Robust ecological analysis of camera trap data labelled by a machine learning model

1. Ecological data are collected over vast geographic areas using digital sensors such as camera traps and bioacoustic recorders. Camera traps have become the standard method for surveying many terrestrial mammals and birds, but camera trap arrays often generate millions of images that are time‐consuming to label. This causes significant latency between data collection and subsequent inference, which impedes conservation at a time of ecological crisis. Machine learning algorithms have been developed to improve the speed of labelling camera trap data, but it is uncertain how the outputs of these models can be used in ecological analyses without secondary validation by a human. 2. Here, we present our approach to developing, testing and applying a machine learning model to camera trap data for the purpose of achieving fully automated ecological analyses. As a case‐study, we built a model to classify 26 Central African forest mammal and bird species (or groups). The model generalizes to new spatially and temporally independent data (n = 227 camera stations, n = 23,868 images), and outperforms humans in several respects (e.g. detecting ‘invisible’ animals). We demonstrate how ecologists can evaluate a machine learning model's precision and accuracy in an ecological context by comparing species richness, activity patterns (n = 4 species tested) and occupancy (n = 4 species tested) derived from machine learning labels with the same estimates derived from expert labels. 3. Results show that fully automated species labels can be equivalent to expert labels when calculating species richness, activity patterns (n = 4 species tested) and estimating occupancy (n = 3 of 4 species tested) in a large, completely out‐of‐sample test dataset. Simple thresholding using the Softmax values (i.e. excluding ‘uncertain’ labels) improved the model's performance when calculating activity patterns and estimating occupancy but did not improve estimates of species richness. 4. We conclude that, with adequate testing and evaluation in an ecological context, a machine learning model can generate labels for direct use in ecological analyses without the need for manual validation. We provide the user‐community with a multi‐platform, multi‐language graphical user interface that can be used to run our model offline.Additional co-authors: Cisquet Kiebou Opepa, Ross T. Pitman, Hugh S. Robinso

Pangolins in global camera trap data: Implications for ecological monitoring

Despite being heavily exploited, pangolins (Pholidota: Manidae) have been subject to limited research, resulting in a lack of reliable population estimates and standardised survey methods for the eight extant species. Camera trapping represents a unique opportunity for broad-scale collaborative species monitoring due to its largely non-discriminatory nature, which creates considerable volumes of data on a relatively wide range of species. This has the potential to shed light on the ecology of rare, cryptic and understudied taxa, with implications for conservation decision-making. We undertook a global analysis of available pangolin data from camera trapping studies across their range in Africa and Asia. Our aims were (1) to assess the utility of existing camera trapping efforts as a method for monitoring pangolin populations, and (2) to gain insights into the distribution and ecology of pangolins. We analysed data collated from 103 camera trap surveys undertaken across 22 countries that fell within the range of seven of the eight pangolin species, which yielded more than half a million trap nights and 888 pangolin encounters. We ran occupancy analyses on three species (Sunda pangolin Manis javanica, white-bellied pangolin Phataginus tricuspis and giant pangolin Smutsia gigantea). Detection probabilities varied with forest cover and levels of human influence for P. tricuspis, but were low (<0.05) for all species. Occupancy was associated with distance from rivers for M. javanica and S. gigantea, elevation for P. tricuspis and S. gigantea, forest cover for P. tricuspis and protected area status for M. javanica and P. tricuspis. We conclude that camera traps are suitable for the detection of pangolins and large-scale assessment of their distributions. However, the trapping effort required to monitor populations at any given study site using existing methods appears prohibitively high. This may change in the future should anticipated technological and methodological advances in camera trapping facilitate greater sampling efforts and/or higher probabilities of detection. In particular, targeted camera placement for pangolins is likely to make pangolin monitoring more feasible with moderate sampling efforts

Pangolins in Global Camera Trap Data: Implications for Ecological Monitoring

Despite being heavily exploited, pangolins (Pholidota: Manidae) have been subject to limited research, resulting in a lack of reliable population estimates and standardised survey methods for the eight extant species. Camera trapping represents a unique opportunity for broad-scale collaborative species monitoring due to its largely non-discriminatory nature, which creates considerable volumes of data on a relatively wide range of species. This has the potential to shed light on the ecology of rare, cryptic and understudied taxa, with implications for conservation decision-making. We undertook a global analysis of available pangolin data from camera trapping studies across their range in Africa and Asia. Our aims were (1) to assess the utility of existing camera trapping efforts as a method for monitoring pangolin populations, and (2) to gain insights into the distribution and ecology of pangolins. We analysed data collated from 103 camera trap surveys undertaken across 22 countries that fell within the range of seven of the eight pangolin species, which yielded more than half a million trap nights and 888 pangolin encounters. We ran occupancy analyses on three species (Sunda pangolin Manis javanica, white-bellied pangolin Phataginus tricuspis and giant pangolin Smutsia gigantea). Detection probabilities varied with forest cover and levels of human influence for P. tricuspis, but were low (M. javanica and S. gigantea, elevation for P. tricuspis and S. gigantea, forest cover for P. tricuspis and protected area status for M. javanica and P. tricuspis. We conclude that camera traps are suitable for the detection of pangolins and large-scale assessment of their distributions. However, the trapping effort required to monitor populations at any given study site using existing methods appears prohibitively high. This may change in the future should anticipated technological and methodological advances in camera trapping facilitate greater sampling efforts and/or higher probabilities of detection. In particular, targeted camera placement for pangolins is likely to make pangolin monitoring more feasible with moderate sampling efforts

Occupancy winners in tropical protected forests: a pantropical analysis

The structure of forest mammal communities appears surprisingly consistent across the continental tropics, presumably due to convergent evolution in similar environments. Whether such consistency extends to mammal occupancy, despite variation in species characteristics and context, remains unclear. Here we ask whether we can predict occupancy patterns and, if so, whether these relationships are consistent across biogeographic regions. Specifically, we assessed how mammal feeding guild, body mass and ecological specialization relate to occupancy in protected forests across the tropics. We used standardized camera-trap data (1002 camera-trap locations and 2–10 years of data) and a hierarchical Bayesian occupancy model. We found that occupancy varied by regions, and certain species characteristics explained much of this variation. Herbivores consistently had the highest occupancy. However, only in the Neotropics did we detect a significant effect of body mass on occupancy: large mammals had lowest occupancy. Importantly, habitat specialists generally had higher occupancy than generalists, though this was reversed in the Indo-Malayan sites. We conclude that habitat specialization is key for understanding variation in mammal occupancy across regions, and that habitat specialists often benefit more from protected areas, than do generalists. The contrasting examples seen in the Indo-Malayan region probably reflect distinct anthropogenic pressures

Robust ecological analysis of camera trap data labelled by a machine learning model

Ecological data are collected over vast geographic areas using digital sensors such as camera traps and bioacoustic recorders. Camera traps have become the standard method for surveying many terrestrial mammals and birds, but camera trap arrays often generate millions of images that are time-consuming to label. This causes significant latency between data collection and subsequent inference, which impedes conservation at a time of ecological crisis. Machine learning algorithms have been developed to improve the speed of labelling camera trap data, but it is uncertain how the outputs of these models can be used in ecological analyses without secondary validation by a human. Here, we present our approach to developing, testing and applying a machine learning model to camera trap data for the purpose of achieving fully automated ecological analyses. As a case-study, we built a model to classify 26 Central African forest mammal and bird species (or groups). The model generalizes to new spatially and temporally independent data (n = 227 camera stations, n = 23,868 images), and outperforms humans in several respects (e.g. detecting ‘invisible’ animals). We demonstrate how ecologists can evaluate a machine learning model's precision and accuracy in an ecological context by comparing species richness, activity patterns (n = 4 species tested) and occupancy (n = 4 species tested) derived from machine learning labels with the same estimates derived from expert labels. Results show that fully automated species labels can be equivalent to expert labels when calculating species richness, activity patterns (n = 4 species tested) and estimating occupancy (n = 3 of 4 species tested) in a large, completely out-of-sample test dataset. Simple thresholding using the Softmax values (i.e. excluding ‘uncertain’ labels) improved the model's performance when calculating activity patterns and estimating occupancy but did not improve estimates of species richness. We conclude that, with adequate testing and evaluation in an ecological context, a machine learning model can generate labels for direct use in ecological analyses without the need for manual validation. We provide the user-community with a multi-platform, multi-language graphical user interface that can be used to run our model offline

Pangolins in global camera trap data: Implications for ecological monitoring

Despite being heavily exploited, pangolins (Pholidota: Manidae) have been subject to limited research, resulting in a lack of reliable population estimates and standardised survey methods for the eight extant species. Camera trapping represents a unique opportunity for broad-scale collaborative species monitoring due to its largely non-discriminatory nature, which creates considerable volumes of data on a relatively wide range of species. This has the potential to shed light on the ecology of rare, cryptic and understudied taxa, with implications for conservation decision-making. We undertook a global analysis of available pangolin data from camera trapping studies across their range in Africa and Asia. Our aims were (1) to assess the utility of existing camera trapping efforts as a method for monitoring pangolin populations, and (2) to gain insights into the distribution and ecology of pangolins. We analysed data collated from 103 camera trap surveys undertaken across 22 countries that fell within the range of seven of the eight pangolin species, which yielded more than half a million trap nights and 888 pangolin encounters. We ran occupancy analyses on three species (Sunda pangolin Manis javanica, white-bellied pangolin Phataginus tricuspis and giant pangolin Smutsia gigantea). Detection probabilities varied with forest cover and levels of human influence for P. tricuspis, but were low (&lt;0.05) for all species. Occupancy was associated with distance from rivers for M. javanica and S. gigantea, elevation for P. tricuspis and S. gigantea, forest cover for P. tricuspis and protected area status for M. javanica and P. tricuspis. We conclude that camera traps are suitable for the detection of pangolins and large-scale assessment of their distributions. However, the trapping effort required to monitor populations at any given study site using existing methods appears prohibitively high. This may change in the future should anticipated technological and methodological advances in camera trapping facilitate greater sampling efforts and/or higher probabilities of detection. In particular, targeted camera placement for pangolins is likely to make pangolin monitoring more feasible with moderate sampling efforts