Package: FuncDiv 1.0.0

FuncDiv: Compute Contributional Diversity Metrics

Compute alpha and beta contributional diversity metrics, which is intended for linking taxonomic and functional microbiome data. See 'GitHub' repository for the tutorial: <https://github.com/gavinmdouglas/FuncDiv/wiki>. Citation: Gavin M. Douglas, Sunu Kim, Morgan G. I. Langille, B. Jesse Shapiro (2023) <doi:10.1093/bioinformatics/btac809>.

Authors:Gavin Douglas [aut, cre]

FuncDiv_1.0.0.tar.gz
FuncDiv_1.0.0.zip(r-4.7-x86_64)FuncDiv_1.0.0.zip(r-4.7-arm64)FuncDiv_1.0.0.zip(r-4.6-x86_64)FuncDiv_1.0.0.zip(r-4.6-arm64)FuncDiv_1.0.0.zip(r-4.5-x86_64)
FuncDiv_1.0.0.tgz(r-4.6-x86_64)FuncDiv_1.0.0.tgz(r-4.6-arm64)FuncDiv_1.0.0.tgz(r-4.5-x86_64)FuncDiv_1.0.0.tgz(r-4.5-arm64)
FuncDiv_1.0.0.tar.gz(r-4.6-arm64)FuncDiv_1.0.0.tar.gz(r-4.7-arm64)FuncDiv_1.0.0.tar.gz(r-4.6-x86_64)FuncDiv_1.0.0.tar.gz(r-4.7-x86_64)
FuncDiv_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
FuncDiv/json (API)

# Install 'FuncDiv' in R:

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

Bug tracker:https://github.com/gavinmdouglas/funcdiv/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.74 score 11 stars 6 scripts 292 downloads 8 exports 11 dependencies

Last updated from:8601891ecc. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	180
linux-devel-x86_64	OK	205
source / vignettes	OK	181
linux-release-arm64	OK	184
linux-release-x86_64	OK	209
macos-release-arm64	OK	196
macos-release-x86_64	OK	330
macos-oldrel-arm64	OK	244
macos-oldrel-x86_64	OK	553
windows-devel-arm64	OK	459
windows-devel-x86_64	OK	255
windows-release-arm64	OK	451
windows-release-x86_64	OK	234
windows-oldrel-x86_64	OK	254
wasm-release	OK	94

Exports:alpha_div_contrib beta_div_contrib compute_alpha_div contrib_to_multitab func_abun_crossproduct FuncDiv_alpha_metrics multitab_to_contrib subset_func_and_abun_tables

Dependencies:ape collapse data.table digest lattice nlme parallelDist Rcpp RcppArmadillo RcppParallel RcppXPtrUtils

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Main function for computing contributional alpha diversity	alpha_div_contrib
Main function for computing contributional beta diversity	beta_div_contrib
Convenience function for running default alpha diversity metrics on a single vector input	compute_alpha_div
Utility function to convert from contributional to multi-table input objects	contrib_to_multitab
Utility function to get community-wide function abundance table	func_abun_crossproduct
List object containing the functions to compute the default alpha diversity metrics	FuncDiv_alpha_metrics
Utility function to convert from multi-table objects to contributional table	multitab_to_contrib
Utility function to subset function copy number and taxonomic abundance tables	subset_func_and_abun_tables