Package index • 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() mpm_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() mpm_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