From 01572c1a2d4f4dd116705b4567168dca5412d852 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Wed, 3 Nov 2021 22:20:47 +0200
Subject: [PATCH 01/16] Initial adjustment for new data source

Switch to using Socrata api to download case list from Colombian open data source. Aggregation to level 1 not yet working.
---
 NAMESPACE       |  2 +
 R/Colombia.R    | 98 ++++++++++++++++++++++++++++++++++---------------
 man/Colombia.Rd | 30 ++++++++++++++-
 3 files changed, 99 insertions(+), 31 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 5cdf4ccd..22eb3cbe 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -44,6 +44,7 @@ export(test_download)
 export(test_processing)
 export(test_return)
 importFrom(R6,R6Class)
+importFrom(RSocrata,read.socrata)
 importFrom(countrycode,countrycode)
 importFrom(countrycode,countryname)
 importFrom(dplyr,"%>%")
@@ -90,6 +91,7 @@ importFrom(lifecycle,deprecated)
 importFrom(lifecycle,is_present)
 importFrom(lubridate,as_date)
 importFrom(lubridate,dmy)
+importFrom(lubridate,dmy_hms)
 importFrom(lubridate,mdy)
 importFrom(lubridate,month)
 importFrom(lubridate,year)
diff --git a/R/Colombia.R b/R/Colombia.R
index c1a3154c..1f41f223 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -3,6 +3,7 @@
 #'  and processing COVID-19 region data for Colombia
 #'
 # nolint start
+#' @source \url{https://www.datos.gov.co/Salud-y-Protecci-n-Social/Casos-positivos-de-COVID-19-en-Colombia/gt2j-8ykr}
 #' @source \url{https://github.com/danielcs88/colombia_covid-19/}
 # nolint end
 #' @export
@@ -21,24 +22,30 @@ Colombia <- R6::R6Class("Colombia",
     #' @field origin name of origin to fetch data for
     origin = "Colombia",
     #' @field supported_levels A list of supported levels.
-    supported_levels = list("1"),
+    supported_levels = list("1", "2"),
     #' @field supported_region_names A list of region names in order of level.
-    supported_region_names = list("1" = "departamento"),
+    supported_region_names = list(
+      "1" = "departamento",
+      "2" = "municipio"
+    ),
     #' @field supported_region_codes A list of region codes in order of level.
-    supported_region_codes = list("1" = "iso_3166_2"),
+    supported_region_codes = list(
+      "1" = "iso_3166_2",
+      "2" = "codigo_municipio"
+    ),
     #' @field common_data_urls List of named links to raw data.
     # nolint start
     common_data_urls = list(
-      "main" = "https://raw.githubusercontent.com/danielcs88/colombia_covid-19/master/datos/cronologia.csv"
+      "main" = "https://www.datos.gov.co/resource/gt2j-8ykr.csv?$select=fecha_diagnostico,departamento_nom,ciudad_municipio_nom,ciudad_municipio"
     ),
     # nolint end
     #' @field source_data_cols existing columns within the raw data
-    source_data_cols = c("cases_total"),
+    source_data_cols = c("cases_new"),
     #' @field source_text Plain text description of the source of the data
-    source_text = "Daniel C\u00e1rdenas",
+    source_text = "Datos abiertos Colombia (Colombia open data)",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://github.com/danielcs88/colombia_covid-19/",
+    source_url = "https://www.datos.gov.co/Salud-y-Protecci-n-Social/Casos-positivos-de-COVID-19-en-Colombia/gt2j-8ykr", # nolint
 
     #' @description Set up a table of region codes for clean data
     #' @importFrom tibble tibble
@@ -47,38 +54,71 @@ Colombia <- R6::R6Class("Colombia",
       self$codes_lookup$`1` <- covidregionaldata::colombia_codes
     },
 
-    #' @description Colombia specific state level data cleaning
-    #' @importFrom dplyr select mutate
-    #' @importFrom lubridate ymd
+    #' @description Colombia specific download using Socrata API
+    #' @importFrom RSocrata read.socrata
+    download = function () {
+      message_verbose(self$verbose,
+                      "Downloading Colombia data. This may take a while.")
+      self$data$raw$main <- read.socrata(self$data_urls[["main"]])
+    },
+
+    #' @description Colombia specific data cleaning
+    #' @importFrom dplyr select mutate rename summarise group_by
+    #' @importFrom lubridate dmy_hms as_date
     #' @importFrom stringr str_replace_all str_to_sentence str_to_title
     #' @importFrom rlang .data
     #'
     clean_common = function() {
       self$data$clean <- self$data$raw[["main"]] %>%
-        select(
-          date = .data$fecha,
-          level_1_region = .data$departamento,
-          cases_total = .data$casos
-        ) %>%
-        mutate(
-          date = ymd(.data$date),
-          level_1_region = iconv(.data$level_1_region,
-            from = "UTF-8",
-            to = "ASCII//TRANSLIT"
-          ),
-          level_1_region = str_replace_all(.data$level_1_region, " D.C.", ""),
-          level_1_region = str_replace_all(
-            .data$level_1_region,
-            "San Andres y Providencia",
-            "San Andres, Providencia y Santa Catalina"
-          ),
-          level_1_region = str_to_sentence(.data$level_1_region),
-          level_1_region = str_to_title(.data$level_1_region)
+        rename(
+          date = .data$fecha_diagnostico,
+          level_1_region = .data$departamento_nom,
+          level_2_region = .data$ciudad_municipio_nom,
+          level_2_region_code = .data$ciudad_municipio
         ) %>%
+        group_by(date, level_1_region, level_2_region, level_2_region_code) %>%
+        summarise(cases_new = n(), .groups = "drop") %>%
+        mutate(date = as_date(dmy_hms(date)),
+               level_1_region = iconv(.data$level_1_region,
+                                      from = "UTF-8",
+                                      to = "ASCII//TRANSLIT"
+               ),
+               level_1_region =
+                 str_replace_all(.data$level_1_region,
+                                 c(" D.C." = "",
+                                   "San Andres y Providencia"
+                                   = "San Andres, Providencia y Santa Catalina",
+                                   "Norte Santander" = "Norte De Santander"
+                                 )
+               ),
+               level_1_region = str_to_sentence(.data$level_1_region),
+               level_1_region = str_to_title(.data$level_1_region)) %>%
         left_join(
           self$codes_lookup$`1`,
           by = c("level_1_region" = "level_1_region")
         )
+    },
+    
+    #' @description Colombia Specific Department Level Data Cleaning
+    #'
+    #' Aggregates data to the level 1 (department) regional level. Data is
+    #' provided by the source at the level 2 (municipality) regional level.
+    #'
+    #' @importFrom dplyr group_by summarise ungroup full_join across if_else
+    #' @importFrom tidyselect vars_select_helpers
+    clean_level_1 = function() {
+      self$data$clean <- self$data$clean %>%
+        group_by(
+          .data$date,
+          .data$level_1_region, .data$level_1_region_code
+        ) %>%
+        summarise(
+          across(
+            tidyselect::vars_select_helpers$where(is.numeric),
+            sum
+          )
+        ) %>%
+        ungroup()
     }
   )
 )
diff --git a/man/Colombia.Rd b/man/Colombia.Rd
index d1f88abb..8fbbdf6d 100644
--- a/man/Colombia.Rd
+++ b/man/Colombia.Rd
@@ -4,6 +4,8 @@
 \alias{Colombia}
 \title{Colombia Class for downloading, cleaning and processing notification data}
 \source{
+\url{https://www.datos.gov.co/Salud-y-Protecci-n-Social/Casos-positivos-de-COVID-19-en-Colombia/gt2j-8ykr}
+
 \url{https://github.com/danielcs88/colombia_covid-19/}
 }
 \description{
@@ -70,7 +72,9 @@ data}
 \subsection{Public methods}{
 \itemize{
 \item \href{#method-set_region_codes}{\code{Colombia$set_region_codes()}}
+\item \href{#method-download}{\code{Colombia$download()}}
 \item \href{#method-clean_common}{\code{Colombia$clean_common()}}
+\item \href{#method-clean_level_1}{\code{Colombia$clean_level_1()}}
 \item \href{#method-clone}{\code{Colombia$clone()}}
 }
 }
@@ -79,7 +83,6 @@ data}
 \itemize{
 \item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="available_regions">}\href{../../covidregionaldata/html/DataClass.html#method-available_regions}{\code{covidregionaldata::DataClass$available_regions()}}\out{</span>}
 \item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="clean">}\href{../../covidregionaldata/html/DataClass.html#method-clean}{\code{covidregionaldata::DataClass$clean()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="download">}\href{../../covidregionaldata/html/DataClass.html#method-download}{\code{covidregionaldata::DataClass$download()}}\out{</span>}
 \item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="download_JSON">}\href{../../covidregionaldata/html/DataClass.html#method-download_JSON}{\code{covidregionaldata::DataClass$download_JSON()}}\out{</span>}
 \item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="filter">}\href{../../covidregionaldata/html/DataClass.html#method-filter}{\code{covidregionaldata::DataClass$filter()}}\out{</span>}
 \item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="get">}\href{../../covidregionaldata/html/DataClass.html#method-get}{\code{covidregionaldata::DataClass$get()}}\out{</span>}
@@ -100,16 +103,39 @@ Set up a table of region codes for clean data
 \if{html}{\out{<div class="r">}}\preformatted{Colombia$set_region_codes()}\if{html}{\out{</div>}}
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-download"></a>}}
+\if{latex}{\out{\hypertarget{method-download}{}}}
+\subsection{Method \code{download()}}{
+Colombia specific download using Socrata API
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Colombia$download()}\if{html}{\out{</div>}}
+}
+
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-clean_common"></a>}}
 \if{latex}{\out{\hypertarget{method-clean_common}{}}}
 \subsection{Method \code{clean_common()}}{
-Colombia specific state level data cleaning
+Colombia specific data cleaning
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{Colombia$clean_common()}\if{html}{\out{</div>}}
 }
 
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clean_level_1"></a>}}
+\if{latex}{\out{\hypertarget{method-clean_level_1}{}}}
+\subsection{Method \code{clean_level_1()}}{
+Colombia Specific Department Level Data Cleaning
+
+Aggregates data to the level 1 (department) regional level. Data is
+provided by the source at the level 2 (municipality) regional level.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Colombia$clean_level_1()}\if{html}{\out{</div>}}
+}
+
 }
 \if{html}{\out{<hr>}}
 \if{html}{\out{<a id="method-clone"></a>}}

From f982a25e8aaf4a7111ef8dff305c0d9c98f53352 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Thu, 4 Nov 2021 22:18:22 +0200
Subject: [PATCH 02/16] Colombia fixes

---
 R/Colombia.R                                  |  33 +++++--------
 data-raw/colombia_codes.R                     |  46 +++++++++++++++++-
 data/all_country_data.rda                     | Bin 3010 -> 3074 bytes
 data/colombia_codes.rda                       | Bin 548 -> 8851 bytes
 man/colombia_codes.Rd                         |   2 +-
 .../testthat/custom_data/Colombia_level_1.rds | Bin 1808 -> 800 bytes
 .../testthat/custom_data/Colombia_level_2.rds | Bin 0 -> 800 bytes
 7 files changed, 56 insertions(+), 25 deletions(-)
 create mode 100644 tests/testthat/custom_data/Colombia_level_2.rds

diff --git a/R/Colombia.R b/R/Colombia.R
index 1f41f223..15792978 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -36,7 +36,7 @@ Colombia <- R6::R6Class("Colombia",
     #' @field common_data_urls List of named links to raw data.
     # nolint start
     common_data_urls = list(
-      "main" = "https://www.datos.gov.co/resource/gt2j-8ykr.csv?$select=fecha_diagnostico,departamento_nom,ciudad_municipio_nom,ciudad_municipio"
+      "main" = "https://www.datos.gov.co/resource/gt2j-8ykr.csv?$select=fecha_diagnostico,ciudad_municipio"
     ),
     # nolint end
     #' @field source_data_cols existing columns within the raw data
@@ -51,7 +51,10 @@ Colombia <- R6::R6Class("Colombia",
     #' @importFrom tibble tibble
     #' @importFrom dplyr mutate
     set_region_codes = function() {
-      self$codes_lookup$`1` <- covidregionaldata::colombia_codes
+      self$codes_lookup$`1` <- covidregionaldata::colombia_codes %>%
+        select(level_1_region, level_1_region_code) %>%
+        unique()
+      self$codes_lookup$`2` <- covidregionaldata::colombia_codes
     },
 
     #' @description Colombia specific download using Socrata API
@@ -72,30 +75,15 @@ Colombia <- R6::R6Class("Colombia",
       self$data$clean <- self$data$raw[["main"]] %>%
         rename(
           date = .data$fecha_diagnostico,
-          level_1_region = .data$departamento_nom,
-          level_2_region = .data$ciudad_municipio_nom,
           level_2_region_code = .data$ciudad_municipio
         ) %>%
-        group_by(date, level_1_region, level_2_region, level_2_region_code) %>%
+        group_by(date, level_2_region_code) %>%
         summarise(cases_new = n(), .groups = "drop") %>%
         mutate(date = as_date(dmy_hms(date)),
-               level_1_region = iconv(.data$level_1_region,
-                                      from = "UTF-8",
-                                      to = "ASCII//TRANSLIT"
-               ),
-               level_1_region =
-                 str_replace_all(.data$level_1_region,
-                                 c(" D.C." = "",
-                                   "San Andres y Providencia"
-                                   = "San Andres, Providencia y Santa Catalina",
-                                   "Norte Santander" = "Norte De Santander"
-                                 )
-               ),
-               level_1_region = str_to_sentence(.data$level_1_region),
-               level_1_region = str_to_title(.data$level_1_region)) %>%
+               level_2_region_code=sprintf("%05d", level_2_region_code)) %>%
         left_join(
-          self$codes_lookup$`1`,
-          by = c("level_1_region" = "level_1_region")
+          self$codes_lookup$`2`,
+          by = c("level_2_region_code" = "level_2_region_code")
         )
     },
     
@@ -104,10 +92,11 @@ Colombia <- R6::R6Class("Colombia",
     #' Aggregates data to the level 1 (department) regional level. Data is
     #' provided by the source at the level 2 (municipality) regional level.
     #'
-    #' @importFrom dplyr group_by summarise ungroup full_join across if_else
+    #' @importFrom dplyr group_by summarise ungroup full_join across if_else select
     #' @importFrom tidyselect vars_select_helpers
     clean_level_1 = function() {
       self$data$clean <- self$data$clean %>%
+        select(-level_2_region_code, -level_2_region) %>%
         group_by(
           .data$date,
           .data$level_1_region, .data$level_1_region_code
diff --git a/data-raw/colombia_codes.R b/data-raw/colombia_codes.R
index 8cb8792b..8c6202a5 100644
--- a/data-raw/colombia_codes.R
+++ b/data-raw/colombia_codes.R
@@ -22,7 +22,7 @@ level_1_region <- read_html(co_iso) %>%
   html_text()
 level_1_region <- level_1_region[1:33]
 
-colombia_codes <- data.frame(
+colombia_departments <- data.frame(
   level_1_region_code,
   level_1_region,
   stringsAsFactors = FALSE
@@ -37,7 +37,7 @@ colombia_codes <- data.frame(
 replacements <- list(
   "Distrito Capital De Bogota" = "Bogota"
 )
-colombia_codes <- colombia_codes %>%
+colombia_departments <- colombia_departments %>%
   mutate(
     level_1_region = ifelse(level_1_region %in% names(replacements),
       replacements[level_1_region],
@@ -46,5 +46,47 @@ colombia_codes <- colombia_codes %>%
     level_1_region = as.character(level_1_region)
   )
 
+# Download list of municipalities and codes
+# 
+
+colombia_municipalities_sheet <- download_excel(
+  "https://www.dane.gov.co/files/censo2005/provincias/subregiones.xls",
+  "colombia_municipalities.xls",
+  verbose = TRUE,
+  transpose = FALSE,
+  sheet = "Hoja1"
+) 
+  colombia_municipalities <- colombia_municipalities_sheet %>%
+  select(level_2_region = NOM_MPIO,
+         level_2_region_code = DPTOC_MPIO,
+         level_1_region = NOM_DEPTO) %>%
+  mutate(
+    level_1_region = stri_trans_general(level_1_region, "latin-ascii"),
+    level_1_region = stri_trim_both(level_1_region),
+    level_1_region = stringr::str_to_title(level_1_region),
+    level_1_region =
+      str_replace_all(.data$level_1_region,
+                      c(" D.c." = "",
+                        "Archipielago De San Andres"
+                        = "San Andres, Providencia Y Santa Catalina",
+                        "Norte Santander" = "Norte De Santander"
+                      )
+      ),
+    level_2_region = stri_trans_general(level_2_region, "latin-ascii"),
+    level_2_region = stri_trim_both(level_2_region),
+    level_2_region =
+      str_replace_all(.data$level_2_region,
+                      c(" D.C." = ""
+                      )
+      ),
+    level_2_region = stringr::str_to_title(level_2_region),
+  ) 
+  
+
+# anti_join(colombia_municipalities, colombia_departments, by=c("level_1_region"))
+colombia_codes <- left_join(colombia_municipalities,
+                            colombia_departments,
+                            by=c("level_1_region"))
+
 # update package region_codes
 usethis::use_data(colombia_codes, overwrite = TRUE)
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index 0d177cf3b295c98fd3073a6bff41fed06d6b0b9d..2555906498bbe297ca0199245f4626e1e9f99491 100644
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diff --git a/data/colombia_codes.rda b/data/colombia_codes.rda
index efc435d6587b37581463d9b043012ca1b64e8b75..81666ce6035ffb9dd66865f9d6afd21dba13249c 100644
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diff --git a/man/colombia_codes.Rd b/man/colombia_codes.Rd
index 2292ad7a..40ff0e81 100644
--- a/man/colombia_codes.Rd
+++ b/man/colombia_codes.Rd
@@ -5,7 +5,7 @@
 \alias{colombia_codes}
 \title{Region Codes for Colombia Dataset.}
 \format{
-An object of class \code{data.frame} with 33 rows and 2 columns.
+An object of class \code{data.frame} with 1119 rows and 4 columns.
 }
 \usage{
 colombia_codes
diff --git a/tests/testthat/custom_data/Colombia_level_1.rds b/tests/testthat/custom_data/Colombia_level_1.rds
index 7f131bb85981280d0a768f614a28bedcda5b58d7..72c9db9b1f25cd3851b1372a3661e716164c913f 100644
GIT binary patch
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diff --git a/tests/testthat/custom_data/Colombia_level_2.rds b/tests/testthat/custom_data/Colombia_level_2.rds
new file mode 100644
index 0000000000000000000000000000000000000000..72c9db9b1f25cd3851b1372a3661e716164c913f
GIT binary patch
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literal 0
HcmV?d00001


From beec5929bad4b8cebb3127c6c2f8def8c12409f2 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Thu, 4 Nov 2021 22:26:36 +0200
Subject: [PATCH 03/16] Add RSocrata to imports

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 20e44186..f1adb951 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -99,6 +99,7 @@ Imports:
     R6,
     readxl,
     rlang,
+    RSocrata,
     stringi,
     stringr,
     tibble,

From 576085a13e2068a1551a7814ad3e76dc8c867d32 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Thu, 4 Nov 2021 22:47:25 +0200
Subject: [PATCH 04/16] Add import of dplyr::n

---
 R/Colombia.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/Colombia.R b/R/Colombia.R
index 15792978..08dc853c 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -66,7 +66,7 @@ Colombia <- R6::R6Class("Colombia",
     },
 
     #' @description Colombia specific data cleaning
-    #' @importFrom dplyr select mutate rename summarise group_by
+    #' @importFrom dplyr select mutate rename summarise group_by n
     #' @importFrom lubridate dmy_hms as_date
     #' @importFrom stringr str_replace_all str_to_sentence str_to_title
     #' @importFrom rlang .data

From d5db53bc87ee4da5d808caf0550a5a5cfb92ad3d Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Thu, 4 Nov 2021 22:48:31 +0200
Subject: [PATCH 05/16] Hand edit to add dplyr::n

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index 22eb3cbe..fa8d9b60 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -68,6 +68,7 @@ importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_at)
 importFrom(dplyr,mutate_if)
+importFrom(dplyr,n)
 importFrom(dplyr,na_if)
 importFrom(dplyr,pull)
 importFrom(dplyr,recode)

From 26a19d070d71f732ceacb91ff20d40e33bb52fd6 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Tue, 9 Nov 2021 20:09:39 +0200
Subject: [PATCH 06/16] Shift to make RSocrata recommended but not required

---
 DESCRIPTION                                   |   2 +-
 NAMESPACE                                     |   1 -
 R/Colombia.R                                  |  18 ++++++++++++++++--
 .../testthat/custom_data/Colombia_level_1.rds | Bin 800 -> 46 bytes
 .../testthat/custom_data/Colombia_level_2.rds | Bin 800 -> 46 bytes
 5 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f1adb951..a07e1f53 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -99,7 +99,6 @@ Imports:
     R6,
     readxl,
     rlang,
-    RSocrata,
     stringi,
     stringr,
     tibble,
@@ -114,6 +113,7 @@ Suggests:
     knitr,
     mockery,
     pkgdown,
+    RSocrata,
     rmarkdown,
     rvest,
     rworldmap,
diff --git a/NAMESPACE b/NAMESPACE
index fa8d9b60..891415c5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -44,7 +44,6 @@ export(test_download)
 export(test_processing)
 export(test_return)
 importFrom(R6,R6Class)
-importFrom(RSocrata,read.socrata)
 importFrom(countrycode,countrycode)
 importFrom(countrycode,countryname)
 importFrom(dplyr,"%>%")
diff --git a/R/Colombia.R b/R/Colombia.R
index 08dc853c..e34266b1 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -58,11 +58,25 @@ Colombia <- R6::R6Class("Colombia",
     },
 
     #' @description Colombia specific download using Socrata API
-    #' @importFrom RSocrata read.socrata
+    #' @importFrom dplyr select
     download = function () {
       message_verbose(self$verbose,
                       "Downloading Colombia data. This may take a while.")
-      self$data$raw$main <- read.socrata(self$data_urls[["main"]])
+      # RSocrata package is recommended but not required
+      if (require("RSocrata", attach.required = TRUE)) {
+        self$data$raw$main <- RSocrata::read.socrata(self$data_urls[["main"]])
+      } else {
+        # If the RSocrata package is not available, we download the full wide
+        # csv (which is at least 8x larger) then select down to what we could
+        # get through the API.
+        #truncated_url <- sub("\\?.*", "", self$data_urls[["main"]])
+        alternate_url <- "https://www.datos.gov.co/api/views/gt2j-8ykr/rows.csv?accessType=DOWNLOAD"
+        massive_co_data <-
+          csv_reader(alternate_url,
+                     self$verbose)
+        self$data$raw$main <- massive_co_data %>%
+          select(.data$fecha_diagnostico, .data$ciudad-municipio)
+      }
     },
 
     #' @description Colombia specific data cleaning
diff --git a/tests/testthat/custom_data/Colombia_level_1.rds b/tests/testthat/custom_data/Colombia_level_1.rds
index 72c9db9b1f25cd3851b1372a3661e716164c913f..70e66ce7e53dbd6f0c9e82fb9618ef4b90f0b617 100644
GIT binary patch
literal 46
xcmb2|=3oE==I#ec2?+^l35h8w32CfGk`d0%cS>{{coGHp83dj>EszH)0{|6-3<UrH

literal 800
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diff --git a/tests/testthat/custom_data/Colombia_level_2.rds b/tests/testthat/custom_data/Colombia_level_2.rds
index 72c9db9b1f25cd3851b1372a3661e716164c913f..70e66ce7e53dbd6f0c9e82fb9618ef4b90f0b617 100644
GIT binary patch
literal 46
xcmb2|=3oE==I#ec2?+^l35h8w32CfGk`d0%cS>{{coGHp83dj>EszH)0{|6-3<UrH

literal 800
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eU#(W#M#LZ1SgN_qg$jmMr2Hz8pgsgb9RL6gbbo6A


From 6828efd1143d65d7fc6b5c09dbe185a0535733cc Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Sat, 20 Nov 2021 18:51:21 +0200
Subject: [PATCH 07/16] Revert "Shift to make RSocrata recommended but not
 required"

This reverts commit 26a19d070d71f732ceacb91ff20d40e33bb52fd6.
---
 DESCRIPTION                                   |   2 +-
 NAMESPACE                                     |   1 +
 R/Colombia.R                                  |  18 ++----------------
 .../testthat/custom_data/Colombia_level_1.rds | Bin 46 -> 800 bytes
 .../testthat/custom_data/Colombia_level_2.rds | Bin 46 -> 800 bytes
 5 files changed, 4 insertions(+), 17 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a07e1f53..f1adb951 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -99,6 +99,7 @@ Imports:
     R6,
     readxl,
     rlang,
+    RSocrata,
     stringi,
     stringr,
     tibble,
@@ -113,7 +114,6 @@ Suggests:
     knitr,
     mockery,
     pkgdown,
-    RSocrata,
     rmarkdown,
     rvest,
     rworldmap,
diff --git a/NAMESPACE b/NAMESPACE
index 891415c5..fa8d9b60 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -44,6 +44,7 @@ export(test_download)
 export(test_processing)
 export(test_return)
 importFrom(R6,R6Class)
+importFrom(RSocrata,read.socrata)
 importFrom(countrycode,countrycode)
 importFrom(countrycode,countryname)
 importFrom(dplyr,"%>%")
diff --git a/R/Colombia.R b/R/Colombia.R
index e34266b1..08dc853c 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -58,25 +58,11 @@ Colombia <- R6::R6Class("Colombia",
     },
 
     #' @description Colombia specific download using Socrata API
-    #' @importFrom dplyr select
+    #' @importFrom RSocrata read.socrata
     download = function () {
       message_verbose(self$verbose,
                       "Downloading Colombia data. This may take a while.")
-      # RSocrata package is recommended but not required
-      if (require("RSocrata", attach.required = TRUE)) {
-        self$data$raw$main <- RSocrata::read.socrata(self$data_urls[["main"]])
-      } else {
-        # If the RSocrata package is not available, we download the full wide
-        # csv (which is at least 8x larger) then select down to what we could
-        # get through the API.
-        #truncated_url <- sub("\\?.*", "", self$data_urls[["main"]])
-        alternate_url <- "https://www.datos.gov.co/api/views/gt2j-8ykr/rows.csv?accessType=DOWNLOAD"
-        massive_co_data <-
-          csv_reader(alternate_url,
-                     self$verbose)
-        self$data$raw$main <- massive_co_data %>%
-          select(.data$fecha_diagnostico, .data$ciudad-municipio)
-      }
+      self$data$raw$main <- read.socrata(self$data_urls[["main"]])
     },
 
     #' @description Colombia specific data cleaning
diff --git a/tests/testthat/custom_data/Colombia_level_1.rds b/tests/testthat/custom_data/Colombia_level_1.rds
index 70e66ce7e53dbd6f0c9e82fb9618ef4b90f0b617..72c9db9b1f25cd3851b1372a3661e716164c913f 100644
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diff --git a/tests/testthat/custom_data/Colombia_level_2.rds b/tests/testthat/custom_data/Colombia_level_2.rds
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From f9087a7669b61624566bc412623a4aece9be0096 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Sat, 20 Nov 2021 20:22:58 +0200
Subject: [PATCH 08/16] Apply require method for using RSocrata package to
 allow it to be suggested in DESCRIPTION

---
 DESCRIPTION                                   |   2 +-
 NAMESPACE                                     |   1 -
 R/Colombia.R                                  |  26 ++++++++++++++----
 man/reexports.Rd                              |   2 +-
 .../testthat/custom_data/Colombia_level_1.rds | Bin 800 -> 848 bytes
 .../testthat/custom_data/Colombia_level_2.rds | Bin 800 -> 848 bytes
 6 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f1adb951..126689af 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -99,7 +99,6 @@ Imports:
     R6,
     readxl,
     rlang,
-    RSocrata,
     stringi,
     stringr,
     tibble,
@@ -115,6 +114,7 @@ Suggests:
     mockery,
     pkgdown,
     rmarkdown,
+    RSocrata,
     rvest,
     rworldmap,
     sf,
diff --git a/NAMESPACE b/NAMESPACE
index fa8d9b60..891415c5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -44,7 +44,6 @@ export(test_download)
 export(test_processing)
 export(test_return)
 importFrom(R6,R6Class)
-importFrom(RSocrata,read.socrata)
 importFrom(countrycode,countrycode)
 importFrom(countrycode,countryname)
 importFrom(dplyr,"%>%")
diff --git a/R/Colombia.R b/R/Colombia.R
index 08dc853c..1c9a9159 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -58,11 +58,25 @@ Colombia <- R6::R6Class("Colombia",
     },
 
     #' @description Colombia specific download using Socrata API
-    #' @importFrom RSocrata read.socrata
-    download = function () {
+    #' @importFrom dplyr select
+    download = function() {
       message_verbose(self$verbose,
                       "Downloading Colombia data. This may take a while.")
-      self$data$raw$main <- read.socrata(self$data_urls[["main"]])
+      # RSocrata package is recommended but not required
+      if (require(RSocrata, attach.required = TRUE)) {
+        self$data$raw$main <- RSocrata::read.socrata(self$data_urls[["main"]])
+      } else {
+        # If the RSocrata package is not available, we download the full wide
+        # csv (which is at least 8x larger) then select down to what we could
+        # get through the API.
+        alternate_url <- "https://www.datos.gov.co/api/views/gt2j-8ykr/rows.csv?accessType=DOWNLOAD" # nolint
+        massive_co_data <-
+          csv_reader(alternate_url,
+                     self$verbose)
+        self$data$raw$main <- massive_co_data %>%
+          select(fecha_diagnostico = .data$`Fecha de diagn\\00f3stico`,
+                 ciudad_municipio = .data$`C\\00f3digo DIVIPOLA municipio`)
+      }
     },
 
     #' @description Colombia specific data cleaning
@@ -80,19 +94,19 @@ Colombia <- R6::R6Class("Colombia",
         group_by(date, level_2_region_code) %>%
         summarise(cases_new = n(), .groups = "drop") %>%
         mutate(date = as_date(dmy_hms(date)),
-               level_2_region_code=sprintf("%05d", level_2_region_code)) %>%
+               level_2_region_code = sprintf("%05d", level_2_region_code)) %>%
         left_join(
           self$codes_lookup$`2`,
           by = c("level_2_region_code" = "level_2_region_code")
         )
     },
-    
+
     #' @description Colombia Specific Department Level Data Cleaning
     #'
     #' Aggregates data to the level 1 (department) regional level. Data is
     #' provided by the source at the level 2 (municipality) regional level.
     #'
-    #' @importFrom dplyr group_by summarise ungroup full_join across if_else select
+    #' @importFrom dplyr group_by summarise ungroup across select
     #' @importFrom tidyselect vars_select_helpers
     clean_level_1 = function() {
       self$data$clean <- self$data$clean %>%
diff --git a/man/reexports.Rd b/man/reexports.Rd
index 3b0d9eb6..eeaa1efc 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -11,6 +11,6 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{rlang}{\code{\link[rlang:tidyeval-data]{.data}}}
+  \item{rlang}{\code{\link[rlang:dot-data]{.data}}}
 }}
 
diff --git a/tests/testthat/custom_data/Colombia_level_1.rds b/tests/testthat/custom_data/Colombia_level_1.rds
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diff --git a/tests/testthat/custom_data/Colombia_level_2.rds b/tests/testthat/custom_data/Colombia_level_2.rds
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From 7f84ec8be2b8731855a460ce2ce929b5cf1f8383 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Sat, 20 Nov 2021 20:27:06 +0200
Subject: [PATCH 09/16] Document specific download function for Colombia, amend
 WORDLIST

---
 R/Colombia.R  | 3 ++-
 inst/WORDLIST | 2 ++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/Colombia.R b/R/Colombia.R
index 1c9a9159..1246c7e9 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -4,7 +4,6 @@
 #'
 # nolint start
 #' @source \url{https://www.datos.gov.co/Salud-y-Protecci-n-Social/Casos-positivos-de-COVID-19-en-Colombia/gt2j-8ykr}
-#' @source \url{https://github.com/danielcs88/colombia_covid-19/}
 # nolint end
 #' @export
 #' @concept dataset
@@ -58,6 +57,8 @@ Colombia <- R6::R6Class("Colombia",
     },
 
     #' @description Colombia specific download using Socrata API
+    #' This uses the `RSocrata` package if it is installed or downloads
+    #' a much larger csv file if that package is not available.
     #' @importFrom dplyr select
     download = function() {
       message_verbose(self$verbose,
diff --git a/inst/WORDLIST b/inst/WORDLIST
index e3fb521e..d197220c 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -131,6 +131,7 @@ rlang
 rmarkdown
 Roxygen
 RoxygenNote
+RSocrata
 rvest
 RVIM
 rworldmap
@@ -143,6 +144,7 @@ seperate
 shapefiles
 sherratt
 Sherratt
+Socrata
 sophie
 SouthAfrica
 spi

From 3063942a49bd010258e8df5fea71c192f01a3275 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Sun, 28 Nov 2021 20:53:52 +0200
Subject: [PATCH 10/16] Document changes to Colombia data.

---
 NEWS.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index efcbe4cf..a56f69d6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -5,7 +5,8 @@ This release is currently under development
 ## New data sets
 
 * Support for level 1 region data in Estonia (thanks to @RichardMN). See `?Estonia` for details.
-* Support for level 1 region data in Vietnam (thanks to @biocyberman). See `?Vietname` for details.
+* Support for level 1 region data in Vietnam (thanks to @biocyberman). See `?Vietnam` for details.
+* Support for level 2 region data in Colombia has been added (thanks to @RichardMN). The package no longer relies on aggregation by another project but takes data direct from the Colombia open data API. This uses the `RSocrata` package, which is suggested but not required. Using the `RSocrata` package cuts download volume and time by a factor of about 8.
 
 ## Other changes
 

From e14e767824b268aaa02291ff663e89e7d57ef5d8 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Sun, 28 Nov 2021 22:48:40 +0200
Subject: [PATCH 11/16] Manual edit of reexports.Rd to get around CMD check
 fail

---
 man/reexports.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/reexports.Rd b/man/reexports.Rd
index eeaa1efc..3b0d9eb6 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -11,6 +11,6 @@ These objects are imported from other packages. Follow the links
 below to see their documentation.
 
 \describe{
-  \item{rlang}{\code{\link[rlang:dot-data]{.data}}}
+  \item{rlang}{\code{\link[rlang:tidyeval-data]{.data}}}
 }}
 

From c2de6c8271c4d91878cafcb7a326579ed3fba962 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Wed, 1 Dec 2021 19:27:29 +0200
Subject: [PATCH 12/16] Replace require with requireNamespace in Colombia.R

---
 R/Colombia.R    | 2 +-
 inst/WORDLIST   | 1 +
 man/Colombia.Rd | 4 ++--
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/Colombia.R b/R/Colombia.R
index 1246c7e9..f5c9fcc2 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -64,7 +64,7 @@ Colombia <- R6::R6Class("Colombia",
       message_verbose(self$verbose,
                       "Downloading Colombia data. This may take a while.")
       # RSocrata package is recommended but not required
-      if (require(RSocrata, attach.required = TRUE)) {
+      if (requireNamespace(RSocrata, quietly = self$verbose)) {
         self$data$raw$main <- RSocrata::read.socrata(self$data_urls[["main"]])
       } else {
         # If the RSocrata package is not available, we download the full wide
diff --git a/inst/WORDLIST b/inst/WORDLIST
index d197220c..1c0d49b7 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -30,6 +30,7 @@ COVID
 covidregionaldata
 cre
 CSSE
+csv
 ctb
 currrently
 DataClass
diff --git a/man/Colombia.Rd b/man/Colombia.Rd
index 8fbbdf6d..f8228ff5 100644
--- a/man/Colombia.Rd
+++ b/man/Colombia.Rd
@@ -5,8 +5,6 @@
 \title{Colombia Class for downloading, cleaning and processing notification data}
 \source{
 \url{https://www.datos.gov.co/Salud-y-Protecci-n-Social/Casos-positivos-de-COVID-19-en-Colombia/gt2j-8ykr}
-
-\url{https://github.com/danielcs88/colombia_covid-19/}
 }
 \description{
 Information for downloading, cleaning
@@ -109,6 +107,8 @@ Set up a table of region codes for clean data
 \if{latex}{\out{\hypertarget{method-download}{}}}
 \subsection{Method \code{download()}}{
 Colombia specific download using Socrata API
+This uses the \code{RSocrata} package if it is installed or downloads
+a much larger csv file if that package is not available.
 \subsection{Usage}{
 \if{html}{\out{<div class="r">}}\preformatted{Colombia$download()}\if{html}{\out{</div>}}
 }

From 3e2f8733de4466449555e438baaf11184b200353 Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Fri, 3 Dec 2021 21:01:34 +0200
Subject: [PATCH 13/16] Remove work-around for when RSocrata package is not
 installed

---
 R/Colombia.R | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/R/Colombia.R b/R/Colombia.R
index f5c9fcc2..39c9c145 100644
--- a/R/Colombia.R
+++ b/R/Colombia.R
@@ -64,19 +64,11 @@ Colombia <- R6::R6Class("Colombia",
       message_verbose(self$verbose,
                       "Downloading Colombia data. This may take a while.")
       # RSocrata package is recommended but not required
-      if (requireNamespace(RSocrata, quietly = self$verbose)) {
+      if (requireNamespace("RSocrata", quietly = self$verbose)) {
         self$data$raw$main <- RSocrata::read.socrata(self$data_urls[["main"]])
       } else {
-        # If the RSocrata package is not available, we download the full wide
-        # csv (which is at least 8x larger) then select down to what we could
-        # get through the API.
-        alternate_url <- "https://www.datos.gov.co/api/views/gt2j-8ykr/rows.csv?accessType=DOWNLOAD" # nolint
-        massive_co_data <-
-          csv_reader(alternate_url,
-                     self$verbose)
-        self$data$raw$main <- massive_co_data %>%
-          select(fecha_diagnostico = .data$`Fecha de diagn\\00f3stico`,
-                 ciudad_municipio = .data$`C\\00f3digo DIVIPOLA municipio`)
+        stop("covidregionaldata::Colombia$download - requires RSocrata package.\n",
+             "Please run install.packages(\"RSocrata\")\n", call.=TRUE)
       }
     },
 

From 190ab71b1e13d0dbfa331558644ec11d2f701dae Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Fri, 4 Feb 2022 21:20:43 +0200
Subject: [PATCH 14/16] Squashed commit of the following:

commit 14e112c23d49ad94699627f3baaff11731a2221f
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Fri Feb 4 15:50:18 2022 +0000

    add github to vscode tools for dev environmenth

commit a851c753dd3e0ce58b5043497afd27d5503eeb46
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Fri Feb 4 15:43:07 2022 +0000

    switch to preferably template for website
---
 .devcontainer/devcontainer.json |  3 +-
 .github/workflows/pkgdown.yaml  | 53 +++++++++++++++++++++++++++++++++
 .pre-commit-config.yaml         |  4 +--
 DESCRIPTION                     |  4 ++-
 NEWS.md                         |  1 +
 5 files changed, 61 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 6717a1de..66b4b139 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -21,7 +21,8 @@
 		"shan.code-settings-sync",
 		"searking.preview-vscode",
 		"tht13.html-preview-vscode",
-		"formulahendry.code-runner"
+		"formulahendry.code-runner",
+		"github.vscode-pull-request-github"
 	],
 
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 00000000..8d695bc1
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,53 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+    tags: ['*']
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: n1hility/cancel-previous-runs@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "curl"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_github("r-lib/pkgdown")
+          remotes::install_github("amirmasoudabdol/preferably", type = "source")
+        shell: Rscript {0}
+        
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 008fa328..f35a2100 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.1.3.9014
+    rev: v0.2.2.9009
     hooks: 
     -   id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]    
@@ -45,7 +45,7 @@ repos:
     -   id: no-browser-statement
     -   id: deps-in-desc
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks: 
     -   id: check-added-large-files
         args: ['--maxkb=800']
diff --git a/DESCRIPTION b/DESCRIPTION
index 91b47f8e..2acdb0e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -107,7 +107,6 @@ Suggests:
     ggspatial,
     knitr,
     mockery,
-    pkgdown,
     rmarkdown,
     RSocrata,
     rvest,
@@ -119,6 +118,9 @@ Suggests:
 VignetteBuilder:
     knitr
 Config/testthat/edition: 3
+Config/Needs/website: 
+    r-lib/pkgdown,
+    amirmasoudabdol/preferably
 Encoding: UTF-8
 Language: en-gb
 LazyData: true
diff --git a/NEWS.md b/NEWS.md
index 4a270315..16faffd2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,7 @@ This release is currently under development
 * Change the data source for Switzerland to draw data from the Swiss Federal Office of Public Health (FOPH)
 * Updated the package logo to include the newly supported data sets.
 * Reduced the number of package dependencies (@bisaloo and @RichardMN)
+
 ## Bug fixes
 
 - Fixed a bug in the data sourced from Germany so that instead of treating it as a line list of individuals it is treated as a relatively finely resolved count data which needs to be summed up (by @sbfnk).

From b607e1fed644d0ce87a84e928bee369fad54016d Mon Sep 17 00:00:00 2001
From: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date: Fri, 4 Feb 2022 21:43:40 +0200
Subject: [PATCH 15/16] Vietnam fix added

---
 DESCRIPTION               |   2 ++
 NAMESPACE                 |   5 +++--
 R/Vietnam.R               |  43 ++++++++++++++++++++++----------------
 data/all_country_data.rda | Bin 3031 -> 3077 bytes
 4 files changed, 30 insertions(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2acdb0e3..7d275b8d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -98,8 +98,10 @@ Imports:
     R6,
     readxl,
     rlang,
+    stringi,
     stringr,
     tidyr (>= 1.0.0),
+    tidyselect,
     vroom,
     xml2
 Suggests:
diff --git a/NAMESPACE b/NAMESPACE
index 6791edbb..0878538c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -118,12 +118,12 @@ importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,syms)
-importFrom(stringr,str_conv)
+importFrom(stringi,stri_trans_general)
+importFrom(stringi,stri_trim_both)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_to_sentence)
 importFrom(stringr,str_to_title)
-importFrom(stringr,str_trim)
 importFrom(tidyr,complete)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,fill)
@@ -133,6 +133,7 @@ importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
+importFrom(tidyselect,vars_select_helpers)
 importFrom(utils,download.file)
 importFrom(utils,untar)
 importFrom(vroom,vroom)
diff --git a/R/Vietnam.R b/R/Vietnam.R
index 44062df8..6f888130 100644
--- a/R/Vietnam.R
+++ b/R/Vietnam.R
@@ -64,7 +64,8 @@ Vietnam <- R6::R6Class("Vietnam",
     #' @importFrom dplyr filter select mutate rename tibble as_tibble full_join
     #' @importFrom tidyr replace_na drop_na separate
     #' @importFrom purrr map
-    #' @importFrom stringr str_conv str_trim str_to_title str_replace_all
+    #' @importFrom stringr str_to_title str_replace_all
+    #' @importFrom stringi stri_trans_general stri_trim_both
     #' @importFrom lubridate dmy
     clean_common = function() {
       # The first three elements of self$data$raw are the data
@@ -80,18 +81,19 @@ Vietnam <- R6::R6Class("Vietnam",
           y %>% separate(date, sep = "[.]+", into = c(NA, "province", "date"))
         }
       )
-      self$data$clean <- full_join(
-        full_join(
-          flat_all$case_by_time, flat_all$death_by_time,
-          by = c("province", "date"),
-          suffix = c(".cases", ".deaths"),
-          copy = TRUE
-        ),
-        flat_all$recovered_by_time,
-        by = c("province", "date"),
-        suffix = c("", ".recovered"),
-        copy = TRUE
-      ) %>%
+      index_cols <- bind_rows(
+        flat_all$case_by_time %>% select("date", "province"),
+        flat_all$death_by_time %>% select("date", "province"),
+        flat_all$recovered_by_time %>% select("date", "province")) %>%
+        unique()
+      
+      self$data$clean <- 
+        left_join(index_cols, flat_all$case_by_time %>% rename(cases_total =value),
+                  by = c("province", "date") ) %>%
+        left_join(flat_all$death_by_time %>% rename(deaths_total =value),
+                  by = c("province", "date") ) %>%
+        left_join(flat_all$recovered_by_time %>% rename(recovered_total =value),
+                  by = c("province", "date") ) %>%
         # The api uses integer codes for provinces which do not
         # line up with ISO 3166-2 (some of which are not numbers)
         # so we use this as a temporary code to line names up
@@ -99,9 +101,14 @@ Vietnam <- R6::R6Class("Vietnam",
         select(
           ncsc_region_code = province,
           date,
-          cases_total = value.cases,
-          deaths_total = value.deaths,
-          recovered_total = value) %>%
+          cases_total,
+          deaths_total,
+          recovered_total
+          # ,
+          # cases_total = value.cases,
+          # deaths_total = value.deaths,
+          # recovered_total = value
+          ) %>%
         mutate(ncsc_region_code = as.numeric(ncsc_region_code)) %>%
         left_join(
           self$data$raw$provinces %>%
@@ -119,8 +126,8 @@ Vietnam <- R6::R6Class("Vietnam",
         #
         #tidyr::drop_na(date, region_name) %>%
         mutate(
-          level_1_region = str_conv(level_1_region, "ASCII"),
-          level_1_region = str_trim(level_1_region, side = "both"),
+          level_1_region = stri_trans_general(level_1_region, "ASCII"),
+          level_1_region = stri_trim_both(level_1_region),
           level_1_region = str_replace_all(level_1_region,
                                            "\\(.*\\)|-| ", ""),
           level_1_region = str_to_title(level_1_region),
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index 5e83bf89bf24c904cddb6dfa807d559d772bf0c9..f305e8ba06a61cf069848f719180bc6c0897113e 100644
GIT binary patch
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From 500ae67dcfa0829a53fd909ba47985fd8aad9be5 Mon Sep 17 00:00:00 2001
From: Sam Abbott <contact@samabbott.co.uk>
Date: Sat, 5 Feb 2022 20:21:54 +0000
Subject: [PATCH 16/16] update news

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index 942c164e..ad8f7d6c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -20,6 +20,7 @@ This release is currently under development
 - Fixed a bug in the data sourced from Germany so that instead of treating it as a line list of individuals it is treated as a relatively finely resolved count data which needs to be summed up (by @sbfnk).
 - Fixed a bug in the Vietnam class due to `stringr` ([#448](https://github.com/epiforecasts/covidregionaldata/pull/448) by @RichardMN).
 - Fixed a bug with the Netherlands class were the lack of Hospitalisation data in the source was causing the class to fail ([#446](https://github.com/epiforecasts/covidregionaldata/pull/446) by @RichardMN).
+- Fixed an issue with the Colombia data and reduced dependencies by making `RSocrata` be a suggested package ([#433](https://github.com/epiforecasts/covidregionaldata/pull/433) by @RichardMN).
 
 ## Depreciations