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

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

## Documentation for package ‘Rcompadre’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D F G H I L M N R S T U V misc

## -- A --

arrange.CompadreDB | Tidyverse methods for CompadreDB objects
as.data.frame.CompadreDB | Methods for CompadreDB objects
as_cdb | Convert legacy COM(P)ADRE database object to CompadreDB
as_tibble.CompadreDB | Methods for CompadreDB objects

## -- C --

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
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
CompadreData | CompadreDB Class
CompadreData-method | CompadreDB Class
CompadreDB | CompadreDB Class
CompadreDB-Methods | Methods for CompadreDB objects
CompadreDB-Subsetting | Subsetting CompadreDB objects
CompadreDB-Tidyverse | Tidyverse methods for CompadreDB objects
CompadreLegacy | Subsample of a legacy version of the COMPADRE Plant Matrix Database for testing and examples
CompadreMatrixMethods | Methods for working with matrices in com(p)adre

## -- D --

DateCreated | CompadreDB Class
DateCreated-method | CompadreDB Class
dim.CompadreDB | Methods for CompadreDB objects

## -- F --

filter.CompadreDB | Tidyverse methods for CompadreDB objects
fortify.CompadreDB | Tidyverse methods for CompadreDB objects
full_join.CompadreDB | Tidyverse methods for CompadreDB objects

## -- G --

group_by.CompadreDB | Tidyverse methods for CompadreDB objects

## -- H --

head.CompadreDB | Methods for CompadreDB objects

## -- I --

inner_join.CompadreDB | Tidyverse methods for CompadreDB objects

## -- L --

left_join.CompadreDB | Tidyverse methods for CompadreDB objects

## -- M --

matA | Methods for working with matrices in com(p)adre
matA-method | Methods for working with matrices in com(p)adre
matC | Methods for working with matrices in com(p)adre
matC-method | Methods for working with matrices in com(p)adre
matF | Methods for working with matrices in com(p)adre
matF-method | Methods for working with matrices in com(p)adre
matrixClass | Methods for working with matrices in com(p)adre
matrixClass-method | Methods for working with matrices in com(p)adre
MatrixClassAuthor | Methods for working with matrices in com(p)adre
MatrixClassAuthor-method | Methods for working with matrices in com(p)adre
MatrixClassNumber | Methods for working with matrices in com(p)adre
MatrixClassNumber-method | Methods for working with matrices in com(p)adre
MatrixClassOrganized | Methods for working with matrices in com(p)adre
MatrixClassOrganized-method | Methods for working with matrices in com(p)adre
matU | Methods for working with matrices in com(p)adre
matU-method | Methods for working with matrices in com(p)adre
mat_mean | Calculate a mean over a list of matrices or CompadreMat objects
mat_median | Calculate a median over a list of matrices or CompadreMat objects
mat_sd | Calculate a standard deviation over a list of matrices or CompadreMat objects
mat_to_string | Convert vectors or square numeric matrices to and from string representation
merge.CompadreDB | Methods for CompadreDB objects
mpm_first_active | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_first_active-method | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_has_active | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_has_active-method | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_has_dorm | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_has_dorm-method | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_has_prop | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_has_prop-method | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_mean | Calculate a mean over a list of matrices or CompadreMat objects
mpm_median | Calculate a median over a list of matrices or CompadreMat objects
mpm_methods | Extract stage-class information from CompadreMat or CompadreDB objects
mpm_sd | Calculate a standard deviation over a list of matrices or CompadreMat objects
mutate.CompadreDB | Tidyverse methods for CompadreDB objects

## -- N --

names.CompadreDB | Methods for CompadreDB objects
NumberAcceptedSpecies | Methods for CompadreDB objects
NumberAcceptedSpecies-method | Methods for CompadreDB objects
NumberMatrices | Methods for CompadreDB objects
NumberMatrices-method | Methods for CompadreDB objects
NumberStudies | Methods for CompadreDB objects
NumberStudies-method | Methods for CompadreDB objects

## -- R --

rename.CompadreDB | Tidyverse methods for CompadreDB objects
right_join.CompadreDB | Tidyverse methods for CompadreDB objects

## -- S --

select.CompadreDB | Tidyverse methods for CompadreDB objects
slice.CompadreDB | Tidyverse methods for CompadreDB objects
string_representation | Convert vectors or square numeric matrices to and from string representation
string_to_mat | Convert vectors or square numeric matrices to and from string representation
string_to_vec | Convert vectors or square numeric matrices to and from string representation
subset.CompadreDB | Subsetting CompadreDB objects
summarise.CompadreDB | Tidyverse methods for CompadreDB objects
summarize.CompadreDB | Tidyverse methods for CompadreDB objects

## -- T --

tail.CompadreDB | Methods for CompadreDB objects

## -- U --

ungroup.CompadreDB | Tidyverse methods for CompadreDB objects

## -- V --

vec_to_string | Convert vectors or square numeric matrices to and from string representation
Version | CompadreDB Class
Version-method | CompadreDB Class
VersionData | CompadreDB Class
VersionData-method | CompadreDB Class

## -- misc --

$-method | CompadreDB Class
$<--method | CompadreDB Class
[-method | Subsetting CompadreDB objects
[[-method | CompadreDB Class
[[<--method | CompadreDB Class