read_com: Community Data Input

In jgmv/comecol: Community Ecology Analysis

Community Data Input

Description

Reads community data from files.

Usage

read_com(
  cdm,
  env,
  tax,
  seq = NULL,
  phy = NULL,
  file = NULL,
  use_saved = F,
  ...
)

Arguments

cdm	the name of the file with the community data matrix. Rows are samples, and columns are species.
env	the name of the file with a table with environmental data. First column must include sample names as in rows of 'cdm'.
tax	the name of the file with a table with taxonomic information. First column must include species names as in columns of 'cdm'.
seq	the name of the file where sequences for each species in fasta format. Sequence headers must be the species names as in columns of 'cdm'.
phy	the name of the file with a phylogenetic tree in Newick format including the species in 'cdm'. Tip labels must be the species names as in columns of 'cdm'. If no tree is provided, a taxonomic tree can be automatically generated using the information in 'tax', using option 'tree_from_tax = T'.
file	the name of the file where the data will be stored as 'RData' object.
use_saved	read data from 'file' instead of importing them from scratch.
...	further arguments to be passed to 'read.table'.

Details

If no phylogenetic tree is provided, the calculation from the taxonomic data provided is performed using the perl script 'taxonomy_to_tree.pl' available at 'https://github.com/mr-y/my_bioinfPerls'.

Value

A list with community data.

Examples

read_com()

jgmv/comecol documentation built on June 6, 2023, 4:07 p.m.