Please read the appropriate sections below, which give specific instructions for installing and testing the software we will be using.

Important note: If you run into problems, send a note to ionides@umich.edu with a detailed description of the problem you’ve encountered. In this message, be certain to include all of the following information:

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.

Update R and RStudio

The latest version is R 3.6.3, and it is helpful to use a recent version, say 3.6.1 or later. If you need to update, go ahead and install version 3.6.3. Source code and binaries are available on CRAN (https://cran.r-project.org/). Install the latest version of RStudio from rstudio.com.

Install needed packages

Open a session in RStudio and run the following:

> update.packages()
> source("https://ionides.github.io/531w20/pomp_prep/packages.R")

[The > is the command prompt; it is not part of the command. Also, depending on your software configuration, you may need to replace the quotation marks with plain keyboard double quotes if you copy-paste the code.]

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 which will install some packages needed to run code from the notes. It is probably helpful to install these.

Windows users

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.

If, having installed the latest version of Rtools compatible with your R, the scripts below fail, try installing a “frozen” version of Rtools.

It is critical that you install these programs before the course starts!

MacOSX users

So that you can compile C code and dynamically link it into an R session, you will need to have the Xcode app installed. This is gratis and can be installed via the App Store or downloaded from developer.apple.com.

Note that you must go beyond merely installing the Xcode app. After you’ve installed the app, open a unix terminal (listed as the Terminal app under “Utilities” in the Finder) and run the following line

xcode-select --install

This will install the “Command Line Tools” that are needed to compile native C codes.

All users

Test pomp

Open a session in RStudio and run the following:

> source("https://ionides.github.io/531w20/pomp_prep/pompTest.R")

This will check whether you can work with pomp.

If it fails, try the following:

> source("https://ionides.github.io/531w20/pomp_prep/hello.R",echo=TRUE)

If this fails to give the “Hello!” message, you will need to follow the instructions below that correspond to your OS before re-trying the pompTest.R script.

Linux and unix

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.

MacOSX

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_github("kingaa/pomp")

If, while trying to install from source, you receive the error,

make: gfortran-4.8: No such file or directory

or 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 email me if these don’t work for you.

Some users have reported receiving an error complaining that

'stdlib.h' file not found

This indicates that the command-line tools from Xcode have not been properly installed. In a unix terminal, run

xcode-select --install

to correct this problem.

Windows

You have probably failed to install the Rtools correctly. Revisit the instructions above.

Acknowledgment

This material leans heavily on Aaron King’s instructions for setting up an R environment for pomp.