Package: nbfar 0.1
Aditya Mishra
nbfar: Negative Binomial Factor Regression Models ('nbfar')
We developed a negative binomial factor regression model to estimate structured (sparse) associations between a feature matrix X and overdispersed count data Y. With 'nbfar', microbiome count data Y can be used, for example, to associate host or environmental covariates with microbial abundances. Currently, two models are available: a) Negative Binomial reduced rank regression (NB-RRR), b) Negative Binomial co-sparse factor regression (NB-FAR). Please refer the manuscript 'Mishra, A. K., & Müller, C. L. (2021). Negative Binomial factor regression with application to microbiome data analysis. bioRxiv.' for more details.
Authors:
nbfar_0.1.tar.gz
nbfar_0.1.zip(r-4.5)nbfar_0.1.zip(r-4.4)nbfar_0.1.zip(r-4.3)
nbfar_0.1.tgz(r-4.4-x86_64)nbfar_0.1.tgz(r-4.4-arm64)nbfar_0.1.tgz(r-4.3-x86_64)nbfar_0.1.tgz(r-4.3-arm64)
nbfar_0.1.tar.gz(r-4.5-noble)nbfar_0.1.tar.gz(r-4.4-noble)
nbfar_0.1.tgz(r-4.4-emscripten)nbfar_0.1.tgz(r-4.3-emscripten)
nbfar.pdf |nbfar.html✨
nbfar/json (API)
| # Install 'nbfar' in R: |
| install.packages('nbfar', repos = c('https://amishra-stats.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/amishra-stats/nbfar/issues
- simulate_nbfar - Simulated data for NBFAR
Last updated 2 years agofrom:b16afe6180. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 31 2024 |
| R-4.5-win-x86_64 | NOTE | Aug 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Aug 31 2024 |
| R-4.4-win-x86_64 | NOTE | Aug 31 2024 |
| R-4.4-mac-x86_64 | NOTE | Aug 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Aug 31 2024 |
| R-4.3-win-x86_64 | NOTE | Aug 31 2024 |
| R-4.3-mac-x86_64 | NOTE | Aug 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Aug 31 2024 |
Exports:nbfarnbfar_controlnbfar_simnbrrr
Dependencies:bstclicodetoolscolorspacedoParallelfansifarverforeachgbmggplot2glmnetgluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmpathmunsellnlmenumDerivpillarpkgconfigpsclR6RColorBrewerRcppRcppArmadilloRcppEigenRcppParallelrlangrpartrrpackscalesshapesurvivaltibbleutf8vctrsviridisLiteWeightSVMwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Negative binomial co-sparse factor regression (NBFAR) | nbfar |
| Control parameters for NBFAR and NBRRR | nbfar_control |
| Simulated data for testing NBFAR and NBRRR model | nbfar_sim |
| Negative binomial reduced rank regression (NBRRR) | nbrrr |
| Suitably generates offset matrix for the multivariate regression problem | offset_sacling |
| Simulated data for NBFAR | simulate_nbfar |