[R] Pairwise testing with pairwise.prop.test

[Jenny Liu]

Thank you very much David, your answers are so clear and helpful!!

Have a great week.

Cheers,
Jenny

On Mon, Apr 1, 2019, 11:53 AM David L Carlson, <dcarlson using tamu.edu> wrote:

> Inline
>
> ----------------------------------------
> David L Carlson
> Department of Anthropology
> Texas A&M University
> College Station, TX 77843-4352
>
> -----Original Message-----
> > From: R-help <r-help-bounces using r-project.org> On Behalf Of Jenny Liu
> > Sent: Sunday, March 31, 2019 6:10 PM
> > To: r-help using r-project.org
> > Subject: [R] Pairwise testing with pairwise.prop.test
> >
> > Hi all,
> >
> > I have a few questions about the pairwise.prop.test function.
> > I run the test using on the attached dataset (EggMortNoTemp) using the
> following
> > code:
> > EggMatrix<-as.matrix(EggMortNoTemp) #making the egg mortality data a
> matrix.
> > pairwise.prop.test needs it to be a matrix
> > EggResults<-pairwise.prop.test(EggMatrix) EggResults
> > I get the attached result (EggResults).
> > 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).
>
> > 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
>
> > 3) Is there a way to assign the numbers to the treatment group that they
> were
> > originally in? For example, "1" in the result should be "3", indicating
> that
> > that was the temperature the experiment took place at. Pairwise.prop.test
> > doesn't seem to accept matrices with more than 2 columns.
>
> No. The test is to do the pairwise comparisons between the samples. The
> treatment group is not considered. You would have to use another test that
> compared the samples by treatment group (instead of pairwise comparisons).
>
> > Any help would be greatly appreciated! Thank you in advance.
> > Cheers,Jenny
>
>

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