analysis/recalculate_temperature.R
In afsc-gap-products/coldpool: AFSC/RACE Groundfish Assessment Program EBS and NBS temperature products
library(ggplot2)
library(dplyr)
library(gapctd)
library(plotly)
channel <- gapctd::get_connected(schema = "AFSC")
# Get vessel/cruise haul data
vc_df <- RODBC::sqlQuery(channel = channel, query = paste0("select vessel, cruise from racebase.haul where region = 'AI' and cruise = 202201")) |>
unique() |>
dplyr::filter(CRUISE %% 10 == 1)
# Retrieve temperature methods
haul_temp_methods <- RODBC::sqlQuery(channel = channel,
query = "select a.cruise_id, a.haul, a.haul_id, a.surface_temperature_method, a.surface_temperature, a.gear_temperature, a.gear_temperature_method from race_data.hauls a") |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel,
query = "select temperature_method_id, name from race_data.temperature_methods") |>
dplyr::mutate(GEAR_TEMPERATURE_METHOD = TEMPERATURE_METHOD_ID,
GEAR_TEMPERATURE_METHOD_NAME = NAME) |>
dplyr::select(-TEMPERATURE_METHOD_ID,
-NAME)) |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel,
query = "select temperature_method_id, name from race_data.temperature_methods") |>
dplyr::mutate(SURFACE_TEMPERATURE_METHOD = TEMPERATURE_METHOD_ID,
SURFACE_TEMPERATURE_METHOD_NAME = NAME) |>
dplyr::select(-TEMPERATURE_METHOD_ID,
-NAME)) |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel, query = "select survey_definition_id, survey_name from race_data.survey_definitions where (survey_definition_id in (47, 52, 98, 143))") |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel, query = "select survey_id, survey_definition_id from race_data.surveys")) |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel, query = "select cruise_id, vessel_id vessel, survey_id, cruise from race_data.cruises")))
aibt <- try(RODBC::sqlQuery(channel = channel, query = paste("select a.vessel_id vessel, a.cruise cruise, b.haul haul,
d.edit_date_time date_time, d.edit_depth depth, d.edit_temperature temperature
from race_data.cruises a, race_data.hauls b, race_data.bathythermic_headers c,
race_data.bathythermics d, race_data.datum_codes e, race_data.surveys f,
race_data.survey_definitions g where g.survey_definition_id = f.survey_definition_id
and year > 2021 and g.survey_name = 'Aleutian Islands Bottom Trawl Survey' and f.survey_id = a.survey_id
and b.cruise_id = a.cruise_id and c.haul_id = b.haul_id and d.bathythermic_header_id = c.bathythermic_header_id and e.datum_code = d.datum_code and d.edit_depth > -0.01
and e.use_in_analysis = 'Y' order by vessel, haul", sep = "")) |>
dplyr::mutate(DATE_TIME = lubridate::force_tz(DATE_TIME, tzone = "America/Anchorage")), silent = TRUE)
ref_depth <- 1
## Upcasts ----
upcast_out_df <- NULL
for(kk in 1:nrow(vc_df)) {
print(paste0(kk, " out of ", nrow(vc_df)))
v_sel <- vc_df$VESSEL[kk]
c_sel <- vc_df$CRUISE[kk]
y_sel <- floor(c_sel/100)
haul_events <- RODBC::sqlQuery(channel = channel, query = paste0("select a.event_type_id, a.date_time, b.haul, c.vessel_id vessel, c.cruise from race_data.events a, race_data.hauls b, race_data.cruises c where a.haul_id = b.haul_id and b.cruise_id = c.cruise_id and c.vessel_id = ", v_sel, "and cruise = ", c_sel))
haul_temp <- RODBC::sqlQuery(channel = channel, query = paste0("select vessel, cruise, haul from racebase.haul where region = 'AI' and vessel = ", v_sel, "and cruise = ", c_sel))
haul_temp$RECALCULATE <- -99
for(ii in 1:nrow(haul_temp)) {
print(ii)
obtime <- (haul_events |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], EVENT_TYPE_ID == 7))
if(!(nrow(obtime) >= 1)) {
next
}
obtime <- obtime$DATE_TIME |>
lubridate::force_tz(tz = "UTC") |>
lubridate::with_tz(tzone = "America/Anchorage")
# DATE_TIME in order
sel_haul <- aibt |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], DATE_TIME > obtime, DEPTH <= (ref_depth + 5)) |>
dplyr::arrange(DATE_TIME)
haul_temp$RECALCULATE[ii] <- gapctd::calc_fixed_depth_var(depth = sel_haul$DEPTH, var = sel_haul$TEMPERATURE, ref_depth = ref_depth)
}
haul_temp <- haul_temp |>
dplyr::inner_join(haul_temp_methods,
by = c("VESSEL", "CRUISE", "HAUL"))
if(is.null(upcast_out_df)) {
upcast_out_df <- haul_temp
} else {
upcast_out_df <- dplyr::bind_rows(upcast_out_df, haul_temp)
}
}
upcast_out_df$RECALCULATE[upcast_out_df$RECALCULATE == -99] <- NA
upcast_out_df$diff <- upcast_out_df$SURFACE_TEMPERATURE - round(upcast_out_df$RECALCULATE, 3)
saveRDS(upcast_out_df, here::here("output", "bt_algorithms_upcast.rds"))
upcast_high_diff <- upcast_out_df |>
dplyr::filter(abs(diff) > 0.15) |>
dplyr::arrange(CRUISE, VESSEL, HAUL)
for(jj in 1:nrow(upcast_high_diff)) {
sel_diff <- aibt |>
dplyr::filter(VESSEL == upcast_high_diff$VESSEL[jj],
CRUISE == upcast_high_diff$CRUISE[jj],
HAUL == upcast_high_diff$HAUL[jj],
DEPTH <= 5) |>
dplyr::mutate(DEPTH = DEPTH * -1)
png(here::here("plots", "surf_temp_diff", paste0("st_diff_upcast_", upcast_high_diff$CRUISE[jj], "_", upcast_high_diff$VESSEL[jj], "_", upcast_high_diff$HAUL[jj], ".png")),
width = 7,
height = 7,
units = "in",
res = 300)
print(ggplot() +
geom_point(data = sel_diff |>
tidyr::pivot_longer(cols = c("DEPTH", "TEMPERATURE")) |>
dplyr::arrange(DATE_TIME),
aes(x = DATE_TIME,
y = value,
color = name)) +
geom_hline(data = upcast_high_diff[jj,] |>
tidyr::pivot_longer(cols = c("SURFACE_TEMPERATURE", "RECALCULATE")) |>
dplyr::rename(type = name) |>
dplyr::mutate(name = "TEMPERATURE"),
mapping = aes(yintercept = value,
lty = type),
size = rel(1.2)) +
facet_wrap(~name, scales = "free_y", nrow = 2) +
ggthemes::scale_color_tableau() +
ggtitle(paste0("Cruise: ", upcast_high_diff[jj,]$CRUISE, ", Vessel: ", upcast_high_diff[jj,]$VESSEL, ", Haul: ", upcast_high_diff[jj,]$HAUL, ", Method: ", upcast_high_diff[jj,]$SURFACE_TEMPERATURE_METHOD)) +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)))
dev.off()
}
## Downcasts ----
downcast_out_df <- NULL
for(kk in 1:nrow(vc_df)) {
print(paste0(kk, " out of ", nrow(vc_df)))
v_sel <- vc_df$VESSEL[kk]
c_sel <- vc_df$CRUISE[kk]
y_sel <- floor(c_sel/100)
haul_events <- RODBC::sqlQuery(channel = channel, query = paste0("select a.event_type_id, a.date_time, b.haul, c.vessel_id vessel, c.cruise from race_data.events a, race_data.hauls b, race_data.cruises c where a.haul_id = b.haul_id and b.cruise_id = c.cruise_id and c.vessel_id = ", v_sel, "and cruise = ", c_sel))
haul_temp <- RODBC::sqlQuery(channel = channel, query = paste0("select vessel, cruise, haul from racebase.haul where region = 'BS' and vessel = ", v_sel, "and cruise = ", c_sel))
haul_temp$RECALCULATE <- -99
for(ii in 1:nrow(haul_temp)) {
print(ii)
obtime <- (haul_events |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], EVENT_TYPE_ID == 3))
if(!(nrow(obtime) >= 1)) {
next
}
obtime <- obtime$DATE_TIME |>
lubridate::force_tz(tz = "UTC") |>
lubridate::with_tz(tzone = "America/Anchorage")
# DATE_TIME in order
sel_haul <- aibt |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], DATE_TIME < obtime, DEPTH <= (ref_depth + 5)) |>
dplyr::arrange(desc(DATE_TIME))
haul_temp$RECALCULATE[ii] <- gapctd::calc_fixed_depth_var(depth = sel_haul$DEPTH, var = sel_haul$TEMPERATURE, ref_depth = ref_depth )
}
haul_temp <- haul_temp |>
dplyr::inner_join(haul_temp_methods,
by = c("VESSEL", "CRUISE", "HAUL"))
# haul_temp$diff <- haul_temp$SURFACE_TEMPERATURE - round(haul_temp$RECALCULATE, 3)
if(is.null(downcast_out_df)) {
downcast_out_df <- haul_temp
} else {
downcast_out_df <- dplyr::bind_rows(downcast_out_df, haul_temp)
}
}
downcast_out_df$RECALCULATE[downcast_out_df$RECALCULATE == -99] <- NA
downcast_out_df$diff <- downcast_out_df$SURFACE_TEMPERATURE - round(downcast_out_df$RECALCULATE, 3)
saveRDS(downcast_out_df, here::here("output", "bt_algorithms_downcast.rds"))
ggplot() +
geom_point(data = downcast_out_df,
aes(x = floor(CRUISE/100),
y = diff,
group = CRUISE)) +
theme_minimal()
ggplot() +
geom_point(data = upcast_out_df,
aes(x = floor(CRUISE/100),
y = diff,
group = CRUISE)) +
theme_minimal()
downcast_high_diff <- downcast_out_df |>
dplyr::filter(abs(diff) > 0.15) |>
dplyr::arrange(CRUISE, VESSEL, HAUL)
for(jj in 1:nrow(downcast_high_diff)) {
sel_diff <- aibt |>
dplyr::filter(VESSEL == downcast_high_diff$VESSEL[jj],
CRUISE == downcast_high_diff$CRUISE[jj],
HAUL == downcast_high_diff$HAUL[jj],
DEPTH <= (ref_depth + 5)) |>
dplyr::mutate(DEPTH = DEPTH * -1)
png(here::here("plots", "surf_temp_diff", paste0("st_diff_downcast_", downcast_high_diff$CRUISE[jj], "_", downcast_high_diff$VESSEL[jj], "_", downcast_high_diff$HAUL[jj], ".png")), width = 7, height = 7, units = "in", res = 300)
print(ggplot() +
geom_point(data = sel_diff |>
tidyr::pivot_longer(cols = c("DEPTH", "TEMPERATURE")) |>
dplyr::arrange(DATE_TIME),
aes(x = DATE_TIME,
y = value,
color = name)) +
geom_hline(data = downcast_high_diff[jj,] |>
tidyr::pivot_longer(cols = c("SURFACE_TEMPERATURE", "RECALCULATE")) |>
dplyr::rename(type = name) |>
dplyr::mutate(name = "TEMPERATURE"),
mapping = aes(yintercept = value,
lty = type),
size = rel(1.2)) +
facet_wrap(~name, scales = "free_y", nrow = 2) +
ggthemes::scale_color_tableau() +
ggtitle(paste0("Cruise: ", downcast_high_diff[jj,]$CRUISE, ", Vessel: ", downcast_high_diff[jj,]$VESSEL, ", Haul: ", downcast_high_diff[jj,]$HAUL, ", Method: ", downcast_high_diff[jj,]$SURFACE_TEMPERATURE_METHOD)) +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)))
dev.off()
}
# Algorithm comparison
readRDS(here::here("output", "bt_algorithms_upcast.rds")) |>
dplyr::mutate(cast = "upcast") |>
dplyr::filter(!is.na(diff)) |>
dplyr::group_by(CRUISE, cast) |>
dplyr::summarise(min_diff = min(diff, na.rm = TRUE),
max_diff = max(diff, na.rm = TRUE),
mean_diff = mean(diff, na.rm = TRUE),
mean_abs_diff = mean(abs(diff), na.rm = TRUE),
sd_diff = sd(diff, na.rm = TRUE),
n = n())
table(upcast_out_df$SURFACE_TEMPERATURE_METHOD_NAME[abs(upcast_out_df$diff) > 0],
upcast_out_df$CRUISE[abs(upcast_out_df$diff) > 0])
table(upcast_out_df$CRUISE[abs(upcast_out_df$diff) > 0],
upcast_out_df$FLAG[abs(upcast_out_df$diff) > 0])
readRDS(here::here("output", "bt_algorithms_downcast.rds")) |>
dplyr::mutate(cast = "downcast") |>
dplyr::filter(!is.na(diff)) |>
dplyr::group_by(CRUISE, cast) |>
dplyr::summarise(min_diff = min(diff, na.rm = TRUE),
max_diff = max(diff, na.rm = TRUE),
mean_diff = mean(diff, na.rm = TRUE),
mean_abs_diff = mean(abs(diff), na.rm = TRUE),
sd_diff = sd(diff, na.rm = TRUE),
n = n())
table(downcast_out_df$CRUISE[abs(downcast_out_df$diff) > 0])
table(upcast_out_df$CRUISE[abs(upcast_out_df$diff) > 0])
table(downcast_out_df$SURFACE_TEMPERATURE_METHOD_NAME[abs(downcast_out_df$diff) > 0],
downcast_out_df$CRUISE[abs(downcast_out_df$diff) > 0])
table(downcast_out_df$CRUISE[abs(downcast_out_df$diff) > 0],
downcast_out_df$FLAG[abs(downcast_out_df$diff) > 0])
# Density plots ----
bt_algorithm_df <- dplyr::bind_rows(
readRDS(here::here("output", "bt_algorithms_upcast.rds")) |>
dplyr::mutate(cast = "upcast"),
readRDS(here::here("output", "bt_algorithms_downcast.rds")) |>
dplyr::mutate(cast = "downcast")) |>
tidyr::pivot_wider(id_cols = c("VESSEL", "CRUISE", "HAUL"), names_from = "cast", values_from = c("RECALCULATE")) |>
dplyr::mutate(diff = upcast - downcast) |>
dplyr::group_by(CRUISE, VESSEL) |>
dplyr::summarise(mean_up_minus_down = mean(diff, na.rm = TRUE))
print(bt_algorithm_df, n = 40)
png(file = here::here("plots", "surf_temp_diff", "0_algorithm_vs_surface"))
print(
ggplot() +
geom_histogram(data = dplyr::bind_rows(
readRDS(here::here("output", "bt_algorithms_upcast.rds")) |>
dplyr::mutate(cast = "upcast"),
readRDS(here::here("output", "bt_algorithms_downcast.rds")) |>
dplyr::mutate(cast = "downcast")),
aes(x = diff, color = cast, fill = cast),
alpha = 0.3,
position = "identity", bins = 20) +
facet_wrap(~floor(CRUISE/100)) +
scale_x_continuous(limits = c(-3,3), name = expression(T["surface,RACEBASE"]-T["surface,algorithm"])) +
scale_y_continuous(limits = c(0, 460), expand = c(0,0)) +
ggthemes::scale_color_tableau() +
ggthemes::scale_fill_tableau() +
theme_bw()
)
dev.off()
afsc-gap-products/coldpool documentation built on Feb. 25, 2024, 9:44 p.m.
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library(ggplot2)
library(dplyr)
library(gapctd)
library(plotly)
channel <- gapctd::get_connected(schema = "AFSC")
# Get vessel/cruise haul data
vc_df <- RODBC::sqlQuery(channel = channel, query = paste0("select vessel, cruise from racebase.haul where region = 'AI' and cruise = 202201")) |>
unique() |>
dplyr::filter(CRUISE %% 10 == 1)
# Retrieve temperature methods
haul_temp_methods <- RODBC::sqlQuery(channel = channel,
query = "select a.cruise_id, a.haul, a.haul_id, a.surface_temperature_method, a.surface_temperature, a.gear_temperature, a.gear_temperature_method from race_data.hauls a") |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel,
query = "select temperature_method_id, name from race_data.temperature_methods") |>
dplyr::mutate(GEAR_TEMPERATURE_METHOD = TEMPERATURE_METHOD_ID,
GEAR_TEMPERATURE_METHOD_NAME = NAME) |>
dplyr::select(-TEMPERATURE_METHOD_ID,
-NAME)) |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel,
query = "select temperature_method_id, name from race_data.temperature_methods") |>
dplyr::mutate(SURFACE_TEMPERATURE_METHOD = TEMPERATURE_METHOD_ID,
SURFACE_TEMPERATURE_METHOD_NAME = NAME) |>
dplyr::select(-TEMPERATURE_METHOD_ID,
-NAME)) |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel, query = "select survey_definition_id, survey_name from race_data.survey_definitions where (survey_definition_id in (47, 52, 98, 143))") |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel, query = "select survey_id, survey_definition_id from race_data.surveys")) |>
dplyr::inner_join(RODBC::sqlQuery(channel = channel, query = "select cruise_id, vessel_id vessel, survey_id, cruise from race_data.cruises")))
aibt <- try(RODBC::sqlQuery(channel = channel, query = paste("select a.vessel_id vessel, a.cruise cruise, b.haul haul,
d.edit_date_time date_time, d.edit_depth depth, d.edit_temperature temperature
from race_data.cruises a, race_data.hauls b, race_data.bathythermic_headers c,
race_data.bathythermics d, race_data.datum_codes e, race_data.surveys f,
race_data.survey_definitions g where g.survey_definition_id = f.survey_definition_id
and year > 2021 and g.survey_name = 'Aleutian Islands Bottom Trawl Survey' and f.survey_id = a.survey_id
and b.cruise_id = a.cruise_id and c.haul_id = b.haul_id and d.bathythermic_header_id = c.bathythermic_header_id and e.datum_code = d.datum_code and d.edit_depth > -0.01
and e.use_in_analysis = 'Y' order by vessel, haul", sep = "")) |>
dplyr::mutate(DATE_TIME = lubridate::force_tz(DATE_TIME, tzone = "America/Anchorage")), silent = TRUE)
ref_depth <- 1
## Upcasts ----
upcast_out_df <- NULL
for(kk in 1:nrow(vc_df)) {
print(paste0(kk, " out of ", nrow(vc_df)))
v_sel <- vc_df$VESSEL[kk]
c_sel <- vc_df$CRUISE[kk]
y_sel <- floor(c_sel/100)
haul_events <- RODBC::sqlQuery(channel = channel, query = paste0("select a.event_type_id, a.date_time, b.haul, c.vessel_id vessel, c.cruise from race_data.events a, race_data.hauls b, race_data.cruises c where a.haul_id = b.haul_id and b.cruise_id = c.cruise_id and c.vessel_id = ", v_sel, "and cruise = ", c_sel))
haul_temp <- RODBC::sqlQuery(channel = channel, query = paste0("select vessel, cruise, haul from racebase.haul where region = 'AI' and vessel = ", v_sel, "and cruise = ", c_sel))
haul_temp$RECALCULATE <- -99
for(ii in 1:nrow(haul_temp)) {
print(ii)
obtime <- (haul_events |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], EVENT_TYPE_ID == 7))
if(!(nrow(obtime) >= 1)) {
next
}
obtime <- obtime$DATE_TIME |>
lubridate::force_tz(tz = "UTC") |>
lubridate::with_tz(tzone = "America/Anchorage")
# DATE_TIME in order
sel_haul <- aibt |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], DATE_TIME > obtime, DEPTH <= (ref_depth + 5)) |>
dplyr::arrange(DATE_TIME)
haul_temp$RECALCULATE[ii] <- gapctd::calc_fixed_depth_var(depth = sel_haul$DEPTH, var = sel_haul$TEMPERATURE, ref_depth = ref_depth)
}
haul_temp <- haul_temp |>
dplyr::inner_join(haul_temp_methods,
by = c("VESSEL", "CRUISE", "HAUL"))
if(is.null(upcast_out_df)) {
upcast_out_df <- haul_temp
} else {
upcast_out_df <- dplyr::bind_rows(upcast_out_df, haul_temp)
}
}
upcast_out_df$RECALCULATE[upcast_out_df$RECALCULATE == -99] <- NA
upcast_out_df$diff <- upcast_out_df$SURFACE_TEMPERATURE - round(upcast_out_df$RECALCULATE, 3)
saveRDS(upcast_out_df, here::here("output", "bt_algorithms_upcast.rds"))
upcast_high_diff <- upcast_out_df |>
dplyr::filter(abs(diff) > 0.15) |>
dplyr::arrange(CRUISE, VESSEL, HAUL)
for(jj in 1:nrow(upcast_high_diff)) {
sel_diff <- aibt |>
dplyr::filter(VESSEL == upcast_high_diff$VESSEL[jj],
CRUISE == upcast_high_diff$CRUISE[jj],
HAUL == upcast_high_diff$HAUL[jj],
DEPTH <= 5) |>
dplyr::mutate(DEPTH = DEPTH * -1)
png(here::here("plots", "surf_temp_diff", paste0("st_diff_upcast_", upcast_high_diff$CRUISE[jj], "_", upcast_high_diff$VESSEL[jj], "_", upcast_high_diff$HAUL[jj], ".png")),
width = 7,
height = 7,
units = "in",
res = 300)
print(ggplot() +
geom_point(data = sel_diff |>
tidyr::pivot_longer(cols = c("DEPTH", "TEMPERATURE")) |>
dplyr::arrange(DATE_TIME),
aes(x = DATE_TIME,
y = value,
color = name)) +
geom_hline(data = upcast_high_diff[jj,] |>
tidyr::pivot_longer(cols = c("SURFACE_TEMPERATURE", "RECALCULATE")) |>
dplyr::rename(type = name) |>
dplyr::mutate(name = "TEMPERATURE"),
mapping = aes(yintercept = value,
lty = type),
size = rel(1.2)) +
facet_wrap(~name, scales = "free_y", nrow = 2) +
ggthemes::scale_color_tableau() +
ggtitle(paste0("Cruise: ", upcast_high_diff[jj,]$CRUISE, ", Vessel: ", upcast_high_diff[jj,]$VESSEL, ", Haul: ", upcast_high_diff[jj,]$HAUL, ", Method: ", upcast_high_diff[jj,]$SURFACE_TEMPERATURE_METHOD)) +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)))
dev.off()
}
## Downcasts ----
downcast_out_df <- NULL
for(kk in 1:nrow(vc_df)) {
print(paste0(kk, " out of ", nrow(vc_df)))
v_sel <- vc_df$VESSEL[kk]
c_sel <- vc_df$CRUISE[kk]
y_sel <- floor(c_sel/100)
haul_events <- RODBC::sqlQuery(channel = channel, query = paste0("select a.event_type_id, a.date_time, b.haul, c.vessel_id vessel, c.cruise from race_data.events a, race_data.hauls b, race_data.cruises c where a.haul_id = b.haul_id and b.cruise_id = c.cruise_id and c.vessel_id = ", v_sel, "and cruise = ", c_sel))
haul_temp <- RODBC::sqlQuery(channel = channel, query = paste0("select vessel, cruise, haul from racebase.haul where region = 'BS' and vessel = ", v_sel, "and cruise = ", c_sel))
haul_temp$RECALCULATE <- -99
for(ii in 1:nrow(haul_temp)) {
print(ii)
obtime <- (haul_events |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], EVENT_TYPE_ID == 3))
if(!(nrow(obtime) >= 1)) {
next
}
obtime <- obtime$DATE_TIME |>
lubridate::force_tz(tz = "UTC") |>
lubridate::with_tz(tzone = "America/Anchorage")
# DATE_TIME in order
sel_haul <- aibt |>
dplyr::filter(VESSEL == haul_temp$VESSEL[ii], CRUISE == haul_temp$CRUISE[ii], HAUL == haul_temp$HAUL[ii], DATE_TIME < obtime, DEPTH <= (ref_depth + 5)) |>
dplyr::arrange(desc(DATE_TIME))
haul_temp$RECALCULATE[ii] <- gapctd::calc_fixed_depth_var(depth = sel_haul$DEPTH, var = sel_haul$TEMPERATURE, ref_depth = ref_depth )
}
haul_temp <- haul_temp |>
dplyr::inner_join(haul_temp_methods,
by = c("VESSEL", "CRUISE", "HAUL"))
# haul_temp$diff <- haul_temp$SURFACE_TEMPERATURE - round(haul_temp$RECALCULATE, 3)
if(is.null(downcast_out_df)) {
downcast_out_df <- haul_temp
} else {
downcast_out_df <- dplyr::bind_rows(downcast_out_df, haul_temp)
}
}
downcast_out_df$RECALCULATE[downcast_out_df$RECALCULATE == -99] <- NA
downcast_out_df$diff <- downcast_out_df$SURFACE_TEMPERATURE - round(downcast_out_df$RECALCULATE, 3)
saveRDS(downcast_out_df, here::here("output", "bt_algorithms_downcast.rds"))
ggplot() +
geom_point(data = downcast_out_df,
aes(x = floor(CRUISE/100),
y = diff,
group = CRUISE)) +
theme_minimal()
ggplot() +
geom_point(data = upcast_out_df,
aes(x = floor(CRUISE/100),
y = diff,
group = CRUISE)) +
theme_minimal()
downcast_high_diff <- downcast_out_df |>
dplyr::filter(abs(diff) > 0.15) |>
dplyr::arrange(CRUISE, VESSEL, HAUL)
for(jj in 1:nrow(downcast_high_diff)) {
sel_diff <- aibt |>
dplyr::filter(VESSEL == downcast_high_diff$VESSEL[jj],
CRUISE == downcast_high_diff$CRUISE[jj],
HAUL == downcast_high_diff$HAUL[jj],
DEPTH <= (ref_depth + 5)) |>
dplyr::mutate(DEPTH = DEPTH * -1)
png(here::here("plots", "surf_temp_diff", paste0("st_diff_downcast_", downcast_high_diff$CRUISE[jj], "_", downcast_high_diff$VESSEL[jj], "_", downcast_high_diff$HAUL[jj], ".png")), width = 7, height = 7, units = "in", res = 300)
print(ggplot() +
geom_point(data = sel_diff |>
tidyr::pivot_longer(cols = c("DEPTH", "TEMPERATURE")) |>
dplyr::arrange(DATE_TIME),
aes(x = DATE_TIME,
y = value,
color = name)) +
geom_hline(data = downcast_high_diff[jj,] |>
tidyr::pivot_longer(cols = c("SURFACE_TEMPERATURE", "RECALCULATE")) |>
dplyr::rename(type = name) |>
dplyr::mutate(name = "TEMPERATURE"),
mapping = aes(yintercept = value,
lty = type),
size = rel(1.2)) +
facet_wrap(~name, scales = "free_y", nrow = 2) +
ggthemes::scale_color_tableau() +
ggtitle(paste0("Cruise: ", downcast_high_diff[jj,]$CRUISE, ", Vessel: ", downcast_high_diff[jj,]$VESSEL, ", Haul: ", downcast_high_diff[jj,]$HAUL, ", Method: ", downcast_high_diff[jj,]$SURFACE_TEMPERATURE_METHOD)) +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)))
dev.off()
}
# Algorithm comparison
readRDS(here::here("output", "bt_algorithms_upcast.rds")) |>
dplyr::mutate(cast = "upcast") |>
dplyr::filter(!is.na(diff)) |>
dplyr::group_by(CRUISE, cast) |>
dplyr::summarise(min_diff = min(diff, na.rm = TRUE),
max_diff = max(diff, na.rm = TRUE),
mean_diff = mean(diff, na.rm = TRUE),
mean_abs_diff = mean(abs(diff), na.rm = TRUE),
sd_diff = sd(diff, na.rm = TRUE),
n = n())
table(upcast_out_df$SURFACE_TEMPERATURE_METHOD_NAME[abs(upcast_out_df$diff) > 0],
upcast_out_df$CRUISE[abs(upcast_out_df$diff) > 0])
table(upcast_out_df$CRUISE[abs(upcast_out_df$diff) > 0],
upcast_out_df$FLAG[abs(upcast_out_df$diff) > 0])
readRDS(here::here("output", "bt_algorithms_downcast.rds")) |>
dplyr::mutate(cast = "downcast") |>
dplyr::filter(!is.na(diff)) |>
dplyr::group_by(CRUISE, cast) |>
dplyr::summarise(min_diff = min(diff, na.rm = TRUE),
max_diff = max(diff, na.rm = TRUE),
mean_diff = mean(diff, na.rm = TRUE),
mean_abs_diff = mean(abs(diff), na.rm = TRUE),
sd_diff = sd(diff, na.rm = TRUE),
n = n())
table(downcast_out_df$CRUISE[abs(downcast_out_df$diff) > 0])
table(upcast_out_df$CRUISE[abs(upcast_out_df$diff) > 0])
table(downcast_out_df$SURFACE_TEMPERATURE_METHOD_NAME[abs(downcast_out_df$diff) > 0],
downcast_out_df$CRUISE[abs(downcast_out_df$diff) > 0])
table(downcast_out_df$CRUISE[abs(downcast_out_df$diff) > 0],
downcast_out_df$FLAG[abs(downcast_out_df$diff) > 0])
# Density plots ----
bt_algorithm_df <- dplyr::bind_rows(
readRDS(here::here("output", "bt_algorithms_upcast.rds")) |>
dplyr::mutate(cast = "upcast"),
readRDS(here::here("output", "bt_algorithms_downcast.rds")) |>
dplyr::mutate(cast = "downcast")) |>
tidyr::pivot_wider(id_cols = c("VESSEL", "CRUISE", "HAUL"), names_from = "cast", values_from = c("RECALCULATE")) |>
dplyr::mutate(diff = upcast - downcast) |>
dplyr::group_by(CRUISE, VESSEL) |>
dplyr::summarise(mean_up_minus_down = mean(diff, na.rm = TRUE))
print(bt_algorithm_df, n = 40)
png(file = here::here("plots", "surf_temp_diff", "0_algorithm_vs_surface"))
print(
ggplot() +
geom_histogram(data = dplyr::bind_rows(
readRDS(here::here("output", "bt_algorithms_upcast.rds")) |>
dplyr::mutate(cast = "upcast"),
readRDS(here::here("output", "bt_algorithms_downcast.rds")) |>
dplyr::mutate(cast = "downcast")),
aes(x = diff, color = cast, fill = cast),
alpha = 0.3,
position = "identity", bins = 20) +
facet_wrap(~floor(CRUISE/100)) +
scale_x_continuous(limits = c(-3,3), name = expression(T["surface,RACEBASE"]-T["surface,algorithm"])) +
scale_y_continuous(limits = c(0, 460), expand = c(0,0)) +
ggthemes::scale_color_tableau() +
ggthemes::scale_fill_tableau() +
theme_bw()
)
dev.off()
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