## R code

A random smattering of R code we've found helpful in the recent past.

R code for a count-based Population Viability Analysis (PVA) with optional density-dependence, environmental stochasticity, catastrophes, and demographic augmentation. Calculates the interval probability of extinction. See chapters 3-5 in Doak and Morris (2002).

R code for estimating minimum viable population size (MVP) via a count-based Population Viability Analysis (PVA) with optional density-dependence, environmental stochasticity, and catastrophes.

R code for performing a Bayesian generalized linear mixed model on pairwise genetic comparisons using the MCMCglmm package in R. This is the analysis employed in the Roberts et al. Freshwater Biology paper to investigate the influences of distance, dams, and genetic drift on pairwise FST.

R code for basic data resampling (bootstrapping, jackknifing, rarification, permutation). This isn't anything all that zoomy, but someone might find it useful.

R code for performing a variety of basic (e.g., diversity estimation, PCA, H-W testing) and more advanced (e.g., outlier detection, data rarefaction, simulation) manipulations and population genetic analyses of SNP datasets. This is continually evolving and not designed as a linear tutorial, but might show you some helpful shortcuts and leads.

R code for a count-based Population Viability Analysis (PVA) with optional density-dependence, environmental stochasticity, catastrophes, and demographic augmentation. Calculates the interval probability of extinction. See chapters 3-5 in Doak and Morris (2002).

R code for estimating minimum viable population size (MVP) via a count-based Population Viability Analysis (PVA) with optional density-dependence, environmental stochasticity, and catastrophes.

R code for performing a Bayesian generalized linear mixed model on pairwise genetic comparisons using the MCMCglmm package in R. This is the analysis employed in the Roberts et al. Freshwater Biology paper to investigate the influences of distance, dams, and genetic drift on pairwise FST.

R code for basic data resampling (bootstrapping, jackknifing, rarification, permutation). This isn't anything all that zoomy, but someone might find it useful.

R code for performing a variety of basic (e.g., diversity estimation, PCA, H-W testing) and more advanced (e.g., outlier detection, data rarefaction, simulation) manipulations and population genetic analyses of SNP datasets. This is continually evolving and not designed as a linear tutorial, but might show you some helpful shortcuts and leads.