Package: corncob 0.4.1

Amy D Willis

corncob: Count Regression for Correlated Observations with the Beta-Binomial

Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.

Authors:Bryan D Martin [aut], Daniela Witten [aut], Sarah Teichman [ctb], Amy D Willis [aut, cre], Thomas W Yee [ctb], Xiangjie Xue [ctb]

corncob_0.4.1.tar.gz
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corncob.pdf |corncob.html✨
corncob/json (API)

# Install 'corncob' in R:
install.packages('corncob', repos = c('https://statdivlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/statdivlab/corncob/issues

Datasets:

On CRAN:

28 exports 102 stars 4.60 score 50 dependencies 1 dependents 4 mentions 222 scripts 563 downloads

Last updated 14 days agofrom:a0309c5f1e. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 04 2024
R-4.5-winNOTESep 04 2024
R-4.5-linuxNOTESep 04 2024
R-4.4-winOKSep 04 2024
R-4.4-macOKSep 04 2024
R-4.3-winOKSep 04 2024
R-4.3-macOKSep 04 2024

Exports:%>%bbdmlcheckNestedclean_taxa_namescontrastsTestconvert_phylocothdifferentialTestfishZgenInitsHDIbetabinomhessianinvfishZinvlogitlogitlrtestotu_to_taxonomypbLRTpbRaopbWaldqbetabinomraotestsand_vcovsandSEscorewaldchisqwaldtwarn_phyloseq

Dependencies:backportscallrcheckmateclicolorspacedescdetectseparationdplyrfansifarverfsgenericsggplot2gluegtableisobandlabelinglatticelifecyclelpSolveAPImagrittrMASSMatrixmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigpkgloadprocessxpsR6RColorBrewerregistryrlangROIROI.plugin.lpsolverprojrootscalesslamtibbletidyselecttrustutf8vctrsVGAMviridisLitewithr

Introduction to corncob

Bryan D Martin

Rendered fromcorncob-intro.Rmdusingknitr::rmarkdownon Sep 04 2024.

Last update: 2024-09-04
Started: 2018-05-11

Introduction to corncob, no phyloseq

Bryan D Martin

Rendered fromcorncob-intro-no-phyloseq.Rmdusingknitr::rmarkdownon Sep 04 2024.

Last update: 2024-09-04
Started: 2024-01-10

Readme and manuals

Help Manual

Help pageTopics
Corncob package documentation.corncob-package corncob
Maximum Likelihood for the Beta-binomial Distributionbbdml
Check for nested modelscheckNested
Rename taxaclean_taxa_names
Identify differentially-abundant and differentially-variable taxa using contrastscontrastsTest
Function to subset and convert phyloseq dataconvert_phylo
Hyperbolic cotangent transformationcoth
Betabinomial densitydbetabin
Negative betabinomial densitydbetabin_neg
Densities of beta binomial distributions, permitting non integer x and sizedbetabinom_cts
Identify differentially-abundant and differentially-variable taxadifferentialTest
Function to run a bootstrap iterationdoBoot
Fisher's z transformationfishZ
Generate initialization for optimizationgenInits
Get index of restricted terms for Wald testgetRestrictionTerms
Parameter Gradient Vectorgr_full
Get highest density interval of beta-binomialHDIbetabinom
Compute Hessian matrix at the MLEhessian
IBD data, OTU count data frame.ibd_phylo_otu
IBD data, sample data frame.ibd_phylo_sample
IBD data, taxonomy data frame.ibd_phylo_taxa
Inverse Fisher's z transformationinvfishZ
Inverse logit transformationinvlogit
Logit transformationlogit
Likelihood ratio testlrtest
Objective functionobjfun
Transform OTUs to their taxonomic labelotu_to_taxonomy
Parametric bootstrap likelihood ratio testpbLRT
Parametric bootstrap Rao testpbRao
Parametric bootstrap Wald testpbWald
Plotting functionplot.bbdml
differentialTest plot functionplot.differentialTest
Print functionprint.bbdml
differentialTest print functionprint.differentialTest
Print summary functionprint.summary.bbdml
Get quantiles of beta binomqbetabinom
Rao-type chi-squared test (model-based or robust)raotest
Compute sandwich estimate of variance-covariance matrixsand_vcov
Compute sandwich standard errors. Legacy function. Use sand_vcov instead.sandSE
Compute score at the MLEscore
Simulate from beta-binomial modelsimulate.bbdml
Soil data, otu table as data frame.soil_phylo_otu
Soil data, sample data.soil_phylo_sample
Soil data, taxa table as data frame.soil_phylo_taxa
Small soil phylum data for contrasts examples, otu table as data framesoil_phylum_contrasts_otu
Small soil phylum data for contrasts examples, sample data as data framesoil_phylum_contrasts_sample
Small soil phylum data for examples, otu table as data framesoil_phylum_small_otu
Small soil phylum data for examples, sample data as data frame combined with counts for OTU 1 and sequencing depth.soil_phylum_small_otu1
Small soil phylum data for examples, sample data as data framesoil_phylum_small_sample
Summary functionsummary.bbdml
Wald-type chi-squared testwaldchisq
Wald-type chi-squared test statistic (model-based or robust)waldchisq_test
Wald-type t test (model-based or robust)waldt
Function to throw error if the `phyloseq` package is called but it is not installedwarn_phyloseq