Analysis-of-Fate-Tracked-Montastraea-cavernosa-Colonies
3D model generation & analysis protocols and statistical analysis pipeline
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version: April 29, 2021
This repository contains protocols, scripts, and data associated with the 3D model generation and analysis of fate-tracked Montastraea cavernosa colonies within Broward County, FL. Found in Combs IR, Studivan MS, Eckert RJ, Voss JD. 2021. Quantifying the impacts of stony coral tissue loss disease on corals in Southeast Florida through surveys and 3D photogrammetry
Analysis and walkthroughs accompanying this repository:
3D Model Analysis
Repository contents:
- code/
- model.analysis.Rmd – analysis of 3D models Rmarkdown
- index.html – colony fate tracking statistical analysis webpage
- fateTracking.Rproj – R project file
- data/
- S2_Dataset.csv – surface Area datasheet for importing into R
- figures/
- Fig1.png – figure of coral colony, 3d model, and typical SCTLD manifestations
- Fig2.eps – map of study sites
- Fig2.png – map of study sites
- Fig4.png – box plot of tissue areas through time
- Fig4.eps – box plot of tissue areas through time
- Fig5.png – box plot and correlation plot of tissue loss metrics
- Fig5.eps – box plot and correlation plot of tissue loss metrics
- Fig6.png – Correlation plot of Disease lesion area and total colony area
-Fig6.eps – Correlation plot of Disease lesion area and total colony area
- protocols/
- 3D_modeling_README – protocol for filming, rendering, and analyzing 3D Models
- scripts/
- ffmpeg.py – batch extract video files using ffmpeg (protocol found in 3D_modeling_README)
- tables/
- Table2.docx – table of Friedman’s test and pairwise comparison outputs for surface area measurements
- TableS1.docx – table of Kruskal-Wallis and pairwise comparison outputs for lesion count and site
- gitignore – .gitignore
- README.md – Repository readme document