R package for combining p-values using Fisher's or Stouffer's method

Question

Is there an R package (or even a base R function) that implements Fisher's or Stouffer's method for combining p-values? Coding this should be almost trivial, but I'd rather use (and cite) a package.

Example code in this question: Fisher's method for combing p-values - what about the lower tail?

score 13 · Accepted Answer · edited Apr 13 '17 at 12:44

13

The metap package by Michael Dewey implements many methods for combining p-values:

sumlog: Fisher's method
sumz: Looks like Stouffer's method (with weights), this isn't mentioned explicitly in the function's documentation but confirmed in the draft vignette (which is not part of the package yet)
meanp: When combining p-values, why not just averaging?
...

edited Apr 13 '17 at 12:44

Community

1

answered Aug 21 '15 at 17:43

krlmlr

779

The vignette is now in the distributed package. – mdewey Apr 09 '16 at 12:12

score 5 · Answer 2 · answered Aug 22 '15 at 12:37

5

There's also the combine.test function in the survcomp package (on Bioconductor). Implements Fisher's and Stouffer's method, as well as the logit method.

answered Aug 22 '15 at 12:37

krlmlr

779

survcomp also works in the edge case of a single pvalue, handles missing values more consistently with base r and encourages contributions by providing an official repo. – jan-glx Jan 16 '19 at 10:17

score 2 · Answer 3 · answered Jun 04 '20 at 06:57

2

There is poolr package by Ozan Cinar and Wolfgang Viechtbauer. It includes functions for both Fisher and Stouffer methods.

answered Jun 04 '20 at 06:57

Maksim Terpilowski

141

Perhaps worth pointing out that it allows for non-independent p-values. – mdewey Jun 16 '20 at 15:55

R package for combining p-values using Fisher's or Stouffer's method

3 Answers3