Function reference • Rcompadre

Data acquisition Functions for acquiring data from COMPADRE/COMADRE.
`cdb_build_cdb()`	Create a CompadreDB object from user-specified data
`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
`mpm_has_prop()` `mpm_has_active()` `mpm_has_dorm()` `mpm_first_active()`	Extract stage-class information from CompadreMat or CompadreDB objects
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_elementwise_apply()`	Apply a function element-wise to a list of matrices
`mat_mean()` `mpm_mean()`	Calculate a mean over a list of matrices or CompadreMat objects
`mat_median()` `mpm_median()`	Calculate a median over a list of matrices or CompadreMat objects
`mat_sd()` `mpm_sd()`	Calculate a standard deviation over a list of matrices or CompadreMat 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_build_cdb()`	Create a CompadreDB object from user-specified 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_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_elementwise_apply()`	Apply a function element-wise to a list of matrices
`mat_mean()` `mpm_mean()`	Calculate a mean over a list of matrices or CompadreMat objects
`mat_median()` `mpm_median()`	Calculate a median 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_sd()` `mpm_sd()`	Calculate a standard deviation over a list of matrices or CompadreMat objects
`mat_to_string()` `vec_to_string()` `string_to_mat()` `string_to_vec()`	Convert vectors or square numeric matrices to and from string representation

Reference

Data acquisition

Data checking

Data management

All functions