Please read the appropriate sections below, which give specific instructions for installing and testing the software we will be using. First follow the instructions for “all users”, then those for your specific operating system (OS).
NB: If you run into problems, send a note to kingaa@umich.edu with a detailed description of the problem you’ve encountered. In this message, be certain to include:
In particular, it is often easiest to send a screenshot or transcript showing the commands you’ve entered and the error messages you’ve received. In R, you can run Sys.info() to get a printout of the operating system and software version numbers.
R and RStudio are free and open-source. You’ll need at least version 3.3.0 of R. The latest version is 3.3.1, so if you need to update, go ahead and install version 3.3.1. Source code and binaries are available on CRAN (http://cran.r-project.org). Install the latest version of RStudio from rstudio.com.
If your machine runs Windows, you must install Rtools. This will give you the ability to compile C code and dynamically link it into an R session.
Download Rtools from CRAN and install it. When installing Rtools, it is sufficient to choose the “Package authoring installation” option. Also during the installation, you must tick the “edit system PATH” box.
Briefly, I had some problems with Rtools33, but none with the last frozen version (Rtools32). I also had some difficulties initially with the latest version of RStudio but these went away when I installed version 0.98.1103 (download here) and now I am having no problems with version RStudio version 0.99.447.
Open a session in RStudio and run the following:
> update.packages()
> source("http://kingaa.github.io/short-course/prep/packages.R")
> source("http://kingaa.github.io/scripts/pompTest.R")[The > is the command prompt; it is not part of the command. Also, depending on your email client program, you may need to replace the quotation marks with plain keyboard double quotes.]
The first command updates your installed packages. You may be prompted to specify a CRAN mirror: choose one geographically near you. In RStudio, you can also push the “Update” button on the “Packages” tab to accomplish this.
The second command runs a script on my website. It will install some needed packages if these are not already installed on your system.
The third command will attempt to install pomp, the principal R package we’ll be using, and will check whether you can work with it. The installed pomp version is more recent than that which is on CRAN; you must install this more recent version.
If the final command fails, try the following:
> source("http://kingaa.github.io/scripts/hello.R",echo=TRUE)If this fails to give the “Hello!” messages, you will need to follow the instructions below that correspond to your OS.
If you have trouble with any of the scripts above, make sure you have the GNU compiler collection (GCC), including gfortran installed on your computer. Linux distributions typically include this by default but it is not impossible that you have somehow avoided this.
So that you can compile C code and dynamically link it into an R session, you will need to have the Xcode app installed before running the pompTest.R script above. This is gratis and can be installed via the App Store or downloaded from developer.apple.com.
If the pompTest.R script fails because you cannot load pomp, try installing it from source. The easiest way to do this is to use the devtools package. Do
install.packages("devtools")
library(devtools)
install_git("kingaa/pomp")If, while trying to install from source, you receive the error,
make: gfortran-4.8: No such file or directoryor one that otherwise refers to gfortran, then it is likely that you do not have the necessary version of gfortran installed. Have a look at these instructions and contact me at the address above if these don’t work for you.
You have probably failed to install the Rtools correctly. Revisit the instructions above.