R/TMB_out.R

In lawlerem/staRVe: Spatio-Temporal Analysis of Research surVEy data

#' @include classes.R getset.R generics.R
NULL

#################
###           ###
### Construct ###
###           ###
#################

#' @param obj Output of TMB::MakeADFun
#' @param opt Output of nlminb
#' @param sdr Output of TMB::sdreport
#'
#' @noRd
setMethod(
  f = "initialize",
  signature = "TMB_out",
  definition = function(
    .Object,
    obj = list(),
    opt = list(convergence = 0, message = "Model not yet fitted."),
    sdr = structure(numeric(0), class = "sdreport")) {
  obj(.Object)<- obj
  opt(.Object)<- opt
  sdr(.Object)<- sdr

  return(.Object)
})



##############
###        ###
### Access ###
###        ###
##############

# #' @param x An object
# #'
# #' @describeIn TMB_out_class Get TMB::MakeADFun object
#' @noRd
setMethod(
    f = "obj",
    signature = "TMB_out",
    definition = function(x) {
  return(x@obj)
})

# #' @param x An object
# #' @param value A replacement value
# #'
# #' @describeIn TMB_out_class Set TMB::MakeADFun object
#' @noRd
setReplaceMethod(
    f = "obj",
    signature = "TMB_out",
    definition = function(x, value) {
  x@obj<- value
  return(x)
})



# #' @param x An object
# #'
# #' @describeIn TMB_out_class Get output of optimizer
#' @noRd
setMethod(
    f = "opt",
    signature = "TMB_out",
    definition = function(x) {
  return(x@opt)
})

# #' @param x An object
# #' @param value A replacement value
# #'
# #' @describeIn TMB_out_class Set output of optimizer
#' @noRd
setReplaceMethod(
    f = "opt",
    signature = "TMB_out",
    definition = function(x, value) {
  x@opt<- value
  return(x)
})



# #' @param x An object
# #'
# #' @describeIn TMB_out_class Get output of TMB::sdreport
#' @noRd
setMethod(
    f = "sdr",
    signature = "TMB_out",
    definition = function(x) {
  return(x@sdr)
})

# #' @param x An object
# #' @param value A replacement value
# #'
# #' @describeIn TMB_out_class Set output of TMB::sdreport
#' @noRd
setReplaceMethod(
    f = "sdr",
    signature = "TMB_out",
    definition = function(x, value) {
  x@sdr<- value
  return(x)
})



###################
### Meta-Access ###
###################

#' @param x An object
#'
#' @describeIn TMB_out_class Get convergence message from optimizer
setMethod(
    f = "convergence",
    signature = "TMB_out",
    definition = function(x) {
  return(opt(x)$message)
})