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:Seungjun Ahn [cre, aut, trl], Somnath Datta [ctb, ths]

SOHPIE_1.0.6.tar.gz
SOHPIE_1.0.6.tar.gz(r-4.5-noble)SOHPIE_1.0.6.tar.gz(r-4.4-noble)
SOHPIE_1.0.6.tgz(r-4.4-emscripten)SOHPIE_1.0.6.tgz(r-4.3-emscripten)
SOHPIE.pdf |SOHPIE.html
SOHPIE/json (API)

# Install 'SOHPIE' in R:
install.packages('SOHPIE', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 562 downloads 15 exports 20 dependencies

Last updated 1 years agofrom:25799e5401. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 16 2024
R-4.5-linuxOKDec 16 2024

Exports:asso_matcoeffcoeff_specific_varDCtaxa_tabpseudoregpseudoreg.summarypvalpval_specific_varqvalqval_specific_varSOHPIE_DNAstderrsstderrs_specific_varthetahatsthetatildefun

Dependencies:cliDEoptimRdplyrfansifdrtoolgenericsgluegtoolslifecyclemagrittrpillarpkgconfigR6rlangrobustbasetibbletidyselectutf8vctrswithr

An Introduction to SOHPIE

Rendered fromUserManualSOHPIE.Rmdusingknitr::rmarkdownon Dec 16 2024.

Last update: 2023-10-23
Started: 2023-06-21

Readme and manuals

Help Manual

Help pageTopics
asso_matasso_mat
coeffcoeff
coeff_specific_varcoeff_specific_var
A Subdata from the American Gut Project study datacombinedamgut
A Subdata from the Diet Swap study datacombineddietswap
DCtaxa_tabDCtaxa_tab
pseudoregpseudoreg
pseudoreg.summary()pseudoreg.summary
pvalpval
pval_specific_varpval_specific_var
qvalqval
qval_specific_varqval_specific_var
SOHPIE_DNASOHPIE_DNA
sparcc wrappersparcc
stderrsstderrs
stderrs_specific_varstderrs_specific_var
thetahatsthetahats
thetatildefunthetatildefun