Description Usage Arguments Details
Calculate Coincidence Index
1  coindex(obs, pred, si, best = "high")

obs 
A named vector of observed phenotypic data 
pred 
A named vector of predicted phenotypic data 
si 
Selection index  value from 0 to 1 
best 
String or number signifying what phenotypic values are considered "best." Must be one of the following:

This function calculates the coincidence index as defined by Hamblin and Zimmerman, 1986. (https://doi.org/10.1002/9781118061015.ch8). In the context of this function, its intended use is to compare direct phenotypic selection with indirect selection based upon genomic data. However, it can be used to compare selections made using any two different methods. The formula for the coincidence index is
CI = (C  R) / (T  R)
where T is the number of observed genotypes selected using the selection index, R is the expected number of genotypes among these correctly selected due to chance, and C is the number of coincident genotypes selected using both methods.
For instance, if we have a population of 100 genotypes and a selection index of 0.1, T = 100 * 0.1 = 10 and R = 10 * 0.1 = 1. The value of C will depend upon how many genotypes are selected based upon both observed and predicted data.
A value of 1 indicates identical selections made using the observed and predicted phenotypic values, while a value of 0 indicates that selections based on predicted values were no better than random chance. Note that CI values can be negative. Small samples sizes will lead to high CI variance.
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