An R package to work with the COM(P)ADRE Plant and Animal Matrix Population Databases. Note this package is at an early stage of development, and may contain bugs.
Install 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_vignettes = TRUE) # use argument 'build_vignettes = FALSE' if the vignette build fails remotes::install_github("jonesor/Rcompadre", build_vignettes = FALSE)
To install the development branch use:
Fetch the most recent database version from compadre-db.org with
or load from a local
.RData file with, for example:
For the most part
CompadreDB objects work like a data frame. They can be subset using
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.
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.
Finally, we’ll use the
lambda function from the library popbio 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
@ tag. You can see details of the existing releases here. Note that the most recent version does not necessarily have an
To install version 0.2.0, our last release before our introduction of the new
CompadreDB class, and associated major changes to the package:
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.