Bayesian Multinomial Logistic Normal Regression

Documentation for package ‘fido’ version 1.1.1

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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