Preface
This document imports the ASE (Sleep environment) and shows descriptive statistics for the site.
Setup
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)
files <- files |>
subset(grepl("ASE", files))
#import files
data <-
read_csv(files, show_col_types = FALSE) |>
rename_with(\(x) str_remove_all(x, "_v2")) |>
drop_na(redcap_repeat_instance)
# drop_na(redcap_repeat_instance)
#check column types
coltype_check <- coltype_checker(codebook, data)
coltype_check$details |> gt()
| slypos_ase_001 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_002 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_003 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_004 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_005 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_006 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_007 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_attentioncheck |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_008 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_009 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_010 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_011 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_012 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
| slypos_ase_0123 |
numeric |
TRUE |
numeric |
TRUE |
ok |
as.numeric(...) |
#collect relevant columns
relevant_columns <-
coltype_check$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 score |
22 |
28.0 (25.0, 30.0) |
| Has too much light |
22 |
|
| Strongly agree |
|
4 (18%) |
| Agree |
|
4 (18%) |
| Disagree |
|
6 (27%) |
| Strongly disagree |
|
8 (36%) |
| Is too dark |
22 |
|
| Strongly agree |
|
8 (36%) |
| Agree |
|
7 (32%) |
| Disagree |
|
4 (18%) |
| Strongly disagree |
|
3 (14%) |
| Is too noisy |
22 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
3 (14%) |
| Disagree |
|
8 (36%) |
| Strongly disagree |
|
11 (50%) |
| Is too quiet |
22 |
|
| Strongly agree |
|
5 (23%) |
| Agree |
|
9 (41%) |
| Disagree |
|
3 (14%) |
| Strongly disagree |
|
5 (23%) |
| Is too warm |
22 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
14 (64%) |
| Disagree |
|
7 (32%) |
| Strongly disagree |
|
1 (4.5%) |
| Is too cool |
22 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
2 (9.1%) |
| Disagree |
|
15 (68%) |
| Strongly disagree |
|
5 (23%) |
| Is too humid |
22 |
|
| Strongly agree |
|
1 (4.5%) |
| Agree |
|
1 (4.5%) |
| Disagree |
|
4 (18%) |
| Strongly disagree |
|
16 (73%) |
| Has an uncomfortable smell |
21 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
0 (0%) |
| Disagree |
|
3 (14%) |
| Strongly disagree |
|
18 (86%) |
| missing |
|
1 |
| Has uncomfortable pillows or blankets |
22 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
1 (4.5%) |
| Disagree |
|
4 (18%) |
| Strongly disagree |
|
17 (77%) |
| Has a mattress or other sleeping surface that is too firm |
21 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
3 (14%) |
| Disagree |
|
8 (38%) |
| Strongly disagree |
|
10 (48%) |
| missing |
|
1 |
| Has a mattress or other sleeping surface that is too soft |
21 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
2 (9.5%) |
| Disagree |
|
10 (48%) |
| Strongly disagree |
|
9 (43%) |
| missing |
|
1 |
| Has a mattress or other sleeping surface that is uncomfortable for another reason |
21 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
1 (4.8%) |
| Disagree |
|
5 (24%) |
| Strongly disagree |
|
15 (71%) |
| missing |
|
1 |
| Does not feel safe or secure |
21 |
|
| Strongly agree |
|
0 (0%) |
| Agree |
|
0 (0%) |
| Disagree |
|
5 (24%) |
| Strongly disagree |
|
16 (76%) |
| missing |
|
1 |
| Attention check successful |
22 |
18 (82%) |
gtsave(table |> as_gt(), filename = "../output/tables/table_ASE.png", vwidth = 800)
file:////var/folders/9p/326_k3kx43qbn_cyl1rqfhb00000gn/T//RtmpUpN6bl/file5c3a7b5867da.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")