Develop (#52)

* release preps 1.1.2

closes #48

Co-authored-by: riccardoporreca <riccardo.porreca@mirai-solutions.com>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Covid19
 Title: Covid-19 Data Analysis
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: 
     c(person("Francesca", "Vitalini", role = c("cre", "aut"),
              email = 'francesca.vitalini@mirai-solutions.com'),

NEWS.md

@@ -1,6 +1,10 @@
+### Covid19 1.1.2 (2020-03-26)
+
+- JHU data source currently deprecated: switch (temporarily) to https://github.com/bumbeishvili/covid19-daily-data (#48). Users are alerted on app launch.
+
 ### Covid19 1.1.1 (2020-03-26)
 
-- fix path to data source
+- Updated JHU data source filenames.
 
 ### Covid19 1.1.0 (2020-03-25)
 

R/app_server.R

@@ -38,4 +38,14 @@ app_server <- function(input, output, session) {
       fade = FALSE
     ))
   })
+
+  # alert popup regarding data source
+  showModal(modalDialog(
+    title = "ALERT: Temporary Data Source",
+    includeMarkdown(system.file("additional_files/alert.md", package = "Covid19")),
+    footer = modalButton("Dismiss"),
+    size = "l",
+    easyClose = TRUE,
+    fade = FALSE
+  ))
 }

R/app_ui.R

@@ -35,11 +35,13 @@ app_ui <- function(request) {
             )
           ),
           a(
-            href = "https://github.com/CSSEGISandData/COVID-19",
+            # href = "https://github.com/CSSEGISandData/COVID-19",
+            href = "https://github.com/bumbeishvili/covid19-daily-data",
             target = "_blank",
             span(
               id = "subtitle",
-              "Data Repository by Johns Hopkins CSSE:",
+              # "Data Repository by Johns Hopkins CSSE:",
+              "Data Repository by bumbeishvili:",
               textOutput("last_update", inline = TRUE)
             )
           )

R/get_data.R

@@ -1,22 +1,22 @@
-# Data taken from here https://github.com/CSSEGISandData/COVID-19
+# Data taken from here https://github.com/bumbeishvili/covid19-daily-data
 
 #' Data Urls confirmed_timeseries
 #' @rdname DataUrls
 #'
 #' @export
-confirmed_timeseries_csv_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
+confirmed_timeseries_csv_url <- "https://raw.githubusercontent.com/bumbeishvili/covid19-daily-data/master/time_series_19-covid-Confirmed.csv"
 
 #' Data Urls deaths_timeseries_csv_url
 #' @rdname DataUrls
 #'
 #' @export
-deaths_timeseries_csv_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
+deaths_timeseries_csv_url <- "https://raw.githubusercontent.com/bumbeishvili/covid19-daily-data/master/time_series_19-covid-Deaths.csv"
 
 #' Data Urls recovered_timeseries_csv_url
 #' @rdname DataUrls
 #'
 #' @export
-recovered_timeseries_csv_url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv"
+recovered_timeseries_csv_url <- "https://raw.githubusercontent.com/bumbeishvili/covid19-daily-data/master/time_series_19-covid-Recovered.csv"
 
 #' Data Urls daily_url
 #' @rdname DataUrls
@@ -83,13 +83,16 @@ get_timeseries_full_data <- function() {
 
   confirmed <- get_timeseries_single_data("confirmed") %>%
     pivot_longer(cols = starts_with("X"), names_to = "date", values_to = "confirmed") %>%
-    convert_date()
+    convert_date() %>%
+    mutate(confirmed = round(confirmed)) # necessary for worldometers data, which is evenly spread across US states
   deaths <- get_timeseries_single_data("deaths")  %>%
     pivot_longer(cols = starts_with("X"), names_to = "date", values_to = "deaths") %>%
-    convert_date()
+    convert_date() %>%
+    mutate(deaths = round(deaths)) # necessary for worldometers data, which is evenly spread across US states
   recovered <- get_timeseries_single_data("recovered")  %>%
     pivot_longer(cols = starts_with("X"), names_to = "date", values_to = "recovered") %>%
-    convert_date()
+    convert_date() %>%
+    mutate(recovered = round(recovered)) # necessary for worldometers data, which is evenly spread across US states
 
   join_by_cols <- c("Province.State", "Country.Region", "Lat", "Long", "date")
 

R/mod_map.R

@@ -171,7 +171,8 @@ align_country_names <- function(data) {
       "Dominican Republic" = "Dominican Rep.",
       "UK" = "United Kingdom",
       "Gibraltar" = "United Kingdom",
-      "US" = "United States",
+      # "US" = "United States",
+      "USA" = "United States",
       "Saint Barthelemy" = "St-Barth\\u00e9lemy", # stringi::stri_escape_unicode("é")
 
       "Faroe Islands" = "Faeroe Is.",

inst/additional_files/alert.md

@@ -0,0 +1,11 @@
+### Update of 2020-03-26
+
+[Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE)](https://github.com/CSSEGISandData/COVID-19) is currently changing its data formats, making the current format [deprecated](https://github.com/CSSEGISandData/COVID-19/issues/1250). 
+
+While we wait for the new format to be released, we are TEMPORARLY relying on the [work](https://github.com/bumbeishvili/covid19-daily-data) of [bumbeishvili](https://github.com/bumbeishvili), who is maintaining the old JHU CSSE data set format with updates declared as from [worldometers](https://www.worldometers.info/coronavirus/). This is a new project and we cannot guarantee the reliability of the data source. We are, however, grateful to [bumbeishvili](https://github.com/bumbeishvili) for his [work](https://github.com/bumbeishvili/covid19-daily-data).
+
+Stability, compatibility and reliability of data is one of the greatest challenges for data scientists, and in this time of turmoil COVID-19 data is in constant change. We are doing our best to keep up to date with the latest data.
+
+Updates regarding data sources to be expected in the upcoming days, so stay tuned!
+
+