hwde | R Documentation |
Fits models for genotypic disequilibria, as described in Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986).
hwde(data = hwde::IndianIrish, gp = "Population", termlist = NULL, refmodel = NULL,
loci = paste("locus", 1:(dim(data)[2] - 1), sep = ""), observed = "Observed",
keep.models = FALSE, aovtable.print = TRUE, group.terms = TRUE, allele.chars = letters)
data |
Must have a column of frequencies, by default called
|
gp |
Gives the name of the column, if any, that has information on groups within the data. |
termlist |
Use to specify a user-defined sequence of models. See the vignette hwde.pdf or hwde.html |
refmodel |
For each model in |
loci |
Gives name(s) of columns that hold information on
genotypes. By default, these are taken to be |
observed |
Name (by default |
keep.models |
Should a list be returned that holds the full sequence of models that were fitted? |
aovtable.print |
Should the anova table be printed? |
group.terms |
Should model terms be grouped according to hierarchy, for the anova table? |
allele.chars |
A sequence of letters used to code for the loci. By default a, b, c, ... are used |
See the document hwde.pdf or hwde.html for details. See the references (below) for information on the interpretation of model parameters.
anovatab |
anova (analysis of deviance) table |
data.df |
Data, and contrasts used in fitting the various models. |
aovtab.terms |
This string holds, for each model that is fitted. the terms that have appeared in the model formula. The text strings for the distinct models are concatenated. |
models |
Optionally, this holds the complete sequence of qmodel objects that were fitted |
J.H. Maindonald
1. Huttley, G.A. and Wilson, S.R. 2000. Testing for concordant
equilibria between population samples. Genetics 156:2127-2135.
2. Weir, B.S. 1996. Genetic Data Analysis II. Sinauer.
3. Weir, B.S. and Wilson, S.R. 1986. Log-linear models for
linked loci. Biometrics 42:665-670.
make.contrasts
, decode.genotypes
data(IndianIrish)
hwde(data=IndianIrish)
data(mendelABC)
hwde(data=mendelABC, loci=c("seedshape", "cotylcolor", "coatcolor"))
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