CODEWITHSUNDEEP
rnormal-distributionanova
mo.frss
mo.frss

Reputation: 11

"contrasts can be applied only to factors with 2 or more levels" Despite having multiple levels in each factor

I am working on a two-way mixed ANOVA using the data below, using one dependent variable, one between-subjects variable and one within-subjects variable. When I tested the normality of the residuals, of the dependent variable, I find that they are not normally distributed. But at this point I am able to perform the two-way ANOVA. Howerver, when I perform a log10 transformation, and run the script again using the log transformed variable, I get the error "contrasts can be applied only to factors with 2 or more levels". 

> str(m_runjumpFREQ)
'data.frame':   564 obs. of  8 variables:
 $ ID1            : int  1 2 3 4 5 6 7 8 9 10 ...
 $ ID             : chr  "ID1" "ID2" "ID3" "ID4" ...
 $ Group          : Factor w/ 2 levels "II","Non-II": 1 1 1 1 1 1 1 1 1 1 ...
 $ Pos            : Factor w/ 3 levels "center","forward",..: 2 1 2 3 2 2 1 3 2 2 ...
 $ Match_outcome  : Factor w/ 2 levels "W","L": 2 2 2 2 2 2 2 2 2 1 ...
 $ time           : Factor w/ 8 levels "runjump_nADJmin_q1",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ runjump        : num  0.0561 0.0858 0.0663 0.0425 0.0513 ...
 $ log_runjumpFREQ: num  -1.25 -1.07 -1.18 -1.37 -1.29 ...

Some answers on StackOverflow to this error have mentioned that one or more factors in the data set, used for the ANOVA, are of less than two levels. But as seen above they are not. Another explanation I have read is that it may be the issue of missing values, where there may be NA's. There is:

 m1_nasum <- sum(is.na(m_runjumpFREQ$log_runjumpFREQ))
> m1_nasum
[1] 88

However, I get the same error even after removing the rows including NA's as follows.

> m_runjumpFREQ <- na.omit(m_runjumpFREQ)
> m1_nasum <- sum(is.na(m_runjumpFREQ$log_runjumpFREQ))
> m1_nasum
[1] 0

I could run the same script without log transformation and it would work, but with it, I get the same error. The factors are the same either way and the missing values do not make a difference. Either I am doing a crucial mistake or the issue is in the line of the log transformation below.

log_runjumpFREQ <- log10(m_runjumpFREQ$runjump)
m_runjumpFREQ <- cbind(m_runjumpFREQ, log_runjumpFREQ)

I appreciate the help.

Upvotes: 0

Views: 422

Answers (1)

G. Grothendieck
G. Grothendieck

Reputation: 269586

It is not good enough that the factors have 2 levels. In addition those levels must actually be present. For example, below f has 2 levels but only 1 is actually present.

y <- (1:6)^2
x <- 1:6

f <- factor(rep(1, 6), levels = 1:2) 
nlevels(f)  # f has 2 levels
## [1] 2

lm(y ~ x + f)
## Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
##   contrasts can be applied only to factors with 2 or more levels

Upvotes: 1

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