mmh

Code for data processing and analysis of the Multimodal Hypersensitivity project.

More details of this project and data can be found on Open Science Framework (DOI: 10.17605/OSF.IO/27KY9).

Packages, functions, and variables that were used across several scripts are located in r-prep.R

Data were processed and analyzed in the following stages:

Stage 1

Raw data were first preprocessed using the following scripts:

• sscodes-prepro.R - prepared master list of participant id numbers
• avisit-1-prepro.R - prepared assessment visit 1 data exported from REDCap
• ppt-prepro.R - prepared data from quantitative sensory testing (PPT, CPM, TS)
• auditory-eprime-prepro.R - prepared the auditory stimulation task data (behavioral)
• visual-eprime-prepro.R - prepared the visual stimulation task data (behavioral)
• screenvisit-prepo.R - prepared data from screen visit

Stage 2

After preprocessing, data were examined and explored for outliers and trends in the following scripts:

• avisit-1-explore.R - explored REDCap data from assessment 1
• ppt-explore.R - explored QST data
• vis-aud-explore.R- explored the visual and auditory tasks
• extradata-explore.R - explored questionnaire data not included in PCA

Stage 3

Data were prepared for PCA analysis by ensuring equivalent size of the dataframes and converting to wide format in the pca-data-prep.R script. Extra data used for coloring was visualized, prepared, and saved out in extradata-explore.R.

To "refresh" the data for PCA analysis, run the data-refresh.R script to compute stage 1 and stage 3 in one go. (This will not refresh "extra data").

Stage 4

Principal component analysis and inferential testing was performed using the pca-proc.R script.

Stage 5

Annual data for the ICSI (our CPP outcome measure) were pulled from Redcap using the API (api-calls.R) and preprocessed using api-prepro.R. As more participants complete their annual questionnaires, these data can be refreshed by running api-calls.R.

Later longitudinal analyses were completed using api-icsiplus-prepro.R and api-icsiplus-explore.R where pelvic pain outcome was more comprehensively modeled.

Sensory analyses were conducted in sensory-analysis.R and sensory-analysis-explore.R. Sensitivity analyses were conducted in sensitivity-analyses-proc.R.

MISC

Annual questionnaires are processed in annuals.R for a grant prep submission.