## 3 Results
### Data-Model Comparisons and Model Adjustment
#### 3.1.3 Soil CO\({}_{2}\) Effluxes  
Measured soil CO\({}_{2}\) effluxes occasionally showed large variation between chambers, as indicated by the error bars in Figure 5a, but the seasonal cycle was clear, from a minimum of 1 g C m\({}^{-2}\) d\({}^{-1}\) in winter to a maximum of 4-6 g C m\({}^{-2}\) d\({}^{-1}\) in summer. The seasonal cycle in the measured effluxes was well reproduced by the simulated mean daily CO\({}_{2}\) efflux, as indicated by the high correlation coefficients for monthly values in Table 5c, although the PSIM module estimated CO\({}_{2}\) effluxes up to two times greater than the PnET module (Figure 5a). The PnET module substantially underestimated the mean daily soil CO\({}_{2}\) effluxes measured during 2008-2012 (significant bias in mean monthly values, M, in Table 5c) but better matched measurements in 2013-2014 (no significant bias). In contrast,  
Figure 4: Average seasonal time course of ecosystem CO\({}_{2}\) flux components for the Straits Inclosure for 1999–2007: (**a**) GPP, (**b**) TER, (**c**) NEP. Each plot shows average daily values of measured eddy covariance fluxes with simulated PnET and PSIM data. Error bars shown on every tenth eddy covariance value are 1 standard deviation of annual variation. the monthly statistics in Table 5c show that PSIM module results more closely matched 2008-2012 measurements (ME = 0.38, CD = 1.20), but significantly overestimated the smaller soil CO\({}_{2}\) effluxes measured in 2013-2014. PnET-simulated annual total soil CO\({}_{2}\) effluxes from 1999-2007 (before thinning) averaged 619 g C m\({}^{-2}\) year\({}^{-1}\) (range 546-745 g C m\({}^{-2}\) year\({}^{-1}\)), whereas equivalent PSIM-simulated effluxes averaged 1042 g C m\({}^{-2}\) year\({}^{-1}\) (range 979-1081 g C m\({}^{-2}\) year\({}^{-1}\)). The proportion of simulated annual soil CO\({}_{2}\) effluxes contributed by autotrophic respiration when using PSIM was 27.5% compared to 32.3% for PnET. For 2008-2014, averages of 547 g C m\({}^{-2}\) year\({}^{-1}\) were obtained using PnET and 1018 g C m\({}^{-2}\) year\({}^{-1}\) using PSIM, compared to a measured value of 807 g C m\({}^{-2}\) year\({}^{-1}\) (Table 6). \begin{table}
\begin{tabular}{c c c c c c c c c c} \hline \hline \multirow{2}{*}{**Year**} & \multicolumn{4}{c}{**Soil CO\({}_{2}\) (g C m\({}^{-2}\) year\({}^{-1}\))**} & \multicolumn{4}{c}{**Soil N\({}_{2}\)O (mg Nm\({}^{-2}\) year\({}^{-1}\))**} \\  & **SC** & **PnET** & **PnET** & **PSIM** & **PSIM** & **SC** & **PnET** & **PnET** & **PSIM** & **PSIM** \\ \hline Thinning: & & 0\% & 30\% & 0\% & 30\% & & 0\% & 30\% & 0\% & 30\% \\ \hline
2006 & Na & 571 & 571 & 1081 & 1081 & Na & 49.1 & 49.1 & 57.3 & 57.3 \\
2007 & Na & 561 & 629 & 1059 & 1026 & Na & 47.0 & 41.7 & 55.2 & 52.7 \\
2008 & 1015.5 & 514 & 758 & 1033 & 904 & Na & 52.6 & 56.5 & 60.3 & 61.1 \\
2009 & 697.0 & 543 & 682 & 1046 & 888 & 155.7 & 43.8 & 61.1 & 52.3 & 61.3 \\
2010 & 797.3 & 496 & 547 & 934 & 793 & 33.8 & 38.9 & 51.8 & 40.7 & 37.6 \\
2011 & 835.8 & 598 & 586 & 1078 & 926 & 15.4 & 41.4 & 51.6 & 43.9 & 37.1 \\
2012 & Na 1 & 514 & 488 & 1007 & 884 & Na 1 & 48.2 & 50.5 & 44.7 & 36.4 \\
2013 & 689.3 2 & 523 & 473 & 941 & 871 & 57.4 2 & 41.7 & 43.3 & 36.9 & 32.7 \\
2014 & Na & 638 & 554 & 1087 & 998 & Na & 55.2 & 52.1 & 51.5 & 46.1 \\ Mean & 807 & 547 & 584 & 1018 & 897 & 65.6 & 46.0 & 52.4 & 47.2 & 46.0 \\ SD & 132.6 & 52.0 & 103.0 & 61.2 & 67.3 & 62.5 & 6.2 & 5.5 & 8.0 & 12.6 \\ Difference & - & \(-\)32\% & & & & & & \(-\)30\% & \(-\)28\% & \\ \hline \hline \end{tabular}  
* \({}^{1}\) = Annual fluxes for 2012 of CO\({}_{2}\) (816.6 g C m\({}^{-2}\) year\({}^{-1}\)) and N\({}_{2}\)O (83.5 mg N m\({}^{-2}\) year\({}^{-1}\)) not included because they were measured only from Jan-Aug 2012; \({}^{2}\) = April 2013-April 2014, (Aug 2013-Aug 2014, CO\({}_{2}\) = 775.8 g C m\({}^{-2}\) year\({}^{-1}\), N\({}_{2}\)O = 52.4 mg N m\({}^{-2}\) year\({}^{-1}\); Na = Not available.  
\end{table}