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Therese L. Johnson

Publications and source records attributed to Therese L. Johnson.

6 recordsLinked to original sources
USGS2019

A hierarchical Bayesian approach for handling missing classification data

Ecologists use classifications of individuals in categories to understand composition of populations and communities. These categories might be defined by demographics, functional traits, or species. Assignment of categories is often imperfect, but frequently treated as observations without error. When individuals are observed but not classified, these “partial” observations must be modified to include the missing data mechanism to avoid spurious inference. We developed two hierarchical Bayesian models to overcome the assumption of perfect assignment to mutually exclusive categories in the multinomial distribution of categorical counts, when classifications are missing. These models incorporate auxiliary information to adjust the posterior distributions of the proportions of membership in categories. In one model, we use an empirical Bayes approach, where a subset of data from one year serves as a prior for the missing data the next. In the other approach, we use a small random sample of data within a year to inform the distribution of the missing data. We performed a simulation to show the bias that occurs when partial observations were ignored and demonstrated the altered inference for the estimation of demographic ratios. We applied our models to demographic classifications of elk ( Cervus elaphus nelsoni ) to demonstrate improved inference for the proportions of sex and stage classes. We developed multiple modeling approaches using a generalizable nested multinomial structure to account for partially observed data that were missing not at random for classification counts. Accounting for classification uncertainty is important to accurately understand the composition of populations and communities in ecological studies.

Ecology and Evolution↗
USGS2018

Development of an aerial population survey method for elk (Cervus elaphus) in Rocky Mountain National Park, Colorado

Executive Summary Since the early 1990s, substantial effort and funding have been expended to conduct research to guide development of a 20-year Elk and Vegetation Management Plan for Rocky Mountain National Park (RMNP) in Colorado. One goal of the plan is to maintain the elk ( Cervus elaphus ) population size at the lower end of the natural range of variation. To implement management actions called for in the plan, accurate and reliable population estimates are needed, as well as a better understanding of the spatial and temporal distribution of elk. The previous aerial survey protocol and population estimation model used by the park had not been updated since the model’s initial calibration more than 15 years ago and the model was developed with an insufficient number (n=44) of observations. Thus we initiated research to reevaluate, update, and improve elk population estimation protocols for RMNP. We considered several alternative survey and analysis methods, and concluded that a hybrid population-estimation model using a simultaneous double-observer technique with sighting covariates was the most appropriate and effective aerial survey methodology for this population and the environmental conditions in RMNP. Instructional protocols for conducting these surveys in the future, along with datasheets, are provided in this report’s appendixes. To develop an improved method for aerial elk surveys, we used elk radio-collar location data from our study and other studies, and applied geographic information system analyses to define the survey area and develop effective, repeatable survey transect lines. We used telemetry data from radio-collared elk to inform our understanding of the temporal and spatial scale of elk movements across the park boundary, elk use of tree cover during potential survey hours, and elk use of different elevations within their range. Determining where elk were during surveys helped to fine-tune a survey design that improved spatial cover-age and decreased costs where possible, while standardizing the method to make it repeatable from year to year. We conducted aerial helicopter surveys to test our methodology in an adaptive, iterative process during three winters: 2007–2008, 2008–2009, and 2009–2010. We gained new information on each survey and used results to refine subsequent surveys. Our results confirm that elk movements were highly dynamic with respect to park boundary crossings; an average of six round trips from the park to Estes Park, Colorado, and back per month were taken by global positioning system-collared bull elk. We observed a strong diurnal temporal pattern of bull elk use of trees; elk were found in dense tree cover from 15:00−22:00 but not as often during morning and early afternoon hours when surveys were conducted. We used information on elk use of different altitudes to refine and establish a more efficient survey area. During the time of our study, a concurrent study in the park deployed 120 very high frequency radio collars on elk cows. We used those collar locations during our flights to increase sample size and to evaluate the level of precision we would gain by using “known fates analysis” (in which elk were known to be in the survey area, out of the survey area, or deceased based on radio-collar locations collected simultaneously during aerial surveys). Using radio-collar locations reduced bias by 1.1–8.8 percent and increased precision (that is, reduced the width of confidence intervals). This report provides final population estimates analyzed with and without radio-collar data to demonstrate what is gained by using marked individuals.

Colorado↗
USGS2018

Estimating abundance of an open population with an N-mixture model using auxiliary data on animal movements

Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground‐based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi‐state mark–recapture methods using a hierarchical N ‐mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state‐space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk ( Cervus elaphus nelsoni ) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N‐mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations.

Ecological Applications↗
USGS2015

Monitoring of vegetation response to elk population and habitat management in Rocky Mountain National Park, 2008–14

Since 2008, Rocky Mountain National Park in Colorado has been implementing an elk and vegetation management plan with the goal of managing elk populations and their habitats to improve the condition of key vegetation communities on elk winter range. Management actions that have been taken thus far include small reductions in the elk herd through culling of animals and temporary fencing of large areas of willow and aspen habitat to protect them from elk browsing. As part of the park’s elk and vegetation management plan (EVMP), a monitoring program was established to assess effectiveness of management actions in achieving vegetation goals. We collected data to monitor offtake (consumption) of upland herbaceous plants and willow annually from 2008 to 2014 and to assess aspen stand structure and regeneration and willow cover and height in 2013, 5 years after plan implementation. Loss of many willow and a few aspen monitoring sites to a fire in late 2012 complicated data collection and interpretation of results but will provide opportunities to observe habitat recovery following fire and in the presence and absence of elk herbivory, which will offer important insights into the use of prescribed fire as an additional management tool in these habitats. Increases in the number of small-diameter, tree-sized (stems greater than 2.5 meter height) aspen stems were observed but only inside fences that excluded ungulates. In unfenced areas, stand structure was stagnant, with many medium- and large-diameter (older) stems and no replacement of small-diameter stems. By 2013, aspen saplings (stems less than or equal to 2.5 meter height) were recruiting on 29 percent of sampled sites, an increase from 13 percent of sites at baseline, but this was mainly due to growth inside fences. Upland herbaceous offtake dropped below baseline levels (61 percent) on both core and noncore winter range in 2010–14. Less than 10 percent of the upland areas had intense herbivory (greater than 85 percent offtake), and less than 30 percent of the landscape had offtake greater than 70 percent after 2009. Offtake levels in 2013 and 2014 indicated an increase in grazing pressure on upland sites compared to 2010–12 levels, but this change may have been in response to loss of large patches of both herbaceous and woody forage in Moraine Park following the 2012 Fern Lake Fire. Winter willow offtake remained steady from 2009 to 2014, and although there were no substantial increases in offtake, there were also no consistent declines. Winter-range willow offtake was below the baseline level of 35 percent only in 2013 and 2014. Willow heights have stayed at or above baseline levels of 0.9 meter. Average heights of willow increased compared to baseline measures within fenced habitat on the core winter range and on noncore (all unfenced) winter range. Willow cover increased at least 75 percent compared to baseline within core winter-range fenced areas and roughly 25 percent in noncore winter range. Overall, during the first 5 years of implementation, the EVMP at Rocky Mountain National Park seems to be making steady progress toward the vegetation objectives set out by the EVMP. Habitat fencing has been the most effective means of improving aspen and willow habitat conditions.

Colorado↗
USGS2011

Monitoring plan for vegetation responses to elk management in Rocky Mountain National Park

Rocky Mountain National Park (RMNP) in north-central Colorado supports numerous species of wildlife, including several large ungulate species among which Rocky Mountain elk (Cervus elaphus) are the most abundant. Elk are native to RMNP but were extirpated from the area by the late 1800s. They were reintroduced to the area in 1913-1914, and the elk herd grew to the point that it was actively managed from 1944 until 1968. In 1969, the active control of elk was discontinued and since then the herd has increased to a high point ranging from 2,800 to 3,500 between 1997 and 2001. In recent years, there has been growing concern over the condition of vegetation in the park and conflicts between elk and humans, both inside and outside the park. In response to these concerns, RMNP implemented an Elk and Vegetation Management Plan (EVMP) in 2009 to guide management actions in the park over a 20-year time period with the goal of reducing the impacts of elk on vegetation and restoring the natural range of variability in the elk population and affected plant and animal communities. The EVMP outlines the desired future condition for three vegetation communities where the majority of elk herbivory impacts are being observed: aspen, montane riparian willow, and upland herbaceous communities. The EVMP incorporates the principle of adaptive management whereby the effectiveness of management actions is assessed and adjusted as needed to successfully achieve objectives. Determination of whether vegetation objectives are being achieved requires monitoring and evaluation of target vegetation communities. The current report describes the design and implementation of a vegetation-monitoring program to help RMNP managers assess the effectiveness of their management actions and determine when and where to alter actions to achieve the EVMP's vegetation objectives. This monitoring plan details the process of selecting variables to be monitored, overall sampling design and structure, site selection, data collection methods, and statistical analyses to be used to conduct this monitoring program in conjunction with the EVMP. We report the baseline conditions observed at the time of the establishment of monitoring sites. We include detailed field protocols for site establishment and data collection, as well as timetables for sampling, so that RMNP staff will be able to continue monitoring the sites established during this implementation stage, and continue to add new sites when necessary, as the execution of the EVMP proceeds over the next 20 years.

Colorado↗