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Uncertainty assessment of the moderate resolution imaging spectroradiometer (MODIS) leaf area index (LAI) and the fraction of photosynthetically active radiation absorbed by vegetation (FPAR) retrieval algorithm can provide a scientific basis for the usage and improvement of this widely-used product. Previous evaluations generally depended on the intercomparison with other datasets as well as direct validation using ground measurements, which mix the uncertainties from the model, inputs, and assessment method. In this study, we adopted the evaluation method based on three-dimensional radiative transfer model (3D RTM) simulations, which helps to separate model uncertainty and other factors. We used the well-validated 3D RTM LESS (large-scale remote sensing data and image simulation framework) for a grassland scene simulation and calculated bidirectional reflectance factors (BRFs) as inputs for the LAI/FPAR retrieval. The dependency between LAI/FPAR truth and model estimation serves as the algorithm uncertainty indicator. This paper analyzed the LAI/FPAR uncertainty caused by inherent model uncertainty, input uncertainty (BRF and biome classification), clumping effect, and scale dependency. We found that the uncertainties of different algorithm paths vary greatly (−6.61% and +84.85% bias for main and backup algorithm, respectively) and the “hotspot” geometry results in greatest retrieval uncertainty. For the input uncertainty, the BRF of the near-infrared (NIR) band has greater impacts than that of the red band, and the biome misclassification also leads to nonnegligible LAI/FPAR bias. Moreover, the clumping effect leads to a significant LAI underestimation (−0.846 and −0.525 LAI difference for two clumping types), but the scale dependency (pixel size ranges from 100 m to 1000 m) has little impact on LAI/FPAR uncertainty. Overall, this study provides a new perspective on the evaluation of LAI/FPAR retrieval algorithms.

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