# Readme: benthic-reefs-and-fish

## Data pedagological context 

These datasets are of benthic and fish surveys at 49 sites. They are useful for teaching spatial ecological analyses, data wrangling, ecological community analysis (multivariate analysis) and GLMs with count data. 

## Survey methodology

Surveys were conducted in benthic ecosystems around mangroves in Kia Province, Solomon Islands. 49 sites were surveyed for benthic organisms and juveniles of two species of fish (*Bolbometopon muricatum* and *Cheilinus undulatus*). All survyes were of standard length. 

The benthic composition data was collected with the point intersect transect method. Divers swam along transects. There were several transects per site.  Along each transect they dropped points and recorded the type of benthic organism (in categories) on that point. Percentage cover for one organism type can then be calculated as the number of points with that organism divided by the total number of points on that transect.

Transects can be averaged to give a single value for each site. 

One fish survey was done at each of the 49 sites. The focus was on finding and counting juveniles of the two key species. 

## Attribution

For reef fish data please attribute: 

[Hamilton RJ, Almany GR, Brown CJ, Pita J, Peterson NA, Choat JH. Logging degrades nursery habitat for an iconic coral reef fish. Biological Conservation. 2017 Jun 1;210:273-80.](https://www.sciencedirect.com/science/article/pii/S0006320716310461?casa_token=BRm2hxABlI0AAAAA:eIcEV7wzDEBCuHSrjwUJ2GcBC2EsQOnWX4gZON0epKo935uaaJgQfU-qHEzbBiFA8IxKgEsKwQ)

For benthic cover data please attribute: 

[Brown, Hamilton. 2018. Estimating the footprint of pollution on coral reefs with models of species turnover. Conservation Biology. DOI: 10.1111/cobi.13079](http://onlinelibrary.wiley.com/doi/10.1111/cobi.13079/abstract)

Bibtex references are below

## Suggested lessons

Join benthic_cover.csv and benthic_variables.csv, then summarize to site level to calculate mean site cover of each habitat type. 

Multivariate community analyses with benthic habitat types. 

GLM with over-dispersed count data using variables in fish-coral-cover-sites.csv (e.g. `pres.topa ~ cb_cover`)

## Meta data 

### benthic_cover.csv

[Benthic cover survey data in long format](https://raw.githubusercontent.com/cbrown5/example-ecological-data/refs/heads/main/data/benthic-reefs-and-fish/benthic_cover.csv)


Variables
- site: Unique site IDs
- trans: transect numbers, there are multiple transects per site
- code: benthic organism code
- cover: Number of points belonging to this habitat type
- n.pts: Total number of points sampled on the transect, used to normalize `Cover` to get per cent cover. 

## benthic_variables.csv

[Database linking benthic codes to full names](https://raw.githubusercontent.com/cbrown5/example-ecological-data/refs/heads/main/data/benthic-reefs-and-fish/benthic_variables.csv)

Variables
- code: benthic organism code, matches `Code` in benthic_cover
- category: Long format name of benthic organism

## fish-coral-cover-sites.csv

![Site level covariates](https://raw.githubusercontent.com/cbrown5/example-ecological-data/refs/heads/main/data/benthic-reefs-and-fish/fish-coral-cover-sites.csv)

Variables
- site: Unique site IDs, use to join to benthic_cover.csv
- reef.ID: Unique reef ID
- pres.topa: number of Topa counted (local name for Bolbometopon)
- pres.habili: number of Habili counted (local name for Cheilinus) 
- secchi: Horizontal secchi depth (m), higher values mean the water is less turbid
- flow: Factor indicating if tidal flow was "Strong" or "Mild" at the site
- logged: Factor indicating if the site was in a region with logging "Logged" or without logging "Not logged"
- coordx: X coordinate in UTM zone 57S
- coordy: Y coordinate in UTM zone 57S
- cb_cover: Number of PIT points for branching coral cover
- soft_cover: Number of PIT points for soft coral cover
- n_pts: Number of PIT points at this site (for normalizing cover to get per cent cover)
- dist_to_logging_km: Linear distance to nearest log pond (site where logging occurs) in kilometres. 

## Bibtext references for attribution

```
@article{brown2018estimating,
  title={Estimating the footprint of pollution on coral reefs with models of species turnover},
  author={Brown, Christopher J and Hamilton, Richard J},
  journal={Conservation Biology},
  volume={32},
  number={4},
  pages={949--958},
  year={2018},
  publisher={Wiley Online Library}
}

@article{hamilton2017logging,
  title={Logging degrades nursery habitat for an iconic coral reef fish},
  author={Hamilton, Richard J and Almany, Glenn R and Brown, Christopher J and Pita, John and Peterson, Nathan A and Choat, J Howard},
  journal={Biological Conservation},
  volume={210},
  pages={273--280},
  year={2017},
  publisher={Elsevier}
}

```