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opencc-zeroMay 2022View details →

Occupancy model for Rattus spp. in high and low human human refuse supplementation conditions

Globally, the genus Rattus is one of the most influential exotic species due to its high rates of competitive exclusion and large dietary breadth. However, the specific foraging strategies of urban and urban-adjacent populations remain largely unknown. We examined Rattus spp. dependency on human food supplementation in a peri-urban population. Through a natural experiment made possible by the COVID-19 shelter in place order in Santa Cruz California, USA, we measured changes in activity between invasive rats and native rodents with and without human supplementation. We measured invasive rat presence in normal (pre-COVID) conditions near dining halls and similar waste sources, and again under COVID lockdown conditions where all sources of human supplementation were removed. We found a decrease in Rattus presence after the removal of human refuse (p < 0.001), while native small mammal presence remained unchanged. These results have strong conservation implications, as they suggest that proper waste management is an effective, targeted, and less-invasive form of population control over conventional forms of poison.

Fig. 7 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 7. Probabilities of flea occupancy (W) for black-tailed prairie dogs (Cynomys ludovicianus) in differing body condition during May–September 2011, at the Vermejo Park Ranch, New Mexico. The solid line depicts estimates of occupancy and dotted lines depict 95% confidence intervals.

Fig. 4 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 4. Model-averaged probabilities for detecting fleas (p) on a black-tailed prairie dog (Cynomys ludovicianus) during May–September 2011, at the Vermejo Park Ranch, New Mexico. Bars depict 95% confidence intervals.

Fig. 3 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 3. Indices for and estimates of flea prevalence on prairie dogs inside old colonies. The estimates are model-averaged values from occupancy models that accounted for imperfect detection of fleas. The naïve indices do not consider imperfect detection. Gains in precision (95% confidence interval) when estimating prevalence are depicted on the right. Confidence intervals for the estimates of prevalence during July–September are very small.

Fig. 2 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 2. The robust design for occupancy models of flea prevalence on black-tailed prairie dogs (Cynomys ludovicianus). Prairie dogs were sampled during primary occasions in different months of the year (May–September 2012). Each primary occasion comprised three secondary occasions (combings) during which fleas might be detected (p = probability of detection, given presence). A prairie dog was ''open'' to colonization by fleas between primary occasions. Once a prairie dog was colonized, it was occupied by fleas during all subsequent primary occasions (thus, the extinction probability, E, was fixed at zero, once a prairie dog was occupied by fleas). Closure was assumed during the secondary occasions, but we used behavioral covariates to account for removal of fleas from hosts during each secondary combing (REMOVAL1 and REMOVAL2, see text). In the example encounter history, a '1' indicates that at least one flea was detected during a combing event, and a '0' indicates that no fleas were detected.

Fig. 5 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 5. Model-averaged probabilities of flea occupancy (W) and flea colonization (γ) for black-tailed prairie dogs (Cynomys ludovicianus) in old and young colonies, and natural and translocation colonies during May–September 2011, at the Vermejo Park Ranch, New Mexico (see Fig. 1 and text for colony descriptions). Bars depict 95% confidence intervals. We do not report estimates of colonization for September, because few prairie dogs were sampled in that month.

Fig. 1 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 1. Map of the study area within the Vermejo Park Ranch, Colfax County, New Mexico, showing old and young, and natural and translocation colonies of black-tailed prairie dogs (Cynomys ludovicianus). Gray areas indicate extent of prairie dog colonies in 2009.

Fig. 6 in Using occupancy models to investigate the prevalence of ectoparasitic vectors on hosts: An example with fleas on prairie dogs

Fig. 6. Probabilities of flea occupancy (W) and flea colonization (γ) for black-tailed prairie dogs (Cynomys ludovicianus) in plots with differing densities of prairie dogs during May–September 2011, at the Vermejo Park Ranch, New Mexico. Solid lines depict estimates and dotted lines depict 95% confidence intervals.

opencc-by-4.0Oct 2024View details →

Occupant Simulation Data based on Honda Accord 2024 Simplified Passenger Model and Full-factorial Sampling with 243 samples and VIRTHUMAN 5, 50, 95 Percentiles

Database with 729 Honda Accord 2014 passenger occupant simulations featuring VIRTHUMAN.

opencc-by-4.0Aug 2021View details →

Using interview surveys and multispecies occupancy models to inform vertebrate conservation

The Excel workbook WGAllSpeciesCov.xlsx contains detection histories of 30 species of vertebrates in 395 sites in the Western Ghats, India obtained from interviews with field staff of the Forest Department, people from local communities and formally trained people. The workbook also contains site level covariates or determinants of species occurrence. The associated README text file contains metadata to describe the data in the xlsx workbook. Complete R code to read in the data and run the model is provided in the R file: FP_MSp_SS_SpR_AllTraitGr.R and the JAGS code for the multispecies occupancy model is provided in the text file FP_MSp_SS_SpR_AllTraitGr_Exp_NoFP.txt

opencc-zeroDec 2021View details →

Data for: Occupancy–detection models with museum specimen data: Promise and pitfalls

Historical museum records provide potentially useful data for identifying drivers of change in species occupancy. However, because museum records are typically obtained via many collection methods, methodological developments are needed in order to enable robust inferences. Occupancy-detection models, a relatively new and powerful suite of statistical methods, are a potentially promising avenue because they can account for changes in collection effort through space and time. We use simulated datasets to identify how and when patterns in data and/or modelling decisions can bias inference. We focus primarily on the consequences of contrasting methodological approaches for dealing with species' ranges and inferring species' non-detections in both space and time. We find that not all datasets are suitable for occupancy-detection analysis but, under the right conditions (namely, datasets that are broken into more time periods for occupancy inference and that contain a high fraction of community-wide collections, or collection events that focus on communities of organisms), models can accurately estimate trends. Finally, we present a case-study on eastern North American odonates where we calculate long-term trends of occupancy by using our most robust workflow. These results indicate that occupancy-detection models are a suitable framework for some research cases and expand the suite of available tools for macroecological analysis available to researchers, especially where structured datasets are unavailable.

opencc-by-4.0Apr 2023View details →

Species detection histories used in Killion et al. (2023): Integrating Spaceborne Estimates of Structural Diversity of Habitat into Wildlife Occupancy Models

Camera trap species detection histories used for occupancy models in "Integrating Spaceborne Estimates of Structural Diversity of Habitat into Wildlife Occupancy Models".

opencc-zeroJul 2023View details →

Data for: Considerations for fitting occupancy models to data from eBird and similar volunteer-collected data

An occupancy model makes use of data that are structured as sets of repeated visits to each of many sites, in order estimate the actual probability of occupancy (i.e., proportion of occupied sites) after correcting for imperfect detection using the information contained in the sets of repeated observations. We explore the conditions under which preexisting, volunteer-collected data from the citizen science project eBird can be used for fitting occupancy models. The data archived here are used to explore two ways in which the single-visit records could be used in occupancy models. First, we use empirical data contained within this archive to assess the potential for space-for-time substitution: aggregating single-visit records from different locations within a region into pseudo-repeat visits. The archived data are used to illustrate that the locations chosen for data collection by observers were not always representative of the habitat in the surrounding area, which would lead to biased estimates of occupancy probabilities when using space-for-time substitution. Second, create a large set of simulated data (output from the simulations contained in this archive) that we used to explore the utility of including data from single-visit records to supplement sets of repeated-visit data.