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microeco (version 1.16.0)

Microbial Community Ecology Data Analysis

Description

A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.

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Install

install.packages('microeco')

Monthly Downloads

4,486

Version

1.16.0

License

GPL-3

Issues

27

Pull Requests

0

Stars

253

Forks

74

Maintainer

Chi Liu

Last Published

October 31st, 2025

Functions in microeco (1.16.0)

microeco

Introduction to microeco package (https://github.com/ChiLiubio/microeco)
clone

Copy an R6 class object
fungi_func_FUNGuild

The FUNGuild database for fungi trait prediction
dropallfactors

Remove all factors in a data frame
microtable

Create microtable object to store and manage all the basic files.
dataset

The dataset structured with microtable class for the demonstration of examples
fungi_func_FungalTraits

The FungalTraits database for fungi trait prediction
env_data_16S

The environmental factors for the 16S example data
otu_table_16S

The OTU table of the 16S example data
Tax4Fun2_KEGG

The KEGG data files used in the trans_func class
prok_func_FAPROTAX

Customized FAPROTAX trait database
tidy_taxonomy

Clean up the taxonomic table to make taxonomic assignments consistent.
trans_abund

Create trans_abund object for taxonomic abundance visualization.
taxonomy_table_ITS

The taxonomic information of ITS example data
sample_info_ITS

The sample information of ITS example data
otu_table_ITS

The OTU table of the ITS example data
phylo_tree_16S

The phylogenetic tree of 16S example data
sample_info_16S

The sample information of 16S example data
taxonomy_table_16S

The taxonomic information of 16S example data
prok_func_NJC19_list

The NJC19 database