Two main sources of data for species distribution models (SDMs) are site-occupancy (SO) data from planned surveys, and presence-background (PB) data from opportunistic surveys and other sources. SO surveys give high quality data about presences and absences of the species in a particular area. However, due to their high cost, they often cover a smaller area relative to PB data, and are usually not representative of the geographic range of a species. In contrast, PB data is plentiful, covers a larger area, but is less reliable due to the lack of information on species absences, and is usually characterised by biased sampling. Here we present a new approach for species distribution modelling that integrates these two data types.
We have used an inhomogeneous Poisson point process as the basis for constructing an integrated SDM that fits both PB and SO data simultaneously. It is the first implementation of an Integrated SO–PB Model which uses repeated survey occupancy data and also incorporates detection probability.
The Integrated Model's performance was evaluated, using simulated data and compared to approaches using PB or SO data alone. It was found to be superior, improving the predictions of species spatial distributions, even when SO data is sparse and collected in a limited area. The Integrated Model was also found effective when environmental covariates were significantly correlated. Our method was demonstrated with real SO and PB data for the Yellow-bellied glider (Petaurus australis) in south-eastern Australia, with the predictive performance of the Integrated Model again found to be superior.
PB models are known to produce biased estimates of species occupancy or abundance. The small sample size of SO datasets often results in poor out-of-sample predictions. Integrated models combine data from these two sources, providing superior predictions of species abundance compared to using either data source alone. Unlike conventional SDMs which have restrictive scale-dependence in their predictions, our Integrated Model is based on a point process model and has no such scale-dependency. It may be used for predictions of abundance at any spatial-scale while still maintaining the underlying relationship between abundance and area.
PBSO
R code and instructions to run the model on the data provided
evaporation_january
A spatial layer of the evaporation in January in the study area used for analysing of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
Evaporation_Jan.zip
evaporation_july
A spatial layer of evaporation in July in the study area used for analysing of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
Evaporation_Jul.zip
log_vertical_distance_major_streams
A spatial layer of the distance to the nearest stream in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
MaxTemp_Jan
A spatial layer of the maximum temperature in January in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
MinTemp_Jul
A spatial layer of the minimum temperature in July in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
RainDays_Jan
A spatial layer of the number of rainy days in January in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
Rainfall_Jul
A spatial layer of the average rainfall in January in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
RainDays_Jul.zip
RainDays_Jul
A spatial layer of the average number of rainy days in January in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
Rainfall_Jan
A spatial layer of the average rainfall in January in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
terrain_ruggedness_index
A spatial layer of the terrain ruggedness index in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
wetness_index
A spatial layer of the wetness index in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
visible_sky
A spatial layer of the proportion of the hemisphere visible from the location in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
SO-data
Site occupancy data. The archive contains the values of the covariates at the survey sites used in the analysis of yellow-bellied glider data (so_occupancy.csv and so_detection) and results of the two repeated surveys (yb-so.csv)
yb-pb-location
List of locations of sightings of yellow-bellied glider in opportunistic surveys
elevation
A spatial layer of the elevation in the study area used for analysing of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
Dem75mInteger.zip