sequential.submatrix: Extract subsampling matrices for a series of subsampling...

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

Description

This function applies submatrix sequencially to all specified sampling schemes and taxonomic groups.

Usage

sequential.submatrix(dataset, sampl.columns, sampl.intervals = NULL,
window.sizes = NULL, gap.sizes = NULL, start.columns = 1, 
all.combinations = TRUE, group.column = NULL, 
include.all.together = TRUE, remove.zeros = TRUE,
keep.nonsampl.columns = TRUE, n.subsampl.columns = NULL)

Arguments

dataset	name of the matrix or dataframe to analyze
sampl.columns	numbers of the consecutive columns with the (daily) sampling data, e.g. 4:180
sampl.intervals	a vector of the intervals at which to extract sampling data, e.g. 5 to take one every five samples
window.sizes	the size (in sampling time units, e.g. days) of the sampling periods
gap.sizes	the size of the gaps between sampling periods
start.columns	vector of start columns, see submatrix
all.combinations	logical, whether to use all window x gap size combinations (the default, TRUE) or just the number corresponding to the length of window.sizes and gap sizes (in which case window.sizes and gap.sizes must have the same length)
group.column	name or index number of the column containing the taxa or groups to analyse separately, e.g. 3 or "Family"; if NULL, all records will be used together
include.all.together	logical, whether to get subsampling matrices also for the complete data (including all groups together)
remove.zeros	logical, whether to remove rows where all extracted samples have zero observations
keep.nonsampl.columns	logical, whether to include also the non-sampling columns of dataset in the resulting submatrices)
n.subsampl.columns	number of subsampl.columns

Value

A list of submatrices

Author(s)

A. Marcia Barbosa

See Also

submatrix, subset

Examples

data(roadkills)

submats1 <- sequential.submatrix(dataset = roadkills, 
sampl.columns = 4:ncol(roadkills), sampl.intervals = c(1, 3), 
group.column = "taxon", include.all.together = TRUE,
remove.zeros = TRUE, keep.nonsampl.columns = TRUE, 
n.subsampl.columns = 85)

names(submats1)
head(submats1[[1]])

submats2 <- sequential.submatrix(dataset = roadkills, 
sampl.columns = 4:ncol(roadkills), window.sizes = c(1,3,5), 
gap.sizes = 1:3, start.columns = 1, all.combinations = TRUE,
group.column = "taxon", include.all.together = TRUE, 
remove.zeros = TRUE, keep.nonsampl.columns = TRUE, 
n.subsampl.columns = 85)

names(submats2)
head(submats2[[1]])

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