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]

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

Uses libs:

c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

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

3.93 score 85 scripts 72 exports 56 dependencies

Last updated 5 months agofrom:4943f8550e. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 04 2024
R-4.5-linux-x86_64	OK	Oct 04 2024

Exports:alr alr_array alrInv alrInv_array basset check_dims clr_array conjugateLinearModel create_default_ilr_base gather_array gradPibbleCollapsed hessPibbleCollapsed lambda_to_iqlr LINEAR loglikPibbleCollapsed miniclo miniclo_array name names_categories names_categories<-names_coords names_covariates names_covariates<-names_samples names_samples<-ncategories ncovariates niter nsamples oalr oalrInv oalrvar2alrvar oalrvar2clrvar oalrvar2ilrvar oclr oclrInv oclrvar2alrvar oclrvar2ilrvar oglr oglrInv oilr oilrInv oilrvar2alrvar oilrvar2clrvar oilrvar2ilrvar optimPibbleCollapsed orthus orthus_sim orthus_tidy_samples orthusfit pibble pibble_sim pibble_tidy_samples pibblefit ppc ppc_summary r2 random_pibble_init reapply_coord refit req sample_prior SE store_coord summarise_posterior to_alr to_clr to_ilr to_proportions uncollapsePibble uncollapsePibble_sigmaKnown verify

Dependencies:abind arrayhelpers backports BH checkmate cli coda colorspace cpp11 distributional dplyr fansi farver generics ggdist ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix matrixStats mgcv munsell nlme numDeriv pillar pkgconfig posterior purrr quadprog R6 RColorBrewer Rcpp RcppEigen RcppGSL RcppNumerical RcppZiggurat rlang scales stringi stringr svUnit tensorA tibble tidybayes tidyr tidyselect utf8 vctrs viridisLite withr

Example of using Fido for measuring and mitigating PCR Bias

Rendered frommitigating-pcrbias.Rmdusingknitr::rmarkdownon Oct 04 2024.

Last update: 2024-05-31
Started: 2022-02-16

Introduction to fido::Pibble

Justin Silverman

Rendered fromintroduction-to-fido.Rmdusingknitr::rmarkdownon Oct 04 2024.

Last update: 2024-05-31
Started: 2022-02-16

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

Justin Silverman

Rendered fromorthus.Rmdusingknitr::rmarkdownon Oct 04 2024.

Last update: 2024-05-31
Started: 2022-02-16

Non-linear models with fido::basset

Justin Silverman

Rendered fromnon-linear-models.Rmdusingknitr::rmarkdownon Oct 04 2024.

Last update: 2024-05-31
Started: 2022-02-16

Picking Priors

Rendered frompicking_priors.Rmdusingknitr::rmarkdownon Oct 04 2024.

Last update: 2024-05-31
Started: 2022-02-16

Citation

Readme and manuals

Help Manual

Help page	Topics
Compute the ALR of a matrix	alr
Compute the ALR of an array	alr_array
Compute the inverse ALR of a matrix	alrInv
Compute the ALR of an array	alrInv_array
Convert object of class orthusfit to a list	as.list.orthusfit
Convert object of class pibblefit to a list	as.list.pibblefit
convert list to orthusfit	as.orthusfit
convert list to pibblefit	as.pibblefit
Interface to fit basset models	basset basset_fit refit.bassetfit
Check vector/matrix/data.frame for expected dimensions or throw error	check_dims
Compute the CLR of an array	clr_array
Return regression coefficients of orthus object	coef.orthusfit
Return regression coefficients of pibblefit object	coef.pibblefit
Solve Bayesian Multivariate Conjugate Linear Model	conjugateLinearModel
Convert orthus covariance matricies between representations	convert_orthus_covariance oalrvar2alrvar oalrvar2clrvar oalrvar2ilrvar oclrvar2alrvar oclrvar2ilrvar oilrvar2alrvar oilrvar2clrvar oilrvar2ilrvar
Create a default ILR base	create_default_ilr_base
fido: Fitting and Analysis of Multinomial Logistic Normal Models	fido-package fido fido_package
Transform Fit fido Parameters to other representations	fido_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 Tibble	gather_array
Multivariate RBF Kernel	kernels 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 Model	gradPibbleCollapsed hessPibbleCollapsed loglikPibbleCollapsed
Data from Silverman et al. (2018) Microbiome	mallard
Data from Silverman et al. (2018) Microbiome	mallard_family
Data from Silverman et al. (2019) bioRxiv	metadata
Closure operator	miniclo
Closure Operation applied to array on margin	miniclo_array
mongrel	mongrel mongrel-deprecated
Generic method for applying names to an object	name
S3 for orthusfit apply names to orthusfit object	name.orthusfit
S3 for pibblefit apply names to pibblefit object	name.pibblefit
Generic method for getting and setting dimension names of fit object	names_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 dimensions	access_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 Model	optimPibbleCollapsed
Interface to fit orthus models	orthus orthus_fit
Log-Ratio transforms for orthus objects	oalr 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 format	orthus_tidy_samples
Create orthusfit object	orthusfit
Data from Silverman et al. (2019) bioRxiv	pcrbias_mock
Interface to fit pibble models	pibble pibble_fit refit.pibblefit
Simulate simple pibble dataset and priors (for testing)	pibble_sim
Convert pibble samples of Eta Lambda and Sigma to tidy format	pibble_tidy_samples
Create pibblefit object	pibblefit
Plot Summaries of Posterior Distribution of pibblefit Parameters	plot.pibblefit
Generic method for visualizing posterior predictive checks	ppc
Generic Method to Plot Posterior Predictive Summaries	ppc_summary ppc_summary.pibblefit
Visualization of Posterior Predictive Check of fit model	ppc.pibblefit
Predict using basset	predict.bassetfit
Predict response from new data	predict.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 Model	r2 r2.bassetfit r2.pibblefit
Provide random initialization for pibble model	random_pibble_init
Generic method for fitting model from passed model fit object	refit
Generic method for ensuring object contains required elements	req
require elements to be non-null in orthusfit or throw error	req.orthusfit
require elements to be non-null in pibblefit or throw error	req.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 object	sample_prior
Sample from the prior distribution of pibblefit object	sample_prior.pibblefit
Holds information on coordinates system to later be reapplied	reapply_coord store_coord
Shortcut for summarize variable with quantiles and mean	summarise_posterior
Summarise orthusfit object and print posterior quantiles	summary.orthusfit
Summarise pibblefit object and print posterior quantiles	summary.pibblefit
Uncollapse output from optimPibbleCollapsed to full pibble Model	uncollapsePibble
Uncollapse output from optimPibbleCollapsed to full pibble Model when Sigma is known	uncollapsePibble_sigmaKnown
Generic method for verifying new objects	verify
Simple verification of passed bassetfit object	verify.bassetfit
Simple verification of passed orthusfit object	verify.orthusfit
Simple verification of passed pibblefit object	verify.pibblefit
Data from Silverman et al. (2019) bioRxiv	Y

Usage by other packages (reverse dependencies)