It looks like the p-value is calculated as follows: pf(summ$fstatistic[1], summ$fstatistic[2], summ$fstatistic[3], lower.tail = FALSE)
You can format it like it is in the summary by wrapping that in format.pval(). Best, Will William Gearty williamgearty.com On Tue, Dec 10, 2019 at 1:33 PM Rafael S Marcondes <raf.marcon...@gmail.com> wrote: > Hi all, > > I'm having a hard time figuring out how to extract the p-value from a PGLS > model fitted in caper. > > When I run summary(mod) and print it, I get, among other things: > > >summ=summary(mod) > >summ > Coefficients: > Estimate Std. Error t value Pr(>|t|) > (Intercept) 0.0179553 0.0243379 0.7378 0.4613664 > scaled_precip -0.0292664 0.0040679 -7.1945 7.474e-12 *** > scaled_temp 0.0162603 0.0048189 3.3743 0.0008592 *** > --- > Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > > Residual standard error: 0.0148 on 247 degrees of freedom > Multiple R-squared: 0.1739, Adjusted R-squared: 0.1672 > F-statistic: 25.99 on 2 and 247 DF, p-value: 5.69e-11 > > What I'm interested in is the very last value printed, 5.69e-11. But I > can't find where it's actually stored in the summ object. I've already > tried every $ in summ but don't see that value anywhere. How can I actually > extract it from the object? > > Thanks! > > > > *--* > *Rafael Sobral Marcondes* > PhD Candidate (Systematics, Ecology and Evolution/Ornithology) > > Museum of Natural Science <http://www.lsu.edu/mns/> > Louisiana State University > 119 Foster Hall > Baton Rouge, LA 70803, USA > > <http://goog_27804804> > www.rafaelmarcondes.com > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
