Displaying 20 results from an estimated 3000 matches similar to: "prcomp: problem with zeros? (PR#8870)"
2004 Jan 15
2
prcomp scale error (PR#6433)
Full_Name: Ryszard Czerminski
Version: 1.8.1
OS: GNU/Linux
Submission from: (NULL) (205.181.102.120)
prcomp(..., scale = TRUE) does not work correctly:
$ uname -a
Linux 2.4.20-28.9bigmem #1 SMP Thu Dec 18 13:27:33 EST 2003 i686 i686 i386
GNU/Linux
$ gcc --version
gcc (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5)
> a <- matrix(rnorm(6), nrow = 3)
> sum((scale(a %*% svd(cov(a))$u, scale
2016 Mar 22
3
Memory usage in prcomp
Hi All:
I am running prcomp on a very large array, roughly [500000, 3650]. The array itself is 16GB. I am running on a Unix machine and am running ?top? at the same time and am quite surprised to see that the application memory usage is 76GB. I have the ?tol? set very high (.8) so that it should only pull out a few components. I am surprised at this memory usage because prcomp uses the SVD
2016 Mar 22
3
Memory usage in prcomp
Hi All:
I am running prcomp on a very large array, roughly [500000, 3650]. The array itself is 16GB. I am running on a Unix machine and am running ?top? at the same time and am quite surprised to see that the application memory usage is 76GB. I have the ?tol? set very high (.8) so that it should only pull out a few components. I am surprised at this memory usage because prcomp uses the SVD
2009 Nov 25
1
which to trust...princomp() or prcomp() or neither?
According to R help:
princomp() uses eigenvalues of covariance data.
prcomp() uses the SVD method.
yet when I run the (eg., USArrests) data example and compare with my own
"hand-written" versions of PCA I get what looks like the opposite.
Example:
comparing the variances I see:
Using prcomp(USArrests)
-------------------------------------
Standard deviations:
[1] 83.732400 14.212402
2006 Jun 16
2
bug in prcomp (PR#8994)
The following seems to be an bug in prcomp():
> test <- ts( matrix( c(NA, 2:5, NA, 7:10), 5, 2))
> test
Time Series:
Start = 1
End = 5
Frequency = 1
Series 1 Series 2
1 NA NA
2 2 7
3 3 8
4 4 9
5 5 10
> prcomp(test, scale.=TRUE, na.action=na.omit)
Erro en svd(x, nu = 0) : infinite or missing values in 'x'
2005 Aug 03
3
prcomp eigenvalues
Hello,
Can you get eigenvalues in addition to eigevectors using prcomp? If so how?
I am unable to use princomp due to small sample sizes.
Thank you in advance for your help!
Rebecca Young
--
Rebecca Young
Graduate Student
Ecology & Evolutionary Biology, Badyaev Lab
University of Arizona
1041 E Lowell
Tucson, AZ 85721-0088
Office: 425BSW
rlyoung at email.arizona.edu
(520) 621-4005
2009 Nov 09
4
prcomp - principal components in R
Hello, not understanding the output of prcomp, I reduce the number of
components and the output continues to show cumulative 100% of the
variance explained, which can't be the case dropping from 8 components
to 3.
How do i get the output in terms of the cumulative % of the total
variance, so when i go from total solution of 8 (8 variables in the data
set), to a reduced number of
2004 Mar 04
1
prcomp: error code 1 from Lapack routine dgesdd
Dear all
I have a big matrix of standardized values (dimensions 285x5829) and R
fails to calculate
the principal components using prcomp() with the following error message:
pc <- prcomp(my.matrix)
Error in La.svd(x, nu, nv, method) : error code 1 from Lapack routine
dgesdd
Is the matrix too big? I'm using R-1.8.1 under Unix (Solaris8) and
Linux(Suse 8.2). I tried to
perform a principal
2016 Mar 24
3
summary( prcomp(*, tol = .) ) -- and 'rank.'
Following from the R-help thread of March 22 on "Memory usage in prcomp",
I've started looking into adding an optional 'rank.' argument
to prcomp allowing to more efficiently get only a few PCs
instead of the full p PCs, say when p = 1000 and you know you
only want 5 PCs.
(https://stat.ethz.ch/pipermail/r-help/2016-March/437228.html
As it was mentioned, we already
2012 Jun 20
1
prcomp: where do sdev values come from?
In the manual page for prcomp(), it says that sdev is "the standard
deviations of the principal components (i.e., the square roots of the
eigenvalues of the covariance/correlation matrix, though the
calculation is actually done with the singular values of the data
matrix)." ?However, this is not what I'm finding. ?The values appear
to be the standard deviations of a reprojection of
2016 Mar 24
3
summary( prcomp(*, tol = .) ) -- and 'rank.'
I agree with Kasper, this is a 'big' issue. Does your method of taking only
n PCs reduce the load on memory?
The new addition to the summary looks like a good idea, but Proportion of
Variance as you describe it may be confusing to new users. Am I correct in
saying Proportion of variance describes the amount of variance with respect
to the number of components the user chooses to show? So
2004 Nov 03
2
Princomp(), prcomp() and loadings()
In comparing the results of princomp and prcomp I find:
1. The reported standard deviations are similar but about 1% from
each other, which seems well above round-off error.
2. princomp returns what I understand are variances and cumulative
variances accounted for by each principal component which are
all equal. "SS loadings" is always 1.
3. Same happens
2011 Aug 17
1
prcomp
Hello
I am trying to run a PCA on the attached file, but I get this error message:
pc<-prcomp(data[,-(1:2)],scale=T)$x
Error in svd(x, nu = 0) : infinite or missing values in 'x'
Thanks in advance
/R
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2004 Apr 14
1
prcomp - error code 18
I am attempting to perform a pca on a data frame of dimension 5000x19, but
when I execute
pcapres<-prcomp(pres,center=TRUE)
the following error message is returned:
Error in La.svd(x, nu, nv, method) : error code 18 from Lapack routine
dgesdd
Where am I going wrong? I am running R-1.8.0 on Debian.
Regards,
Laura
2016 Mar 25
2
summary( prcomp(*, tol = .) ) -- and 'rank.'
> On 25 Mar 2016, at 10:41 am, peter dalgaard <pdalgd at gmail.com> wrote:
>
> As I see it, the display showing the first p << n PCs adding up to 100% of the variance is plainly wrong.
>
> I suspect it comes about via a mental short-circuit: If we try to control p using a tolerance, then that amounts to saying that the remaining PCs are effectively zero-variance, but
2013 Aug 08
1
Reason for difference in singular value decomposition produced by function La.svd (via prcomp)?
Dear expeRts,
I have run some simulations under R 2.15.1 on a Mac, and I have rerun a
sample of them under R 3.0.1 on Windows (and also for comparison under
R2.14.1 on Windows). For most cases, I get exactly the same results in
all three runs. However, for those cases that depend on principal
components computed with prcomp, where the particular choice of the
orthogonalization is arbitrary
2013 Aug 08
1
Reason for difference in singular value decomposition produced by function La.svd (via prcomp)?
Dear expeRts,
I have run some simulations under R 2.15.1 on a Mac, and I have rerun a
sample of them under R 3.0.1 on Windows (and also for comparison under
R2.14.1 on Windows). For most cases, I get exactly the same results in
all three runs. However, for those cases that depend on principal
components computed with prcomp, where the particular choice of the
orthogonalization is arbitrary
1998 Apr 24
1
Warning: ignored non function "scale"
I've been working on a revised version of prcomp and princomp. Below is my
current draft of prcomp, which is marginally different from V&R. I've added
center and scale as optional arguments. However, scale causes the following:
> zi _ prcomp(iris[,,2])
Warning: ignored non function "scale"
because scale is both a variable and a function. Is there any way to avoid this
2009 Dec 23
1
prcomp : plotting only explanatory axis arrows
Dear all,
I have a very large dataset (1712351 , 20) and would like
to plot only the arrows that represent the
contribution of each variables.
On the sample below I woild like to plot
only the explanatory variables (Murder, Assault..)
and not the sites.
prcomp(USArrests) # inappropriate
prcomp(USArrests, scale = TRUE)
prcomp(~ Murder + Assault + Rape, data = USArrests, scale = TRUE)
2002 Oct 29
0
patch to mva:prcomp to use La.svd instead of svd (PR#2227)
Per the discussion about the problems with prcomp() when n << p, which
boils down to a problem with svd() when n << p,
here is a patch to prcomp() which substitutes La.svd() instead of svd().
-Greg
(This is really a feature enhancement, but submitted to R-bugs to make sure
it doesn't get lost. )
*** R-1.6.0/src/library/mva/R/prcomp.R Mon Aug 13 17:41:50 2001
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