Computational protocol: The “Flexi-Chamber”: A Novel Cost-Effective In Situ Respirometry Chamber for Coral Physiological Measurements

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Protocol publication

[…] Daily PN, R, and net G were each compared across species and habitats using Linear Mixed Effects (LME) models, with day as a random effect. Before model application, data was explored (as per []). Cleveland dot-plots were used to determine if there were any outliers, and boxplots and scatterplots were used to check for co-linearity. Assumptions of linearity, independence, homoscedasticity and normality were met. The model was fitted using the lme function in the nlme package in R software []. Model simplification was undertaken using ANOVA to compare models with progressively simplified fixed effects; thus ensuring correct p values []. The acceptability of the model was tested by plotting the residuals against: a) the fitted values to check for homogeneity and b) each explanatory variable in the model and dropped during model selection to check for violations of independence []. Parameter estimation in lme models was done based on Restricted Maximum Likelihood (REML). The final model applied was: CJ = α + β1* RespirometrychamberJ + εJ(4) Where C is metabolic parameter being measured, J is the day, α is the intercept, β is the slope of the respirometrychamber and εJ is the residual error. […]

Pipeline specifications

Software tools lme4, nlme
Application Mathematical modeling