CBASSED50

Overview

R package to process CBASS-derived PAM data. Minimal requirements are PAM data (or data from any other continuous variable that changes with temperature, e.g. relative bleaching scores) from 4 samples (e.g., nubbins) subjected to 4 temperature profiles of at least 2 colonies from 1 coral species from 1 site. Please refer to the following papers for in-depth information regarding CBASS acute thermal stress assays, ED50 thermal thresholds, etc.

Voolstra, C. R., Buitrago-López, C., Perna, G., Cárdenas, A., Hume, B. C. C., Rädecker, N., & Barshis, D. J. (2020). Standardized Short-Term Acute Heat Stress Assays Resolve Historical Differences in Coral Thermotolerance across Microhabitat Reef Sites. Global Change Biology 26 (8). Wiley: 4328–43. https://doi.org/10.1111/gcb.15148

Evensen, N. R., Parker, K. E., Oliver, T. A., Palumbi, S. R., Logan, C. A., Ryan, J. S., Klepac, C. N., Perna, G., Warner, M. E., Voolstra, C. R., & Barshis, D. J. (2023). The Coral Bleaching Automated Stress System (CBASS): A low‐cost, portable system for standardized empirical assessments of coral thermal limits. Limnology and Oceanography, Methods / ASLO, 21(7), 421--434. https://doi.org/10.1002/lom3.10555

Voolstra, C. R., Alderdice, R., Colin, L., Staab, S., Apprill, A., and Raina, J.-R. (2025). Standardized Methods to Assess the Impacts of Thermal Stress on Coral Reef Marine Life. Annual Review of Marine Science 17 (1). Annual Reviews: 193–226. https://doi.org/10.1146/annurev-marine-032223-024511

Get Started

Install CBASSED50

Install the current version of CBASSED50 from CRAN:

r install.packages("CBASSED50")

Demo File

Download CBASSED50_tutorial.qmd. GitHub allows you to do this directly from the web interface:

This is a document with a notebook interface that contains explanatory text together with the code. Open the document in RStudio and explore it.

RStudio will offer to install missing packages required for running the CBASSED50_tutorial.qmd, please do this:

Input file format

An example input file can be downloaded from this repository.

The R package contains an internal dataset. Alternativley, you can run demo using your own inputfile for processing (CSV or XLSX format).

The following columns are mandatory:

• Project free text field; we recommend to use a unique identifier for your project, e.g. 202211_DEU_Zugspitze-Feldberg (YYYYMMDDCountrySite).
• Date format YYYYMMDD.
• Country format 3-letter ISO country code.
• Latitude and Longitude in decimal degrees (e.g., 47.42123, 10.98632).
• Site free text field (e.g., name of the reef).
• Condition Descriptor to set apart samples from the same species and site, e.g. probiotic treatment vs. control; nursery vs. wild; diseased vs. healthy; can be used to designate experimental treatments besides heat stress. If no other treatments, write 'not available'.
• Species free text field; we recommend providing the name of the coral as accurate as possible, e.g. Porites lutea or Porites sp.
• Genotype free text field; denotes samples/fragments/nubbins from distinct colonies in a given dataset; we recommend to use integers, i.e. 1, 2, 3, 4, 5, etc.
• Temperature CBASS treatment temperatures; must be ≥ 4 different temperatures; must be integer; e.g. 30, 33, 36, 39. Typical CBASS temperature ranges are average summer mean MMM, MMM+3°C, MMM+6°C, MMM+9°C).
• Timepoint timepoint of PAM measurements in minutes from start of the thermal cycling profile; typically: 420 (7 hours after start, i.e., after ramping up, heat-hold, ramping down) or 1080 (18 hours after start, i.e. at the end of the CBASS thermal cycling profile); differences in ED50s between timepoints 420 and 1080 may be indicative of resilience/recovery (if 1080 ED50 > 420 ED50) or collapse (if 1080 ED50 < 420 ED50).
• Pam_value Fv/Fm value of a given sample (format: ≥0 and ≤1, e.g. 0.387); note that technically any continuous variable can be used for ED50 calculation (e.g., coral whitening; black/white pixel intensity; etc.) and be provided in this column.

This is how your input file should look like:

| Project | Date | Country | Latitude | Longitude | Site | Condition | Species | Genotype | Temperature | Timepoint | Pamvalue | |-------------------------------|----------|---------|----------|-----------|-----------|-----------|-------------------|----------|-------------|-----------|-----------| | 202211DEUZugspitze-Feldberg | 20221114 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 1 | 29 | 420 | 0.636 | | 202211DEUZugspitze-Feldberg | 20221114 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 2 | 29 | 420 | 0.615 | | 202211DEUZugspitze-Feldberg | 20221114 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 3 | 29 | 420 | 0.64 | | 202211DEUZugspitze-Feldberg | 20221114 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 4 | 29 | 420 | 0.669 | | 202211DEUZugspitze-Feldberg | 20221114 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 5 | 29 | 420 | 0.64 | | 202211DEUZugspitze-Feldberg | 20221115 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 6 | 29 | 420 | 0.664 | | 202211DEUZugspitze-Feldberg | 20221115 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 7 | 29 | 420 | 0.638 | | 202211DEUZugspitze-Feldberg | 20221115 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 8 | 29 | 420 | 0.685 | | 202211DEU_Zugspitze-Feldberg | 20221115 | DEU | 47.42123 | 10.98632 | Zugspitze | Nursery | Acropora germania | 9 | 29 | 420 | 0.658 |

Contributing

If you want to contribute to a project and make it better, your help is very welcome.

You can always report an issue or fork this repository, implement/fix your feature, and create a pull request.

FAQ

In Ubuntu, you may face the issue with R package dependencies installation. To fix this, you should install missing system libraries first.

Error installing 'devtools'

commandline sudo apt-get install \ libssl-dev \ libfontconfig1-dev \ libxml2-dev \ libharfbuzz-dev \ libfribidi-dev \ libcurl4-openssl-dev \ libfreetype6-dev \ libpng-dev \ libtiff5-dev \ libjpeg-dev

Error installing 'mvtnorm'

commandline sudo apt-get install gfortran liblapack-dev libblas-dev

Error installing 'nloptr'

commandline sudo apt-get install cmake

Getting Help

You can always report the GitHub issue or email the current maintainer: Luigi Colin.

Cite Us

If you use this software, please cite it as below:

commandline Iakovleva, Y., Colin, L., & Voolstra, C. R. (2025). CBASSED50: R package to process CBASS-derived PAM data. Zenodo. https://doi.org/10.5281/zenodo.8370644.