You want to transform variables by performing operations on groups of data, as specified by a grouping variable.

Use ddply() from the plyr package with the transform() function, and specify the operations:

library(MASS) # For the data set
library(plyr)
cb <- ddply(cabbages, "Cult", transform, DevWt = HeadWt - mean(HeadWt))

 Cult Date HeadWt VitC       DevWt
  c39  d16    2.5   51 -0.40666667
  c39  d16    2.2   55 -0.70666667
 ...
  c52  d21    1.5   66 -0.78000000
  c52  d21    1.6   72 -0.68000000

Let’s take a closer look at the cabbages data set. It has two grouping variables (factors): Cult, which has levels c39 and c52, and Date, which has levels d16, d20, and d21. It also has two measured numeric variables, HeadWt and VitC: