CNVRG v0.1
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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>).
Readme
CNVRG
**Beta release This is the first release of this software. Please let us know if you find any errors.
A package to provide a user-friendly wrapper for 'RStan' to implement Dirichlet-multinomial modeling of relative abundance count data. For vignette information see below.
A github repo for this package exists at: https://github.com/JHarrisonEcoEvo/CNVRG Please check that repo out for new versions of this software that are under development. Also, if you discover issues or have questions please post them there so that others may benefit from answers.
To install from source. Download repo and unzip it then use the following command from within the 'R' interpreter. Change the path to the 'CNVRG' directory as appropriate.
install.packages("./CNVRG/", repos = NULL, type = "source")
VIGNETTE
Please view the pdf vignette available at the repo linked above.
Functions in CNVRG
| Name | Description | |
| isd_transform | @encoding UTF-8 Transform data into estimates of absolute abundances using an ISD | |
| varInf | @encoding UTF-8 Perform variational inference sampling | |
| CNVRG-package | The 'CNVRG' package. | |
| varHMC | @encoding UTF-8 Perform Hamiltonian Monte Carlo sampling | |
| extract_point_estimate | @encoding UTF-8 Extract point estimates of pi parameters | |
| diff_abund | @encoding UTF-8 | |
| fungi | Fungal endophytes of Astragalus lentiginosus grown near Reno, NV | |
| diversity_calc | @encoding UTF-8 Calculate diversity entropies for each replicate | |
| No Results! | ||
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Details
| License | GPL-3 |
| Encoding | UTF-8 |
| LazyData | true |
| RoxygenNote | 7.1.1 |
| Biarch | true |
| LinkingTo | BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) |
| SystemRequirements | GNU make |
| Repository | CRAN |
| NeedsCompilation | yes |
| Packaged | 2020-09-08 18:54:42 UTC; joshuaharrison |
| Date/Publication | 2020-09-16 09:40:06 UTC |
| linkingto | BH (>= 1.66.0) , RcppEigen (>= 0.3.3.3.0) , RcppParallel (>= 5.0.1) , StanHeaders (>= 2.18.0) |
| imports | methods , Rcpp (>= 0.12.0) , rstan (>= 2.18.1) , vegan |
| depends | R (>= 3.4.0) |
| Contributors | Vivaswat Shastry, W. John Calder, C. Alex Buerkle |
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