Requirements | Load the study data from SOHPIE R package: | Example I: American Gut Project Data | Data processing for the toy example using sample dataset from American Gut Project: | Fit a pseudo-value regression via SOHPIE_DNA() function: | Additional features available in SOHPIE package: | Example II: Diet Exchange Study Data | References
Package: SOHPIE 1.0.6
Seungjun Ahn
SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation
'SOHPIE' (pronounced as SOFIE) is a novel pseudo-value regression approach for differential co-abundance network analysis of microbiome data, which can include additional clinical covariate in the model. The full methodological details can be found in Ahn S and Datta S (2023) <arxiv:2303.13702v1>.
Authors:
SOHPIE_1.0.6.tar.gz
SOHPIE_1.0.6.tar.gz(r-4.7-any)SOHPIE_1.0.6.tar.gz(r-4.6-any)
SOHPIE_1.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SOHPIE/json (API)
| # Install 'SOHPIE' in R: |
| install.packages('SOHPIE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- combinedamgut - A Subdata from the American Gut Project study data
- combineddietswap - A Subdata from the Diet Swap study data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:25799e5401. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 154 | ||
| source / vignettes | OK | 207 | ||
| linux-release-x86_64 | OK | 177 | ||
| wasm-release | OK | 111 |
Exports:asso_matcoeffcoeff_specific_varDCtaxa_tabpseudoregpseudoreg.summarypvalpval_specific_varqvalqval_specific_varSOHPIE_DNAstderrsstderrs_specific_varthetahatsthetatildefun
Dependencies:cliDEoptimRdplyrfdrtoolgenericsgluegtoolslifecyclemagrittrpillarpkgconfigR6rlangrobustbasetibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| asso_mat | asso_mat |
| coeff | coeff |
| coeff_specific_var | coeff_specific_var |
| A Subdata from the American Gut Project study data | combinedamgut |
| A Subdata from the Diet Swap study data | combineddietswap |
| DCtaxa_tab | DCtaxa_tab |
| pseudoreg | pseudoreg |
| pseudoreg.summary() | pseudoreg.summary |
| pval | pval |
| pval_specific_var | pval_specific_var |
| qval | qval |
| qval_specific_var | qval_specific_var |
| SOHPIE_DNA | SOHPIE_DNA |
| sparcc wrapper | sparcc |
| stderrs | stderrs |
| stderrs_specific_var | stderrs_specific_var |
| thetahats | thetahats |
| thetatildefun | thetatildefun |