Title Linear Mixed-Effects Models using 'Eigen' and S4Contact LME4 Authors Description Fit linear and generalized linear mixed-effects models.The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen'``glue''.Depends R (>= 3.2.0), Matrix (>= 1.2-1), methods, statsLinkingTo Rcpp (>= 0.10.5), RcppEigen

Agassiz's desert tortoise (Gopherus agassizii), a threatened species of the southwestern United States, has severely declined to the point where 76% of populations in critical habitat (Tortoise Conservation Areas) are below viability. The potential for rapid recovery of wild populations is low because females require 12-20 years to reach reproductive maturity and produce few eggs annually. We report on a 34-year mark-recapture study of tortoises initiated in 1979 at the Desert Tortoise Research Natural Area in the western Mojave Desert, California, USA, and provide substantive data on challenges faced by the species. In 1980, the United States Congress designated the Research Natural Area and protected the land from recreational vehicles, livestock grazing, and mining with a wildlife-permeable fence. The 7.77-km 2 study area, centered on interpretive facilities, included land both within the Natural Area and outside the fence. We expected greater benefits to accrue to the tortoises and habitat inside compared to outside. Our objectives were to conduct a demographic study, analyze and model changes in the tortoise population and habitat, and compare the effectiveness of fencing to protect populations and habitat inside the fence versus outside, where populations and habitat were unprotected. We conducted surveys in spring in each of 7 survey years from 1979, when the fence was under construction, through 2012. We compared populations inside to those outside the fence by survey year for changes in distribution, structure by size and relative age, sex ratios, death rates of adults, and causes of death for all sizes of tortoises. We used a Bayesian implementation of a Jolly Seber model for mark-recapture data. We modeled detection, density, growth and transition of tortoises to larger size-age classes, movements from inside the protective fence to outside and vice versa, and survival. After the second and subsequent survey years, we added surveys to monitor vegetation and habitat changes, conduct health assessments, and collect data on counts of predators and predator sign. At the beginning of the study, counts and densities for all sizes of tortoises were high, but densities were approximately 24% higher inside the fence than outside. By 2002, the low point in densities, densities had declined 90% inside the fence and 95% outside. Between 2002 and 2012, the population inside the fence showed signs of improving with a 54% increase in density. Outside the fence, densities remained low. At the end of the study, when we considered the initial differences in location, densities inside the fence were roughly 2.5 times higher than outside. The pattern of densities was similar for male and female adults. When evaluating survival by blocks of years, survivorship was higher in 1979-1989 than in 1989-2002 (the low point) and highest from 2002 to 2012. Recruitment and survival of adult females into the population was important for growing the population, but survival of all sizes, including juveniles, was also critical.Major ...

Wildlife managers face complex problems in attempting to achieve contemporary conservation goals while maintaining ecosystem function. Anthropogenically altered environments can subsidize certain species, causing them to become overabundant and straining the remaining natural system. Such is the case with the widespread avian generalist and subsidized predator, the common raven (Corvus corax). Ravens depredate nests and prey on small animals, with locally focused high impacts to the ecosystem during rearing of their nestlings. Limiting predator abundance reduces the spatially concentrated predation rates by eliminating nestling provisioning needs. We investigated avenues to limit the reproduction of common raven using customized theoretical and practical tools. Specifically, we developed an online interactive tool, a mathematical model, that calculates the predator's population growth rate under any given proportion of reproductive management. This quantitative tool models an assessment of ravens in a defined area and results in the degree to which raven fitness would need to be reduced to control their populations. To implement the model's results in a field‐practical way and manage reproduction with minimal disturbance, we developed novel technology, a Remote Fluid Application System (RFAS). The RFAS applies the egg addling technique of egg oiling to high (usually out of reach) nesting situations. We tested these tools in the Mojave Desert, CA, where the raven is a heavily human‐subsidized predator. We mounted our RFAS on telescoping poles and unmanned aerial vehicles (UAVs; drones) and found that we were able to aerially, and precisely, spray‐oil eggs high in trees or cliffs/rock faces, halting 100% (n = 46) of raven nesting events. With these tools, we enable managers to calculate the intensity of, and the ability to carry out, egg addling needed to stem or halt predator population growth. We conclude that the combination of the interactive software (StallPOPd Interactive Tool, https://cwhl.vet.cornell.edu/tools/stallpopd; publicly available at https://ecommons.cornell.edu/handle/1813/65718) and the RFAS is the most effective wildlife management strategy to date for the offset or control of undesirable population growth in high‐nesting avian predators.