from absolute numbers to proportion in two level data (R! SAC? plyr?)

Question

I have data nested in to levels:

L1 L2   x1 x2 x3 x4
A  This 20 14 12 15
A  That 11 NA 8  16
A  Bat  Na 22 13  9
B  This 10  9 11  6
B  That 3   3  1 NA
B  Bat  4  10  2  8

Now I want something simply - and I feel I have been able to do this just last month. But something has gone missing in my head: I want percentages (ignoring NA), summing to 100 for each variable in L1

L1 L2   x1  x2   x3   x4
A  This 65% 39%  36%  38%
A  That 35%  0%  24%  40%
A  Bat   0% 61%  40%  22%

I can get the totals I need with

cast(L1~variable, data=melt(d, na.rm=T),sum)

But I guess it should be possible to cook up a function that gives me what I want? I tried various approaches with cast and plyr... But it seams xmas has already brought to many beers to my frail brain.

Any help will be appreciated - as will any refrain from a downvote.

Thanx

this is my data:

d <- structure(list(level1 = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 
2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 
6L, 6L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 10L, 10L, 10L, 10L, 
11L, 11L, 11L, 11L, 11L, 11L, 9L, 9L, 9L, 9L, 9L, 12L, 12L, 12L, 
12L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L, 14L, 14L, 14L, 14L, 
15L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 16L, 16L, 17L, 17L, 
17L, 17L, 17L, 18L, 18L, 18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L, 
19L, 19L), .Label = c("a", "b", "c", "d", "e", "f", "g", "h", 
"i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s"), class = "factor"), 
level2 = structure(c(6L, 2L, 1L, 3L, 5L, 6L, 1L, 3L, 5L, 
6L, 1L, 3L, 5L, 6L, 5L, 6L, 1L, 3L, 5L, 4L, 6L, 2L, 1L, 3L, 
5L, 6L, 1L, 5L, 4L, 6L, 2L, 1L, 3L, 5L, 6L, 1L, 3L, 5L, 6L, 
2L, 1L, 3L, 5L, 4L, 6L, 2L, 1L, 3L, 5L, 6L, 1L, 3L, 5L, 6L, 
2L, 1L, 3L, 5L, 4L, 6L, 2L, 1L, 3L, 5L, 4L, 6L, 2L, 1L, 3L, 
5L, 6L, 2L, 1L, 3L, 5L, 4L, 6L, 2L, 1L, 3L, 5L, 6L, 2L, 1L, 
3L, 5L, 4L, 6L, 2L, 1L, 3L, 5L, 4L), .Label = c("This", "That", 
"Phat", "Bat", "Man", "Hat"), class = "factor"), X2002 = c(28L, 
9L, 17L, 8L, 95L, 18L, NA, NA, 36L, 40L, 15L, 10L, 71L, NA, 
14L, 25L, 18L, NA, 56L, 5L, 29L, 5L, 13L, 8L, 65L, 23L, 8L, 
34L, NA, 14L, 5L, 5L, NA, 51L, 18L, NA, 5L, 56L, 30L, 8L, 
9L, 11L, 77L, 5L, 53L, 12L, 16L, 13L, 114L, 30L, 8L, NA, 
52L, 38L, NA, 12L, 5L, 87L, 5L, 35L, NA, 10L, 6L, 92L, 10L, 
41L, NA, 22L, 8L, 115L, 27L, 6L, 9L, NA, 47L, 9L, 29L, 6L, 
11L, NA, 56L, 38L, 7L, 10L, NA, 93L, 6L, 22L, 9L, 9L, NA, 
59L, 5L), X2003 = c(32L, NA, 16L, 9L, 76L, 10L, NA, 5L, 24L, 
22L, 12L, 9L, 63L, 12L, 9L, 36L, 9L, 6L, 83L, 5L, 35L, NA, 
12L, 8L, 82L, 19L, 5L, 53L, 5L, 10L, NA, 7L, NA, 35L, 15L, 
6L, 6L, 40L, 30L, NA, 10L, 8L, 85L, 9L, 46L, NA, 14L, 9L, 
106L, 24L, 6L, 7L, 56L, 33L, NA, 12L, 9L, 106L, NA, 37L, 
7L, 11L, 8L, 79L, 5L, 54L, 5L, 10L, 6L, 100L, 25L, 9L, 5L, 
6L, 49L, NA, 31L, NA, 13L, 10L, 79L, 46L, NA, 14L, NA, 82L, 
5L, 21L, 7L, 11L, NA, 69L, NA), X2004 = c(35L, 6L, 13L, 8L, 
82L, 12L, 5L, NA, 35L, 34L, 5L, 6L, 75L, 9L, 9L, 40L, 13L, 
9L, 70L, NA, 41L, NA, 17L, 10L, 83L, 10L, 6L, 40L, NA, 18L, 
NA, 6L, NA, 34L, 10L, NA, NA, 45L, 38L, 6L, 11L, NA, 74L, 
NA, 45L, 5L, 12L, 9L, 131L, 34L, NA, NA, 64L, 28L, 5L, NA, 
NA, 93L, NA, 32L, NA, 9L, 11L, 99L, NA, 40L, NA, 18L, 8L, 
104L, 14L, NA, 13L, 6L, 67L, NA, 23L, NA, 6L, 8L, 85L, 49L, 
NA, 19L, 7L, 102L, NA, 28L, 5L, 7L, 7L, 74L, NA), X2005 = c(36L, 
NA, 20L, 10L, 93L, 22L, NA, NA, 35L, 38L, 13L, 9L, 99L, NA, 
14L, 48L, 17L, 7L, 70L, NA, 35L, NA, 13L, 9L, 103L, 16L, 
5L, 49L, NA, 12L, NA, 5L, 8L, 51L, 15L, 7L, 5L, 45L, 40L, 
NA, 12L, 5L, 102L, NA, 40L, NA, 21L, 16L, 141L, 25L, 9L, 
10L, 70L, 41L, NA, 10L, NA, 111L, NA, 37L, NA, 10L, 9L, 124L, 
NA, 37L, NA, 12L, 12L, 124L, 32L, NA, 16L, 6L, 45L, NA, 33L, 
NA, 8L, NA, 101L, 51L, NA, 19L, 5L, 117L, NA, 17L, NA, 11L, 
5L, 73L, NA), X2006 = c(38L, NA, 22L, 13L, 103L, 15L, NA, 
7L, 44L, 39L, 11L, 6L, 95L, NA, 15L, 53L, 16L, 9L, 89L, NA, 
41L, NA, 12L, 13L, 87L, 30L, 6L, 43L, NA, 14L, NA, 6L, 5L, 
50L, 19L, 5L, NA, 63L, 23L, NA, 6L, NA, 75L, NA, 38L, NA, 
12L, 19L, 142L, 32L, 7L, 7L, 64L, 49L, NA, 13L, 12L, 114L, 
NA, 48L, NA, 23L, 5L, 136L, NA, 52L, NA, 15L, 16L, 127L, 
24L, NA, 6L, NA, 57L, NA, 32L, NA, NA, 13L, 96L, 20L, NA, 
10L, 21L, 102L, NA, 31L, NA, 5L, 12L, 93L, NA)), .Names = c("level1", 
"level2", "X2002", "X2003", "X2004", "X2005", "X2006"), row.names = c(NA, 
-93L), class = "data.frame")

Answer 1

This should do the trick I think:

by(d, d$level1, function(x) cbind(x[,1:2], t(t(x[,-1:-2]) / colSums(x[,-1:-2], na.rm=TRUE))))

You can run a do.call(rbind,...) on that if you want everything in one data frame.

Answer 2

As I understand the question, you have the totals, using:

totals <- cast(level1 ~ variable, data=melt(d, na.rm=T),sum)

... and you want to convert them to percentages. (Note that you called the first column "L1" in your question text, but the data structure calls the column "level1".)

Going from totals to percentages is more straightforward than you think.

prc <- 100 * totals[,-1] / colSums(totals[,-1])
rownames(prc) <- totals[,1]