Author: Douglas Bates and Ana Ines Vazquez,

Description: Provides functions to estimate mixed probit models using, for
instance, pedigree data like in <doi:10.1002/sim.1603>. The models are also
commonly called liability threshold models. The approximation is
based on direct log marginal likelihood approximations like the randomized
Quasi-Monte Carlo suggested by <doi:10.1198/106186002394> with a similar
procedure to approximate the derivatives. Graph-based methods are also
provided that can be used to simplify pedigrees.
LinkingTo: Rcpp, RcppArmadillo, BH, testthat
Suggests: testthat, mvtnorm, xml2, knitr, rmarkdown, R.rsp, abind,

procedure to approximate the derivatives. The minimax tilting method
suggested by <doi:10.1111/rssb.12162> is also supported. Graph-based methods
are also provided that can be used to simplify pedigrees.
LinkingTo: Rcpp, RcppArmadillo, BH, testthat, psqn

Title: Mutation Models for Pedigree Likelihood Computations
Description: A collection of functions for modeling mutations in pedigrees with
marker data, as used e.g. in likelihood computations with microsatellite data.
Implemented models include proportional and stepwise models, as well as random
models for experimental work, and custom models allowing the user to apply any
valid mutation matrix. Allele lumping is done following the lumpability criteria
of Kemeny and Snell (1976), ISBN:0387901922.

Description: A collection of functions for modelling mutations in pedigrees with

Authors@R: c(person("Alessandro Samuel-Rosa", role = c("aut", "cre"), email = "alessandrosamuelrosa@gmail.com"),
person("Lucia H. C. Anjos", role = "ths", email = "lanjos@ufrrj.br"),
person("Gustavo M. Vasques", role = "ths", email = "gustavo.vasques@embrapa.br"),
person("Gerard B. M. Heuvelink", role = "ths", email = "gerard.heuvelink@wur.nl"))
Author: Alessandro Samuel-Rosa [aut, cre],
Imports: spsurvey, xtable, XML, stringr, sp, car, pbapply, MASS, plyr,
lattice, latticeExtra, grid, VecStatGraphs2D, mvtsplot
Description: This package contains functions to employ many tools and techniques used in the field of pedometrics (see http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics). These functions were developed to fulfill the demands created by the PhD research project (2012-2016) entitled Contribution to the Construction of Models for Predicting Soil Properties, developed by Alessandro Samuel-Rosa under the supervision of Dr Lucia HC Anjos (Federal Rural University of Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Soils, Brazil), and Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands). The project is supported by the CAPES Foundation, Ministry of Education of Brazil, Brasilia - DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions are simple wrapper functions that extend the functionalities of other functions commonly used for the analysis of pedometric data. It should be noted that changes are likely to occur quite often and using this package as a dependency for other packages is strongly discouraged.