on getCatchWgt

[einarhjorleifsson]

This issue is not a bug, but rather a question of preventing inadvertent use of the dataproduct downstream.

Now the help file states: "Calculate the total reported catch weight by species and haul." I initially interpreted this to be the actual catch in the haul. But if I understand things correctly the interpretation of the value in CatCatchWeight in the HL-data is dependent on the DataType in the HH-data. I.e. standardized to one hour if DataType is "C", otherwise ias reported in the haul.

So question if this function should not in addition return an explicit cpue value and make a clear distinction between that value and CatchWgt in the help file (also if zero's should not explicitly be returned, see sidenote below).

Below is a code that illustrate the difference these two values would give in a typical downstream user analysis:

library(icesDatras)
library(tidyverse)
dr_add_id <- function (d) {
  d |> 
    dplyr::mutate(.id = paste(Survey, Year, Quarter, Country, 
                               Ship, Gear, StNo, HaulNo, sep = ":"))
}
cw <- 
  icesDatras::getCatchWgt("NS-IBTS", years = 2020:2025, quarters = 1, aphia = 126437) |> 
  dr_add_id() |>  
  select(.id, Valid_Aphia, CatchWgt)
hh <- 
  icesDatras::getDATRAS("HH", "NS-IBTS", 2020:2025, 1) |> 
  dr_add_id() |> 
  select(.id, DataType, HaulDur, Year)
d <- 
  hh |> 
  left_join(cw,
            by = join_by(.id)) |> 
  as_tibble() |> 
  mutate(CatchWgt = replace_na(CatchWgt, 0),    # This may not be kosher is some cases
         wgt = case_when(DataType == "C" ~ CatchWgt/60 * HaulDur,
                         .default = CatchWgt),
         cpue = wgt / HaulDur * 60)
d |> 
  count(Year, DataType) |> 
  ggplot(aes(Year, n, colour = DataType)) +
  geom_point()
d |> 
  select(.id, Year, CatchWgt, cpue) |> 
  gather(var, value, -c(.id, Year)) |> 
  ggplot(aes(Year, value, colour = var)) +
  stat_summary(fun.data = "mean_cl_boot")

Side note: In the above the missing CatchWgt are interpreted as zero. I have however come across cases where the CatCatchWgt may be missing for some CatIdentifier within the same tow. I guess these should return an NA in the CatchWgt of a particular haul (or possibly be a QC-flag issue), but cases where the species is not reported at all in the HL-data for a given haul should be explicitly set to zero.

Just some food for thought.