# Standardized Processing and Analysis of Thermal Imaging Data in Animal Studies

## Documentation for package ‘BioThermR’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

aggregate_replicates | Aggregate Technical Replicates for Statistical Rigor
analyze_thermal_stats | Calculate Comprehensive Thermal Statistics
assess_replicates | Assess replicate consistency and repeatability
as_EBImage | Convert BioThermR Object to EBImage Object
compile_batch_stats | Compile Batch Statistics into a Tidy Data Frame
correlate_thermal_traits | Pairwise Correlation Analysis for Thermal and External Traits
create_BioThermR | Create BioThermR Object from Data
from_EBImage | Import EBImage Object into BioThermR
load_biothermr | Load BioThermR Data from Disk
merge_clinical_data | Merge Thermal Stats with Clinical Data
plot_roi_overlap | Visualize ROI Overlap and Dice Coefficient
plot_thermal_3d | Interactive 3D Thermal Surface Plot
plot_thermal_cloud | Generate a "Thermal Cloud" Visualization (Phyllotaxis Layout)
plot_thermal_density | Visualize Temperature Distribution (Density Plot)
plot_thermal_heatmap | Visualize Thermal Matrix as 2D Heatmap
plot_thermal_montage | Create a Gap-Free Thermal Image Montage
read_thermal_batch | Batch Read .raw Files
read_thermal_flir | Read FLIR Radiometric JPG File
read_thermal_raw | Read a Single .raw Thermal Image File
roi_filter_interactive | Interactive ROI Selector with Denoising (Shiny App)
roi_filter_threshold | Filter Thermal Image by Temperature Thresholds
roi_segment_ebimage | Automated ROI Segmentation via EBImage
save_biothermr | Save BioThermR Data Objects to Disk
viz_cor_heatmap | Visualize Thermal Correlation Heatmap
viz_cor_scatter | Visualize Correlation Scatter Plot
viz_thermal_barplot | Generate Publication-Ready Comparative Barplots
viz_thermal_boxplot | Generate Publication-Ready Comparative Boxplots
viz_thermal_montage2 | Create a Thermal Image Montage