# Microbial Community Ecology Data Analysis

## Documentation for package ‘microeco’ version 2.3.0

- DESCRIPTION file.

## Help Pages

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 data.
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 | Customized FAPROTAX trait database
prok_func_NJC19_list | The NJC19 database
sample_info_16S | The sample information of 16S example data
sample_info_ITS | The sample information of ITS example data
soil_metab | Microtable object of non-targeted metabolome data from bulk soil and maize rhizosphere soil in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).
soil_microb | Microtable object of prokaryotic sequencing data from soil and maize in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).
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_metab | Create 'trans_metab' object for metabolite analysis.
trans_network | Create 'trans_network' object for network analysis.
trans_niche | Create 'trans_niche' object for niche breadth and niche overlap analysis.
trans_norm | Feature abundance normalization/transformation.
trans_nullmodel | Create 'trans_nullmodel' object for null model related analysis.
trans_phylo | trans_phylo class
trans_venn | Create 'trans_venn' object for the Venn diagram, petal plot and UpSet plot.