MPM-errors

This is the repository for analysis and writing associated with the paper "Persistent problems in the construction of matrix population models," to be submitted to the special issue of Ecological Modelling on matrix population models.

To reproduce the analyses, you will need to:

• Clone or download the repository
• Download the COMPADRE and COMADRE databases from http://www.compadre-db.org. Put the files in the data subdirectory. Note that reproducibility is only guaranteed if you use v. 2.0.1 of COMADRE and v. 4.0.1 of COMPADRE
• Install the ProjectTemplate library, and run ProjectTemplate::load.project() at the beginning of your session. More details are below.

Collaborators: Please use the issue tracker on github (https://github.com/BruceKendall/MPM-errors/issues) to make comments and to-do items.

Required libraries

• Mage (devtools::install_github("jonesor/compadreDB/Mage"))

ProjectTemplate

The compadre-plus project was set up with the ProjectTemplate package, as described below:

ProjectTemplate is an R package that helps you organize your statistical analysis projects. Since you're reading this file, we'll assume that you've already called create.project() to set up this project and all of its contents.

To load your new project, you'll first need to setwd() into the directory where this README file is located. Then you need to run the following two lines of R code:

library('ProjectTemplate')
load.project()

After you enter the second line of code, you'll see a series of automated messages as ProjectTemplate goes about doing its work. This work involves:

• Reading in the global configuration file contained in config.
• Loading any R packages you listed in he configuration file.
• Reading in any datasets stored in data or cache.
• Preprocessing your data using the files in the munge directory.

Once that's done, you can execute any code you'd like. For every analysis you create, we'd recommend putting a separate file in the src directory. If the files start with the two lines mentioned above:

library('ProjectTemplate')
load.project()

You'll have access to all of your data, already fully preprocessed, and all of the libraries you want to use.

For more details about ProjectTemplate, see http://projecttemplate.net