R/roleData-rawStats.R

In role-model/roleR: Rules of Life Engine

#' @title Get raw data from `roleData` objects.
#' @description Gets raw data according to the function specification.
#' @param x A `roleData` object.
#' @param ... Additional parameters, ignored.
#' 
#' @return A list with one element. Inside that one element is a vector of the
#'     raw data.
#' 
#' @details These functions return a list of length one (with summary statistics as a vector
#'     inside that list) because the summary statistics themselves can be variable
#'     length. This is distinct from other summary statistic functions which will
#'     always return a fixed length value.  When using raw summary statistic
#'     functions in `getSumStats` they will be returned in a list-column.
#'     rawAbundance gets the unordered abundance of species, 
#'     while rawSpAbundance gets the ordered abundance of species which is a much longer vector
#' 
#' @rdname raw-sumStats
#' @export

# abundance of each 
setGeneric('rawAbundance', 
           def = function(x, ...) standardGeneric('rawAbundance'), 
           signature = 'x')



#' rawAbundance on roleData
#' @name rawAbundance
#' @aliases rawAbundance,roleData-method
#' @docType methods
#' @rdname raw-sumStats

setMethod('rawAbundance', 
          signature = 'roleData', 
          definition = function(x) {
              list(tabulate(x@localComm@indSpecies))
          }
)

#' abundance
#' @rdname rawSpAbundance
#' @param x x
#' @param ... ignored
#' @export
setGeneric('rawSpAbundance', 
           def = function(x, ...) standardGeneric('rawSpAbundance'), 
           signature = 'x')



#' abundance on roleData
#' @name rawSpAbundance
#' @aliases rawSpAbundance,roleData-method
#' @docType methods
#' @rdname rawSpAbundance
setMethod('rawSpAbundance', 
          signature = 'roleData', 
          definition = function(x) {
              list(tabulate(x@localComm@spAbund))
          }
)

# spp IDs
#' @rdname raw-sumStats
#' @export

setGeneric('rawSppID', 
           def = function(x, ...) standardGeneric('rawSppID'), 
           signature = 'x')



#' spp IDs on roleData
#' @name rawSppID
#' @aliases rawSppID,roleData-method
#' @docType methods
#' @rdname raw-sumStats
setMethod('rawSppID', 
          signature = 'roleData', 
          definition = function(x) {
              list(x@localComm@indSpecies) #list(x@localComm@indSppTrt[, 1])
          }
)

# traits
#' @rdname raw-sumStats
#' @export

setGeneric('rawTraits', 
           def = function(x, ...) standardGeneric('rawTraits'), 
           signature = 'x')


#' raw traits on roleData
#' @name rawTraits
#' @aliases rawTraits,roleData-method
#' @docType methods
#' @rdname raw-sumStats
setMethod('rawTraits', 
          signature = 'roleData', 
          definition = function(x) {
              list(x@localComm@indTrait)
          }
)


# gen div
#' @rdname raw-sumStats
#' @export

setGeneric('rawGenDiv', 
           def = function(x, ...) standardGeneric('rawGenDiv'), 
           signature = 'x')



#' raw gen div on roleData
#' @name rawGenDiv
#' @aliases rawGenDiv,roleData-method
#' @docType methods
#' @rdname raw-sumStats
setMethod('rawGenDiv', 
          signature = 'roleData', 
          definition = function(x) {
              list(x@localComm@spGenDiv)  #list(x@localComm@sppGenDiv[, 1])
          }
)



# gen seqs
#' @rdname raw-sumStats
#' @export

setGeneric('rawSeqs', 
           def = function(x, ...) standardGeneric('rawSeqs'), 
           signature = 'x')


#' raw seqs on roleData
#' @name rawSeqs
#' @aliases rawSeqs,roleData-method
#' @docType methods
#' @rdname raw-sumStats
setMethod('rawSeqs', 
          signature = 'roleData', 
          definition = function(x) {
              list(x@localComm@indSeqs)
          }
)


# branch lengths
#' @rdname raw-sumStats
#' @export

setGeneric('rawBranchLengths', 
           def = function(x, ...) standardGeneric('rawBranchLengths'), 
           signature = 'x')


#' raw branch lengths on roleData
#' @name rawBranchLengths
#' @aliases rawBranchLengths,roleData-method
#' @docType methods
#' @rdname raw-sumStats
setMethod('rawBranchLengths', 
          signature = 'roleData', 
          definition = function(x) {
              list(x@phylo@l[x@phylo@e[, 1] != -1])
          }
)


# ape phylo
#' @rdname raw-sumStats
#' @export

setGeneric('rawApePhylo', 
           def = function(x, ...) standardGeneric('rawApePhylo'), 
           signature = 'x')


#' raw ape phylo  on roleData
#' @name rawApePhylo
#' @aliases rawApePhylo,roleData-method
#' @docType methods
#' @rdname raw-sumStats
setMethod('rawApePhylo', 
          signature = 'roleData', 
          definition = function(x) {
              list(as(x@phylo, 'phylo'))
          }
)