Dataset: Imaging Pulse Amplitude Modulator Fluorometer Data 2016
Deployment: Muller_Looe_Key_Reef_Acropora

Data Processing: 
We derived four key parameters from the IPAM photophysiology data set: maximum yield (mY), maximum electron transport rate (mETR), the irradiance at which maximum ETR is reached (mPAR), and the initial slope of the ETR curve (alpha). Only mY was transformed, using a skewed and heavy-tailed LambertWxN back-transform to induce normality, though the lower and upper tails still remain heavier and lighter than the normal distribution respectively. 
PAM dataset parameters: Maximum electron transport rate (mETR) was estimated using a linear search algorithm that used the slopes between adjacent (PAR, ETR) data points to determine the first local critical point (maximum or plateau). The algorithm first searches for three data points between which the slope changes sign. If no sign change is detected, the algorithm then looks for largest set of two data points between which the slope is less than a user defined threshold (default is 0.1). In the former case, the middle point is chosen as the (mPAR, mETR) coordinate, while in the later case the second endpoint is used. If neither search yields a solution, the threshold is increased by 0.01 and the two linear searches are repeated, until a solution is found. The slope alpha is calculated with a similar algorithm that searches all PAR levels x such that min(PAR) = 55 < x < mPAR for pairs of points between which the ratio of the local slope to the initial slope (slope between (0,0) and first non-zero datapoint) is less than a user defined threshold (default is 0.1). If not solution is found, the threshold is increased by 0.01 and the search is repeated. Once a pair of points i and i+1 have been identified, all data points with PAR levels less than that of point i are used to calculate the slope.  If the threshold increases to greater than 0.25, the algorithm terminates by returning the slope of all points with PAR < mPAR. Both algorithms return NA when given zero vectors and are both implemented in R. 

BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* alpha values rounded to three decimal places