Import Sleep environment ASE

Preface

This document imports the ASE (Sleep environment) 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",
  "attention_check",
  "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_sleep_environment_ase")
#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.

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

col	expected	present	actual	type_ok	issue	expected_example
slypos_ase_001	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_002	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_003	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_004	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_005	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_006	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_007	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_attentioncheck	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_008	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_009	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_010	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_011	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_012	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
slypos_ase_0123	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")

Attention check

data <- 
  data |> 
  attention_check(slypos_ase_attentioncheck, "Strongly disagree")

ASE score

data <- 
data |> 
  rowwise() |> 
  mutate(
across(starts_with("slypos_ase_0"),
       \(x) {x <- x |> as.numeric()
       x-1
       }, .names = "{.col}_num"),
ASE = sum(c_across(ends_with("_num")), na.rm = TRUE),
.after = record_id
) |> select(-ends_with("_num"))

data <- 
add_labels(data, c(ASE = "ASE score"))

Summarize results

table <- 
table_general(data, "ASE: Sleep environment")
table

ASE: Sleep environment	N	N = 26¹
ASE score	26	27.5 (26.0, 31.0)
Has too much light	26
Strongly agree		1 (3.8%)
Agree		3 (12%)
Disagree		10 (38%)
Strongly disagree		12 (46%)
Is too dark	26
Strongly agree		0 (0%)
Agree		3 (12%)
Disagree		11 (42%)
Strongly disagree		12 (46%)
Is too noisy	26
Strongly agree		1 (3.8%)
Agree		3 (12%)
Disagree		8 (31%)
Strongly disagree		14 (54%)
Is too quiet	26
Strongly agree		2 (7.7%)
Agree		7 (27%)
Disagree		6 (23%)
Strongly disagree		11 (42%)
Is too warm	26
Strongly agree		4 (15%)
Agree		4 (15%)
Disagree		15 (58%)
Strongly disagree		3 (12%)
Is too cool	26
Strongly agree		0 (0%)
Agree		6 (23%)
Disagree		11 (42%)
Strongly disagree		9 (35%)
Is too humid	26
Strongly agree		2 (7.7%)
Agree		2 (7.7%)
Disagree		11 (42%)
Strongly disagree		11 (42%)
Has an uncomfortable smell	26
Strongly agree		0 (0%)
Agree		0 (0%)
Disagree		9 (35%)
Strongly disagree		17 (65%)
Has uncomfortable pillows or blankets	26
Strongly agree		0 (0%)
Agree		4 (15%)
Disagree		14 (54%)
Strongly disagree		8 (31%)
Has a mattress or other sleeping surface that is too firm	26
Strongly agree		1 (3.8%)
Agree		2 (7.7%)
Disagree		11 (42%)
Strongly disagree		12 (46%)
Has a mattress or other sleeping surface that is too soft	26
Strongly agree		2 (7.7%)
Agree		4 (15%)
Disagree		14 (54%)
Strongly disagree		6 (23%)
Has a mattress or other sleeping surface that is uncomfortable for another reason	26
Strongly agree		1 (3.8%)
Agree		3 (12%)
Disagree		12 (46%)
Strongly disagree		10 (38%)
Does not feel safe or secure	26
Strongly agree		0 (0%)
Agree		1 (3.8%)
Disagree		4 (15%)
Strongly disagree		21 (81%)
Attention check successful	26	25 (96%)
¹ Median (Q1, Q3); n (%)

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

file:////var/folders/9p/326_k3kx43qbn_cyl1rqfhb00000gn/T//RtmpcBd2va/file5d44426943de.html screenshot completed

Export

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