# Carbon Dynamics of _Pinus palustris_ Ecosystems Following Drought
## Materials and Methods
### Data Processing  
Raw EC data were processed using EdiRe (version 1.4.3.1184; [38]), which carried out a 2-day coordinate rotation of the horizontal wind velocities to obtain turbulence statistics perpendicular to the local streamline. The covariance between turbulence and scalar concentrations was maximized through the examination of the time series at 0.1-s intervals on both sides of a fixed lag-time (in this case, \(\sim\)0.3 s). Because of the relatively short roughness lengths and uniform canopy structure at these sites, we assumed that the influence of coherent structures and low frequency effects were captured by this approach. Fluxes were calculated for half-hour intervals and then corrected for the mass transfer resulting from changes in density not accounted for by the IRGA [39; 40]. Barometric pressure data were used to correct the fluxes to 1 standard atmosphere. Flux data screening was applied to eliminate 30-min fluxes resulting from systematic errors, such as: (i) rain and condensation in the sampling path; (ii) incomplete 30-min datasets during system calibration or maintenance; (iii) poor coupling of the canopy with the external atmospheric conditions, as defined by the friction velocity, frictional velocity of wind (u*), using a threshold \(<\)0.20 m\(\cdot\)s\({}^{-1}\)[41; 42]; and (iv) excessive variation from the half-hourly mean based on an analysis of standard deviations for u, v, and w wind and CO\({}_{2}\) statistics. Quality assurance of the flux data was also maintained by examining plausibility tests (e.g., \(-\)30 \(<\) NEE \(<\)\(-\)30 \(\mu\)mol m\({}^{-2}\cdot\)s\({}^{-1}\)), stationarity criteria, and integral turbulent statistics [43; 44]. Eddy covariance measurements of NEE were estimated at a temporal resolution of one hour or less [45; 46], such that:  
\[N\!E\approx-N\!E \tag{2a}\] \[G\!P\!P\approx\!GEE\;=\;-N\!E\;+\;R_{eco} \tag{2b}\]  
where, NEP is net ecosystem production and GPP is gross primary production. GPP cannot be measured directly, but rather is estimated from the right hand terms in Equation (2b). Half hourly fluxes of NEE (\(\mu\)mol m\({}^{-2}\cdot\)s\({}^{-1}\)) were used to calculate GEE and R\({}_{eco}\) in g C m\({}^{-2}\cdot\)s\({}^{-1}\) from Equations (2a) and (2b) based on the logic provided in References [46; 47; 48]. To estimate seasonal and annual NEE, GEE, and R\({}_{eco}\) values, missing half hourly data were gap-filled using separate functions for day and night (NEEday, NEEnight). When photosynthetically active radiation (PAR) was \(\geqslant\)10 \(\mu\)mol m\({}^{-2}\cdot\)s\({}^{-1}\), daytime NEE data were gap-filled using a Michaelis-Menten approach [49]:  
\[N\!E\!E\!_{day}=\frac{\alpha\phi P_{\rm max}}{\alpha\phi+P_{\rm max}}+R_{d} \tag{3}\]  
and, when PAR was \(<\)10 \(\mu\)mol m\({}^{-2}\cdot\)s\({}^{-1}\), nighttime NEE data were gap-filled using a modification of [PERSON] and Taylor [50] approach:  
\[N\!E\!E\!_{night}\approx R_{eco}=R_{0}e^{bT_{air}} \tag{4}\]  
where, \(\alpha\) is the apparent quantum efficiency (\(-\)\(\mu\)mol CO\({}_{2}\)\(\mu\)mol quanta\({}^{-1}\)), \(\phi\) is PAR (\(\mu\)mol quanta), \(R_{d}\) is ecosystem respiration (\(\mu\)mol CO\({}_{2}\) m\({}^{-2}\cdot\)s\({}^{-1}\)), \(P_{max}\) is the maximum ecosystem CO\({}_{2}\) uptake rate (\(\mu\)mol CO\({}_{2}\) m\({}^{-2}\cdot\)s\({}^{-1}\)), \(R_{0}\) is the base respiration rate when air temperature is 0 \({}^{\circ}\)C, and \(b\) is an empirical coefficient (_i.e.,_ [PERSON]n't [PERSON]'s exponential function [51]). These functional relationships were estimated on a monthly basis to gap-fill where enough data were available. When too few observations were available to produce stable and biologically reasonable parameter estimates, equations estimated from annual data were used to gap-fill data by site. Gap-filled data accounted for 31% and 33% of daytime and 61% and 66% of nighttime values for mesic and xeric sites, respectively. Error estimation from gap-filled values of NEE was performed via bootstrap methods following [PERSON] _et al_. [18].