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When comparing the results of assignClones and GenoType using my own data, the only differences I have seen have been the result of rounding a decimal that was slightly above the threshold in when analyzed in R was rounded down to the threshold when analyzed in GenoType.
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Note that GenoType requires that distances be integers rather than decimals, so you will have to multiply the distances produced by polysat by a large number and round them to the nearest integer if you wish to export them to GenoType. If a distance matrix from polysat is exported to GenoType, the results will be the same as those from assignClones assuming the same threshold is used.
#GENODIVE SAMPLE DATA MATRIX SOFTWARE#
Each clone or group is given a number, and the number for each sample indicates the clone or group to which it belongs.ĭetails: This function groups individuals very similarly to the software GenoType (Meirmans and van Tienderen, 2004). Return Values: A numeric vector, named by samples. # assign clones with a threshold of zero or 0.5 # set up a simple matrix with three samples Install.packages("polysat", repo="", dep=T) A number indicating the maximum distance between two individuals that will be placed into the same group.
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