AA.Aa.aa: The AA-Aa-aa Blood Group System In VGAM: Vector Generalized Linear and Additive Models

 AA.Aa.aa R Documentation

The AA-Aa-aa Blood Group System

Description

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

Usage

ipA = NULL, ifp = NULL, zero = NULL)

Arguments

 linkp, linkf Link functions applied to pA and f. See Links for more choices. ipA, ifp Optional initial values for pA and f. inbreeding Logical. Is there inbreeding? zero See CommonVGAMffArguments for information.

Details

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.

Value

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

Warning

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

Note

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

References

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

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

Examples

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
summary(fit1)

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