Import current conditions

Author

Johannes Zauner

Preface

This document imports the current conditions and shows descriptive statistics for the site.

Setup

library(tidyverse)

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

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

library(LightLogR)

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

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

site <- "MPI"

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

c("labeling",
  "radio_factors",
  "time_summaries",
  "prepare_codebook",
  "filefinder",
  "general_parameters",
  "coltype_checker",
  "diarydate",
  "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("MeLiDosCurrentConditions4xday_DataDictionary_2024-10-16.csv")
#collect files
files <- filefinder("currenconditions", continuous = TRUE, individual = TRUE)
#import files
data <- 
  read_csv2(files, show_col_types = FALSE) |> 
  drop_na(redcap_repeat_instance) |> 
  mutate(record_id = paste0("MPI_S", record_id),
         across(c(startdate_4, enddate_4),
                \(x) parse_date_time(x, c("ymdHMS", "dmyHM")))
         )

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
ema_light	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
currentight	numeric	TRUE	character	FALSE	wrong_type	as.numeric(...)
additional_light	numeric	TRUE	character	FALSE	wrong_type	as.numeric(...)
currentmood	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
anxious	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
elated	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
sad	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
angry	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
irritable	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
energetic	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
kss_instr	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
kss	numeric	TRUE	numeric	TRUE	ok	as.numeric(...)
status_4	numeric	FALSE	NA	FALSE	missing	as.numeric(...)
check_mixedlight	logical	TRUE	numeric	FALSE	wrong_type	as.logical(...)
startdate_4	Date	TRUE	POSIXct	FALSE	wrong_type	as.Date(...)
enddate_4	Date	TRUE	POSIXct	FALSE	wrong_type	as.Date(...)
scheduledate_4	Date	FALSE	NA	FALSE	missing	as.Date(...)
record_id	character	TRUE	character	TRUE	ok	as.character(...)
uuid_4	character	FALSE	NA	FALSE	missing	as.character(...)
supplementaldata_4	character	FALSE	NA	FALSE	missing	as.character(...)
serializedresult_4	character	FALSE	NA	FALSE	missing	as.character(...)

#collect relevant columns: POSIXct, Date & numeric
relevant_columns <- 
  coltype_check$details |> 
  pull(col)
relevant_columns <- 
  c("record_id", relevant_columns)
#select relevant columns
data <- 
  data |> 
  select(any_of(relevant_columns)) |> 
  select(-c( 
            ema_light, currentmood, kss_instr)) |> 
  mutate(check_mixedlight = as.logical(check_mixedlight)) |> 
  filter(!is.na(currentight))
#label variables
data <-
data |> 
  add_radio_factors(codebook, 
                    var_col = `Variable / Field Name`, 
                    type_col = `Field Type`,
                    levels_col = `Choices, Calculations, OR Slider Labels`
                    ) |> 
  add_col_labels(codebook, var_col = `Variable / Field Name`, label_col = `Field Label`) |> 
  relocate(record_id, any_of(codebook$`Variable / Field Name`)) |> 
  mutate(across(where(is.POSIXct), \(x) force_tz(x, tzs[[site]]))) |> 
  rename(Datetime = startdate_4, 
         currentlight = currentight) |> 
  relocate(Datetime, .after = record_id)

Warning in add_radio_factors(data, codebook, var_col = `Variable / Field Name`,
: Radio variables provided but not in `data`: ema_light, currentmood, kss_instr

Warning in add_col_labels(add_radio_factors(data, codebook, var_col = `Variable
/ Field Name`, : Labels provided for variables not in `data`: ema_light,
currentmood, kss_instr, uuid_4, scheduledate_4, status_4, supplementaldata_4,
serializedresult_4

attr(data$Datetime, "label") <- "EMA time (start)"
attr(data$enddate_4, "label") <- "EMA time (finish)"

Summarize results

table_currentconditions(data)

Warning in add_col_labels(mutate(data, across(anxious:kss, as.numeric)), :
Labels provided for variables not in `data`: ema_light, currentight,
currentmood, kss_instr, uuid_4, startdate_4, scheduledate_4, status_4,
supplementaldata_4, serializedresult_4

Current conditions (EMA)	N	N = 682¹
Select the main light source you are currently exposed to. If you are unsure which one this is, think about it as the biggest and brightest source from which you are receiving light	682
Electric light source indoors (e.g.: LED/halogen/fluorescent lamps)		269 (39%)
Electric light source outdoors (e.g.: street lights)		8 (1.2%)
Daylight indoors (through windows)		295 (43%)
Daylight outdoors (including being in the shade)		91 (13%)
Emissive displays (e.g.: smartphone, laptop etc.)		13 (1.9%)
Darkness (outdoors and/or indoors)		6 (0.9%)
Light entering from outside during sleep (e.g.: skyglow, street lights etc.)		0 (0%)
Are you also being exposed to an additional, secondary light source?	682	363 (53%)
Please select the additional light source you are currently exposed to	363
Electric light source indoors (e.g.: LED/halogen/fluorescent lamps)		59 (16%)
Electric light source outdoors (e.g.: street lights)		6 (1.7%)
Daylight indoors (through windows)		75 (21%)
Daylight outdoors (including being in the shade)		3 (0.8%)
Emissive displays (e.g.: smartphone, laptop etc.)		215 (59%)
Darkness (outdoors and/or indoors)		4 (1.1%)
Light entering from outside during sleep (e.g.: skyglow, street lights etc.)		1 (0.3%)
missing		319
Anxious	682	1.00 (1.00, 2.00)
Elated	682	2.00 (1.00, 4.00)
Sad	682	1.00 (1.00, 1.00)
Angry	682	1.00 (1.00, 1.00)
Irritable	682	1.00 (1.00, 2.00)
Energetic	682	4.00 (2.00, 5.00)
Please rate your sleepiness in the last 5 minutes	682	3.00 (2.00, 5.00)
¹ n (%); Median (Q1, Q3)

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

Warning in add_col_labels(mutate(data, across(anxious:kss, as.numeric)), :
Labels provided for variables not in `data`: ema_light, currentight,
currentmood, kss_instr, uuid_4, startdate_4, scheduledate_4, status_4,
supplementaldata_4, serializedresult_4

file:////var/folders/9p/326_k3kx43qbn_cyl1rqfhb00000gn/T//RtmpoDUtMs/filebfd87bf96cb6.html screenshot completed

Export

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