I am using the HSD.test function from the agricolae package in R to conduct a TukeyHSD post hoc test. The function works fine except I'm not sure where the p values are hidden. The letters in groups denote significance, but where are the actual p values? Thank you
library(agricolae)
data(sweetpotato)
model<-aov(yield~virus, data=sweetpotato)
out <- HSD.test(model,"virus", group=TRUE,console=TRUE,
main="Yield of sweetpotato\nDealt with different virus")
Study: Yield of sweetpotato
Dealt with different virus
HSD Test for yield
Mean Square Error: 22.48917
virus, means
yield std r Min Max
cc 24.40000 3.609709 3 21.7 28.5
fc 12.86667 2.159475 3 10.6 14.9
ff 36.33333 7.333030 3 28.0 41.8
oo 36.90000 4.300000 3 32.1 40.4
Alpha: 0.05 ; DF Error: 8
Critical Value of Studentized Range: 4.52881
Minimun Significant Difference: 12.39967
Treatments with the same letter are not significantly different.
yield groups
oo 36.90000 a
ff 36.33333 ab
cc 24.40000 bc
fc 12.86667 c
Changing group to FALSE returns the comparisons instead of the compact letter display.
out = HSD.test(model, "virus", group = FALSE)
print(out$comparison)
difference pvalue signif. LCL UCL
cc - fc 11.5333333 0.0686 . -0.8663365 23.9330031
cc - ff -11.9333333 0.0592 . -24.3330031 0.4663365
cc - oo -12.5000000 0.0482 * -24.8996698 -0.1003302
fc - ff -23.4666667 0.0014 ** -35.8663365 -11.0669969
fc - oo -24.0333333 0.0012 ** -36.4330031 -11.6336635
ff - oo -0.5666667 0.9988 -12.9663365 11.8330031