This paper describes the software package KELVIN, which supports the PPL (posterior probability of linkage) framework for the measurement of statistical evidence in human (or more generally, diploid) genetic studies. In terms of scope, KELVIN supports two-point (trait-marker or marker-marker) and multipoint linkage analysis, based on either sex-averaged or sex-specific genetic maps, with an option to allow for imprinting; trait-marker linkage disequilibrium (LD), or association analysis, in case-control data, trio data, and/or multiplex family data, with options for joint linkage and trait-marker LD or conditional LD given linkage; dichotomous trait, quantitative trait and quantitative trait threshold models; and certain types of gene-gene interactions and covariate effects. Features and data (pedigree) structures can be freely mixed and matched within analyses. The statistical framework is specifically tailored to accumulate evidence in a mathematically rigorous way across multiple data sets or data subsets while allowing for multiple sources of heterogeneity, and KELVIN itself utilizes sophisticated software engineering to provide a powerful and robust platform for studying the genetics of complex disorders.

Statistical analysis is used throughout biomedical research and elsewhere to assess strength of evidence. We have previously argued that typical outcome statistics (including p values and maximum likelihood ratios) have poor measure-theoretic properties: they can erroneously indicate decreasing evidence as data supporting an hypothesis accumulate; and they are not amenable to calibration, necessary for meaningful comparison of evidence across different study designs, data types, and levels of analysis. We have also previously proposed that thermodynamic theory, which allowed for the first time derivation of an absolute measurement scale for temperature (T), could be used to derive an absolute scale for evidence (E). Here we present a novel thermodynamically based framework in which measurement of E on an absolute scale, for which “one degree” always means the same thing, becomes possible for the first time. The new framework invites us to think about statistical analyses in terms of the flow of (evidential) information, placing this work in the context of a growing literature on connections among physics, information theory, and statistics.

Statistical modeling is often used to measure the strength of evidence for or against hypotheses about given data. We have previously proposed an information-dynamic framework in support of a properly calibrated measurement scale for statistical evidence, borrowing some mathematics from thermodynamics, and showing how an evidential analogue of the ideal gas equation of state could be used to measure evidence for a one-sided binomial hypothesis comparison ("coin is fair" vs. "coin is biased towards heads"). Here we take three important steps forward in generalizing the framework beyond this simple example, albeit still in the context of the binomial model. We: (1) extend the scope of application to other forms of hypothesis comparison; (2) show that doing so requires only the original ideal gas equation plus one simple extension, which has the form of the Van der Waals equation; (3) begin to develop the principles required to resolve a key constant, which enables us to calibrate the measurement scale across applications, and which we find to be related to the familiar statistical concept of degrees of freedom. This paper thus moves our information-dynamic theory substantially closer to the goal of producing a practical, properly calibrated measure of statistical evidence for use in general applications.