fn-qa.R

# Function to apply quality assurance
qa <- function(input, study_dates) {

  # Specify consort table --------------------------------------------------------
  
  print('Specify consort table')

  consort <- data.frame(Description = "Input", 
                        N = nrow(input),
                        stringsAsFactors = FALSE)

  print('Quality assurance: Year of birth is after year of death or patient only has year of death')
  
  input <- input[!((input$qa_num_birth_year > (format(input$cens_date_death, format="%Y")) & 
                      is.na(input$qa_num_birth_year)== FALSE & is.na(input$cens_date_death) == FALSE) | 
                     (is.na(input$qa_num_birth_year)== TRUE & is.na(input$cens_date_death) == FALSE)),]
  consort[nrow(consort)+1,] <- c("Quality assurance: Year of birth is after year of death or patient only has year of death",
                                 nrow(input))
  
  print('Quality assurance: Year of birth is before 1793 or year of birth exceeds current date')
  
  input <- input[!((input$qa_num_birth_year < 1793 | 
                      (input$qa_num_birth_year >format(Sys.Date(),"%Y"))) & 
                     is.na(input$qa_num_birth_year) == FALSE),]
  consort[nrow(consort)+1,] <- c("Quality assurance: Year of birth is before 1793 or year of birth exceeds current date",
                                 nrow(input))
  
  print('Quality assurance: Date of death is invalid (on or before 1/1/1900 or after current date)')
  
  input <- input[!((input$cens_date_death <= as.Date(study_dates$earliest_expec) | 
                      input$cens_date_death > format(Sys.Date(),"%Y-%m-%d")) & is.na(input$cens_date_death) == FALSE),]
  consort[nrow(consort)+1,] <- c("Quality assurance: Date of death is invalid (on or before 1/1/1900 or after current date)",
                                 nrow(input))
  
  print('Quality assurance: Pregnancy/birth codes for men')
  
  input <- input[!(input$qa_bin_pregnancy == TRUE & input$cov_cat_sex=="Male") | is.na(input$cov_cat_sex),]
  consort[nrow(consort)+1,] <- c("Quality assurance: Pregnancy/birth codes for men",
                                 nrow(input))
  
  print('Quality assurance: HRT or COCP meds for men')
  
  input <- input[!(input$cov_cat_sex=="Male" & input$qa_bin_hrtcocp==TRUE) | is.na(input$cov_cat_sex),]
  consort[nrow(consort)+1,] <- c("Quality assurance: HRT or COCP meds for men",
                                 nrow(input))
  
  print('Quality assurance: Prostate cancer codes for women')
  
  input <- input[!(input$qa_bin_prostate_cancer == TRUE & 
                     input$cov_cat_sex=="Female") | is.na(input$cov_cat_sex),]
  consort[nrow(consort)+1,] <- c("Quality assurance: Prostate cancer codes for women",
                                 nrow(input))

  return(list(input = input, consort = consort))
}