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fido (version 1.1.2)

Bayesian Multinomial Logistic Normal Regression

Description

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) . Key functionality is implemented in C++ for scalability. 'fido' replaces the previous package 'stray'.

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Version

Install

install.packages('fido')

Monthly Downloads

354

Version

1.1.2

License

GPL-3

Maintainer

Justin Silverman

Last Published

February 27th, 2025

Functions in fido (1.1.2)

Interface to fit basset models

conjugateLinearModel

Solve Bayesian Multivariate Conjugate Linear Model

loglikPibbleCollapsed

Calculations for the Collapsed Pibble Model

Derivative of Log of Multivariate Gamma Function - Gamma_p(a)

S3 for orthusfit apply names to orthusfit object

Generic method for applying names to an object

Return regression coefficients of pibblefit object

Gather Multidimensional Array to Tidy Tibble

convert list to pibblefit

convert list to orthusfit

Check vector/matrix/data.frame for expected dimensions or throw error

Compute the ALR of a matrix

Multivariate RBF Kernel

Closure Operation applied to array on margin

mongrel-deprecated

Compute the CLR of an array

fido: Fitting and Analysis of Multinomial Logistic Normal Models

Return regression coefficients of orthus object

fido_transforms

Transform Fit fido Parameters to other representations

Compute the inverse ALR of a matrix

predict.pibblefit

Predict response from new data

print.orthusfit

Print dimensions and coordinate system information for orthusfit object.

sample_prior.pibblefit

Sample from the prior distribution of pibblefit object

Holds information on coordinates system to later be reapplied

orthus_lr_transforms

Log-Ratio transforms for orthus objects

as.list.orthusfit

Convert object of class orthusfit to a list

as.list.pibblefit

Convert object of class pibblefit to a list

create_default_ilr_base

Create a default ILR base

convert_orthus_covariance

Convert orthus covariance matricies between representations

Simulate simple orthus dataset and priors (for testing)

orthus_tidy_samples

Convert orthus samples of Eta Lambda and Sigma to tidy format

uncollapsePibble_sigmaKnown

Uncollapse output from optimPibbleCollapsed to full pibble Model when Sigma is known

Plot Summaries of Posterior Distribution of pibblefit Parameters

Create orthusfit object

S3 for pibblefit apply names to pibblefit object

Create pibblefit object

Simulate simple pibble dataset and priors (for testing)

names_covariates.pibblefit

Generic method for getting and setting dimension names of fit object

pibble_tidy_samples

Convert pibble samples of Eta Lambda and Sigma to tidy format

summarise_posterior

Shortcut for summarize variable with quantiles and mean

summary.orthusfit

Summarise orthusfit object and print posterior quantiles

verify.bassetfit

Simple verification of passed bassetfit object

verify.orthusfit

Simple verification of passed orthusfit object

ppc_summary.pibblefit

Generic Method to Plot Posterior Predictive Summaries

predict.bassetfit

Predict using basset

Interface to fit orthus models

Data from Silverman et al. (2018) Microbiome

Data from Silverman et al. (2018) Microbiome

optimPibbleCollapsed

Function to Optimize the Collapsed Pibble Model

Visualization of Posterior Predictive Check of fit model

Generic method for sampling from prior distribution of object

require elements to be non-null in pibblefit or throw error

Generic method for visualizing posterior predictive checks

Generic method for verifying new objects

verify.pibblefit

Simple verification of passed pibblefit object

Transform Lambda into IQLR (Inter-Quantile Log-Ratio)

Log of Multivarate Gamma Function - Gamma_p(a)

Data from Silverman et al. (2019) bioRxiv

random_pibble_init

Provide random initialization for pibble model

Generic method for fitting model from passed model fit object

Data from Silverman et al. (2019) bioRxiv

Closure operator

Interface to fit pibble models

Generic method for ensuring object contains required elements

require elements to be non-null in orthusfit or throw error

print.pibblefit

Print dimensions and coordinate system information for pibblefit object.

Generic Method to Calculate R2 for Fitted Model

summary.pibblefit

Summarise pibblefit object and print posterior quantiles

uncollapsePibble

Uncollapse output from optimPibbleCollapsed to full pibble Model

ncategories.pibblefit

Generic method for accessing model fit dimensions

Data from Gevers et al. (2014)

Data from Gevers et al. (2014)

Compute the ALR of an array

Compute the ALR of an array

Data from Gevers et al. (2014)

Data from Gevers et al. (2014)

Data from Silverman et al. (2019) bioRxiv