pldist_all: pldist_all
In aplantin/pldist: Paired and Longitudinal Ecological Dissimilarities

Function that calculates multiple paired and longitudinal ecological distance/dissimilarity matrices. Includes qualitative and quantitative versions of Bray-Curtis, Jaccard, Kulczynski, Gower, and unweighted and generalized UniFrac distances/dissimilarities. UniFrac-based metrics are based in part on GUniFrac (Jun Chen & Hongzhe Li (2012)). Both quantitative and qualitative versions of each requested metric are returned.

pldist_all(
  otus,
  metadata,
  paired = FALSE,
  clr = FALSE,
  pseudoct = NULL,
  method = c("b", "g", "j", "k", "u"),
  tree = NULL,
  gam = c(0, 0.5, 1),
  norm = FALSE
)

`otus`	OTU count or frequency table, containing one row per sample and one column per OTU.
`metadata`	Data frame with three columns: subject identifiers (n unique values, column name "subjID"), sample identifiers (must match row names of otu.tab, column name "sampID"), and time point or group identifier (if using longitudinal distances, this must be numeric or convertable to numeric).
`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.
`clr`	Logical indicating whether to use CLR-transformed abundances (TRUE) or original proportions (FALSE) in quantitative distances/dissimilarities. Default FALSE.
`pseudoct`	Pseudocount value to be added to each cell of the matrix prior to CLR transformation. Default is NULL; if NULL, 0.5 will be added if data are counts, min(1e-06, 0.5*min(nonzero p)) will be added if data are proportions, and nothing will be added if no cells have zero values.
`method`	Desired distance metric(s). Include a vector with any combination of braycurtis, jaccard, kulczynski, gower, and unifrac, or any unambiguous abbreviation thereof.
`tree`	Rooted phylogenetic tree of R class "phylo". Default NULL; only needed for UniFrac family distances.
`gam`	Parameter controlling weight on abundant lineages for UniFrac family distances. The same weight is used within a subject as between subjects. Default (0, 0.5, 1); only needed for UniFrac family distances.
`norm`	Indicator of whether to normalize the difference to average taxon abundance or not (default FALSE)

Returns a list containing all n x n distance (or dissimilarity) matrices requested, with both quantitative and qualitative versions of the metric, named as "D_metric_quant" or "D_metric_qual".

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