Initial commit of dashboard version 2

- Clean slate for dashboard #41
- Update dashboard to use CovidTimelineCanada #45
- Add basic plot of case time series by province/territory (mainly as an example, plot will be removed/altered later)
- Add sidebar with link to top of page (eventually, each section will be linked here)

app.R

@@ -1,11 +1,10 @@
-# define global
-source("global.R")
+# load pipe
+library(magrittr)
 
-# define UI
+# source components
+source("global.R")
 source("ui.R")
-
-# define server
 source("server.R")
 
 # run app
-shinyApp(ui, server)
+shiny::shinyApp(ui, server)

data_updater.R

@@ -1,71 +1,39 @@
-# load libraries
-library(dplyr)
-library(RJSONIO)
-
 # create data directory, if it doesn't already exist
 dir.create("data", showWarnings = FALSE)
 
-# download most recent data from GitHub and unzip into temporary folder
-temp <- tempfile()
-tempd <- tempdir()
-download.file("https://github.com/ccodwg/Covid19Canada/archive/master.zip", temp, mode = "wb")
-unzip(temp, exdir = tempd)
+# download data from GitHub
 
-# copy into local data directories
+# update time
+curl::curl_download("https://raw.githubusercontent.com/ccodwg/CovidTimelineCanada/main/update_time.txt", "data/update_time.txt")
 
-## copy data
-if (dir.exists(paste(tempd, "Covid19Canada-master", sep = "/"))) {
-  for (f in list.files(paste(tempd, "Covid19Canada-master", sep = "/"), recursive = TRUE, full.names = TRUE)[basename(list.files(paste(tempd, "Covid19Canada-master", sep = "/"), recursive = TRUE)) %in% c(
-    "update_time.txt", "data_notes.txt",
-    "cases_timeseries_prov.csv", "mortality_timeseries_prov.csv", "recovered_timeseries_prov.csv", "testing_timeseries_prov.csv", "active_timeseries_prov.csv",
-    "cases_timeseries_hr.csv", "mortality_timeseries_hr.csv",
-    "cases_timeseries_canada.csv", "mortality_timeseries_canada.csv", "recovered_timeseries_canada.csv", "testing_timeseries_canada.csv", "active_timeseries_canada.csv",
-    "vaccine_administration_timeseries_prov.csv", "vaccine_administration_timeseries_canada.csv",
-    "vaccine_distribution_timeseries_prov.csv", "vaccine_distribution_timeseries_canada.csv",
-    "vaccine_completion_timeseries_prov.csv", "vaccine_completion_timeseries_canada.csv",
-    "vaccine_additionaldoses_timeseries_prov.csv", "vaccine_additionaldoses_timeseries_canada.csv",
-    "sk_new_cases_timeseries_hr.csv","sk_new_mortality_timeseries_hr.csv"
-    )]) {
-    file_destination <- paste0("data/", basename(f))
-    message("Copying: ", file_destination)
-    file.copy(f, file_destination, overwrite = TRUE)
-  }
-}
+# geo data
+curl::curl_download("https://raw.githubusercontent.com/ccodwg/CovidTimelineCanada/main/geo/pt.csv", "data/pt.csv")
+curl::curl_download("https://raw.githubusercontent.com/ccodwg/CovidTimelineCanada/main/geo/pt.geojson", "data/pt.geojson")
+curl::curl_download("https://raw.githubusercontent.com/ccodwg/CovidTimelineCanada/main/geo/health_regions.csv", "data/health_regions.csv")
+curl::curl_download("https://raw.githubusercontent.com/ccodwg/CovidTimelineCanada/main/geo/health_regions.geojson", "data/health_regions.geojson")
 
-## copy other files
-if (dir.exists(paste(tempd, "Covid19Canada-master", sep = "/"))) {
-  for (f in list.files(paste(tempd, "Covid19Canada-master", sep = "/"), recursive = TRUE, full.names = TRUE)[basename(list.files(paste(tempd, "Covid19Canada-master", sep = "/"), recursive = TRUE)) %in% c(
-    "prov_map.csv", "hr_map.csv","hr_map_sk_new.csv"
-  )]) {
-    file_destination <- paste0("data/", basename(f))
-    message("Copying: ", file_destination)
-    file.copy(f, file_destination, overwrite = TRUE)
-  }
+# health region data
+for (d in c(
+  "cases",
+  "deaths"
+  )) {
+  curl::curl_download(paste0("https://github.com/ccodwg/CovidTimelineCanada/raw/main/data/hr/", d, "_hr.csv"), paste0("data/", d, "_hr.csv"))
 }
 
-# download hospitalization data
-hosp <- fromJSON("https://api.covid19tracker.ca/summary/split")$data %>%
-  lapply(function(x) {
-    x[sapply(x, is.null)] <- NA
-    unlist(x)
-  }) %>%
-  {as.data.frame(t(do.call("cbind", .)), stringsAsFactors = FALSE)} %>%
-  rename(
-    prov_short = province,
-    hosp_cases = total_hospitalizations,
-    hosp_cases_change = change_hospitalizations) %>%
-  inner_join(
-    data.frame("prov_short" = c("NL", "PE", "NS", "NB", "QC", "ON", "MB", "SK", "AB", "BC", "YT", "NT", "NU"),
-               "province" = c("NL", "PEI", "Nova Scotia", "New Brunswick", "Quebec", "Ontario", "Manitoba",
-                              "Saskatchewan", "Alberta", "BC", "Yukon", "NWT", "Nunavut"),
-               stringsAsFactors = FALSE),
-    by = "prov_short"
-  ) %>%
-  select(province, hosp_cases, hosp_cases_change)
-
-# write hospitalization data
-write.csv(hosp, "data/hosp.csv", row.names = FALSE)
+# province/territory data
+for (d in c(
+  "cases",
+  "deaths",
+  "tests_completed",
+  "vaccine_coverage_dose_1",
+  "vaccine_coverage_dose_2",
+  "vaccine_coverage_dose_3",
+  "vaccine_coverage_dose_4"
+  )) {
+  curl::curl_download(paste0("https://github.com/ccodwg/CovidTimelineCanada/raw/main/data/pt/", d, "_pt.csv"), paste0("data/", d, "_pt.csv"))
+}
 
-# delete temporary files
-unlink(temp) # delete GitHub download
-unlink(paste(tempd, "Covid19Canada-master", sep = "/"), recursive = TRUE) # delete unzipped files
+# metadata
+for (d in c("cases", "deaths")) {
+  curl::curl_download(paste0("https://github.com/ccodwg/CovidTimelineCanada/raw/main/data/can/", d, "_can_completeness.json"), paste0("data/", d, "_can_completeness.json"))
+}