Package: microeco 1.10.1

microeco: Microbial Community Ecology Data Analysis

A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.

Authors:Chi Liu [aut, cre], Felipe R. P. Mansoldo [ctb], Minjie Yao [ctb], Xiangzhen Li [ctb]

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microeco.pdf |microeco.html✨
microeco/json (API)

# Install 'microeco' in R:

install.packages('microeco', repos = c('https://chiliubio.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/chiliubio/microeco/issues

Datasets:

Tax4Fun2_KEGG - The KEGG data files used in the trans_func class
dataset - The dataset structured with microtable class for the demonstration of examples
env_data_16S - The environmental factors for the 16S example data
fungi_func_FUNGuild - The FUNGuild database for fungi trait prediction
fungi_func_FungalTraits - The FungalTraits database for fungi trait prediction
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
taxonomy_table_16S - The taxonomic information of 16S example data
taxonomy_table_ITS - The taxonomic information of ITS example data

On CRAN:

9.86 score 204 stars 3 packages 160 scripts 3.3k downloads 1 mentions 15 exports 44 dependencies

Last updated 4 days agofrom:85f2e9f4c9. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 14 2024
R-4.5-win	NOTE	Nov 14 2024
R-4.5-linux	NOTE	Nov 14 2024
R-4.4-win	NOTE	Nov 14 2024
R-4.4-mac	NOTE	Nov 14 2024
R-4.3-win	NOTE	Nov 14 2024
R-4.3-mac	NOTE	Nov 14 2024

Exports:clone dropallfactors microtable tidy_taxonomy trans_abund trans_alpha trans_beta trans_classifier trans_diff trans_env trans_func trans_network trans_norm trans_nullmodel trans_venn

Dependencies:ape cli cluster colorspace cpp11 data.table digest dplyr fansi farver generics ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme permute pillar pkgconfig plyr R6 RColorBrewer Rcpp reshape2 rlang scales stringi stringr tibble tidyselect utf8 vctrs vegan viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

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