_003f)".
If you would like to upgrade your R installation, please refer to the
respective
[FAQ entry](http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f).
### Installing gmkin and gWidgetsWWW2
Windows and Linux users running R 3.1.0 or later can make use of the
package repository on R-Forge. Before installing gmkin, you should update
your R packages already installed, e.g. by starting R, and pasting the
command
```s
update.packages()
```
or similar, depending on your R installation.
For installing gmkin or upgrading to the latest released version, please
use the command
```s
install.packages("gmkin", repos = c("http://r-forge.r-project.org", getOption("repos")))
```
If you have not set your CRAN mirror yet, you may have to select one from the list that
appears.
The above command temporarily adds the R-Forge repository to your package
sources. It should pull the gmkin package and its dependencies, notably the
gWidgetsWWW2 package which is not available from the CRAN archive (see below).
Mac users that have the necessary development files installed can probably
install from the source files in this repository (not tested).
In a previous version of this README I have described how to permanently add
the R-Forge repository to your options. However, I noticed this has unwanted
side effects, so I do not recommend it any longer. Therefore, you may want
to revert such changes to your R startup options.
The latest changes to gmkin are recorded in the
[NEWS](https://github.com/jranke/gmkin/blob/master/NEWS.md) file,
more details can be found in the
[commit history](https://github.com/jranke/gmkin/commits/master).
## Usage
Without further preparation, you can start the GUI by starting R and pasting the following
commands into the R terminal (R console on Windows):
```s
require(gmkin)
gmkin()
```
You may also want to adapt the browser that R starts (using e.g.
`options(browser="/usr/bin/firefox")` on linux, or setting the default browser
on Windows).
## Documentation
For a complete overview of the functionality of the gmkin graphical user
interface please refer to the
[manual](http://kinfit.r-forge.r-project.org/gmkin_static/vignettes/gmkin_manual.html)
available at the gmkin [documentation website](http://kinfit.r-forge.r-project.org/gmkin_static).
In case you would like to see the documentation of the underlying mkin package, please
refer to its
[documentation website](http://kinfit.r-forge.r-project.org/mkin_static).
## Status and known issues
- gmkin was developed in the hope that it will be useful. However, no warranty can be
given that it will meet your expectations. There may be bugs, so please be
careful, check your results for plausibility and use your own expertise to judge
yourself.
- Starting the GUI takes some time. If the GUI does not come up after 10-15
seconds, close your browser and start gmkin again using the command 'gmkin()'.
Once the GUI is started, it is reasonably responsive.
- Please check the [issues](https://github.com/jranke/gmkin/issues) reported on github
- The R console starting the graphical user interface is not secured against manipulations
from local users on multiuser systems
(see [gWidgetsWWW2 issue](https://github.com/jverzani/gWidgetsWWW2/issues/22)).
### Notes on the gWidgetsWWW2 package
The R package gWidgetsWWW2 is not available on CRAN because it contains
path names with more then 100 characters in the JavaScript files which limits
its portability. Also, it attaches some R objects to the search path, which is,
in its current form, not fully in line with the CRAN package policy. It is not
a widely used library for creating graphical user interfaces and is not supported
by a commercial company. However it makes it possible to create a reasonably
complex user interface by just writing R code, and is therefore used by gmkin.
### Installation using the devtools package
Users of the `devtools` package can also install gWidgetsWWW2 and gmkin directly from
the respective github repositories:
```s
require(devtools)
install_github("jverzani/gWidgetsWWW2", quick = TRUE)
install_github("jranke/gmkin", quick = TRUE)
```
Installing gWidgetsWWW2 in this way yields a lot of warnings concerning overly
long path names (see Notes on gWidgetsWWW2 above). Using `quick = TRUE` skips
docs, multiple-architecture builds, demos, and vignettes, to make installation
as fast and painless as possible.
## Simplifying the start of gmkin under Windows
You can put the commands
```s
require(gmkin)
gmkin()
while (TRUE) {
Sys.sleep(10)
}
```
into an R script (e.g. under `C:\Users\<your username>\AppData\Roaming\gmkin_start.R`),
and create a Windows shortcut, e.g. on the Desktop, with the target
`"C:\Program Files\R\R-3.x.y\bin\R.exe" --slave -f c:\Users\<your username>\AppData\Roaming\gmkin_start.R`,
where R.x.y is the version of R that you would like to use with gmkin. This
will start a non-interactive R console that runs the gmkin GUI. In the
properties dialogue of the shortcut, you can also set the working directory in
which it starts gmkin. Thanks to Jonas Klein of the Umweltbundesamt for the
trick with using Sys.sleep in a while loop and for suggesting the AppData
directory for the start script.
## Acknowledgements
Financial support, feedback and suggestions by the German Federal Environmental
Agency ([Umweltbundesamt](http://www.umweltbundesamt.de)) in two projects in
2014 and 2015 was crucial for reaching version 0.6.3 in November 2015 and is
gratefully acknowledged. In particular, Stefan Meinecke contributed with a lot
of user feedback and suggestions for improvement in that time.
