Letters group Games-Howell post hoc in R - r

Question

I use the sweetpotato database included in library agricolae of R:
data(sweetpotato)
This dataset contains two variables: yield(continous variable) and virus(factor variable).
Due to Levene test is significant I cannot assume homogeneity of variances and I apply Welch test in R instead of one-way ANOVA followed by Tukey posthoc.
Nevertheless, the problems come from when I apply posthoc test. In Tukey posthoc test I use library(agricolae) and displays me the superscript letters between virus groups. Therefore there are no problems.
Nevertheless, to perform Games-Howell posthoc, I use library(userfriendlyscience) and I obtain Games-Howell output but it's impossible for me to obtain a letter superscript comparison between virus groups as it is obtained through library(agricolae).
The code used it was the following:
library(userfriendlyscience)
data(sweetpotato)
oneway<-oneway(sweetpotato$virus, y=sweetpotato$yield, posthoc =
'games-howell')
oneway
I try with cld() importing previously library(multcompView) but doesn't work.
Can somebody could helps me?
Thanks in advance.

Answer 1

This functionality does not exist in userfriendlyscience at the moment. You can see which means differ, and with which p-values, by looking at the row names of the dataframe with the post-hoc test results. I'm not sure which package contains the sweetpotato dataset, but using the ChickWeight dataset that comes with R (and is used on the oneway manual page):
oneway(y=ChickWeight$weight, x=ChickWeight$Diet, posthoc='games-howell');
Yields:
### (First bit removed as it's not relevant.)
### Post hoc test: games-howell
diff ci.lo ci.hi t df p
2-1 19.97 0.36 39.58 2.64 201.38 .044
3-1 40.30 17.54 63.07 4.59 175.92 <.001
4-1 32.62 13.45 51.78 4.41 203.16 <.001
3-2 20.33 -6.20 46.87 1.98 229.94 .197
4-2 12.65 -10.91 36.20 1.39 235.88 .507
4-3 -7.69 -33.90 18.52 0.76 226.16 .873
The first three rows compare groups 2, 3 and 4 to 1: using alpha = .05, 1 and 2 have the same means, but 3 and 4 are higher. This allows you to compute the logical vector you need for multCompLetters in multcompView. Based on the example from the manual page at ?multcompView:
### Run oneway anova and store result in object 'res'
res <- oneway(y=ChickWeight$weight, x=ChickWeight$Diet, posthoc='games-howell');
### Extract dataframe with post hoc test results,
### and overwrite object 'res'
res <- res$intermediate$posthoc;
### Extract p-values and comparison 'names'
pValues <- res$p;
### Create logical vector, assuming alpha of .05
dif3 <- pValues > .05;
### Assign names (row names of post hoc test dataframe)
names(dif3) <- row.names(res);
### convert this vector to the letters to compare
### the group means (see `?multcompView` for the
### references for the algorithm):
multcompLetters(dif3);
This yields as final result:
2 3 4 1
"a" "b" "c" "abc"
This is what you need, right?
I added this functionality to userfriendlyscience, but it will be a while before this new version will be on CRAN. In the meantime, you can get the source code for this update at https://github.com/Matherion/userfriendlyscience/blob/master/R/oneway.R if you want (press the 'raw' button to get an easy-to-download version of the source code).
Note that if you need this updated version, you need to set parameter posthocLetters to TRUE, because it's FALSE by default. For example:
oneway(y=ChickWeight$weight,
x=ChickWeight$Diet,
posthoc='games-howell',
posthocLetters=TRUE);

Answer 2

shouldn't it be
dif3 <- pValues < .05, instead of dif3 <- pValues > .05 ?
This way the letters are the same if the distributions are 'the same' (this is, no evidence that they are different).
Please correct me if I'm interpreting this wrong.