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

Source: R/data.R
CompadreLegacy.Rd

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