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merge1 <- within(merge(df1, df2, by=c("ID"),all=F),

 AD <- A.x - A.y                                                  

 BD <- B.x - B.y                                                

 CD <- C.x - C.y

 DC <- ifelse(df1$D != df2$D | df1$D == "TOT" | df2$D == "TOT", 1, 0)

})[,c("ID","AD","BD","CD","DC")] 

I want to compare statistics of IDs across two data sets. Imagine each df representing data from one year. This works exactly like I want it to except when I try to add the "DC" variable using an ifelse statement. Some information about the data set is that they are not of equal length and IDs that existed in df1 may not exist in df2 and vice versa. The D variable in each data frame is comprised of organizations. However, I want the new merged df to be a binary of whether or not the ID changed organizations or not. This is why I have an ifelse statement where if D from df1 does not match D from df2 then I want it to output 1. Also if D from either or both data frames happen to be labeled as TOT then I want it to output 1. I only want it to output 0 if df1$D = df2$D and TOT is not assigned to the ID. Can ifelse( statements be used this way or am I doing something wrong? I am a bit new to R so I appreciate the help in advance.

Edit

Here is the resulting error code:

Error in `[<-.data.frame`(`*tmp*`, nl, value = list(TmC = c(1, 1, 0, 1,  : 

 replacement element 1 has 486 rows, need 576

In addition: Warning messages:

1: In if (all.x) all.x <- (nxx <- length(m$x.alone)) > 0L :

 the condition has length > 1 and only the first element will be used

2: In if (all.y) all.y <- (nyy <- length(m$y.alone)) > 0L :

 the condition has length > 1 and only the first element will be used  

3: In is.na(e1) | is.na(e2) :

 longer object length is not a multiple of shorter object length

4: In `!=.default`(nbasumadv1617$Tm, nbasumadv1516$Tm) :

 longer object length is not a multiple of shorter object length

5: In nbasumadv1617$Tm != nbasumadv1516$Tm | nbasumadv1617$Tm == "TOT" |  :

 longer object length is not a multiple of shorter object length

I described a simplified version of the variable names I have here. It worked as I wanted to without the fourth "DC" variable which is actually labeled TmC in my actual code. I believe this code actually produces nothing since it shows me nothing different from what I created without that fourth variable. The first two error messages still showed up without the fourth "DC" variable but that's fine. The last 3 error messages and the TmC replacement element mismatch error are new.

Simply adjust the ifelse call to use the actual merged columns, D.x and D.y, and not their original sources. When you merged, you rendered all columns equal length since by definition a data frame is a list of equal length atomic vectors. But referencing df1$D and df2$D as you originally do can involve different lengths and hence your error.

merge1 <- within(merge(df1, df2, by=c("ID"), all=FALSE),

                 {

                   AD <- A.x - A.y                                                  

                   BD <- B.x - B.y                                                

                   CD <- C.x - C.y

                   DC <- ifelse(D.x != D.y | D.x == "TOT" | D.y == "TOT", 1, 0)

                 } 

          )[,c("ID","AD","BD","CD","DC")]