Supplement 1. Symbiont population dynamics data set and cost or benefit model implementation in R.

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<br> Time: Time point within each experiment<br> Colony: Nominal coral colony ID number from which sample was taken<br> Sym: The dominant <i>Symbiodinium</i> clade in the coral colony<br> 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<br> 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<br> Time: Time point within each experiment<br> i mean: Irradiance mean for time point (mol m-2 d-1)<br> i se: Irradiance SEM for time point (mol m-2 d-1)<br> t mean: Temperature mean for time point (°C)<br> 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