R/pull-covid-jhu.R

In CBDRH/COVIDreconnoitR: Pulls and Analyses COVID data

#' read in raw covid19 data
#'
#' @return dataframe
#' @export
covid_jhu_read <- function(){
  readr::read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv",
           col_types = readr::cols(
             .default = readr::col_double(),
             `Province/State` = readr::col_character(),
             `Country/Region` = readr::col_character()
           ))
}

#' clean variable names of covid19 raw data (from `covid_read`)
#'
#' @param x covid19 raw data
#'
#' @return data.frame with tidied names
#' @export
covid_jhu_clean_names <- function(x){
  x %>%
    tibble::as_tibble(.name_repair = janitor::make_clean_names) %>%
    dplyr::rename(province = province_state)
}

#' pivots the covid19 data into longer form
#'
#' @param x data that has been imported and cleaned
#'
#' @return longer form pivoted data
#' @export
covid_jhu_pivot_longer <- function(x){
  tidyr::pivot_longer(data = x,
                      cols = -c(province:long),
                      names_to = "date",
                      values_to="cumulative_cases")
}


#' Pulls and tidies the latest covid19 data
#'
#' @return covid19 data with columns..
#' @export
covid_jhu <- function(){
  covid_jhu_read() %>%
    covid_jhu_clean_names() %>%
    covid_jhu_pivot_longer() %>%
    dplyr::mutate(date = covid_jhu_clean_date(date)) %>%
    dplyr::arrange(country_region,
                   province,
                   date) %>%
    dplyr::group_by(country_region, province) %>%
    dplyr::mutate(incident_cases = c(0, diff(cumulative_cases))) %>%
    dplyr::ungroup() %>%
    add_continent(country_source = country_region)

}


#' Filter covid countries to provided countries
#'
#' @param data covid19 data
#' @param countries vector of countries
#'
#' @return dataset filtered to existing countries
#' @export
covid_jhu_filter_countres <- function(data, countries){
  data %>%
    dplyr::filter(country_region %in% countries)
}