Nothing
reorganize <- function(dat, wald, lm, ct, tsr){
var <- dat$var
map <- dat$map
use <- dat$use
if(use$shared.x){
np <- length(wald$par)
tmp <- diag(np)
rownames(tmp) <- rownames(wald$vcov)
colnames(tmp) <- colnames(wald$vcov)
tmp[map$gam.x, map$bet] <- -wald$par[map$phi.x]
tmp[map$gam.x, map$phi.x] <- wald$par[map$bet]
wald$vcov <- tmp %*% wald$vcov %*% t(tmp)
wald$par[map$gam.x] <- wald$par[map$gam.x] - wald$par[map$bet] * wald$par[map$phi.x]
tmp[map$gam.x, map$bet] <- -tsr$par[map$phi.x]
tmp[map$gam.x, map$phi.x] <- tsr$par[map$bet]
tsr$vcov <- tmp %*% tsr$vcov %*% t(tmp)
tsr$par[map$gam.x] <- tsr$par[map$gam.x] - tsr$par[map$bet] * tsr$par[map$phi.x]
}
wald$map <- map
wald$var <- var
wald$use <- use
par <- wald$par
vcov <- wald$vcov
residuals <- wald$diag$residuals
fitted.values <- wald$diag$fitted.values
mu <- dat$mu
sigma <- dat$sigma
residuals <- residuals * sigma
fitted.values <- fitted.values * sigma
wald$par <- NULL
wald$vcov <- NULL
wald$diag <- NULL
###############
tmp <- rescale(par, vcov, map, mu, sigma)
par <- tmp$par
vcov <- tmp$vcov
sigma2 <- par[c(map$c0, map$c1)]
lm$ci <- lm$ci / sigma
tmp <- rescale(tsr$par, tsr$vcov, map, mu, sigma)
tsr$par <- tmp$par
tsr$vcov <- tmp$vcov
# par and vcov returned are different from the estimated parameters
# if shared covariates are used in both models.
# returned par and its vcov are subject to parameterization used in underlying models
# see Assumptions 1 and 2 for underlying models and their parameters
fit <- list(sigma2 = sigma2,
residuals = residuals, fitted.values = fitted.values,
coefficients = par, vcov = vcov,
wald = wald, lm = lm, ct = ct, tsr = tsr)
}
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