R/get_SC125_Lamprey.R

In AdamCottrill/glfishr: Fetch fisheries assessment data from the FN Portal

#' Get SC125_Lamprey - Lamprey Wound data from Creel_Portal API
#'
#' This function accesses the api endpoint to for SC125 Lamprey
#' records. SC125 Lam records contain information about the individual
#' lamprey wounds observed on a sampled fish.  Historically, lamprey
#' wounds were reported as a single field (XLAM) in the SC125 table.
#' In the early 2000 the Great Lakes fishery community agreed to
#' capture lamprey wounding data in a more consistent fashion the
#' basin, using the conventions described in Ebener et al. 2006.  The
#' SC125Lam table captures data from individual lamprey wounds
#' collected using those conventions.  A sampled fish with no observed
#' wound will have a single record in this table (with lamijc value of
#' 0), while fish with lamprey wounds, will have one record for every
#' observed wound. This function takes an optional filter list which
#' can be used to return records based on several different attributes
#' of the wound (wound type, degree of healing, and wound size) as
#' well as, attributes of the sampled fish such as the species, or
#' group code, or attributes of the interview, or the creel(s) that
#' the samples were collected in.
#'
#' Use \code{show_filters("sc125lamprey")} to see the full list of
#' available filter keys (query parameters). Refer to
#' \url{https://intra.glis.mnr.gov.on.ca/creels/api/v1/swagger/} and
#' filter by "sc125lamprey" for additional information.
#'
#' @param filter_list list
#' @param show_id When 'FALSE', the default, the 'id' and 'slug'
#'   fields are hidden from the data frame. To return these columns as
#'   part of the data frame, use 'show_id = TRUE'.
#' @param to_upper - should the names of the dataframe be converted to
#'   upper case?
#'
#' @author Adam Cottrill \email{adam.cottrill@@ontario.ca}
#' @return dataframe
#' @export
#' @examples
#'
#' sc125Lam <- get_SC125_Lamprey(list(lake = "HU", spc = "081", year = 2000))
#'
#'
#' filters <- list(lake = "HU", spc = "076", year__gte = 2018)
#' sc125Lam <- get_SC125_Lamprey(filters)
#' sc125Lam <- get_SC125_Lamprey(filters, show_id = TRUE)
get_SC125_Lamprey <- function(filter_list = list(), show_id = FALSE,
                              to_upper = TRUE) {
  recursive <- ifelse(length(filter_list) == 0, FALSE, TRUE)
  query_string <- build_query_string(filter_list)
  check_filters("sc125lamprey", filter_list, api_app = "creels")
  my_url <- sprintf(
    "%s/sc125lamprey/%s",
    get_sc_portal_root(),
    query_string
  )
  payload <- api_to_dataframe(my_url, recursive = recursive)
  payload <- prepare_payload(payload, show_id, to_upper)

  return(payload)
}