[R] sapply following using by with a list of factors
McClatchie, Sam (PIRSA-SARDI)
mcclatchie.sam at saugov.sa.gov.au
Mon May 30 04:48:11 CEST 2005
Background:
OS: Linux Mandrake 10.1
release: R 2.0.0
editor: GNU Emacs 21.3.2
front-end: ESS 5.2.3
---------------------------------
Colleagues
I am having some trouble extracting results from the function by, used to
average variables in a data.frame first by one factor (depth) and then by a
second factor (station). The real data.frame is quite large
> dim(data.2001)
[1] 32049 11
Here is a snippet of code:
## bin density data for each station into 1 m depth bins, containing means
data.2001.test$integer.Depth <- as.factor(round(data.2001.test$Depth,
digits=0))
attach(data.2001.test)
binned.data.2001 <- by(data.2001.test[,5:11], list(depth=integer.Depth,
station=Station), mean)
and here is a snippet of the data.frame
> dim(data.2001.test)
[1] 150 11
> dump("data.2001.test", file=stdout())
data.2001.test <-
structure(list(Cruise = structure(as.integer(c(1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Label =
"Ngerin01", class = "factor"),
Station = structure(as.integer(c(2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 5, 5)), .Label = c("a1", "a2", "a3",
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24.5016, 24.5592, 21.4044, 11.1924, 7.70434, -4.09892, -4.29682,
0.10429, 15.62, 15.2757, 1.12576, 12.3537, 6.28031, 6.28031,
6.28031, 9.70625, 9.70625, 16.6939, 16.6939, -16.9003, -16.9003,
-16.5469, -16.5469, -1.24881, 2.12382, -8.88365, 11.8552,
18.6224, 22.4818, 17.7073, 7.05875, 5.60178, 7.24009, 3.48756,
9.56937, 10.7906, 13.3156, 2.31384, -11.7071, -5.06014, 11.9814,
9.25461, 10.2528, 1.04765, -3.92472, 0.97033, -6.84208, 7.41494,
13.7583, 6.60244, 5.18133, -9.85804, -4.08612, 10.1503, 5.32709,
4.55223, -0.413365, -5.7495, 3.18065, -5.70216, -7.24117,
-7.31205, 12.0855, 4.33021, -4.98771, -2.93681), integer.Depth = c(5,
5, 6, 6, 6, 6, 7, 7, 7, 8, 8, 9, 9, 9, 9, 9, 10, 10, 10,
11, 12, 12, 13, 13, 14, 15, 15, 16, 16, 17, 17, 17, 18, 18,
18, 19, 19, 19, 19, 20, 20, 20, 21, 21, 22, 22, 23, 23, 23,
24, 24, 24, 25, 25, 5, 6, 6, 7, 7, 8, 8, 8, 8, 9, 9, 10,
10, 11, 11, 12, 12, 13, 13, 14, 14, 14, 15, 15, 15, 16, 16,
17, 17, 18, 18, 18, 19, 19, 20, 20, 21, 22, 22, 23, 23, 24,
24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 6, 6, 6, 6,
7, 7, 8, 8, 8, 9, 9, 10, 10, 10, 11, 11, 11, 12, 12, 13,
13, 14, 14, 14, 15, 15, 16, 16, 17, 17, 18, 19, 19, 20, 21,
21, 22, 22, 23, 23, 5, 6)), .Names = c("Cruise", "Station",
"Lon", "Lat", "Depth", "Temperature.oC", "Salinity", "Fluoresence.Volts",
"Density.kg.m3", "Brunt.Vaisala.Freq.cycl.h", "integer.Depth"
), row.names = c("19", "20", "21", "22", "23", "24", "25", "26",
"27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37",
"38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48",
"49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59",
"60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70",
"71", "72", "88", "89", "90", "91", "92", "93", "94", "95", "96",
"97", "98", "99", "100", "101", "102", "103", "104", "105", "106",
"107", "108", "109", "110", "111", "112", "113", "114", "115",
"116", "117", "118", "119", "120", "121", "122", "123", "124",
"125", "126", "127", "128", "129", "130", "131", "132", "133",
"134", "135", "136", "137", "138", "139", "140", "154", "155",
"156", "157", "158", "159", "160", "161", "162", "163", "164",
"165", "166", "167", "168", "169", "170", "171", "172", "173",
"174", "175", "176", "177", "178", "179", "180", "181", "182",
"183", "184", "185", "186", "187", "188", "189", "190", "191",
"192", "193", "194", "209", "210"), class = "data.frame")
When I run this code on the full dataset, calculations continue long enough
to suggest I am generating a huge matrix, so perhaps I'm doing something
silly? Eventually (well, after maybe 5 minutes) I get a by class object of
109 rows (depth category) by 288 columns (station category), so it does seem
to be working.
I know that you use sapply to get the by class back to a data.frame. I want
to extract a matrix of mean densities (one of the original variables) at
each of the 109 depths and 288 stations.
I have not quite got this right...can you help?
Thanks in advance
Sam
----
Sam McClatchie,
Biological oceanography
South Australian Aquatic Sciences Centre
PO Box 120, Henley Beach 5022
Adelaide, South Australia
email <mcclatchie.sam at saugov.sa.gov.au>
Telephone: (61-8) 8207 5448
FAX: (61-8) 8207 5481
Research home page <http://www.members.iinet.net.au/~s.mcclatchie/>
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