make_pages: Make synopsis pages
In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

make_pages

R Documentation

Make synopsis pages

Description

This is the main workhorse function that creates the synopsis pages.

Usage

make_pages(
  dat,
  dat_iphc,
  spp,
  d_geostat_index,
  aspect = 1.35,
  short_page_height_ratio = 0.78,
  width = 11.5,
  debug = FALSE,
  resolution = 170,
  png_format = TRUE,
  spp_file = clean_name(spp),
  report_folder = "report",
  report_lang_folder = "report",
  include_map_square = FALSE,
  map_xlim = c(360, 653),
  map_ylim = c(5275, 6155),
  save_gg_objects = FALSE,
  survey_cols = c(`SYN WCHG` = "#E41A1C", `SYN WCVI` = "#984EA3", `SYN HS` = "#377EB8",
    `SYN QCS` = "#4DAF4A", `HBLL OUT N` = "#FF7F00", `HBLL OUT S` = "#FDBF6F",
    `HBLL INS N/S` = "#A65628", `IPHC FISS` = "#F781BF", `MSSM WCVI` = "#6c6c6c",
    `MSSM Geostat` = "#6c6c6c", `MSA HS` = "#6c6c6c", `SYN HS/QCS/WCHG/WCVI` = "#6c6c6c",
    `SYN HS/QCS/WCVI` = "#6c6c6c", `HBLL OUT N/S` = "#6c6c6c", Commercial = "#303030"),
  mat_min_n = 20,
  survey_map_outlier = 1,
  synoptic_max_survey_years = list(`SYN WCHG` = 2020, `SYN HS` = 2019, `SYN WCVI` = 2018,
    `SYN QCS` = 2019),
  hbll_out_max_survey_years = list(`HBLL OUT N` = 2019, `HBLL OUT S` = 2020),
  iphc_max_survey_year = 2022,
  parallel = FALSE,
  french = FALSE,
  final_year_comm = 2021,
  final_year_surv = 2022,
  length_ticks = NULL,
  all_survey_years = NULL,
  stitch_model_type = "st-rw",
  grid_dir,
  hbll_bait_counts,
  iphc_hook_counts,
  index_ggplot
)

Arguments

`dat`	A data list object from `gfdata::cache_pbs_data()`.
`dat_iphc`	A data list object from `gfiphc::cache_pbs_data_iphc()`.
`spp`	A species common name.
`d_geostat_index`	`d_geostat_index` data
`aspect`	The aspect ratio of the 2nd page.
`short_page_height_ratio`	The aspect ratio of the shorter first page.
`width`	The width of a page.
`debug`	If `TRUE` then a debugging grid will be added to the plot layout.
`resolution`	The resolution for a png page.
`png_format`	If `TRUE` then the pages will be png instead of PDF.
`spp_file`	A version of the species name to be used when generating file names.
`report_folder`	The folder in which to create the report.
`include_map_square`	If `TRUE` then a perfect square will be added to the maps to help adjust the figure layout to get the aspect ratio of these maps correct.
`map_xlim`	The X axis limits in UTM coordinates.
`map_ylim`	The Y axis limits in UTM coordinates.
`save_gg_objects`	If `TRUE` then the ggplot2 objects will be saved as a list object in `file.path(report_folder, 'ggplot-objects')`. This will also cause the CPUE model to be cached.
`survey_cols`	A vector of colors for the surveys.
`mat_min_n`	The minimum number of samples before the maturity ogives are plotted.
`survey_map_outlier`	A quantile above which of the colors in the map should be squashed the same color. Useful to avoid a small number of outlying cells from distorting the color scale.
`synoptic_max_survey_years`	A vector of length 2 giving the maximum synoptic survey years to include.
`parallel`	Parallel CPUE index fitting?
`length_ticks`	A data frame indicating optional length composition x-axis breaks and labels.
`all_survey_years`	DF with `survey_abbrev` and all `year`
`stitch_model_type`	A string indicating what type of stitch model to fit. Matching one of: "st-rw" (the default), "st-rw_tv-rw". See `get_stitched_index()`.
`index_ggplot`	Pre-made ggplots for survey indices.