AFSC Gulf of Alaska • surveyresamplr

# Get rid of memory limits -----------------------------------------------------
options(future.globals.maxSize = 1 * 1024^4) # Allow up to 1 TB for globals

# Install Libraries ------------------------------------------------------------

# Here we list all the packages we will need for this whole process
# We'll also use this in our works cited page.
PKG <- c(
  "surveyresamplr",
  "dplyr",
  "tidyr",
  "purrr",
  "ggplot2",
  "future.callr",
  "flextable", 
  "sdmTMB"
)

pkg_install <- function(p) {
  if (!require(p, character.only = TRUE)) {
    install.packages(p)
  }
  require(p, character.only = TRUE)
}
base::lapply(unique(PKG), pkg_install)
#> Loading required package: surveyresamplr
#> Loading required package: dplyr
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> Loading required package: tidyr
#> Loading required package: purrr
#> Loading required package: ggplot2
#> Loading required package: future.callr
#> Loading required package: future
#> Loading required package: flextable
#> 
#> Attaching package: 'flextable'
#> The following object is masked from 'package:purrr':
#> 
#>     compose
#> Loading required package: sdmTMB
#> [[1]]
#> [1] TRUE
#> 
#> [[2]]
#> [1] TRUE
#> 
#> [[3]]
#> [1] TRUE
#> 
#> [[4]]
#> [1] TRUE
#> 
#> [[5]]
#> [1] TRUE
#> 
#> [[6]]
#> [1] TRUE
#> 
#> [[7]]
#> [1] TRUE
#> 
#> [[8]]
#> [1] TRUE

# Set directories --------------------------------------------------------------
wd <- paste0(here::here(), "/vignettes/")
dir_out <- paste0(wd, "output/")
dir_final <- paste0(dir_out, "GOA_0results/")

Run scenarios


### Define study species -------------------------------------------------------

spp_list <- data.frame(
  srvy = "GOA",
  common_name = c(
    "walleye pollock", "Pacific cod",
    "Pacific ocean perch", "flathead sole",
    "northern rockfish", "arrowtooth flounder"
  ),
  species_code = as.character(c(
    21740, 21720,
    30060, 10130,
    30420, 10110
  )),
  filter_lat_lt = NA,
  filter_lat_gt = NA,
  filter_depth = NA,
  model_fn = "total_catch_wt_kg ~ 0 + factor(year)",
  model_family = "delta_gamma",
  model_anisotropy = TRUE,
  model_spatiotemporal = "iid, iid"
) |>
  dplyr::mutate(
    file_name = gsub(pattern = " ", replacement = "_", x = (tolower(common_name)))
  )

### Load survey data -----------------------------------------------------------

# source(paste0(wd, "code/data_dl_ak.r"))
catch <- surveyresamplr::noaa_afsc_catch |>
  dplyr::filter(srvy == "GOA")

### Load grid data -------------------------------------------------------------

grid_yrs <- replicate_df(surveyresamplr::noaa_afsc_goa_pred_grid_depth, "year", unique(catch$year))

### Variables ------------------------------------------------------------------

srvy <- "GOA"
seq_from <- 0.2
seq_to <- 1.0
seq_by <- 0.2
tot_dataframes <- 13
replicate_num <- 3

### Run ------------------------------------------------------------------------

purrr::map(
  1:nrow(spp_list),
  ~ clean_and_resample(spp_list[.x, ],
    catch, seq_from, seq_to, seq_by,
    tot_dataframes, replicate_num, grid_yrs, dir_out,
    test = TRUE
  )
)

### Plot indices --------------------------------------------------------------

out <- plot_results(srvy = srvy, dir_out = dir_out, dir_final = dir_final)

out$plots
#> $index_boxplot_log_biomass

#> 
#> $index_boxplot_log_biomass_SE

#> 
#> $index_boxplot_biomass

#> 
#> $index_timeseries_biomass

Parameter output:

i <- 1
print(names(out$tables)[i])
#> [1] "fit_df"
head(out$tables[i][[1]]) |>
  flextable::flextable()

X.1	X	srvy	common_name	species_code	model_fn	model_family	model_anisotropy	model_spatiotemporal	file_name	effort	term	estimate	std.error	conf.low	conf.high
1	1	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	factor(year)1990	22.20962	3,623.130	-7,078.994	7,123.414
2	2	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	factor(year)1993	22.15425	3,324.978	-6,494.683	6,538.992
3	3	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	factor(year)1996	22.02771	3,275.996	-6,398.807	6,442.862
4	4	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	factor(year)1999	23.34060	6,546.774	-12,808.102	12,854.783
5	5	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	factor(year)2001	21.66088	3,589.083	-7,012.812	7,056.134
6	6	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	factor(year)2003	22.09698	3,319.433	-6,483.873	6,528.066

i <- 1 + i
print(names(out$tables)[i])
#> [1] "fit_pars"
head(out$tables[i][[1]]) |>
  flextable::flextable()

X.1	X	srvy	common_name	species_code	model_fn	model_family	model_anisotropy	model_spatiotemporal	file_name	effort	term	estimate	std.error	conf.high
1	1	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	range	0.4230446	3,307.7298	Inf
2	2	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	sigma_O	0.2235829	1,245.4340	Inf
3	3	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	sigma_E	0.2061478	797.8968	Inf
4		GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	1_1	range	3.2400616	16,000.5812	Inf
5		GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	1_1	sigma_O	0.3181234	1,172.7933	Inf
6		GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	1_1	sigma_E	0.2486639	1,162.1914	Inf

i <- 1 + i
print(names(out$tables)[i])
#> [1] "fit_check"
head(out$tables[i][[1]]) |>
  flextable::flextable()

X.1	X	srvy	common_name	species_code	model_fn	model_family	model_anisotropy	model_spatiotemporal	file_name	effort	hessian_ok	eigen_values_ok	nlminb_ok	range_ok	gradients_ok	se_magnitude_ok	se_na_ok	sigmas_ok	all_ok
1	1	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	TRUE	TRUE	TRUE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE
2		GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	1_1	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE
1	1	GOA	northern rockfish	30,420	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	northern_rockfish	08_3	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE
2		GOA	northern rockfish	30,420	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	northern_rockfish	1_1	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE
1	1	GOA	Pacific cod	21,720	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	pacific_cod	08_3	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	TRUE	FALSE	FALSE
2		GOA	Pacific cod	21,720	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	pacific_cod	1_1	FALSE	TRUE	TRUE	TRUE	TRUE	FALSE	TRUE	TRUE	FALSE

i <- 1 + i
print(names(out$tables)[i])
#> [1] "index"
head(out$tables[i][[1]]) |>
  flextable::flextable()

X.1	X	srvy	common_name	species_code	model_fn	model_family	model_anisotropy	model_spatiotemporal	file_name	effort	year	est	lwr	upr	log_est	se	type
1	1	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	1,990	13,633,865	11,327,310	16,410,100	16.42807	0.09456306	index
2	2	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	1,993	12,573,858	10,014,298	15,787,616	16.34713	0.11612763	index
3	3	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	1,996	9,991,137	7,583,964	13,162,355	16.11721	0.14064669	index
4	4	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	1,999	7,146,546	5,486,662	9,308,594	15.78214	0.13485400	index
5	5	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	2,001	11,322,791	8,269,930	15,502,623	16.24233	0.16030479	index
6	6	GOA	flathead sole	10,130	total_catch_wt_kg ~ 0 + factor(year)	delta_gamma	TRUE	iid, iid	flathead_sole	08_3	2,003	11,073,005	8,457,789	14,496,865	16.22002	0.13746288	index