Helper function for PLN initialization. — compute_PLN_starting

Barebone function to compute starting points for B, M and S when fitting a PLN. Mostly intended for internal use.

compute_PLN_starting_point(Y, X, O, w, s = 0.1)

Arguments

Y: Response count matrix
X: Covariate matrix
O: Offset matrix (in log-scale)
w: Weight vector (defaults to 1)
s: Scale parameter for S (defaults to 0.1)

Value

a named list of starting values for model parameter B and variational parameters M and S used in the iterative optimization algorithm of PLN()

Details

The default strategy to estimate B and M is to fit a linear model with covariates X to the response count matrix (after adding a pseudocount of 1, scaling by the offset and taking the log). The regression matrix is used to initialize B and the residuals to initialize M. S is initialized as a constant conformable matrix with value s.

Examples

if (FALSE) { # \dontrun{
data(barents)
Y <- barents$Abundance
X <- model.matrix(Abundance ~ Latitude + Longitude + Depth + Temperature, data = barents)
O <- log(barents$Offset)
w <-- rep(1, nrow(Y))
compute_PLN_starting_point(Y, X, O, w)
} # }