# Bayesian Multinomial Logistic Normal Regression

## Documentation for package ‘fido’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C F G H K L M N O P R S T U V Y

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

## -- A --

access_dims | Generic method for accessing model fit dimensions
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

## -- B --

basset | Interface to fit basset models
basset_fit | Interface to fit basset models

## -- C --

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

## -- F --

fido | fido: Fitting and Analysis of Multinomial Logistic Normal Models
fido_package | fido: Fitting and Analysis of Multinomial Logistic Normal Models
fido_transforms | Transform Fit fido Parameters to other representations

## -- G --

gather_array | Gather Multidimensional Array to Tidy Tibble
gradPibbleCollapsed | Calculations for the Collapsed Pibble Model

## -- H --

hessPibbleCollapsed | Calculations for the Collapsed Pibble Model

## -- K --

kernels | Multivariate RBF Kernel

## -- L --

lambda_to_iqlr | Transform Lambda into IQLR (Inter-Quantile Log-Ratio)
LINEAR | Multivariate RBF Kernel
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

## -- M --

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 | mongrel
mongrel-deprecated | mongrel

## -- N --

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_categories | Generic method for getting and setting dimension names of fit object
names_categories.pibblefit | Generic method for getting and setting dimension names of fit object
names_categories<- | Generic method for getting and setting dimension names of fit object
names_categories<-.pibblefit | Generic method for getting and setting dimension names of fit object
names_coords | Generic method for getting and setting dimension names of fit object
names_coords.pibblefit | Generic method for getting and setting dimension names of fit object
names_covariates | Generic method for getting and setting dimension names of fit object
names_covariates.pibblefit | Generic method for getting and setting dimension names of fit object
names_covariates<- | Generic method for getting and setting dimension names of fit object
names_covariates<-.pibblefit | Generic method for getting and setting dimension names of fit object
names_samples | Generic method for getting and setting dimension names of fit object
names_samples.pibblefit | Generic method for getting and setting dimension names of fit object
names_samples<- | Generic method for getting and setting dimension names of fit object
names_samples<-.pibblefit | Generic method for getting and setting dimension names of fit object
name_dims | Generic method for getting and setting dimension names of fit object
ncategories | Generic method for accessing model fit dimensions
ncategories.orthusfit | Generic method for accessing model fit dimensions
ncategories.pibblefit | Generic method for accessing model fit dimensions
ncovariates | Generic method for accessing model fit dimensions
ncovariates.orthusfit | Generic method for accessing model fit dimensions
ncovariates.pibblefit | Generic method for accessing model fit dimensions
niter | Generic method for accessing model fit dimensions
niter.orthusfit | Generic method for accessing model fit dimensions
niter.pibblefit | Generic method for accessing model fit dimensions
nsamples | Generic method for accessing model fit dimensions
nsamples.orthusfit | Generic method for accessing model fit dimensions
nsamples.pibblefit | Generic method for accessing model fit dimensions

## -- O --

oalr | Log-Ratio transforms for orthus objects
oalrInv | Log-Ratio transforms for orthus objects
oalrvar2alrvar | Convert orthus covariance matricies between representations
oalrvar2clrvar | Convert orthus covariance matricies between representations
oalrvar2ilrvar | Convert orthus covariance matricies between representations
oclr | Log-Ratio transforms for orthus objects
oclrInv | Log-Ratio transforms for orthus objects
oclrvar2alrvar | Convert orthus covariance matricies between representations
oclrvar2ilrvar | Convert orthus covariance matricies between representations
oglr | Log-Ratio transforms for orthus objects
oglrInv | Log-Ratio transforms for orthus objects
oilr | Log-Ratio transforms for orthus objects
oilrInv | Log-Ratio transforms for orthus objects
oilrvar2alrvar | Convert orthus covariance matricies between representations
oilrvar2clrvar | Convert orthus covariance matricies between representations
oilrvar2ilrvar | Convert orthus covariance matricies between representations
optimPibbleCollapsed | Function to Optimize the Collapsed Pibble Model
orthus | Interface to fit orthus models
orthusfit | Create orthusfit object
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

## -- P --

pcrbias_mock | Data from Silverman et al. (2019) bioRxiv
pibble | Interface to fit pibble models
pibblefit | Create pibblefit object
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
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 | Generic Method to Plot Posterior Predictive Summaries
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.

## -- R --

r2 | Generic Method to Calculate R2 for Fitted Model
r2.bassetfit | Generic Method to Calculate R2 for Fitted Model
r2.pibblefit | Generic Method to Calculate R2 for Fitted Model
random_pibble_init | Provide random initialization for pibble model
reapply_coord | Holds information on coordinates system to later be reapplied
refit | Generic method for fitting model from passed model fit object
refit.bassetfit | Interface to fit basset models
refit.pibblefit | Interface to fit pibble models
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
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)

## -- S --

sample_prior | Generic method for sampling from prior distribution of object
sample_prior.pibblefit | Sample from the prior distribution of pibblefit object
SE | Multivariate RBF Kernel
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

## -- T --

to_alr | Transform Fit fido Parameters to other representations
to_alr.orthusfit | Transform Fit fido Parameters to other representations
to_alr.pibblefit | Transform Fit fido Parameters to other representations
to_clr | Transform Fit fido Parameters to other representations
to_clr.orthusfit | Transform Fit fido Parameters to other representations
to_clr.pibblefit | Transform Fit fido Parameters to other representations
to_ilr | Transform Fit fido Parameters to other representations
to_ilr.orthusfit | Transform Fit fido Parameters to other representations
to_ilr.pibblefit | Transform Fit fido Parameters to other representations
to_proportions | Transform Fit fido Parameters to other representations
to_proportions.orthusfit | Transform Fit fido Parameters to other representations
to_proportions.pibblefit | Transform Fit fido Parameters to other representations

## -- U --

uncollapsePibble | Uncollapse output from optimPibbleCollapsed to full pibble Model
uncollapsePibble_sigmaKnown | Uncollapse output from optimPibbleCollapsed to full pibble Model when Sigma is known

## -- V --

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

## -- Y --

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