3. factorplot- factorplot provides numerical and graphical summaries of factor-level differences in GLMs. It produces all pairwise hypotheses tests with either the exact pairwise difference and variance or user-supplied quasi-variances or floating absolute risks.
4. OUwie- Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models that allow the strength of selection and drift to vary across selective regimes.
7. Bayesian Biclustering- This package uses a Bayesian spike-and-slab model to construct bidendrograms using log posterior as the natural distance defined by the model and calculates importance using log Bayes factor.
8. Evolution simulation and classification- After measuring gene frequencies of modern populations that have a common ancestor, we estimate ancestral allele frequency and selection state for each gene. A bayesian model is used and verified using the included simulator.
9. Test for point containment in polyhedron- This project provides a function to test whether a point is contained within a closed three-dimensional polyhedron, defined by a triangular mesh. A two-dimensional version for polygons is also provided.
13. CShapes Dataset and Utilities- This package provides a link between R and CShapes, a GIS dataset of country boundaries (1946-2008). The package includes functions for data extraction and the computation of weights matrices.
14. Hierarchical Generalized Linear Models- The aim of the project is to develop a series of packages, including the hglm package, which implement the estimation algorithm of different random effects models based on the hierarchical likelihood theory.
16. Monte Carlo IBD Matrix Estimation- Flexible Monte Carlo Identity-By-Descent (IBD) Matrix Estimation with Within-Line Segregation for Use of Quantitative Trait Loci (QTL) Detection in F2 Intercross Designs.