timeDecay: Plot the time decay.

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Plot the time decay.

Description

Plot time elapsed against the community dissimilarity for all possible pairs of time points.

Usage

timeDecay(x, time = c(1:ncol(x)), dissim = "bray", normtaxa = FALSE,
  logdissim = FALSE, logtime = FALSE, header = "", units = "",
  plot = TRUE)

Arguments

x	a taxon matrix with rows representing taxa and columns samples
time	vector with time steps
dissim	sample dissimilarity to use, should be supported by vegdist
normtaxa	divide each taxon vector in x by its sum
logdissim	take the logarithm of the dissimilarity before fitting a line
logtime	take the logarithm of the time interval before fitting a line
header	a string to be appended to the plot title (Time decay)
units	a string to describe the units of the time points (days, weeks etc)
plot	whether to do the plot

Value

a list with the time intervals, dissimilarity values, intersection, slope, p-value, adjusted R2, dissimilarity measure used and log status of dissimilarity measure

Examples

data("david_stoolA_otus")
data=rarefyFilter(david_stoolA_otus,min=10000)[[1]]
out.decay=timeDecay(data[,1:50], header="Stool subject A")

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.