RISK_CCFA               Data from Gevers et al. (2014)
RISK_CCFA_otu           Data from Gevers et al. (2014)
RISK_CCFA_sam           Data from Gevers et al. (2014)
RISK_CCFA_tax           Data from Gevers et al. (2014)
Y                       Data from Silverman et al. (2019) bioRxiv
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
basset_fit              Interface to fit basset models
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
convert_orthus_covariance
                        Convert orthus covariance matricies between
                        representations
create_default_ilr_base
                        Create a default ILR base
fido_package            fido: Fitting and Analysis of Multinomial
                        Logistic Normal Models
fido_transforms         Transform Fit fido Parameters to other
                        representations
gather_array            Gather Multidimensional Array to Tidy Tibble
kernels                 Multivariate RBF Kernel
lambda_to_iqlr          Transform Lambda into IQLR (Inter-Quantile
                        Log-Ratio)
lmvgamma                Log of Multivarate Gamma Function - Gamma_p(a)
lmvgamma_deriv          Derivative of Log of Multivariate Gamma
                        Function - Gamma_p(a)
loglikPibbleCollapsed   Calculations for the Collapsed Pibble Model
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
miniclo                 Closure operator
miniclo_array           Closure Operation applied to array on margin
mongrel-deprecated      mongrel
name                    Generic method for applying names to an object
name.orthusfit          S3 for orthusfit apply names to orthusfit
                        object
name.pibblefit          S3 for pibblefit apply names to pibblefit
                        object
names_covariates.pibblefit
                        Generic method for getting and setting
                        dimension names of fit object
ncategories.pibblefit   Generic method for accessing model fit
                        dimensions
optimPibbleCollapsed    Function to Optimize the Collapsed Pibble Model
orthus_fit              Interface to fit orthus models
orthus_lr_transforms    Log-Ratio transforms for orthus objects
orthus_sim              Simulate simple orthus dataset and priors (for
                        testing)
orthus_tidy_samples     Convert orthus samples of Eta Lambda and Sigma
                        to tidy format
orthusfit               Create orthusfit object
pcrbias_mock            Data from Silverman et al. (2019) bioRxiv
pibble_fit              Interface to fit pibble models
pibble_sim              Simulate simple pibble dataset and priors (for
                        testing)
pibble_tidy_samples     Convert pibble samples of Eta Lambda and Sigma
                        to tidy format
pibblefit               Create pibblefit object
plot.pibblefit          Plot Summaries of Posterior Distribution of
                        pibblefit Parameters
ppc                     Generic method for visualizing posterior
                        predictive checks
ppc.pibblefit           Visualization of Posterior Predictive Check of
                        fit model
ppc_summary.pibblefit   Generic Method to Plot Posterior Predictive
                        Summaries
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.
r2                      Generic Method to Calculate R2 for Fitted Model
random_pibble_init      Provide random initialization for pibble model
refit                   Generic method for fitting model from passed
                        model fit object
req                     Generic method for ensuring object contains
                        required elements
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
sample_prior            Generic method for sampling from prior
                        distribution of object
sample_prior.pibblefit
                        Sample from the prior distribution of pibblefit
                        object
store_coord             Holds information on coordinates system to
                        later be reapplied
summarise_posterior     Shortcut for summarize variable with quantiles
                        and mean
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                  Generic method for verifying new objects
verify.bassetfit        Simple verification of passed bassetfit object
verify.orthusfit        Simple verification of passed orthusfit object
verify.pibblefit        Simple verification of passed pibblefit object
