confint and adjust in R [General Sta­tis­tics]

posted by ElMaestro  – Belgium?, 2019-01-07 18:12 (622 d 02:41 ago) – Posting: # 19754
Views: 2,710

Dear d_labes,

» What you describe must be an effect of using an add-on package with comes with the possibility to consider multiplicity in calculation of confidence intervals.

Thanks a lot for commenting :-)

Can you try this:

library("lsmeans")
set.seed(12341)
v1=c(rep("A",10),rep( "B",10), rep( "C", 10))
v2=c(rep("Q",10),rep( "W",10), rep( "E",10))
Foo=sample(v1)
Bar=sample(v2)
y=runif(30)
M=lm(y~factor(Foo)+factor(Bar))

confint(pairs(lsmeans(M, "Foo")), adjust="none")
confint(pairs(lsmeans(M, "Foo")), adjust="bonferroni")
confint(pairs(lsmeans(M, "Foo")), adjust="eat.my.shorts")
confint(pairs(lsmeans(M, "Foo")))
# HAPPY NEW YEAR


It gives four different results here. You can see adjust is passed as an argument to the confint function so can't see how it would be part of lsmeans or pairs args.

I could be wrong, but...

Best regards,
ElMaestro

R's base package has 274 reserved words and operators, along with 1761 functions. I can use 18 of them (about 14 of them properly). I believe this makes me the Donald Trump of programming.

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