|Project||Main branch||Devel branch|
An R package to facilitate working with the COM(P)ADRE Plant and Animal Matrix Population Databases.
Install the stable release package from CRAN with:
Install the package from GitHub with:
# install package 'remotes' if necessary # will already be installed if 'devtools' is installed install.packages("remotes") # argument 'build_opts = NULL' only needed if you want to build vignettes remotes::install_github("jonesor/Rcompadre", build_opts = NULL)
To install from the development branch use:
remotes::install_github("jonesor/Rcompadre", ref = "devel")
Fetch the most recent database version from compadre-db.org with
compadre <- cdb_fetch("compadre") # or use 'comadre' for the animal database
or load from a local
.RData file with
compadre <- cdb_fetch("path/to/file/COMPADRE_v.4.0.1.RData")
First we’ll use the function
cdb_flag() to add columns to the database flagging potential issues with the projection matrices, such as missing values, or matrices that don’t meet assumptions like ergodicity, irreducibility, or primitivity.
compadre_flags <- cdb_flag(compadre)
We’ll only be able to calculate population growth rates from matrices that don’t contain missing values, and we only want to use matrices that meet the assumption of ergodicity, so we’ll subset the database accordingly.
compadre_sub <- subset( compadre_flags, check_NA_A == FALSE & check_ergodic == TRUE )
Finally, we’ll use the
eigs() function from the popdemo package to calculate the population growth rate for every matrix in
In the code above, the accessor function
matA() is used to extract a list of projection matrices (the full matrix,
matA) from every row of
compadre_sub. There are also accessor functions for the matrix subcomponents (
matC()), and for many other parts of the database too.
Specific earlier releases of this package can be installed using the appropriate
For example to install version 0.1.0:
See the Changelog for more details.
Jones, Owen R., Patrick Barks, Iain M. Stott, Tamora D. James, Sam C. Levin, William K. Petry, Pol Capdevila, et al. 2021. “Rcompadre and Rage – Two R Packages to Facilitate the Use of the COMPADRE and COMADRE Databases and Calculation of Life History Traits from Matrix Population Models.” bioRxiv. doi: 10.1101/2021.04.26.441330.
All contributions are welcome. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
There are numerous ways of contributing.