R/zzz.R

In Meiosis: Simulation of Meiosis in Plant Breeding Research

.onAttach <- function(libname, pkgname) {
##   artwork <- "
##   /\\\\,/\\\\,
##  /| || ||         '              '
##  || || ||   _-_  \\  /'\\\\  _-_, \\\\  _-_,
##  ||=|= ||  || \\\\ || || || ||_.  || ||_.
## ~|| || ||  ||/   || || ||  ~ || ||  ~ ||
##  |, \\\\,\\\\, \\\\,/  \\\\ \\\\,/  ,-_-  \\\\ ,-_-
## _-
## "
  artwork <- "
  __  __        _              _      
 |  \\/  |  ___ (_)  ___   ___ (_) ___ 
 | |\\/| | / _ \\| | / _ \\ / __|| |/ __|
 | |  | ||  __/| || (_) |\\__ \\| |\\__ \\
 |_|  |_| \\___||_| \\___/ |___/|_||___/
                                      
"

  packageStartupMessage(artwork)
  packageStartupMessage(sprintf('Package Meiosis, version %s', utils::packageVersion(pkgname)))
  packageStartupMessage('Dominik Mueller')
  packageStartupMessage("Use Meiosis::seed_rng to seed the RNG of the C++ routines ",
                        "(Mersenne Twister)")
  packageStartupMessage("Otherwise a random seed is used.")
  invisible()
}

.onLoad <- function(libname, pkgname) {
  seed_rng()
  invisible()
}

.onUnload <- function (libpath) {
  library.dynam.unload("Meiosis", libpath)
}

Rcpp::loadModule("Module", TRUE)

#' @name Converter
#' @docType class
#'
#' @title Converter reference class
#'
#' @description An object of type Converter is used to efficiently convert data from the
#' segmental to the genotypic representation. This class has two methods that should be
#' employed by the user: \code{insert_founder} and \code{convert}. Please look up their
#' documentation with \code{help(Converter$insert_founder)} and \code{help(Converter$convert)}.
#' Before starting conversion, all founder alleles and founder genotypes have to be added via
#' the method \code{insert_founder}. Conversion is then done by the method \code{convert}.
#'
#' The constructor has two parameters, \code{positions} and \code{use_names}
#' (optional, defaults to \code{FALSE}).
#' Parameter \code{positions} must be a list of vectors with the genetic positions.
#' If these vectors are named, and if \code{use_names} is \code{TRUE},
#' the result of a conversion via \code{convert} will also be named.
#'
#' Please see the vignette (\code{vignette('Introduction', package = 'Meiosis')}) for an example.
#'
NULL
## xyz <- setRefClass("xyz",
##             methods = list(
##               new = function(channel.labels=NA, green.channels=NA, avg.green.channel.label=NA) {
##                 "Create a new instance of the hvdvm class"
##                 NULL
##               },
##               digest = function(photo.conds.file.name, crop.files.path='./') {
##                 "Collect statistics from the raw images files sdfasdfsadf"
##                 NULL
##               }
##             ))

#' @name Converter$convert
#'
#' @title convert
#'
#' @description Convert an individual from its segmental to its genotypic representation.
#'
#' @param individual List. An individual to be converted.
NULL


#' @name Converter$insert_founder
#'
#' @title insert_founder
#'
#' @description Insert founder genotypes.
#'
#' @param keys Integer vector. The two (unique) founder alleles.
#' @param geno List. The genotypic data.
NULL


## ## destroy dummy class
## rm(xyz)