In psHarmonize: Creates a Harmonized Dataset Based on a Set of Instructions

  ## Table ---------

      table_summ <- data_intermediate %>%
      group_by(cohort, visit) %>%
      summarise(n = n(),
                n_missing = sum(is.na(value)),
                min = min(value, na.rm = TRUE),
                Q1 = quantile(value, probs = c(0.25), na.rm = TRUE),
                median = median(value, na.rm = TRUE),
                Q3 = quantile(value, probs = c(0.75), na.rm = TRUE),
                max = max(value, na.rm = TRUE),
                mean = mean(value, na.rm = TRUE),
                std = sd(value, na.rm = TRUE)) %>%
      ungroup() %>%
      mutate(n = format(n, big.mark = ','),
             n_missing = format(n_missing, big.mark = ','),
             min = round(min, digits = 1),
             Q1 = round(Q1, digits = 1),
             median = round(median, digits = 1),
             Q3 = round(Q3, digits = 1),
             max = round(max, digits = 1),
             mean = round(mean, digits = 1),
             std = round(std, digits = 1))

  kable(table_summ) %>%
    kable_styling()


  cat('\n')
  cat('\n')


  ## Plot ----------


    ggplot(data_intermediate, aes(x = value)) +
       geom_histogram(bins = 30) +
       theme_bw() +
       labs(title = glue('Distribution of {current_cat}')) +
       xlab(units)

     cat('\n')
     cat('\n')

psHarmonize documentation built on April 4, 2025, 1:50 a.m.