Get summary statistics for RoLE objects.

Applies different summary statistics functions to `roleExperiment`, `roleModel`, or `roleData` objects.

Usage

getSumStats(x, funs = .getDefaultSumStatsFuns(), moreArgs, ...)

# S4 method for roleData
getSumStats(x, funs, moreArgs)

# S4 method for roleModel
getSumStats(x, funs, moreArgs)

# S4 method for roleExperiment
getSumStats(x, funs, moreArgs)

Arguments

x

The object to calculate summary statistics on.

funs

A named list of functions to calculate the summary statistics; can be a named list with a single function or many functions, but must be a named list of functions. If unspecified, defaults to including several standard stats. Included diversity index functions in roleR are: `hillAbund`, `hillGenetic`,`hillPhylo` & `richness`. Included raw stats functions are `rawAbundance`, `rawSpAbundance`,`rawSppId`,`rawTraits`,`rawGenDiv`,`rawSeqs`, `rawBranchLengths` & `rawApePhylo`.

moreArgs

An optional named list of additional arguments to pass to the functions listed in `funs`. If given, list names must match those in `funs`. Note: not all names in `funs` need to appear in `moreArgs`

...

ignored

Value

data.frame containing summary stats where each row is a model snapshot and each column is a summary stat requested by a function provided to `funs`

Details

Users can define their own functions, so long as they work on any object of class `roleData`.

Examples

# get the species richness 
# rich_stat <- getSumStats(model, funs = list(rich = richness))
# get many default summary stats
# stats <- getSumStats(model)