# Microbial Community Ecology Data Analysis

## Documentation for package ‘microeco’ version 0.7.1

- DESCRIPTION file.

## Help Pages

clone | Copy an R6 class object completely
color_palette_20 | A color palette for 20 elements.
dataset | The dataset in the microeco package
dropallfactors | Remove all factors in a data frame
env_data_16S | The environmental factors for the 16S dataset in the microeco package
fungi_func_FungalTraits | The FungalTraits database for fungi trait identification in the microeco package
fungi_func_FUNGuild | The FUNGuild database for fungi trait identification in the microeco package
microtable | Create microtable object to store and manage all the basic files.
otu_table_16S | The OTU table of the 16S dataset in the microeco package
otu_table_ITS | The OTU table of the ITS dataset in the microeco package
phylo_tree_16S | The phylogenetic tree of 16S dataset in the microeco package
prok_func_FAPROTAX | The modified FAPROTAX trait database in the microeco package
prok_func_NJC19_list | The modified NJC19 database in the microeco package
rep_fasta_16S | The fasta file of 16S dataset used in tax4fun2 method.
sample_info_16S | The sample information of 16S dataset in the microeco package
sample_info_ITS | The sample information of ITS dataset in the microeco package
Tax4Fun2_KEGG | The KEGG data files used in the cal_tax4fun2 function of trans_func class.
taxonomy_table_16S | The taxonomic information of 16S dataset in the microeco package
taxonomy_table_ITS | The taxonomic information of ITS dataset in the microeco package
tidy_taxonomy | Clear up the taxonomic table to make taxonomic assignments consistent.
trans_abund | Create trans_abund object to transform taxonomic abundance for plotting.
trans_alpha | Create trans_alpha object for alpha diveristy statistics and plotting.
trans_beta | Create trans_beta object for the analysis of distance matrix of beta-diversity.
trans_classifier | Create trans_classifier object for machine-learning-based model prediction.
trans_diff | Create trans_diff object for the differential analysis on the taxonomic abundance.
trans_env | Create trans_env object for the analysis of the effects of environmental factors on communities.
trans_func | Create trans_func object for functional analysis.
trans_network | Create trans_network object for co-occurrence network analysis.
trans_nullmodel | Create trans_nullmodel object.
trans_venn | Create trans_venn object.