1.In forest ecosystems, many functional processes are governed by local canopy gap dynamics, caused by either natural or anthropogenic factors. Quantifying the size and spatial distribution of canopy gaps enables an improved understanding and predictive modeling of multiple environmental phenomena. For instance, knowledge of canopy gap dynamics can help us elucidate time‐integrated effects of tree mortality, regrowth and succession rates, carbon flux patterns, species heterogeneity, and three‐dimensional spacing within structurally complex forest ecosystems. 2.Airborne Laser Scanning (ALS) has emerged as a technology that is well‐suited for mapping forest canopy gaps in a wide variety of forest ecosystems and across spatial scales. New technological and algorithmic advances, including ALS remote‐sensing, coupled with optimized frameworks for data processing and detection of forest canopy gaps, are allowing an enhanced understanding of forest structure and functional processes. 3.This paper introduces ForestGapR, a cutting‐edge open source R package for forest gap analysis from canopy height models derived from ALS and other remote sensing sources. The ForestGapR package offers tools to i) automate forest canopy gap detection, ii) compute a series of gap statistics, including gap‐size frequency distributions and spatial distribution, iii) map gap dynamics (when multi‐temporal ALS data are available), and iv) convert forest canopy gaps detected into raster or vector layers as per user requirements. 4.As case studies, we run ForestGapR on ALS data collected over four different tropical forest regions worldwide. We hope this new package will enable further research towards understanding the distribution, dynamics, and role of canopy gaps not only in tropical forests, but in other forest types elsewhere.

Forest degradation is common in tropical landscapes, but estimates of the extent and duration of degradation impacts are highly uncertain. In particular, selective logging is a form of forest degradation that alters canopy structure and function, with persistent ecological impacts following forest harvest. In this study, we employed airborne laser scanning in 2012 and 2014 to estimate three-dimensional changes in the forest canopy and understory structure and aboveground biomass following reduced-impact selective logging in a site in Eastern Amazon. Also, we developed a binary classification model to distinguish intact versus logged forests. We found that canopy gap frequency was significantly higher in logged versus intact forests even after 8 years (the time span of our study). In contrast, the understory of logged areas could not be distinguished from the understory of intact forests after 6–7 years of logging activities. Measuring new gap formation between LiDAR acquisitions in 2012 and 2014, we showed rates 2 to 7 times higher in logged areas compared to intact forests. New gaps were spatially clumped with 76 to 89% of new gaps within 5 m of prior logging damage. The biomass dynamics in areas logged between the two LiDAR acquisitions was clearly detected with an average estimated loss of −4.14 ± 0.76 MgC ha⁻¹ y⁻¹. In areas recovering from logging prior to the first acquisition, we estimated biomass gains close to zero. Together, our findings unravel the magnitude and duration of delayed impacts of selective logging in forest structural attributes, confirm the high potential of airborne LiDAR multitemporal data to characterize forest degradation in the tropics, and present a novel approach to forest classification using LiDAR data.

Leaf area index (LAI) is an important parameter to describe the capacity of forests to intercept light and thus affects the microclimate and photosynthetic capacity of canopies. In general, tropical forests have a higher leaf area index and it is a challenge to estimate LAI in a forest with a very dense canopy. In this study, it is assumed that the traditional Light Detection and Ranging (LiDAR)-derived fractional vegetation cover (fCover) has weak relationship with leaf area index in a dense forest. We propose a partial least squares (PLS) regression model using the height percentile metrics derived from airborne LiDAR data to estimate the LAI of a dense forest. Ground inventory and airborne LiDAR data collected in a selectively logged tropical forest area in Eastern Amazonia are used to map LAI from the plot level to the landscape scale. The results indicate that the fCover, derived from the first return or the last return, has no significant correlations with the ground-based LAI. The PLS model evaluated by the leave-one-out validation shows that the estimated LAI is significantly correlated with the ground-based LAI with an R² of 0.58 and a root mean square error (RMSE) of 1.13. A data comparison indicates that the Moderate Resolution Imaging Spectrometer (MODIS) LAI underestimates the landscape-level LAI by about 22%. The MODIS quality control data show that in the selected tile, the cloud state is not the primary factor affecting the MODIS LAI performance; rather, the LAI from the main radiative transfer (RT) algorithm contributes much to the underestimation of the LAI in the tropical forest. In addition, the results show that the LiDAR-based LAI has a better response to the logging activities than the MODIS-based LAI, and that the leaf area reduction caused by logging is about 13%. In contrast, the MODIS-based LAI exhibits no apparent spatial correlation with the LiDAR-based LAI. It is suggested that the main algorithm of MODIS should be improved with regard to tropical forests. The significance of this study is the proposal of a framework to produce ground-based LAI using forest inventory data and determine the plot-level LAI at the airborne and satellite scale using LiDAR data.

Background: Tropical forests are critical for the global carbon budget, yet they have been threatened by deforestation and forest degradation by fire, selective logging, and fragmentation. Existing uncertainties on land cover classification and in biomass estimates hinder accurate attribution of carbon emissions to specific forest classes. In this study, we used textural metrics derived from PlanetScope images to implement a probabilistic classification framework to identify intact, logged and burned forests in three Amazonian sites. We also estimated biomass for these forest classes using airborne lidar and compared biomass uncertainties using the lidar-derived estimates only to biomass uncertainties considering the forest degradation classification as well. Results: Our classification approach reached overall accuracy of 0.86, with accuracy at individual sites varying from 0.69 to 0.93. Logged forests showed variable biomass changes, while burned forests showed an average carbon loss of 35%. We found that including uncertainty in forest degradation classification significantly increased uncertainty and decreased estimates of mean carbon density in two of the three test sites. Conclusions: Our findings indicate that the attribution of biomass changes to forest degradation classes needs to account for the uncertainty in forest degradation classification. By combining very high-resolution images with lidar data, we could attribute carbon stock changes to specific pathways of forest degradation. This approach also allows quantifying uncertainties of carbon emissions associated with forest degradation through logging and fire. Both the attribution and uncertainty quantification provide critical information for national greenhouse gas inventories.