Compadre: Subsamples of the COMPADRE Plant Matrix Database and COMADRE...

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

Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples

Description

Compadre (plant matrices) and Comadre (animal matrices) are subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database, respectively, that are used for testing and examples. Each object is of class 'CompadreDB' and therefore has the following two slots: data and version.

For full documentation see the COMPADRE User Guide.

Usage

Compadre

Comadre

Format

Slot data - A tibble-style data frame with the following 48 columns:

• mat - A list of 'CompadreMat' objects, each with the following slots:

  • 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 data frame with the following columns:

    • MatrixClassOrganized - Standardized stage class of the matrix population model

    • MatrixClassAuthor - Stage description from the original publication

    • MatrixClassNumber - Integer stage number

• 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

• 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)

• 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
  

Slot version - A list with the following elements:

• Version - The version number of the database

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

• Agreement - Link to the COMADRE license agreement

An object of class CompadreDB with 150 rows and 49 columns.

An object of class CompadreDB with 150 rows and 49 columns.

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