R/EnvNeg_logLik.R

In knygren/glmbayes: Bayesian Generalized Linear Models (iid Samples)

#' Negative Log-Likelihood for a Generalized Linear Model
#'
#' @param b a matrix where each row represents a point at which Negative Log-Likelihood is to be calculated
#' @param y A vector
#' @param x A matrix
#' @param alpha A vector
#' @param wt A vector
#' @param family A family
#' @return The sum of \code{x} and \code{y}
#' @keywords internal
#' @examples
#' 1+1
#' 10+1


Neg_logLik<-function(b, y, x, alpha, wt,family){
  
  ## Add required checks on other inputs at the top
  
  if (is.character(family)) 
    family <- get(family, mode = "function", envir = parent.frame())
  if (is.function(family)) 
    family <- family()
  if (is.null(family$family)) {
    print(family)
    stop("'family' not recognized")
  }
  
  okfamilies <- c("gaussian","poisson","binomial","quasipoisson","quasibinomial","Gamma")
  if(family$family %in% okfamilies){
    if(family$family=="gaussian") oklinks<-c("identity")
    if(family$family=="poisson"||family$family=="quasipoisson") oklinks<-c("log")		
    if(family$family=="binomial"||family$family=="quasibinomial") oklinks<-c("logit","probit","cloglog")		
    if(family$family=="Gamma") oklinks<-c("log")		
    if(family$link %in% oklinks){
      
      ## This may be the R version of these files so may not be using the efficiency of C++
      ## This may be safer
      
      famfunc<-glmbfamfunc(family)
      f1<-famfunc$f1
      f2<-famfunc$f2
      f3<-famfunc$f3
#      f5<-famfunc$f5
#      f6<-famfunc$f6
    }
    else{
      stop(gettextf("link \"%s\" not available for selected family; available links are %s", 
                    family$link , paste(sQuote(oklinks), collapse = ", ")), 
           domain = NA)
      
    }	
    
  }		
  else {
    stop(gettextf("family \"%s\" not available in glmb; available families are %s", 
                  family$family , paste(sQuote(okfamilies), collapse = ", ")), 
         domain = NA)
  }
  
  return(f1(b, y, x, alpha, wt)) 

}