R/figs.R
In afsc-gap-products/coldpool: AFSC/RACE Groundfish Assessment Program EBS and NBS temperature products
Defines functions
plot_stn_doy
#' Map survey stations and regions w/ sampling day of year
#'
#' Make a plot showing survey stations and sampling day of year
#'
#' @noRd
plot_stn_doy <- function() {
channel <- coldpool::get_connected(schema = "AFSC")
# Retrieve haul data from RACEBASE
qry_haul <- "select a.* from RACEBASE.HAUL a, RACE_DATA.V_CRUISES b where a.cruisejoin = b.cruisejoin and b.survey_definition_id in (98, 143) and a.region = 'BS' and a.abundance_haul = 'Y' and a.cruise > 198200 and a.performance >=0 and a.haul_type = 3"
# Day of year of hauls
haul_dat <- RODBC::sqlQuery(channel = channel,
query = qry_haul) |>
dplyr::filter(STATIONID %in% akgfmaps::get_survey_stations(select.region = "ebs")) |>
dplyr::mutate(DOY = yday(as.POSIXct(START_TIME)))
# Retrieve EBS base layers
ebs_layers <- akgfmaps::get_base_layers(select.region = "ebs", set.crs = "EPSG:3338")
# Join with survey grid and calculate mean day of year grid cells were sampled
start_df <- ebs_layers$survey.grid |>
sf::st_intersection(ebs_layers$survey.area |>
dplyr::mutate(REGION = "EBS") |>
dplyr::group_by(REGION) |>
dplyr::summarise()) |>
dplyr::inner_join(haul_dat |>
dplyr::group_by(STATIONID) |>
dplyr::summarise(MEAN_DOY = mean(DOY),
MEAN_DEPTH = mean(BOTTOM_DEPTH, na.rm = TRUE)))
# Define plot exent (through trial end error)
panel_extent <- data.frame(x = c(-1326559.21, -87636.05),
y = c(533099.5, 1894909.7))
# Combine strata by main survey region + SEBS plus NW
agg_stratum <- ebs_layers$survey.strata |>
dplyr::mutate(agg_stratum = Stratum) |>
dplyr::mutate(agg_stratum = replace(agg_stratum, agg_stratum %in% c(31,32,30,41,42,43,61,62,60,10,20,50), "EBS Shelf\nStandard"),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(82, 90), "EBS\nPlus NW"),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(70,71,81), "NBS")) |>
dplyr::group_by(agg_stratum) |>
dplyr::summarise()
plot_ebs_nbs_survey_stations <- ggplot() +
geom_sf(data = ebs_layers$akland,
fill = "grey70",
color = "black") +
geom_sf(data = start_df,
aes(fill = MEAN_DOY)) +
ggplot2::geom_sf(data = agg_stratum,
fill = NA,
color = "black",
size = rel(1.1)) +
shadowtext::geom_shadowtext(data = data.frame(agg_stratum = sf::st_centroid(agg_stratum)$agg_stratum, # Centroid of aggregate stratum polygons
x = sf::st_coordinates(sf::st_centroid(agg_stratum))[,1], # Coordinates of centroid of aggregate stratum polygons
y = sf::st_coordinates(sf::st_centroid(agg_stratum))[,2]),# Coordinates of centroid of aggregate stratum polygons
aes(x = x,
y = y,
label = agg_stratum),
size = rel(4.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -158.5,
y = 62.4,
lab = "Alaska") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(6),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -166.2,
y = 60.08,
lab = "Nunivak\nIsland") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(2.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = c(-169, -159.5),
y = c(66.3, 57.7),
lab = c("Bering\nStrait", "Bristol\nBay")) |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(3),
color = "black",
bg.color = "white") +
scale_fill_viridis_c(name = "Sample Mean\nDay of Year",
option = "B") +
scale_color_brewer() +
coord_sf(xlim = panel_extent$x,
ylim = panel_extent$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = ebs_layers$lat.breaks) +
theme_bw() +
ggplot2::theme(axis.title = element_blank(),
panel.border = element_rect(color = "black", fill = NA),
legend.title = element_text(size = 9, color = "black"),
legend.text = element_text(size = 8, color = "black"),
axis.text = element_text(size = 8, color = "black"),
panel.grid = element_blank(),
panel.background = element_rect(color = "black", fill = "#bee8ff"),
legend.margin = margin(-12,0,0,0),
legend.position = "right",
legend.background = element_blank())
doy_for_tm <- ggplot() +
geom_sf(data = ebs_layers$akland,
fill = "grey70",
color = "black") +
geom_sf(data = start_df,
aes(fill = MEAN_DOY)) +
geom_sf_text(data = start_df,
aes(label = round(MEAN_DOY))) +
ggplot2::geom_sf(data = agg_stratum,
fill = NA,
color = "black",
size = rel(1.1)) +
shadowtext::geom_shadowtext(data = data.frame(agg_stratum = sf::st_centroid(agg_stratum)$agg_stratum, # Centroid of aggregate stratum polygons
x = sf::st_coordinates(sf::st_centroid(agg_stratum))[,1], # Coordinates of centroid of aggregate stratum polygons
y = sf::st_coordinates(sf::st_centroid(agg_stratum))[,2]),# Coordinates of centroid of aggregate stratum polygons
aes(x = x,
y = y,
label = agg_stratum),
size = rel(4.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -158.5,
y = 62.4,
lab = "Alaska") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(6),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -166.2,
y = 60.08,
lab = "Nunivak\nIsland") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(2.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = c(-169, -159.5),
y = c(66.3, 57.7),
lab = c("Bering\nStrait", "Bristol\nBay")) |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(3),
color = "black",
bg.color = "white") +
scale_fill_viridis_c(name = "Sample Mean\nDay of Year",
option = "B") +
scale_color_brewer() +
coord_sf(xlim = panel_extent$x,
ylim = panel_extent$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = ebs_layers$lat.breaks) +
theme_bw() +
ggplot2::theme(axis.title = element_blank(),
panel.border = element_rect(color = "black", fill = NA),
legend.title = element_text(size = 9, color = "black"),
legend.text = element_text(size = 8, color = "black"),
axis.text = element_text(size = 8, color = "black"),
panel.grid = element_blank(),
panel.background = element_rect(color = "black", fill = "#bee8ff"),
legend.margin = margin(-12,0,0,0),
legend.position = "right",
legend.background = element_blank())
png(filename = here::here("plots", "ebs_nbs_survey_area.png"), width = 5, height = 5, units = "in", res = 600)
print(plot_ebs_nbs_survey_stations)
dev.off()
png(filename = here::here("plots", "doy_for_tm.png"), width = 10, height = 10, units = "in", res = 120)
print(doy_for_tm)
dev.off()
}
afsc-gap-products/coldpool documentation built on Feb. 25, 2024, 9:44 p.m.
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Defines functions plot_stn_doy
#' Map survey stations and regions w/ sampling day of year
#'
#' Make a plot showing survey stations and sampling day of year
#'
#' @noRd
plot_stn_doy <- function() {
channel <- coldpool::get_connected(schema = "AFSC")
# Retrieve haul data from RACEBASE
qry_haul <- "select a.* from RACEBASE.HAUL a, RACE_DATA.V_CRUISES b where a.cruisejoin = b.cruisejoin and b.survey_definition_id in (98, 143) and a.region = 'BS' and a.abundance_haul = 'Y' and a.cruise > 198200 and a.performance >=0 and a.haul_type = 3"
# Day of year of hauls
haul_dat <- RODBC::sqlQuery(channel = channel,
query = qry_haul) |>
dplyr::filter(STATIONID %in% akgfmaps::get_survey_stations(select.region = "ebs")) |>
dplyr::mutate(DOY = yday(as.POSIXct(START_TIME)))
# Retrieve EBS base layers
ebs_layers <- akgfmaps::get_base_layers(select.region = "ebs", set.crs = "EPSG:3338")
# Join with survey grid and calculate mean day of year grid cells were sampled
start_df <- ebs_layers$survey.grid |>
sf::st_intersection(ebs_layers$survey.area |>
dplyr::mutate(REGION = "EBS") |>
dplyr::group_by(REGION) |>
dplyr::summarise()) |>
dplyr::inner_join(haul_dat |>
dplyr::group_by(STATIONID) |>
dplyr::summarise(MEAN_DOY = mean(DOY),
MEAN_DEPTH = mean(BOTTOM_DEPTH, na.rm = TRUE)))
# Define plot exent (through trial end error)
panel_extent <- data.frame(x = c(-1326559.21, -87636.05),
y = c(533099.5, 1894909.7))
# Combine strata by main survey region + SEBS plus NW
agg_stratum <- ebs_layers$survey.strata |>
dplyr::mutate(agg_stratum = Stratum) |>
dplyr::mutate(agg_stratum = replace(agg_stratum, agg_stratum %in% c(31,32,30,41,42,43,61,62,60,10,20,50), "EBS Shelf\nStandard"),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(82, 90), "EBS\nPlus NW"),
agg_stratum = replace(agg_stratum, agg_stratum %in% c(70,71,81), "NBS")) |>
dplyr::group_by(agg_stratum) |>
dplyr::summarise()
plot_ebs_nbs_survey_stations <- ggplot() +
geom_sf(data = ebs_layers$akland,
fill = "grey70",
color = "black") +
geom_sf(data = start_df,
aes(fill = MEAN_DOY)) +
ggplot2::geom_sf(data = agg_stratum,
fill = NA,
color = "black",
size = rel(1.1)) +
shadowtext::geom_shadowtext(data = data.frame(agg_stratum = sf::st_centroid(agg_stratum)$agg_stratum, # Centroid of aggregate stratum polygons
x = sf::st_coordinates(sf::st_centroid(agg_stratum))[,1], # Coordinates of centroid of aggregate stratum polygons
y = sf::st_coordinates(sf::st_centroid(agg_stratum))[,2]),# Coordinates of centroid of aggregate stratum polygons
aes(x = x,
y = y,
label = agg_stratum),
size = rel(4.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -158.5,
y = 62.4,
lab = "Alaska") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(6),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -166.2,
y = 60.08,
lab = "Nunivak\nIsland") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(2.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = c(-169, -159.5),
y = c(66.3, 57.7),
lab = c("Bering\nStrait", "Bristol\nBay")) |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(3),
color = "black",
bg.color = "white") +
scale_fill_viridis_c(name = "Sample Mean\nDay of Year",
option = "B") +
scale_color_brewer() +
coord_sf(xlim = panel_extent$x,
ylim = panel_extent$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = ebs_layers$lat.breaks) +
theme_bw() +
ggplot2::theme(axis.title = element_blank(),
panel.border = element_rect(color = "black", fill = NA),
legend.title = element_text(size = 9, color = "black"),
legend.text = element_text(size = 8, color = "black"),
axis.text = element_text(size = 8, color = "black"),
panel.grid = element_blank(),
panel.background = element_rect(color = "black", fill = "#bee8ff"),
legend.margin = margin(-12,0,0,0),
legend.position = "right",
legend.background = element_blank())
doy_for_tm <- ggplot() +
geom_sf(data = ebs_layers$akland,
fill = "grey70",
color = "black") +
geom_sf(data = start_df,
aes(fill = MEAN_DOY)) +
geom_sf_text(data = start_df,
aes(label = round(MEAN_DOY))) +
ggplot2::geom_sf(data = agg_stratum,
fill = NA,
color = "black",
size = rel(1.1)) +
shadowtext::geom_shadowtext(data = data.frame(agg_stratum = sf::st_centroid(agg_stratum)$agg_stratum, # Centroid of aggregate stratum polygons
x = sf::st_coordinates(sf::st_centroid(agg_stratum))[,1], # Coordinates of centroid of aggregate stratum polygons
y = sf::st_coordinates(sf::st_centroid(agg_stratum))[,2]),# Coordinates of centroid of aggregate stratum polygons
aes(x = x,
y = y,
label = agg_stratum),
size = rel(4.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -158.5,
y = 62.4,
lab = "Alaska") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(6),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = -166.2,
y = 60.08,
lab = "Nunivak\nIsland") |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(2.5),
color = "black",
bg.color = "white") +
shadowtext::geom_shadowtext(data = data.frame(x = c(-169, -159.5),
y = c(66.3, 57.7),
lab = c("Bering\nStrait", "Bristol\nBay")) |>
akgfmaps::transform_data_frame_crs(out.crs = coldpool:::ebs_proj_crs),
mapping = aes(x = x,
y = y,
label = lab),
size = rel(3),
color = "black",
bg.color = "white") +
scale_fill_viridis_c(name = "Sample Mean\nDay of Year",
option = "B") +
scale_color_brewer() +
coord_sf(xlim = panel_extent$x,
ylim = panel_extent$y) +
ggplot2::scale_x_continuous(name = "Longitude",
breaks = ebs_layers$lon.breaks) +
ggplot2::scale_y_continuous(name = "Latitude",
breaks = ebs_layers$lat.breaks) +
theme_bw() +
ggplot2::theme(axis.title = element_blank(),
panel.border = element_rect(color = "black", fill = NA),
legend.title = element_text(size = 9, color = "black"),
legend.text = element_text(size = 8, color = "black"),
axis.text = element_text(size = 8, color = "black"),
panel.grid = element_blank(),
panel.background = element_rect(color = "black", fill = "#bee8ff"),
legend.margin = margin(-12,0,0,0),
legend.position = "right",
legend.background = element_blank())
png(filename = here::here("plots", "ebs_nbs_survey_area.png"), width = 5, height = 5, units = "in", res = 600)
print(plot_ebs_nbs_survey_stations)
dev.off()
png(filename = here::here("plots", "doy_for_tm.png"), width = 10, height = 10, units = "in", res = 120)
print(doy_for_tm)
dev.off()
}
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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