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Electroencephalography during acute painful procedures in neonates: a scoping review.

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  1. [1] § 2. Methods › 2.5. Data extraction and variable explanation ↔ r/scripts/analyse_data.R, lines 52–135 · score 0.52 · electrode placements, variables, interventions, sex, age, clinical

Paper

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The authors' code

R · 135 lines · 6.2 KB · Apache-2.0 · 1 match

  1. # Load required functions from external scripts
  2. source("functions/count_occurrences.R") # Function to count categorical variable values
  3. source("functions/multiple_entries_to_vector.R") # Function to split comma-separated values
  4. source("functions/save_figure.R") # Wrapper for saving figures to file
  5. source("functions/summary_stats.R") # Function to calculate summary statistics
  6. source("functions/plot_country_map.R") # Function to create country distribution map
  7. source("functions/plot_publication_year.R") # Function to plot histogram of publication years
  8. source("functions/export_raincloud_data.R") # Function to export CSVs for raincloud plotting
  9. source("functions/plot_electrode_frequencies.R") # Function to create electrode distribution map
  11. # Load required libraries
  12. library(readr) # Efficient CSV reading
  13. library(ggplot2) # Data visualization
  14. library(dplyr) # Data manipulation
  15. library(tidyr) # Data reshaping
  17. # Define the results folder for output files
  18. results_folder <- "results/"
  20. # Create results folder if it doesn't exist
  21. if (!dir.exists(results_folder)) {
  22. dir.create(results_folder)
  23. }
  25. # Load dataset from CSV file
  26. data_path <- "data/data_extraction_form.csv"
  27. df <- read_csv(data_path, show_col_types = FALSE)
  29. # Define consistent color scheme and font size for plots
  30. blue_colour <- "#AECDE1"
  31. axis_font_size <- 12
  33. # Filter dataset to include only relevant groups for descriptive figures
  34. df_analysis_1 <- df %>% dplyr::filter(analysis_group %in% c(1, 2, 3))
  36. # Generate and save country count table and map
  37. country_count_table <- count_occurrences(df_analysis_1$data_country, paste0(results_folder, "fig_country_count_table.csv"))
  38. plot_country_map(country_count_table, paste0(results_folder, "fig_country_map.pdf"))
  40. # Generate and save publication year plot
  41. years_range <- seq(min(df_analysis_1$publication_year, na.rm = TRUE),
  42. max(df_analysis_1$publication_year, na.rm = TRUE), by = 1)
  44. years_counts <- df_analysis_1 %>%
  45. dplyr::filter(!is.na(publication_year)) %>%
  46. count(publication_year) %>%
  47. right_join(data.frame(publication_year = years_range), by = "publication_year") %>%
  48. dplyr::mutate(n = replace_na(n, 0))
  50. plot_publication_year(df_analysis_1, paste0(results_folder, "fig_publication_year.pdf"))
  52. # Filter for primary analysis group (group 3)
  53. df_analysis_2 <- df %>% dplyr::filter(analysis_group == 3)
  55. # Export CSV files for external raincloud plotting in JASP
  56. export_single_raincloud_data(df_analysis_2)
  57. export_paired_raincloud_data(df_analysis_2)
  59. # Compute summary statistics and export summary statistics table
  60. summary_vars <- c("Sample Size (N)", "Age at Birth (weeks)", "Age at Study (weeks)",
  61. "EEG Data Loss (%)", "Males (%)", "Females (%)")
  63. T_summary_stats <- data.frame(
  64. Min = numeric(length(summary_vars)),
  65. Q1 = numeric(length(summary_vars)),
  66. Median = numeric(length(summary_vars)),
  67. Q3 = numeric(length(summary_vars)),
  68. Max = numeric(length(summary_vars)),
  69. row.names = summary_vars
  70. )
  72. T_summary_stats["Sample Size (N)", ] <- summary_stats(df_analysis_2$sample_size, "Sample Size (N)")
  73. T_summary_stats["Age at Birth (weeks)", ] <- summary_stats(df_analysis_2$pma_birth_avg, "Age at Birth (weeks)")
  74. T_summary_stats["Age at Study (weeks)", ] <- summary_stats(df_analysis_2$pma_study_avg, "Age at Study (weeks)")
  75. T_summary_stats["EEG Data Loss (%)", ] <- summary_stats(df_analysis_2$eeg_data_loss_pct, "EEG Data Loss (%)")
  76. T_summary_stats["Males (%)", ] <- summary_stats(df_analysis_2$sex_male_pct, "Males (%)")
  77. T_summary_stats["Females (%)", ] <- summary_stats(df_analysis_2$sex_female_pct, "Females (%)")
  79. write.csv(T_summary_stats, paste0(results_folder, "summary_stats.csv"), row.names = TRUE)
  81. # Generate and save electrode count table and map
  82. electrode_count_table <- count_occurrences(df_analysis_2$electrode_positions, paste0(results_folder, "fig_electrode_count_table.csv"))
  84. plot_electrode_frequencies(
  85. electrode_data = electrode_count_table,
  86. output_pdf = paste0(results_folder, "electrode_frequency_map.pdf")
  87. )
  89. # Plot and export selected categorical variables
  90. categorical_vars <- c("pain_procedure", "analgesic_intervention", "epoch_rej_method",
  91. "clinical_pain_scale", "non_eeg_recording", "electrode_placement_method")
  93. file_names <- c("fig_pain_procedure.pdf", "fig_analgesic_intervention.pdf", "fig_epoch_rej_method.pdf",
  94. "fig_clinical_pain_scale.pdf", "fig_non_eeg_recording.pdf", "fig_electrode_placement_method.pdf")
  96. # Plot and export selected categorical variables
  97. categorical_vars <- c("pain_procedure", "analgesic_intervention", "epoch_rej_method",
  98. "clinical_pain_scale", "non_eeg_recording", "electrode_placement_method")
  100. file_names <- c("fig_pain_procedure.pdf", "fig_analgesic_intervention.pdf", "fig_epoch_rej_method.pdf",
  101. "fig_clinical_pain_scale.pdf", "fig_non_eeg_recording.pdf", "fig_electrode_placement_method.pdf")
  103. for (i in seq_along(categorical_vars)) {
  104. var_name <- categorical_vars[i]
  105. file_name <- paste0(results_folder, file_names[i])
  106. csv_file <- gsub(".pdf", ".csv", file_name)
  108. count_table <- count_occurrences(df_analysis_2[[var_name]], csv_file) %>%
  109. dplyr::arrange(Count)
  111. plot_categorical <- ggplot(count_table, aes(x = reorder(Category, Count), y = Count)) +
  112. geom_bar(stat = "identity", fill = blue_colour, width = 0.8) + # fixed width for uniform bars
  113. coord_flip() +
  114. labs(x = "", y = "Count") +
  115. theme_minimal(base_size = 22) +
  116. theme(
  117. panel.grid.major.x = element_line(color = "grey85"), # keep only x-axis major gridlines
  118. panel.grid.major.y = element_blank(),
  119. panel.grid.minor = element_blank(),
  120. axis.text.x = element_text(size = 22, color = "black"),
  121. axis.text.y = element_text(size = 22, color = "black"),
  122. axis.title.y = element_text(size = 22),
  123. axis.title.x = element_text(size = 22),
  124. axis.line.x = element_line(color = "black"),
  125. axis.ticks.x = element_line(color = "black"),
  126. axis.ticks.y = element_blank()
  127. )
  129. # Adaptive figure sizing
  130. num_cats <- nrow(count_table)
  131. height <- max(4, 0.6 * num_cats)
  132. width <- 10
  134. ggsave(file_name, plot = plot_categorical, width = width, height = height, units = "in")
  135. }

analyse_data.R at commit 6ea0fdb, under Apache-2.0 · at the source

Overview

Authors: Patricia Y. Gunawan1,2, Luke Baxter1, Maria M. Cobo1,3, Marianne van der Vaart1, Samyuktha Iyer1, Vaneesha Monk1, Kanwaljeet J.S. Anand4,5,6, Charles B. Berde7,8, Caterina Coviello9, Mohammad Reza Daliri10, Guy Dumont11,12, Vineta Fellman13,14, Behnood Gholami15, Caroline Hartley1, Pierre Kuhn16, Nathalie L. Maitre17,18, Roshni C. Mansfield1, Simon Marchant1, Sofie Nilsson13, Elisabeth Norman13,19
and 13 other authorsSafa Talebi20, Sonya Wang21,22, Karel Allegaert23,24,25, Jonathan M. Davis26, Mark A. Turner27,28, Robert M. Ward29, Edress Darsey30, James P. Sheppard31, Aomesh Bhatt1, John van den Anker1,32, An N. Massaro33, Kanwaljit Singh34, Rebeccah Slater1
ORCID iDs: Luke Baxter, Vineta Fellman, Sonya Wang, Karel Allegaert, Mark A. Turner
34 affiliations
  1. Department of Paediatrics, University of Oxford, Oxford, United Kingdom
  2. Department of Pediatrics, Faculty of Medicine, Pelita Harapan University, Tangerang, Indonesia
  3. Colegio de Ciencias Biologicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
  4. Stanford Child Wellness Lab, Maternal & Child Health Research Institute, Stanford University School of Medicine, Stanford, CA, USA
  5. Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
  6. Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
  7. Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
  8. Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
  9. Division of Neonatology, Careggi University Hospital of Florence, Florence, Italy
  10. Biomedical Engineering Department, School of Electrical Engineering, Iran University of Science and Technology, Tehran, Iran
  11. Department of Electrical & Computer Engineering, The University of British Columbia, Vancouver, Canada
  12. British Columbia Children's Hospital Research Institute, Vancouver, Canada
  13. Paediatrics, Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden
  14. Children's Hospital, University of Helsinki, Helsinki, Finland
  15. Autonomous Healthcare, Santa Clara, CA, USA
  16. Department of Neonatology, University of Strasbourg, Strasbourg, France
  17. Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
  18. Children's Healthcare of Atlanta Inc, Atlanta, GA, USA
  19. Department of Neonatology, Skåne University Hospital, Lund, Sweden
  20. Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran
  21. Departments of Neurology and
  22. Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
  23. Department of Development and Regeneration, KU Leuven, Leuven, Belgium
  24. Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
  25. Department of Hospital Pharmacy, Erasmus Medical Center, Rotterdam, Netherlands
  26. Department of Pediatrics, Tufts Medical Center, Boston, MA, USA
  27. Department of Women's and Children's Health, University of Liverpool, Liverpool, United Kingdom
  28. Conect4children Stichting, Utrecht, Netherlands
  29. Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
  30. Pediatric Development Strategy, Clinical Research Group, Thermo Fisher Scientific, Waltham, MA, USA
  31. Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
  32. Center for Translational Research, Children's National Hospital, Washington, DC, USA
  33. Office of Pediatric Therapeutics, Food and Drug Administration (FDA), Silver Spring, MD, USA
  34. INC, Critical Path Institute (C-Path), Tucson, AZ, USA
Institutions: Pelita Harapan University (Indonesia); University of Oxford (United Kingdom); Universidad San Francisco de Quito (Ecuador); Stanford Medicine (United States); Stanford Maternal and Child Health Research Institute; Stanford University (United States); Boston Children's Hospital (United States); Harvard University (United States); Azienda Ospedaliero-Universitaria Careggi (Italy); Iran University of Science and Technology (Iran); University of British Columbia (Canada); BC Children's Hospital Research Institute (Canada); University of Helsinki (Finland); Lund University (Sweden); Skåne University Hospital (Sweden); Université de Strasbourg (France); Emory University (United States); Children's Healthcare of Atlanta (United States); University of Tabriz (Iran); University of Minnesota (United States); Pediatrics and Genetics (United States); Erasmus MC (Netherlands); KU Leuven (Belgium); Tufts Medical Center (United States); University of Liverpool (United Kingdom); University of Utah (United States); Thermo Fisher Scientific (United States) (United States); Children's National (United States); United States Food and Drug Administration (United States); Critical Path Institute (United States)
Journal: Pain reports, volume 11, issue 3, article e1437
Dates: received 2 December 2025; accepted 2 March 2026; published online 9 April 2026
Type: Review · Language: English
License: CC BY
Identifiers: DOI 10.1097/pr9.0000000000001437 · PMID 41972211 · PMCID PMC13068459 · OpenAlex W7153868512
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: EEG (modality), human (organism), pain (population), developmental (subfield)
Keywords: Pain, EEG, Neonate, Evidence synthesis
Journal subjects: Pediatric
Topic: Pediatric Pain Management Techniques (Pediatrics, Perinatology and Child Health, Medicine), according to OpenAlex
Funding: International Neonatal Consortium
Citations: not cited yet (Europe PMC); 110 references in the paper

Abstract

Although electroencephalography (EEG) is used to assess neonatal pain in research settings, EEG assessments have not been sufficiently characterized for use as end points to assess the efficacy of analgesics in regulatory-endorsed, industry-sponsored trials. We aimed to identify all studies conducted in neonates with EEG recordings during acute somatic nociceptive skin-breaking procedures, and to create a network of authors who will be invited to contribute their individual participant data (IPD) to an IPD meta-analysis to establish the validity, reliability, and clinical interpretability of an EEG-based neonatal pain measure. To identify literature, we searched MEDLINE, Embase, CINAHL, Web of Science, Scopus, Google Scholar, ClinicalTrials.gov, and the WHO ICTRP from database inception to July 2, 2025. Eligible studies were primary empirical studies that included neonates with EEG recordings during acute skin-breaking procedures. We identified 55 studies across 11 countries. Heel lance was the most common painful procedure; others included venipuncture, immunization, and lumbar puncture. The impact of 12 analgesic interventions has been studied to date, mostly nonpharmacological interventions. Individual-electrode EEG is more common than EEG caps. We noted relatively high data loss due to EEG data-quality concerns. A wide range of non-EEG pain-relevant measures have been recorded alongside EEG (eg, behavior, vital signs). Coauthorship network analysis highlighted that authors commonly work within discrete authorship hubs, with limited coauthorship across hubs. The predominance of studies was from European and American institutions, which limits generalizability. We conclude that sufficient data are available to undertake an IPD meta-analysis.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

lukebax/neonate-eeg-pain-scr

License: Apache-2.0
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 6ea0fdbba362ce0b73b80b2898bcddf0af0edf8c, 17 October 2025
Languages: R (9)
Size: 21 files, 9 scripts
Software Heritage: not archived
Found in: the acknowledgements
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (5 files), ggplot2 (4 files)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
11 files
At the source: github.com/lukebax/neonate-eeg-pain-scr

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 9 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

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Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 33 authors, 4 keywords, 1 funder, 65 references.

Cite

This paper

Gunawan, P. Y., Baxter, L., Cobo, M. M., van der Vaart, M., Iyer, S., Monk, V., Anand, K. J., Berde, C. B., Coviello, C., Daliri, M. R., Dumont, G., Fellman, V., Gholami, B., Hartley, C., Kuhn, P., Maitre, N. L., Mansfield, R. C., Marchant, S., Nilsson, S., . . . Slater, R. (2026). Electroencephalography during acute painful procedures in neonates: a scoping review. Pain reports, 11(3), e1437. https://doi.org/10.1097/pr9.0000000000001437

BibTeX

@article{gunawan2026electroencephalograp,
author = {Gunawan, Patricia Y. and Baxter, Luke and Cobo, Maria M. and van der Vaart, Marianne and Iyer, Samyuktha and Monk, Vaneesha and Anand, Kanwaljeet J.S. and Berde, Charles B. and Coviello, Caterina and Daliri, Mohammad Reza and Dumont, Guy and Fellman, Vineta and Gholami, Behnood and Hartley, Caroline and Kuhn, Pierre and Maitre, Nathalie L. and Mansfield, Roshni C. and Marchant, Simon and Nilsson, Sofie and Norman, Elisabeth and Talebi, Safa and Wang, Sonya and Allegaert, Karel and Davis, Jonathan M. and Turner, Mark A. and Ward, Robert M. and Darsey, Edress and Sheppard, James P. and Bhatt, Aomesh and van den Anker, John and Massaro, An N. and Singh, Kanwaljit and Slater, Rebeccah},
title = {{Electroencephalography during acute painful procedures in neonates: a scoping review}},
journal = {Pain reports},
year = {2026},
month = apr,
volume = {11},
number = {3},
pages = {e1437},
publisher = {Wolters Kluwer Health},
issn = {2471-2531},
doi = {10.1097/pr9.0000000000001437},
url = {https://doi.org/10.1097/pr9.0000000000001437},
pmid = {41972211},
pmcid = {PMC13068459}
}

RIS

TY - JOUR
AU - Gunawan, Patricia Y.
AU - Baxter, Luke
AU - Cobo, Maria M.
AU - van der Vaart, Marianne
AU - Iyer, Samyuktha
AU - Monk, Vaneesha
AU - Anand, Kanwaljeet J.S.
AU - Berde, Charles B.
AU - Coviello, Caterina
AU - Daliri, Mohammad Reza
AU - Dumont, Guy
AU - Fellman, Vineta
AU - Gholami, Behnood
AU - Hartley, Caroline
AU - Kuhn, Pierre
AU - Maitre, Nathalie L.
AU - Mansfield, Roshni C.
AU - Marchant, Simon
AU - Nilsson, Sofie
AU - Norman, Elisabeth
AU - Talebi, Safa
AU - Wang, Sonya
AU - Allegaert, Karel
AU - Davis, Jonathan M.
AU - Turner, Mark A.
AU - Ward, Robert M.
AU - Darsey, Edress
AU - Sheppard, James P.
AU - Bhatt, Aomesh
AU - van den Anker, John
AU - Massaro, An N.
AU - Singh, Kanwaljit
AU - Slater, Rebeccah
TI - Electroencephalography during acute painful procedures in neonates: a scoping review
T2 - Pain reports
J2 - Pain Rep
PY - 2026
DA - 2026/04/09
VL - 11
IS - 3
SP - e1437
SN - 2471-2531
PB - Wolters Kluwer Health
DO - 10.1097/pr9.0000000000001437
UR - https://doi.org/10.1097/pr9.0000000000001437
LA - en
ER -

CSL-JSON

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