[R] Problems with LSD.test

[arun]

Hi,
You didn't provide a reproducible example (http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example)  So, it is difficult to comment.

Using the dataset(sweetpotato)

library(agricolae)
data(sweetpotato)
m1<-aov(yield~virus, data=sweetpotato)
df1<-df.residual(m1)
MSerror1<-deviance(m1)/df1
out <- LSD.test(sweetpotato$yield,sweetpotato$virus,df1,MSerror1)

out$statistics
#    Mean      CV  MSerror      LSD
 # 27.625 17.1666 22.48917 8.928965

A.K.


Hi, 
I have been trying to do a LSD test on some data but I get everything except the actual LSD value 

m1 <- aov(T50~WPT , data = P) 
m1 
TukeyHSD(m1) 
df<-df.residual(m1) 
MSerror<-deviance(m1)/df 
LSD.test(P$T50,P$WPT,df,MSerror) 

also tried a few variations but kept getting this same result 

Study: 

LSD t Test for T50 

Mean Square Error:  21.78628 

WPT,  means and individual ( 95 %) CI 

        T50   std.err r       LCL       UCL      Min.      Max. 
a 135.64286 4.0864385 4 127.31905 143.96666 126.00000 144.00000 
b  40.30594 0.5911702 4  39.10177  41.51012  39.00000  41.76923 
c  77.33800 1.9456540 4  73.37483  81.30116  72.00000  81.23077 
d  39.50893 1.6959821 4  36.05433  42.96353  36.42857  42.85714 
e  42.34801 1.3507746 4  39.59657  45.09945  39.56250  46.00000 
f  33.52500 4.1474251 4  25.07697  41.97303  21.60000  40.28571 
g  94.16450 2.9264069 3  88.20361 100.12540  90.85714 100.00000 
h  54.11667 1.4952703 4  51.07090  57.16243  51.00000  58.00000 
i  79.00879 1.2037678 4  76.55680  81.46079  75.69231  81.42857 
j  74.39560 2.1751581 4  69.96495  78.82626  68.00000  77.53846 
k  73.35000 1.6317169 4  70.02630  76.67370  69.00000  76.80000 

alpha: 0.05 ; Df Error: 32 
Critical Value of t: 2.036933 

Minimum difference changes for each comparison 

Means with the same letter are not significantly different. 

Groups, Treatments and means 
a        a       135.6 
b        g       94.16 
c        i       79.01 
c        c       77.34 
c        j       74.4 
c        k       73.35 
d        h       54.12 
e        e       42.35 
e        b       40.31 
ef       d       39.51 
f        f       33.52 

How do I get a LSD value??? 

Thanks