R/get_agecases.R

In Andreaierardi/disCOVIDer19: Covid_19 outbreak analysis

#' Data acquisition of cases age region from Epicentro ISS
#' 
#' Data acquisition of cases age from Epicentro ISS \href{https://www.epicentro.iss.it/}{(Link)} of summary information and age cases per region
#'
#'
#' @examples
#' \dontrun{
#' get_agecases(regNames)
#' }
#' 
#' @param regNames vector. Name of italian regions
#' @return list. Return a list of region containing a list of dataframe  
#' @export
#' 
#' 
#' 

get_agecases <- function(regNames) {
  
  
  #start_url = "https://www.epicentro.iss.it/coronavirus/bollettino/Bolletino-sorveglianza-integrata-COVID-19_"
  #Sys.setlocale("LC_TIME", "Italian")
  #url_file = format(Sys.Date(), "%d-%B-%Y")
  #end_url = "_appendix.pdf"
  #files = paste0(start_url,url_file,end_url)*/
  #day = 0
  #document = NULL
  #while(day <30)
  #{
   # url_file = format(Sys.Date()-day, "%d-%B-%Y")
  #  files = paste0(start_url,url_file,end_url)
  #  message("checking URL : ",files)
  #  x <- tryCatch(
  #    {
      #  quiet(pdftools::pdf_text(files))
   #     ddpcr::quiet( pdftools::pdf_text(files))
        
    #    document =  pdftools::pdf_text(files)
     #   day = 50

        
      #},
      #error = function(e){
      # message("Trying the day before..")

      #}
  #  )
    #
   # day = day+1
#  }
 
#  https://www.epicentro.iss.it/coronavirus/bollettino/Bolletino-sorveglianza-integrata-COVID-19_30-marzo-2020_appendix.pdf
  files = "https://www.epicentro.iss.it/coronavirus/bollettino/Bolletino-sorveglianza-integrata-COVID-19_20-maggio-2020_appendix.pdf"
  document = pdftools::pdf_text(files)
  #"https://www.epicentro.iss.it/coronavirus/bollettino/Bollettino-sorveglianza-integrata-COVID-19_30-marzo-2020.pdf"
#  lapply(document, length) 
  alldocument_pages = document
  
  
  condition_split = "Sintesi dei dati principali -"

  splitted = strsplit(alldocument_pages, condition_split)
  length(splitted)
  interested_pages = c()
  regNames_extend = c(regNames, c("Trento","Bolzano","Friuli-Venezia-Giulia","Valle D’Aosta"))
  
  for (i in 1:length(splitted))
  {
    splitted[[i]] = stringr::str_trim(splitted[[i]])
    splitted[[i]]= splitted[[i]][splitted[[i]]!=""]
    tmp = startsWith(splitted[[i]],regNames_extend)
    if(length(tmp[tmp ==T])>0)
    {
      filter_doc = splitted[[i]]
      interested_pages <- c(interested_pages, filter_doc)
    }
  }
  #Friuli
  
  pages_split =  strsplit(interested_pages, "•")
  regions = c()
  age_lis = list()
  for (reg in 1:length(pages_split))
  {
    clean = stringr::str_trim(pages_split[[reg]])
    
    m = gregexpr('[0-9]+',clean[2:4])
    partition = regmatches(clean[2:4], m)
    
    regione = clean[1]
    casi_totali = as.integer(partition[[1]])
    eta_mediana = as.integer(partition[[2]][1])
    deceduti = as.integer(partition[[3]][1])
  #  operatori_sanitari = as.integer(partition[[4]][1])
    
#    summary = data.frame(casi_totali,eta_mediana,deceduti,operatori_sanitari)
    summary = data.frame(casi_totali,eta_mediana,deceduti)
    
    m2 = gregexpr('[0-9]+-[0-9]+|[+-]?(?:[0-9]+(?:[.][0-9]*)?|[.][0-9]+)',clean[4])
    part2 = regmatches(clean[4], m2)[[1]]
    
    age_cases = data.frame()
    
    for (i in seq(2,length(part2)-1, by =3))
    {
      age_int = part2[i]
      cases = as.integer(part2[i+1])
      perc_cases =  as.numeric(part2[i+2])
      
      if(i == length(part2)-2)
      {
        age_int = "Not known"
        cases = as.integer(part2[i])
        perc_cases =  as.numeric(part2[i+1])
        
      }
      tmp =  data.frame(age_int,cases,perc_cases)
      age_cases = rbind(age_cases,tmp)
    }
    regions =  c(regions, regione)
    age_lis[[reg]] = list(summary, age_cases)
    names(age_lis[[reg]]) = c("summary","age_cases")
    
  }
  age_lis
  names(age_lis) = regions
  return(age_lis)
  
}