From 0dfb79fb47846de44b35ef71f112e1c9afbf002b Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Mon, 14 Mar 2022 22:09:13 +0200
Subject: [PATCH 1/5] Initial change to use InPhyT data for Italy

Currently fails in single class test but seems to work to generate results.
---
 R/Italy.R                                    |  39 ++++++++++---------
 data/all_country_data.rda                    | Bin 2965 -> 3078 bytes
 tests/testthat/custom_data/Italy_level_1.rds | Bin 17726 -> 1252 bytes
 3 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/R/Italy.R b/R/Italy.R
index 18fd963e..2766056b 100644
--- a/R/Italy.R
+++ b/R/Italy.R
@@ -30,16 +30,16 @@ Italy <- R6::R6Class("Italy",
     #' only entry, is be named main.
     # nolint start
     common_data_urls = list(
-      "main" = "https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"
+      "main" = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/raw/use_initial_conditions/epiforecasts_covidregionaldata/COVID19-Italy-Integrated-Surveillance-Data.csv"
     ),
     # nolint end
     #' @field source_data_cols existing columns within the raw data
-    source_data_cols = c("cases_total", "deaths_total", "tested_total"),
+    source_data_cols = c("cases_new", "deaths_new", "hosp_new"),
     #' @field source_text Plain text description of the source of the data
-    source_text = "Department of Civil Protection, Italy",
+    source_text = "Pietro Monticone and Claudio Moroni, Interdisciplinary Physics Team (InPhyT)",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://github.com/pcm-dpc/COVID-19/blob/master/README_EN.md",
+    source_url = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/blob/797ceacaee6e0e418715d235506d28656b8333ba/README.md",
 
     #' @description Set up a table of region codes for clean data
     #' @importFrom dplyr tibble
@@ -61,37 +61,38 @@ Italy <- R6::R6Class("Italy",
     },
 
     #' @description State level data cleaning
-    #' @importFrom dplyr mutate select arrange recode group_by ungroup
-    #' @importFrom lubridate as_date ymd_hms
+    #' @importFrom dplyr mutate select arrange recode group_by summarise
+    #' @importFrom lubridate as_date ymd
     #' @importFrom rlang .data
     #'
     clean_common = function() {
       self$data$clean <- self$data$raw[["main"]] %>%
+        group_by(date,region,indicator) %>%
+        summarise(across(where(is.double), sum), .groups = "drop") %>%
         mutate(
-          date = suppressWarnings(as_date(ymd_hms(.data$data))),
-          level_1_region = as.character(.data$denominazione_regione),
-          cases_total = .data$totale_casi,
-          deaths_total = .data$deceduti,
-          tested_total = .data$tamponi
+          date = suppressWarnings(as_date(ymd(.data$date))),
+          level_1_region = as.character(.data$region)
+        ) %>%
+        pivot_wider(
+          id_cols = c("date", "level_1_region"),
+          names_from = c("indicator"),
+          values_from = c("count")
         ) %>%
         arrange(.data$date) %>%
         mutate(level_1_region = recode(.data$level_1_region,
           "P.A. Trento" = "Trentino-Alto Adige",
           "P.A. Bolzano" = "Trentino-Alto Adige"
         )) %>%
-        group_by(.data$date, .data$level_1_region) %>%
-        summarise(
-          cases_total = sum(.data$cases_total, na.rm = TRUE),
-          deaths_total = sum(.data$deaths_total, na.rm = TRUE),
-          tested_total = sum(.data$tested_total, na.rm = TRUE),
-        ) %>%
-        ungroup() %>%
         full_join(self$codes_lookup[["1"]],
           by = c("level_1_region" = "region")
         ) %>%
         select(.data$date, .data$level_1_region,
           level_1_region_code = .data$code,
-          .data$cases_total, .data$deaths_total, .data$tested_total
+          cases_new = .data$confirmed,
+          deaths_new = .data$deceased,
+          hosp_new = .data$hospitalizations,
+          symp_new = .data$symptomatic,
+          care_new = .data$care
         )
     }
   )
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index 8e1c4d4f00988a562f7dceaf9af5db1633c3514e..298309ceb8ef00c071e146737f3afa9acc158e78 100644
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diff --git a/tests/testthat/custom_data/Italy_level_1.rds b/tests/testthat/custom_data/Italy_level_1.rds
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From d780dc3e15a150b9cbd027ac8c7a5c7f4423539d Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Tue, 15 Mar 2022 22:05:02 +0200
Subject: [PATCH 2/5] Adjust to upstream changes and add comment about
 Trentino-Alto Adige

---
 R/Italy.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/Italy.R b/R/Italy.R
index 2766056b..f3aac640 100644
--- a/R/Italy.R
+++ b/R/Italy.R
@@ -79,6 +79,8 @@ Italy <- R6::R6Class("Italy",
           values_from = c("count")
         ) %>%
         arrange(.data$date) %>%
+        # The region of Trentino-Alto Adige is made up of two self-governing
+        # provinces of Trento and Bolzano
         mutate(level_1_region = recode(.data$level_1_region,
           "P.A. Trento" = "Trentino-Alto Adige",
           "P.A. Bolzano" = "Trentino-Alto Adige"
@@ -90,9 +92,9 @@ Italy <- R6::R6Class("Italy",
           level_1_region_code = .data$code,
           cases_new = .data$confirmed,
           deaths_new = .data$deceased,
-          hosp_new = .data$hospitalizations,
+          hosp_new = .data$ordinary_hospital_admission,
           symp_new = .data$symptomatic,
-          care_new = .data$care
+          icu_new = .data$ICU_admission
         )
     }
   )

From d87a3ac9805c8583067b49b787ade2592f916e36 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Wed, 6 Apr 2022 22:09:00 +0300
Subject: [PATCH 3/5] Adjust source url for Italy from InPhyT

---
 R/Italy.R                            |   4 ++--
 data-raw/render_available_datasets.R |   1 +
 data/all_country_data.rda            | Bin 3078 -> 3070 bytes
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/Italy.R b/R/Italy.R
index f3aac640..7887d154 100644
--- a/R/Italy.R
+++ b/R/Italy.R
@@ -30,7 +30,7 @@ Italy <- R6::R6Class("Italy",
     #' only entry, is be named main.
     # nolint start
     common_data_urls = list(
-      "main" = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/raw/use_initial_conditions/epiforecasts_covidregionaldata/COVID19-Italy-Integrated-Surveillance-Data.csv"
+      "main" = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/blob/main/epiforecasts_covidregionaldata/COVID19-Italy-Integrated-Surveillance-Data.csv"
     ),
     # nolint end
     #' @field source_data_cols existing columns within the raw data
@@ -39,7 +39,7 @@ Italy <- R6::R6Class("Italy",
     source_text = "Pietro Monticone and Claudio Moroni, Interdisciplinary Physics Team (InPhyT)",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/blob/797ceacaee6e0e418715d235506d28656b8333ba/README.md",
+    source_url = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data",
 
     #' @description Set up a table of region codes for clean data
     #' @importFrom dplyr tibble
diff --git a/data-raw/render_available_datasets.R b/data-raw/render_available_datasets.R
index 214d2edc..b904d26c 100644
--- a/data-raw/render_available_datasets.R
+++ b/data-raw/render_available_datasets.R
@@ -2,3 +2,4 @@
 
 all_country_data <- get_available_datasets(render = TRUE)
 usethis::use_data(all_country_data, overwrite = TRUE)
+# 
\ No newline at end of file
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index 298309ceb8ef00c071e146737f3afa9acc158e78..e574dfc6fc9d3898252745530cce666b05a72b47 100644
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From 7960bba4121a56ecff8a95c953d705693c94c5a3 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Wed, 6 Apr 2022 22:21:56 +0300
Subject: [PATCH 4/5] Append raw=true for url downloading large CSV from github

---
 R/Italy.R                            |   2 +-
 data-raw/render_available_datasets.R |   1 -
 data/all_country_data.rda            | Bin 3070 -> 3065 bytes
 3 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/Italy.R b/R/Italy.R
index 7887d154..0a37acf9 100644
--- a/R/Italy.R
+++ b/R/Italy.R
@@ -30,7 +30,7 @@ Italy <- R6::R6Class("Italy",
     #' only entry, is be named main.
     # nolint start
     common_data_urls = list(
-      "main" = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/blob/main/epiforecasts_covidregionaldata/COVID19-Italy-Integrated-Surveillance-Data.csv"
+      "main" = "https://github.com/InPhyT/COVID19-Italy-Integrated-Surveillance-Data/raw/main/epiforecasts_covidregionaldata/COVID19-Italy-Integrated-Surveillance-Data.csv?raw=true"
     ),
     # nolint end
     #' @field source_data_cols existing columns within the raw data
diff --git a/data-raw/render_available_datasets.R b/data-raw/render_available_datasets.R
index b904d26c..214d2edc 100644
--- a/data-raw/render_available_datasets.R
+++ b/data-raw/render_available_datasets.R
@@ -2,4 +2,3 @@
 
 all_country_data <- get_available_datasets(render = TRUE)
 usethis::use_data(all_country_data, overwrite = TRUE)
-# 
\ No newline at end of file
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index e574dfc6fc9d3898252745530cce666b05a72b47..ce13307ca2b6dc0f6bbd7278552ac795734a9721 100644
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From 690d731424ef05364b14ed89d9ed5e34964d0886 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Mon, 6 Jun 2022 22:48:32 +0300
Subject: [PATCH 5/5] Update all_country_data.rda

---
 data/all_country_data.rda | Bin 3065 -> 3043 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index ce13307ca2b6dc0f6bbd7278552ac795734a9721..06a68019418dbdcddf19eb6b064529cf10690ca3 100644
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