Hi useRs,
I am trying to compare several distance matrices obtained from subsets
of variables from the same experiment. I put all the subsets in a list
and then calculated the distance matrices with lapply. In order to do a
mantel test between them I wrote a function the returns a list with the
output of single tests. I would like to include the name of the tests,
so I know what each element of the result list is. My code is as follows:
land <- list(s1536 = s1536, s384L = s384L, s96L = s96L, s384c = s384c,
s96c = s96c, s384r = s384r, s96r = s96r)
library(analogue)
ldis <- lapply(land, function(x) as.dist(distance(x, method = "mixed")))
mantel.list <- function(x, ...) {
require(ade4)
for (i in 2:length(x)) {
x1 <- x[[i - 1]]
x2 <- x[[i]]
y[[i]] <- mantel.rtest(x1, x2)
}
return(y)
}
lmantel <- mantel.list(ldis)
> str(ldis)
List of 7
$ s1536:Class 'dist' atomic [1:15400] 0.357 0.260 0.341 0.342 0.267 ...
.. ..- attr(*, "Labels")= chr [1:176] "CS301" "CS302" "CS303" "CS304" ...
.. ..- attr(*, "Size")= int 176
.. ..- attr(*, "call")= language as.dist.default(m = distance(x,
method = "mixed"))
.. ..- attr(*, "Diag")= logi FALSE
.. ..- attr(*, "Upper")= logi FALSE
$ s384L:Class 'dist' atomic [1:15400] 0.497 0.243 0.453 0.440 0.277 ...
.. ..- attr(*, "Labels")= chr [1:176] "CS301" "CS302" "CS303" "CS304" ...
.. ..- attr(*, "Size")= int 176
.. ..- attr(*, "call")= language as.dist.default(m = distance(x,
method = "mixed"))
.. ..- attr(*, "Diag")= logi FALSE
.. ..- attr(*, "Upper")= logi FALSE
(...)
> str(lmantel)
List of 7
$ :List of 5
..$ sim : num [1:99] 0.007734 0.002429 -0.021489 -0.000181
0.021703 ...
..$ obs : num 0.785
..$ rep : int 99
..$ pvalue: num 0.01
..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet)
..- attr(*, "class")= chr "rtest"
$ :List of 5
..$ sim : num [1:99] 0.00749 0.02850 -0.01301 -0.01376 0.00883 ...
..$ obs : num 0.785
..$ rep : int 99
..$ pvalue: num 0.01
..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet)
..- attr(*, "class")= chr "rtest"
(...)
I would like to get something like
> str(lmantel)
List of 7
$ s1536_s384L
:List of 5
..$ sim : num [1:99] 0.007734 0.002429 -0.021489 -0.000181
0.021703 ...
..$ obs : num 0.785
..$ rep : int 99
..$ pvalue: num 0.01
..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet)
..- attr(*, "class")= chr "rtest"
(...)
Thanks for your help.
Marc.
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