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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

528

Version

1.1.2

License

GPL-3

Maintainer

Justin Silverman

Last Published

February 27th, 2025

Functions in fido (1.1.2)

basset_fit

Interface to fit basset models
conjugateLinearModel

Solve Bayesian Multivariate Conjugate Linear Model
loglikPibbleCollapsed

Calculations for the Collapsed Pibble Model
lmvgamma_deriv

Derivative of Log of Multivariate Gamma Function - Gamma_p(a)
name.orthusfit

S3 for orthusfit apply names to orthusfit object
name

Generic method for applying names to an object
coef.pibblefit

Return regression coefficients of pibblefit object
gather_array

Gather Multidimensional Array to Tidy Tibble
as.pibblefit

convert list to pibblefit
as.orthusfit

convert list to orthusfit
check_dims

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

Compute the ALR of a matrix
kernels

Multivariate RBF Kernel
miniclo_array

Closure Operation applied to array on margin
mongrel-deprecated

mongrel
clr_array

Compute the CLR of an array
fido_package

fido: Fitting and Analysis of Multinomial Logistic Normal Models
coef.orthusfit

Return regression coefficients of orthus object
fido_transforms

Transform Fit fido Parameters to other representations
alrInv

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
store_coord

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
orthus_sim

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.pibblefit

Plot Summaries of Posterior Distribution of pibblefit Parameters
orthusfit

Create orthusfit object
name.pibblefit

S3 for pibblefit apply names to pibblefit object
pibblefit

Create pibblefit object
pibble_sim

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
orthus_fit

Interface to fit orthus models
mallard_family

Data from Silverman et al. (2018) Microbiome
mallard

Data from Silverman et al. (2018) Microbiome
optimPibbleCollapsed

Function to Optimize the Collapsed Pibble Model
ppc.pibblefit

Visualization of Posterior Predictive Check of fit model
sample_prior

Generic method for sampling from prior distribution of object
req.pibblefit

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

Generic method for visualizing posterior predictive checks
verify

Generic method for verifying new objects
verify.pibblefit

Simple verification of passed pibblefit object
lambda_to_iqlr

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

Log of Multivarate Gamma Function - Gamma_p(a)
metadata

Data from Silverman et al. (2019) bioRxiv
random_pibble_init

Provide random initialization for pibble model
refit

Generic method for fitting model from passed model fit object
pcrbias_mock

Data from Silverman et al. (2019) bioRxiv
miniclo

Closure operator
pibble_fit

Interface to fit pibble models
req

Generic method for ensuring object contains required elements
req.orthusfit

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

Print dimensions and coordinate system information for pibblefit object.
r2

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
RISK_CCFA_otu

Data from Gevers et al. (2014)
RISK_CCFA_tax

Data from Gevers et al. (2014)
alrInv_array

Compute the ALR of an array
alr_array

Compute the ALR of an array
RISK_CCFA

Data from Gevers et al. (2014)
RISK_CCFA_sam

Data from Gevers et al. (2014)
Y

Data from Silverman et al. (2019) bioRxiv