orthusfit: Create orthusfit object

In jsilve24/mongrel: Bayesian Multinomial Logistic Normal Regression

Description

Create orthusfit object

Usage

orthusfit(D, N, Q, P, coord_system, iter = NULL, alr_base = NULL,
  ilr_base = NULL, Eta = NULL, Lambda = NULL, Sigma = NULL,
  Sigma_default = NULL, Z = NULL, Y = NULL, X = NULL,
  upsilon = NULL, Theta = NULL, Xi = NULL, Xi_default = NULL,
  Gamma = NULL, init = NULL, names_categories = NULL,
  names_samples = NULL, names_Zdimensions = NULL,
  names_covariates = NULL)

Arguments

D	number of multinomial categories
N	number of samples
Q	number of covariates
P	Dimension of second dataset (e.g., nrows(Z) )
coord_system	coordinate system objects are represented in (options include "alr", "clr", "ilr", and "proportions")
iter	number of posterior samples
alr_base	integer category used as reference (required if coord_system=="alr")
ilr_base	(D x D-1) contrast matrix (required if coord_system=="ilr")
Eta	Array of samples of Eta
Lambda	Array of samples of Lambda
Sigma	Array of samples of Sigma (null if coord_system=="proportions")
Sigma_default	Array of samples of Sigma in alr base D, used if coord_system=="proportions"
Z	PxN matrix of real valued observations
Y	DxN matrix of observed counts
X	QxN design matrix
upsilon	scalar prior dof of inverse wishart prior
Theta	prior mean of Lambda
Xi	Matrix of prior covariance for inverse wishart (null if coord_system=="proportions")
Xi_default	Matrix of prior covariance for inverse wishart in alr base D (used if coord_system=="proportions")
Gamma	QxQ covariance matrix prior for Lambda
init	matrix initial guess for Lambda used for optimization
names_categories	character vector
names_samples	character vector
names_Zdimensions	character vector
names_covariates	character vector

Value

object of class pibblefit

See Also

pibble

jsilve24/mongrel documentation built on Jan. 27, 2022, 9:54 p.m.