Data acquisition

Functions for acquiring data from COMPADRE/COMADRE.

cdb_fetch()

Fetch the COM(P)ADRE database from compadre-db.org or a local file

cdb_metadata()

Extract metadata from a COM(P)ADRE database

Data checking

Functions for checking data.

cdb_check_species()

Check whether a COM(P)ADRE database contains one or more species of interest

cdb_collapse()

Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variables

cdb_compare()

Compare two versions or subsets of a COM(P)ADRE database

cdb_flag()

Flag potential issues in matrices of a COM(P)ADRE database

Data management

Functions for manipulating and managing data.

cdb_flatten()

Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representation

cdb_id()

Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columns

cdb_id_stages()

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

cdb_id_studies()

Create a vector of unique study identifiers from a COM(P)ADRE database

cdb_mean_matF()

Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE database

cdb_rbind()

Merge two COM(P)ADRE databases via row-bind

cdb_unflatten()

Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB object

cdb_unnest()

Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columns

mat_mean() mpm_mean()

Calculate a mean over a list of matrices or CompadreMat objects

mpm_has_prop() mpm_has_active() mpm_has_dorm() mpm_first_active()

Extract stage-class information from CompadreMat or CompadreDB objects

mat_to_string() vec_to_string() string_to_mat() string_to_vec()

Convert vectors or square numeric matrices to and from string representation

All functions

All functions listed alphabetically.

Compadre Comadre

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

as.data.frame(<CompadreDB>) as_tibble(<CompadreDB>) head(<CompadreDB>) tail(<CompadreDB>) names(<CompadreDB>) dim(<CompadreDB>) merge(<CompadreDB>) NumberAcceptedSpecies() NumberStudies() NumberMatrices()

Methods for CompadreDB objects

`[`(<CompadreDB>,<ANY>,<ANY>,<ANY>) subset(<CompadreDB>)

Subsetting CompadreDB objects

fortify.CompadreDB() filter.CompadreDB() slice.CompadreDB() arrange.CompadreDB() mutate.CompadreDB() group_by.CompadreDB() ungroup.CompadreDB() summarize.CompadreDB() summarise.CompadreDB() select.CompadreDB() rename.CompadreDB() left_join.CompadreDB() right_join.CompadreDB() inner_join.CompadreDB() full_join.CompadreDB()

Tidyverse methods for CompadreDB objects

CompadreData() `$`(<CompadreDB>) `$<-`(<CompadreDB>) `[[`(<CompadreDB>,<ANY>,<missing>) `[[<-`(<CompadreDB>,<ANY>,<missing>) VersionData() Version() DateCreated()

CompadreDB Class

CompadreLegacy

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

matA() matU() matF() matC() matrixClass() MatrixClassAuthor() MatrixClassOrganized() MatrixClassNumber()

Methods for working with matrices in com(p)adre

as_cdb()

Convert legacy COM(P)ADRE database object to CompadreDB

cdb_check_species()

Check whether a COM(P)ADRE database contains one or more species of interest

cdb_collapse()

Collapse a COM(P)ADRE database by averaging matrices over levels of one or more grouping variables

cdb_compare()

Compare two versions or subsets of a COM(P)ADRE database

cdb_fetch()

Fetch the COM(P)ADRE database from compadre-db.org or a local file

cdb_flag()

Flag potential issues in matrices of a COM(P)ADRE database

cdb_flatten()

Convert a COM(P)ADRE database to a flat data frame with matrices and vectors stored in string representation

cdb_id()

Create integer identifiers for a COM(P)ADRE database corresponding to unique combinations of a given set of columns

cdb_id_stages()

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

cdb_id_studies()

Create a vector of unique study identifiers from a COM(P)ADRE database

cdb_mean_matF()

Calculate a population-specific mean fecundity matrix for each set of matrices in a COM(P)ADRE database

cdb_metadata()

Extract metadata from a COM(P)ADRE database

cdb_rbind()

Merge two COM(P)ADRE databases via row-bind

cdb_unflatten()

Reconstitute a flattened COM(P)ADRE database (created by cdb_flatten) as a CompadreDB object

cdb_unnest()

Unnest a COM(P)ADRE database by spreading the components of CompadreMat into separate list-columns

mat_mean() mpm_mean()

Calculate a mean over a list of matrices or CompadreMat objects

mpm_has_prop() mpm_has_active() mpm_has_dorm() mpm_first_active()

Extract stage-class information from CompadreMat or CompadreDB objects

mat_to_string() vec_to_string() string_to_mat() string_to_vec()

Convert vectors or square numeric matrices to and from string representation