Package: banocc 1.31.0
George Weingart
banocc: Bayesian ANalysis Of Compositional Covariance
BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.
Authors:
banocc_1.31.0.tar.gz
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banocc.pdf |banocc.html✨
banocc/json (API)
| # Install 'banocc' in R: |
| install.packages('banocc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- compositions_hard_null - Simulated compositional data with no feature correlations
- compositions_neg_spike - Simulated compositional data with a negative count correlation
- compositions_null - Simulated compositional data with no feature correlations
- compositions_pos_spike - Simulated compositional data with a positive count correlation
- counts_hard_null - Simulated count data with no feature correlations
- counts_neg_spike - Simulated count data with one negative feature correlation
- counts_null - Simulated count data with no feature correlations
- counts_pos_spike - Simulated count data with one positive feature correlation
On BioConductor:banocc-1.29.0(bioc 3.20)banocc-1.28.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologymetagenomicssoftwarebayesian
Last updated 23 days agofrom:eef3ada16f. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:banocc_modelget_banocc_outputrun_banocc
Dependencies:abindbackportsBHcallrcheckmateclicodacolorspacedescdistributionalfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellmvtnormnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanscalesStanHeadersstringistringrtensorAtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| banocc: A package for Bayesian ANalysis of Compositional Correlation | banocc-package banocc |
| The stan model used in the Bayesian fit | banocc_model |
| Simulated compositional data with no feature correlations | compositions_hard_null |
| Simulated compositional data with a negative count correlation | compositions_neg_spike |
| Simulated compositional data with no feature correlations | compositions_null |
| Simulated compositional data with a positive count correlation | compositions_pos_spike |
| Simulated count data with no feature correlations | counts_hard_null |
| Simulated count data with one negative feature correlation | counts_neg_spike |
| Simulated count data with no feature correlations | counts_null |
| Simulated count data with one positive feature correlation | counts_pos_spike |
| Takes a model fit from BAnOCC, evaluates convergence and generates appropriate convergence metrics and inference | get_banocc_output |
| Runs BAnOCC to fit the model and generate appropriate convergence metrics and inference. | run_banocc |
