Fetch the COM(P)ADRE database from compadre-db.org or a local file

Fetches the current version of a COM(P)ADRE database from https://compadre-db.org, or load any version stored in a local .RData file.

cdb_fetch(cdb, version = NULL, flag = FALSE, userComment = NULL, quiet = FALSE)

Arguments

cdb

Either "comadre" or "compadre" (case insensitive) to fetch the most recent database from https://compadre-db.org, or a path to an existing COMPADRE database (i.e. .RData file) stored on the local machine.

version

Optional. The version number of a particular database to be downloaded e.g. "3.0.0". If this is not included (as default) the latest versions are downloaded.

flag

Logical argument where `TRUE` will automatically run cdb_flag to add logical columns to the metadata to flag potential problems in the matrix population models. Default is `FALSE`.

userComment

An optional string to enable users to add a comment as an attribute to the returned data frame. This could be useful for keeping track of multiple versions of the database. Accessed by `attributes(db)$comment`.

quiet

A logical argument. If `TRUE` the download message that includes version information and link to the user agreement is suppressed. Default is `FALSE`.

Value

A CompadreDB object

Note

The downloaded databases include a set of attributes accessible with `attributes`. These include version information and date and time of creation.

See also

Other data acquisition: cdb_build_cdb(), cdb_metadata()

Author

Owen R. Jones <jones@biology.sdu.dk>

Patrick M. Barks <patrick.barks@gmail.com>

Examples

if (FALSE) {
# Download latest version of COMPADRE direct from the website
compadre <- cdb_fetch("compadre")

# Examine the attributes of the downloaded database
attributes(compadre)

# Download COMPADRE version 3.0.0 direct from the website
compadre <- cdb_fetch("compadre", version = "3.0.0")

# using file path to downloaded data
compadre <- cdb_fetch("data/COMPADRE_v.5.0.1.RData")
}