R. Cunning, N. Vaughan, P. Gillette, T. R. Capo, J. L. Maté, and A. C. Baker. 2015. Dynamic regulation of partner abundance mediates response of reef coral symbioses to environmental change. Ecology 96:1411–1420. http://dx.doi.org/10.1890/14-0449.1


Supplement

Symbiont population dynamics data set and cost or benefit model implementation in R.
Ecological Archives E096-125-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

Ross Cunning
Department of Marine Biology and Ecology
Rosenstiel School of Marine and Atmospheric Science
University of Miami
Miami, FL USA
Email: ross.cunning@gmail.com

Nathan Vaughan
Department of Marine Biology and Ecology
Rosenstiel School of Marine and Atmospheric Science
University of Miami
Miami, FL USA
E-mail: nvaughan@rsmas.miami.edu

Philip Gillette
Department of Marine Biology and Ecology
Rosenstiel School of Marine and Atmospheric Science
University of Miami
Miami, FL USA

Tom R. Capo
Department of Marine Biology and Ecology
Rosenstiel School of Marine and Atmospheric Science
University of Miami
Miami, FL USA

Juan L. Maté
Smithsonian Tropical Research Institute
Panama, Republic of Panama

Andrew C. Baker
Department of Marine Biology and Ecology
Rosenstiel School of Marine and Atmospheric Science
University of Miami
Miami, FL USA


File list

Pdam_dataset.csv (MD5: f339fb38a32a02c75d8af0b2658d146d)

Pdam_metadata.csv (MD5: 50a904eedb36ce85111a3e674d09a449)

Pdam_fitModel.R (MD5: c8104a06f0574a6eb4ffb2ddb1c08b19)

Pdam_runModel.R (MD5: 6860a90a42c2fc5bb356faed79afa874)

Description

These supplements are designed to allow the reader to reproduce the cost or benefit model implemented in this study using the statistical package R. The first two files contain the symbiont population dynamics data set (Pdam_dataset.csv) and environmental metadata (Pdam_metadata.csv) from the two experiments. The R code is divided into two files, one which fits the model structure to the data by a gradient search routine that optimizes scaling parameters (Pdam_fitModel.R), and one which implements a fitted version of the model and generates all of the figures presented in the manuscript (Pdam_runModel.R). This code will allow users to adjust and test the cost-benefit model structure and its output.

Pdam_dataset.csv -- Data set used in this study

Experiment: Classifies data from experiment 1 or 2
Time: Time point within each experiment
Colony: Nominal coral colony ID number from which sample was taken
Sym: The dominant Symbiodinium clade in the coral colony
Total: The total symbiont to host cell ratio, calculated as the sum of clade C and D symbiont to host cell ratios based on qPCR assay results
logTotal: Logarithm (base 10) of the total symbiont to host cell ratio

Pdam_metadata.csv -- Environmental metadata from this study

Experiment: Classifies data from experiment 1 or 2
Time: Time point within each experiment
i mean: Irradiance mean for time point (mol m-2 d-1)
i se: Irradiance SEM for time point (mol m-2 d-1)
t mean: Temperature mean for time point (°C)
t se: Temperature SEM for time point (°C)

Pdam_fitModel.R -- R code for fitting model scaling parameters

Pdam_runModel.R -- R code for running fitted model and generating the figures presented in this manuscript