remove recovered

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: coronavirus
 Title: Tracking the Coronavirus
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: person('John', 'Coene', email = 'jcoenep@gmail.com', role = c('cre', 'aut'))
 Description: Tracking the Coronavirus.
 License: MIT + file LICENSE

NEWS.md

@@ -1,3 +1,7 @@
+# coronavirus 0.1.4
+
+- Updated JHU data source, no longer provides recovered data
+
 # coronavirus 0.1.3
 
 - Meet new country naming convention of John Hopkins data.

R/app_server.R

@@ -61,7 +61,6 @@ app_server <- function(input, output,session) {
   # counts jhu
   callModule(mod_count_server, "count_ui_1", df = df, type_filter = "confirmed")
   callModule(mod_count_server, "count_ui_2", df = df, type_filter = "death")
-  callModule(mod_count_server, "count_ui_3", df = df, type_filter = "recovered")
 
   # counts weixin
   callModule(
@@ -145,7 +144,6 @@ app_server <- function(input, output,session) {
       # jhu tab
       callModule(mod_count_server, "count_ui_1_jhu", df = df, type_filter = "confirmed")
       callModule(mod_count_server, "count_ui_2_jhu", df = df, type_filter = "death")
-      callModule(mod_count_server, "count_ui_3_jhu", df = df, type_filter = "recovered")
 
       # trend
       callModule(mod_trend_server, "trend_ui_1", df = df)

R/app_ui.R

@@ -55,9 +55,6 @@ app_ui <- function() {
               ),
               f7Col(
                 mod_count_ui("count_ui_2", "Deaths")
-              ),
-              f7Col(
-                mod_count_ui("count_ui_3", "Recovered")
               )
             ),
             h2("Weixin Data", class = "center"),
@@ -98,9 +95,6 @@ app_ui <- function() {
               f7Col(
                 mod_count_ui("count_ui_2_jhu", "Deaths")
               ),
-              f7Col(
-                mod_count_ui("count_ui_3_jhu", "Recovered")
-              )
             ),
             mod_new_cases_ui("new_cases"),
             f7Row(

R/crawl.R

@@ -23,26 +23,26 @@ crawl_coronavirus <- function(){
   # read data
   suppressMessages({
     confirmed <- readr::read_csv(confirmed_sheet, col_types = readr::cols())
-    recovered <- readr::read_csv(recovered_sheet, col_types = readr::cols())
+    #recovered <- readr::read_csv(recovered_sheet, col_types = readr::cols())
     deaths <- readr::read_csv(deaths_sheet, col_types = readr::cols())
   })
 
   # add col
   confirmed$type <- "confirmed"
-  recovered$type <- "recovered"
+  #recovered$type <- "recovered"
   deaths$type <- "death"
 
   # rename
   confirmed <- rename_sheets(confirmed)
-  recovered <- rename_sheets(recovered)
+  #recovered <- rename_sheets(recovered)
   deaths <- rename_sheets(deaths)
 
   # pivot longer
   confirmed <- pivot(confirmed)
-  recovered <- pivot(recovered)
+  #recovered <- pivot(recovered)
   deaths <- pivot(deaths)
 
-  df <- dplyr::bind_rows(confirmed, recovered, deaths) %>% 
+  df <- dplyr::bind_rows(confirmed, deaths) %>% 
     dplyr::mutate(
       date = as.Date(date, format = "%m/%d/%y"),
       cases = trimws(cases),

R/mod_jhu_death_rate.R

@@ -21,7 +21,7 @@ mod_jhu_death_rate_ui <- function(id){
     echarts4r::echarts4rOutput(ns("trend"), height = 395),
     footer = f7Row(
       f7Col(uiOutput(ns("copy_ui"))),
-      f7Col("deaths / (confirmed + recovered)")
+      f7Col("deaths / confirmed")
     )
   )
 }
@@ -65,7 +65,7 @@ mod_jhu_death_rate_echarts <- function(df){
       )
     ) %>%
     dplyr::mutate(
-      rate = death / (confirmed + recovered),
+      rate = death / (confirmed),
       rate = round(rate * 100, 3)
     ) %>% 
     echarts4r::e_charts(date) %>% 

R/mod_table.R

@@ -44,13 +44,11 @@ mod_china_server <- function(input, output, session, df){
       dplyr::arrange(-confirmed) %>% 
       dplyr::mutate(
         confirmed = as.integer(confirmed),
-        recovered = as.integer(recovered),
         death = as.integer(death)
       ) %>% 
       dplyr::select(
         Province = state,
         Confirmed = confirmed, 
-        Recovered = recovered,
         Deaths = death
       ) %>% 
       as_f7_table(card = TRUE)

R/mod_table_world.R

@@ -47,13 +47,11 @@ mod_table_world_server <- function(input, output, session, df){
       dplyr::arrange(-confirmed) %>% 
       dplyr::mutate(
         confirmed = as.integer(confirmed),
-        recovered = as.integer(recovered),
         death = as.integer(death)
       ) %>% 
       dplyr::select(
         Country = country,
         Confirmed = confirmed, 
-        Recovered = recovered,
         Deaths = death
       ) %>% 
       as_f7_table(card = TRUE)

R/utils.R

@@ -4,8 +4,8 @@ theme <- "dark"
 dxy_url <- "https://ncov.dxy.cn/ncovh5/view/pneumonia"
 
 # jhu
-confirmed_sheet <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv"
-deaths_sheet <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Deaths.csv"
+confirmed_sheet <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
+deaths_sheet <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
 recovered_sheet <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Recovered.csv"
 
 # pallettes for DXY

docs/_coverpage.md

@@ -2,7 +2,7 @@
 
 ![logo](_media/microbe.png)
 
-# Coronavirus <small>0.1.0</small>
+# Coronavirus <small>0.1.4</small>
 
 > An open-source nCov-2019 tracker.
 

docs/news.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## coronavirus 0.1.4
+
+- Updated JHU data source, no longer provides recovered data
+
 ## coronavirus 0.1.3
 
 - Meet new country naming convention of John Hopkins data.