Package: CNVRG 1.0.0
CNVRG: Dirichlet-Multinomial Modelling of Relative Abundance Data
Implements Dirichlet multinomial modelling of relative abundance data using functionality provided by the 'Stan' software. The purpose of this package is to provide a user friendly way to interface with 'Stan' that is suitable for those new to modelling. For more regarding the modelling mathematics and computational techniques we use see our publication in Molecular Ecology Resources titled "Dirichlet multinomial modelling outperforms alternatives for analysis of ecological count data" (Harrison et al. 2020 <doi:10.1111/1755-0998.13128>).
Authors:
CNVRG_1.0.0.tar.gz
CNVRG_1.0.0.zip(r-4.5)CNVRG_1.0.0.zip(r-4.4)CNVRG_1.0.0.zip(r-4.3)
CNVRG_1.0.0.tgz(r-4.4-x86_64)CNVRG_1.0.0.tgz(r-4.4-arm64)CNVRG_1.0.0.tgz(r-4.3-x86_64)CNVRG_1.0.0.tgz(r-4.3-arm64)
CNVRG_1.0.0.tar.gz(r-4.5-noble)CNVRG_1.0.0.tar.gz(r-4.4-noble)
CNVRG.pdf |CNVRG.html✨
CNVRG/json (API)
| # Install 'CNVRG' in R: |
| install.packages('CNVRG', repos = c('https://jharrisonecoevo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jharrisonecoevo/cnvrg/issues
- fungi - Fungal endophytes of Astragalus lentiginosus grown near Reno, NV
Last updated 3 years agofrom:ba34997803. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win-x86_64 | WARNING | Sep 13 2024 |
| R-4.5-linux-x86_64 | WARNING | Sep 13 2024 |
| R-4.4-win-x86_64 | WARNING | Sep 13 2024 |
| R-4.4-mac-x86_64 | WARNING | Sep 13 2024 |
| R-4.4-mac-aarch64 | WARNING | Sep 13 2024 |
| R-4.3-win-x86_64 | WARNING | Sep 13 2024 |
| R-4.3-mac-x86_64 | WARNING | Sep 13 2024 |
| R-4.3-mac-aarch64 | WARNING | Sep 13 2024 |
Exports:cnvrg_HMCcnvrg_VIdiff_abunddiversity_calcextract_pi_quantilesextract_point_estimateindexerisd_transform
Dependencies:abindbackportsBHcallrcheckmatecliclustercolorspacedescdistributionalfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpermutepillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsveganviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'CNVRG' package. | CNVRG-package CNVRG |
| Perform Hamiltonian Monte Carlo sampling | cnvrg_HMC |
| Perform variational inference sampling | cnvrg_VI |
| Calculate features with different abundances between treatment groups | diff_abund |
| Calculate diversity entropies for each replicate | diversity_calc |
| Extract quantiles of pi parameters | extract_pi_quantiles |
| Extract point estimates of multinomial and Dirichlet parameters | extract_point_estimate |
| Fungal endophytes of Astragalus lentiginosus grown near Reno, NV | fungi |
| Determine indices for treatment groups | indexer |
| Transform data into estimates of absolute abundances using an ISD | isd_transform |
