Sleep diary analysis

R analyses of my long-term sleep diary and bedroom sensor measurements. The project examines how coffee, bedtime, exercise, stress, illness, and the sleep environment relate to sleep within one person.

Each focused report produces a main figure, supporting figures, and model summaries. Coffee reports examine previous-night sleep, 3- and 5-night sleep history, and medication. The magnesium report uses the proposed experiment period, starting one day before the first recorded use.

Project layout

• data/raw/: private input files; never commit these data.
• data/derived/: intermediate datasets generated during analysis.
• Numbered scripts under scripts/: ordered data preparation and core analyses; lag analysis is separate.
• scripts/run_core_pipeline.R and scripts/run_variable_specific_reports.R: analysis entry points.
• scripts/variable_specific/: focused reports for individual variables or themes.
• scripts/helpers/: shared validation, date, and analysis helpers.
• tests/: synthetic-data checks for the pipeline and reports.
• ANALYSIS_NOTES.md: analysis decisions, exclusions, and interpretation notes.
• outputs/figures/core/: figures from the numbered core pipeline.
• outputs/figures/variable_specific/: figures from focused reports.
• outputs/synthetic_test_previews/: temporary previews produced by report tests.
• archive/: retired scripts; not part of the analysis workflow.

The root-level figures/ directory contains legacy generated images only; active scripts now save figures under outputs/figures/.

Run analyses

Open Uni.Rproj. Install tidyverse, readxl, here, fixest, patchwork, gridExtra, and zoo. Place the private input files in data/raw/: loki.xlsx and, for environmental analyses, mittari_kaikki.xlsx.

Run the core pipeline or all focused reports with:

source("scripts/run_core_pipeline.R")
source("scripts/run_variable_specific_reports.R")

To run one focused report, source its script directly, for example scripts/variable_specific/coffee.R. Automated checks use synthetic data; private diary and sensor files are not included in the repository.

Interpretation

The diary date identifies the exposure day and the night starting that day. Sensor nights run from 21:00 to 08:00 in Helsinki time. Unsupported values exclude the entire diary row and are reported during loading. Zero-hour sleep is valid. Models account for calendar timing and serial dependence where appropriate; observational associations do not establish causation.

See analysis notes for coding, exclusions, and model assumptions.

Johannes Piipponen