R/convert_lengths.R

In Delta-Stewardship-Council/deltafish: Accesses an Integrated Fish Count and Length Dataset from the San Francisco Delta

#' Convert fish length
#'
#' Converts fish length data using the length conversion table. Returns an arrow dataset.
#' This function is only needed to convert Suisun survey data.
#'
#' @param data A DBI table that can be treated like a data.frame, with fish data. See `open_fish()`
#'
#' @importFrom magrittr %>%
#' @importFrom rlang .data
#'
#' @return data_conv A DBI table with converted lengths
#' @export
#'
#' @examples
#' \dontrun{
#' library(dplyr)
#' con <- open_database()
#' fish <- open_fish(con) %>%
#'   filter(Taxa %in% c("Dorosoma petenense", "Morone saxatilis", "Spirinchus thaleichthys"))
#'
#' fish_conv <- convert_lengths(fish) %>%
#'   collect()
#' close_database(con)
#' }
#'
convert_lengths <- function(data) {
  if (any(!c("Taxa", "Length") %in% colnames(data))) {
    stop("Input data must have Taxa and Length column names")
  }
  if (!("Source" %in% colnames(data))) {
    con <- data[["src"]][["con"]]
    surv <- open_survey(con) %>%
      dplyr::select("SampleID", "Source")

    data_prep <- dplyr::left_join(data, surv)
  } else {
    data_prep <- data
  }

  sources <- data_prep %>%
    dplyr::distinct(.data$Source) %>%
    dplyr::collect() %>%
    dplyr::pull("Source")

  if (!("Suisun" %in% sources)) {
    warning("No Suisun data found in input data. This function only operates on Suisun data.")
    return(data)
  }

  con <- data[["src"]][["con"]]
  l <- open_length_conv(con)

  sp <- l %>%
    dplyr::distinct(.data$Species) %>%
    dplyr::collect() %>%
    dplyr::pull("Species")

  data_f <- data_prep %>%
    dplyr::left_join(l, by = c("Taxa" = "Species")) %>%
    dplyr::mutate(Length = ifelse(.data$Source == "Suisun" & .data$Taxa %in% sp,
      .data$Intercept + .data$Slope * .data$Length,
      .data$Length
    )) %>%
    dplyr::select(-"Intercept", -"Slope")

  # if source wasn't in input data drop it
  if (!("Source" %in% colnames(data))) {
    data_f <- data_f %>%
      dplyr::select(-"Source")
  }

  return(data_f)
}