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Meta-analysis of learning and memory in PTSD

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Systematic review and meta-analysis as described in:

  • Milou S.C. Sep, Elbert Geuze, Marian Joëls. Impaired learning, memory, and extinction in posttraumatic stress disorder: translational meta-analysis of clinical and preclinical studies. medRxiv 2021.07.19.21260790; doi: https://doi.org/10.1101/2021.07.19.21260790 [preprint]
  • Sep, M.S.C., Geuze, E. & Joëls, M. Impaired learning, memory, and extinction in posttraumatic stress disorder: translational meta-analysis of clinical and preclinical studies. Transl Psychiatry 13, 376 (2023). https://doi.org/10.1038/s41398-023-02660-7

Index

_ README.md: an overview of the project
|___ data: data files used in the project
|___ processed_data: intermediate files from the analysis
|___ results: results of the analyses (data, tables, figures)
|___ R: contains all R-code in the project

TRACE: Meta-analysis of learning and memory in PTSD

Step 1: Prepare data

Merge datasets

Recode data

  • script: Recode variables and add method codes with prepare_recode.rmd.
  • input:TRACEmerged.RDS, TRACE_method_codes.xlsx
  • output: TRACErecoded.RDS

Process QA data

  • script: process QA data with prepare_QA.rmd
  • input: TRACE_RoBQA_data.xlsx,
  • output: TRACE_QA_animal.RData, TRACE_QA_human.RData, and RoB.jpeg (optional: RoB_clinical.jpeg, RoB_preclinical.jpeg)

Calculate effect sizes

  • script: prepare data for analysis in prepare_effect_size_QA.rmd
  • input: TRACErecoded.RDS, TRACE_QA_animal.RData, and TRACE_QA_human.RData
  • output: TRACEprepared.RData (nb n=1647)

Step 2: Meta-regression Valence x Phase

  • script: meta-regression Valence x Phase: meta_regression.rmd. This script uses meta_regression_influentials.r to calculate potential influential case and outliers
  • input: TRACEprepared.RData
  • output: datasets used in analyses: clinical.data.metaregression.RDS, preclinical.data.metaregression.RDS and results (main, diagnostics, sensitivity, graphs)
    • clinical: phase_valence_PTSD_clinical.csv, phase_valence_PTSD_clinical.tiff, funnel.colours.clinical.tiff, phase_valence_PTSD_clinical.FSN.csv, influentials.clinical.rds, sens.clinical.infout.csv, sens.mod.A.csv, sens.mod.B.csv, sens.mod.C.csv
    • preclinical: phase_valence_PTSD_preclinical.csv, phase_valence_PTSD_preclinical.tiff, funnel.colours.preclinical.tiff, phase_valence_PTSD_preclinical.FSN.csv, influentials.preclinical.rds, sens.preclinical.infout.csv, sens.mod.E.csv, sens.mod.D.csv, sens.mod.F.csv
    • figure: PTSD.clinical.preclinical.tiff

Step 3: MetaForest and MetaCART

  • script: meta_forest_meta_cart.rmd
  • input: TRACEprepared.RData
  • output: data.explore.rds (NB: also used for descriptives table)
    • clinical: clinical.data.explorative.RDS, preclinical.data.explorative.RDS, fitted.clinicalMetaForest.RDS, metaforest_Clinical_convergence.tiff, metaforest_Clinical_varImportance.tiff, important_variables_clinical_metaforest.csv, metaforest_PD_clinical.tiff
    • preclinical: fitted.preclinicalMetaForest.RDS, metaforest_Preclinical_convergence.tiff, metaforest_Preclinical_varImportance.tiff, REtree.P.rds, metaCART.preclinical.tiff, important_variables_preclinical_metaforest.csv, metaforest_PD_preclinical.tiff, metaforest_PD_preclinical_metaCARTfollowup.tiff, VarImp.clinical.preclinical.tiff

Step 4: Vizualization and Study descriptives

Flowchart

Characteristics of the included studies

  • Script: descriptives.rmd
  • input: data.explore.rds, created in DataDrivenAnalysis.rmd
  • output: tables in word files: descriptives.comparison.doc, descriptives.csv (optional), descriptives.combined.doc, descriptives.clinical.doc, descriptives.preclinical.doc

Visualize QA

  • script: visualize_QA.Rmd
  • input: TRACE_QA_animal.RData, TRACE_QA_human.RData, clinical.data.metaregression.RDS preclinical.data.metaregression.RDS (Note: these objects are outputs from prepare_QA.RMD and meta_regression.rmd)
  • output: RoB.jpeg