plot_iphc_map: Plot the locations of the IPHC stations for a given year,...

In pbs-assess/gfiphc: Data Extraction and Analysis for Groundfish Data from the IPHC Longline Survey in BC

Plot the locations of the IPHC stations for a given year, with various

Description

Options include whether or not a given species was caught in that year, or indicating showing stations within a given area, or not referencing a particular species (just showing stations), or showing non-standard stations.

Usage

plot_iphc_map(
  set_counts_of_sp,
  sp_short_name = NULL,
  years,
  main_title = NULL,
  mar_val = c(1.8, 2, 1, 0.5),
  mgp_val = c(1.6, 0.5, 0),
  lat_cut_off = 50.6,
  lon_cut_off_1 = -130,
  lon_cut_off_2 = -128.25,
  pch_pos_count = 19,
  pch_zero_count = 1,
  pch_non_standard = 4,
  cex_val = 1,
  add_to_existing = FALSE,
  indicate_in_area = FALSE,
  indicate_standard = TRUE,
  include_legend = TRUE,
  ...
)

Arguments

set_counts_of_sp	input tibble of the species of interest, likely generated from cache_pbs_data_iphc (which seems to save a list with the first element the desired tibble), with column names year, station, lat, lon, E_it, N_it, C_it, E_it20, N_it20, C_it20, usable, and in_area if indicate_in_area is TRUE
sp_short_name	short name species of interest to have in legend, if NULL then plots all stations labelled as usable and unusable, but with no catch rates. Still needs set_counts_of_sp input tibble (can be any species, as they all have all stations documented).
years	year of interest. See vignettes for movie code.
main_title	title for map, if NULL then is All years stations
mar_val	mar values to reduce whitespace around maps
mgp_val	mgp values to reduce whitespace around maps
lat_cut_off	latitudinal cut off near top of Vancouver Island, below which stations are excluded when constructing Series A and B; this is just below all stations from 1995-1998, so that Series A and B include all stations for 1995-1998. If NULL then nothing plotted
lon_cut_off_1	left-hand end of line (longitude) to show cut off
lon_cut_off_2	right-hand end of line (longitude) to show cut off
pch_pos_count	pch for positive counts (or sets inside area if indicate_in_area is TRUE)
pch_zero_count	pch for zero counts (or sets outside area if indicate_in_area is FALSE)
pch_non_standard	pch for showing non-standard stations for that year
cex_val	cex size of plotted circles (or whatever is chosen using above pch options
add_to_existing	if TRUE then add to an existing plot, if FALSE then create new map using plot_BC()
indicate_in_area	indicate whether or not station is within a specficied area, as indicated by TRUE/FALSE in set_counts_of_sp$in_area
indicate_standard	indicate whether or not station is part of the standard stations or an expansion (in 2018, 2020, and later), as indicated by Y/N in set_counts_of_sp$standard
include_legend	whether to include legend or not (TRUE/FALSE)
...	extra arguments to par()

Details

If possible, also show whether the species was caught in the first 20 hooks and only caught after the first 20 hooks. Uses PBSmapping style of plot, as used in the Redbanded and Yelloweye Rockfish stock assessments.

Value

A map of the IPHC survey stations for that year and species, with a legend describing the points.

Author(s)

Andrew Edwards

Examples

## Not run: 
# See vignette `data_for_one_species`
sp <- "yelloweye rockfish"
sp_set_counts <- readRDS(sp_hyphenate(sp))    # Need .rds
  saved already
plot_iphc_map(sp_set_counts$set_counts, sp_short_name = "Yelloweye", years =
  2003)  # one year
# many years (matches maps in Yamanka et al. (2018) Yelloweye assessment,
#  except stations 14A, 19IC, and 3D that are now marked as unusable):
for(i in unique(sp_set_counts$set_counts$year)){
  plot_iphc_map(sp_set_counts$set_counts,
                sp_short_name = "Yelloweye",
                years = i)
  invisible(readline(prompt="Press [enter] to continue"))
}

# Hooks with no bait, showing non-standard as crosses :
plot_iphc_map(hooks_with_bait$set_counts,
              sp = "Hooks with bait",
              years = 2018,
              indicate_standard = TRUE)

# Just the stations, with no species information:
plot_iphc_map(sp_set_counts$set_counts,
              sp_short_name = NULL,
              years = 2008)

## End(Not run)

pbs-assess/gfiphc documentation built on July 4, 2023, 1:13 p.m.