R/Severity.R

In romanceline/Severity:

#' Severity per country
#'
#' This is reading the excel file made of many sheets and returns a single long dataset for the selected country
#' @param infile,country
#' @keywords
#' @export
#' @examples
#' SeverityPerCountry()


SeverityPerCountry<-function(infile,country){
    df <- read_excel(infile, sheet = country,col_names=FALSE) #DataFrame
    dft <- t(df) #Dataframe has become a character matrix due to transposition
    colnames(dft) <- dft[1,] #Rewriting the column names
    colnames(dft)<-make.names(colnames(dft)) #Make sure column names are in acceptable format, no special character, no space,...
    dft<-dft[-c(1), ] #Removing useless row
    Severity<-dft[,c("X1.4_IND","X4.1_IND","X4.2_IND","X4.3_IND","X4.5_IND","X5_IND","PHSM.SI","Date")] #Selects only fields we are interested in
    Severity<-as.data.frame(Severity) %>% mutate(Date=as.numeric(Date)) %>%
      mutate(Date=as.Date(Date,origin = "1899-12-30")) %>%
      convert(num("X1.4_IND","X4.1_IND","X4.2_IND","X4.3_IND","X4.5_IND","X5_IND","PHSM.SI"))
    #Retransforms the matrix in a dataframe where different types of data are allowed, converts characters into dates or numbers
    Severity$ADM0NAME<-country #Creates new field with country name as the final aim is to have a global dataset with all countries
    Severity<-Severity %>% select(
      Date,
      ADM0NAME,
      GlobalIndex=PHSM.SI,
      Masks= X1.4_IND,
      School = X4.1_IND,
      Workplace=X4.2_IND,
      Gatherings=X4.3_IND,
      StayHome=X4.5_IND,
      Travels=X5_IND,
    ) #Gives understandable column names
    return(Severity)
}


#' Severity for all countries
#'
#' This is reading the excel file made of many sheets and returns a single long dataset for all countries
#' @param infile
#' @keywords
#' @export
#' @examples
#' SeverityForAllCountries()

SeverityForAllCountries<-function(infile){
ListCountries<-excel_sheets(infile)
Severity<-data.frame()
for (country in ListCountries){
  Severity_<-SeverityPerCountry(infile,country)
  Severity<-bind_rows(Severity,Severity_)
}}