Dataset: coral colony size
Deployment: Donahue_2014

In each photoquadrat, every colony (defined as contiguous coral tissue) was traced and measured using Adobe Photoshop CS5.1 (the scale bar was set for each image). Individual colonies were named and tracked from year to year, and we used a custom JavaScript to export these measurements from Photoshop. For QA/QC, we flagged and checked colonies with unusual perimeter to area ratio. Substantial further analysis of growth, mortality, fission, and fusion rates flagged anomalous colonies, which we checked and retraced or relabeled as necessary. The primary source of error in these measurements comes from parallax when the camera angle changes slightly from year to year; as a percent of area, this error is larger for smaller colonies.

Colony numbering code methodology: A distinct colony code was assigned. It applies to each physiologically distinct colony in the quadrat. Individual colonies of each species in each quadrat were numbered starting from 01. A physiologically distinct colony retained the same colony number across all years. If a colony recruited after the first year, the next number in the series would be used. In colonies that underwent fission, the largest colony retained the original number and any smaller colonies resulting from the fission event were given the same number as the parent colony (largest fragment) with the addition of a lowercase letter starting from 'a'. If a colony assigned a number/letter combination underwent fission, resulting colonies were given the same name as the parent with a second letter added to the end of the name. For instance, if colony 01 underwent fission and made one smaller colony, the larger colony would continue with the name 01 and the smaller colony would be named 01a. If, in a subsequent year, colony 01a underwent fission and made one smaller colony, the larger colony would retain the name 01a and the smaller colony would be named 01aa.

Each year, every colony was assigned a fate observed between year t and year t-1. D = death, I = fission (one colony splits into two or more colonies), M = fission and fusion (one colony undergoes both fission and fusion in one year), N = new (code given to the measurement of a colony in the first year of the project), R = recruit (new, small colony), S = survival (colony persists from year t to t+1), U = fusion (two physiologically distinct colonies merge into a single colony and take the name of the larger colony), X = phoenix (colony was present in year t-1, not visible in year t, but reappeared in year t+1).

When two colonies fused together, the largest colony retains its colony number and the smaller colonies (now a part of this larger colony) are not recorded in subsequent years.  Fusee is the name of the large colony with which the smaller colony fused that year.

References:

Brown, E.K., Cox, E., Jokiel, P.L., Rodgers, S.K., Smith, W.R., Tissot, B., Coles, S.L., and Hultquist, J. (2004) Development of Benthic Sampling Methods for the Coral Reef Assessment and Monitoring Program (CRAMP) in Hawai'i. Pacific Science 58:2 pp. 145-158 doi: 10.1353/psc.2004.0013

Jokiel, P.L., Brown, E.K., Friedlander, A., Rodgers, S.K., and Smith, W.R. (2004) Hawai'i Coral Reef Assessment and Monitoring Program: Spatial Patterns and Temporal Dynamics in Reef Coral Communities. Pacific Science 58:2, pp. 159-174 doi: 10.1353/psc.2004.0018