data_raw/data_refresh.R
In RamiKrispin/covid19sf: The Covid19 San Francisco Dataset
data_refresh <- function(){
`%>%` <- magrittr::`%>%`
# covid19sf_age ----
# cat(paste0("\033[4;", 36, "m","covid19sf_age dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
# age_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_age.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
# covid19sf_age <- read.csv("https://data.sfgov.org/resource/sunc-2t3k.csv?$limit=10000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
# if(max(covid19sf_age$specimen_collection_date) > max(age_csv$specimen_collection_date) ||
# nrow(covid19sf_age) > nrow(age_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_age, overwrite = TRUE)
# write.csv(covid19sf_age, "csv/covid19sf_age.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_summary ----
# cat(paste0("\033[4;", 36, "m","covid19sf_summary dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
#
#
# covid19sf_summary <- read.csv("https://data.sfgov.org/resource/tvq9-ec9w.csv?$limit=5000",
# stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at, -last_updated)
#
#
#
# summary_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_summary.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_summary$specimen_collection_date) > max(summary_csv$specimen_collection_date) || nrow(covid19sf_summary) > nrow(summary_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_summary, overwrite = TRUE)
# write.csv(covid19sf_summary, "csv/covid19sf_summary.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_hospitalizations ----
cat(paste0("\033[4;", 36, "m","covid19sf_hospitalizations dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_hospitalizations <- read.csv("https://data.sfgov.org/resource/nxjg-bhem.csv?$limit=5000", stringsAsFactors = FALSE) %>%
dplyr::mutate(reportdate = as.Date(lubridate::ymd_hms(reportdate,
tz = "America/Los_Angeles")))
hospitalizations_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_hospitalizations.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(reportdate = as.Date(reportdate, tz = "America/Los_Angeles"))
if(max(covid19sf_hospitalizations$reportdate) > max(hospitalizations_csv$reportdate) ||
nrow(covid19sf_hospitalizations) > nrow(hospitalizations_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_hospitalizations, overwrite = TRUE)
write.csv(covid19sf_hospitalizations, "csv/covid19sf_hospitalizations.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_tests ----
cat(paste0("\033[4;", 36, "m","covid19sf_tests dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_tests <- read.csv("https://data.sfgov.org/resource/nfpa-mg4g.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
tz = "America/Los_Angeles")),
last_updated = lubridate::ymd_hms(last_updated_at,
tz = "America/Los_Angeles")) %>%
dplyr::select(-last_updated_at, - last_updated, - data_loaded_at)
tests_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_tests.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
tz = "America/Los_Angeles"))
if(max(covid19sf_tests$specimen_collection_date) > max(tests_csv$specimen_collection_date) ||
nrow(covid19sf_tests) > nrow(tests_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_tests, overwrite = TRUE)
write.csv(covid19sf_tests, "csv/covid19sf_tests.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_demo ----
# cat(paste0("\033[4;", 36, "m","covid19sf_demo dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
# covid19sf_demo <- read.csv("https://data.sfgov.org/resource/vqqm-nsqg.csv?$limit=5000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
#
# demo_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_demo.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_demo$specimen_collection_date) > max(demo_csv$specimen_collection_date) ||
# nrow(covid19sf_demo) > nrow(demo_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_demo, overwrite = TRUE)
# write.csv(covid19sf_demo, "csv/covid19sf_demo.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_population ----
cat(paste0("\033[4;", 36, "m","covid19sf_population dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_population <- read.csv("https://data.sfgov.org/resource/j7i3-u9ke.csv?$limit=50000",
stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
tz = "America/Los_Angeles")),
last_updated = lubridate::ymd_hms(data_loaded_at,
tz = "America/Los_Angeles")) %>%
dplyr::select(-data_loaded_at, - data_as_of, - last_updated)
population_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_population.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
tz = "America/Los_Angeles"),
last_updated = lubridate::ymd_hms(last_updated,
tz = "America/Los_Angeles"))
if(max(covid19sf_population$specimen_collection_date) > max(population_csv$specimen_collection_date) ||
nrow(covid19sf_population) > nrow(population_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_population, overwrite = TRUE)
write.csv(covid19sf_population, "csv/covid19sf_population.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_housing ----
cat(paste0("\033[4;", 36, "m","covid19sf_housing dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_housing <- read.csv("https://data.sfgov.org/resource/qu2c-7bqh.csv?$limit=5000", stringsAsFactors = FALSE) %>%
dplyr::mutate(date_updated = as.Date(lubridate::ymd_hms(date_updated,
quiet = TRUE,
tz = "America/Los_Angeles")))
housing_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_housing.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(date_updated = as.Date(date_updated,tz = "America/Los_Angeles"))
if(max(covid19sf_housing$date_updated) > max(housing_csv$date_updated) ||
nrow(covid19sf_housing) > nrow(housing_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_housing, overwrite = TRUE)
write.csv(covid19sf_housing, "csv/covid19sf_housing.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_geo ----
cat(paste0("\033[4;", 36, "m","covid19sf_geo dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_geo <- sf::st_read("https://data.sfgov.org/resource/tpyr-dvnc.geojson",
stringsAsFactors = FALSE,
quiet = TRUE) %>%
dplyr::select(area_type, id, count, rate, deaths, acs_population, last_updated = last_updated_at, geometry)
covid19sf_geo$count <- as.numeric(covid19sf_geo$count)
covid19sf_geo$rate <- as.numeric(covid19sf_geo$rate)
covid19sf_geo$deaths <- as.numeric(covid19sf_geo$deaths)
covid19sf_geo$acs_population <- as.numeric(covid19sf_geo$acs_population)
covid19sf_geo$id <- as.character(covid19sf_geo$id)
covid19sf_geo$area_type <- as.character(covid19sf_geo$area_type)
geo_csv <- sf::st_read("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_geo.geojson",
stringsAsFactors = FALSE,
quiet = TRUE)
if(max(as.Date(covid19sf_geo$last_updated)) > max(as.Date(geo_csv$last_updated)) ||
nrow(covid19sf_geo) > nrow(geo_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_geo, overwrite = TRUE)
sf::write_sf(covid19sf_geo, "csv/covid19sf_geo.geojson")
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_vaccine_geo ----
cat(paste0("\033[4;", 36, "m","covid19sf_vaccine_geo dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_vaccine_geo <- sf::st_read("https://data.sfgov.org/resource/4e7h-hjt4.geojson",
stringsAsFactors = FALSE,
quiet = TRUE) %>%
dplyr::select(id, area_type,
count_vaccinated_by_dph, count_vaccinated,
count_series_completed, acs_population,
percent_pop_series_completed, geometry,
last_updated = data_loaded_at) %>%
dplyr::mutate(count_vaccinated_by_dph = as.numeric(count_vaccinated_by_dph),
count_vaccinated = as.numeric(count_vaccinated),
count_series_completed = as.numeric(count_series_completed),
acs_population = as.numeric(acs_population),
percent_pop_series_completed = count_series_completed / acs_population)
vacccine_geo_csv <- sf::st_read("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_vaccine_geo.geojson",
stringsAsFactors = FALSE,
quiet = TRUE)
if(max(as.Date(covid19sf_vaccine_geo$last_updated)) > max(as.Date(vacccine_geo_csv$last_updated))){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_vaccine_geo, overwrite = TRUE)
unlink("csv/covid19sf_vaccine_geo.geojson")
sf::write_sf(covid19sf_vaccine_geo, "csv/covid19sf_vaccine_geo.geojson")
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_hospital ----
cat(paste0("\033[4;", 36, "m","covid19sf_hospital dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_hospital <- read.csv("https://data.sfgov.org/resource/rh24-ebzg.csv?$limit=5000", stringsAsFactors = FALSE) %>%
dplyr::mutate(date = as.Date(lubridate::ymd_hms(date,
tz = "America/Los_Angeles")))
hospital_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_hospital.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(date = as.Date(date, z = "America/Los_Angeles"))
if(max(covid19sf_hospital$date) > max(hospital_csv$date) ||
nrow(covid19sf_hospital) > nrow(hospital_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_hospital, overwrite = TRUE)
write.csv(covid19sf_hospital, "csv/covid19sf_hospital.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_test_loc ----
cat(paste0("\033[4;", 36, "m","covid19sf_test_loc dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_test_loc <- sf::st_read("https://data.sfgov.org/resource/dtit-7gp4.geojson",
stringsAsFactors = FALSE,
quiet = TRUE) %>%
dplyr::select(id, medical_home, name,address, phone_number, phone_number_formatted,
testing_hours, popup_or_permanent, location_type, eligibility,
cta_text, cta_link, sample_collection_method, lab,
latitude, longitude, geometry)
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_test_loc, overwrite = TRUE)
sf::write_sf(covid19sf_test_loc, "csv/covid19sf_test_loc.geojson")
# covid19sf_gender ----
# cat(paste0("\033[4;", 36, "m","covid19sf_gender dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
#
#
# covid19sf_gender <- read.csv("https://data.sfgov.org/resource/nhy6-gqam.csv?$limit=5000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
#
#
# gender_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_gender.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_gender$specimen_collection_date) > max(gender_csv$specimen_collection_date) ||
# nrow(covid19sf_gender) > nrow(gender_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_gender, overwrite = TRUE)
# write.csv(covid19sf_gender, "csv/covid19sf_gender.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_homeless ----
# cat(paste0("\033[4;", 36, "m","covid19sf_homeless dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
#
#
# covid19sf_homeless <- read.csv("https://data.sfgov.org/resource/b45x-2crv.csv?$limit=5000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
#
#
# homeless_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_homeless.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_homeless$specimen_collection_date) > max(homeless_csv$specimen_collection_date) ||
# nrow(covid19sf_homeless) > nrow(homeless_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_homeless, overwrite = TRUE)
# write.csv(covid19sf_homeless, "csv/covid19sf_homeless.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# Vaccine demographic summary ----
cat(paste0("\033[4;", 36, "m","covid19sf_vaccine_demo dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_vaccine_demo <- read.csv("https://data.sfgov.org/resource/wv2h-rqwk.csv?$limit=1000", stringsAsFactors = FALSE)
covid19sf_vaccine_demo$data_as_of <- lubridate::ymd_hms(covid19sf_vaccine_demo$data_as_of)
covid19sf_vaccine_demo$data_loaded_at <- lubridate::ymd_hms(covid19sf_vaccine_demo$data_loaded_at)
covid19sf_vaccine_demo_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_vaccine_demo.csv", stringsAsFactors = FALSE)
covid19sf_vaccine_demo_csv$data_as_of <- lubridate::ymd_hms(covid19sf_vaccine_demo_csv$data_as_of)
covid19sf_vaccine_demo_csv$data_loaded_at <- lubridate::ymd_hms(covid19sf_vaccine_demo_csv$data_loaded_at)
if(round(as.numeric(max(covid19sf_vaccine_demo$data_loaded_at, na.rm = TRUE))) >
round(as.numeric(max(covid19sf_vaccine_demo_csv$data_loaded_at, na.rm = TRUE)))){
usethis::use_data(covid19sf_vaccine_demo, overwrite = TRUE)
write.csv(covid19sf_vaccine_demo, "csv/covid19sf_vaccine_demo.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# Vaccine demographic time series ----
cat(paste0("\033[4;", 36, "m","covid19sf_vaccine_demo_ts dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_vaccine_demo_ts <- read.csv("https://data.sfgov.org/resource/xjh5-h442.csv?$limit=50000", stringsAsFactors = FALSE)
covid19sf_vaccine_demo_ts$date_administered <- lubridate::ymd_hms(covid19sf_vaccine_demo_ts$date_administered)
covid19sf_vaccine_demo_ts$data_as_of <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts$data_as_of)
covid19sf_vaccine_demo_ts$data_loaded_at <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts$data_loaded_at)
covid19sf_vaccine_demo_ts_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_vaccine_demo_ts.csv", stringsAsFactors = FALSE)
covid19sf_vaccine_demo_ts_csv$date_administered <- lubridate::ymd(covid19sf_vaccine_demo_ts_csv$date_administered)
# covid19sf_vaccine_demo_ts_csv$data_as_of <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts_csv$data_as_of)
# covid19sf_vaccine_demo_ts_csv$data_loaded_at <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts_csv$data_loaded_at)
if(round(as.numeric(max(covid19sf_vaccine_demo_ts$date_administered, na.rm = TRUE))) >
round(as.numeric(max(covid19sf_vaccine_demo_ts_csv$date_administered, na.rm = TRUE)))){
usethis::use_data(covid19sf_vaccine_demo_ts, overwrite = TRUE)
write.csv(covid19sf_vaccine_demo_ts, "csv/covid19sf_vaccine_demo_ts.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
return(invisible(NULL))
}
data_refresh()
RamiKrispin/covid19sf documentation built on April 3, 2023, 4:11 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
data_refresh <- function(){
`%>%` <- magrittr::`%>%`
# covid19sf_age ----
# cat(paste0("\033[4;", 36, "m","covid19sf_age dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
# age_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_age.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
# covid19sf_age <- read.csv("https://data.sfgov.org/resource/sunc-2t3k.csv?$limit=10000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
# if(max(covid19sf_age$specimen_collection_date) > max(age_csv$specimen_collection_date) ||
# nrow(covid19sf_age) > nrow(age_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_age, overwrite = TRUE)
# write.csv(covid19sf_age, "csv/covid19sf_age.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_summary ----
# cat(paste0("\033[4;", 36, "m","covid19sf_summary dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
#
#
# covid19sf_summary <- read.csv("https://data.sfgov.org/resource/tvq9-ec9w.csv?$limit=5000",
# stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at, -last_updated)
#
#
#
# summary_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_summary.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_summary$specimen_collection_date) > max(summary_csv$specimen_collection_date) || nrow(covid19sf_summary) > nrow(summary_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_summary, overwrite = TRUE)
# write.csv(covid19sf_summary, "csv/covid19sf_summary.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_hospitalizations ----
cat(paste0("\033[4;", 36, "m","covid19sf_hospitalizations dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_hospitalizations <- read.csv("https://data.sfgov.org/resource/nxjg-bhem.csv?$limit=5000", stringsAsFactors = FALSE) %>%
dplyr::mutate(reportdate = as.Date(lubridate::ymd_hms(reportdate,
tz = "America/Los_Angeles")))
hospitalizations_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_hospitalizations.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(reportdate = as.Date(reportdate, tz = "America/Los_Angeles"))
if(max(covid19sf_hospitalizations$reportdate) > max(hospitalizations_csv$reportdate) ||
nrow(covid19sf_hospitalizations) > nrow(hospitalizations_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_hospitalizations, overwrite = TRUE)
write.csv(covid19sf_hospitalizations, "csv/covid19sf_hospitalizations.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_tests ----
cat(paste0("\033[4;", 36, "m","covid19sf_tests dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_tests <- read.csv("https://data.sfgov.org/resource/nfpa-mg4g.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
tz = "America/Los_Angeles")),
last_updated = lubridate::ymd_hms(last_updated_at,
tz = "America/Los_Angeles")) %>%
dplyr::select(-last_updated_at, - last_updated, - data_loaded_at)
tests_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_tests.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
tz = "America/Los_Angeles"))
if(max(covid19sf_tests$specimen_collection_date) > max(tests_csv$specimen_collection_date) ||
nrow(covid19sf_tests) > nrow(tests_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_tests, overwrite = TRUE)
write.csv(covid19sf_tests, "csv/covid19sf_tests.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_demo ----
# cat(paste0("\033[4;", 36, "m","covid19sf_demo dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
# covid19sf_demo <- read.csv("https://data.sfgov.org/resource/vqqm-nsqg.csv?$limit=5000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
#
# demo_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_demo.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_demo$specimen_collection_date) > max(demo_csv$specimen_collection_date) ||
# nrow(covid19sf_demo) > nrow(demo_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_demo, overwrite = TRUE)
# write.csv(covid19sf_demo, "csv/covid19sf_demo.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_population ----
cat(paste0("\033[4;", 36, "m","covid19sf_population dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_population <- read.csv("https://data.sfgov.org/resource/j7i3-u9ke.csv?$limit=50000",
stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
tz = "America/Los_Angeles")),
last_updated = lubridate::ymd_hms(data_loaded_at,
tz = "America/Los_Angeles")) %>%
dplyr::select(-data_loaded_at, - data_as_of, - last_updated)
population_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_population.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
tz = "America/Los_Angeles"),
last_updated = lubridate::ymd_hms(last_updated,
tz = "America/Los_Angeles"))
if(max(covid19sf_population$specimen_collection_date) > max(population_csv$specimen_collection_date) ||
nrow(covid19sf_population) > nrow(population_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_population, overwrite = TRUE)
write.csv(covid19sf_population, "csv/covid19sf_population.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_housing ----
cat(paste0("\033[4;", 36, "m","covid19sf_housing dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_housing <- read.csv("https://data.sfgov.org/resource/qu2c-7bqh.csv?$limit=5000", stringsAsFactors = FALSE) %>%
dplyr::mutate(date_updated = as.Date(lubridate::ymd_hms(date_updated,
quiet = TRUE,
tz = "America/Los_Angeles")))
housing_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_housing.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(date_updated = as.Date(date_updated,tz = "America/Los_Angeles"))
if(max(covid19sf_housing$date_updated) > max(housing_csv$date_updated) ||
nrow(covid19sf_housing) > nrow(housing_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_housing, overwrite = TRUE)
write.csv(covid19sf_housing, "csv/covid19sf_housing.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_geo ----
cat(paste0("\033[4;", 36, "m","covid19sf_geo dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_geo <- sf::st_read("https://data.sfgov.org/resource/tpyr-dvnc.geojson",
stringsAsFactors = FALSE,
quiet = TRUE) %>%
dplyr::select(area_type, id, count, rate, deaths, acs_population, last_updated = last_updated_at, geometry)
covid19sf_geo$count <- as.numeric(covid19sf_geo$count)
covid19sf_geo$rate <- as.numeric(covid19sf_geo$rate)
covid19sf_geo$deaths <- as.numeric(covid19sf_geo$deaths)
covid19sf_geo$acs_population <- as.numeric(covid19sf_geo$acs_population)
covid19sf_geo$id <- as.character(covid19sf_geo$id)
covid19sf_geo$area_type <- as.character(covid19sf_geo$area_type)
geo_csv <- sf::st_read("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_geo.geojson",
stringsAsFactors = FALSE,
quiet = TRUE)
if(max(as.Date(covid19sf_geo$last_updated)) > max(as.Date(geo_csv$last_updated)) ||
nrow(covid19sf_geo) > nrow(geo_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_geo, overwrite = TRUE)
sf::write_sf(covid19sf_geo, "csv/covid19sf_geo.geojson")
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_vaccine_geo ----
cat(paste0("\033[4;", 36, "m","covid19sf_vaccine_geo dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_vaccine_geo <- sf::st_read("https://data.sfgov.org/resource/4e7h-hjt4.geojson",
stringsAsFactors = FALSE,
quiet = TRUE) %>%
dplyr::select(id, area_type,
count_vaccinated_by_dph, count_vaccinated,
count_series_completed, acs_population,
percent_pop_series_completed, geometry,
last_updated = data_loaded_at) %>%
dplyr::mutate(count_vaccinated_by_dph = as.numeric(count_vaccinated_by_dph),
count_vaccinated = as.numeric(count_vaccinated),
count_series_completed = as.numeric(count_series_completed),
acs_population = as.numeric(acs_population),
percent_pop_series_completed = count_series_completed / acs_population)
vacccine_geo_csv <- sf::st_read("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_vaccine_geo.geojson",
stringsAsFactors = FALSE,
quiet = TRUE)
if(max(as.Date(covid19sf_vaccine_geo$last_updated)) > max(as.Date(vacccine_geo_csv$last_updated))){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_vaccine_geo, overwrite = TRUE)
unlink("csv/covid19sf_vaccine_geo.geojson")
sf::write_sf(covid19sf_vaccine_geo, "csv/covid19sf_vaccine_geo.geojson")
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_hospital ----
cat(paste0("\033[4;", 36, "m","covid19sf_hospital dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_hospital <- read.csv("https://data.sfgov.org/resource/rh24-ebzg.csv?$limit=5000", stringsAsFactors = FALSE) %>%
dplyr::mutate(date = as.Date(lubridate::ymd_hms(date,
tz = "America/Los_Angeles")))
hospital_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_hospital.csv", stringsAsFactors = FALSE) %>%
dplyr::mutate(date = as.Date(date, z = "America/Los_Angeles"))
if(max(covid19sf_hospital$date) > max(hospital_csv$date) ||
nrow(covid19sf_hospital) > nrow(hospital_csv)){
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_hospital, overwrite = TRUE)
write.csv(covid19sf_hospital, "csv/covid19sf_hospital.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# covid19sf_test_loc ----
cat(paste0("\033[4;", 36, "m","covid19sf_test_loc dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_test_loc <- sf::st_read("https://data.sfgov.org/resource/dtit-7gp4.geojson",
stringsAsFactors = FALSE,
quiet = TRUE) %>%
dplyr::select(id, medical_home, name,address, phone_number, phone_number_formatted,
testing_hours, popup_or_permanent, location_type, eligibility,
cta_text, cta_link, sample_collection_method, lab,
latitude, longitude, geometry)
cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
usethis::use_data(covid19sf_test_loc, overwrite = TRUE)
sf::write_sf(covid19sf_test_loc, "csv/covid19sf_test_loc.geojson")
# covid19sf_gender ----
# cat(paste0("\033[4;", 36, "m","covid19sf_gender dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
#
#
# covid19sf_gender <- read.csv("https://data.sfgov.org/resource/nhy6-gqam.csv?$limit=5000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
#
#
# gender_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_gender.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_gender$specimen_collection_date) > max(gender_csv$specimen_collection_date) ||
# nrow(covid19sf_gender) > nrow(gender_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_gender, overwrite = TRUE)
# write.csv(covid19sf_gender, "csv/covid19sf_gender.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# covid19sf_homeless ----
# cat(paste0("\033[4;", 36, "m","covid19sf_homeless dataset","\033[0m","\n"))
# cat("Checking for updates...\n")
#
#
#
# covid19sf_homeless <- read.csv("https://data.sfgov.org/resource/b45x-2crv.csv?$limit=5000", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(lubridate::ymd_hms(specimen_collection_date,
# tz = "America/Los_Angeles")),
# last_updated = lubridate::ymd_hms(last_updated_at,
# tz = "America/Los_Angeles")) %>%
# dplyr::select(-last_updated_at)
#
#
#
# homeless_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_homeless.csv", stringsAsFactors = FALSE) %>%
# dplyr::mutate(specimen_collection_date = as.Date(specimen_collection_date,
# tz = "America/Los_Angeles"),
# last_updated = lubridate::ymd_hms(last_updated,
# tz = "America/Los_Angeles"))
#
#
#
#
# if(max(covid19sf_homeless$specimen_collection_date) > max(homeless_csv$specimen_collection_date) ||
# nrow(covid19sf_homeless) > nrow(homeless_csv)){
# cat(paste0("\033[0;", 42, "m","Updates are available, saving the changes","\033[0m","\n"))
#
# usethis::use_data(covid19sf_homeless, overwrite = TRUE)
# write.csv(covid19sf_homeless, "csv/covid19sf_homeless.csv", row.names = FALSE)
# } else{
# cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
# }
# Vaccine demographic summary ----
cat(paste0("\033[4;", 36, "m","covid19sf_vaccine_demo dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_vaccine_demo <- read.csv("https://data.sfgov.org/resource/wv2h-rqwk.csv?$limit=1000", stringsAsFactors = FALSE)
covid19sf_vaccine_demo$data_as_of <- lubridate::ymd_hms(covid19sf_vaccine_demo$data_as_of)
covid19sf_vaccine_demo$data_loaded_at <- lubridate::ymd_hms(covid19sf_vaccine_demo$data_loaded_at)
covid19sf_vaccine_demo_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_vaccine_demo.csv", stringsAsFactors = FALSE)
covid19sf_vaccine_demo_csv$data_as_of <- lubridate::ymd_hms(covid19sf_vaccine_demo_csv$data_as_of)
covid19sf_vaccine_demo_csv$data_loaded_at <- lubridate::ymd_hms(covid19sf_vaccine_demo_csv$data_loaded_at)
if(round(as.numeric(max(covid19sf_vaccine_demo$data_loaded_at, na.rm = TRUE))) >
round(as.numeric(max(covid19sf_vaccine_demo_csv$data_loaded_at, na.rm = TRUE)))){
usethis::use_data(covid19sf_vaccine_demo, overwrite = TRUE)
write.csv(covid19sf_vaccine_demo, "csv/covid19sf_vaccine_demo.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
# Vaccine demographic time series ----
cat(paste0("\033[4;", 36, "m","covid19sf_vaccine_demo_ts dataset","\033[0m","\n"))
cat("Checking for updates...\n")
covid19sf_vaccine_demo_ts <- read.csv("https://data.sfgov.org/resource/xjh5-h442.csv?$limit=50000", stringsAsFactors = FALSE)
covid19sf_vaccine_demo_ts$date_administered <- lubridate::ymd_hms(covid19sf_vaccine_demo_ts$date_administered)
covid19sf_vaccine_demo_ts$data_as_of <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts$data_as_of)
covid19sf_vaccine_demo_ts$data_loaded_at <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts$data_loaded_at)
covid19sf_vaccine_demo_ts_csv <- read.csv("https://raw.githubusercontent.com/RamiKrispin/covid19sf/master/csv/covid19sf_vaccine_demo_ts.csv", stringsAsFactors = FALSE)
covid19sf_vaccine_demo_ts_csv$date_administered <- lubridate::ymd(covid19sf_vaccine_demo_ts_csv$date_administered)
# covid19sf_vaccine_demo_ts_csv$data_as_of <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts_csv$data_as_of)
# covid19sf_vaccine_demo_ts_csv$data_loaded_at <- NULL #lubridate::ymd_hms(covid19sf_vaccine_demo_ts_csv$data_loaded_at)
if(round(as.numeric(max(covid19sf_vaccine_demo_ts$date_administered, na.rm = TRUE))) >
round(as.numeric(max(covid19sf_vaccine_demo_ts_csv$date_administered, na.rm = TRUE)))){
usethis::use_data(covid19sf_vaccine_demo_ts, overwrite = TRUE)
write.csv(covid19sf_vaccine_demo_ts, "csv/covid19sf_vaccine_demo_ts.csv", row.names = FALSE)
} else{
cat(paste0("\033[0;", 41, "m","No updates are available","\033[0m","\n"))
}
return(invisible(NULL))
}
data_refresh()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.