Analyses to test a site selection framework for seeded coral deployments. We test the framework proposed by Humanes et al. (2025) using spat survival data from deployments occurring between 2021 and 2023.
There should be three folders: data (contains the raw data), scripts (contains two R scripts, one that contains the functions -functions.R- and one that runs the analyses and generates the figures - analyses.R), and outputs (where the plots will be saved).
The Data folder has two files: environment.csv and survival.csv, which contain the environmental factors associated to the deployment sites and the spat survival data, respectively.
The environment.csv has one deployment site per row and includes the following variables:
- Lead Researcher- researcher leading the coral seeding deployment
- Reef- name of reef where the coral spat where deployed
- Site - unique identification for each deployment site
- Longitude- site longitude
- Latitude - site latitude
- Deployment.year - years in which the spat were deployed
- Deployment.date - date of deployment
- Census.date - date of spat survival census
- Deployment.duration - number of days between deployment and census
- Species - name of species deployed at the site
- Deployment.method - type of attachment to the substratum (fixed directly, freely deployed or tethered)
- Sedimentation - sedimentation category
- Rugosity - categorical measurement of rugosity
- Slope - slope of the site obtained from bathymetry maps
- Water.velocity - estimates of mean horizontal water velocity at the seabed (in m s-1) from Callaghan et al. 2023
- Consolidated.substrate - estimate of the percentage of hard substrate at the site
- Hard.coral - estimate of the percentage of hard coral cover at the site
- Macroalgae - estimate of the percentage of macroalgal cover at the site
- Free.space - estimate of the percentage of free consolidated substrate at the site
- score.X - score assigned to each (X) environmental factor following Humanes et al. (2025)
- Reference - study from which the deployment information was obtained
The survival.csv has survival data for one seeding unit and species combination per row and includes the following variables:
- Reef- name of reef where the coral spat where deployed
- Site - unique identification for each deployment site
- Deployment.year - years in which the spat were deployed
- Deployment.duration - number of days between deployment and census
- Species - species for which the survival was recorded
- n_trial - number of tabs/plugs with spat from at the time of deployment
- n_surv - number of tabs/plugs with living spat at the time of census
- Lead Researcher- researcher leading the coral seeding deployment
Humanes, A., Fabricius, K.E., Ferrari, R. & Ortiz, J.C. (2025) Ecological quantitative criteria for reef site prioritisation to maximise survivorship and growth of outplanted corals. Journal of Environmental Management, 392, 126585.