Вот один вариант с data.table
library(data.table)
setDT(df1)[, .SD[c(.N+1, seq_len(.N))], Scenario][
!duplicated(Scenario), Scenario := 0][]
# Scenario Month A B C
# 1: 0 NA NA NA NA
# 2: 1 1 -0.5931863 1.04555081 -0.5938163
# 3: 1 2 0.1786261 2.04308443 0.1113706
# 4: 1 3 1.2057797 -0.32408372 -1.3977169
# 5: 0 NA NA NA NA
# 6: 2 1 0.9336152 0.05264706 -0.6564862
# 7: 2 2 1.6472917 -1.06579367 0.7990405
# 8: 2 3 1.6136631 -1.95556723 -1.8174580
# 9: 0 NA NA NA NA
#10: 3 1 -0.6219918 1.63406940 -1.4049816
#11: 3 2 -1.8993269 -0.83632239 -1.8263515
#12: 3 3 0.1642351 -1.16070181 1.2382465
Или как @ chinsoon12, упомянутый в комментариях
setDT(df1)[, rbindlist(.(.(Scenario=0L), c(.(Scenario=rep(Scenario, .N)),
.SD)), use.names=TRUE, fill=TRUE), by=.(Scenario)][, -1L]
data
df1 <- structure(list(Scenario = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L
), Month = c(1L, 2L, 3L, 1L, 2L, 3L, 1L, 2L, 3L), A = c(-0.593186301,
0.178626141, 1.205779717, 0.933615199, 1.647291688, 1.613663101,
-0.621991775, -1.899326887, 0.164235141), B = c(1.045550808,
2.043084432, -0.324083723, 0.052647056, -1.065793671, -1.955567231,
1.634069402, -0.836322394, -1.160701812), C = c(-0.593816304,
0.111370583, -1.397716949, -0.656486153, 0.799040546, -1.817457972,
-1.404981646, -1.826351541, 1.238246459)), class = "data.frame",
row.names = c(NA,
-9L))