Peirce's sign theory as an open-source R package.

Throughout Peirce’s writing, we witness his developing vision of a machine that scientists will eventually be able to create. Nadin (2010) raised the question:Why do computer scientists continue to ignore Peirce’s sign theory? A review of the literature on Peirce’s theory and the semiotics machine reveals that many authors discussed the machine;however, they donot differentiate between a physical computer machine and its software. This paper discusses the problematic issues involved in converting Peirce’s theory into a programming language, machine and software application. We demonstrate this challenge by introducing Peirce’s sign theory as a software application that runs under an open-source R environmen

Beyond Age and Stage: Consequences of Individual Variation in Demographic Traits

Within natural populations, individuals vary in their propensity to grow, survive and produce offspring. Additionally, fates of individuals are often correlated and non-independent as a result of shared genes, rearing environment or both. Variation in demographic traits can change population dynamics over time. The effects of variation in individual growth rate on population growth rate, net reproductive rate and generation time are examined, along with quantifying the sources of variation in survival of a long-lived cooperatively breeding bird, the Florida Scrub-Jay (Aphelocoma coerulescens). I built a 2 stage population model with two growth phenotypes, fast and slow, and simulated all parameter values using R 3.3.1. Variation in individual maturation rate changes population dynamics, especially in the presence of phenotypic correlation between parents and offspring in growth phenotype. I used Cox Proportional Hazard models with a covariance structure derived from a kinship matrix using the R packages survival and kinship2. Survival of juvenile Florida Scrub-Jays is strongly dependent on kinship, or the degree of relatedness between individuals, in addition to body mass, social structure of the natal territory, natal territory quality and environmental conditions of the rearing period. Breeder Florida Scrub-Jay survival is mainly structured by group size, kinship, yearly variation in environmental conditions and territory quality

Remains to Be Seen: Execution and Embodiment in the Early English Atlantic World

This dissertation explores the development of capitalism in the early English Atlantic World (1580 - 1752) and the manipulation of the legal system to criminalize the laboring body in order to more fully exploit the productive output of labor