Package: breakaway 4.8.4

breakaway: Species Richness Estimation and Modeling
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis. 'breakaway' is the premier package for statistical analysis of microbial diversity. 'breakaway' implements the latest and greatest estimates of species richness, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arxiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.
Authors:
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breakaway.pdf |breakaway.html✨
breakaway/json (API)
# Install 'breakaway' in R: |
install.packages('breakaway', repos = c('https://adw96.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/adw96/breakaway/issues
Pkgdown site:https://adw96.github.io
- apples - (Data) Frequency count table of soil microbes in an apples orchard.
- hawaii - (Data) Frequency count table of soil microbes in Hawaii.
- pasolli_et_al - (Data) Data frame of covariate information about pasolli_et_al.
- soil_phylo - (Data) Data frame of soil data from whitman_et_al.
- toy_metadata - (Data) Data frame of covariate information about toy_otu_table.
- toy_otu_table - (Data) A toy OTU table.
- toy_taxonomy - (Data) The taxonomy of the OTUs in 'toy_otu_table'.
Last updated 1 years agofrom:6d3c912963. Checks:8 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Feb 23 2025 |
R-4.5-win | OK | Feb 23 2025 |
R-4.5-mac | OK | Feb 23 2025 |
R-4.5-linux | OK | Feb 23 2025 |
R-4.4-win | OK | Feb 23 2025 |
R-4.4-mac | OK | Feb 23 2025 |
R-4.3-win | OK | Feb 23 2025 |
R-4.3-mac | OK | Feb 23 2025 |
Exports:%>%alpha_estimatealpha_estimatesbettabetta_lincombetta_picbetta_randombreakawaybreakaway_nof1build_frequency_count_tableschao_bungechao_shenchao1chao1_bcconvertF_testgood_turingkempmake_design_matrixmake_frequency_count_tableobjective_bayes_geometricobjective_bayes_mixedgeoobjective_bayes_negbinobjective_bayes_poissonpoisson_modelpoisson_model_nof1proportions_insteadrnbinomtablerztnbinomtablesample_inverse_simpsonsample_richnesssample_shannonsample_shannon_esample_simpsonsample_size_estimatesample_size_figuretest_submodeltrue_ginitrue_hilltrue_inverse_simpsontrue_shannontrue_shannon_etrue_simpsonwlrm_transformedwlrm_untransformed
Dependencies:ade4apeaskpassBiobaseBiocGenericsbiomformatBiostringsbootcliclustercodetoolscolorspacecpp11crayoncurldata.tabledigestfansifarverforeachgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehttrigraphIRangesisobanditeratorsjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixmgcvmimeminqamulttestmunsellnlmenloptropensslpermutephyloseqpillarpixmappkgconfigplyrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreshape2rhdf5rhdf5filtersRhdf5librlangS4VectorsscalesspstringistringrsurvivalsystibbleUCSC.utilsutf8vctrsveganviridisLitewithrXVector
Getting started with breakaway
Rendered frombreakaway.Rmd
usingknitr::rmarkdown
on Feb 23 2025.Last update: 2022-10-04
Started: 2017-09-21
Introduction to diversity estimation
Rendered fromintro-diversity-estimation.Rmd
usingknitr::rmarkdown
on Feb 23 2025.Last update: 2022-11-22
Started: 2019-07-31
Introduction to hypothesis testing for diversity
Rendered fromdiversity-hypothesis-testing.Rmd
usingknitr::rmarkdown
on Feb 23 2025.Last update: 2022-11-22
Started: 2019-08-15