Package: meconetcomp 0.8.0

meconetcomp: Compare Microbial Networks of 'trans_network' Class of 'microeco' Package

Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>. This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.

Authors:Chi Liu [aut, cre], Minjie Yao [ctb], Xiangzhen Li [ctb]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
meconetcomp/json (API)

# Install 'meconetcomp' in R:

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

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

Datasets:

soil_amp - The soil_amp data
soil_amp_network - The soil_amp_network data
soil_measure_diversity - The soil_measure_diversity data
stool_met - The stool_met data

On CRAN:

4.72 score 12 stars 22 scripts 364 downloads 13 exports 87 dependencies

Last updated from:f52f5277de. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	211
source / vignettes	OK	281
linux-release-x86_64	ERROR	181
macos-release-arm64	ERROR	112
macos-oldrel-arm64	ERROR	129
windows-devel	ERROR	145
windows-release	ERROR	152
windows-oldrel	ERROR	148
wasm-release	OK	160

Exports:cal_module cal_network_attr cohesionclass edge_comp edge_node_distance edge_tax_comp get_edge_table get_node_table node_comp robustness subnet_property subset_network vulnerability

Dependencies:abind ape backports boot broom car carData cli cluster colorspace corrplot cowplot cpp11 data.table Deriv digest doBy dplyr farver forecast Formula fracdiff generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable igraph isoband labeling lattice lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels mgcv microbenchmark microeco minqa modelr nlme nloptr nnet numDeriv pbkrtest permute pillar pkgconfig plyr polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rstatix S7 scales SparseM stringi stringr survival tibble tidyr tidyselect timeDate urca utf8 vctrs vegan viridisLite withr zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assign modules to each network	cal_module
Calculate network topological property for each network	cal_network_attr
Calculate the cohesion of samples for each network	cohesion
Calculate the cohesion of samples for each network	cohesionclass
Generate a 'microtable' object with paired nodes distributions of edges across networks	edge_comp
Perform the distance distribution of paired nodes in edges across networks.	edge_node_distance
Taxonomic sum of linked nodes in edges across networks	edge_tax_comp
Get edge property table for each network	get_edge_table
Get node property table for each network	get_node_table
Introduction to meconetcomp package (https://github.com/ChiLiubio/meconetcomp)	meconetcomp
Generate a microtable object with node distributions across networks	node_comp
Calculate robustness across networks.	robustness
The soil_amp data	soil_amp
The soil_amp_network data	soil_amp_network
The soil_measure_diversity data	soil_measure_diversity
The stool_met data	stool_met
Calculate properties of sub-networks selected according to features in samples	subnet_property
Extract subset of network according to the edge intersection of networks	subset_network
Calculate the vulnerability of each node for each network	vulnerability