# Phenology and Seasonal Ecosystem Productivity in an Amazonian Floodplain Forest
## Materials and Methods
### Flux Tower and Field Data  
Data from the flux tower have been recorded daily since October 2003 and include the following variables: GPP (\(\mu\)mol CO\({}_{2}\) m\({}^{-2}\) s\({}^{-1}\)), air temperature (Ta, \({}^{\circ}\)C), rainfall (mm), net radiation (Rn, in w m\({}^{-2}\)), latent heat (LE, in w m\({}^{-2}\)), specific humidity (q, g Kg\({}^{-1}\)), pressure (press, kPa) and vapour pressure deficit (VPD, kPa). A detailed description of the methods used in eddy covariance technique the CO\({}_{2}\) ecosystem exchange at this site is reported in [PERSON] et al. (2003) and [PERSON] (2004).  
Evapotranspiration was calculated from LE and Ta as a function of latent heat of water vaporization (\(\lambda\)) (Equation (1)).  
\[\text{ET}=\text{LE}*\lambda, \tag{1}\]  
\[\text{where }\lambda\left(\text{J kg}^{-1}\right)=10^{3}*\left(2500-2.37*\text{Ta}\right)\]  
Vapour Pressure Deficit was calculated through [PERSON] (1980) equations using a script available freely for the R language ([PERSON] 2018). The input parameters are air temperature, specific humidity, and pressure.  
Soil moisture has been measured close to the tower using FDR (frequency domain reflectometer) probes installed at four depths 0.2, 0.4, 0.8, and 1.5 m from 2004 to 2006 and from 2006 onwards, two more probes were added at 2.0 and 2.9 m depths.  
The Javaes river level record of the Barreira da Cruz station was obtained from the Agencia Nacional de Aguas (ANA) in Brazil ([[http://hidroweb.ana.gov.br](http://hidroweb.ana.gov.br)]([http://hidroweb.ana.gov.br](http://hidroweb.ana.gov.br))), from 1990 to 2017. The river level describes the flood pulse and the flood height measured at the tower base (r = 0.76, \(p<0.05\)) (Figure S1).  
We performed gap filling on night and daily CO\({}_{2}\) estimates according to the method described in [PERSON] et al. (2003). There was an underestimation of night positive CO\({}_{2}\) fluxes due to insufficient turbulent mixing. We filled each missing nighttime value from an average of all valid nighttime values (from 6 pm to 5 am) within a 5-day window. The data was replaced by the average of this 5-day window, and when this was not possible we applied windows varying 11-31 days. The correction performed in this paper involved 35% of the total night data for a friction velocity (u*) threshold of 0.19 m s\({}^{-1}\) for the rainy season and 0.17 m s\({}^{-1}\) for the dry season. Our data can be considered below the thresholds and percentage of gaps found in the literature for other sites in the Amazon region ([PERSON], 2016).  
The relationship between photosynthetically active radiation (PAR) and the observed data of NEE (net ecosystem exchange) was used for filling daytime NEE (NEE, assumed as a proxy for turbulent flux) ([PERSON], 2016; [PERSON], 2016). The hyperbolic relationship pattern between these variables included coefficients which represented the maximum photosynthetic efficiency of the canopy (a2), its yield (a3) and the mean ecosystem nocturnal respiration (a1) ([PERSON], 2016), as described in Equation (2).  
\[NEE=a1+\frac{a2*PAR}{a3+PAR} \tag{2}\]  
NEE values for PAR \(<\) 40 \(\mu\)mol CO\({}_{2}\) m\({}^{-2}\) s\({}^{-1}\) were excluded from this analysis since this condition is generally associated with invalid turbulence and abrupt changes in light levels ([PERSON], 2016). Further details are described in [PERSON] et al. (2003).