If your goal is to convert the three colors to long this can be accomplished with the base R reshape function:
reshape(sample.df, idvar="subject", varying=2:length(sample.df), sep="", direction="long")
Subject time BlueTime RedTime GreenTime subject
1.1 1 1 2 2 2 1
2.1 2 1 5 5 5 2
3.1 3 1 6 6 6 3
1.2 1 2 4 4 4 1
2.2 2 2 6 6 6 2
3.2 3 2 7 7 7 3
1.3 1 3 1 1 1 1
2.3 2 3 2 2 2 2
3.3 3 3 3 3 3 3
The time variable captures the 1,2,3 in the names of the wide variables. The varying argument tells reshape which variables should be converted to long. The sep argument tells reshape to look for numbers at the end of the varying variables that are not separated by any characters, while the direction argument tells the function to attempt a long conversion.
I always add the id variable, even if it is not necessary for future reference.
If your data.frame doesn't have actually have the numbers for the time variable, a fairly simple solution is to change the variable names so that they do. For example, the following would replace "_Pre" with "1" at the end of any such variables.
names(df)[grep("_Pre$", names(df))] <- gsub("_Pre$", "1",
names(df)[grep("_Pre$", names(df))])
