r - using multcompLetters to add connecting letters -

r - using multcompLetters to add connecting letters -

i hope there has 2 minutes explain me 2 things. have code run on pretty big dataset. using multcompletters add together connecting letters boxplots. have experiment setup 4 treatments , 2 genotypes aov y ~ treat+geno+geno:treat. when run code treatment (3df) or interaction (7df) seems work quite ok time. when run on geno(here x) error.

error in multcompletters(t$x[, 1]) : names required t$x[, 1]

and cant find out why.

2nd question -

what [,4] mean in

groups2 <- multcompletters(t$x[,4])

??

the code mockup made u:

#rgr ~ geno boxplot y<-c(1,2,6,4,5,7,2,3,9,7,5,6,4,3,2,3,4,5,4,5) x<-c("no","yes","no","yes","no","yes","no","yes","no","yes", "no","yes","no","yes","no","yes","no","yes","no","yes") fit <- aov(y~x) summary(fit) t <- tukeyhsd(aov(fit)) t names(t) boxplot(y~x, data=for.r, ylim=c(0,10),xlab="some", ylab="else") tp <- extract_p(t) tp groups2 <- multcompletters(t$x[,4]) lets <- groups2$letters[c(4,1:3)] text(1:4, 95 ,lets)

thanks.

what multcompletters expects matrix of values, because expected more 1 comparison. in data, have 1 comparison, yes vs no. if within t$x variable, can see matrix:

t$x # diff lwr upr p adj # yes-no 0.3 -1.631884 2.231884 0.747998

typically, there many rows here. unfortunately, when select 1 row matrix, of row names dropped, , multcompletters needs names. example:

t$x[,4] # [1] 0.747998 # no names.

to prevent this, have add together parameter subselect:

t$x[,4,drop=false] # p adj # yes-no 0.747998 # names intact multcompletters(t$x[,4,drop=false]) # works. # $letters # yes-no # "a" # # $lettermatrix # # yes-no true

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