cdb_id_stages: Create integer identifiers for a COM(P)ADRE database...

In jonesor/Rcompadre: Utilities for using the 'COM(P)ADRE' Matrix Model Database

Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of species and matrix stage class definitions

Description

Creates a vector of integer identifiers corresponding to the rows of a CompadreDB object, based on unique combinations of the column 'SpeciesAccepted' and a list of matrix stage class definitions (either 'MatrixClassAuthor' or 'MatrixClassOrganized').

Usage

cdb_id_stages(cdb, stage_def = "MatrixClassAuthor")

Arguments

cdb	A CompadreDB object
stage_def	Whether to define matrix stage class based on "MatrixClassAuthor" or "MatrixClassOrganized" (see Details). Defaults to "MatrixClassAuthor".

Details

The vector 'MatrixClassOrganized' reflects standardized stage classes ('prop', 'active', or 'dorm'), whereas 'MatrixClassAuthor' reflects a description of the stage classes as defined by the original author (e.g. c('Seedling', 'Medium rosette', 'Large (2 rosettes)', 'Flowering')).

Because the 'MatrixClassAuthor' definitions are less standardized, they are more prone to typos that could lead to slight differences between stage descriptions of matrices that really do have the same stage classes (e.g. a set of matrices from a single study/species/population). Therefore, using 'MatrixClassAuthor' to define stage classes is potentially prone to mistakenly 'splitting' identifiers that should really be the same.

'MatrixClassOrganized' has the opposite problem. It's possible for two matrices from a given study to have the same stage definitions based on 'MatrixClassOrganized', but legitimately differ in stage definitions as defined by the author. Therefore, using 'MatrixClassAuthor' to define stage classes is potentially prone to mistakenly 'lumping' identifiers that should actually differ.

Because the majority of studies in COM(P)ADRE use a single set of stage definitions for all matrices, and typos are rare, results for the different stage definitions will usually be similar. Note, however, that the actual integers returned for the different stage definitions are likely to be very different (because they are based on alphabetical order).

Value

Vector of integer identifiers corresponding to the rows of cdb.

Author(s)

Patrick Barks <[e-mail]>

See Also

cdb_id

Other data management: cdb_flatten(), cdb_id_studies(), cdb_id(), cdb_mean_matF(), cdb_rbind(), cdb_unflatten(), cdb_unnest(), mpm_elementwise_apply(), mpm_mean(), mpm_median(), mpm_sd(), string_representation

Examples

cdb_id_stages(Compadre, stage_def = "MatrixClassOrganized")

jonesor/Rcompadre documentation built on Jan. 16, 2024, 12:48 a.m.