fido1.1.2 package

Generic method for accessing model fit dimensions

Compute the ALR of an array

Compute the ALR of a matrix

Compute the ALR of an array

Compute the inverse ALR of a matrix

Convert object of class orthusfit to a list

Convert object of class pibblefit to a list

convert list to orthusfit

convert list to pibblefit

Interface to fit basset models

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

Compute the CLR of an array

Return regression coefficients of orthus object

Return regression coefficients of pibblefit object

Solve Bayesian Multivariate Conjugate Linear Model

Convert orthus covariance matricies between representations

Create a default ILR base

fido: Fitting and Analysis of Multinomial Logistic Normal Models

Transform Fit fido Parameters to other representations

Gather Multidimensional Array to Tidy Tibble

Multivariate RBF Kernel

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

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

Log of Multivarate Gamma Function - Gamma_p(a)

Calculations for the Collapsed Pibble Model

Data from Silverman et al. (2019) bioRxiv

Closure Operation applied to array on margin

Closure operator

mongrel

Generic method for getting and setting dimension names of fit object

S3 for orthusfit apply names to orthusfit object

S3 for pibblefit apply names to pibblefit object

Generic method for applying names to an object

Function to Optimize the Collapsed Pibble Model

Interface to fit orthus models

Log-Ratio transforms for orthus objects

Simulate simple orthus dataset and priors (for testing)

Convert orthus samples of Eta Lambda and Sigma to tidy format

Create orthusfit object

Interface to fit pibble models

Simulate simple pibble dataset and priors (for testing)

Convert pibble samples of Eta Lambda and Sigma to tidy format

Create pibblefit object

Plot Summaries of Posterior Distribution of pibblefit Parameters

Generic Method to Plot Posterior Predictive Summaries

Visualization of Posterior Predictive Check of fit model

Generic method for visualizing posterior predictive checks

Predict using basset

Predict response from new data

Print dimensions and coordinate system information for orthusfit objec...

Print dimensions and coordinate system information for pibblefit objec...

Generic Method to Calculate R2 for Fitted Model

Provide random initialization for pibble model

Generic method for fitting model from passed model fit object

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

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

Generic method for ensuring object contains required elements

Data from Gevers et al. (2014)

Data from Gevers et al. (2014)

Data from Gevers et al. (2014)

Sample from the prior distribution of pibblefit object

Generic method for sampling from prior distribution of object

Holds information on coordinates system to later be reapplied

Shortcut for summarize variable with quantiles and mean

Summarise orthusfit object and print posterior quantiles

Summarise pibblefit object and print posterior quantiles

Uncollapse output from optimPibbleCollapsed to full pibble Model when ...

Uncollapse output from optimPibbleCollapsed to full pibble Model

Simple verification of passed bassetfit object

Simple verification of passed orthusfit object

Simple verification of passed pibblefit object

Generic method for verifying new objects

Data from Silverman et al. (2019) bioRxiv