acceptanceProbability |
Compute the acceptance probability for each updated design |

arrayUpdate |
Update array allocation |

conditionAllocation |
Allocate the selected RILs into different conditions |

conditionCombination |
Generate a matrix indicating all possible levels for environmental factors |

conditionLevel |
Levels of all environmental factors |

conditionUpdate |
Update condition allocation |

design genetical genomics experiment |
Optimal design for genetical genomics experiments |

designGG |
Optimal design for genetical genomics experiments |

designScore |
Calculate the A- or D- optimality score based on current experimental design |

exampleArrayDesignTable |
Example output of ArrayDesignTable data |

exampleConditionDesignTable |
Example ConditionDesignTable data |

examplePlotObj |
Example PlotObj data |

experimentDesignTable |
Make experiment table based design matrix |

genotype |
Example genotype data |

initialDesign |
Initialize an experiment design matrix |

interactionLevel |
Generate levels for all interacting factors |

pairLevel |
Pair levels for paired RILs (or strains) |

plotAllScores |
Plot scores profiles |

temperatureStep |
Calculate the temperature decreasing step for simulated annealing process |

updateDesign |
Updates current design |

variableNames |
Generate variable names for all factors |

variableNumber |
Compute the number of variables in the experiment |