Overview

The RMark package is a collection of R functions that can be used as an interface to MARK for analysis of capture-recapture data. The package contains various functions that import/export capture data, build capture-recapture models, run the FORTRAN program MARK.EXE, and extract and display output. Program MARK has its own user interface; however, model development can be rather tedious and error-prone because the parameter structure and design matrix are created by hand. This interface in R was created to use the formula and design matrix functions in R to ease model development and reduce errors. For more details about its capabilities, download the following RMark documentation archive.

Installing and using RMark...

To use RMark under MS Windows, you must do the following:

  • If you haven't already done so, you must install MARK on your computer. Click here to download the most recent version of MARK. If you choose the default options during the installation process, MARK.EXE will be stored in the default location of c:/Program Files/Mark (or c:/Program Files (x86)/Mark on 64bit machines) where the R package will expect it. If you modify the default location, you'll need to put that location in your path or create a MarkPath variable in R. See the help for "mark" once you have completed step 5 below.
  • If you haven't already done so, you must install R from the CRAN website http://cran.r-project.org. Select Windows, then select base and finally Download R vvvv for Windows (where vvvv is the current version. Version R2.13.0 or greater is required for the current version of RMark. Select run and then follow the directions and choose the default setup by clicking on "next"at each prompt.
  • Next run R, and use Packages/Install Packages to install RMark from CRAN (select a local mirror site).
  • Next you need to use the command library(RMark) to attach the package so you can use the functions. Every time you start R you need to issue the command library(RMark) to attach the package but you only need to install it once.
  • To avoid entering library(RMark) each time you initiate R, you have a couple of options. You can enter the library(RMark) command by editing the file rprofile.site located in the directory C:\Program Files\R\R-vvvvv\etc\. If you choose that option, the RMark package will be loaded anytime you load R. Or you can write a function .First<-function() library(RMark) and save it into any .Rdata file from which you will do MARK analyses. The rprofile.site file is also a good place to make generic modifications. For example, can use options(htmlhelp=TRUE) to use html help. Enter "?mark" at the bottom of the page click on index to see the complete list of help topics. The "rprofile.site" file or ".First" function is also a good place to change options like the default editor etc. See help for "options" and "Startup" from within R.
  • You can also download the source for the RMark package by going to the RMark page under contributed packages on CRAN (http://cran.r-project.org/).