CompadreLegacy: Subsample of a legacy version of the COMPADRE Plant Matrix...

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

Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples

Description

CompadreLegacy is a subsample of the COMPADRE Plant Matrix Database in the legacy format (class 'list'), for use in testing and examples. For full documentation see the COMPADRE User Guide.

Usage

CompadreLegacy

Format

A list with four elements:

metadata - A data frame with the following 47 columns:

• SpeciesAuthor - Binomial species name given by the paper's author

• SpeciesAccepted - Accepted binomial species name taken from The Plant List or Catalogue of Life

• CommonName - Common name for species used in the publication

• Genus - Taxonomic genus that the accepted species belongs to

• Family - Family that the species belongs to

• Order - Order that the species belongs to

• Class - Class that the species belongs to

• Phylum - Phylum that the species belongs to

• Kingdom - Kingdom that the species belongs to

• OrganismType - Organism type (see COMPADRE User Guide for documentation)

• DicotMonoc - Whether the species is a dicot or monocot. Non-angiosperms are NA.

• AngioGymno - Whether the species is an angiosperm or gymnosperm. Non-plants are NA.

• Authors - Last name of all authors (separated with ";")

• Journal - Abbreviated journal title, or type of source document (e.g. "PhD thesis")

• YearPublication - Year of publication

• DOI.ISBN - Digital Object Identifier or International Standard Book Number codes to identify each publication (note that the name has changed to DOI_ISBN in later database versions.)

• AdditionalSource - Additional source(s) used to reconstruct the matrix or obtain additional metadata for the matrix (if applicable)

• StudyDuration - Number of years of observation in study (StudyEnd - StudyStart)

• StudyStart - Study start year

• StudyEnd - Study end year

• AnnualPeriodicity - Inverse of the length of the projection interval (in years). Note that the name has changed to ProjectionInterval in later database versions.

• NumberPopulations - The number of study populations as defined by the authors. Within site replication of permanent plots is not defined as separate populations

• MatrixCriteriaSize - Indicates whether the matrix contains stages based on size. If so, indicates what that measure of size is

• MatrixCriteriaOntogeny - Indicates whether the matrix contains stages based on ontogenic/developmental stages

• MatrixCriteriaAge - Indicates whether the matrix contains stages based on age

• MatrixPopulation - Population name or definition of where the matrix was recorded, usually given by the author. See COMPADRE User Guide.

• Lat - Latitude in decimal degrees

• Lon - Longitude in decimal degrees

• Altitude - Altitude of study site (m above sea level)

• Country - 3-letter ISO country code for the country in which the study took place (multiple countries separated with ";")

• Continent - Continent on which study took place

• Ecoregion - Ecoregion in which study took place. See COMPADRE User Guide.

• StudiedSex - Whether study included only males ("M"), only females ("F"), or both sexes ("M/F")

• MatrixComposite - Indicates the type of matrix population model. Possible values are Individual, Mean, Pooled, and Seasonal. See COMPADRE User Guide.

• MatrixTreatment - Describes if a treatment was applied to the population or not. If yes, includes a brief description of the treatment. If not, Unmanipulated

• MatrixCaptivity - Whether species was studied in the wild (W), captivity (C), or captured from a wild population (CW)

• MatrixStartYear - First year of matrix

• MatrixStartSeason - First season of matrix as described by author (hemisphere-specific)

• MatrixStartMonth - First month of matrix

• MatrixEndYear - Final year of matrix

• MatrixEndSeason - Final season of matrix as described by author (hemisphere-specific)

• MatrixEndMonth - Final month of matrix

• MatrixSplit - Whether the A matrix has been split into components U, F, and C ("Divided") or not ("Indivisible"). If not, elements of matU, matF, and matC are filled with NA

• MatrixFec - Whether fecundity was measured for the matrix model

• Observation - Additional observations recorded by database compilers

• MatrixDimension - Dimension of the A matrix

• SurvivalIssue - Denotes the maximum stage-specific survival value

mat - A list of population projection models, which are also in list format. Each list element contains four matrices:

• matA - A matrix population model

• matU - The survival- and growth-related component of matA

• matF - The sexual reproduction component of matA

• matC - The clonal reproduction component of matA

matrixClass - A list of data frames, each with the following columns:

• MatrixClassOrganized - Standardized stage class of the matrix population model

• MatrixClassAuthor - Stage description from the original publication

• MatrixClassNumber - Integer stage number

version - A list with the following elements:

• Version - The version number of the database

• DateCreated - The date that the .RData file was created

• NumberAcceptedSpecies - The number of accepted species in the original version

• NumberStudies - The number of studies in the original version

• NumberMatrices - The number of matrices in the original version

• Agreement - Link to the COMADRE license agreement

Rcompadre documentation built on Oct. 17, 2024, 1:07 a.m.