calc.nnfit: Calculate the nearest neighbour fit.
In MDSMap: High Density Genetic Linkage Mapping using Multidimensional Scaling

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.