cbass_dataset: CBASS Dataset

In CBASSED50: Process CBASS-Derived PAM Data

CBASS Dataset

Description

A dataset containing example simulated experimental data.

Usage

data(cbass_dataset)

Format

A data frame with 240 observations and 9 variables:

Project

Name to identify the project/experiment.

Latitude

Latitude of the observation collection site in decimal format.

Longitude

Longitude of the observation collection site in decimal format.

Date

Date of the observation in YYYYMMDD format.

Country

Country of the observation in 3-letter ISO country code format.

Site

Site of the observation, 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

Species of the observation. We recommend providing the name of the coral as accurate as possible, e.g. Porites lutea or Porites sp.

Genotype

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 \ge 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: \ge0 and \le1, 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.

Details

This dataset provides experimental data with various attributes for demonstration and testing purposes.

Examples

# Load the sample dataset
data(cbass_dataset)
head(cbass_dataset)

CBASSED50 documentation built on June 8, 2025, 10:27 a.m.