make_pages | R Documentation |
This is the main workhorse function that creates the synopsis pages.
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,
spatiotemporal_cpue = FALSE,
raw_cpue = NULL
)
dat |
A data list object from |
dat_iphc |
A data list object from |
spp |
A species common name. |
d_geostat_index |
|
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 |
resolution |
The resolution for a png page. |
png_format |
If |
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 |
map_xlim |
The X axis limits in UTM coordinates. |
map_ylim |
The Y axis limits in UTM coordinates. |
save_gg_objects |
If |
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 |
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
|
index_ggplot |
Pre-made ggplots for survey indices. |
spatiotemporal_cpue |
Logical: use commercial trawl CPUE sdmTMB model output? |
This function generates 2 png files with all of the plots for a given species.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.