Temporal resolution of hydrogen peroxide (H2O2) dynamics during heat stress do not support a causative role in coral bleaching

The goal of this repository is to reproduce all analyses and figures of the paper

Title: Temporal resolution of hydrogen peroxide (H2O2) dynamics during heat stress do not support a causative role in coral bleaching

Authors: Schlotheuber M, Voolstra CR, de Beer D, Camp EF, Klatt JM, Ghilardi M, Neumüller K, Ousley S, Bejarano S

Link to open access paper: (https://link.springer.com/article/10.1007/s00338-023-02448-7)

Content

This repository is structured as follow:

• 📁data/: contains all raw and processed data and images used for Visual Bleaching Assessment (VBA).
• 📁R/: contains all the R code used to reproduce analyses and figures.
• 📁figures/: contains all figures created during the analyses.

Instructions

• Clone this repository (for those not familiar with GitHub, click on the green button Code on the project main page on GitHub and then on Download ZIP to download the entire repository, thus unzip it).

• Open the .Rproj file in RStudio or open an R session with working directory set to the root of the project.

• Reproduce the entire project by running:

# Install dependencies
devtools::install_deps()
# Run all scripts
scripts <- list.files("R/")
lapply(paste("R", scripts, sep = "/"), source)

For questions related to the data please contact Marlen Schlotheuber at marlen.schlotheuber@uni-konstanz.de. For questions related to the code please contact Mattia Ghilardi at mattia.ghilardi91@gmail.com.

Working environment

#> R version 4.1.3 (2022-03-10)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.6 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_4.1.3  magrittr_2.0.1  fastmap_1.1.0   cli_3.4.1      
#>  [5] tools_4.1.3     htmltools_0.5.5 rstudioapi_0.13 yaml_2.2.1     
#>  [9] stringi_1.7.3   rmarkdown_2.14  knitr_1.33      stringr_1.4.0  
#> [13] xfun_0.31       digest_0.6.27   rlang_1.0.6     evaluate_0.14