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

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Documentation for package ‘Rcompadre’ version 1.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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