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wisconsin_crashes/scripts/school_maps_parallel.R

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added scripts
2024-04-02 12:36:56 -05:00
library(tidyverse)
library(ggmap)
library(sf)
library(osrm)
library(smoothr)
library(ggnewscale)
library(RColorBrewer)
library(magick)
library(rsvg)
library(parallel)
## add data from WiscTransPortal Crash Data Retrieval Facility ----
## query: SELECT *
## FROM DTCRPRD.SUMMARY_COMBINED C
## WHERE C.CRSHDATE BETWEEN TO_DATE('2022-JAN','YYYY-MM') AND
## LAST_DAY(TO_DATE('2022-DEC','YYYY-MM')) AND
## (C.BIKEFLAG = 'Y' OR C.PEDFLAG = 'Y')
## ORDER BY C.DOCTNMBR
## Load TOPS data ----
## load TOPS data for the whole state (crashes involving bikes and pedestrians),
TOPS_data <- as.list(NULL)
for (file in list.files(path = "data/TOPS", pattern = "crash-data-download")) {
message(paste("importing data from file: ", file))
year <- substr(file, 21, 24)
csv_run <- read_csv(file = paste0("data/TOPS/",file), col_types = cols(.default = "c"))
TOPS_data[[file]] <- csv_run
}
rm(csv_run)
TOPS_data <- bind_rows(TOPS_data)
## clean up data
TOPS_data <- TOPS_data %>%
mutate(date = mdy(CRSHDATE),
age1 = as.double(AGE1),
age2 = as.double(AGE2),
latitude = as.double(LATDECDG),
longitude = as.double(LONDECDG)) %>%
mutate(month = month(date, label = TRUE),
year = as.factor(year(date)))
# county index
counties <- data.frame(name = c("Dane", "Milwaukee"),
CNTYCODE = c(13, 40),
COUNTY = c("DANE", "MILWAUKEE"))
# Injury Severy Index and Color -------------------------------------------
# injury severity index
injury_severity <- data.frame(InjSevName = c("No apparent injury", "Possible Injury", "Suspected Minor Injury","Suspected Serious Injury","Fatality"),
code = c("O", "C", "B", "A", "K"),
color = c("#fafa6e", "#edc346", "#d88d2d", "#bd5721", "#9b1c1c"))
TOPS_data <- left_join(TOPS_data, injury_severity %>% select(InjSevName, code), join_by(INJSVR == code)) %>% mutate(InjSevName = factor(InjSevName, levels = injury_severity$InjSevName))
# ---- add additional data
## add school enrollment data
enrollment <- read_csv(file = "data/Schools/Enrollement_2022-2023/enrollment_by_gradelevel_certified_2022-23.csv",
col_types = "ccccccccccccciid")
enrollment_wide <-
enrollment %>%
mutate(district_school = paste0(DISTRICT_CODE, SCHOOL_CODE),
variable_name = paste0(GROUP_BY, "__", GROUP_BY_VALUE)) %>%
mutate(variable_name = str_replace_all(variable_name, "[ ]", "_")) %>%
pivot_wider(id_cols = c(district_school, GRADE_LEVEL, SCHOOL_NAME, DISTRICT_NAME, GRADE_GROUP, CHARTER_IND), names_from = variable_name, values_from = PERCENT_OF_GROUP) %>%
group_by(district_school, SCHOOL_NAME, DISTRICT_NAME, GRADE_GROUP, CHARTER_IND) %>%
summarise_at(vars("Disability__Autism":"Migrant_Status__[Data_Suppressed]"), mean, na.rm = TRUE)
district_info <- data.frame(name = c("Madison Metropolitan", "Milwaukee"),
code = c("3269","3619"),
walk_boundary_hs = c(1.5, 2),
walk_boundary_ms = c(1.5, 2),
walk_boundary_es = c(1.5, 1))
## load school locations
WI_schools <- st_read(dsn = "data/Schools/WI_schools.gpkg")
WI_schools <- left_join(WI_schools %>% mutate(district_school = paste0(SDID, SCH_CODE)),
enrollment_wide,
join_by(district_school))
## load bike LTS networks
# bike_lts <- as.list(NULL)
# for(file in list.files("data/bike_lts")) {
# county <- str_sub(file, 10, -9)
# lts_run <- st_read(paste0("data/bike_lts/", file))
# lts_run[["lts"]] <- as.factor(lts_run$LTS_F)
# bike_lts[[county]] <- lts_run
# }
# bike_lts_scale <- data.frame(code = c(1, 2, 3, 4, 9),
# color = c("#1a9641",
# "#a6d96a",
# "#fdae61",
# "#d7191c",
# "#d7191c"))
# register stadia API key ----
register_stadiamaps(key = substr(read_file(file = "api_keys/stadia_api_key"), 1, 36))
#options(ggmap.file_drawer = "data/basemaps")
# dir.create(file_drawer(), recursive = TRUE, showWarnings = FALSE)
# saveRDS(list(), file_drawer("index.rds"))
#readRDS(file_drawer("index.rds"))
#file_drawer("index.rds")
# load census api key ----
#census_api_key(key = substr(read_file(file = "api_keys/census_api_key"), 1, 40))
# load logo
logo <- image_read(path = "other/BFW_Logo_180_x_200_transparent_background.png")
school_symbol <- image_read_svg(path = "other/school_FILL0_wght400_GRAD0_opsz24.svg")
## ---- generate charts/maps ----
## set parameters of run
county_focus <- str_to_upper(unique(WI_schools %>% pull(CTY_DIST)))
#county_focus <- c("DANE")
#county_focus <- c("MILWAUKEE")
#county_focus <- c("WINNEBAGO")
#county_focus <- c("DANE", "MILWAUKEE", "BROWN")
#county_focus <- c("VILAS", "BROWN")
#county_focus <- c("BROWN")
school_type_focus <- unique(WI_schools %>% filter(CTY_DIST %in% str_to_title(county_focus)) %>% pull(SCHOOLTYPE))
#school_type_focus <- c("High School")
district_focus <- unique(WI_schools %>% filter(CTY_DIST %in% str_to_title(county_focus), SCHOOLTYPE %in% school_type_focus, !is.na(DISTRICT_NAME)) %>% pull(DISTRICT_NAME))
#district_focus <- c("Madison Metropolitan")
#district_focus <- c("Milwaukee")
#district_focus <- c("Charter")
#district_focus <- c("Madison Metropolitan", "Milwaukee")
#district_focus <- c("Middleton-Cross Plains Area")
#district_focus <- c("Oregon")
# WI_schools <- st_as_sf(
# data.frame(SCHOOL = c("Escuela Verde"),
# SCHOOLTYPE = c("High School"),
# CTY_DIST = c("Milwaukee"),
# DISTRICT_NAME = c("Charter"),
# district_school = c("001001"),
# latitude = c(43.02387627250446),
# longitude = c(-87.95981501028392)
# ), coords = c("longitude", "latitude"), crs = 4326) %>% mutate(geom = geometry)
school_number <- length(unique(WI_schools %>% filter(CTY_DIST %in% str_to_title(county_focus),
SCHOOLTYPE %in% school_type_focus,
DISTRICT_NAME %in% district_focus) %>%
pull(district_school)))
## * generate county charts ----
for(county in county_focus) {
message(county)
TOPS_data %>%
filter(CNTYNAME %in% county) %>%
filter(ROLE1 %in% c("BIKE", "PED") & age1 < 18 | ROLE2 %in% c("BIKE", "PED") & age2 < 18) %>%
group_by(year) %>% summarise(count = n_distinct(DOCTNMBR)) %>%
ggplot() +
geom_col(aes(x = year,
y = count),
fill = "darkred") +
scale_y_continuous(expand = expansion(mult = c(0,0.07))) +
labs(title = paste0("Pedestrians/bicyclists under 18 years old hit by cars in ",
str_to_title(county),
" County"),
x = "Year",
y = "Number of crashes",
caption = "data from UW TOPS Laboratory")
ggsave(file = paste0("figures/crash_maps/Crash Maps/",
str_to_title(county),
" County/_",
str_to_title(county),
" County_year.pdf"),
title = paste0(county, " County Youth Pedestrian/Bike crashes"),
device = pdf,
height = 8.5,
width = 11,
units = "in",
create.dir = TRUE)
# # generate map for county
# county_data <- WI_schools %>% filter(CTY_DIST %in% str_to_title(county))
# bbox <- st_bbox(st_transform(st_buffer(county_data %>% pull(geom), dist = 4000), crs = 4326))
# bbox <- c(left = as.double(bbox[1]), bottom = as.double(bbox[2]), right = as.double(bbox[3]), top = as.double(bbox[4]))
#
# #get basemap
# basemap <- get_stadiamap(bbox = bbox, zoom = 12, maptype = "stamen_toner_lite")
#
# # generate map
# ggmap(basemap) +
# labs(title = paste0("Crashes between cars and youth (under 18) pedestrians/bicyclists in ",
# str_to_title(county),
# " County"),
# subtitle = paste0(min(year(TOPS_data$date), na.rm = TRUE), " - ", max(year(TOPS_data$date), na.rm = TRUE)),
# caption = "data from Wisconsin DOT, UW TOPS Laboratory, Wisconsin DPI, and OpenStreetMap",
# x = NULL,
# y = NULL) +
# theme(axis.text=element_blank(),
# axis.ticks=element_blank()) +
#
# # add crash heatmap
# # stat_density_2d(data = TOPS_data %>%
# # filter(ROLE1 %in% c("BIKE", "PED") & age1 < 18 | ROLE2 %in% c("BIKE", "PED") & age2 < 18),
# # inherit.aes = FALSE,
# # geom = "polygon",
# # aes(fill = after_stat(level),
# # x = longitude,
# # y = latitude),
# # alpha = 0.2,
# # color = NA,
# # na.rm = TRUE,
# # bins = 12,
# # n = 300) +
# # scale_fill_distiller(type = "div", palette = "YlOrRd", guide = "none", direction = 1) +
#
# # add crashes
# new_scale_color() +
# geom_point(data = TOPS_data %>%
# filter(ROLE1 %in% c("BIKE", "PED") & age1 < 18 | ROLE2 %in% c("BIKE", "PED") & age2 < 18) %>%
# filter(longitude >= as.double(bbox[1]),
# latitude >= as.double(bbox[2]),
# longitude <= as.double(bbox[3]),
# latitude <= as.double(bbox[4])),
# aes(x = longitude,
# y = latitude,
# color = InjSevName),
# shape = 18,
# size = 1) +
# scale_color_manual(values = injury_severity$color, name = "Crash Severity")
#
# # add school location
# # new_scale_color() +
# # geom_sf(data = st_transform(WI_schools, crs = 4326),
# # inherit.aes = FALSE,
# # aes(color = "school"),
# # size = 2,
# # shape = 0) +
# # scale_color_manual(values = "black", name = NULL)
#
# ggsave(file = paste0("figures/crash_maps/Crash Maps/",
# str_to_title(county), " County/_",
# str_to_title(county), " County.pdf"),
# title = paste0(str_to_title(county), " County Youth Pedestrian/Bike crashes"),
# device = pdf,
# height = 8.5,
# width = 11,
# units = "in",
# create.dir = TRUE)
}
# * generate individual school maps ----
options(osrm.server = "http://127.0.0.1:5000/")
options(osrm.profile = "walk")
districts_done <- read_csv(file = "other/districts_done.csv")
district_focus <- district_focus[! district_focus %in% districts_done$district]
generate_school_maps <- function(district) {
message(paste("***", district, "School District |", match(district, district_focus), "/271"))
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options(ggmap.file_drawer = paste0("basemaps/districts/", district))
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dir.create(file_drawer(), recursive = TRUE, showWarnings = FALSE)
saveRDS(list(), file_drawer("index.rds"))
readRDS(file_drawer("index.rds"))
file_drawer("index.rds")
for(school in WI_schools %>%
filter(DISTRICT_NAME %in% district,
SCHOOLTYPE %in% school_type_focus,
!st_is_empty(geom)) %>%
pull(district_school)) {
school_data <- WI_schools %>% filter(district_school == school)
message(paste(school_data %>% pull(SCHOOL_NAME), "-", district, "School District", "-", school_data %>% pull(CTY_DIST), "County"))
#find walk boundary distance for school
if(length(which(district_info$name == district)) > 0) {
ifelse((school_data %>% pull(SCHOOLTYPE)) %in% "High School",
walk_boundary_mi <- district_info$walk_boundary_hs[district_info$name == district],
ifelse((school_data %>% pull(SCHOOLTYPE)) %in% c("Junior High School", "Middle School"),
walk_boundary_mi <- district_info$walk_boundary_ms[district_info$name == district],
ifelse((school_data %>% pull(SCHOOLTYPE)) %in% c("Combined Elementary/Secondary School", "Elementary School"),
walk_boundary_mi <- district_info$walk_boundary_es[district_info$name == district],
walk_boundary <- 2)))
} else {
walk_boundary_mi <- 2
}
walk_boundary_m <- walk_boundary_mi * 1609
walk_boundary_poly <- fill_holes(st_make_valid(osrmIsodistance(
loc = st_transform(school_data %>% pull(geom), crs = 4326),
breaks = c(walk_boundary_m),
res = 80)
), units::set_units(1, km^2))
# create bounding box from school, 5km away.
bbox <- st_bbox(st_transform(st_buffer(school_data %>% pull(geom), dist = walk_boundary_m + 500), crs = 4326))
bbox <- c(left = as.double(bbox[1]),
bottom = as.double(bbox[2]),
right = as.double(bbox[3]),
top = as.double(bbox[4]))
#get basemap
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basemap <- get_stadiamap(bbox = bbox, zoom = 15, maptype = "stamen_toner_lite")
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# generate map
ggmap(basemap) +
labs(title = paste0("Crashes between cars and youth (<18) pedestrians/bicyclists near ",
school_data %>% pull(SCHOOL_NAME),
" School"),
subtitle = paste0(school_data %>% pull(DISTRICT_NAME),
" School District | ",
min(year(TOPS_data$date), na.rm = TRUE),
" - ",
max(year(TOPS_data$date), na.rm = TRUE)),
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caption = "crash data from UW TOPS lab - retrieved 3/2024 per direction of the WisDOT Bureau of Transportation Safety\nbasemap from StadiaMaps and OpenStreetMap Contributers",
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x = NULL,
y = NULL) +
theme(axis.text=element_blank(),
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axis.ticks=element_blank(),
plot.caption = element_text(color = "grey")) +
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## add bike lts
#geom_sf(data = bike_lts[[county]],
# inherit.aes = FALSE,
# aes(color = lts)) +
#scale_color_manual(values = bike_lts_scale$color, name = "Bike Level of Traffic Stress") +
# add crash locations
new_scale_fill() +
geom_point(data = TOPS_data %>%
filter(ROLE1 %in% c("BIKE", "PED")
& age1 < 18
| ROLE2 %in% c("BIKE", "PED")
& age2 < 18
) %>%
filter(longitude >= as.double(bbox[1]),
latitude >= as.double(bbox[2]),
longitude <= as.double(bbox[3]),
latitude <= as.double(bbox[4])),
aes(x = longitude,
y = latitude,
fill = InjSevName),
shape = 23,
size = 3) +
scale_fill_manual(values = injury_severity$color, name = "Crash Severity") +
# add walk boundary
new_scale_color() +
new_scale_fill() +
geom_sf(data = walk_boundary_poly,
inherit.aes = FALSE,
aes(color = paste0(walk_boundary_mi, " mile walking boundary")),
fill = NA,
linewidth = 1) +
scale_color_manual(values = "black", name = NULL) +
# add school location
# geom_sf(data = st_transform(school_data, crs = 4326), inherit.aes = FALSE) +
annotation_raster(school_symbol,
# Position adjustments here using plot_box$max/min/range
ymin = as.double((st_transform(school_data, crs = 4326) %>% pull(geom))[[1]])[2] - 0.001,
ymax = as.double((st_transform(school_data, crs = 4326) %>% pull(geom))[[1]])[2] + 0.001,
xmin = as.double((st_transform(school_data, crs = 4326) %>% pull(geom))[[1]])[1] - 0.0015,
xmax = as.double((st_transform(school_data, crs = 4326) %>% pull(geom))[[1]])[1] + 0.0015) +
geom_sf_label(data = st_transform(school_data, crs = 4326),
inherit.aes = FALSE,
mapping = aes(label = paste(SCHOOL_NAME, "School")),
nudge_y = 0.0015,
label.size = 0.04,
size = 2) +
annotation_raster(logo,
# Position adjustments here using plot_box$max/min/range
ymin = bbox['top'] - (bbox['top']-bbox['bottom']) * 0.16,
ymax = bbox['top'],
xmin = bbox['right'] + (bbox['right']-bbox['left']) * 0.05,
xmax = bbox['right'] + (bbox['right']-bbox['left']) * 0.20) +
coord_sf(clip = "off")
ggsave(file = paste0("figures/crash_maps/Crash Maps/",
str_to_title(school_data %>% pull(CTY_DIST)),
" County/",
school_data %>% pull(DISTRICT_NAME),
" School District/",
str_replace_all(school_data %>% pull(SCHOOLTYPE), "/","-"),
"s/",
str_replace_all(school_data %>% pull(SCHOOL_NAME), "/", "-"),
" School.pdf"),
title = paste0(school_data %>% pull(SCHOOL), " Youth Pedestrian/Bike crashes"),
device = pdf,
height = 8.5,
width = 11,
units = "in",
create.dir = TRUE)
}
districts_done <<- c(districts_done, district)
}
## generate maps in parallel ----
mclapply(district_focus,
generate_school_maps,
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mc.cores = 8,
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mc.cleanup = TRUE,
mc.preschedule = TRUE,
mc.silent = FALSE)
# double check that all schools have a map ----
double_check <- list(NULL)
for(school in WI_schools$district_school) {
school_data <- WI_schools %>% filter(district_school %in% school)
school_check <- data.frame(district_school = c(school),
exists = c(file.exists(paste0("figures/crash_maps/Crash Maps/",
str_to_title(school_data %>% pull(CTY_DIST)),
" County/",
school_data %>% pull(DISTRICT_NAME),
" School District/",
str_replace_all(school_data %>% pull(SCHOOLTYPE), "/","-"),
"s/",
str_replace_all(school_data %>% pull(SCHOOL_NAME), "/", "-"),
" School.pdf"))))
double_check[[school]] <- school_check
}
double_check <- bind_rows(double_check)
unique(WI_schools %>%
filter(district_school %in% (double_check %>%
filter(exists == FALSE) %>%
pull(district_school)),
!st_is_empty(geom)) %>%
pull(DISTRICT_NAME))
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