counting the frequency of value in a column [duplicate]

Answer 1

Assuming your data is called dat:

intm <- aggregate(Likelihood ~ Pathway, data=dat, FUN=table)
data.frame(Pathway=intm$Pathway, intm$Likelihood)

#  Pathway likely possible unlikely
#1       A      0        1        3
#2       B      0        2        2
#3       C      2        2        0
#4       D      0        4        0
#5       E      1        2        1

Or all in one line:

do.call(data.frame, aggregate(Likelihood ~ Pathway, data=dat, FUN=table))

#  Pathway Likelihood.likely Likelihood.possible Likelihood.unlikely
#1       A                 0                   1                   3
#2       B                 0                   2                   2
#3       C                 2                   2                   0
#4       D                 0                   4                   0
#5       E                 1                   2                   1