Microbial Community Ecology Data Analysis

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Documentation for package ‘microeco’ version 0.2.1

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clone Copy an R6 class object completely
clr_matrix Centered log ratio tranformation for the matrix
cor2cov Convert a symmetric correlation matrix to a covariance matrix given the standard deviation
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 The fungi function database in the microeco package
ko_map The KEGG pathway annotation database 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 The prokaryotic function database in the microeco package
pval.sparccboot SparCC p-vals
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
sparcc sparcc wrapper
sparccboot Bootstrap SparCC
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_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.