submatrix: Extract a submatrix for a given taxomic group and/or sampling...

In DeadCanMove: Assess How Spatial Roadkill Patterns Change with Temporal Sampling Scheme

Description

Given a baseline dataset, this function extracts a sub-dataset for a given taxomic group and/or sampling scheme, defined either by a sampling interval (periodicity) or by a window size (consecutive sampling days each time) and a gap size (gaps between sampling windows).

Usage

submatrix(dataset, sampl.columns, sampl.interval = NULL, 
window.size = NULL, gap.size = NULL, start.column = 1, 
group.column = NULL, group.names = NULL, remove.zeros = TRUE, 
keep.nonsampl.columns = TRUE)

Arguments

dataset	name of the matrix or dataframe to analyze
sampl.columns	index numbers of the (consecutive) columns containing the baseline (daily) sampling data, e.g. 3:180
sampl.interval	interval at which to extract sampling data, e.g. 5 (to take one every five samples)
window.size	instead of sampl.interval (for one sampling every so many time units), size (in sampling time units, e.g. days) of each sampling window (e.g. 3 for 3 consecutive days sampling each time); must be complemented with gap.size, for the gap between sampling windows.
gap.size	size (in sampling time units, e.g. days) of the gaps between sampling windows – e.g. 1 for 1 gap (non-sampled) day between sampling windows.
start.column	column of sampl.columns where to actually start the sampling (e.g. with a gap size of 1 between sampling windows, the start column can be either 1 or 2)
group.column	name or index number of the column containing the taxa or groups to analyse, e.g. 3 or "Family"
group.names	name(s) of the group(a) to extract, e.g. c("Mustelidae", "Procyonidae"); if NULL (the default), all groups in group.names are extracted
remove.zeros	logical indicating whether to remove rows where all extracted days have zero observations
keep.nonsampl.columns	logical indicating whether to keep the non-sampling columns in the extracted result

Value

This function returns a subset of dataset containing the taxonomic groups and sampling columns resulting from the given sampling scheme.

Author(s)

A. Marcia Barbosa, J. Tiago Marques

See Also

sequential.submatrix, subset

Examples

data(roadkills)

submat1 <- submatrix(dataset = roadkills, sampl.columns = 4:ncol(roadkills),
sampl.interval = 3, start.column = 1, group.column = "taxon", group.names = NULL)

head(submat1)

submat2 <- submatrix(dataset = roadkills, sampl.columns = 4:ncol(roadkills),
window.size = 5, gap.size = 2, start.column = 1, group.column = "taxon",
group.names = NULL)

head(submat2)

DeadCanMove documentation built on May 2, 2019, 6:48 p.m.