Title: Admixture Graph Manipulation and Fitting
Authors@R: c(person("Thomas", "Mailund", email = "mailund@birc.au.dk", role = c("cre", "aut")),
person("Kalle", "Leppala", email = "kalle.m.leppala@gmail.com", role = c("aut")))
Description: Implements tools for building and visualising admixture graphs
and for extracting equations from them. These equations can be compared to f-
statistics obtained from data to test the consistency of a graph against data --
for example by comparing the sign of f_4-statistics with the signs predicted by
the graph -- and graph parameters (edge lengths and admixture proportions) can
Imports: doParallel, dplyr, foreach, ggplot2, graphics, MASS,
neldermead, parallel, pracma, stats, utils

person("Kalle", "Leppala", email = "kalle.m.leppala@gmail.com", role = c("aut")),
person("Svend", "Nielsen", email = "svn@cs.au.dk", role = c("aut")))
neldermead, parallel, pracma, stats, utils, grDevices

Imports: doParallel, dplyr, foreach, ggplot2, graphics, MASS, methods,

Title: Alternating Direction Method of Multipliers to Solve Dense
Author: Brendan Ames <bpames@ua.edu>, Polina Bombina <pbombina@crimson.ua.edu>
Description: Solves the problem of identifying the densest submatrix in a given or sampled binary matrix, Bombina et al. (2019) <arXiv:1904.03272>.
Packaged: 2019-10-28 18:58:15 UTC; polinabombina

Title: No-U-Turn MCMC Sampling for 'ADMB' and 'TMB' Models
Authors@R: person("Cole", "Monnahan", email = "monnahc@uw.edu", role = c("aut", "cre"))
Description: Bayesian inference using the no-U-turn (NUTS) algorithm by
Hoffman and Gelman (2014) <http://www.jmlr.org/papers/v15/hoffman14a.html>.
Designed for 'AD Model Builder' ('ADMB') models,
or when R functions for log-density and log-density gradient
are available, such as 'Template Model Builder' ('TMB')
models and other special cases. Functionality is similar to 'Stan',
and the 'rstan' and 'shinystan' packages are used for diagnostics and
Suggests: snowfall (>= 1.84.6.1), shinystan (>= 2.3.0), R2admb (>=

Suggests: snowfall (>= 1.84.6.1), shinystan (>= 2.5.0), matrixcalc (>=
1.0.3), TMB (>= 1.7.15), stats, knitr, rmarkdown
Packaged: 2019-04-04 18:38:45 UTC; cole.monnahan