[R] two-sample test of multinomial proportion

[Gustaf Rydevik]

Hi all,

This is perhaps more a statistics question than an R question, but I
hope it's OK anyhow.

I have some data (see below) with the number of tests positive to
subtype H1 of a virus, the number of tests postive to subtype H3, and
the total number of tests. This is for two different groups, and the
two subtypes are mutually exclusive.

What is the best way to test if the proportion of H1 tests to all
positive tests differ between the two groups?
I could run prop.test() on just the H1 and H3 part of the data,
ignoring the total number of tests. But this seem to skip some
information regarding variance of H1/H3 in the two groups, so I don't
think it is correct.

I've tried using a bootstrap approach on the ratio of the two
proportions, but there must be a smarter way.
Any help is much appreciated!

Best regards,

Gustaf Rydevik


####data and bootstrap attempt ###
multi.data<-data.frame(
                  group=c("a","b"),
                  H1=c(2,12),
                  H3=c(21,46),
                  tests=c(189,411)
)
multi.ind<-data.frame(Type=
rep(c("H1","H3","Neg"),c(2+12,21+46,189+411-2-12-21-46)),
group=rep(c("a","b","a","b","a","b"),c(2,12,21,46,189-2-21,411-12-46))
)

props1<-vector(mode="numeric",length=1000)
props2<-vector(mode="numeric",length=1000)
for(i in 1:1000){
sub.tab<-t(table(Subtyp.orig[sample(1:nrow(Subtyp.orig),nrow(Subtyp.orig),replace=TRUE),]))
props1[i]<-sub.tab[1,1]/(sub.tab[1,1]+sub.tab[1,2])
props2[i]<-sub.tab[2,1]/(sub.tab[2,1]+sub.tab[2,2])
}
sub.kvot<-props1/props2
sort(sub.kvot)[50]
sort(sub.kvot)[950]



-- 
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik