Function reference • stray

Main Model Functions Main interface for fitting models and returning model objects
`pibble()` `refit(<pibblefit>)`	Interface to fit pibble models
`basset()` `refit(<bassetfit>)`	Interface to fit basset models
`orthus()`	Interface to fit orthus models
`maltipoo()`	Interface to fit maltipoo models
Rcpp Model Interfaces Low level interfaces for fitting models
`optimPibbleCollapsed()`	Function to Optimize the Collapsed Pibble Model
`optimMaltipooCollapsed()`	Function to Optimize the Collapsed Maltipoo Model
`conjugateLinearModel()`	Solve Bayesian Multivariate Conjugate Linear Model
`uncollapsePibble()`	Uncollapse output from optimPibbleCollapsed to full pibble Model
`loglikPibbleCollapsed()` `gradPibbleCollapsed()` `hessPibbleCollapsed()`	Calculations for the Collapsed Pibble Model
`loglikMaltipooCollapsed()` `gradMaltipooCollapsed()` `hessMaltipooCollapsed()`	Calculations for the Collapsed Maltipoo Model
`SE()` `LINEAR()`	Multivariate RBF Kernel
Object Methods Methods for working with model objects
`ncategories()` `nsamples()` `ncovariates()` `niter()`	Generic method for accessing model fit dimensions
`as.list(<pibblefit>)`	Convert object of class pibblefit to a list
`coef(<pibblefit>)`	Return regression coefficients of 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
`refit()`	Generic method for fitting model from passed model fit object
`ppc()`	Generic method for visualizing posterior predictive checks
`ppc_summary()`	Generic Method to Plot Posterior Predictive Summaries
`print(<pibblefit>)`	Print dimensions and coordinate system information for pibblefit object.
`predict(<pibblefit>)`	Predict response from new data
`plot(<pibblefit>)`	Plot Summaries of Posterior Distribution of pibblefit Parameters
`sample_prior()`	Generic method for sampling from prior distribution of object
`to_proportions()` `to_alr()` `to_ilr()` `to_clr()`	Transform Fit Stray Parameters to other representations
`req()`	Generic method for ensuring object contains required elements
`verify()`	Generic method for verifying new objects
`summary(<pibblefit>)`	Summarise pibblefit object and print posterior quantiles
`summary(<orthusfit>)`	Summarise orthusfit object and print posterior quantiles
Helpful Utility Methods Just that, mostly support other package functions
`random_pibble_init()`	Provide random initialization for pibble model
`lambda_to_iqlr()`	Transform Lambda into IQLR (Inter-Quantile Log-Ratio)
`pibble_sim()`	Simulate simple pibble dataset and priors (for testing)
`orthus_sim()`	Simulate simple orthus dataset and priors (for testing)
`pibble_tidy_samples()`	Convert pibble samples of Eta Lambda and Sigma to tidy format
`orthus_tidy_samples()`	Convert orthus samples of Eta Lambda and Sigma to tidy format
`store_coord()` `reapply_coord()`	Holds information on coordinates system to later be reapplied
`check_dims()`	Check vector/matrix/data.frame for expected dimensions or throw error
Utility Math Functions Fast, C++, mostly for internal use
`lmvgamma()`	Log of Multivarate Gamma Function - Gamma_p(a)
`lmvgamma_deriv()`	Derivative of Log of Multivariate Gamma Function - Gamma_p(a)
Datasets Example Datasets
`mallard`	Data from Silverman et al. (2018) Microbiome
`mallard_family`	Data from Silverman et al. (2018) Microbiome

Reference

Main Model Functions

Rcpp Model Interfaces

Object Methods

Helpful Utility Methods

Utility Math Functions

Datasets