Demerelate(inputdata, tab.dist = "NA", ref.pop = "NA", object = FALSE, value = "Mxy", Fis = FALSE, file.output = FALSE, p.correct = FALSE, iteration = 1000, pairs = 1000, dis.data = "relative", NA.rm = TRUE, genotype.ref = TRUE)
ref.pop = "NA"
) all information on loci are used as reference by omitting population information.prop.test(...)
be used in $\chi^2$ statistics when calculating p-values on differences between empirical and randomized relatedness in populations.tab.dist
or "decimal" for geographic decimal degrees.return
following objects as one list:NA
. If no additional reference populations are defined, inputdata omitting population information are used to calculate references. If no good reference populations are available you need to take care of bias in calculations. In any case you should consult for example Oliehoek et al. 2006 to get an idea of bias in relatedness calculations.
Geographic distances between individual pairs are calculated when tab.dist =
... . Distances calculated from x-y coordinates by simple Pythagorean mathematics can be applied to any metrical positions in sampling. Geographic coordinates from e.g. GPS need to be transformed to decimal GPS coordinates. Be sure to have positions for each individual or remove missing values from inputdata.
Each calculation will have its unique bar-code and is named with the date and population name. Calculations are performed for each population in the inputdata.
inputformat
Emp.calc
stat.pops
F.stat
## Data set is used to calculate Blouins allele sharing index on
## population data. Pairs are set to 10 for convenience.
## For statistical reason for your final results you may want to
## use more pairs to model relatedness (1000 pairs are recommended).
data(demerelpop)
dem.results <- Demerelate(demerelpop[,1:6], value="Mxy",
file.output=FALSE, object=TRUE, pairs=10)
## Demerelate can be executed with several different values
## should consult the references to decided which estimator may
## be useful in your case.
## Be careful some estimators may be biased in situations with
## no reference populations or violatin of Hardy-Weinberg
## Equilibrium.
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