microeco

The KEGG data files used in the cal_tax4fun2 function of trans_func class.

Copy an R6 class object completely

A color palette for 20 elements.

The dataset in the microeco package

Remove all factors in a data frame

The environmental factors for the 16S dataset in the microeco package

The FUNGuild database for fungi trait identification in the microeco package

The FungalTraits database for fungi trait identification in the microeco package

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

The OTU table of the 16S dataset in the microeco package

The OTU table of the ITS dataset in the microeco package

The phylogenetic tree of 16S dataset in the microeco package

The modified FAPROTAX trait database in the microeco package

The modified NJC19 database in the microeco package

The fasta file of 16S dataset used in tax4fun2 method.

The sample information of 16S dataset in the microeco package

The sample information of ITS dataset in the microeco package

The taxonomic information of 16S dataset in the microeco package

The taxonomic information of ITS dataset in the microeco package

Clean up the taxonomic table to make taxonomic assignments consistent.

Create trans_abund object to transform taxonomic abundance for plotting.

Create trans_alpha object for alpha diveristy statistics and plotting.

Create trans_beta object for the analysis of distance matrix of beta-diversity.

Create trans_classifier object for machine-learning-based model prediction.

Create trans_diff object for the differential analysis on the taxonomic abundance.

Create trans_env object for the analysis of the effects of environmental factors on communities.

Create trans_func object for functional analysis.

Create trans_network object for co-occurrence network analysis.

Create trans_nullmodel object for phylogeny- and taxonomy-based null model analysis.

Create trans_venn object.