R/Module_Polyps.R

In sebastiz/EndoMineR_devlop: Functions to mine endoscopic and associated pathology datasets

########################### Diagnostic yield functions #######

#' Create GRS metrics by endoscopist (X-ref with pathology)
#'
#' This extracts the polyps types from the data
#' (for colonoscopy and flexible sigmoidosscopy data)
#' and output the adenoma,adenocarcinoma and
#' hyperplastic detection rate by endoscopist as well
#' as overall number of colonoscopies.
#' This will be extended to other GRS outputs in the future.
#' @param dataframe The dataframe
#' @param ProcPerformed The column containing the Procedure type performed
#' @param Endo_Endoscopist column containing the Endoscopist name
#' @param Dx The column with the Histological diagnosis
#' @param Histol The column with the Histology text in it
#' @importFrom dplyr group_by_ do full_join
#' @keywords Withdrawal
#' @export
#' @examples # Firstly merge histology and endoscopy datasets for the colon:
#'
#' nn<-GRS_Type_Assess_By_Unit(vColon,'ProcedurePerformed',
#' 'Endoscopist','Diagnosis','Histology')
#' rm(vColon)
#' rm(MypathColon)
#' rm(MyendoColon)


GRS_Type_Assess_By_Unit <-
  function(dataframe,
           ProcPerformed,
           Endo_Endoscopist,
           Dx,
           Histol) {
    dataframe <- data.frame(dataframe)
    dataframe <- dataframe[grepl("Colonoscopy", dataframe[, ProcPerformed]),]
    
    #Function should get proportions of a procedure that result in a finding:
    
    Adenoma<-dataframe %>% group_by_(Endo_Endoscopist) %>% summarise(Adenoma=(sum(grepl("[Aa]denoma", Original.y))/dplyr::n())*100)
    Adenocarcinoma<-dataframe %>% group_by_(Endo_Endoscopist) %>% summarise(Adenocarcinoma=(sum(grepl(".*denoca.*", Original.y))/dplyr::n())*100)
    HGD<-dataframe %>% group_by_(Endo_Endoscopist) %>% summarise(HGD=(sum(grepl(".*[Hh]igh [Gg]rade.*", Original.y))/dplyr::n())*100)
    LGD<-dataframe %>% group_by_(Endo_Endoscopist) %>% summarise(LGD=(sum(grepl(".*[Ll]ow [Gg]rade.*", Original.y))/dplyr::n())*100)
    Serrated<-dataframe %>% group_by_(Endo_Endoscopist) %>% summarise(Serrated=(sum(grepl(".*[Ss]errated.*", Original.y))/dplyr::n())*100)
    Hyperplastic<-dataframe %>% group_by_(Endo_Endoscopist) %>% summarise(Hyperplastic=(sum(grepl(".*yperplastic.*", Original.y))/dplyr::n())*100)
    
    FinalTable <-
      full_join(Adenoma, Adenocarcinoma, by = Endo_Endoscopist)
    FinalTable <-
      full_join(FinalTable, HGD, by = Endo_Endoscopist)
    FinalTable <-
      full_join(FinalTable, LGD, by = Endo_Endoscopist)
    FinalTable <-
      full_join(FinalTable, Serrated, by = Endo_Endoscopist)
    FinalTable <-
      full_join(FinalTable, Hyperplastic, by = Endo_Endoscopist)
    
    # Need to add the total colonoscopy count in here
    FinalTable<-data.frame(FinalTable)
    return(FinalTable)
  }