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fido (version 1.0.4)

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

993

Version

1.0.4

License

GPL-3

Maintainer

Michelle Nixon

Last Published

March 24th, 2023

Functions in fido (1.0.4)

coef.orthusfit

Return regression coefficients of orthus object
conjugateLinearModel

Solve Bayesian Multivariate Conjugate Linear Model
name.pibblefit

S3 for pibblefit apply names to pibblefit object
basset_fit

Interface to fit basset models
lmvgamma_deriv

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

Calculations for the Collapsed Maltipoo Model
as.pibblefit

convert list to pibblefit
name.orthusfit

S3 for orthusfit apply names to orthusfit object
create_default_ilr_base

Create a default ILR base
gather_array

Gather Multidimensional Array to Tidy Tibble
mallard_family

Data from Silverman et al. (2018) Microbiome
kernels

Multivariate RBF Kernel
maltipoo_fit

Interface to fit maltipoo models
optimPibbleCollapsed

Function to Optimize the Collapsed Pibble Model
pcrbias_mock

Data from Silverman et al. (2019) bioRxiv
pibble_fit

Interface to fit pibble models
lambda_to_iqlr

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

Closure Operation applied to array on margin
miniclo

Closure operator
names_covariates.pibblefit

Generic method for getting and setting dimension names of fit object
lmvgamma

Log of Multivarate Gamma Function - Gamma_p(a)
optimMaltipooCollapsed

Function to Optimize the Collapsed Maltipoo Model
orthus_tidy_samples

Convert orthus samples of Eta Lambda and Sigma to tidy format
orthusfit

Create orthusfit object
pibble_sim

Simulate simple pibble dataset and priors (for testing)
ppc_summary.pibblefit

Generic Method to Plot Posterior Predictive Summaries
predict

Predict response from new data
pibblefit

Create pibblefit object
loglikPibbleCollapsed

Calculations for the Collapsed Pibble Model
mallard

Data from Silverman et al. (2018) Microbiome
mongrel-deprecated

mongrel
name

Generic method for applying names to an object
predict.bassetfit

Predict using basset
store_coord

Holds information on coordinates system to later be reapplied
sample_prior.pibblefit

Sample from the prior distribution of pibblefit object
verify.orthusfit

Simple verification of passed orthusfit object
random_pibble_init

Provide random initialization for pibble model
uncollapsePibble

Uncollapse output from optimPibbleCollapsed to full pibble Model
print.pibblefit

Print dimensions and coordinate system information for pibblefit object.
verify

Generic method for verifying new objects
pibble_tidy_samples

Convert pibble samples of Eta Lambda and Sigma to tidy format
print

Print dimensions and coordinate system information for an orthusfit or pibblefit object.
plot.pibblefit

Plot Summaries of Posterior Distribution of pibblefit Parameters
print.orthusfit

Print dimensions and coordinate system information for orthusfit object.
fido_package

fido: Fitting and Analysis of Multinomial Logistic Normal Models
ppc

Generic method for visualizing posterior predictive checks
req.pibblefit

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

Visualization of Posterior Predictive Check of fit model
orthus_fit

Interface to fit orthus models
sample_prior

Generic method for sampling from prior distribution of object
summary.orthusfit

Summarise orthusfit object and print posterior quantiles
summary.pibblefit

Summarise pibblefit object and print posterior quantiles
summarise_posterior

Shortcut for summarize variable with quantiles and mean
req

Generic method for ensuring object contains required elements
refit

Generic method for fitting model from passed model fit object
predict.pibblefit

Predict response from new data
summary

Summarise pibblefit or orthusfit object and print posterior quantiles
fido_transforms

Transform Fit fido Parameters to other representations
verify.pibblefit

Simple verification of passed pibblefit object
maltipoofit

Create maltipoofit object
orthus_sim

Simulate simple orthus dataset and priors (for testing)
req.maltipoofit

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

Simple verification of passed multipoo object
req.orthusfit

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

Log-Ratio transforms for orthus objects
verify.bassetfit

Simple verification of passed bassetfit object
metadata

Data from Silverman et al. (2019) bioRxiv
alrInv_array

Compute the ALR of an array
as.list.pibblefit

Convert object of class pibblefit to a list
alr

Compute the ALR of a matrix
alr_array

Compute the ALR of an array
alrInv

Compute the inverse ALR of a matrix
as.list.orthusfit

Convert object of class orthusfit to a list
as.list

Generic method to convert to list
Y

Data from Silverman et al. (2019) bioRxiv
as.orthusfit

convert list to orthusfit
ncategories.pibblefit

Generic method for accessing model fit dimensions
coef

Return regression coefficients of pibblefit or orthusfit object
convert_orthus_covariance

Convert orthus covariance matricies between representations
check_dims

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

Compute the CLR of an array
coef.pibblefit

Return regression coefficients of pibblefit object