Microbial Community Ecology Data Analysis

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Documentation for package ‘microeco’ version 1.15.0

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clone Copy an R6 class object
dataset The dataset structured with microtable class for the demonstration of examples
dropallfactors Remove all factors in a data frame
env_data_16S The environmental factors for the 16S example data
fungi_func_FungalTraits The FungalTraits database for fungi trait prediction
fungi_func_FUNGuild The FUNGuild database for fungi trait prediction
microeco Introduction to microeco package (https://github.com/ChiLiubio/microeco)
microtable Create 'microtable' object to store and manage all the basic files.
otu_table_16S The OTU table of the 16S example data
otu_table_ITS The OTU table of the ITS example data
phylo_tree_16S The phylogenetic tree of 16S example data
prok_func_FAPROTAX The modified FAPROTAX trait database
prok_func_NJC19_list The modified NJC19 database
sample_info_16S The sample information of 16S example data
sample_info_ITS The sample information of ITS example data
Tax4Fun2_KEGG The KEGG data files used in the trans_func class
taxonomy_table_16S The taxonomic information of 16S example data
taxonomy_table_ITS The taxonomic information of ITS example data
tidy_taxonomy Clean up the taxonomic table to make taxonomic assignments consistent.
trans_abund Create 'trans_abund' object for taxonomic abundance visualization.
trans_alpha Create 'trans_alpha' object for alpha diversity statistics and visualization.
trans_beta Create 'trans_beta' object for beta-diversity analysis
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 to analyze the association between environmental factor and microbial community.
trans_func Create 'trans_func' object for functional prediction.
trans_network Create 'trans_network' object for network analysis.
trans_norm Feature abundance normalization/transformation.
trans_nullmodel Create 'trans_nullmodel' object for null model related analysis.
trans_venn Create 'trans_venn' object for the Venn diagram, petal plot and UpSet plot.