Salakhutdinov (2006) <DOI:10.1126/science.1127647>). This method includes a
pre training with the contrastive divergence method published by G.E Hinton
Imports: stats, methods, ggplot2, reshape2, futile.logger (>= 1.4.1),
Suggests: foreach, doRNG, NeuralNetTools, gputools, testthat, plyr (>=
Collate: 'RcppExports.R' 'autosave.R' 'net.Class.R' 'darch.Class.R'
'momentum.R' 'net.Getter.R' 'newDArch.R' 'params.R' 'plot.R'

Title: Package for deep architectures and Restricted-Bolzmann-Machines
Description: The darch package is build on the basis of the code from G. E.
nets : last visit: 01.08.2013). This package is for generating neural
networks with many layers (deep architectures) and train them with the
method introduced by the publications "A fast learning algorithm for deep
belief nets" (G. E. Hinton, S. Osindero, Y. W. Teh) and "Reducing the
Salakhutdinov). This method includes a pre training with the contrastive
divergence method publishing by G.E Hinton (2002) and a fine tuning with
common known training algorithms like backpropagation or conjugate

Collate: 'net.R' 'darch.R' 'backpropagation.R' 'darch.Getter.R'

Title: Tools to Work with the Dark Sky API
person("Bob", "Rudis", email = "bob@rud.is", role = c("aut", "cre")),
Description: Provides programmatic access to the Dark Sky API
<https://darksky.net/dev/docs>, which provides current or historical global
Imports: stats, httr, dplyr, grid, gridExtra, gtable, ggplot2

Title: Tools to Work with the 'Dark Sky' 'API'
person("Lasse", "Vilhelmsen", role = "ctb"),
person("David", "Severski", email = "davidski@deadheaven.com", role = "ctb")
Description: Provides programmatic access to the 'Dark Sky' 'API'
Imports: stats, httr, grid, gridExtra, gtable, ggplot2, plyr, utils

Title: Importing and Analysing Snp and Silicodart Data Generated by
person("Peter J.", "Unmack", email="peter.mail2@unmack.net", rol="ctb"),
person("Oliver", "Berry", email="oliver.berry@csiro.au", rol="ctb" )  )
Description: Functions are provided that facilitate the import and analysis of
snp and silicodart (presence/absence) data. The main focus is on data generated
by DarT (Diversity Arrays Technology). However, once SNP or related fragment
presence/absence data from any source is imported into a genlight object many
of the functions can be used. Functions are available for input and output of
snp and silicodart data, for reporting on and filtering on various criteria
(e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency).
Advanced filtering is based on Linkage Disequilibrium and HWE. Other functions
are available for visualization after PCoA, or to facilitate transfer of data
between genlight/genind objects and newhybrids, related, phylip packages etc.
Imports: plyr, tidyr, reshape2, MASS, ggplot2, directlabels, quadprog,
rgl, misc3d, pca3d, utils, Demerelate, seqinr, pegas, SNPassoc,
methods, doParallel, stats, data.table, parallel, foreach,
Suggests: knitr, rmarkdown, StAMPP, mmod