Function reference • fido

Model functions

Functions for fitting the main models

pibble() refit(<pibblefit>): Interface to fit pibble models

refit(): Generic method for fitting model from passed model fit object

basset() refit(<bassetfit>): Interface to fit basset models

orthus(): Interface to fit orthus models

Model checking

plot(<pibblefit>): Plot Summaries of Posterior Distribution of pibblefit Parameters

ppc(<pibblefit>): Visualization of Posterior Predictive Check of fit model

ppc(): Generic method for visualizing posterior predictive checks

ppc_summary(): Generic Method to Plot Posterior Predictive Summaries

Useful functions for determining model fit

plot(<pibblefit>): Plot Summaries of Posterior Distribution of pibblefit Parameters

ppc(<pibblefit>): Visualization of Posterior Predictive Check of fit model

ppc(): Generic method for visualizing posterior predictive checks

ppc_summary(): Generic Method to Plot Posterior Predictive Summaries

r2(): Generic Method to Calculate R2 for Fitted Model

sample_prior(<pibblefit>): Sample from the prior distribution of pibblefit object

sample_prior(): Generic method for sampling from prior distribution of object

summarise_posterior(): Shortcut for summarize variable with quantiles and mean

Transformation functions

to_proportions() to_alr() to_ilr() to_clr(): Transform Fit fido Parameters to other representations

Helper functions

alr(): Compute the ALR of a matrix

alrInv(): Compute the inverse ALR of a matrix

alrInv_array(): Compute the ALR of an array

alr_array(): Compute the ALR of an array

as.list(<orthusfit>): Convert object of class orthusfit to a list

as.list(<pibblefit>): Convert object of class pibblefit to a list

as.orthusfit(): convert list to orthusfit

as.pibblefit(): convert list to pibblefit

check_dims(): Check vector/matrix/data.frame for expected dimensions or throw error

clr_array(): Compute the CLR of an array

coef(<orthusfit>): Return regression coefficients of orthus object

coef(<pibblefit>): Return regression coefficients of pibblefit object

conjugateLinearModel(): Solve Bayesian Multivariate Conjugate Linear Model

oilrvar2ilrvar() oilrvar2clrvar() oclrvar2ilrvar() oalrvar2clrvar() oclrvar2alrvar() oalrvar2alrvar() oalrvar2ilrvar() oilrvar2alrvar(): Convert orthus covariance matricies between representations

create_default_ilr_base(): Create a default ILR base

gather_array(): Gather Multidimensional Array to Tidy Tibble

SE() LINEAR(): Multivariate RBF Kernel

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

loglikPibbleCollapsed() gradPibbleCollapsed() hessPibbleCollapsed(): Calculations for the Collapsed Pibble Model

lmvgamma(): Log of Multivarate Gamma Function - Gamma_p(a)

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

miniclo(): Closure operator

miniclo_array(): Closure Operation applied to array on margin

mongrel(): mongrel

name(<orthusfit>): S3 for orthusfit apply names to orthusfit object

name(<pibblefit>): S3 for pibblefit apply names to pibblefit object

name(): Generic method for applying names to an object

names_covariates() names_samples() names_categories() names_coords() `names_covariates<-`() `names_samples<-`() `names_categories<-`(): Generic method for getting and setting dimension names of fit object

ncategories() nsamples() ncovariates() niter(): Generic method for accessing model fit dimensions

optimPibbleCollapsed(): Function to Optimize the Collapsed Pibble Model

orthusfit(): Create orthusfit object

oglr() oglrInv() oalr() oalrInv() oilr() oilrInv() oclr() oclrInv(): Log-Ratio transforms for orthus objects

orthus_tidy_samples(): Convert orthus samples of Eta Lambda and Sigma to tidy format

pibblefit(): Create pibblefit object

predict(<bassetfit>): Predict using basset

predict(<pibblefit>): Predict response from new data

print(<orthusfit>): Print dimensions and coordinate system information for orthusfit object.

print(<pibblefit>): Print dimensions and coordinate system information for pibblefit object.

pibble_tidy_samples(): Convert pibble samples of Eta Lambda and Sigma to tidy format

random_pibble_init(): Provide random initialization for pibble model

req(<orthusfit>): require elements to be non-null in orthusfit or throw error

req(<pibblefit>): require elements to be non-null in pibblefit or throw error

req(): Generic method for ensuring object contains required elements

store_coord() reapply_coord(): Holds information on coordinates system to later be reapplied

summary(<orthusfit>): Summarise orthusfit object and print posterior quantiles

summary(<pibblefit>): Summarise pibblefit object and print posterior quantiles

uncollapsePibble(): Uncollapse output from optimPibbleCollapsed to full pibble Model

uncollapsePibble_sigmaKnown(): Uncollapse output from optimPibbleCollapsed to full pibble Model when Sigma is known

verify(<bassetfit>): Simple verification of passed bassetfit object

verify(<orthusfit>): Simple verification of passed orthusfit object

verify(<pibblefit>): Simple verification of passed pibblefit object

verify(): Generic method for verifying new objects

Data sets and data simulators

fido fido-package fido_package: fido: Fitting and Analysis of Multinomial Logistic Normal Models

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

orthus_sim(): Simulate simple orthus dataset and priors (for testing)

pcrbias_mock: Data from Silverman et al. (2019) bioRxiv

pibble_sim(): Simulate simple pibble dataset and priors (for testing)

Y: Data from Silverman et al. (2019) bioRxiv