- chronobiome.sh
- Shell script, runs the scripts below
- install.R
- Installs necessary R dependencies
- Saves record of installation with checkpoint package
- Outputs:
- session.info.txt
- Process_Activity_Communication_BP.R
- Assigns common hour/subject index to all datapoints in activity, communication, blood pressure/HR, and energy data
- Transforms activity and communication variables to improve normality
- Outputs:
- transformed.community.activity.csv
- community.activity.csv
- heartrate.bp.csv
- energy.csv
- PCAPlot.R
- Performs PCA on combined activity and communication data across all 4 months
- Plots activity and communication PCA, and plots metabolomic and microbiomic PCAs performed by Seth Rhodes
- Outputs:
- Act_Com_PCAPlotAll.eps
- Act_Com_PCAPlot_48.eps
- Facets_Act_Com_PC2PC3.eps
- Facets_Act_Com_PC1PC3.eps
- Facets_Act_Com_PC2PC3.eps
- Saliva_Metabs_PCA.eps
- Saliva_Microbes_PCA.eps
- Plasma_Proteins_PCA.eps
- Plasma_Metabs_PCA.eps
- Macronutrients.eps
- Variance_Explained_WithEnergy.eps
- Variance_Correlation_Plot.R
- Generates R-squared (variability explained) heatmaps for activity & communication variables for all 4 months and for activity, communication, and blood pressure / heart rate variables
- Generates .pdf of scatterplots for each activity, communication, energy, and blood pressure/heartrate variable against each other
- Outputs:
- HCR001_Variance.4months.eps
- HCR003_Variance.4months.eps
- HCR004_Variance.4months.eps
- HCR006_Variance.4months.eps
- HCR008_Variance.4months.eps
- HCR009_Variance.4months.eps
- Variability.Activity.Communication.eps
- HCR001_Variance.4months_withEnergy
- HCR003_Variance.4months_withEnergy
- HCR004_Variance.4months_withEnergy
- HCR006_Variance.4months_withEnergy
- HCR008_Variance.4months_withEnergy
- HCR009_Variance.4months_withEnergy
- Variability.Activity.Communication_WithEnergy.eps
- HCR001_Variance_BothVisits
- HCR003_Variance_BothVisits
- HCR004_Variance_BothVisits
- HCR006_Variance_BothVisits
- HCR008_Variance_BothVisits
- HCR009_Variance_BothVisits
- HCR001_Variance_visit1
- HCR003_Variance_visit1
- HCR004_Variance_visit1
- HCR006_Variance_visit1
- HCR008_Variance_visit1
- HCR009_Variance_visit1
- HCR001_Variance_visit2
- HCR003_Variance_visit2
- HCR004_Variance_visit2
- HCR006_Variance_visit2
- HCR009_Variance_visit2