R/show.R

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

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

#' @param object An object
#'
#' @describeIn dag_class Print method
setMethod(
    f = "show",
    signature = "dag",
    definition = function(object) {
  n_nodes<- length(edges(object))
  cat("\n")
  if( n_nodes > 0 ) {
    avg_deg<- median(
      do.call(
        c,
        lapply(
          edges(object),
          function(x) length(x[[2]])
        )
      )
    )
    avg_dist<- mean(
      do.call(
        c,
        lapply(
          distances(object),
          c
        )
      )
    )
    print(paste0(
      "A directed acyclic graph with ", n_nodes, " nodes, with an median in-degree of ", avg_deg, "."
    ))
    print(paste0(
      "The average edge distance is ", round(avg_dist, 2), "", distance_units(object), "."
    ))
  } else {
    print(paste0("An empty directed acyclic graph."))
  }

  return(invisible(object))
})

# setMethod(f = "show",
#           signature = "process_parameters",
#           definition = function(object) {
# Default is fine
# })

# setMethod(f = "show",
#           signature = "process",
#           definition = function(object) {
# Default is fine
# })

# setMethod(f = "show",
#           signature = "observation_parameters",
#           definition = function(object) {
# Default is fine
# })

# setMethod(f = "show",
#           signature = "observations",
#           definition = function(object) {
# Default is fine
# })

# setMethod(f = "show",
#           signature = "settings",
#           definition = function(object) {
# Default is fine
# })

#' @param object An object
#'
#' @export
#' @describeIn tracing_class Print method
setMethod(
    f = "show",
    signature = "tracing",
    definition = function(object) {
  cat("\n")

  cat("Time elapsed while fitting the model:")
  cat("\n")
  print(timing(object))
  cat("\n\n")

  cat("Estimated parameter hessian matrix:")
  cat("\n")
  print(parameter_hessian(object))
  cat("\n\n")

  cat("Estimated parameter covariance matrix:")
  cat("\n")
  print(parameter_covariance(object))
  cat("\n")

  return(invisible(object))
})

#' @param object An object
#'
#' @export
#' @describeIn TMB_out_class Print method
setMethod(
    f = "show",
    signature = "TMB_out",
    definition = function(object) {
  cat("\n")
  cat("An class containing TMB objects: obj, opt, and sdr.")
  cat("\n")

  return(invisible(object))
})



#' @param object An object
#'
#' @export
#' @describeIn starve_class Print method
setMethod(
    f = "show",
    signature = "starve",
    definition = function(object) {
  cat("A starve model object\n\n")
  cat("Model formula: ")
  print(formula(object))

  cat("Response distribution: ")
  cat(response_distribution(object))
  cat("\n")

  cat("Link function: ")
  cat(link_function(object))
  cat("\n")

  cat("Optimizer message: ")
  cat(convergence(object))
  cat("\n\n")


  cat(paste(
    "Data is a simple feature collection with", nrow(dat(object)), "features\n"
  ))
  cat("CRS: ")
  cat(format(sf::st_crs(dat(object))))
  cat("\n")
  cat("Bounding times: ")
  t<- time_from_formula(formula(object), dat(object))
  cat(c(min(t), max(t)))
  cat("\n")
  cat("Bounding box:\n")
  print(sf::st_bbox(dat(object)))
  cat("\n")


  return(invisible(object))
})


# setMethod(f = "show",
#           signature = "parameters",
#           definition = function(object) {
# Default is fine
# })