Package: codacore 0.0.4
codacore: Learning Sparse Log-Ratios for Compositional Data
In the context of high-throughput genetic data, CoDaCoRe identifies a set of sparse biomarkers that are predictive of a response variable of interest (Gordon-Rodriguez et al., 2021) <doi:10.1093/bioinformatics/btab645>. More generally, CoDaCoRe can be applied to any regression problem where the independent variable is Compositional (CoDa), to derive a set of scale-invariant log-ratios (ILR or SLR) that are maximally associated to a dependent variable.
Authors:
codacore_0.0.4.tar.gz
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codacore.pdf |codacore.html✨
codacore/json (API)
NEWS
| # Install 'codacore' in R: |
| install.packages('codacore', repos = c('https://egr95.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 years agofrom:039d1b2767. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 30 2025 |
| R-4.5-win | OK | Mar 30 2025 |
| R-4.5-mac | OK | Mar 30 2025 |
| R-4.5-linux | OK | Mar 30 2025 |
| R-4.4-win | OK | Mar 30 2025 |
| R-4.4-mac | OK | Mar 30 2025 |
| R-4.4-linux | OK | Mar 30 2025 |
| R-4.3-win | OK | Mar 30 2025 |
| R-4.3-mac | OK | Mar 30 2025 |
Exports:activeInputs.codacorecodacoregetBinaryPartitionsgetDenominatorPartsgetLogRatiosgetNumeratorPartsgetNumLogRatiosgetSlopesgetTidyTableplotROCsimulateHTS
Dependencies:backportsbase64enccliconfiggenericsgluegtoolsherejsonlitekeraslatticelifecyclemagrittrMatrixplyrpngpROCprocessxpsR6rappdirsRcppRcppTOMLreticulaterlangrprojrootrstudioapitensorflowtfautographtfrunstidyselectvctrswhiskerwithryamlzeallot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| activeInputs | activeInputs.codacore |
| codacore | codacore |
| Microbiome composition related to Crohn`s disease study | Crohn |
| Metabolite relative abundances (Franzosa et al., 2019) | FranzosaMetabolite |
| Micriobiome relative abundances (Franzosa et al., 2019) | FranzosaMicrobiome |
| getBinaryPartitions | getBinaryPartitions |
| getDenominatorParts | getDenominatorParts |
| getLogRatios | getLogRatios |
| getNumeratorParts | getNumeratorParts |
| getNumLogRatios | getNumLogRatios |
| getSlopes | getSlopes |
| getTidyTable | getTidyTable |
| Microbiome, HIV infection and MSM factor | HIV |
| plot | plot.codacore |
| plotROC | plotROC |
| predict | predict.codacore |
| print.codacore | |
| Microbiome and sCD14 inflammation parameter | sCD14 |
| simulateHTS | simulateHTS |
