Paired t-test in R - r

Question

I am trying to run a paired t-test in R on data grouped by factors:
> head(i.o.diff,n=20)
# Difference Tree.ID Tree.Name Ins Outs
#1 0.20 AK-1 Akun 1.20 1.0
#2 -1.60 AK-2 Akun 0.40 2.0
#3 -0.60 AK-3 Akun 1.40 2.0
#4 0.40 AK-4 Akun 0.40 0.0
#5 1.30 AK-5 Akun 1.80 0.5
#6 2.70 J-1 Jaror 10.20 7.5
#7 6.60 J-2 Jaror 10.60 4.0
#8 2.50 J-3 Jaror 6.00 3.5
#9 7.50 J-4 Jaror 22.00 14.5
#10 -4.50 J-5 Jaror 5.00 9.5
#11 3.50 Ce-1 Ku'ch 4.00 0.5
#12 -0.70 Ce-2 Ku'ch 4.80 5.5
#13 1.60 Ce-3 Ku'ch 2.60 1.0
#14 -2.40 Ce-4 Ku'ch 2.60 5.0
#15 -1.75 Ce-5 Ku'ch 2.25 4.0
I first tried using:
pairwise.t.test(i.o.diff$In,i.o.diff$Out,g=i.o.diff$Tree.Name,paired=TRUE,pool=FALSE,p.adj="none",alternative=c("less"),mu=0)
but I get the error
Error in complete.cases(x, y) : not all arguments have the same length
which doesn't make a whole lot of sense to me.
I considered using ddply(), apply(), and summaryBy(), but couldn't get it to work because the inputs for the paired t-test require 2 vectors and most of the previous functions I mention seem to work best when only one column is being "operated" upon.
In order to get around this, I tried to use a for loop to achieve the same end:
for(i in unique(i.o.diff$Tree.Name)) {
pair_sub<-subset(i.o.diff,Tree.Name==i)
t.pair<-t.test(pair_sub$Ins,pair_sub$Outs,paired="True")
print(t.pair)
}
However when I do this, I get error
in paired || !is.null(y) : invalid 'x' type in x||y
So I checked typeof(pair_sub$Ins). Turns out that type is double, which is numeric, so I am not sure why the paired t-test is not working. Any ideas as to how to fix either of these methods?

Answer 1

Removed the quotes around TRUE in the for loop. Works great now.

Answer 2

From R documentation:
t.test {stats} R Documentation Student’s t-Test:
Description:
Performs one and two sample t-tests on vectors of data. Usage t.test(x, …)
Default S3 method:
t.test(x, y = NULL, alternative = c(“two.sided”, “less”, “greater”), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, …)