BiodiversityR CAPdiscrim error
Hi Kendra, (sorry I got your name wrong, missed the comma.)
[cc'ing the list: better to keep stuff there, so others could comment.]
Ah, that's the trouble: your matrix is a matrix, not a dist object.
Assuming you do know which distance metric is applied, and you chose the
right one, you could simply use:
MD.2.tyc <- as.dist(MD.2.tyc)
# As you did not provide the environmental data: random factors.
MD.2.env <- as.data.frame(c(rep("a", 10), rep("b", 3), rep("c", 21) ))
names(MD.2.env) <- "z.om"
# And there you go:
CAPdiscrim(MD.2.tyc~z.om, data=MD.2.env, axes=2, m=0)
HTH.
Regards,
arne
On 19.02.2014 19:30, Mitchell, Kendra wrote:
Pretty much the same error just different number of negative eigenvalues
CAPdiscrim(MD.2.tyc~MD.2.env$z.om, data=MD.2.env$z.om, axes=2, m=0)
Error in y[, group] : incorrect number of dimensions In addition: Warning message: In cmdscale(distmatrix, k = nrow(x) - 1, eig = T, add = F) : only 29 of the first 33 eigenvalues are > 0
dput(MD.2.tyc)
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0.999218, 0.927436, 0.948375, 0.94201, 0.901174, 0.905485, 0.924442, 0.941102, 0.943876, 0.793747, 0.99723, 0.999566, 0.843149, 0.943907, 0.989472, 0.859977, 0.914263, 0.795808, 0.93327, 0.812763, 0.865374, 0.851265, 0.839837, 0.780646, 0.868732, 0), .Dim = c(34L, 34L))
________________________________________
From: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] on behalf of Arne Erpenbach [arne.erpenbach at gmx.de]
Sent: Wednesday, February 19, 2014 2:56 AM
To: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] BiodiversityR CAPdiscrim error
Mitchell,
I suspect that the indexing is not working.
I just ran it on one of my datasets, having a distance matrix on the
left hand side of the formula, and a variable on the right hand side
(and define data=envir).
So: just split up your matrix in a distance matrix and an environmental
matrix, perhaps?
env <- MD.2.tyc.om[,35]
MD.2.tyc.om <- MD.2.tyc.om[,-35]
CAPdiscrim(MD.2.tyc.om~V35, data=env, axes=2)
If not working, please provide your matrix dput(){base}. Makes it much
easier to copy-paste it.
Cheers,
arne
On 19.02.2014 02:06, Mitchell, Kendra wrote:
I'm trying to run CAPdiscrim on a dissimilarity matrix with a catagorical variable attached on the right with cbind
str(MD2.tyc.om)
num [1:34, 1:35] 0 0.53 0.857 0.962 0.763 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:35] "" "" "" "" ...
CAPdiscrim(MD.2.tyc.om~MD.2.tyc.om[,35], data=MD.2.tyc.om, axes=2)
I keep getting this error, even if I set m=10 (as in much smaller than 24).
Error in y[, group] : no 'dimnames' attribute for array
In addition: Warning message:
In cmdscale(distmatrix, k = nrow(x) - 1, eig = T, add = F) :
only 24 of the first 33 eigenvalues are > 0
I can't find any examples using CAPdiscrim on previously calculated distance matrices even though that's an option in the manual. Any guidance on this error would be appreciated.
Thanks, Kendra
Here is the full matrix
"","V1","V2","V3","V4","V5","V6","V7","V8","V9","V10","V11","V12","V13","V14","V15","V16","V17","V18","V19","V20","V21","V22","V23","V24","V25","V26","V27","V28","V29","V30","V31","V32","V33","V34","V35"
"1",0,0.530104,0.856862,0.962188,0.763469,0.847752,0.784871,0.981281,0.994992,0.852796,0.885253,0.892708,0.801034,0.896041,0.790542,0.905549,0.91111,0.89411,0.976961,0.997093,0.784175,0.903232,0.93154,0.801226,0.792943,0.647447,0.895218,0.943309,0.668771,0.764815,0.739676,0.882644,0.870289,0.944295,2
"2",0.530104,0,0.848909,0.96033,0.714506,0.800896,0.741563,0.980028,0.997491,0.846717,0.878128,0.857846,0.725213,0.870564,0.765767,0.877561,0.878336,0.852742,0.986353,0.999126,0.822573,0.897483,0.955899,0.828633,0.780688,0.745419,0.823416,0.943878,0.708038,0.723605,0.774255,0.873241,0.838629,0.944567,2
"3",0.856862,0.848909,0,0.982097,0.508784,0.92577,0.909307,0.973827,0.996873,0.942398,0.837959,0.964803,0.942049,0.970062,0.921683,0.965747,0.865674,0.96621,0.970599,0.998697,0.95216,0.857683,0.946018,0.930482,0.927475,0.913383,0.792996,0.982603,0.910284,0.917016,0.920965,0.962759,0.94806,0.981199,2
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