R/logLik.fitRMU.R

In phenology: Tools to Manage a Parametric Function that Describes Phenology and More

#' logLik.fitRMU Return Log Likelihood of a fit for fitRMU
#' @title Return Log Likelihood of a fit generated by fitRMU
#' @author Marc Girondot
#' @return The Log Likelihood value for the fitted model with data
#' @param object A result file generated by fitRMU
#' @param ... Not used
#' @description Return Log Likelihood of a fit generated by fitRMU
#' @family Fill gaps in RMU
#' @examples
#' \dontrun{
#' library(phenology)
#' RMU.name.AtlanticW <- data.frame(mean=c("Yalimapo.French.Guiana", 
#'                                          "Galibi.Suriname", 
#'                                          "Irakumpapy.French.Guiana"), 
#'                                  se=c("se_Yalimapo.French.Guiana", 
#'                                       "se_Galibi.Suriname", 
#'                                       "se_Irakumpapy.French.Guiana"))
#' data.AtlanticW <- data.frame(Year=c(1990:2000), 
#'       Yalimapo.French.Guiana=c(2076, 2765, 2890, 2678, NA, 
#'                                6542, 5678, 1243, NA, 1566, 1566),
#'       se_Yalimapo.French.Guiana=c(123.2, 27.7, 62.5, 126, NA, 
#'                                  230, 129, 167, NA, 145, 20),
#'       Galibi.Suriname=c(276, 275, 290, NA, 267, 
#'                        542, 678, NA, 243, 156, 123),
#'       se_Galibi.Suriname=c(22.3, 34.2, 23.2, NA, 23.2, 
#'                            4.3, 2.3, NA, 10.3, 10.1, 8.9),
#'       Irakumpapy.French.Guiana=c(1076, 1765, 1390, 1678, NA, 
#'                                3542, 2678, 243, NA, 566, 566),
#'       se_Irakumpapy.French.Guiana=c(23.2, 29.7, 22.5, 226, NA, 
#'                                  130, 29, 67, NA, 15, 20))
#'                            
#' cst <- fitRMU(data=data.AtlanticW, RMU.name=RMU.name.AtlanticW, 
#'                colname.year="Year", model.trend="Constant", 
#'                model.SD="Zero")
#' logLik(cst)
#' AIC(cst)
#' }
#' @method logLik fitRMU
#' @export


logLik.fitRMU <- function(object, ...) {
  l <- -object$value
  n <- sum(!is.na(as.numeric(as.matrix(object$data))))
  attributes(l) <- list(nall=n , nobs=n , df=length(object$par) , class="logLik")
  return(l)
}