Import Light sensitivity VLSQ8

Preface

This document imports the VLSQ8 (Light sensitivity) and shows descriptive statistics for the site.

Setup

library(tidyverse)

Warning: package 'ggplot2' was built under R version 4.5.2

Warning: package 'tidyr' was built under R version 4.5.2

Warning: package 'dplyr' was built under R version 4.5.2

library(LightLogR)
library(glue)
library(readxl)
library(gt)
library(gtsummary)

remote <- 
  "https://raw.githubusercontent.com/MeLiDosProject/Data_Metadata_Conventions/main/scripts/"

c("labeling",
  "radio_factors",
  "add_label",
  "prepare_codebook",
  "filefinder",
  "general_parameters",
  "coltype_checker",
  "tables"
) |> walk(\(x) source(paste0(remote, x, ".R")))

Warning: package 'rlang' was built under R version 4.5.2

Preparation

#collect codebook
codebook <- 
  prepare_codebook("MeLiDosDischargeQuestionnaire_DataDictionary_2024-10-16.csv",
                   "your_light_sensitivity_vlsq8")
#collect files
files <- filefinder("discharge",individual = FALSE)
#import files
data <- 
  read_csv2(files, show_col_types = FALSE) |> 
  mutate(record_id = paste0("MPI_S", record_id)) |> 
  filter(!redcap_survey_identifier %in% c(200, 217))

ℹ Using "','" as decimal and "'.'" as grouping mark. Use `read_delim()` for more control.

#check column types
coltype_check <- coltype_checker(codebook, data)
coltype_check$details |> gt()

col	expected	present	actual	type_ok	issue	expected_example
sensitivity	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
glare	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
flicker	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
sensitivity_severity	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
headache	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
blurry_vision	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
ability	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
glasses	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)

#collect relevant columns
relevant_columns <- 
  coltype_check$details |> 
  pull(col) |> 
  c("record_id")
#select relevant columns
data <- data |> select(any_of(relevant_columns))
#label
data <-
data |> 
  add_radio_factors(codebook, 
                    var_col = `Variable / Field Name`, 
                    type_col = `Field Type`,
                    levels_col = `Choices, Calculations, OR Slider Labels`
                    ) |> 
  add_col_labels(codebook, var_col = `Variable / Field Name`, label_col = `Field Label`)

#reorder variables
data <- 
  data |> 
  relocate(record_id, any_of(codebook$`Variable / Field Name`))

data$record_id <- add_label(data$record_id, "Record ID")

Calculate composit score

data <- 
data |> 
  rowwise() |> 
  mutate(VLSQ8 = sum(c_across(sensitivity:glasses) |> as.numeric())) |> 
  ungroup() |> 
  relocate(.after = record_id, VLSQ8)
data$VLSQ8 <- add_label(data$VLSQ8, "VLSQ-8 sum score (light sensitivity)")

Summarize results

table <- 
table_general(data, "VLSQ-8: light sensitivity")
table

VLSQ-8: light sensitivity	N	N = 261
VLSQ-8 sum score (light sensitivity)	26	18.0 (15.0, 25.0)
How often did you have visual light sensitivity outdoors during daylight?	26
Never		8 (31%)
Rarely		8 (31%)
Sometimes		8 (31%)
Often		1 (3.8%)
Always		1 (3.8%)
How often did you have a sense of glare in your eyes?	26
Never		8 (31%)
Rarely		9 (35%)
Sometimes		7 (27%)
Often		2 (7.7%)
Always		0 (0%)
How often did you have visual light sensitivity from flickering lights or bright colors?	26
Never		8 (31%)
Rarely		9 (35%)
Sometimes		3 (12%)
Often		5 (19%)
Always		1 (3.8%)
Please rate the severity of the worst visual light sensitivity you experienced in the past week.	26
None		13 (50%)
Mild		9 (35%)
Moderate		4 (15%)
Significant		0 (0%)
Severe		0 (0%)
When you have sensitivity to light, do you also experience headache?	26
Never		13 (50%)
Rarely		6 (23%)
Sometimes		4 (15%)
Often		1 (3.8%)
Always		2 (7.7%)
When you have sensitivity to light, how often is your vision blurry?	26
Never		14 (54%)
Rarely		6 (23%)
Sometimes		4 (15%)
Often		2 (7.7%)
Always		0 (0%)
How often does sensitivity to light limit your ability to read, watch TV, or use the computer?	26
Never		10 (38%)
Rarely		10 (38%)
Sometimes		5 (19%)
Often		1 (3.8%)
Always		0 (0%)
How often did you need to wear dark glasses on cloudy days or indoors?	26
Never		22 (85%)
Rarely		3 (12%)
Sometimes		1 (3.8%)
Often		0 (0%)
Always		0 (0%)
1 Median (Q1, Q3); n (%)

gtsave(table |> as_gt(), filename = "../output/tables/table_vlsq8.png", vwidth = 800)

file:////var/folders/9p/326_k3kx43qbn_cyl1rqfhb00000gn/T//RtmprVDfbw/fileee164ba31573.html screenshot completed

Export

data <- data |> rename(Id = record_id)
vlsq8 <- data
path <- "../data/imported/"
if(!dir.exists(path)) dir.create(path, recursive = TRUE)
save(vlsq8, file = "../data/imported/vlsq8.RData")