Package: Rcompadre 1.4.0.9000

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

Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.

Authors:Patrick Barks [aut], Danny Buss [aut], Roberto Salguero-Gomez [aut], Iain Stott [aut], William K. Petry [aut], Tamora James [aut], Owen Jones [aut, cre], Julia Jones [aut], Gesa Römer [aut], Sam Levin [aut]

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Rcompadre.pdf |Rcompadre.html✨
Rcompadre/json (API)
NEWS

# Install 'Rcompadre' in R:
install.packages('Rcompadre', repos = c('https://jonesor.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jonesor/rcompadre/issues

Datasets:
  • Comadre - Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples
  • Compadre - Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examples
  • CompadreLegacy - Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples

On CRAN:

8.00 score 11 stars 2 packages 51 scripts 560 downloads 47 exports 23 dependencies

Last updated 1 months agofrom:e741b33645. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winOKNov 15 2024
R-4.5-linuxOKNov 15 2024
R-4.4-winNOTENov 15 2024
R-4.4-macNOTENov 15 2024
R-4.3-winNOTENov 15 2024
R-4.3-macNOTENov 15 2024

Exports:as_cdbcdb_build_cdbcdb_check_speciescdb_collapsecdb_comparecdb_fetchcdb_flagcdb_flattencdb_idcdb_id_stagescdb_id_studiescdb_mean_matFcdb_metadatacdb_rbindcdb_unflattencdb_unnestCompadreDataDateCreatedmat_elementwise_applymat_meanmat_medianmat_sdmat_to_stringmatAmatCmatFmatrixClassMatrixClassAuthorMatrixClassNumberMatrixClassOrganizedmatUmpm_elementwise_applympm_first_activempm_has_activempm_has_dormmpm_has_propmpm_meanmpm_medianmpm_sdNumberAcceptedSpeciesNumberMatricesNumberStudiesstring_to_matstring_to_vecvec_to_stringVersionVersionData

Dependencies:clicodaexpmfansigluelatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackpillarpkgconfigpopdemoquantregrlangSparseMsurvivaltibbleutf8vctrs

Getting started with Rcompadre

Owen Jones

Rendered froma01_GettingStarted.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-10-16
Started: 2021-02-21

Obtaining references

Owen Jones

Rendered froma04_ObtainingReferences.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2023-09-02
Started: 2021-02-21

Using Rcompadre with the tidyverse

Patrick Barks & Owen Jones

Rendered froma02_RcompadreTidy.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-10-16
Started: 2021-02-21

Using your own matrix data

Owen Jones

Rendered froma05_UsingYourOwnData.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-10-15
Started: 2021-06-20

Vectorising with Rcompadre

Patrick Barks

Rendered froma03_VectorisingRcompadre.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2024-10-15
Started: 2021-03-13

Readme and manuals

Help Manual

Help pageTopics
Convert legacy COM(P)ADRE database object to CompadreDBas_cdb
Create a CompadreDB object from user-specified datacdb_build_cdb
Check whether a COM(P)ADRE database contains one or more species of interestcdb_check_species
Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variablescdb_collapse
Compare two versions or subsets of a COM(P)ADRE databasecdb_compare
Fetch the COM(P)ADRE database from compadre-db.org or a local filecdb_fetch
Flag potential issues in matrices of a COM(P)ADRE databasecdb_flag
Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representationcdb_flatten
Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columnscdb_id
Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of species and matrix stage class definitionscdb_id_stages
Create a vector of unique study identifiers from a COM(P)ADRE databasecdb_id_studies
Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE databasecdb_mean_matF
Extract metadata from a COM(P)ADRE databasecdb_metadata
Merge two COM(P)ADRE databases via row-bindcdb_rbind
Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB objectcdb_unflatten
Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columnscdb_unnest
Subsamples of the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database for testing and examplesComadre Compadre
CompadreDB Class$,CompadreDB-method $<-,CompadreDB-method CompadreData CompadreData,CompadreDB-method CompadreDB DateCreated DateCreated,CompadreDB-method Version Version,CompadreDB-method VersionData VersionData,CompadreDB-method [[,CompadreDB,ANY,missing-method [[<-,CompadreDB,ANY,missing-method
Methods for CompadreDB objectsas.data.frame.CompadreDB as_tibble.CompadreDB CompadreDB-Methods dim.CompadreDB head.CompadreDB merge.CompadreDB names.CompadreDB NumberAcceptedSpecies NumberAcceptedSpecies,CompadreDB-method NumberMatrices NumberMatrices,CompadreDB-method NumberStudies NumberStudies,CompadreDB-method tail.CompadreDB
Subsetting CompadreDB objectsCompadreDB-Subsetting subset.CompadreDB [,CompadreDB,ANY,ANY,ANY-method
Tidyverse methods for CompadreDB objectsarrange.CompadreDB CompadreDB-Tidyverse filter.CompadreDB fortify.CompadreDB full_join.CompadreDB group_by.CompadreDB inner_join.CompadreDB left_join.CompadreDB mutate.CompadreDB rename.CompadreDB right_join.CompadreDB select.CompadreDB slice.CompadreDB summarise.CompadreDB summarize.CompadreDB ungroup.CompadreDB
Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examplesCompadreLegacy
Methods for working with matrices in com(p)adreCompadreMatrixMethods matA matA,CompadreDB-method matA,CompadreMat-method matA,list-method matC matC,CompadreDB-method matC,CompadreMat-method matC,list-method matF matF,CompadreDB-method matF,CompadreMat-method matF,list-method matrixClass matrixClass,CompadreDB-method matrixClass,CompadreMat-method matrixClass,list-method MatrixClassAuthor MatrixClassAuthor,CompadreDB-method MatrixClassAuthor,CompadreMat-method MatrixClassAuthor,list-method MatrixClassNumber MatrixClassNumber,CompadreDB-method MatrixClassNumber,CompadreMat-method MatrixClassNumber,list-method MatrixClassOrganized MatrixClassOrganized,CompadreDB-method MatrixClassOrganized,CompadreMat-method MatrixClassOrganized,list-method matU matU,CompadreDB-method matU,CompadreMat-method matU,list-method
Apply a function element-wise to a list of matricesmat_elementwise_apply mpm_elementwise_apply
Calculate a mean over a list of matrices or CompadreMat objectsmat_mean mpm_mean
Calculate a median over a list of matrices or CompadreMat objectsmat_median mpm_median
Extract stage-class information from CompadreMat or CompadreDB objectsmpm_first_active mpm_first_active,CompadreDB-method mpm_first_active,CompadreMat-method mpm_has_active mpm_has_active,CompadreDB-method mpm_has_active,CompadreMat-method mpm_has_dorm mpm_has_dorm,CompadreDB-method mpm_has_dorm,CompadreMat-method mpm_has_prop mpm_has_prop,CompadreDB-method mpm_has_prop,CompadreMat-method mpm_methods
Calculate a standard deviation over a list of matrices or CompadreMat objectsmat_sd mpm_sd
Convert vectors or square numeric matrices to and from string representationmat_to_string string_representation string_to_mat string_to_vec vec_to_string