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0_update_indicator.R
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0_update_indicator.R
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library(akfishcondition)
# Make ESR/ESP settings ----
ESR_SETTINGS <- list(ESR_SPECIES = data.frame(common_name = c(
"walleye pollock", "walleye pollock (100-250 mm)", "walleye pollock (>250 mm)", "Pacific cod",
"Pacific cod (juvenile)", "Pacific cod (adult)", "Atka mackerel", "arrowtooth flounder",
"flathead sole", "yellowfin sole", "northern rock sole", "southern rock sole", "Alaska plaice",
"Pacific ocean perch", "dusky rockfish", "northern rockfish", "Dover sole", "rex sole", "shortraker rockfish", "rougheye rockfish", "blackspotted rockfish", "sharpchin rockfish"),
species_code = c(21740, 21741, 21742, 21720, 21721, 21722, 21921, 10110, 10130,
10210, 10261, 10262, 10285, 30060, 30152, 30420, 10180, 10200, 30576, 30051, 30052, 30560),
AI = c(FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE),
GOA = c(FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE),
EBS = c(FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE),
NBS = c(FALSE, TRUE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE)),
VAST_SETTINGS = data.frame(species_code = c(30420, 30060, 10262, 21720, 21740, 10110, 30152,
30420, 30060, 10262, 21720, 21740, 21921, 10110, 21741, 21742,
10130, 10210, 10285, 21740, 21720, 10110, 10261, 21741, 21742,
21740, 21720, 10210, 10285, 21741, 21742
),
region = c("GOA", "GOA", "GOA", "GOA", "GOA", "GOA", "GOA",
"AI", "AI", "AI", "AI", "AI", "AI", "AI", "AI", "AI",
"EBS", "EBS", "EBS", "EBS", "EBS", "EBS", "EBS", "EBS", "EBS",
"NBS", "NBS", "NBS", "NBS", "NBS", "NBS"),
ObsModel_1 = c(2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2),
ObsModel_2 = c(1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1),
ObsModel_3 = c(3, 3, 3, 3, 4, 4, 4,
3, 3, 3, 3, 4, 3, 4, 4, 4,
3, 3, 3, 4, 3, 4, 3, 4, 4,
4, 4, 3, 4, 4, 4),
ObsModel_4 = c(3, 3, 3, 3, 4, 4, 4,
3, 3, 3, 3, 4, 3, 4, 4, 4,
3, 3, 3, 4, 3, 4, 3, 4, 4,
4, 4, 3, 4, 4, 4),
fl_min = c(0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 100, 251,
0, 0, 0, 0, 0, 0, 0, 100, 251,
0, 0, 0, 0, 100, 251),
fl_max = c(1e7, 1e7, 1e7, 1e7, 1e7, 1e7, 1e7,
1e7, 1e7, 1e7, 1e7, 1e7, 1e7, 1e7, 250, 1e7,
1e7, 1e7, 1e7, 1e7, 1e7, 1e7, 1e7, 250, 1e7,
1e7, 1e7, 1e7, 1e7, 250, 1e7),
n_knots = c(400, 400, 400, 400, 400, 400, 400,
400, 600, 400, 400, 400, 400, 400, 400, 400,
400, 600, 400, 400, 750, 400, 400, 400, 400,
200, 200, 200, 200, 200, 200))
)
ESP_SETTINGS <- list(ESP_SPECIES =
data.frame(
common_name = c("Pacific cod (juvenile)", "Pacific cod (adult)"),
species_code = c(21721, 21722),
AI = c(TRUE, TRUE),
GOA = c(TRUE, TRUE),
EBS = c(TRUE, TRUE),
NBS = c(FALSE, FALSE)),
VAST_SETTINGS = data.frame(species_code = c(21721, 21722,
21721, 21722,
21721, 21722),
region = c("GOA", "GOA",
"AI", "AI",
"EBS", "EBS"),
ObsModel_1 = c(2, 2,
2, 2,
2, 2),
ObsModel_2 = c(1, 1,
1, 1,
1, 1),
ObsModel_3 = c(3, 3,
4, 4,
3, 3),
ObsModel_4 = c(3, 3,
4, 4,
3, 3),
n_knots = c(400, 400,
400, 600,
750, 750),
fl_min = c(0, 504,
0, 581,
0, 581),
fl_max = c(503, 1e7,
580, 1e7,
580, 1e7))
)
devtools::install()
# Get data ---
library(akfishcondition)
channel <- akfishcondition:::get_connected(schema = "AFSC")
akfishcondition::get_condition_data(channel = channel)
# Generate data visualizations ---
akfishcondition:::make_data_summary(dat_csv = here::here("data", "nbs_all_species.csv"), region = "NBS")
akfishcondition:::make_data_summary(dat_csv = here::here("data", "ebs_all_species.csv"), region = "EBS")
akfishcondition:::make_data_summary(dat_csv = here::here("data", "ai_all_species.csv"), region = "AI")
akfishcondition:::make_data_summary(dat_csv = here::here("data", "goa_all_species.csv"), region = "GOA")
# Calculate residual condition indicator ----
ai_sbw <- akfishcondition:::run_sbw_condition_multimodel(
region = "AI",
covariates_to_use = c('sex', 'stratum'),
min_n = 10)
goa_sbw <- akfishcondition:::run_sbw_condition_multimodel(
region = "GOA",
covariates_to_use = c('sex', 'stratum'),
min_n = 10)
ebs_sbw <- akfishcondition:::run_sbw_condition_multimodel(
region = "EBS",
covariates_to_use = c('sex', 'stratum'),
min_n = 10)
nbs_sbw <- akfishcondition:::run_sbw_condition_multimodel(
region = "NBS",
covariates_to_use = c('sex', 'stratum'),
min_n = 10)
# Add updated indicator to built-in data sets ----
EBS_INDICATOR <- list(
FULL_REGION = as.data.frame(
ebs_sbw$full_sbw) |>
dplyr::filter(common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$EBS]),
STRATUM = as.data.frame(
dplyr::filter(
ebs_sbw$stratum_sbw,
common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$EBS])
),
LAST_UPDATE = Sys.Date()
)
NBS_INDICATOR <- list(
FULL_REGION = as.data.frame(
nbs_sbw$full_sbw) |>
dplyr::filter(
common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$NBS]),
STRATUM = as.data.frame(
dplyr::filter(
nbs_sbw$stratum_sbw,
common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$EBS])
),
LAST_UPDATE = Sys.Date()
)
GOA_INDICATOR <- list(
FULL_REGION = as.data.frame(
goa_sbw$full_sbw) |>
dplyr::filter(common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$GOA]),
STRATUM = as.data.frame(
dplyr::filter(
goa_sbw$stratum_sbw,
common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$GOA])
),
LAST_UPDATE = Sys.Date()
)
AI_INDICATOR <- list(
FULL_REGION = as.data.frame(
ai_sbw$full_sbw) |>
dplyr::filter(common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$AI]),
STRATUM = as.data.frame(
dplyr::filter(
ai_sbw$stratum_sbw,
common_name %in% ESR_SETTINGS$ESR_SPECIES$common_name[ESR_SETTINGS$ESR_SPECIES$AI])
),
LAST_UPDATE = Sys.Date()
)
PCOD_ESP <- list(
FULL_REGION_EBS = as.data.frame(
dplyr::filter(ebs_sbw$full_sbw,
common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
FULL_REGION_GOA = as.data.frame(
dplyr::filter(goa_sbw$full_sbw,
common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
FULL_REGION_AI = as.data.frame(
dplyr::filter(ai_sbw$full_sbw,
common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
FULL_REGION_NBS = as.data.frame(
dplyr::filter(
nbs_sbw$full_sbw, common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
STRATUM_EBS = as.data.frame(
dplyr::filter(
ebs_sbw$stratum_sbw, common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
STRATUM_GOA = as.data.frame(
dplyr::filter(
goa_sbw$stratum_sbw, common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
STRATUM_AI = as.data.frame(
dplyr::filter(
ai_sbw$stratum_sbw, common_name %in% ESP_SETTINGS$ESP_SPECIES$common_name
)),
stratum_NBS = NA,
LAST_UPDATE = Sys.Date()
)
usethis::use_data(EBS_INDICATOR, overwrite = TRUE)
usethis::use_data(AI_INDICATOR, overwrite = TRUE)
usethis::use_data(GOA_INDICATOR, overwrite = TRUE)
usethis::use_data(NBS_INDICATOR, overwrite = TRUE)
usethis::use_data(PCOD_ESP, overwrite = TRUE)
save(
EBS_INDICATOR,
NBS_INDICATOR,
GOA_INDICATOR,
AI_INDICATOR,
PCOD_ESP,
ESR_SETTINGS,
ESP_SETTINGS,
file = here::here("R", "sysdata.rda")
)
AI_raw <- ai_sbw$input_data
GOA_raw <- goa_sbw$input_data
EBS_raw <- ebs_sbw$input_data
NBS_raw <- nbs_sbw$input_data
save(AI_raw,
GOA_raw,
EBS_raw,
NBS_raw,
file = here::here("inst", "extdata", "raw_lw_bio.rda"))
# Check update ----
library(akfishcondition)
print(akfishcondition::AI_INDICATOR$LAST_UPDATE)
print(akfishcondition::GOA_INDICATOR$LAST_UPDATE)
print(akfishcondition::EBS_INDICATOR$LAST_UPDATE)
print(akfishcondition::NBS_INDICATOR$LAST_UPDATE)