SETTING UP THE ENVIRONMENT
R is available for virtually any platform and can be installed from the
R Project website. Please note that throughout this paper all R commands are distinguished from ordinary text using a bold-face font, and blocks of R commands are set apart in monospace font. All commands are preceded by a chevron (>) that does not need to be entered, but simply represents the beginning of a new command.
Throughout much of this paper, I use a theoretical data set called fdata, consisting of three parts. fdata.list is a table with each row representing an individual species occurrence and columns for locality name, species name, species abundance, latitude and longitude. fdata.mat is a matrix (12 by 12) with each unique species as a row and each locality as a column. The last part is fdata.lats, a SpatialPoints object containing the longitude and latitude for each locality. All of this data is found as part of the fossil package. As well, the entirety of the code used to analyse the data and create figures for this paper is available as a supplementary file, along with full instructions on how to use it.
To begin using the fossil package in an interactive session, you must first ensure the package has been installed on your computer. It is available online from CRAN and can be downloaded from within an R session by typing install.packages ('fossil') at the command prompt. You will be prompted to choose a download location; simply try to choose one closest to your location. Once the
fossil package is available on your computer, you can load it in to R using the command library (fossil). Every time you start a new session, you will have to load the package again using the library() command as extra libraries are not loaded by default to keep the memory use as low as possible.