Nothing
lmm.diago <- function(Y, X = matrix(1, nrow=length(Y)), eigenK, p = 0, method = c("newton", "brent"), min_h2 = 0, max_h2 = 1,
verbose = getOption("gaston.verbose", TRUE), tol = .Machine$double.eps^0.25) {
if( any(is.na(Y)) )
stop('Missing data in Y.')
if(!is.null(X)) {
if( length(Y)<(ncol(X)+max(p)) )
stop('The total number of covariables and PCs as fixed effects cannot exceed the number of observations.')
if( length(Y)!=nrow(X) )
stop('Length of Y and the number of rows of X differ.')
} else if( length(Y) < max(p) )
stop('The total number of covariables and PCs as fixed effects cannot exceed the number of observations.')
Sigma <- eigenK$values
if( length(Y)!=length(Sigma) )
stop('Length of Y and number of eigenvalues differ.')
w <- which(Sigma < 1e-6)
Sigma[w] <- 1e-6
U <- eigenK$vectors
method <- match.arg(method)
brent <- (method == "brent")
if(is.null(X))
return(.Call('gg_fit_diago_nocovar', PACKAGE = "gaston", Y, p, Sigma, U, min_h2, max_h2, tol, verbose, brent))
else
return(.Call('gg_fit_diago', PACKAGE = "gaston", Y, X, p, Sigma, U, min_h2, max_h2, tol, verbose, brent))
}
lmm.diago.likelihood <- function(tau, s2, h2, Y, X = matrix(1, nrow=length(Y)), eigenK, p = 0) {
if( any(is.na(Y)) )
stop('Missing data in Y.')
if(!is.null(X)) {
if( length(Y)<(ncol(X)+max(p)) )
stop('The total number of covariables and PCs as fixed effects cannot exceed the number of observations.')
if( length(Y)!=nrow(X) )
stop('Length of Y and the number of rows of X differ.')
} else if( length(Y) < max(p) )
stop('The total number of covariables and PCs as fixed effects cannot exceed the number of observations.')
Sigma <- eigenK$values
if( length(Y)!=length(Sigma) )
stop('Length of Y and number of eigenvalues differ.')
if(!missing(tau) & !missing(s2))
if(is.null(X))
.Call("gg_diago_likelihood2_nocovar", PACKAGE = "gaston", tau, s2, p, Y, Sigma, eigenK$vectors)
else
.Call("gg_diago_likelihood2", PACKAGE = "gaston", tau, s2, p, Y, X, Sigma, eigenK$vectors)
else if(!missing(h2))
if(is.null(X))
.Call("gg_diago_likelihood1_nocovar", PACKAGE = "gaston", h2, p, Y, Sigma, eigenK$vectors)
else
.Call("gg_diago_likelihood1", PACKAGE = "gaston", h2, p, Y, X, Sigma, eigenK$vectors)
else
stop("To compute likelihood, provide tau and s2 values, or h2 value")
}
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