Thank you Stephen and Peter for your code and your answers!
Stephen, your NaN explanation makes sense - thank you for putting it so clearly.
Cheers,
Jenny
On Tue, Apr 2, 2019 11:10 AM, peter dalgaard pda...@gmail.com wrote:
>> My questions:1) Why is there a "-" instead of a numerical result for pairs
1-2,
>> 1-16, and 2-16?
>
> When the difference between the pair is zero, the p.value is NaN (not a
number).
>
Not quite: When both groups have 0 successes (or both 0 failures), the test stat
has a divide-by-zero condition.
>> 2) Is there an easy way to export/convert the result to a list with two
columns
>> instead of the matrix? Column 1 would be the pair being compared, and column
2
>> would be the p-value. For example, Column 1 would say "6-8" so column 2 would
>> say "0.9532".
>
> Fairly easy:
>
> idx <- expand.grid(2:16, 1:15)
> pair <- as.matrix(idx[idx[,1] > idx[,2], ])
> mode(pair) <- "character"
> comp <- apply(pair, 1, paste0, collapse="-")
> tbl <- data.frame(comp, p.value=EggResults$p.value[pair])
> head(tbl)
> # comp p.value
> # 1 2-1 NaN
> # 2 3-1 2.706354e-24
> # 3 4-1 1.487240e-23
> # 4 5-1 1.946384e-31
> # 5 6-1 4.888537e-25
> # 6 7-1 7.683167e-41
>
Somewhat neater:
> out <- pairwise.prop.test(smokers, patients)
[....]
> pmat <- out$p.value
> ix <- lower.tri(pmat, diag=TRUE)
> R <- rownames(pmat)[row(pmat)[ix]]
> C <- colnames(pmat)[col(pmat)[ix]]
> data.frame(row.vs.col = paste(R,C,sep="-"), adj.p = pmat[ix])
row.vs.col adj.p
1 2-1 1.00000000
2 3-1 1.00000000
3 4-1 0.11856482
4 3-2 1.00000000
5 4-2 0.09321728
6 4-3 0.12376805
Also, labeling seems to work if you label the original data appropriately, e.g.
> names(smokers) <- names(patients) <- as.roman(1:4)
> out <- pairwise.prop.test(smokers, patients)
[....]
> ix <- lower.tri(pmat, diag=TRUE)
> pmat <- out$p.value
> R <- rownames(pmat)[row(pmat)[ix]]
> C <- colnames(pmat)[col(pmat)[ix]]
> data.frame(row.vs.col = paste(R,C,sep="-"), adj.p = pmat[ix])
row.vs.col adj.p
1 II-I 1.00000000
2 III-I 1.00000000
3 IV-I 0.11856482
4 III-II 1.00000000
5 IV-II 0.09321728
6 IV-III 0.12376805
-pd
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd....@cbs.dk Priv: pda...@gmail.com
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