Extracting output from statistical tests - r

Question

I run a statistical test in R (running in RStudio). I save the result using a variable name. I want to extract one part of the result. How do I do this?
Here is an example with the R code at the end.
I set up an experiment with four treatments, and gather data. I next run ANOVA and perform a Tukey HSD test. The result is stored in a variable called "posthoc."
I look and note that posthoc is a list of 1. In RStudio I see a little blue arrow to the left of the name, and clicking on that gives more information. I am not sure how to interpret it in a way that I can use to answer my own question.
I can print(posthoc) and I get the following.
# Tukey multiple comparisons of means
# 95% family-wise confidence level
#
#Fit: aov(formula = Expt1$Treat1 ~ Expt1$Trt)
#
#$`Expt1$Trt`
# diff lwr upr p adj
#B-A 6.523841 2.664755 10.38292569 0.0001372
#C-A 18.584160 14.725075 22.44324507 0.0000000
#D-A 2.643719 -1.215367 6.50280370 0.2854076
#C-B 12.060319 8.201234 15.91940456 0.0000000
#D-B -3.880122 -7.739207 -0.02103681 0.0482260
#D-C -15.940441 -19.799527 -12.08135619 0.0000000
I can also type class(posthoc) and I get this:
[1] "TukeyHSD" "multicomp"
In this case, what I need are all the p-values in a new variable. The general problem is that R gives me output and I need to be able to figure out how to extract specific elements of that output. I might be using aov, lm, nlme, or something else.
Mean1=3.2
Sd1=3.2
Mean2=9.4
Sd2=2.4
Mean3=21.4
Sd3=6.4
Mean4=3.9
Sd4=10.7
Size1=30
Treat1=rnorm(Size1,mean=Mean1, sd=Sd1)
Trt="A"
Treat1M <- data.frame(Treat1, Trt)
Treat1=rnorm(Size1,mean=Mean2, sd=Sd2)
Trt="B"
Treat2M <- data.frame(Treat1, Trt)
Treat1=rnorm(Size1,mean=Mean3, sd=Sd3)
Trt="C"
Treat3M <- data.frame(Treat1, Trt)
Treat1=rnorm(Size1,mean=Mean4, sd=Sd4)
Trt="D"
Treat4M <- data.frame(Treat1, Trt)
Expt1=rbind(Treat1M, Treat2M, Treat3M, Treat4M)
Expt1R<-aov(Expt1$Treat1 ~ Expt1$Trt)
posthoc <-TukeyHSD(x=Expt1R, 'Expt1$Trt', conf.level=.95)

Answer 1

simply use subsetting of your posthoc variable.
posthoc$`Expt1$Trt`[,4]
or you can try the broom package.
library(broom)
res <- tidy(posthoc)
res
term comparison estimate conf.low conf.high adj.p.value
1 Expt1$Trt B-A 5.904138 1.3639293 10.444346 5.223255e-03
2 Expt1$Trt C-A 16.886340 12.3461316 21.426548 3.919087e-14
3 Expt1$Trt D-A 4.283597 -0.2566111 8.823805 7.189220e-02
4 Expt1$Trt C-B 10.982202 6.4419940 15.522410 3.226398e-08
5 Expt1$Trt D-B -1.620540 -6.1607487 2.919668 7.886097e-01
6 Expt1$Trt D-C -12.602743 -17.1429509 -8.062534 3.235351e-10
The output of the tidy function is a data.frame. Thus, you can access the p-values using res$adj.p.value.
class(res)
[1] "data.frame"

Answer 2

Jimbou has already provided an excellent solution. I would also go for broom especially when doing plots with ggplot2. I would just like to expound on the comment by John Coleman.
You can inspect the object by using str. In case of posthoc,
str(posthoc)
gives
List of 1
$ Expt1$Trt: num [1:6, 1:4] 6.46 18.19 -0.76 11.74 -7.22 ...
Typing
posthoc$`Expt1$Trt`
gives
diff lwr upr p adj
B-A 6.4562 2.130 10.782 9.530e-04
C-A 18.1922 13.866 22.519 2.454e-14
D-A -0.7598 -5.086 3.566 9.680e-01
C-B 11.7360 7.410 16.062 7.427e-10
D-B -7.2160 -11.542 -2.890 1.725e-04
D-C -18.9521 -23.278 -14.626 1.588e-14
So you can access the fourth column by typing
posthoc$`Expt1$Trt`[,4]
or
posthoc$`Expt1$Trt`[,'p adj']
For some objects like Expt1R, the output of str() can sometimes be overwhelming. Using names() to look at the different objects inside it is also helpful.
names(Expt1R)
[1] "coefficients" "residuals" "effects" "rank" "fitted.values" "assign"
[7] "qr" "df.residual" "contrasts" "xlevels" "call" "terms"
[13] "model"
So
Expt1R$df.residual
will give you the degrees of freedom of the residual.