calcSizeComps: Create "size" compositions from a dataframe with count data
In wStockhausen/wtsSizeComps: Various functions for dealing with size compositions

calcSizeComps

R Documentation

Create "size" compositions from a dataframe with count data

Description

Function to create a dataframe of "size" compositions from a dataframe with count data.

Usage

calcSizeComps(
  dfrZ,
  id.size = "size",
  id.value = "abundance",
  id.facs = "",
  cutpts = NULL,
  truncate.low = FALSE,
  truncate.high = FALSE,
  expandToAllFactorCombos = FALSE,
  normalize = FALSE,
  id.normfacs = "",
  rescale = FALSE,
  dfrScalars = NULL,
  id.scalevalue,
  id.scalefacs = id.normfacs,
  verbose = FALSE
)

Arguments

`dfrZ`	- input dataframe with count/abundance data by size and other factors
`id.size`	- name of column in dfr with "size" data
`id.value`	- name of column in dfrZ with count (or abundance) values
`id.facs`	- character vector of column names to use as factors in calculating size compositions
`cutpts`	- cut points for size bins
`truncate.low`	-flag to truncate counts/abundance below the minimum size or include in first size bin (FALSE)
`truncate.high`	- flag to truncate counts/abundance above the maximum size (TRUE) or include in final size bin (FALSE)
`expandToAllFactorCombos`	- flag (T/F) to expand size comps to include all factor combinations
`normalize`	- flag (T/F) to normalize size comps (i.e., sum to 1 acorss normalizing factors)
`id.normfacs`	- character vector of column names of factors to normalize the size compositions across when scaling to total abundance
`rescale`	- flag to rescale size compositions by factor combination using scalars in dfrA
`dfrScalars`	- [optional] input dataframe with scalars to apply by a subset of the factors in dfr
`id.scalevalue`	- column name for scale value in dfrA
`id.scalefacs`	- character vector of column names of factors in dfrA to scale the size compositions across
`verbose`	- flag to print diagnostic output to console

Details

Non-standard column names should be back-quoted. The names of columns (id.normfacs) used to normalize the composition data in dfrZ prior to expanding to total abundance using dfrScalars should represent the same factors (id.scalefacs) and levels in both datasets.