bnlearn, fastDummies, lavaan, Rgraphviz, semPlot, xlsx
Elias Carvalho, Joao R N Vissoci, Luciano Andrade, Wagner Machado, Emerson P Cabrera, Julio C Nievola
This project aims to enable the method of Path Analysis to infer causalities
from data. For this we propose a hybrid approach, which uses Bayesian network
structure learning algorithms from data to create the input file for creation of a
PA model. The process is performed in a semi-automatic way by our intermediate
algorithm, allowing novice researchers to create and evaluate their own PA models
from a data set. The references used for this project are:
Koller, D., & Friedman, N. (2009). Probabilistic graphical models: principles and techniques. MIT press. <doi:10.1017/S0269888910000275>.
Nagarajan, R., Scutari, M., & Lèbre, S. (2013). Bayesian networks in r. Springer, 122, 125-127. Scutari, M., & Denis, J. B. <doi:10.1007/978-1-4614-6446-4>.
Scutari M (2010). Bayesian networks: with examples in R. Chapman and Hall/CRC. <doi:10.1201/b17065>.
Rosseel, Y. (2012). lavaan: An R Package for Structural Equation Modeling. Journal of Statistical Software, 48(2), 1 - 36. <doi:10.18637/jss.v048.i02>.

Implements the Bayesian nonparametric monotonic regression
method described in Bornkamp & Ickstadt (2009), Biometrics, 65,
198-205.

Implements the Bayesian nonparametric monotonic regression
method described in Bornkamp & Ickstadt (2009), Biometrics, 65, 198-205.

Simulate Genotypes from the BN-PSD Admixture Model
c(
person("Alejandro", "Ochoa", email = "ochoa@princeton.edu", role = c("aut", "cre")),
person("John D.", "Storey", email = "jstorey@princeton.edu", role = c("aut"))
)
The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions.  The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters.  The BN-PSD model can be used to yield complex population structures.  Method described in Ochoa and Storey (2016) <doi:10.1101/083923>.
popkin, testthat, knitr, rmarkdown, RColorBrewer
Alejandro Ochoa [aut, cre],
John D. Storey [aut]