neutral.rand: Fit Sloan et al. (2006) Neutral Model several times

In Russel88/MicEco: Various functions for microbial community data

Fit Sloan et al. (2006) Neutral Model several times

Description

Fit neutral model developed by Sloan et al. (2006, Environ Microbiol 8(4):732-740) and implemented by Burns et al. (2015, ISME J 10(3):655-664) several times on ramdomly picked samples and with 16S rRNA gene copy number corrected rarefaction.

Usage

neutral.rand(
  data,
  n = NULL,
  s = NULL,
  rRNA = NULL,
  rn = NULL,
  cores = 1,
  naming = NULL
)

Arguments

data	A phyloseq object
n	Integer. Number of times to repeat analysis
s	Integer. Number of random samples to for each repetition.
rRNA	What Greengenes database version was used to find OTUs. Atm only "v13.5" is available. Alternatively, A dataframe with two variables: "ID" is the OTU id matched by names in x and "Copy" is the copy number.
rn	Integer. Number of reads to sample for rarefaction
cores	Integer. Number of cores to use for parallel computing.
naming	Optional. A list for naming the output e.g. list(Time="1 Week",Type="Gut")

Value

A list of length two; first element contains fit statistics, the second element contains predictions.

Russel88/MicEco documentation built on Nov. 24, 2022, 2:33 a.m.