AA.Aa.aa: The AA-Aa-aa Blood Group System

View source: R/family.genetic.R

AA.Aa.aaR Documentation

The AA-Aa-aa Blood Group System


Estimates the parameter of the AA-Aa-aa blood group system, with or without Hardy Weinberg equilibrium.


AA.Aa.aa(linkp = "logitlink", linkf = "logitlink", inbreeding = FALSE,
         ipA = NULL, ifp = NULL, zero = NULL)


linkp, linkf

Link functions applied to pA and f. See Links for more choices.

ipA, ifp

Optional initial values for pA and f.


Logical. Is there inbreeding?


See CommonVGAMffArguments for information.


This one or two parameter model involves a probability called pA. The probability of getting a count in the first column of the input (an AA) is pA*pA. When inbreeding = TRUE, an additional parameter f is used. If inbreeding = FALSE then f = 0 and Hardy-Weinberg Equilibrium (HWE) is assumed. The EIM is used if inbreeding = FALSE.


An object of class "vglmff" (see vglmff-class). The object is used by modelling functions such as vglm and vgam.


Setting inbreeding = FALSE makes estimation difficult with non-intercept-only models. Currently, this code seems to work with intercept-only models.


The input can be a 3-column matrix of counts, where the columns are AA, Ab and aa (in order). Alternatively, the input can be a 3-column matrix of proportions (so each row adds to 1) and the weights argument is used to specify the total number of counts for each row.


T. W. Yee


Weir, B. S. (1996). Genetic Data Analysis II: Methods for Discrete Population Genetic Data, Sunderland, MA: Sinauer Associates, Inc.

See Also

AB.Ab.aB.ab, ABO, A1A2A3, MNSs.


y <- cbind(53, 95, 38)
fit1 <- vglm(y ~ 1, AA.Aa.aa, trace = TRUE)
fit2 <- vglm(y ~ 1, AA.Aa.aa(inbreeding = TRUE), trace = TRUE)
rbind(y, sum(y) * fitted(fit1))
Coef(fit1)  # Estimated pA
Coef(fit2)  # Estimated pA and f

VGAM documentation built on Sept. 19, 2023, 9:06 a.m.