ComMA-package: ComMA R documentation

In walterxie/ComMA: Community Matrix Analysis

Description

This package is a collection of tools for community matrix analyse, especially for eDNA data, but it also can be used for traditional species survey data. The package not only wraps bioinformatic, ecological methods and figure plotting into one-line functions, but also create utility functions to procced data easily. All functions are available by typing help(package="ComMA") in R.

Details

Community matrix in ComMA is a community data from file as a matrix, where rows are OTUs (therefore this matrix is called OTU table) or individual species and columns are sites or samples. Matrix elements are abundance data or proportion (e.g. counts, percentage). For example,

OTU_id	plot01	plot02	...
OTU_1	1	0	...
OTU_2	100	200	...
OTU_3	56	3	...

Variable t.community.matrix is a transposed matrix from community matrix we defined here, where columns are OTUs or individual species and rows are sites or samples. It is also the abundances argument in vegetarian d.

The taxa.table is a data frame to contain taxonomic classifications of OTUs. Rows are OTUs or individual species, which have to be the subset of (or matching) rows in the community matrix from getCommunityMatrix). Columns are taxonomy at the rank, such as c("superkingdom", "kingdom", "phylum", "class", "order", "family", "genus", "species"), or full taxonomic lineage but it is optional. If it is from RDP, then column "confidence" is required. For example,

OTU_id	kingdom	phylum	...
OTU_1	Bacteria	Firmicutes	...
OTU_2	Bacteria	Proteobacteria	...
OTU_3	Not assigned	Not assigned	...

The enviornmental data env is also called as the meta data of samples, where rows are sites or samples, and columns are the measurement, such as elevation, tempurature, soil chemistry, forest type, etc. For example,

Plot	Elevation(m)	pH	...
plot01	50	5.89	...
plot02	90	5.12	...
plot03	160	5.46	...

The phyloTree is a rooted tree of phylo object, which is created from ape read.tree.

Source

https://github.com/walterxie/ComMA

Install all depdent packages: installAllPackages

walterxie/ComMA documentation built on May 3, 2019, 11:51 p.m.