Package: fido 1.1.1
fido: Bayesian Multinomial Logistic Normal Regression
Provides methods for fitting and inspection of Bayesian Multinomial Logistic Normal Models using MAP estimation and Laplace Approximation as developed in Silverman et. Al. (2022) <https://www.jmlr.org/papers/v23/19-882.html>. Key functionality is implemented in C++ for scalability. 'fido' replaces the previous package 'stray'.
Authors:
fido_1.1.1.tar.gz
fido_1.1.1.tar.gz(r-4.5-noble)fido_1.1.1.tar.gz(r-4.4-noble)
fido.pdf |fido.html✨
fido/json (API)
NEWS
# Install 'fido' in R: |
install.packages('fido', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jsilve24/fido/issues
Pkgdown:https://jsilve24.github.io
- RISK_CCFA_otu - Data from Gevers et al.
- RISK_CCFA_sam - Data from Gevers et al.
- RISK_CCFA_tax - Data from Gevers et al.
- Y - Data from Silverman et al. (2019) bioRxiv
- mallard - Data from Silverman et al. (2018) Microbiome
- mallard_family - Data from Silverman et al. (2018) Microbiome
- metadata - Data from Silverman et al. (2019) bioRxiv
Last updated 6 months agofrom:4943f8550e. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 03 2024 |
R-4.5-linux-x86_64 | OK | Dec 03 2024 |
Exports:alralr_arrayalrInvalrInv_arraybassetcheck_dimsclr_arrayconjugateLinearModelcreate_default_ilr_basegather_arraygradPibbleCollapsedhessPibbleCollapsedlambda_to_iqlrLINEARloglikPibbleCollapsedminiclominiclo_arraynamenames_categoriesnames_categories<-names_coordsnames_covariatesnames_covariates<-names_samplesnames_samples<-ncategoriesncovariatesniternsamplesoalroalrInvoalrvar2alrvaroalrvar2clrvaroalrvar2ilrvaroclroclrInvoclrvar2alrvaroclrvar2ilrvaroglroglrInvoilroilrInvoilrvar2alrvaroilrvar2clrvaroilrvar2ilrvaroptimPibbleCollapsedorthusorthus_simorthus_tidy_samplesorthusfitpibblepibble_simpibble_tidy_samplespibblefitppcppc_summaryr2random_pibble_initreapply_coordrefitreqsample_priorSEstore_coordsummarise_posteriorto_alrto_clrto_ilrto_proportionsuncollapsePibbleuncollapsePibble_sigmaKnownverify
Dependencies:abindarrayhelpersbackportsBHcheckmateclicodacolorspacecpp11distributionaldplyrfansifarvergenericsggdistggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgconfigposteriorpurrrquadprogR6RColorBrewerRcppRcppEigenRcppGSLRcppNumericalRcppZigguratrlangscalesstringistringrsvUnittensorAtibbletidybayestidyrtidyselectutf8vctrsviridisLitewithr
Example of using Fido for measuring and mitigating PCR Bias
Rendered frommitigating-pcrbias.Rmd
usingknitr::rmarkdown
on Dec 03 2024.Last update: 2024-05-31
Started: 2022-02-16
Introduction to fido::Pibble
Rendered fromintroduction-to-fido.Rmd
usingknitr::rmarkdown
on Dec 03 2024.Last update: 2024-05-31
Started: 2022-02-16
Joint Modeling (e.g., Multiomics) with fido::Orthus
Rendered fromorthus.Rmd
usingknitr::rmarkdown
on Dec 03 2024.Last update: 2024-05-31
Started: 2022-02-16
Non-linear models with fido::basset
Rendered fromnon-linear-models.Rmd
usingknitr::rmarkdown
on Dec 03 2024.Last update: 2024-05-31
Started: 2022-02-16
Picking Priors
Rendered frompicking_priors.Rmd
usingknitr::rmarkdown
on Dec 03 2024.Last update: 2024-05-31
Started: 2022-02-16