Installation instructions

pomp version 2 installation instructions

Because it is not fully backward-compatible, pomp version 2 is being made available temporarily as the pomp2 package. pomp2 is not available on CRAN but it can be installed directly from the pomp package repository.

pomp2 will be phased out, replaced by version 2 of pomp, around the middle of 2019. At that point, pomp versions <2 will no longer be supported.

It is recommended that users begin making the transition to version 2 now. An upgrade guide is available to help you transition your codes to the new version. In the interim period, you can have both pomp and pomp2 installed on your system simultaneously.

There are three ways to install pomp2.

  1. Run the following in an R session:
    install.packages("pomp2",repos="https://kingaa.github.io/")
    
  2. Use devtools:
    devtools::install_github("kingaa/pomp")
    

    Note that this installs pomp2.

  3. Download the source tarball and install locally.

pomp versions <2, from CRAN:

Source and binaries for the CRAN version are available here.

Important note for Windows users

To make use of pomp’s facilities for accelerated computation using compiled C code, and to compile the package from source, you will need the ability to compile C code and dynamically link it into an R session. For this reason, you must install the Rtools suite, which can be downloaded from cran.r-project.org. Rtools is needed both to compile and install the development version from source and to obtain full value from any version of the package.

When installing Rtools, it is sufficient to choose the “Package authoring installation” option. Also during the installation, tick the “edit system PATH” box.

Important note for Mac OS X users

To make use of the package facilities for accelerated computation using compiled C code, you will need the ability to compile C code and dynamically link it into an R session. These facilities are provided in the Xcode app, which is free and can be installed via the App Store or downloaded from developer.apple.com.

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.


NSF
NCEAS
NIH

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.