Installation instructions
From CRAN:
Source and binaries are available on CRAN.
Install pomp from CRAN just like any other R package:
install.packages("pomp")
From Github:
The latest development release is usually several weeks ahead of the version on CRAN. You can install it from the Github repository by executing the following in an R session:
install.packages("pomp",repos="https://kingaa.github.io/")
On Windows and MacOS systems, this will cause a precompiled version of the latest release of pomp to be installed, if one is available, and will install from source if a binary is not available.
Download and install locally
You can also download the latest release and install it locally as you would any R package.
Testing your installation
To make use of pomp’s facilities for accelerated computation using compiled C code, and to compile the package from source, you will want the ability to compile C code and dynamically link it into an R session. To test this, run the following in an R session:
source("https://kingaa.github.io/scripts/helloC.R",echo=TRUE)
This script attempts to compile a simple C program. Upon success, you’ll see a “Hello!” message.
If this fails, consult the instructions below, according to your operating system.
Important note for Windows users
To use pomp’s compilation facility, you need to have the Rtools suite installed. This can be downloaded from CRAN. Rtools is needed to obtain full value from pomp, but also to compile R packages from source, if you ever want to do that.
A video tutorial on installing Rtools is available here.
To test your Rtools installation, run the following in an R session:
source("https://kingaa.github.io/scripts/hello.R",echo=TRUE)
On success, you will see two “Hello!” messages.
Important note for Mac OS users
To use pomp’s compilation facility, you need to have the Xcode app installed.
Xcode is free and can be installed according to these instructions.
In addition, some users report problems installing pomp from source due to lack of an appropriate gfortran installation, which is not included by default in all versions of Xcode.
If you have this problem, see these instructions.
To test your Xcode and Fortran installations, run the following in an R session:
source("https://kingaa.github.io/scripts/hello.R",echo=TRUE)
On success, you will see two “Hello!” messages.
Important note for Linux users
To install pomp from source, you will need the gfortran compiler on your machine and will therefore may need to install it.
To do so on a Debian-based system (e.g., Ubuntu), for example, run:
sudo apt install gfortran
On an RPM-based system, run:
sudo yum install gcc-gfortran
|
This software has been made possible by support from the U.S. National Science Foundation (Grants #EF-0545276, #EF-0430120), by the “Inference for Mechanistic Models” Working Group supported by the National Center for Ecological Analysis and Synthesis (a Center funded by N.S.F. (Grant #DEB-0553768), the University of California, Santa Barbara, and the State of California), and by the RAPIDD program of the Science & Technology Directorate, Department of Homeland Security and the Fogarty International Center, U.S. National Institutes of Health. |