pltransform: pltransform

In aplantin/pldist: Paired and Longitudinal Ecological Dissimilarities

Description

OTU transformation for paired and longitudinal data. Computes average within-subject change (in presence for qualitative metrics, proportional or CLR-transformed abundance for quantitative metrics) during one unit of time for each taxon.

Usage

pltransform(otu.data, paired, norm = TRUE)

Arguments

otu.data	OTU data after pre-processing using data_prep() function. List with elements otu.props, otu.clr, and metadata.
paired	Logical indicating whether to use the paired version of the metric (TRUE) or the longitudinal version (FALSE). Paired analyis is only possible when there are exactly 2 unique time points/identifiers for each subject or pair.
norm	Logical indicating whether quantitative differences should be normalized by taxon abundance (default TRUE)

Value

List with the following elements. Data matrices have subject identifiers as row names and OTU identifiers as column names.

dat.binary	n x p matrix of data after binary/qualitative transformation
dat.quant.prop	n x p matrix of data after quantitative transformation applied to proportions
dat.quant.prop	n x p matrix of data after quantitative transformation applied to CLR-transformed proportions
avg.prop	n x p matrix with overall average proportion of each taxon
type	Type of transformation that was used (paired, balanced longitudinal, unbalanced longitudinal) with a warning if unbalanced longitudinal.

Examples

data("paired.otus")
data("paired.meta")
 # paired transformation
otudat <- data_prep(paired.otus, paired.meta, paired = TRUE) 
res1 <- pltransform(otudat, paired = TRUE, norm = TRUE) 
 # longitudinal transformation 
otudat <- data_prep(paired.otus, paired.meta, paired = FALSE)
res2 <- pltransform(otudat, paired = FALSE, norm = TRUE) 
    

aplantin/pldist documentation built on Feb. 26, 2021, 2:19 p.m.