[R] pls package
Hi All, I am using the cppls function in the pls package, and I want to use cross validation to determine the best number of components. Since Hastie et al recommended a "one standard error rule", i.e., choose the most parsimonious model whose error is no more than one standard error above the error of the best model, I am wondering how I can get the standard error of misclassification rate from pls package? Thank you, Cindy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Re: [R] help plsr function
Ok, yes, I can match them now. Thank you very much!
On Tue, Jun 24, 2014 at 3:58 AM, Bjørn-Helge Mevik b.h.me...@usit.uio.no
wrote:
annie Zhang annie.zhang2...@gmail.com writes:
## the predicted scores from the model
(pred - predict(data.cpls,n.comp=1:2,newdata=x.new,type=score))
## the predicted scores using x%*%projection
cbind(x.new.centered%*%data.cpls$projection[,1],x.new.centered%*%data.cpls$projection[,2])
Can someone please tell me why the two predicted scores don't match?
If you look at the code that does the prediction:
pls:::predict.mvr
function (object, newdata, ncomp = 1:object$ncomp, comps, type =
c(response,
scores), na.action = na.pass, ...)
{
[...]
TT - (newX - rep(object$Xmeans, each = nobs)) %*%
object$projection[, comps]
you will see that it subtracts the _old X_ coloumn means from the new X
matrix, not the _new X_ coloumn means. So
sweep(x.new, 2, data.cpls$Xmeans, -) %*% data.cpls$projection[,1:2]
will reproduce the values from predict().
--
Regards,
Bjørn-Helge Mevik
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[R] calculate probability circles
Hi, All, I want to have the 1%, 2%, 3%, ... contours for Dirichlet distribution. I need the exact contour circles (mathematically) instead of contour plots. Can anyone help me with this? Many thanks, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] integration
'integrate' does not allow parameter limits. For example, the limits of x is (z/y, Inf) while z and y are unkonwn. On Fri, Apr 8, 2011 at 9:46 PM, Ravi Varadhan rvarad...@jhmi.edu wrote: ?integrate From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of cindy Guo [cindy.g...@gmail.com] Sent: Friday, April 08, 2011 9:21 PM To: r-help@r-project.org Subject: [R] integration Hi, All, I have a density function with 3 variables which is defined on some irregular domain, and I want to get the marginal distribution of each variable. Is there any function doing this? A simple example is p(x,y,z)=x*y*z*I(xyz). So each marginal distribution is a function of the other two variables. My density form is very complicated, so I cannot do it by hand. I was just wondering if there is any function in R for this? Thanks, Cindy [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
[R] integration
Hi, All, I have a density function with 3 variables which is defined on some irregular domain, and I want to get the marginal distribution of each variable. Is there any function doing this? A simple example is p(x,y,z)=x*y*z*I(xyz). So each marginal distribution is a function of the other two variables. My density form is very complicated, so I cannot do it by hand. I was just wondering if there is any function in R for this? Thanks, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] pairs
I forgot to say that there are no ties in each row. So any number can occur only once in each row. Also as I mentioned earlier, actually I only need the top 50 most frequent pairs, is there a more efficient way to do it? Because I have 15000 numbers, output of all the pairs would be too long. Thank you, Cindy On Mon, Nov 16, 2009 at 7:02 AM, David Winsemius dwinsem...@comcast.netwrote: I stuck in another 7 in one of the lines with a 2 and reasoned that we could deal with the desire for non-ordered pair counting by pasting min(x,y) to max(x,y); dput(prmtx) structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim = c(4L, 4L)) prmtx [,1] [,2] [,3] [,4] [1,]2516 [2,]1772 [3,]3762 [4,]9857 pair.str - sapply(1:nrow(prmtx), function(z) apply(combn(prmtx[z,], 2), 2,function(x) paste(min(x[2],x[1]), max(x[2],x[1]), sep=.))) The logic: sapply(1:nrow(prmtx), ... just loops over the rows of the matrix. combn(prmtx[z,], 2) ... returns a two row matrix of combination in a single row. apply(combn(prmtx[z,], 2), 2 ... since combn( , 2) returns a matrix that has two _rows_ I needed to loop over the columns. paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the minimum of a pair in front of the max and separates them with a period to prevent two+ digits from being non-unique Then using table() and logical tests in an index for the desired multiple pairs: tpair -table(pair.str) tpair pair.str 1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8 7.9 8.9 2 1 1 2 1 1 2 3 1 1 1 1 1 1 1 1 1 1 1 tpair[tpair1] pair.str 1.2 1.7 2.6 2.7 2 2 2 3 -- David. On Nov 16, 2009, at 7:02 AM, David Winsemius wrote: I'm not convinced it's right. In fact, I'm pretty sure the last step taking only the first half of the list is wrong. I also do not know if you have considered how you want to count situations like: 3 2 7 4 5 7 ... 7 3 8 6 1 2 9 2 .. How many pairs of 2-7/7-2 would that represent? -- David On Nov 15, 2009, at 11:06 PM, cindy Guo wrote: Hi, David, The matrix has 20 columns. Thank you very much for your help. I think it's right, but it seems I need some time to figure it out. I am a green hand. There are so many functions here I never used before. :) Cindy On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net wrote: Assuming that the number of columns is 4, then consider this approach: prs -scan() 1: 2 5 1 6 5: 1 7 8 2 9: 3 7 6 2 13: 9 8 5 7 17: Read 16 items prmtx - matrix(prs, 4,4, byrow=T) #Now make copus of x.y and y.x pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x) paste(x[2],x[1], sep=.))) ) tpair -table(pair.str) # This then gives you a duplicated list tpair[tpair1] pair.str 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7 2 2 2 2 2 2 2 2 # So only take the first half of the pairs: head(tpair[tpair1], sum(tpair1)/2) pair.str 1.2 2.1 2.6 2.7 2 2 2 2 -- David. On Nov 15, 2009, at 8:06 PM, David Winsemius wrote: I could of course be wrong but have you yet specified the number of columns for this pairing exercise? On Nov 15, 2009, at 5:26 PM, cindy Guo wrote: Hi, All, I have an n by m matrix with each entry between 1 and 15000. I want to know the frequency of each pair in 1:15000 that occur together in rows. So for example, if the matrix is 2 5 1 6 1 7 8 2 3 7 6 2 9 8 5 7 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return the value 2 for this pair as well as that for all pairs. Is there a fast way to do this avoiding loops? Loops take too long. and provide commented, minimal, self-contained, reproducible code. ^^ David Winsemius, MD Heritage Laboratories 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT David Winsemius, MD Heritage Laboratories 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https
Re: [R] pairs
Do you mean if the numbers in each row are ordered? They are not, but if it's needed, we can order them. The matrix only has 5000 rows. On Mon, Nov 16, 2009 at 1:34 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 16, 2009, at 2:32 PM, cindy Guo wrote: I forgot to say that there are no ties in each row. So any number can occur only once in each row. Also as I mentioned earlier, actually I only need the top 50 most frequent pairs, is there a more efficient way to do it? Because I have 15000 numbers, output of all the pairs would be too long. ?order Thank you, Cindy On Mon, Nov 16, 2009 at 7:02 AM, David Winsemius dwinsem...@comcast.netwrote: I stuck in another 7 in one of the lines with a 2 and reasoned that we could deal with the desire for non-ordered pair counting by pasting min(x,y) to max(x,y); dput(prmtx) structure(c(2, 1, 3, 9, 5, 7, 7, 8, 1, 7, 6, 5, 6, 2, 2, 7), .Dim = c(4L, 4L)) prmtx [,1] [,2] [,3] [,4] [1,]2516 [2,]1772 [3,]3762 [4,]9857 pair.str - sapply(1:nrow(prmtx), function(z) apply(combn(prmtx[z,], 2), 2,function(x) paste(min(x[2],x[1]), max(x[2],x[1]), sep=.))) The logic: sapply(1:nrow(prmtx), ... just loops over the rows of the matrix. combn(prmtx[z,], 2) ... returns a two row matrix of combination in a single row. apply(combn(prmtx[z,], 2), 2 ... since combn( , 2) returns a matrix that has two _rows_ I needed to loop over the columns. paste(min(x[2],x[1]), max(x[2],x[1]), sep=.) ... stick the minimum of a pair in front of the max and separates them with a period to prevent two+ digits from being non-unique Then using table() and logical tests in an index for the desired multiple pairs: tpair -table(pair.str) tpair pair.str 1.2 1.5 1.6 1.7 2.3 2.5 2.6 2.7 3.6 3.7 5.6 5.7 5.8 5.9 6.7 7.7 7.8 7.9 8.9 2 1 1 2 1 1 2 3 1 1 1 1 1 1 1 1 1 1 1 tpair[tpair1] pair.str 1.2 1.7 2.6 2.7 2 2 2 3 -- David. On Nov 16, 2009, at 7:02 AM, David Winsemius wrote: I'm not convinced it's right. In fact, I'm pretty sure the last step taking only the first half of the list is wrong. I also do not know if you have considered how you want to count situations like: 3 2 7 4 5 7 ... 7 3 8 6 1 2 9 2 .. How many pairs of 2-7/7-2 would that represent? -- David On Nov 15, 2009, at 11:06 PM, cindy Guo wrote: Hi, David, The matrix has 20 columns. Thank you very much for your help. I think it's right, but it seems I need some time to figure it out. I am a green hand. There are so many functions here I never used before. :) Cindy On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.net wrote: Assuming that the number of columns is 4, then consider this approach: prs -scan() 1: 2 5 1 6 5: 1 7 8 2 9: 3 7 6 2 13: 9 8 5 7 17: Read 16 items prmtx - matrix(prs, 4,4, byrow=T) #Now make copus of x.y and y.x pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x) paste(x[2],x[1], sep=.))) ) tpair -table(pair.str) # This then gives you a duplicated list tpair[tpair1] pair.str 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7 2 2 2 2 2 2 2 2 # So only take the first half of the pairs: head(tpair[tpair1], sum(tpair1)/2) pair.str 1.2 2.1 2.6 2.7 2 2 2 2 -- David. On Nov 15, 2009, at 8:06 PM, David Winsemius wrote: I could of course be wrong but have you yet specified the number of columns for this pairing exercise? On Nov 15, 2009, at 5:26 PM, cindy Guo wrote: Hi, All, I have an n by m matrix with each entry between 1 and 15000. I want to know the frequency of each pair in 1:15000 that occur together in rows. So for example, if the matrix is 2 5 1 6 1 7 8 2 3 7 6 2 9 8 5 7 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return the value 2 for this pair as well as that for all pairs. Is there a fast way to do this avoiding loops? Loops take too long. and provide commented, minimal, self-contained, reproducible code. ^^ David Winsemius, MD Heritage Laboratories 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT David Winsemius, MD Heritage Laboratories 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.htmlhttp://www.r-project.org
Re: [R] pairs
Thank you. I will check that. Cindy On Mon, Nov 16, 2009 at 1:45 PM, cls59 ch...@sharpsteen.net wrote: David Winsemius wrote: ?order cindy Guo wrote: Do you mean if the numbers in each row are ordered? They are not, but if it's needed, we can order them. The matrix only has 5000 rows. No, he's suggesting you check out the order() function by calling it's help page: ?order order() will sort your results into ascending or descending order. You could then pick off the top 50 by using head(). Hope that helps! -Charlie - Charlie Sharpsteen Undergraduate Environmental Resources Engineering Humboldt State University -- View this message in context: http://old.nabble.com/pairs-tp26364801p26378236.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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
[R] pairs
Hi, All, I have an n by m matrix with each entry between 1 and 15000. I want to know the frequency of each pair in 1:15000 that occur together in rows. So for example, if the matrix is 2 5 1 6 1 7 8 2 3 7 6 2 9 8 5 7 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return the value 2 for this pair as well as that for all pairs. Is there a fast way to do this avoiding loops? Loops take too long. Thank you, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] pairs
Hi, Charlie,
Thank you for the reply. Maybe I don't need the frequency of each pair. I
only need the top, say 50, pairs with the highest frequency. Is there anyway
which can avoid calculating for all the pairs?
Thanks,
Cindy
On Sun, Nov 15, 2009 at 4:18 PM, cls59 ch...@sharpsteen.net wrote:
cindy Guo wrote:
Hi, All,
I have an n by m matrix with each entry between 1 and 15000. I want to
know
the frequency of each pair in 1:15000 that occur together in rows. So for
example, if the matrix is
2 5 1 6
1 7 8 2
3 7 6 2
9 8 5 7
Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return
the value 2 for this pair as well as that for all pairs. Is there a fast
way
to do this avoiding loops? Loops take too long.
Thank you,
Cindy
Use %in% to check for the presence of the numbers in a row and apply() to
efficiently execute the test for each row:
tstMatrix - matrix( c(2,5,1,6,
1,7,8,2,
3,7,6,2,
9,8,5,7), nrow=4, byrow=T )
matches - apply( tstMatrix, 1, function( row ){
if( 2 %in% row 6 %in% row ){
return( 2 )
} else {
return( 0 )
}
})
matches
[1] 2 0 2 0
If you have more than one pair, it gets a little tricky. Say you are also
looking for the pair (7,8). Store them as a list:
pairList - list( c(2,6), c(7,8) )
Then use sapply() to efficiently iterate over the pair list and execute the
apply() test:
matchMatrix - sapply( pairList, function( pair ){
matches - apply( tstMatrix, 1, function( row ){
if( pair[1] %in% row pair[2] %in% row ){
return( pair[1] )
} else {
return( 0 )
}
})
return( matches )
})
matchMatrix
[,1] [,2]
[1,]20
[2,]07
[3,]20
[4,]07
If you're looking to apply the above method to every possible permutation
of
2 numbers that may be generated from the range of numbers 1:15000... that's
225,000,000 pairs. expand.grid() can generate the required pair list-- but
that step alone causes a memory allocation of ~6 GB on my machine.
If you don't have a pile of CPU cores and RAM at your disposal, you can
probably:
1. Restrict the upper end of your range to the maximal entry present in
your matrix since all other combinations have zero occurrences.
2. Break the list of pairs up into several sublists, run the tests, and
aggregate the results.
Either way, the analysis will take some time despite the efficiencies of
the
apply family of functions due to the shear size of the problem. If you
have
more than one CPU, I would recommend taking a look at parallelized apply
functions, perhaps using a package like snowfall, as the testing of the
pairs is an embarrassingly parallel problem.
Hopefully I'm misunderstanding the scope of your problem.
Good luck!
-Charlie
-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
--
View this message in context:
http://old.nabble.com/pairs-tp26364801p26365206.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] pairs
Hi, David, The matrix has 20 columns. Thank you very much for your help. I think it's right, but it seems I need some time to figure it out. I am a green hand. There are so many functions here I never used before. :) Cindy On Sun, Nov 15, 2009 at 5:19 PM, David Winsemius dwinsem...@comcast.netwrote: Assuming that the number of columns is 4, then consider this approach: prs -scan() 1: 2 5 1 6 5: 1 7 8 2 9: 3 7 6 2 13: 9 8 5 7 17: Read 16 items prmtx - matrix(prs, 4,4, byrow=T) #Now make copus of x.y and y.x pair.str - sapply(1:nrow(prmtx), function(z) c(apply(combn(prmtx[z,], 2), 2,function(x) paste(x[1],x[2], sep=.)) , apply(combn(prmtx[z,], 2), 2,function(x) paste(x[2],x[1], sep=.))) ) tpair -table(pair.str) # This then gives you a duplicated list tpair[tpair1] pair.str 1.2 2.1 2.6 2.7 6.2 7.2 7.8 8.7 2 2 2 2 2 2 2 2 # So only take the first half of the pairs: head(tpair[tpair1], sum(tpair1)/2) pair.str 1.2 2.1 2.6 2.7 2 2 2 2 -- David. On Nov 15, 2009, at 8:06 PM, David Winsemius wrote: I could of course be wrong but have you yet specified the number of columns for this pairing exercise? On Nov 15, 2009, at 5:26 PM, cindy Guo wrote: Hi, All, I have an n by m matrix with each entry between 1 and 15000. I want to know the frequency of each pair in 1:15000 that occur together in rows. So for example, if the matrix is 2 5 1 6 1 7 8 2 3 7 6 2 9 8 5 7 Pair (2,6) (un-ordered) occurs together in rows 1 and 3. I want to return the value 2 for this pair as well as that for all pairs. Is there a fast way to do this avoiding loops? Loops take too long. and provide commented, minimal, self-contained, reproducible code. ^^ David Winsemius, MD Heritage Laboratories 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT [[alternative HTML version deleted]] __ 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.
[R] SSVS
Hi, ALL, Is there any R/bioconductor package to do SSVS (stochastic search variable selection) for glm? Thanks, Cindy [[alternative HTML version deleted]] __ 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.
[R] matrix power
Hi, All, If I have a symmetric matrix, how can I get the negative square root of the matrx, ie. X^(-1/2) ? Thanks, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] matrix power
Hi, Ted, Thanks for the sample code. It is exactly what I want. But can I ask another question? The matrix for which I want the negative square root is a covariance matrix. I suppose it should be positive definite, so I can do 1/sqrt(V) as you wrote. But the covariance matrix I got in R using the function cov has a lot of negative eigenvalues, like -5.338634e-17, so 1/sqrt(V) generates NA's. Can you tell what's the problem here. Thanks, Cindy On Mon, Aug 10, 2009 at 2:53 PM, Ted Harding ted.hard...@manchester.ac.ukwrote: On 10-Aug-09 21:31:30, cindy Guo wrote: Hi, All, If I have a symmetric matrix, how can I get the negative square root of the matrx, ie. X^(-1/2) ? Thanks, Cindy X - matrix(c(2,1,1,2),nrow=2) X # [,1] [,2] # [1,]21 # [2,]12 E - eigen(X) V - E$values Q - E$vectors Y - Q%*%diag(1/sqrt(V))%*%t(Q) Y #[,1] [,2] # [1,] 0.7886751 -0.2113249 # [2,] -0.2113249 0.7886751 solve(Y%*%Y)## i.e. find its inverse # [,1] [,2] # [1,]21 # [2,]12 Hence (Y%*%Y)^(-1) = X, or Y = X^(-1/2) Hopingb this helps, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 10-Aug-09 Time: 22:53:25 -- XFMail -- [[alternative HTML version deleted]] __ 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.
Re: [R] matrix power
Hi, Ted, Now I understand the problem. Thank you for the explanation. It's very helpful. I appreciate it. Cindy On Mon, Aug 10, 2009 at 3:58 PM, Ted Harding ted.hard...@manchester.ac.ukwrote: On 10-Aug-09 22:36:03, cindy Guo wrote: Hi, Ted, Thanks for the sample code. It is exactly what I want. But can I ask another question? The matrix for which I want the negative square root is a covariance matrix. I suppose it should be positive definite, so I can do 1/sqrt(V) as you wrote. But the covariance matrix I got in R using the function cov has a lot of negative eigenvalues, like -5.338634e-17, so 1/sqrt(V) generates NA's. Can you tell what's the problem here. Thanks, Cindy Cindy, If that -5.338634e-17 is typical of the lot of negative eigenvalues, then what you are seeing is the result of R's attempt to calculate zero eigenvalues, but defeated by the inevitable rounding errors. In other words, your covariance matrix is singular, and the variables involved are not linearly independent. The only thing that is guaranteed about a covariance matrix is that it is positive semi-definite (not positive definite); in other words all eigenvalues are positive or zero (mathematically). For example, if Y=X, var(X) = var(Y) = 1, then cov(X,Y) = 1 1 1 1 which is singular (eigenvalues = 2, 0). The result of attempting to compute them is subject to rounding errors, which (for zero eigenvalues) can be slightly negative. So the covariance matrix in your case would not have an inverse, still less a negative square root! The basic problem is that you have luinear dependence between the variables. To make progress, you would need to find a maximal linearly independent set (or possibly find the principal components with nozero weights). Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 10-Aug-09 Time: 23:58:00 -- XFMail -- [[alternative HTML version deleted]] __ 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.
Re: [R] matrix power
Hi, Dan, Yes, this is what I want. Is there better way to solve this? Cindy On Mon, Aug 10, 2009 at 2:52 PM, Nordlund, Dan (DSHS/RDA) nord...@dshs.wa.gov wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of cindy Guo Sent: Monday, August 10, 2009 2:32 PM To: r-help@r-project.org Subject: [R] matrix power Hi, All, If I have a symmetric matrix, how can I get the negative square root of the matrx, ie. X^(-1/2) ? Thanks, Cindy Cindy, Just to be sure we are all on the same page. Are saying you have a matrix X, and you want to find the a matrix A such that X = A %*% A And you want to then find the matrix inverse of A ? Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
Re: [R] matrix power
I think it may be important, but I am not sure. Actually I am trying to program the adaptive nearest neighbor method proposed by Hastie and Tibshirani. I am following the steps in the book 'The elements of statistical learning' by Hastie, Tibshirani and Friedman, in which the local metric is defined as W^(-1/2)[B*+I]W^(-1/2), where W is the pooled within-class covariance matrix. Cindy On Mon, Aug 10, 2009 at 4:28 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: If its not important which of many solutions you use then the generalized inverse can be used, say. Just use 0 for each small eigenvalue and 1/sqrt(x) for the others. On Mon, Aug 10, 2009 at 6:36 PM, cindy Guocindy.g...@gmail.com wrote: Hi, Ted, Thanks for the sample code. It is exactly what I want. But can I ask another question? The matrix for which I want the negative square root is a covariance matrix. I suppose it should be positive definite, so I can do 1/sqrt(V) as you wrote. But the covariance matrix I got in R using the function cov has a lot of negative eigenvalues, like -5.338634e-17, so 1/sqrt(V) generates NA's. Can you tell what's the problem here. Thanks, Cindy On Mon, Aug 10, 2009 at 2:53 PM, Ted Harding ted.hard...@manchester.ac.ukwrote: On 10-Aug-09 21:31:30, cindy Guo wrote: Hi, All, If I have a symmetric matrix, how can I get the negative square root of the matrx, ie. X^(-1/2) ? Thanks, Cindy X - matrix(c(2,1,1,2),nrow=2) X # [,1] [,2] # [1,]21 # [2,]12 E - eigen(X) V - E$values Q - E$vectors Y - Q%*%diag(1/sqrt(V))%*%t(Q) Y #[,1] [,2] # [1,] 0.7886751 -0.2113249 # [2,] -0.2113249 0.7886751 solve(Y%*%Y)## i.e. find its inverse # [,1] [,2] # [1,]21 # [2,]12 Hence (Y%*%Y)^(-1) = X, or Y = X^(-1/2) Hopingb this helps, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 10-Aug-09 Time: 22:53:25 -- XFMail -- [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
[R] nearest neighbors
Hi, All, I am wondering if there is any package which can give the index of the k nearest neighbors. Thank you, Cindy [[alternative HTML version deleted]] __ 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.
[R] diagonal lda and qda
Hi, all, I am wondering if there is any package doing lda and qda which allows assuming diagonal covariance matrices. I checked the lda function in MASS, and it seems it does not support this. Thanks, Cindy [[alternative HTML version deleted]] __ 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.
[R] diagonal LDA and QDA
Hi, all, I am wondering if there is any package doing lda and qda which allows assuming diagonal covariance matrices. I checked the lda function in MASS, and it seems it does not support this. Thanks, Cindy [[alternative HTML version deleted]] __ 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.
[R] diagonal LDA and QDA
Hi, all, I am wondering if there is any package doing lda and qda which allows assuming diagonal covariance matrices. I checked the lda function in MASS, and it seems it does not support this. Thanks, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] local regression using loess
Bert, Ryan, Alain, You suggestions are very helpful. Thank you. I learned a lot from the discussion. Cindy On Tue, Jul 28, 2009 at 8:53 AM, Ryan rha...@purdue.edu wrote: Bert Gunter gunter.berton at gene.com writes: Actually, loess is much more than an interpolant. I wouldn't even call it that. It is a local regression technique that comes with all the equipment you get in classical regression. But it is meant for normal-like errors, which is not what you have. Bert - when I hear interpolate, I think of connecting the data points, like using something like divided differences or hermite interpolation, so I thought that's what you meant. Sorry for the misunderstanding. True that loess was designed to be robust, but when I said it is meant for normal-like errors, I was referring to loess with statistical procedures analagous to the classical regression setting, such as confidence intervals, anova, etc. (see Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting, 1988). __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
[R] install package from CRAN
Hi, I have a very basic question about install packages from CRAN on unix. I only installed on Windows before. Should I use the command install.package? The error message I got is syntax error near unexpected token `mvtnorm' Is it because I didn't set the path? Which path should I specify? Thanks, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] install package from CRAN
Hi, Steve,
Thanks for the response.
I did the same thing:
install.packages('mvtnorm')
-bash: syntax error near unexpected token `'mvtnorm''
I think what may cause difference is that I am using a unix cluster of my
university, so I am not the administrator. Do I need to set the path?
Cindy
On Tue, Jul 28, 2009 at 5:31 PM, Steve Lianoglou
mailinglist.honey...@gmail.com wrote:
On Jul 28, 2009, at 8:15 PM, cindy Guo wrote:
Hi,
I have a very basic question about install packages from CRAN on unix. I
only installed on Windows before. Should I use the command
install.package?
The error message I got is
syntax error near unexpected token `mvtnorm'
Is it because I didn't set the path? Which path should I specify?
You should use install.packages (note the last s)... how did you call
that function to get that error you are showing us?
It looks like you're trying to install the 'mvtnorm' package, and you'd do
so like this:
install.packages('mvtnorm')
Is that what you did?
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R] install package from CRAN
Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I didn't set the path? Which path should I specify? a) You use install.packages() only from __inside R__. As you got an error from bash, you must have done this from the command prompt. b) At the command prompt, use 'R CMD INSTALL mvtnorm' instead. In either case, you need proper permissions to install in global directories, so if you can run this, try either 'sudo R' to start R so that 'install.packages(mvtnorm)' will succeed, or use 'sudo R CMD INSTALL mvtnorm. Also, if you are on Debian / Ubuntu, you can do sudo apt-get install r-cran-mvtnorm as we provide a prebuild version. Dirk -- Three out of two people have difficulties with fractions. [[alternative HTML version deleted]] __ 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.
Re: [R] install package from CRAN
Hi, Thank you for asking. Actually I downloaded the tar.gz file as Mark said and used R CMD INSTALL -l . package.tar.gz to install. I didn't know I can download CRAN packages from the internet. I am not a unix person, so I struggled a lot with the commands on unix and directories especially. I don't know how to deal with it when I don't have enough privilege. Cindy On Tue, Jul 28, 2009 at 7:33 PM, stephen sefick ssef...@gmail.com wrote: What was the problem- out of curiosity? Stephen Sefick On Tue, Jul 28, 2009 at 9:23 PM, cindy Guocindy.g...@gmail.com wrote: Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I didn't set the path? Which path should I specify? a) You use install.packages() only from __inside R__. As you got an error from bash, you must have done this from the command prompt. b) At the command prompt, use 'R CMD INSTALL mvtnorm' instead. In either case, you need proper permissions to install in global directories, so if you can run this, try either 'sudo R' to start R so that 'install.packages(mvtnorm)' will succeed, or use 'sudo R CMD INSTALL mvtnorm. Also, if you are on Debian / Ubuntu, you can do sudo apt-get install r-cran-mvtnorm as we provide a prebuild version. Dirk -- Three out of two people have difficulties with fractions. [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis [[alternative HTML version deleted]] __ 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.
Re: [R] normal mixture model
Hi, Christian, Yes, it works. Thank you very much. It's really helpful. Cindy On Mon, Jul 27, 2009 at 5:39 AM, Christian Hennig chr...@stats.ucl.ac.ukwrote: Hi Cindy, you need the summary function mclustsummary - summary(mclustBICoutputobject,data) to get all the information. Some (like best model) is given if you just print out the summary object. Some other information (like estimated parameter values) are accessible as components of the summary object, like mclustsummary$parameters$... Try str(mclustsummary) to see what's there (unfortunately this is not fully documented). For more detail see the help pages. Hope this helps, Christian On Sun, 26 Jul 2009, cindy Guo wrote: Hi, Christian, Thank you for the reply. I just tried. Does the function mclustBIC only give the best model, or does it also do EM to get the cluster means and variances according to the best model it picks? I didn't find it. Is there a way to automatically select the best number of components and do EM? Because I need to do the normal mixture model in a loop (one EM at an iteration), so I want it to do everything automatically. Thanks, Cindy On Sun, Jul 26, 2009 at 3:46 PM, Christian Hennig chr...@stats.ucl.ac.uk wrote: You can use mclustBIC in package mclust (uses the BIC for deciding about the number of components and hierarchical clustering for initialisation). Christian On Sun, 26 Jul 2009, cindy Guo wrote: Hi, All, I want to fit a normal mixture model. Which package in R is best for this? I was using the package 'mixdist', but I need to group the data into groups before fitting model, and different groupings seem to lead to different results. What other package can I use which is stable? And are there packages that can automatically determine the number of components? Thank you, Cindy [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 chr...@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 chr...@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche [[alternative HTML version deleted]] __ 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.
Re: [R] local regression using loess
Hi, Bert, Thanks for the response. But then in this case, can I use loess to fit the data? If yes, then how to interpret the results? Cindy On Mon, Jul 27, 2009 at 4:32 PM, Bert Gunter gunter.ber...@gene.com wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of cindy Guo Sent: Monday, July 27, 2009 4:06 PM To: r-help@r-project.org Subject: [R] local regression using loess Hi, All, I have a dataset with binary response ( 0 and 1) and some numerical covariates. I know I can use logistic regression to fit the data. But I want to consider more locally. So I am wondering how can I fit the data with 'loess' function in R? And what will be the response: 0/1 or the probability in either group like in logistic regression? -- Neither. Loess is an algorithm that smoothly interpolates the data. It makes no claim of modeling the probability for a binary response variable. -- Bert Gunter Genentech Nonclinical Statistics Thank you, Cindy [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
Re: [R] local regression using loess
Hi, Ryan, Thank you for the information. I tried it. But there are some error messages. When I use fit - locfit(Y~X1*X2,family='binomial'), the error message is error lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : compparcomp: parameters out of bounds And when I use fit - locfit(Y~X1*X2), the error message is error lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space This happens sometimes, not every time for different data. Do you know what's the reason? Thank you, Cindy On Mon, Jul 27, 2009 at 5:25 PM, Ryan rha...@purdue.edu wrote: Hi, All, I have a dataset with binary response ( 0 and 1) and some numerical covariates. I know I can use logistic regression to fit the data. But I want to consider more locally. So I am wondering how can I fit the data with 'loess' function in R? And what will be the response: 0/1 or the probability in either group like in logistic regression? -- Neither. Loess is an algorithm that smoothly interpolates the data. It makes no claim of modeling the probability for a binary response variable. -- Bert Gunter Genentech Nonclinical Statistics Thank you, Cindy [[alternative HTML version deleted]] Actually, loess is much more than an interpolant. I wouldn't even call it that. It is a local regression technique that comes with all the equipment you get in classical regression. But it is meant for normal-like errors, which is not what you have. I would recommend that you take a look at the locfit package. It fits local likelihood models. I've never tried it with binary data, but if y is your 0/1 response and x is a covariate, you might try something like: locfit(y ~ x, ..., family=binomial) If you have a good library at your disposal, try picking up Loader's book Local Regression and Likelihood. __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
[R] mixdist package in R
Hi, All, I fitted a 3-component normal mixture model with the mixdist package in R. How can I get the density of a new data after I fit the model? Is there any function to do it? Thanks, Cindy [[alternative HTML version deleted]] __ 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.
[R] normal mixture model
Hi, All, I want to fit a normal mixture model. Which package in R is best for this? I was using the package 'mixdist', but I need to group the data into groups before fitting model, and different groupings seem to lead to different results. What other package can I use which is stable? And are there packages that can automatically determine the number of components? Thank you, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] normal mixture model
Hi, Christian, Thank you for the reply. I just tried. Does the function mclustBIC only give the best model, or does it also do EM to get the cluster means and variances according to the best model it picks? I didn't find it. Is there a way to automatically select the best number of components and do EM? Because I need to do the normal mixture model in a loop (one EM at an iteration), so I want it to do everything automatically. Thanks, Cindy On Sun, Jul 26, 2009 at 3:46 PM, Christian Hennig chr...@stats.ucl.ac.ukwrote: You can use mclustBIC in package mclust (uses the BIC for deciding about the number of components and hierarchical clustering for initialisation). Christian On Sun, 26 Jul 2009, cindy Guo wrote: Hi, All, I want to fit a normal mixture model. Which package in R is best for this? I was using the package 'mixdist', but I need to group the data into groups before fitting model, and different groupings seem to lead to different results. What other package can I use which is stable? And are there packages that can automatically determine the number of components? Thank you, Cindy [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 chr...@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche [[alternative HTML version deleted]] __ 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.
[R] question about mean
Hello, everyone, I have a matrix like following: school value A .1 A .2 A .15 A .2 B .3 B .5 C .3 C .3 C .4 C .5 C .6 C .9 C 1 I want to get the mean 'value' for each 'school', but each school has different length. Is there any way to do this fast? Because my data has hundreds of thousands of rows. Thank you, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] R-package install
Thank you, Brian and Mark, I tried the win-builder on http://win-builder.r-project.org/. Is this what you mean? I uploaded the source code, and I didn't get any email after couple of hours. It should arrive after half an hour, as it is said on the webpage. Do you know what can happen? Cindy On 7/25/08, Prof Brian Ripley [EMAIL PROTECTED] wrote: We write manuals so that you can know how to do things in R. Package installation is covered in the 'R Installation and Administration' manual. We don't have the attachment, but assuming this was a source package I sugest you look into Uwe Ligges' win-builder service mentioned in that manual (and in 'Writing R Extensions'). On Thu, 24 Jul 2008, cindy Guo wrote: Hi, Mark, Thank you for your response. No, I don't know how to compile it. Do I need to use unix to compile? After compiling, can I use it in Windows R? Attached is the package. Cindy On 7/24/08, Mark Difford [EMAIL PROTECTED] wrote: Hi Cindy, Hi, I have a R package, which is a .tar.tar file. And it is said to be source code for all platforms. ... I am wondering if I can use this package in Windows R. If it is source code you would first need to compile it to binary format before you can use it. Can you do that? Which package is it? Regards, Mark. cindy Guo wrote: Hi, I have a R package, which is a .tar.tar file. And it is said to be source code for all platforms. And the author said it should install on any system (but he didn't know about Windows). I am wondering if I can use this package in Windows R. Thank you, Cindy [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/R-package-install-tp18636993p18639516.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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ 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.
[R] R-package install
Hi, I have a R package, which is a .tar.tar file. And it is said to be source code for all platforms. And the author said it should install on any system (but he didn't know about Windows). I am wondering if I can use this package in Windows R. Thank you, Cindy [[alternative HTML version deleted]] __ 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.
Re: [R] R-package install
Hi, Mark, Thank you for your response. No, I don't know how to compile it. Do I need to use unix to compile? After compiling, can I use it in Windows R? Attached is the package. Cindy On 7/24/08, Mark Difford [EMAIL PROTECTED] wrote: Hi Cindy, Hi, I have a R package, which is a .tar.tar file. And it is said to be source code for all platforms. ... I am wondering if I can use this package in Windows R. If it is source code you would first need to compile it to binary format before you can use it. Can you do that? Which package is it? Regards, Mark. cindy Guo wrote: Hi, I have a R package, which is a .tar.tar file. And it is said to be source code for all platforms. And the author said it should install on any system (but he didn't know about Windows). I am wondering if I can use this package in Windows R. Thank you, Cindy [[alternative HTML version deleted]] __ 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. -- View this message in context: http://www.nabble.com/R-package-install-tp18636993p18639516.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. __ 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.
[R] truncated normal
Hi, I want to generate random samples from truncated normal say Normal(0,1)Indicator((0,1),(2,4)). It has more than one intervals. In the library msm, it seems to me that the 'lower' and 'upper' arguments can only be a number. I tried rtnorm(1,mean=0,sd=1, lower=c(0,2),upper=c(1,4)) and it didn't work. Can you tell me how I can do truncated normal at more than one intervals? Thank you. [[alternative HTML version deleted]] __ 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.
