README

Cornelius Hennch 21.02.2024

PreTHOD: Prediction of Therapy Outcome in Depression

Cornelius Hennch, last updated: 21.02.2024

R-Version: R version 4.3.1 (2023-06-16)

RStudio-Version: 2023.6.1.524

Project summary

PreTHOD is a data analysis project at the St. Hedwig university hospital of the Charité - Universitätsmedizin Berlin that tries to identify prognostic factors for the treatment outcome of depression by analyzing a dataset from routine clinical practice. The data were collected with tablet-based standardized self-rating tools both in the day clinic as well as the specialized ward for depression. Both settings work with the same cognitive-behavioral therapy program that consists of group and single therapeutic sessions as well as complementary therapies.

Project plan and current status

Project plan and timeline

• Timeline and goals → ✅
• Detailed project plan → 🚧
• Team responsibilities
  • C. Hennch (lead author) 🧑‍🔬
  • H. Stuke (methodological support) 👨‍💻
  • N. Schoofs (supervisor) 👩‍⚕️
  • K.Priebe (data) ❓
• Regular team meetings → ❓

Preregistration and Registered Reports

• Preregistration → 🚧
• Registered reports → journals ❓

Data and Code Management

• Clean, well-documented code → Code written according to Hadley Wickhams tidyverse style guide ✅
• Version control tools (e.g., Git) → This repository on github. ✅
• README file → 🚧
• Acquisition, storage, and sharing → PEQ, sharing after publication ✅
• Data and code management plan → clear repository structure 🚧
• Ethical and legal requirements → Written informed consent available :white_check_mark:

Statistical Analysis

• Plan statistical analysis
• Reporting guidelines
• Handling of Missing data

Publication and Dissemination

• Literature review
• Manuscript writing
• Open access journal ❓
• Sharing data and code

Project plan and timeline

First draft for timeline:

Preregistration and Registered Reports

Preregistration

Which preregistration template → ❓

• PRP-QUANT

• aspredicted.org

Registered Reports

Available journals for registered reports

Statistical Analysis

→ Analysis plan included in preregistration?

Describe methods and packages here.

Reporting guidelines

• TRIPOD → multivariable prediction models

• JARS-Quant → reporting standards for quantitative research in psychology

Data and Code Management

Project folder structure

This repository aspires to meet the principles of a research compendium.

• markdown/figures is for figures that are ready to be included in .Rmd reports
• output/plots take all other graphics, e.g. large PDF files with plots on multiple pages
• src home of the main R scripts

## .
## ├── README_files
## │   └── figure-gfm
## ├── data
## │   ├── processed
## │   └── raw
## │       └── archive
## ├── markdown
## │   └── img
## ├── output
## │   ├── plots
## │   ├── reports
## │   │   ├── presentations
## │   │   └── report_files
## │   │       └── figure-latex
## │   └── tables
## └── src

Data sharing

→ Which repository?

Publication and Dissemination

Transparency statement on usage of AI tools

We would like to transparently report the use of ChatGPT, a large language model trained by OpenAI, based on the GPT-3.5 architecture, for guiding the planning of our research project, as well as for providing code completion suggestions during data analysis in R. Additionally, we utilized perplexity.ai, an AI-powered tool, for literature research and brainstorming. These tools were used in combination with our own expertise and knowledge to enhance the quality and efficiency of our work.