Package: fido 1.1.1

Michelle Nixon

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:Justin Silverman [aut], Kim Roche [ctb], Michelle Nixon [ctb, cre]

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fido.pdf |fido.html✨
fido/json (API)
NEWS

# Install 'fido' in R:
install.packages('fido', repos = c('https://jsilve24.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jsilve24/fido/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

8.21 score 20 stars 92 scripts 563 downloads 72 exports 56 dependencies

Last updated 1 months agofrom:a4e6c2c4b9. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64OKOct 31 2024
R-4.5-linux-x86_64OKOct 31 2024
R-4.4-win-x86_64OKOct 31 2024
R-4.4-mac-x86_64OKOct 31 2024
R-4.4-mac-aarch64OKOct 31 2024
R-4.3-win-x86_64OKOct 31 2024
R-4.3-mac-x86_64OKOct 31 2024
R-4.3-mac-aarch64OKOct 31 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.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-05-30
Started: 2020-09-22

Introduction to fido::Pibble

Justin Silverman

Rendered fromintroduction-to-fido.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-05-20
Started: 2020-08-06

Joint Modeling (e.g., Multiomics) with fido::Orthus

Justin Silverman

Rendered fromorthus.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-05-03
Started: 2019-08-06

Non-linear models with fido::basset

Justin Silverman

Rendered fromnon-linear-models.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-05-14
Started: 2019-04-25

Picking Priors

Rendered frompicking_priors.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-06-14
Started: 2019-06-22

Readme and manuals

Help Manual

Help pageTopics
Compute the ALR of a matrixalr
Compute the ALR of an arrayalr_array
Compute the inverse ALR of a matrixalrInv
Compute the ALR of an arrayalrInv_array
Convert object of class orthusfit to a listas.list.orthusfit
Convert object of class pibblefit to a listas.list.pibblefit
convert list to orthusfitas.orthusfit
convert list to pibblefitas.pibblefit
Interface to fit basset modelsbasset basset_fit refit.bassetfit
Check vector/matrix/data.frame for expected dimensions or throw errorcheck_dims
Compute the CLR of an arrayclr_array
Return regression coefficients of orthus objectcoef.orthusfit
Return regression coefficients of pibblefit objectcoef.pibblefit
Solve Bayesian Multivariate Conjugate Linear ModelconjugateLinearModel
Convert orthus covariance matricies between representationsconvert_orthus_covariance oalrvar2alrvar oalrvar2clrvar oalrvar2ilrvar oclrvar2alrvar oclrvar2ilrvar oilrvar2alrvar oilrvar2clrvar oilrvar2ilrvar
Create a default ILR basecreate_default_ilr_base
fido: Fitting and Analysis of Multinomial Logistic Normal Modelsfido-package fido fido_package
Transform Fit fido Parameters to other representationsfido_transforms to_alr to_alr.orthusfit to_alr.pibblefit to_clr to_clr.orthusfit to_clr.pibblefit to_ilr to_ilr.orthusfit to_ilr.pibblefit to_proportions to_proportions.orthusfit to_proportions.pibblefit
Gather Multidimensional Array to Tidy Tibblegather_array
Multivariate RBF Kernelkernels LINEAR SE
Transform Lambda into IQLR (Inter-Quantile Log-Ratio)lambda_to_iqlr
Log of Multivarate Gamma Function - Gamma_p(a)lmvgamma
Derivative of Log of Multivariate Gamma Function - Gamma_p(a)lmvgamma_deriv
Calculations for the Collapsed Pibble ModelgradPibbleCollapsed hessPibbleCollapsed loglikPibbleCollapsed
Data from Silverman et al. (2018) Microbiomemallard
Data from Silverman et al. (2018) Microbiomemallard_family
Data from Silverman et al. (2019) bioRxivmetadata
Closure operatorminiclo
Closure Operation applied to array on marginminiclo_array
mongrelmongrel mongrel-deprecated
Generic method for applying names to an objectname
S3 for orthusfit apply names to orthusfit objectname.orthusfit
S3 for pibblefit apply names to pibblefit objectname.pibblefit
Generic method for getting and setting dimension names of fit objectnames_categories names_categories.pibblefit names_categories<- names_categories<-.pibblefit names_coords names_coords.pibblefit names_covariates names_covariates.pibblefit names_covariates<- names_covariates<-.pibblefit names_samples names_samples.pibblefit names_samples<- names_samples<-.pibblefit name_dims
Generic method for accessing model fit dimensionsaccess_dims ncategories ncategories.orthusfit ncategories.pibblefit ncovariates ncovariates.orthusfit ncovariates.pibblefit niter niter.orthusfit niter.pibblefit nsamples nsamples.orthusfit nsamples.pibblefit
Function to Optimize the Collapsed Pibble ModeloptimPibbleCollapsed
Interface to fit orthus modelsorthus orthus_fit
Log-Ratio transforms for orthus objectsoalr oalrInv oclr oclrInv oglr oglrInv oilr oilrInv orthus_lr_transforms
Simulate simple orthus dataset and priors (for testing)orthus_sim
Convert orthus samples of Eta Lambda and Sigma to tidy formatorthus_tidy_samples
Create orthusfit objectorthusfit
Data from Silverman et al. (2019) bioRxivpcrbias_mock
Interface to fit pibble modelspibble pibble_fit refit.pibblefit
Simulate simple pibble dataset and priors (for testing)pibble_sim
Convert pibble samples of Eta Lambda and Sigma to tidy formatpibble_tidy_samples
Create pibblefit objectpibblefit
Plot Summaries of Posterior Distribution of pibblefit Parametersplot.pibblefit
Generic method for visualizing posterior predictive checksppc
Generic Method to Plot Posterior Predictive Summariesppc_summary ppc_summary.pibblefit
Visualization of Posterior Predictive Check of fit modelppc.pibblefit
Predict using bassetpredict.bassetfit
Predict response from new datapredict.pibblefit
Print dimensions and coordinate system information for orthusfit object.print.orthusfit
Print dimensions and coordinate system information for pibblefit object.print.pibblefit
Generic Method to Calculate R2 for Fitted Modelr2 r2.bassetfit r2.pibblefit
Provide random initialization for pibble modelrandom_pibble_init
Generic method for fitting model from passed model fit objectrefit
Generic method for ensuring object contains required elementsreq
require elements to be non-null in orthusfit or throw errorreq.orthusfit
require elements to be non-null in pibblefit or throw errorreq.pibblefit
Data from Gevers et al. (2014)RISK_CCFA
Data from Gevers et al. (2014)RISK_CCFA_otu
Data from Gevers et al. (2014)RISK_CCFA_sam
Data from Gevers et al. (2014)RISK_CCFA_tax
Generic method for sampling from prior distribution of objectsample_prior
Sample from the prior distribution of pibblefit objectsample_prior.pibblefit
Holds information on coordinates system to later be reappliedreapply_coord store_coord
Shortcut for summarize variable with quantiles and meansummarise_posterior
Summarise orthusfit object and print posterior quantilessummary.orthusfit
Summarise pibblefit object and print posterior quantilessummary.pibblefit
Uncollapse output from optimPibbleCollapsed to full pibble ModeluncollapsePibble
Uncollapse output from optimPibbleCollapsed to full pibble Model when Sigma is knownuncollapsePibble_sigmaKnown
Generic method for verifying new objectsverify
Simple verification of passed bassetfit objectverify.bassetfit
Simple verification of passed orthusfit objectverify.orthusfit
Simple verification of passed pibblefit objectverify.pibblefit
Data from Silverman et al. (2019) bioRxivY