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. |