###### postSim ######

setGeneric("postSim", 
           function(object, n.sims=1000){
             standardGeneric("postSim")
           }
)

setClass("postSim", 
         slots = c(coef = "matrix",
                   sigma = "numeric")
)

setClass("postSim.polr", 
         slots = c(coef = "matrix",
                   zeta = "matrix")
)

setMethod("postSim", signature(object = "lm"),
          function(object, n.sims=1000)
          {
            object.class <- class(object)[[1]]
            summ <- summary (object)
            coef <- summ$coef[,1:2,drop=FALSE]
            dimnames(coef)[[2]] <- c("coef.est","coef.sd")
            sigma.hat <- summ$sigma
            beta.hat <- coef[,1,drop = FALSE]
            V.beta <- summ$cov.unscaled
            n <- summ$df[1] + summ$df[2]
            k <- summ$df[1]
            sigma <- rep (NA, n.sims)
            beta <- array (NA, c(n.sims,k))
            dimnames(beta) <- list (NULL, rownames(beta.hat))
            for (s in 1:n.sims){
              sigma[s] <- sigma.hat*sqrt((n-k)/rchisq(1,n-k))
              beta[s,] <- MASS::mvrnorm (1, beta.hat, V.beta*sigma[s]^2)
            }
            
            ans <- new("postSim",
                       coef = beta,
                       sigma = sigma)
            return (ans)
          }
)


setMethod("postSim", signature(object = "glm"),
          function(object, n.sims=1000)
          {
            object.class <- class(object)[[1]]
            summ <- summary (object, correlation=TRUE, dispersion = object$dispersion)
            coef <- summ$coef[,1:2,drop=FALSE]
            dimnames(coef)[[2]] <- c("coef.est","coef.sd")
            beta.hat <- coef[,1,drop=FALSE]
            sd.beta <- coef[,2,drop=FALSE]
            corr.beta <- summ$corr
            n <- summ$df[1] + summ$df[2]
            k <- summ$df[1]
            V.beta <- corr.beta * array(sd.beta,c(k,k)) * t(array(sd.beta,c(k,k)))
            beta <- array (NA, c(n.sims,k))
            dimnames(beta) <- list (NULL, dimnames(beta.hat)[[1]])
            for (s in 1:n.sims){
              beta[s,] <- MASS::mvrnorm (1, beta.hat, V.beta)
            }
            # Added by Masanao
            beta2 <- array (0, c(n.sims,length(coefficients(object))))
            dimnames(beta2) <- list (NULL, names(coefficients(object)))
            beta2[,dimnames(beta2)[[2]]%in%dimnames(beta)[[2]]] <- beta
            # Added by Masanao
            sigma <- rep (sqrt(summ$dispersion), n.sims)
            
            ans <- new("postSim",
                       coef = beta2,
                       sigma = sigma)
            return(ans)
          }
)


setMethod("postSim", signature(object = "polr"),
          function(object, n.sims=1000){
            x <- as.matrix(model.matrix(object))
            coefs <- coef(object)
            k <- length(coefs)
            zeta <- object$zeta
            Sigma <- vcov(object)
            
            if(n.sims==1){
              parameters <- t(MASS::mvrnorm(n.sims, c(coefs, zeta), Sigma))
            }else{
              parameters <- MASS::mvrnorm(n.sims, c(coefs, zeta), Sigma)
            }
            ans <- new("postSim.polr",
                       coef = parameters[,1:k,drop=FALSE],
                       zeta = parameters[,-(1:k),drop=FALSE])
            return(ans)
          }
)


setMethod("postSim", signature(object = "svyglm"),
          function(object, n.sims=1000)
          {
            object.class <- class(object)[[2]]
            summ <- summary (object, correlation=TRUE, dispersion = object$dispersion)
            coef <- summ$coef[,1:2,drop=FALSE]
            dimnames(coef)[[2]] <- c("coef.est","coef.sd")
            beta.hat <- coef[,1,drop=FALSE]
            sd.beta <- coef[,2,drop=FALSE]
            corr.beta <- summ$corr
            n <- summ$df[1] + summ$df[2]
            k <- summ$df[1]
            V.beta <- corr.beta * array(sd.beta,c(k,k)) * t(array(sd.beta,c(k,k)))
            beta <- array (NA, c(n.sims,k))
            dimnames(beta) <- list (NULL, dimnames(beta.hat)[[1]])
            for (s in 1:n.sims){
              beta[s,] <- MASS::mvrnorm (1, beta.hat, V.beta)
            }
            beta2 <- array (0, c(n.sims,length(coefficients(object))))
            dimnames(beta2) <- list (NULL, names(coefficients(object)))
            beta2[,dimnames(beta2)[[2]]%in%dimnames(beta)[[2]]] <- beta
            sigma <- rep (sqrt(summ$dispersion), n.sims)
            
            ans <- new("postSim",
                       coef = beta2,
                       sigma = sigma)
            return(ans)
          }
)