FitConstrainedGLLVM: Fits a GLLVM to data

In oharar/LatentINLA: Package to Write GLLVMs in INLA

Fits a GLLVM to data

Description

Fits a GLLVM to data

Usage

FitConstrainedGLLVM(Y, X, formula = NULL, nLVs = 1, Family = "gaussian", ColScorePriorsd = 10, INLAobj = FALSE, ...)

Arguments

Y	A data frame or matrix with the response
X	A data frame or matrix of covariates
formula	for predictors in the ordination
nLVs	The number of latent variables required
Family	A string indicating the likelihood family. If length 1, it gets repeated with one for each column of the data.
ColScorePriorsd	Prior standard deviation for column scores (the betas for INLA insiders), defaults to 10
INLAobj	Should the full INLA object be included in the output object? Defaults to FALSE
...	More arguments to be passed to inla()

Value

A list with fixed, colscores, and roweffs: the posterior summaries for the fixed effects, the column scores and the row effects respectively

Examples

set.seed(2021)
NRows <- 200
nLVs <- 1
NCol <- 20
NCovs <- 2
Intercept <- 2
CovBeta <- matrix(c(-0.2, 0.7, 0.7, -0.2), nrow=2)
ColEffs <- matrix(c(1,rnorm(nLVs*(NCol-1), 0, 0.5)), ncol=NCol)
X <- matrix(10+1:(NCovs*NRows), nrow=NRows,
            dimnames = list(NULL, paste0("X", 1:NCovs)))
LV.true <- rowSums(apply(X, 2, scale)%*%CovBeta)
E.Y <- Intercept+LV.true%*%ColEffs
TrueFixed <- c(Intercept, CovBeta)
Y.mat <- apply(E.Y, 2, function(e) rpois(length(e), exp(e)))
colnames(Y.mat) <- paste0("Col", 1:ncol(Y.mat))
## Not run: 
  Try1 <- FitConstrainedGLLVM(Y=Y.mat, X=X, nLVs=1, Family="poisson", INLAobj = FALSE)
  Try2 <- FitConstrainedGLLVM(Y=Y.mat, X=X, nLVs=2, Family="poisson",
                              INLAobj = FALSE, verbose=TRUE)

## End(Not run)

oharar/LatentINLA documentation built on Sept. 13, 2023, 5:18 p.m.