diff --git a/DESCRIPTION b/DESCRIPTION
index 86fd1d5f..87d1d841 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -86,6 +86,7 @@ Imports:
countrycode (>= 1.2.0),
dplyr,
httr,
+ jsonlite,
lifecycle,
lubridate,
magrittr,
@@ -100,7 +101,7 @@ Imports:
tidyselect,
vroom,
withr,
- xml2
+ xml2,
Suggests:
ggplot2,
ggspatial,
diff --git a/NAMESPACE b/NAMESPACE
index 37b43471..4c694bca 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -74,12 +74,14 @@ importFrom(dplyr,slice_tail)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,tally)
+importFrom(dplyr,tibble)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars)
importFrom(httr,GET)
importFrom(httr,POST)
importFrom(httr,content)
importFrom(httr,status_code)
+importFrom(jsonlite,fromJSON)
importFrom(lifecycle,deprecate_warn)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
diff --git a/R/Vietnam.R b/R/Vietnam.R
index 9afa1eea..22ed8302 100644
--- a/R/Vietnam.R
+++ b/R/Vietnam.R
@@ -4,9 +4,7 @@
#' @description Information for downloading, cleaning
#' and processing covid-19 region data for Vietnam.
#'
-# nolint start
-#' @source \url{https://github.com/biocyberman/covidregionaldata/}
-# nolint end
+#' @source \url{https://covid.ncsc.gov.vn}
#' @export
#' @concept dataset
#' @family subnational
@@ -15,11 +13,12 @@
#' region <- Vietnam$new(verbose = TRUE, steps = TRUE, get = TRUE)
#' region$return()
#' }
+# nolint start
Vietnam <- R6::R6Class("Vietnam",
inherit = DataClass,
public = list(
- # Core Attributes (amend each paramater for country specific infomation)
+ # Core Attributes (amend each parameter for country specific information)
#' @field origin name of country to fetch data for
origin = "Vietnam",
#' @field supported_levels List of supported levels.
@@ -27,22 +26,15 @@ Vietnam <- R6::R6Class("Vietnam",
#' @field supported_region_names List of region names in order of level.
supported_region_names = list("1" = "region"),
#' @field supported_region_codes List of region codes in order of level.
- supported_region_codes = list("1" = "is_3166_2"),
+ supported_region_codes = list("1" = "iso_3166_2"),
#' @field common_data_urls List of named links to raw data.
- # nolint start
- common_data_urls = list(
- "case_by_time" = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time',
- "death_by_time" = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time',
- "recovered_by_time" = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time'
-
- ),
- # nolint end
+ common_data_urls = list(),
#' @field source_data_cols existing columns within the raw data
source_data_cols = c(
"cases_total", "deaths_total", "recovered_total"
),
#' @field source_text Plain text description of the source of the data
- source_text = "Public COVID-19 data curated by 5F team",
+ source_text = "Public COVID-19 for Vietnam, curated by NCSC's COVID-19 team",
#' @field source_url Website address for explanation/introduction of the
#' data
source_url = "https://covid.ncsc.gov.vn", # nolint
@@ -53,26 +45,28 @@ Vietnam <- R6::R6Class("Vietnam",
self$codes_lookup$`1` <- covidregionaldata::vietnam_codes
},
- #' @description Provincial Level Data
- #' cleaning
- #' @param ... pass additional arguments
- #'
- #' @importFrom dplyr filter select mutate rename
+ #' @description download function to get raw data
#' @importFrom tidyr replace_na drop_na
- #' @importFrom lubridate dmy
+ #' @importFrom lubridate dmy
#' @importFrom jsonlite fromJSON
- clean_common = function() {
- Sys.setenv("VROOM_CONNECTION_SIZE" = 131072*4) # Fix VROOM error
+ download = function() {
+ bundles_urls = list(
+ "case_by_time" = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time',
+ "death_by_time" = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time',
+ "recovered_by_time" = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time'
+
+ )
+ Sys.setenv("VROOM_CONNECTION_SIZE" = 131072*4) # Fix VROOM error
provines_url = 'https://covid.ncsc.gov.vn/api/v3/covid/provinces'
- bundles = names(self$data$raw)
- provines_data = jsonlite::fromJSON(provines_url)
+ bundles = names(bundles_urls)
+ provines_data = fromJSON(provines_url)
get_bundles_data = function(bundles){
bundles_data = list()
- for (bundle in bundles){
+ for (bundle in bundles){
url = paste0('https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=', bundle)
- data = jsonlite::fromJSON(url)
- bundles_data = c(bundles_data, setNames(list(data), bundle))
+ data = fromJSON(url)
+ bundles_data = c(bundles_data, setNames(list(data), bundle))
}
bundles_data
}
@@ -82,30 +76,39 @@ Vietnam <- R6::R6Class("Vietnam",
get_province = function(id, data){
row_dat = provines_data[(id=id),]
death_by_time= do.call(cbind, data$death_by_time[id])
- case_by_time=do.call(cbind, data$case_by_time[id])
- recovered_by_time=do.call(cbind, data$recovered_by_time[id])
+ case_by_time=do.call(cbind, data$case_by_time[id])
+ recovered_by_time=do.call(cbind, data$recovered_by_time[id])
if (!identical(row.names(death_by_time), row.names(death_by_time))) {
stop("Dates on case_by_time and death_by_time do not match!")
}
- df = dplyr::tibble(date= lubridate::dmy(row.names(case_by_time)),
- id = row_dat$id,
- name = row_dat$name,
- case_by_time= case_by_time,
- death_by_time= death_by_time,
- recovered_by_time= recovered_by_time)
+ df = tibble(date= dmy(row.names(case_by_time)),
+ id = row_dat$id,
+ name = row_dat$name,
+ case_by_time= case_by_time,
+ death_by_time= death_by_time,
+ recovered_by_time= recovered_by_time)
df
}
df = do.call(rbind, lapply(provines_data$id, function(id){get_province(id, bundles_data)}))
names(df) <- c("date", "id", "region_name", "cases_total", "deaths_total", "recovered_total")
-
- self$data$clean <- df %>%
+ self$data$raw[['main']] = df
+ },
+
+ #' @description Provincial Level Data
+ #' cleaning
+ #' @param ... pass additional arguments
+ #'
+ #' @importFrom dplyr filter select mutate rename tibble
+ #' @importFrom tidyr replace_na drop_na
+ clean_common = function() {
+ self$data$clean <- self$data$raw[['main']] %>%
select( date, region_name, cases_total, deaths_total, recovered_total) %>%
mutate(cases_total = as.numeric(cases_total),
deaths_total = as.numeric(deaths_total),
recovered_total = as.numeric(recovered_total),
region_name = stringr::str_replace_all(region_name, 'TP HCM', 'Hochiminh'),
- ) %>%
+ ) %>%
tidyr::drop_na(date, region_name) %>%
rename(level_1_region = region_name) %>%
mutate(
@@ -120,5 +123,7 @@ Vietnam <- R6::R6Class("Vietnam",
by = c("level_1_region" = "level_1_region")
)
}
+
)
)
+# nolint end
diff --git a/man/Vietnam.Rd b/man/Vietnam.Rd
index 20f22e4b..56f9876e 100644
--- a/man/Vietnam.Rd
+++ b/man/Vietnam.Rd
@@ -5,7 +5,7 @@
\title{Vietnam Class for downloading, cleaning and processing
notification data}
\source{
-\url{https://github.com/biocyberman/covidregionaldata/}
+\url{https://covid.ncsc.gov.vn}
}
\description{
Information for downloading, cleaning
@@ -70,6 +70,7 @@ data}
\subsection{Public methods}{
\itemize{
\item \href{#method-set_region_codes}{\code{Vietnam$set_region_codes()}}
+\item \href{#method-download}{\code{Vietnam$download()}}
\item \href{#method-clean_common}{\code{Vietnam$clean_common()}}
\item \href{#method-clone}{\code{Vietnam$clone()}}
}
@@ -79,7 +80,6 @@ data}
\itemize{
\item \out{}\href{../../covidregionaldata/html/DataClass.html#method-available_regions}{\code{covidregionaldata::DataClass$available_regions()}}\out{}
\item \out{}\href{../../covidregionaldata/html/DataClass.html#method-clean}{\code{covidregionaldata::DataClass$clean()}}\out{}
-\item \out{}\href{../../covidregionaldata/html/DataClass.html#method-download}{\code{covidregionaldata::DataClass$download()}}\out{}
\item \out{}\href{../../covidregionaldata/html/DataClass.html#method-filter}{\code{covidregionaldata::DataClass$filter()}}\out{}
\item \out{}\href{../../covidregionaldata/html/DataClass.html#method-get}{\code{covidregionaldata::DataClass$get()}}\out{}
\item \out{}\href{../../covidregionaldata/html/DataClass.html#method-initialize}{\code{covidregionaldata::DataClass$initialize()}}\out{}
@@ -99,6 +99,16 @@ Set up a table of region codes for clean data
\if{html}{\out{}}\preformatted{Vietnam$set_region_codes()}\if{html}{\out{
}}
}
+}
+\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-download}{}}}
+\subsection{Method \code{download()}}{
+download function to get raw data
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{Vietnam$download()}\if{html}{\out{
}}
+}
+
}
\if{html}{\out{
}}
\if{html}{\out{}}