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

knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)

library(tidyverse)
library(knitr)
library(janitor)
library(kableExtra)

error_log <- params$error_log

Harmonization completed status:

error_log %>%
  tabyl(completed_status) %>%
  adorn_totals(where = 'row') %>%
  adorn_pct_formatting() %>%
  kable(align = 'lrr') %>%
  kable_styling(full_width = F) %>%
  column_spec(column = 1, width = '2in') %>%
  column_spec(column = 2, width = '1in') %>%
  column_spec(column = 3, width = '1in')

vars_not_completed <- any(error_log$completed_status == 'Not completed')

if(vars_not_completed)
{

  cat('\n\n')
  cat('## Reasons variables were not harmonized: \n\n')
  cat('\n\n')

  error_log %>%
    filter(completed_status == 'Not completed') %>%
    tabyl(completed_reason) %>%
    adorn_totals(where = 'row') %>%
    adorn_pct_formatting() %>%
    kable(align = 'lrr') %>%
    kable_styling(full_width = F) %>%
    column_spec(column = 1, width = '2in') %>%
    column_spec(column = 2, width = '1in') %>%
    column_spec(column = 3, width = '1in') %>%
    cat()

  cat('<br>')

  cat('\n\n')
  cat('## Variables not harmonized: \n\n')
  cat('\n\n')

  error_log %>%
    filter(completed_status == 'Not completed') %>%
    select(study, item, visit, completed_reason) %>%
    kable(align = 'llrl') %>%
    kable_styling(full_width = F) %>%
    column_spec(column = 1, width = '2in') %>%
    column_spec(column = 2, width = '2in') %>%
    column_spec(column = 3, width = '1in') %>%
    column_spec(column = 4, width = '2in') %>%
    cat()

}

Variables set to NA (out of range)

# Number of variables where possible_range was used
num_vars_range <- sum(!is.na(error_log$possible_range) & error_log$possible_range != '', na.rm = T)

# Number of variables where values where set to NA, due to possible range
num_vars_set_to_na = sum(error_log$range_set_to_na > 0, na.rm = T)

Number of variables with a possible range set (column possible_range ): r num_vars_range

Number of variables with values out of possible range (set to NA): r num_vars_set_to_na

if(num_vars_range)
{

  cat('\n\n')
  cat('## variables with a possible range: \n\n')
  cat('\n\n')

  cat('<br>')

  error_log %>%
    filter(!is.na(possible_range) & possible_range != '') %>%
    select(study, item, visit, possible_range) %>%
    kable(align = 'llrr') %>%
    kable_styling(full_width = F) %>%
    column_spec(column = 1, width = '2in') %>%
    column_spec(column = 2, width = '2in') %>%
    column_spec(column = 3, width = '1in') %>%
    column_spec(column = 4, width = '2in') %>%
    cat()

}

cat('<br>')

if(num_vars_set_to_na)
{

  cat('\n\n')
  cat('## Variables with values out of possible range (set to NA): \n\n')
  cat('\n\n')

  cat('<br>')

  error_log %>%
    filter(range_set_to_na > 0) %>%
    select(study, item, visit, possible_range, range_set_to_na) %>%
    kable(align = 'llrrr') %>%
    kable_styling(full_width = F) %>%
    column_spec(column = 1, width = '2in') %>%
    column_spec(column = 2, width = '2in') %>%
    column_spec(column = 3, width = '1in') %>%
    column_spec(column = 4, width = '2in') %>%
    column_spec(column = 4, width = '2in') %>%
    cat()

}