This repository includes data and analysis scripts to accompany: Patterns of bleaching and recovery of Montipora capitata in Kāneʻohe Bay, Hawaiʻi, USA Authors: Ross Cunning, Raphael Ritson-Williams, Ruth D. Gates Journal: Marine Ecology Progress Series Link: doi:10.3354/meps11733 Description: This work analyzes bleaching and recovery dynamics of Symbiodinium in Montipora capitata corals following a thermal stress event in Kāneʻohe Bay, Oʻahu (Hawaiʻi, USA) in late 2014. Corals were tagged and resampled 6 times between October 2014 and May 2015, and extracted DNA from each sample was used to measure symbiont to host cell ratios for both clade C and clade D Symbiodinium. Contents: Scripts: setup.R: R script that imports and quality controls qPCR data in preparation for analysis. analysis.R: R script for all data analyses and figures presented in the manuscript. suppmethods.R: R script for analyses presented in the Supplement (fluorescence normalization, copy number estimation, ITS2 analysis, environmental data analysis). ITS2_analysis.txt: Shell script for bioinformatic analysis of Symbiodinium ITS2 data. Data: data/coast_n83.shp/: Hawaii coastline shapefile, originally downloaded from here data/bleachedpair.png: Photograph of a bleached and non-bleached pair of M. capitata colonies used in Figure 1 (photo credit: R. Ritson-Williams). data/qPCR/: Directory containing .csv files of symbiont and host quantification data exported directly from Applied Biosystems StepOnePlus Software qPCR platform. data/ITS2/: Directory containing ITS2 sequence data .fastq files (raw data) and OTU tables (final result of bioinformatic analysis). Note that intermediate/temporary data files in bioinformatic analysis are not included in the repository. data/supp/: Directory containing data for fluorescence normalization and gene copy number estimation, presented in the Supplement. data/temp_light/: Directory containing temperature and light data recorded during the study, originally downloaded from Zenodo. Links to Zenodo data repositories: Temperature data: doi:10.5281/zenodo.53226 Light data: doi:10.5281/zenodo.53227 Output: output/: Directory containing the figures and tables produced by the analysis scripts and presented in the manuscript and the Supplement.