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:
remotes::install_github("jonesor/Rcompadre", ref = "devel")library(Rcompadre)Fetch the most recent database version from compadre-db.org with
compadre <- cdb_fetch("compadre") # or use 'comadre' for the animal databaseor load from a local .RData file with, for example:
compadre <- cdb_fetch("path/to/file/COMPADRE_v.4.0.1.RData")If you prefer using load() to load your local copy of a legacy
database, use as_cdb() to convert it to the ‘CompadreDB’ class
load("COMPADRE_v.4.0.1.RData") # loads object 'compadre'
compadre <- as_cdb(compadre)For the most part CompadreDB objects work like a data frame. They can
be subset using [ or subset()
# subset to the first 10 rows
compadre[1:10,]
# subset to the species 'Echinacea angustifolia'
subset(compadre, SpeciesAccepted == "Echinacea angustifolia")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 lambda function from the library
popbio to calculate the population
growth rate for every matrix in compadre_sub.
library(popbio)
compadre_sub$lambda <- sapply(matA(compadre_sub), lambda)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 (matU(), matF(), 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 @ tag.
To install version 0.2.0, our last release before our introduction of
the new CompadreDB class, and associated major changes to the package:
remotes::install_github("jonesor/Rcompadre@v0.2.0")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.