Functions to support master thesis

boxplots_with_checks | Boxplots with checks alongside the boxes |

calculateH2 | Compute the broad-sense heritability from a mixed model... |

crossValidate | Cross-validation function |

CVcommit | Function to make a CV scheme based on a commited test set. |

CVincompleteTrial | Function to make a CV scheme based on random sampling of... |

CVrandomAccrossFactor | Function to make a CV scheme based on random sampling of... |

CVrandomByID | Function to make a CV scheme based on random sampling of... |

CVrandomWithinFactor | Function to make a CV scheme based on random sampling of... |

data-exampleCV | Example data for CV functionalities used in thesis |

dataframe.to.list | Convert data frame to list |

data-G | Realization of the G-matrix used in thesis |

data-genotypes | Raw SNP marker data used in thesis |

data-M | Cleaned numeric SNP marker data used in thesis |

data-Mraw | Numeric SNP marker data used in thesis |

data-P | Modeled cleaned phenotypic data used in thesis |

data-phenotypes | Raw phenotype data used in thesis |

data-Praw | Modeled phenotypic data used in thesis |

inferenceBGLR | Function to make inference on a cross validation analysis and... |

list.to.dataframe | Transform a list of data frames to one data frame |

LR.test.asreml | Likelihood ratio test for two asreml-models. |

make_design_rectangular | Add observations to a data frame so that the design is... |

makeG | Make genomic relationship matrix using Van Raden (2008) |

makeZ | Make a centered (scaled) genetic marker matrix |

MaStatThesisRuud | MaStatThesisRuud |

permute | Function to generate a table of combinations when applying... |

plotCV | Plot a CV scheme based on crossValidate function |

plotCVThesisData | Plot a CV scheme for the data used in the thesis |

plotFields | Create a field-layout plot from a data frame. |

plotResiduals | Plot a series of residual plots obtained from a linear mixed... |

plotVariogram | Plot variogram from residuals |

summarizeInference | Summarize the inference results from from inferenceBGLR |

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