Package: ncmR 0.3.1

ncmR: Fit Neutral Community Model to Microbiome or Ecological Data

Provides tools for fitting the neutral community model (NCM) to assess the role of stochastic processes in community assembly. The package implements the framework of Sloan et al. (2006) <doi:10.1111/j.1462-2920.2005.00956.x>, enabling users to evaluate neutral dynamics in ecological and microbial communities.

Authors:Yuxuan He [aut, cre, cph]

ncmR_0.3.1.tar.gz
ncmR_0.3.1.zip(r-4.7)ncmR_0.3.1.zip(r-4.6)ncmR_0.3.1.zip(r-4.5)
ncmR_0.3.1.tgz(r-4.6-any)ncmR_0.3.1.tgz(r-4.5-any)
ncmR_0.3.1.tar.gz(r-4.7-any)ncmR_0.3.1.tar.gz(r-4.6-any)
ncmR_0.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ncmR/json (API)

# Install 'ncmR' in R:

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

Bug tracker:https://github.com/h-xuanjiu/ncmr/issues

Datasets:

example_data - Example OTU table and grouping information for NCM demonstration

On CRAN:

3.48 score 1 stars 1 scripts 473 downloads 3 exports 87 dependencies

Last updated from:53fad71efd. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	141
source / vignettes	OK	191
linux-release-x86_64	OK	142
macos-release-arm64	OK	81
macos-oldrel-arm64	OK	92
windows-devel	OK	137
windows-release	OK	102
windows-oldrel	OK	122
wasm-release	OK	122

Exports:fit_ncm run_app scatter_plot

Dependencies:backports base64enc bslib cachem checkmate cli cluster colorspace colourpicker commonmark cpp11 crosstalk curl data.table digest dplyr DT evaluate farver fastmap fontawesome foreign Formula fs generics ggplot2 ggtext glue gridExtra gridtext gtable highr Hmisc htmlTable htmltools htmlwidgets httpuv isoband jpeg jquerylib jsonlite knitr labeling later lazyeval lifecycle litedown magrittr markdown memoise mime miniUI minpack.lm nnet otel pillar pkgconfig png promises R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rpart rstudioapi S7 sass scales shiny shinyjs sourcetools stringi stringr tibble tidyselect tinytex utf8 vctrs viridisLite withr xfun xml2 xtable yaml zip

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Example OTU table and grouping information for NCM demonstration	example_data
Fit Neutral Community Model (NCM) with optional grouping and total pooling	fit_ncm
Print summary of NCM model	print.summary_ncm
Print summary of NCM group results	print.summary_ncm_group
Launch the ncmR Shiny Application	run_app
Scatter plot for NCM results and data frames	scatter_plot scatter_plot.data.frame scatter_plot.default scatter_plot.NCM
Summary method for NCM objects	summary.NCM
Summary method for NCM group results	summary.NCM_group