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 CBASS method paper for in-depth information regarding CBASS acute thermal stress assays, ED50 thermal thresholds, etc.

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

Get Started

Updates

• Release 0.1.5: Added ED5 and ED95 to functions and minor documentation updates

Demo File

To get started download CBASSED50_demo.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_demo.qmd, please do this:

Install CBASSED50

You can install the latest version of CBASSED50 from GitHub:

if(!require(devtools)){
   install.packages("devtools")
}

devtools::install_github("reefgenomics/[email protected]", force=TRUE)

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:

• Date format YYYYMMDD.
• Country format 3-letter ISO country code.
• 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 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:

Date	Country	Site	Condition	Species	Genotype	Temperature	Timepoint	PAM
20221113	DEU	Zugspitze	Wild	Acropora germania	1	29	420	0.608
20221113	DEU	Zugspitze	Wild	Acropora germania	2	29	420	0.651
20221113	DEU	Zugspitze	Wild	Acropora germania	3	29	420	0.558
20221113	DEU	Zugspitze	Wild	Acropora germania	4	29	420	0.635
20221113	DEU	Zugspitze	Wild	Acropora germania	5	29	420	0.618
20221114	DEU	Zugspitze	Nursery	Acropora germania	1	29	420	0.636
20221114	DEU	Zugspitze	Nursery	Acropora germania	2	29	420	0.615
20221114	DEU	Zugspitze	Nursery	Acropora germania	3	29	420	0.64
20221114	DEU	Zugspitze	Nursery	Acropora germania	4	29	420	0.669
20221114	DEU	Zugspitze	Nursery	Acropora germania	5	29	420	0.64

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'

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'

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

Error installing 'nloptr'

sudo apt-get install cmake

Getting Help

You can always report the GitHub issue or email the current maintainer: [email protected].

Cite Us

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

Yulia Iakovleva & Christian R Voolstra. (2023).
CBASSED50: R package to process CBASS-derived PAM data.
Zenodo. https://doi.org/10.5281/zenodo.8370644.