Initial data analysis in the context of regression modeling

Repository for IDA for regression modeling

The focus of this report is to provide examples on conducting initial data analysis in a reproducible manner in the context of intended regression analyses.

Project Description

Objective: Develop initial data analysis plan (IDAP) and provide sample reports for IDA before executing the statistical analysis plan (SAP) for regression modeling.

Six steps of the IDA framework [Ref 1] are

1. Meta data set-up
2. Data cleaning
3. Data screening
4. Initial data reporting
5. Updating/refining the statistical analysis plan
6. Reporting of IDA findings in research papers [Ref 2]

For our objective, we assume that meta data exist and data cleaning has already been done. We created hypothetical statistical analyses plans for each of the data sets.

Project Outcomes

1. Sample IDA plans and IDA reports to illustrate data screening and initial reporting (steps 3 and 4 of the IDA framework)
2. Recommendations for numerical and graphical summaries (step 3 of IDA framework)
3. Explanation and elaboration of potential consequences to the SAP as a result of IDA findings (step 5 of IDA framework)
4. Recommendations for reporting of IDA for regression analyses (step 6 of IDA framework)
5. Manuscript with scope of regression model, generic IDA strategy, examples with IDA discoveries and consequences

Structure

• main - General report files
• data-raw - Repository for original data sets and their data dictionaries
• data - Repository for analysis data sets
• R - R functions for data visualization and transformations used in the R markdown files
• docs - report in website
• report - report in MS word format

Data set specifications and tracker

https://docs.google.com/spreadsheets/d/1Ft5eyenvDnMBoLvJmcBaklfrYcwyW-rkt-ivIkaphdA/edit?usp=sharing

References

Initial data analysis

[1] Huebner M, le Cessie S, Schmidt CO, Vach W . A contemporary conceptual framework for initial data analysis. Observational Studies 2018; 4: 171-192. Link

[2] Huebner M, Vach W, le Cessie S, Schmidt C, Lusa L. Hidden Analyses: a review of reporting practice and recommendations for more transparent reporting of initial data analyses. BMC Med Res Meth 2020; 20:61 Link

Bacteremia data set

[3] Ratzinger F, Dedeyan M, Rammerstorfer M, Perkmann T, Burgmann H, et al. (2014) A Risk Prediction Model for Screening Bacteremic Patients: A Cross Sectional Study. PLoS ONE 9(9): e106765. doi:10.1371/journal.pone.0106765

Abbreviations

SAP - statistical analysis plan
IDA - initial data analysis
IDAP - initial data analysis plan

Funding

None.
Contributors are from the STRATOS Initiative.

-TG2: Selection of variables and functional forms in multivariable analyses.
-TG3: Initial data analysis

Authors

Mark Baillie
Novartis,
Email: mark.baillie@novartis.com

Georg Heinze
Medical University, Vienna, Austria
Email: georg.heinze@meduniwien.ac.at

Marianne Huebner
Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
Email: huebner@msu.edu