DOC: A wrapper to run the whole DOC analysis

In Russel88/DOC: DOC analysis of microbial communities

A wrapper to run the whole DOC analysis

Description

A wrapper to run the whole DOC analysis

Usage

DOC(otu, R = 100, subr = NULL, pair = NULL, mov.avg = 5,
  ci = c(0.025, 0.5, 0.975), span = 0.2, degree = 1,
  family = "symmetric", iterations = 4, surface = "interpolate",
  cores = 1)

Arguments

otu	An OTU-table (taxa as rows)
R	Number of bootstraps
subr	If NULL will do bootstrap, alternatively an integer denoting size of subsample
pair	A vector of length two with names of pairs mathcing colnames in otu
mov.avg	Moving average window to use for estimating where negative slope starts
ci	Vector with quantiles for confidence intervals
span	Span of loess smoothing
degree	Degree of loess smoothing (If 1 linear, >1 polynomial)
family	"gaussian" is least-squares fitting, "symmetric" is robust fitting
iterations	Number of iterations for robust fitting
surface	"direct" estimation (slow exact) or "interpolate" estimation (fast approximate)
cores	Number of cores to use

Value

Output: A list with class DOC:

• DO: A dataframe with Overlap and Dissimilarity (rJSD)

• LME: A dataframe with estimates of negative slope

• LOWESS: A dataframe with loess(lowess) results of non-bootstraped data

• NEG: A dataframe with Overlap values where negative slope starts

• FNS: A dataframe with Fns values

• BOOT: A dataframe with loess results for each bootstrap

• CI: A dataframe with quantiles for the BOOT dataframe

Russel88/DOC documentation built on Nov. 14, 2022, 3:50 p.m.