Description Usage Arguments Details Value See Also

Calculates the total, mean and individual differences between the observed and estimated distances from all loci and their nearest neighbours with non-zero LOD scores.

1 | ```
calc.nnfit(distmap, lodmap, estmap)
``` |

`distmap` |
Symmetric matrix of pairwise inter-marker distances with columns and rows corresponding to the estimated map order. |

`lodmap` |
Symmetric matrix of pairwise lod scores with columns and rows corresponding to the estimated map order. |

`estmap` |
Vector of estimated marker positions. |

The nearest neighbour fit for a marker is the sum of the difference between the observed and estimated distances between the marker and its nearest informative neighbour. A neighbour is informative if the LOD score for the inter-marker distance is greater than zero. This function calculates the nearest neighbour fit for each marker and returns the fit for each point and the sum of all the fits.

A list with the elements:

`fit` |
Sum of the nearest neighbour fits over all markers. |

`pointfits` |
Vector of nearest neighbour fits for each marker. |

`meanfit` |
Mean of the nearest neighbour fits over all markers. |

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