Merge data frames based on rownames in R

See ?merge:

the name “row.names” or the number 0 specifies the row names.

Example:

R> de <- merge(d, e, by=0, all=TRUE)  # merge by row names (by=0 or by="row.names")
R> de[is.na(de)] <- 0                 # replace NA values
R> de
  Row.names   a   b   c   d   e   f   g   h   i  j  k  l  m  n  o  p  q  r  s
1         1 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10 11 12 13 14 15 16 17 18 19
2         2 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9  1  0  0  0  0  0  0  0  0  0
3         3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0  0 21 22 23 24 25 26 27 28 29
   t
1 20
2  0
3 30

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