Bradley-Terry model for contingency table
This function calculates statistics under Bradley-Terry model.
bt(x)
x |
the data table |
The returned value is a list containing:
y |
A column of 1 |
count |
the frequency count/weight |
allele |
the design matrix |
bt.glm |
a glm.fit object |
etdt.dat |
a data table that can be used by ETDT |
Bradley RA, Terry ME (1952) Rank analysis of incomplete block designs I. the method of paired comparisons. Biometrika 39:324–345
Sham PC, Curtis D (1995) An extended transmission/disequilibrium test (TDT) for multi-allelic marker loci. Ann. Hum. Genet. 59:323-336
Adapted from a SAS macro for data in the example section
Jing Hua Zhao
## Not run:
# Copeman JB, Cucca F, Hearne CM, Cornall RJ, Reed PW,
# Ronningen KS, Undlien DE, Nistico L, Buzzetti R, Tosi R, et al.
# (1995) Linkage disequilibrium mapping of a type 1
# diabetes susceptibility gene (IDDM7) to chromosome 2q31-q33.
# Nat Genet 9: 80-5
x <- matrix(c(0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
0,0, 1, 3, 0,0, 0, 2, 3, 0, 0, 0,
2,3,26,35, 7,0, 2,10,11, 3, 4, 1,
2,3,22,26, 6,2, 4, 4,10, 2, 2, 0,
0,1, 7,10, 2,0, 0, 2, 2, 1, 1, 0,
0,0, 1, 4, 0,1, 0, 1, 0, 0, 0, 0,
0,2, 5, 4, 1,1, 0, 0, 0, 2, 0, 0,
0,0, 2, 6, 1,0, 2, 0, 2, 0, 0, 0,
0,3, 6,19, 6,0, 0, 2, 5, 3, 0, 0,
0,0, 3, 1, 1,0, 0, 0, 1, 0, 0, 0,
0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
0,0, 1, 0, 0,0, 0, 0, 0, 0, 0, 0),nrow=12)
# Bradley-Terry model, only deviance is available in glm
# (SAS gives score and Wald statistics as well)
bt.ex<-bt(x)
anova(bt.ex$bt.glm)
summary(bt.ex$bt.glm)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.