On Feb 6, 2011, at 9:35 PM, B77S wrote:
I figured there would be an even more straightforward way, but that
works
David, thanks.
I am rather puzzled. What prior experience with computing would lead
you to believe that one line of code was not a straightforward method
to do multinomial sampling from 4 different sets of probabilities???
There has to be a way to get the output I want/need (see below). I
tried to
bind or merge the elements of "apply(samptbl, 2, table)" but with no
success. I could probably make a for loop with a merge statement,
it would
work.. but I'm guessing unnecessary and just plain ugly.
## what I want/need
spA spB spC spD spa spF spG
site1 8 13 6 13 32 0 28
site2 31 25 0 0 25 19 0
site3 0 0 9 51 0 0 40
site4 27 19 0 0 22 32 0
If you know, I'd appreciate it.. thanks again for the help.
In order to keep the zero entries straight, there needs to be some
sort of structure that records the fact that there were not
occurrences in a column. Using a factor construct is the method R uses
for that purpose. Factors work better in data.frames:
> set.seed(123)
> samptbl <- apply(abund2, 1, function(x) sample(colnames(abund2),
100, prob=x, replace=TRUE) )
> sampdf <- as.data.frame(samptbl)
> sampdf[[1]] <- factor( sampdf[[1]], levels= colnames(abund2) )
> sampdf[[2]] <- factor( sampdf[[2]], levels= colnames(abund2) )
> sampdf[[3]] <- factor( sampdf[[3]], levels= colnames(abund2) )
> sampdf[[4]] <- factor( sampdf[[4]], levels= colnames(abund2) )
> sapply(sampdf, table)
site1 site2 site3 site4
spA 14 20 0 31
spB 12 30 0 20
spC 8 0 7 0
spD 13 0 41 0
spa 0 20 0 19
spF 26 30 0 30
spG 27 0 52 0
Again, the t() function would flip that:
> t( sapply(sampdf, table) )
spA spB spC spD spa spF spG
site1 14 12 8 13 0 26 27
site2 20 30 0 0 20 30 0
site3 0 0 7 41 0 0 52
site4 31 20 0 0 19 30 0
--
david.
David Winsemius wrote:
On Feb 6, 2011, at 3:25 PM, B77S wrote:
Hello,
How can I randomly sample individuals within a sites from a site
(row) X
species abundance (column) data frame or matrix? As an example, the
matrix
"abund2" made below.
##### (sorry, Im a newbie and this is the only way I know to get an
example
on here)
abund1 <- c(150, 300, 0, 360, 150, 300, 0, 240, 150,
0, 60,
0, 150, 0, 540, 0, 0, 300, 0, 240, 300, 300, 0, 360, 300, 0, 600,
0)
abund2 <- matrix(data=abund1, nrow=4, ncol=7)
colnames(abund2) <- c("spA", "spB", "spC", "spD", "spa", "spF",
"spG")
rownames(abund2)<-c("site1", "site2", "site3", "site4")
Perfect. Best submission of an example by a newbie in weeks.
#####
abund2
spA spB spC spD spa spF spG
site1 150 150 150 150 0 300 300
site2 300 300 0 0 300 300 0
site3 0 0 60 540 0 0 600
site4 360 240 0 0 240 360 0
How can I make a random subsample of 100 individuals from the
abundances
given for each site?
samptbl <- apply(abund2, 1, function(x) sample(colnames(abund2), 100,
prob=x, replace=TRUE) )
samptbl
site1 site2 site3 site4
[1,] "spG" "spa" "spD" "spF"
[2,] "spF" "spF" "spG" "spB"
[3,] "spF" "spB" "spC" "spA"
[4,] "spD" "spa" "spG" "spA"
[5,] "spF" "spa" "spD" "spa"
[6,] "spA" "spB" "spD" "spF"
[7,] "spA" "spF" "spD" "spA"
[8,] "spG" "spF" "spG" "spa"
[9,] "spF" "spF" "spG" "spa"
[10,] "spG" "spB" "spD" "spA"
Snipped
apply() always transposes the results when called with row margins.
The t() function would "fix" this if it needed to be arranged with
rows by site. You could check by further apply-(cation) of table to
the columns:
apply(samptbl, 2, table)
$site1
spA spB spC spD spF spG
8 13 6 13 32 28
$site2
spa spA spB spF
25 31 25 19
$site3
spC spD spG
9 51 40
$site4
spa spA spB spF
22 27 19 32
This is probably really easy.
Thanks.
Bubba
--
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______________________________________________
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://r.789695.n4.nabble.com/Subsampling-out-of-site-abundance-matrix-tp3263148p3263488.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
