Merge pull request #113 from miraisolutions/develop

Release 2.0.0

DESCRIPTION

@@ -1,6 +1,6 @@
-Package: Covid19
+Package: Covid19Mirai
 Title: Covid-19 Data Analysis
-Version: 1.2.2
+Version: 2.0.0
 Authors@R: 
     c(person("Francesca", "Vitalini", role = c("cre", "aut"),
              email = 'francesca.vitalini@mirai-solutions.com'),
@@ -38,6 +38,7 @@ Imports:
     sp,
     markdown,
     scales,
+    COVID19,
     grDevices,
     rlang,
     zoo

NAMESPACE

@@ -23,8 +23,10 @@ export(from_contagion_day_bar_plot)
 export(getTableOptions)
 export(get_Covid19_version)
 export(get_daily_data)
+export(get_datahub)
 export(get_date_data)
 export(get_pop_data)
+export(get_pop_datahub)
 export(get_timeseries_by_contagion_day_data)
 export(get_timeseries_country_data)
 export(get_timeseries_data)
@@ -33,6 +35,7 @@ export(get_timeseries_global_data)
 export(get_timeseries_province_data)
 export(get_timeseries_single_data)
 export(load_countries_data_map)
+export(load_countries_datahub_map)
 export(merge_pop_data)
 export(new_case_colors)
 export(new_total_colors)
@@ -60,6 +63,7 @@ import(sp)
 import(stringr)
 import(tidyr)
 import(zoo)
+importFrom(COVID19,covid19)
 importFrom(DT,DTOutput)
 importFrom(DT,datatable)
 importFrom(DT,renderDT)

NEWS.md

@@ -1,3 +1,12 @@
+### Covid19Mirai 2.0.0
+- Update data source from covid19datahub (#104)
+https://github.com/covid19datahub/COVID19
+- Population size taken from covid19datahub, some variables over 1M will differ
+- Package name renamed to Covid19Mirai to avoid conflict with COVID19
+- SP data saved in RDS for faster reading
+- updated info on data source, updated ReadMe page
+- correction on color palette for new active maps when there are no negative values
+
 ### Covid19 1.2.2 (2020-06-23)
 - Fix colors in lineplot (#95)
 - Align graph colors in continent map (#105)

R/app_config.R

@@ -1,33 +1,33 @@
 #' Access files in the current app
-#' 
+#'
 #' @param ... Character vector specifying directory and or file to
 #'     point to inside the current package.
-#' 
+#'
 #' @noRd
 app_sys <- function(...){
-  system.file(..., package = "Covid19")
+  system.file(..., package = "Covid19Mirai")
 }
 
 
 #' Read App Config
-#' 
-#' @param value Value to retrieve from the config file. 
-#' @param config R_CONFIG_ACTIVE value. 
+#'
+#' @param value Value to retrieve from the config file.
+#' @param config R_CONFIG_ACTIVE value.
 #' @param use_parent Logical, scan the parent directory for config file.
-#'     
+#'
 #' @importFrom config get
-#' 
+#'
 #' @noRd
 get_golem_config <- function(
-  value, 
-  config = Sys.getenv("R_CONFIG_ACTIVE", "default"), 
+  value,
+  config = Sys.getenv("R_CONFIG_ACTIVE", "default"),
   use_parent = TRUE
 ){
   config::get(
-    value = value, 
-    config = config, 
+    value = value,
+    config = config,
     # Modify this if your config file is somewhere else:
-    file = app_sys("golem-config.yml"), 
+    file = app_sys("golem-config.yml"),
     use_parent = use_parent
   )
 }

R/app_server.R

@@ -10,19 +10,24 @@
 #' @noRd
 app_server <- function(input, output, session) {
 
+#profvis({
   # Params ----
   n <- 1000 #  min number of cases for a country to be considered. Default 1000
   w <- 7 # number of days of outbreak. Default 7
 
   # Data ----
   # map
-  countries_data_map <- load_countries_data_map(destpath = system.file("./countries_data", package = "Covid19"))
-  orig_data <- reactive({
-    get_timeseries_full_data() %>%
+  #countries_data_map <- load_countries_datahub_map(destpath = system.file("./countries_data", package = "Covid19Mirai"))
+  rds_map = "WorldMap_sp_rds"
+  message("read map from RDS ", rds_map)
+  countries_data_map = readRDS(file =  file.path(system.file("./countries_data", package = "Covid19Mirai"),rds_map))
+
+  orig_data <- #reactive({
+    get_datahub() %>%
       get_timeseries_by_contagion_day_data()
-  })
+  #})
 
-  pop_data = get_pop_data()
+  pop_data = get_pop_datahub()
 
   #align continents from map with pop
   #country_name <- as.character(unique(as.character(countries_data_map$NAME))[charmatch(pop_data$Country.Region, unique(as.character(countries_data_map$NAME)))])
@@ -44,49 +49,35 @@ app_server <- function(input, output, session) {
   pop_data = res$pop
   countries_data_map = res$map
   # remove small countries, population <=1000
-  pop_data = pop_data %>% filter(population >1000)
-  # clean countries_data_map
-  orig_data_aggregate <- reactive({
-    orig_data_aggregate <- orig_data() %>%
-      aggregate_province_timeseries_data() %>%
-      add_growth_death_rate() %>%
-      arrange(Country.Region) %>%
-      #align_country_names_pop() %>%
-      merge_pop_data(pop_data) %>% # compute additional variables
-      #align_country_names_pop_reverse() %>%
-      mutate(mortality_rate_1M_pop = round(10^6*deaths/population, digits = 3),
-             prevalence_rate_1M_pop = round(10^6*confirmed/population, digits = 3),
-             new_prevalence_rate_1M_pop = round(10^6*new_confirmed/population, digits = 3))
-    orig_data_aggregate
-  })
+  # TODO pop_data = pop_data %>% filter(population >1000)
+
+  orig_data_aggregate <-
+    build_data_aggr(orig_data, pop_data)
+
 
   output$last_update <- renderText({
     paste0("Last updated: ",
-           max(orig_data()$date)
+           max(orig_data$date)
     )
   })
 
-  data_filtered <- reactive({
-    orig_data_aggregate() %>%
+  data_filtered <-
+    orig_data_aggregate %>%
       rescale_df_contagion(n = n, w = w)
-  })
+
 
   countries <- reactive({
-    data_filtered() %>%
+    data_filtered %>%
       select(Country.Region) %>%
       distinct()
   })
 
 
-  # continents <- reactive({
-  #   data_filtered() %>%
-  #     select(continent) %>%
-  #     distinct()
-  # })
-
   # Modules ----
+
   callModule(mod_global_server, "global", orig_data = orig_data, orig_data_aggregate = orig_data_aggregate,
              data_filtered = data_filtered, countries_data_map)
+
   callModule(mod_continent_comparison_server, "continent_comparison", orig_data_aggregate = orig_data_aggregate, n = n, w = w, pop_data = pop_data)
 
   # select continents in tabs
@@ -98,12 +89,10 @@ app_server <- function(input, output, session) {
                orig_data_aggregate = orig_data_aggregate, n = n, w = w,
                pop_data = pop_data, countries_data_map = countries_data_map,
                cont = continents[i.cont], uicont = uicontinents[i.cont])
-
   }
+  callModule(mod_country_server, "country", data_filtered = data_filtered, countries = countries, n = n, w = w)
 
-
-  callModule(mod_country_server, "country", orig_data_aggregate = orig_data_aggregate, data_filtered = data_filtered, countries = countries, n = n, w = w)
-  callModule(mod_country_comparison_server, "country_comparison", orig_data_aggregate = orig_data_aggregate, data_filtered = data_filtered, countries = countries, n = n, w = w)
+  callModule(mod_country_comparison_server, "country_comparison", data_filtered = data_filtered, countries = countries, n = n, w = w)
 
   # Modal ----
   # what is new pop-up
@@ -117,5 +106,7 @@ app_server <- function(input, output, session) {
       fade = FALSE
     ))
   })
+#})
 
 }
+

R/app_ui.R

@@ -39,13 +39,17 @@ app_ui <- function(request) {
           ),
           a(
             # href = "https://github.com/CSSEGISandData/COVID-19",
-            href = "https://github.com/bumbeishvili/covid19-daily-data",
+            #href = "https://github.com/bumbeishvili/covid19-daily-data",
+            href =  "https://covid19datahub.io/",
             target = "_blank",
             span(
               id = "subtitle",
-              "Data source: worldometers from 26.03.2020, JHU CSSE before.",
+              #"Data source: worldometers from 26.03.2020, JHU CSSE before.",
+              "Data source: COVID-19 Data Hub",
               textOutput("last_update", inline = TRUE) %>%
-                bs_embed_tooltip(title = "Data Repository by bumbeishvili. More information on the README.", placement = "right")
+                #bs_embed_tooltip(title = "Data Repository by bumbeishvili. More information on the README.", placement = "right")
+                bs_embed_tooltip(title = "Data Repository by COVID-19 Data Hub. More information in the README on our github page.", placement = "right")
+
             )
           )
         ), # end header-left

R/get_Covid19_version.R

@@ -8,5 +8,5 @@
 #'
 #' @export
 get_Covid19_version <- function() {
-  as.character(utils::packageVersion("Covid19"))
+  as.character(utils::packageVersion("Covid19Mirai"))
 }