The Thorn and the Petal (A Ghazal)

Poe

The analysis of test coverage using mutation operator BSR

Code coverage is a measure used to describe the degree to which the source code of a program or paths through the program has been tested by a particular test suite. In this thesis we have designed and implemented a Java tool for code coverage analysis which is based on principles of mutation testing. Mutations are small modifications of source code which are deliberately seeded into the source code under testing in order to evaluate the quality of existing test suite and improve it. We used the mutation operator BSR to systematically seed so-called bombs into Java source code. In mutation testing a bomb is a statement which causes an exception when executed. After that we ran the test suite against the mutated code and checked whether it finished successfully. Based on the test suite results it is possible to assess the code coverage at the position where the bomb was placed. We put a lot of effort in algorithm optimization because mutation testing is known to be extremely time-consuming process. We designed the application as a plugin for Maven, software project management and comprehension tool, which makes it simple to use on any Maven based Java project. Our goal was to develop a tool similar to EMMA by functionality and code coverage measurement methodology. By running the code coverage analysis on a few real-world open source projects, the application proved to be pretty accurate and comparable to EMMA

Holes in the Skein

Short stor

A clear and present danger: impacts of poisoning on a vulture population and the effect of poison response activities

Vultures in Africa are being poisoned deliberately by poachers to prevent the birds alerting authorities to the poachers’ illegal activities, or for harvesting and sale of body parts for use in witchcraft. Hundreds of vultures can be killed at a single poisoned elephant Loxodonta africana carcass, and although field staff trained in poison response activities can limit the damage, mortalities remain numerous. We used the population viability analysis programme VORTEX to simulate seven 100-year-long scenarios investigating various rates of poisoning mortalities and the remedial effects of poison response activities on a population of Critically Endangered white-backed vultures Gyps africanus breeding in Kruger National Park, South Africa. In six scenarios the population declined; in three scenarios the population remained extant over the 100-year simulations but declined by 60-90% from a starting size of 2,400 individuals.In two scenarios one poisoned elephant carcass left untreated and causing the greatest number of vulture deaths was modelled as a catastrophic event with a 50% probability of annual occurrence, which resulted in a 100% probability of population extinction, with a mean time to extinction of 55-62 years. Effective poison response activities were modelled as a 70% reduction of mortality at each poisoned elephant carcass and resulted in population persistence after 100 years but with a c. 90% reduction in size (final n = 205). We highlight that although poison response activities will not prevent poisoning from occurring, they form an essential part of wider conservation actions designed to prevent local extinctions of vultures or other vulnerable species

Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys

Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey method

'No Man is an Island' - Crossing Thresholds: Journeying with the recent poetry of Syd Harrex

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