Question

I’m working in R. I have a dataframe, df that looks like this:

> str(exp)
'data.frame':   691200 obs. of  19 variables:
 $ groupname: Factor w/ 8 levels "rowA","rowB",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ location : Factor w/ 96 levels "c1","c10","c11",..: 1 2 3 4 12 23 34 45 56 67 ...
 $ starttime: num  0 0 0 0 0 0 0 0 0 0 ...
 $ inadist  : num  0 0.2 0 0.2 0.6 0 0 0 0 0 ...
 $ smldist  : num  0 2.1 0 1.8 1.2 0 0 0 0 3.3 ...
 $ lardist  : num  0 0 0 0 0 0 0 0 0 1.3 ...
 $ fPhase   : Factor w/ 2 levels "Light","Dark": 2 2 2 2 2 2 2 2 2 2 ...
 $ fCycle   : Factor w/ 6 levels "predark","Cycle 1",..: 1 1 1 1 1 1 1 1 1 1 ...

I’d like to add another column, timepoint, that gives the starttime relative to the beginning of the fCycle it is in. So starttime=1801 would be timepoint=1 for fCycle='Cycle 1'.

What is the best way to create df$timepoint?

ETA toy dataset:

starttime fCycle timepoint
1         1      1
2         1      2
3         1      3
4         1      4
5         2      1
6         2      2
7         2      3
8         2      4
9         3      1
10        3      2
11        3      3
12        4      1
13        4      2
14        4      3
15        5      1
16        5      2
17        6      1
18        6      2
19        6      3
20        6      4

Answer 1

You can combine rle with sequence. Here is some sample code. Is the output what you were looking for?

require(plyr)

mydf = data.frame(
  starttime = 1:20,
  fCycle    = c(rep(1:3, each = 4), rep(4:5, each = 3), rep(6, 2))
)

# sort data in increasing order of cycle and starttime
mydf = arrange(mydf, fCycle, starttime)

mydf = transform(mydf, timepoint = sequence(rle(fCycle)$lengths))

NOTE: In the light of the fact that there could be identical starttimes within the same fCycle, here is an alternate approach using rank and ddply

# treat same starttimes in an fcycle identically
ddply(mydf, .(fCycle), transform, timepoint = rank(starttime, ties = 'min'))

# treat same starttimes in an fcycle using average
ddply(mydf, .(fCycle), transform, timepoint = rank(starttime, ties = 'average'))