Re: [R] Package installation in Windows
On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: As a sys admin, how do I install packages so that there is one common library for all users of the MS Windows computer, instead of the default individual location for each user? I've done this for Linux. The same way. You set R_LIBS_SITE in etc/Renviron.site. See ?.Library.site . This was discussed on this list with the last couple of weeks, so please do check the archives. Thanks, in advance, for your help. Mike -- 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 __ 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] Problem with starting and using R
On Wed, 10 Sep 2008, Thomas Lo wrote: The patched version (r46512) solves the problem!! Thanks! Thank you for confirming this. In the meantime I tracked down the exact problem. The standards for a locale name are 'language_country.encoding', as in 'en_GB.utf8' or 'English_United Kingdom.1252'. In Windows XP (at least) Microsoft gives 'Chinese_Hong Kong S.A.R..950'. This is ambiguous, and in at least two places it was parsed as an encoding of 'A.R..950'. There seem to be only three locales with dots in the country name (Hong Kong, Macau, U.A.E.), so it perhaps not surprising that this has gone undetected for so long. On Tue, Sep 9, 2008 at 12:20 AM, Thomas Lo <[EMAIL PROTECTED]> wrote: Hi Brian and Duncan, Many thanks for your responses. Setting the 'Current format' in 'Regional and language options' under Control Panel to English (Singapore) solved the R usage problem for me. I will have a go at R-patched build 46507 after it is released. Regards, Thomas On Mon, Sep 8, 2008 at 7:20 PM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: On Mon, 8 Sep 2008, Duncan Murdoch wrote: On 08/09/2008 6:56 AM, Prof Brian Ripley wrote: On Mon, 8 Sep 2008, Prof Brian Ripley wrote: This reflects a problem in your locale (traditional Chinese): we cannot reproduce it. Try running R in a different locale (e.g. append LC_ALL=en to the target when you start R). Maybe I have found this as a bug in iconv. Please try a version of R-patched with svn revision 46507 or later. Unfortunately, something stopped the daily builds of R-patched on Saturday, and I haven't been in to the office yet to fix things. So it's likely to be tomorrow before the Windows build of r46507 or later is available on CRAN. I only found r46507 this morning, as a side effect of something else. So it would not be in a build until tomorrow. Duncan Murdoch On Sun, 7 Sep 2008, Thomas Lo wrote: Dear all, I encountered a problem on starting and using the R v 2.7.2 installation on my PC running Windows Vista and would appreciate your help. When R was first started, the Rgui returned several error messages: Error in structure(.Internal(Sys.getenv(as.character(x), as.character(unset)$ unsupported conversion Error in file.exists(name) : unsupported conversion in 'filenameToWchar' In addition, a dialog box called 'Information' popped up with the following message: Fatal error: unable to restore saved data in .RData On clicking 'OK', R closed immediately and the same thing occurs on restarting R. After checking for previous related messages online, I followed one of the recommendations from before and appended --no-restore-data to the R shorcut target line. After that, R could start without the 'fatal error'. However,
Re: [R] Genmod in SAS vs. glm in R
Rolf Turner wrote:
For one thing your call to glm() is wrong --- didn't you notice the
warning messages about ``non-integer #successes in a binomial glm!''?
You need to do either:
glm(r/k ~ x, family=binomial(link='cloglog'), data=bin_data,
offset=log(y), weights=k)
or:
glm(cbind(r,k-r) ~ x, family=binomial(link='cloglog'), data=bin_data,
offset=log(y))
You get the same answer with either, but this answer still does not
agree with your
SAS results. Perhaps you have an error in your SAS syntax as well. I
wouldn't know.
The data created in the data step are not those used in the analysis.
Changing to
data nelson;
gives the same result as R on the versions I have available:
Analysis Of Parameter Estimates
Standard Wald 95%
Confidence Chi-
ParameterDFEstimate Error Limits
SquarePr > ChiSq
Intercept 1 -3.5866 2.2413 -7.9795
0.8064 2.560.1096
x 1 0.9544 2.8362 -4.6046
6.5133 0.110.7365
Scale 0 1. 0. 1. 1.
and
Call:
glm(formula = r/k ~ x, family = binomial(link = "cloglog"), data = bin_data,
weights = k, offset = log(y))
Deviance Residuals:
1234
0.5407 -0.9448 -1.0727 0.7585
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -3.5866 2.2413 -1.6000.110
x 0.9544 2.8362 0.3360.736
cheers,
Rolf Turner
On 10/09/2008, at 10:37 AM, sandsky wrote:
Hello,
I have different results from these two softwares for a simple
binomial GLM
problem.
From Genmod in SAS: LogLikelihood=-4.75, coeff(intercept)=-3.59,
coeff(x)=0.95
From glm in R: LogLikelihood=-0.94, coeff(intercept)=-3.99,
coeff(x)=1.36
Is there anyone tell me what I did wrong?
Here are the code and results,
1) SAS Genmod:
% r: # of failure
% k: size of a risk set
data bin_data;
input r k y x;
os=log(y);
cards;
1350.5
0250.5
0241.0
1241.0
;
proc genmod data=nelson;
model r/k = x / dist = binomial link =cloglog offset =
os ;
Log Likelihood -4.7514
ParameterDFEstimate Error Limits
SquarePr > ChiSq
Intercept 1 -3.6652 1.9875 -7.5605 0.2302
3.400.0652
x1 0.8926 2.4900 -3.9877 5.7728
0.130.7200
Scale 0 1. 0. 1. 1.
2) glm in R
bin_data <-
data.frame(cbind(y=c(5,5,4,4),r=c(1,0,0,1),k=c(3,2,2,2),x=c(0.5,0.5,1.0,1.0)))
glm(r/k ~ x, family=binomial(link='cloglog'), data=bin_data,
offset=log(y))
Coefficients:
(Intercept)x
-3.9911.358
'log Lik.' -0.9400073 (df=2)
##
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--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] building a package that contains S4 classes and methods
Marie Pierre Sylvestre wrote:
Hello R users,
I am trying to make a my first package and I get an error that I can
understand. The package is build out of three files (one for functions, 1
for s4 classes and 1 for s4 methods).
Once I source them I run
package.skeleton( name="TDC" )
within a R session and I get
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './TDC/Read-and-delete-me'.
Warning messages:
1: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
2: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
3: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
4: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse may be incomplete
I keep going in spite of the warnings with
R CMD check --no-examples TDC
and I get
* checking for working pdflatex ... OK
* using log directory
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: UTF-8
* checking for file 'TDC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TDC' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'TDC' can be installed ... ERROR
Installation failed.
The error file says:
* Installing *source* package 'TDC' ...
** R
** preparing package for lazy loading
Error in parse(n = -1, file = file) : unexpected '<' at
102: `.__C__BindArgs` <-
103: <
Calls: -> code2LazyLoadDB -> sys.source -> parse
Execution halted
ERROR: lazy loading failed for package 'TDC'
** Removing
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck/TDC'
The problem is with my classes and methods. The respective files contain:
setClass("BindArgs", signature( "function" ))
setClass("BindArgs2", signature( "function" ))
and
setMethod("initialize", "BindArgs", function( .Object, f, ... )
callNextMethod( .Object, function( x ) f( x, ... ) ))
setMethod("initialize", "BindArgs2", function( .Object, f, ...)
callNextMethod( .Object, function( x, y ) f( x, y, ... ) ))
Everything works well within a R session but I can build the package.
If I look at the internal R file that this created I get
`.__C__BindArgs` <-
`.__C__BindArgs2` <-
`.__M__initialize:methods` <-
`.__T__initialize:methods` <-
Well, let just say that I am new to classes so this confuses me greatly. I
have checked the documentation and tried a few things but I reached my
personal limits!
I am using R 2.7.1 on Linux Fedora 8.
Any comments on what is happening and/or help would be greatly appreciated.
The main point is that you should not rely on R putting sensible code in
the package source files, but rather stay in control yourself. What the
warnings are telling you is that you cannot deparse an S4 object in a
way that can be reparsed, so dump() doesn't work. What you get is
obj <-
and the syntax error from source() if you try using it. So what you need
to is to delete it and put in the appropriate class/methods definitions
from your original sources. It might help to look at an existing
S4-using package.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] "figure margins too large" issue
Thank you Marc, I have checked two versions following your suggestions and the default setting of mar in both versions are same to each other as c(5,4,4,2)+0.1. Besides, I dont change any default settings about the graphics devices. For more info, following is my two sessions of R. *1.* R version 2.6.2 (2008-02-08) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base *2.* R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Thank you in advance!! Hui-Yi On Tue, Sep 9, 2008 at 9:04 PM, Marc Schwartz <[EMAIL PROTECTED]>wrote: > on 09/09/2008 05:19 PM Hui-Yi Chu wrote: > > Hi everyone, > > > > I updated R from 2.6.2 to 2.7.2 recently but keep getting the error > "figure > > margins too large" when plot pictures which never happened to me when > using > > 2.6.2. After googling and searching the mailing list, I still have no > idea > > how to optimize it. One of my packages fixed bugs in 2.7.2 version, so > that > > I have to use it. Any suggestions are really appreciated!!! > > > > Best regards, > > Hui-Yi Chu > > There were substantial changes in the graphics devices for 2.7.0. More > information here: > > https://svn.r-project.org/R/branches/R-2-7-branch/NEWS > > and review the sections for 2.7.0 and newer, which now includes 2.7.2 > patched. > > Without knowing your OS and which graphics device you are using and > having an issue with, preferably along with sample (working) code that > reproduces the issue, it will be difficult to know the exact source of > the problem. > > A first place to start however would be to see ?par and review 'mar'. > You will likely need to adjust either the default values or any adjusted > values you have in your code. > > HTH, > > Marc Schwartz > > [[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] yahoo finance into R
thanks a lot. i thought it was more difficult.
however i am dissapointed that i get so little data.
thanks again
thomas
Peter Dalgaard wrote:
>
> thomastos wrote:
>> Hi R,
>>
>> I am familiar with the basics of R.
>> To learn more I would like how to get data from Yahoo!finance directly
>> into
>> R. So basically I want a data frame or matrix to do some data analysis.
>> How do I do this?
>>
> RSiteSearch("yahoo")
>
> get.hist.quote() from tseries
> yahooSeries() from fImport (untried)
>
> --
>O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
> ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
>
> __
> 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/yahoo-finance-into-R-tp19385481p19405623.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] extract variance components
Hi,
Thanks for all. I now know how to extract the \sigma's.
For the unbalanced model y_{ijk}=x\beta+\alpha_i+\beta_{ij}+e_{ijk}
i=1,2,\dots,a, j=1,2,\dots,b_i, k=1,2,\dots,n_{ij}
How can I extract the variance matrix $V$? The variance for the ith group is
also of help. Suppose the ith group has totally 10 observations. b_i=4,
n_{i1}=1,n_{i2}=3,n_{i3}=2 and n_{i4}=1. $V_i=\sigma_a^2 J_{10}+\sigma_b^2
diag(J_1,J_3,J_2, J_1)+\sigma_e^2 I_{10}$, where I is the identity matrix
and J_d is the matrix of 1's with dimention d \by d. J_d reduces to 1 if
d=1. I only know how to extract the design matrix for the fixed effect by
model.matrix(lme.fit2). How to deal with the parts for the random effects?
Thank you.
Huang
On Fri, Aug 29, 2008 at 11:30 AM, huang min <[EMAIL PROTECTED]> wrote:
> HI,
>
> I would like to extract the variance components estimation in lme function
> like
>
> a.fit<-lme(distance~age, data=aaa, random=~day/subject)
>
> There should be three variances \sigma_day, \sigma_{day %in% subject } and
> \sigma_e.
>
> I can extract the \sigma_e using something like a.fit$var. However, I
> cannot manage to extract the first two variance components. I can only see
> the results in summary(a.fit).
>
> I have some problem in the lme4 package and hence use the nlme package. The
> example data also has some problem so I just list the function here using
> some imaginary data set. Thank you.
>
> Huang
>
[[alternative HTML version deleted]]
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Re: [R] Substitute Values in a Matrix?
on 09/09/2008 06:12 PM Chris82 wrote:
> Hi,
>
> I'm searching for a function to subistute Values in a Matrix to new Values.
> For example:
>
> old value new value
> 1.1 6
> 1.2 7
> ..
> ..
> ..
> 1.9 14
> 2.0 15
>
> and
>
> 2.1 15.5
> 2.2 16
> ..
> ..
> 2.9 19.5
> 3.0 20
>
> There is a difference between the correlation old to new value
>
> For the present my code is like this:
>
> y <- matrix(c(1,2,1, 3,2,4, 1,1,1), ncol=3, byrow=TRUE)
>
> for (i in 1:3) {
> for (j in 1:3) {
>if y[i,j] = 1:2 substitute y[i,j] = 6:15
>
>
> }
> }
>
> But I don't find a correct syntax for this term " if y[i,j] = 1:2 substitute
> y[i,j] = 6:15" and I'm not sure if my idea is to simple and it's more
> complex than I think.
>
> thanks.
It is made more complicated because you are using floating point values
in the table lookup process, rather than integer or character based
comparisons. See R FAQ 7.31 for why floating point comparisons are
problematic.
In this case, we need to set up a process by which we can include a
tolerance for the floating point comparisons for the Search vector in
the source matrix and then generate the matching indices into the
Replace vector.
In traditional floating point comparison applications, you would look to
use all.equal(), but it is not suitably 'vectorized' for this
application, so we set up a parallel process.
There are likely to be further optimizations applicable here, for
someone with fresher eyes, but here is a first pass function:
SR <- function(x, Search, Replace, tol = .Machine$double.eps ^ 0.5)
{
Ind <- sapply(x, function(i) which(abs(i - Search) < tol))
names(Ind) <- seq(length(Ind))
Ind <- unlist(Ind)
x[as.integer(names(Ind))] <- Replace[Ind]
x
}
The arguments are the source matrix, the Search vector, the Replace
vector and the required tolerance for the comparison. In this case, I
took the default tolerance from all.equal().
Within the function body, we loop over each value in the source matrix
and subtract the Search vector. We then compare the absolute values of
the result vector to the tolerance value and get the index using which()
for any values within the tolerance. We thus presume that this is a
'match' between the matrix value and a Search vector value, within the
tolerance level.
They key is that if there is no value that matches, which() returns
integer(0), not NA, so there is additional code to deal with that
possibility. In this case, 'Ind' would be a list, rather than a vector,
but the additional code will work in either case, perhaps adding a bit
of overhead in lieu of an if/else construct.
So let's set up two test matrices. The first only has the values in the
Search vector, whereas the second has four additional values that do not
match.
Search <- seq(1.1, 3.0, 0.1)
Replace <- c(6:15, seq(15.5, 20, 0.5))
mat <- matrix(seq(1.1, 3.0, 0.1), ncol = 4)
mat2 <- matrix(c(seq(1.1, 3.0, 0.1), 0, 4, 5, 6), ncol = 4)
> Search
[1] 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7
[18] 2.8 2.9 3.0
> Replace
[1] 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 15.5 16.0 16.5
[14] 17.0 17.5 18.0 18.5 19.0 19.5 20.0
> mat
[,1] [,2] [,3] [,4]
[1,] 1.1 1.6 2.1 2.6
[2,] 1.2 1.7 2.2 2.7
[3,] 1.3 1.8 2.3 2.8
[4,] 1.4 1.9 2.4 2.9
[5,] 1.5 2.0 2.5 3.0
> mat2
[,1] [,2] [,3] [,4]
[1,] 1.1 1.7 2.3 2.9
[2,] 1.2 1.8 2.4 3.0
[3,] 1.3 1.9 2.5 0.0
[4,] 1.4 2.0 2.6 4.0
[5,] 1.5 2.1 2.7 5.0
[6,] 1.6 2.2 2.8 6.0
# Let's do 'mat'
> SR(mat, Search, Replace)
[,1] [,2] [,3] [,4]
[1,]6 11 15.5 18.0
[2,]7 12 16.0 18.5
[3,]8 13 16.5 19.0
[4,]9 14 17.0 19.5
[5,] 10 15 17.5 20.0
# Now on 'mat2'
> SR(mat2, Search, Replace)
[,1] [,2] [,3] [,4]
[1,]6 12.0 16.5 19.5
[2,]7 13.0 17.0 20.0
[3,]8 14.0 17.5 0.0
[4,]9 15.0 18.0 4.0
[5,] 10 15.5 18.5 5.0
[6,] 11 16.0 19.0 6.0
My solution is likely to become rather inefficient on 'large' matrices,
for some suitable definition of 'large'.
HTH,
Marc Schwartz
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Re: [R] bootstrapping - number of items to replace is not a multiple of replacement length
Hello,
Your theta() function is returning different
sets of coefficients depending on the results of
step().
You'll need to add code to theta() to figure
out which variables were selected, and store
them into the right positions of a vector
of length 20 (the apparent number of covariates
you describe below), so that your theta()
function always returns the same sized output.
(Google
stepwise regression random forest
and you'll get a number of hits
about using random forests instead
of stepwise regression, and pointers
about bootstrapping the random forest.)
HTH
Steve McKinney
> -Original Message-
> From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
> On Behalf Of Gabriela Bucini
> Sent: Tuesday, September 09, 2008 5:02 PM
> To: r-help@r-project.org
> Subject: [R] bootstrapping - number of items to replace is not a
multiple
> ofreplacement length
>
> Hello,
>
> I'm new to boostrapping and I'd need some help to understand the error
> message that pops up when I run my script.
>
> I have a data.frame with 73 lines and 21 column.
> I am running a stepwise regression to find the best model using the R
> function "step".
> I apply bootstrapping to obtain model coefficients.
> This is my script:
>
> # "datare80" is the name of the data.frame and "woodycover" is the
> response
> variable
> theta <- function(datare80, indices) {
> d <- datare80[indices, ]# allows boot to select
subsample
> datasets
> full <- lm(d$woodycover~ ., data= d )
> lmbroadst <- step(full, data=d , direction = "both", k=2,
> trace=0)
> coefficients(lmbroadst) # return coef. vector
> }
> resb <- boot(data = datare80, statistic = theta, R=1000)
>
>
>
> When I run it, I get these two messages:
> If I omit the last line "coefficients(lmbroadst)" in the function
> definition, I get :
> "Error in t.star[r, ] <- statistic(data, i[r, ], ...) :
> incorrect number of subscripts on matrix"
> If I have the last line "coefficients(lmbroadst)", then I get:
> "Error in t.star[r, ] <- statistic(data, i[r, ], ...) :
> number of items to replace is not a multiple of replacement
> length"
>
>
> Thank you very much for any help!
>
> Gabriela
>
> __
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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.
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Re: [R] "figure margins too large" issue
It is not the default setting for par("mar") that changed.
There are other device specific changes that occurred in 2.7.0,
including, for some devices (eg. pdf and bitmap), the default device
dimensions.
See the bullets in the NEWS file under "SIGNIFICANT USER-VISIBLE
CHANGES" and "GRAPHICS CHANGES" for 2.7.0. It could be something subtle,
having to do with any font/symbol selections and/or sizes (eg. cex.*).
You still did not provide a small reproducible example, which would
better help us help you. The fundamental error message suggests that you
need to either reduce one or more of the par("mar") settings to reduce
the margin size, increase the device dimensions, or alter some other
attribute. This is further complicated if you might be using layout() or
par(mfrow/mfcol) to create a matrix of plots.
Regards,
Marc
on 09/09/2008 09:05 PM Hui-Yi Chu wrote:
> Thank you Marc,
> I have checked two versions following your suggestions and the default
> setting of mar in both versions are same to each other as
> c(5,4,4,2)+0.1. Besides, I dont change any default settings about the
> graphics devices.
> For more info, following is my two sessions of R.
>
> *1.*
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
>
> *2.*
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
>
> Thank you in advance!!
> Hui-Yi
>
> On Tue, Sep 9, 2008 at 9:04 PM, Marc Schwartz <[EMAIL PROTECTED]
> > wrote:
>
> on 09/09/2008 05:19 PM Hui-Yi Chu wrote:
> > Hi everyone,
> >
> > I updated R from 2.6.2 to 2.7.2 recently but keep getting the
> error "figure
> > margins too large" when plot pictures which never happened to me
> when using
> > 2.6.2. After googling and searching the mailing
> list, I still have no idea
> > how to optimize it. One of my packages fixed bugs in 2.7.2
> version, so that
> > I have to use it. Any suggestions are really appreciated!!!
> >
> > Best regards,
> > Hui-Yi Chu
>
> There were substantial changes in the graphics devices for 2.7.0.
> More
> information here:
>
> https://svn.r-project.org/R/branches/R-2-7-branch/NEWS
>
> and review the sections for 2.7.0 and newer, which now includes 2.7.2
> patched.
>
> Without knowing your OS and which graphics device you are using and
> having an issue with, preferably along with sample (working) code that
> reproduces the issue, it will be difficult to know the exact source of
> the problem.
>
> A first place to start however would be to see ?par and review 'mar'.
> You will likely need to adjust either the default values or any adjusted
> values you have in your code.
>
> HTH,
>
> Marc Schwartz
>
>
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] "figure margins too large" issue
on 09/09/2008 05:19 PM Hui-Yi Chu wrote: > Hi everyone, > > I updated R from 2.6.2 to 2.7.2 recently but keep getting the error "figure > margins too large" when plot pictures which never happened to me when using > 2.6.2. After googling and searching the mailing list, I still have no idea > how to optimize it. One of my packages fixed bugs in 2.7.2 version, so that > I have to use it. Any suggestions are really appreciated!!! > > Best regards, > Hui-Yi Chu There were substantial changes in the graphics devices for 2.7.0. More information here: https://svn.r-project.org/R/branches/R-2-7-branch/NEWS and review the sections for 2.7.0 and newer, which now includes 2.7.2 patched. Without knowing your OS and which graphics device you are using and having an issue with, preferably along with sample (working) code that reproduces the issue, it will be difficult to know the exact source of the problem. A first place to start however would be to see ?par and review 'mar'. You will likely need to adjust either the default values or any adjusted values you have in your code. HTH, Marc Schwartz __ 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: error handling in try
First time to post and searched archive for this problem with no clue. My
version is 2.5.1.
Below is a function to check if a given date is a valid date to a given date
function object. It uses try (also tried tryCatch but with same problem). When
given an invalid date, I am hoping try will generate en error message which
would be picked up by the geterrmessage and thus expecting a false result. but
this is not the case when it is inside a function. However, if simply run the
body of function, the ret is indeed a false value. Why are they different?
Many thanks
is.Date=
# adate: a scalar value
# fun: the date function object
# format: the designated date format to date function
function(adate,fun,format) {
ret=NA;
error.old=geterrmessage();
.Internal(seterrmessage('no error'));
try(fun(adate,format),silent=T);
error=geterrmessage();
if (error=='no error') {
ret=T;
} else {
ret=F;
}
.Internal(seterrmessage(error.old));
return(ret);
}
adate='12/2000';
fun=as.Date;
format='%b %Y';
is.Date(adate,fun,format) # returns true which is not correct.
ret=NA;
error.old=geterrmessage();
.Internal(seterrmessage('no error'));
try(fun(adate,format),silent=T);
error=geterrmessage();
if (error=='no error') {
ret=T;
} else {
ret=F;
}
.Internal(seterrmessage(error.old));
ret # shows false which is correct
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[R] Substitute Values in a Matrix?
Hi,
I'm searching for a function to subistute Values in a Matrix to new Values.
For example:
old value new value
1.1 6
1.2 7
..
..
..
1.9 14
2.0 15
and
2.1 15.5
2.2 16
..
..
2.9 19.5
3.0 20
There is a difference between the correlation old to new value
For the present my code is like this:
y <- matrix(c(1,2,1, 3,2,4, 1,1,1), ncol=3, byrow=TRUE)
for (i in 1:3) {
for (j in 1:3) {
if y[i,j] = 1:2 substitute y[i,j] = 6:15
}
}
But I don't find a correct syntax for this term " if y[i,j] = 1:2 substitute
y[i,j] = 6:15" and I'm not sure if my idea is to simple and it's more
complex than I think.
thanks.
--
View this message in context:
http://www.nabble.com/Substitute-Values-in-a-Matrix--tp19403197p19403197.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] densities with overlapping area of 0.35
Hi, I just findout that the KL Divengence depends on the variances of the distrubutions too and I'm trying to figureout how to do this. please help me. let's say X ~n(0,1) and Y~n(2*a, sigma^2). Is there any way I can calculate the "sigma" and "a" corresponding to an overlapping area of 0.35. Thank you, Lavan Lavan wrote: > > Hi, > > I like to generate two normal densities such that the overlapping area > between them is 0.35. Is there any code/package available in R to do > that?? > > Regards, > > Lavan > -- View this message in context: http://www.nabble.com/densities-with-overlapping-area-of-0.35-tp19384741p19404352.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.
Re: [R] Problem with starting and using R
The patched version (r46512) solves the problem!! Thanks!
On Tue, Sep 9, 2008 at 12:20 AM, Thomas Lo <[EMAIL PROTECTED]> wrote:
> Hi Brian and Duncan,
>
> Many thanks for your responses. Setting the 'Current format' in 'Regional
> and language options' under Control Panel to English (Singapore) solved the
> R usage problem for me. I will have a go at R-patched build 46507 after it
> is released.
>
> Regards,
> Thomas
>
> On Mon, Sep 8, 2008 at 7:20 PM, Prof Brian Ripley <[EMAIL PROTECTED]
> > wrote:
>
>> On Mon, 8 Sep 2008, Duncan Murdoch wrote:
>>
>> On 08/09/2008 6:56 AM, Prof Brian Ripley wrote:
>>>
On Mon, 8 Sep 2008, Prof Brian Ripley wrote:
This reflects a problem in your locale (traditional Chinese): we cannot
> reproduce it. Try running R in a different locale (e.g. append LC_ALL=en
> to
> the target when you start R).
>
Maybe I have found this as a bug in iconv. Please try a version of
R-patched with svn revision 46507 or later.
>>>
>>> Unfortunately, something stopped the daily builds of R-patched on
>>> Saturday, and I haven't been in to the office yet to fix things. So it's
>>> likely to be tomorrow before the Windows build of r46507 or later is
>>> available on CRAN.
>>>
>>
>> I only found r46507 this morning, as a side effect of something else. So
>> it would not be in a build until tomorrow.
>>
>>
>>
>>
>>> Duncan Murdoch
>>>
>>>
On Sun, 7 Sep 2008, Thomas Lo wrote:
>
> Dear all,
>>
>> I encountered a problem on starting and using the R v 2.7.2
>> installation on
>> my PC running Windows Vista and would appreciate your help.
>>
>> When R was first started, the Rgui returned several error messages:
>>
>> Error in structure(.Internal(Sys.getenv(as.character(x),
>> as.character(unset)$ unsupported conversion
>> Error in file.exists(name) : unsupported conversion in
>> 'filenameToWchar'
>>
>> In addition, a dialog box called 'Information' popped up with the
>> following
>> message:
>>
>> Fatal error: unable to restore saved data in .RData
>>
>> On clicking 'OK', R closed immediately and the same thing occurs on
>> restarting R.
>>
>> After checking for previous related messages online, I followed one of
>> the
>> recommendations from before and appended --no-restore-data to the R
>> shorcut
>> target line. After that, R could start without the 'fatal error'.
>> However,
>> some functions such as 'help' and 'setwd' do not work:
>>
>> e.g. >help()
>> Error: could not find function "help"
>>
>> setwd("DirName")
>>>
>> Error in setwd("DirName") : unsupported conversion in
>> 'filenameToWchar'
>> I then typed 'Sys.getlocale()' and got this:
>>
>> Sys.getlocale()
>>>
>> [1] "LC_COLLATE=Chinese (Traditional)_Hong Kong
>> S.A.R..950;LC_CTYPE=Chinese
>> (Traditional)_Hong Kong S.A.R..950;LC_MONETARY=Chinese
>> (Traditional)_Hong
>> Kong S.A.R..950;LC_NUMERIC=C;LC_TIME=Chinese (Traditional)_Hong Kong
>> S.A.R..950"
>> Setting LC_ALL=en in the shortcut target does not appear to work in
>> this
>> case as I got
>>
>> During startup - Warning message:
>> Setting LC_CTYPE=en failed
>>
>> Furthermore, I tried the patched version of R 2.7.2 and the same
>> problem
>> occurs.
>>
>> I would be very grateful if anybody could help. Many thx.
>>
>> Thomas
>>
>>[[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.
>>
>> --
> 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
>
>
>>>
>> --
>> 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
>>
>
>
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] test for a single variance
Edna Bell gmail.com> writes:
>
> Dear R Gurus:
>
> Is there a test for a single variance available in R, please?
>
> Thanks,
> Edna Bell
>
Do you mean a test for homogeneity of variance?
If so, try RSiteSearch("variance homogeneity")
and see what you get ...
Ben Bolker
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Re: [R] NMDS and varimax rotation
At 9:54 PM +0200 9/9/08, Bernd Panassiti wrote: hello, subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is it possible to rotate the axis through a varimax-rotation? Thanks in advance. Bernd Panassiti Bernd, Yes. The output of isoMDS is an object with points and stress. consider the following example: test.data <- Harman74.cor$cov #twenty four mental measurements harm.dist <- sqrt(2*(1- test.data) ) #convert correlations to distances harm.iso <- isoMDS(harm.dist,k=2) # find the multidimensional solution harm.varimax <- varimax(harm.iso$points) #rotate with varimax op <- par(mfrow=c(1,2)) plot(harm.iso$points, main="unrotated") plot(harm.varimax$loadings,main="rotated") Bill __ 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. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Use R for psychology http://personality-project.org/r __ 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] bootstrapping - number of items to replace is not a multiple of replacement length
Hello,
I'm new to boostrapping and I'd need some help to understand the error
message that pops up when I run my script.
I have a data.frame with 73 lines and 21 column.
I am running a stepwise regression to find the best model using the R
function "step".
I apply bootstrapping to obtain model coefficients.
This is my script:
# "datare80" is the name of the data.frame and "woodycover" is the response
variable
theta <- function(datare80, indices) {
d <- datare80[indices, ]# allows boot to select subsample
datasets
full <- lm(d$woodycover~ ., data= d )
lmbroadst <- step(full, data=d , direction = "both", k=2,
trace=0)
coefficients(lmbroadst) # return coef. vector
}
resb <- boot(data = datare80, statistic = theta, R=1000)
When I run it, I get these two messages:
If I omit the last line "coefficients(lmbroadst)" in the function
definition, I get :
"Error in t.star[r, ] <- statistic(data, i[r, ], ...) :
incorrect number of subscripts on matrix"
If I have the last line "coefficients(lmbroadst)", then I get:
"Error in t.star[r, ] <- statistic(data, i[r, ], ...) :
number of items to replace is not a multiple of replacement length"
Thank you very much for any help!
Gabriela
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Re: [R] Genmod in SAS vs. glm in R
For one thing your call to glm() is wrong --- didn't you notice the
warning messages about ``non-integer #successes in a binomial glm!''?
You need to do either:
glm(r/k ~ x, family=binomial(link='cloglog'), data=bin_data,
offset=log(y), weights=k)
or:
glm(cbind(r,k-r) ~ x, family=binomial(link='cloglog'), data=bin_data,
offset=log(y))
You get the same answer with either, but this answer still does not
agree with your
SAS results. Perhaps you have an error in your SAS syntax as well.
I wouldn't know.
cheers,
Rolf Turner
On 10/09/2008, at 10:37 AM, sandsky wrote:
Hello,
I have different results from these two softwares for a simple
binomial GLM
problem.
From Genmod in SAS: LogLikelihood=-4.75, coeff(intercept)=-3.59,
coeff(x)=0.95
From glm in R: LogLikelihood=-0.94, coeff(intercept)=-3.99, coeff
(x)=1.36
Is there anyone tell me what I did wrong?
Here are the code and results,
1) SAS Genmod:
% r: # of failure
% k: size of a risk set
data bin_data;
input r k y x;
os=log(y);
cards;
1 3 5 0.5
0 2 5 0.5
0 2 4 1.0
1 2 4 1.0
;
proc genmod data=nelson;
model r/k = x / dist = binomial link =cloglog offset
= os ;
Log Likelihood -4.7514
ParameterDFEstimate Error Limits
SquarePr > ChiSq
Intercept 1 -3.6652 1.9875 -7.5605 0.2302
3.400.0652
x1 0.8926 2.4900 -3.9877 5.7728
0.130.7200
Scale 0 1. 0. 1. 1.
2) glm in R
bin_data <-
data.frame(cbind(y=c(5,5,4,4),r=c(1,0,0,1),k=c(3,2,2,2),x=c
(0.5,0.5,1.0,1.0)))
glm(r/k ~ x, family=binomial(link='cloglog'), data=bin_data,
offset=log(y))
Coefficients:
(Intercept)x
-3.9911.358
'log Lik.' -0.9400073 (df=2)
##
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Re: [R] probably easy methods question
On Tue, 9 Sep 2008, Edna Bell wrote:
Dear R Gurus:
I want to look at the code for the t.test function. I did the following:
t.test
function (x, ...)
UseMethod("t.test")
getAnywhere("t.test")
A single object matching 't.test' was found
It was found in the following places
package:stats
registered S3 method for t from namespace stats
namespace:stats
with value
function (x, ...)
UseMethod("t.test")
methods("t.test")
[1] t.test.default* t.test.formula*
Non-visible functions are asterisked
Ok. Now what, please? I'm sure it's really simple.
Thanks,
Edna Bell
getAnywhere(t.test.default)
David Scott
_
David Scott Department of Statistics, Tamaki Campus
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000
Email: [EMAIL PROTECTED]
Graduate Officer, Department of Statistics
Director of Consulting, Department of Statistics
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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.
[R] probably easy methods question
Dear R Gurus:
I want to look at the code for the t.test function. I did the following:
> t.test
function (x, ...)
UseMethod("t.test")
> getAnywhere("t.test")
A single object matching 't.test' was found
It was found in the following places
package:stats
registered S3 method for t from namespace stats
namespace:stats
with value
function (x, ...)
UseMethod("t.test")
> methods("t.test")
[1] t.test.default* t.test.formula*
Non-visible functions are asterisked
>
Ok. Now what, please? I'm sure it's really simple.
Thanks,
Edna Bell
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[R] Genmod in SAS vs. glm in R
Hello, I have different results from these two softwares for a simple binomial GLM problem. >From Genmod in SAS: LogLikelihood=-4.75, coeff(intercept)=-3.59, coeff(x)=0.95 >From glm in R: LogLikelihood=-0.94, coeff(intercept)=-3.99, coeff(x)=1.36 Is there anyone tell me what I did wrong? Here are the code and results, 1) SAS Genmod: % r: # of failure % k: size of a risk set data bin_data; input r k y x; os=log(y); cards; 1 3 5 0.5 0 2 5 0.5 0 2 4 1.0 1 2 4 1.0 ; proc genmod data=nelson; model r/k = x / dist = binomial link =cloglog offset = os ; Log Likelihood -4.7514 ParameterDFEstimate Error Limits SquarePr > ChiSq Intercept 1 -3.6652 1.9875 -7.5605 0.2302 3.400.0652 x1 0.8926 2.4900 -3.9877 5.7728 0.130.7200 Scale 0 1. 0. 1. 1. 2) glm in R bin_data <- data.frame(cbind(y=c(5,5,4,4),r=c(1,0,0,1),k=c(3,2,2,2),x=c(0.5,0.5,1.0,1.0))) glm(r/k ~ x, family=binomial(link='cloglog'), data=bin_data, offset=log(y)) Coefficients: (Intercept)x -3.9911.358 'log Lik.' -0.9400073 (df=2) -- View this message in context: http://www.nabble.com/Genmod-in-SAS-vs.-glm-in-R-tp19402751p19402751.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] fBasics package: dnig
Hi, I am trying to calculate probability density of normal inverse gaussian distribution. I am using dnig function of fBasics package. However, I am getting following result. The density at x = 0.003042866 is: > dnig(x= 0.003042866, alpha=5.184868, beta= 0.11841, delta= 0.06038513, mu= > -0.0003520626) [1] 6.550251 I am not sure why it is 6.550251. Can anyone tell me why density is more than 1? Thank you for your time. --Raj __ 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] Package installation in Windows
As a sys admin, how do I install packages so that there is one common library for all users of the MS Windows computer, instead of the default individual location for each user? I've done this for Linux. Thanks, in advance, for your help. Mike __ 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] New member with question on multiple comparisons in mixed effects models
Dear fellow R.users/.lovers, I am very new to both R and this list, so I hope you will be patient with me in the beginning if my enquiries are inappropriate/unclear. I am trying to perform some rather complex statistical modelling using mixed-effects models. I have, after a rather difficult beginning, finally boiled down my model (using the lme function in nlme) to a couple of fixed effects and their interactions, plus a couple of nested random effects. For the moment I will not include the details because the dataset is rather large and without it is difficult to be more specific, but I can provide them if requested. My question is maybe a bit trivial, but I would like to get out of the model the pairwise comparisons for all the factor levels using TukeyHSD, but when I try to do this using the "glht" method in the multcomp library I get an error message which seems to indicate a wrong synthax, yet I think I am following the instructions given on the package documentation. Below are the code lines and the R reply. > glht(inner.exch.M9.lme,linfct=mcp(Personality:Day = "Tukey")) Error: unexpected '=' in "glht(inner.exch.M9.lme,linfct=mcp(Personality:Day =" (inner.exch.M9.lme is the model object, Personality and Day are the two fixed factors the levels of which I want to compare) I also tried without the interaction symbol and only one factor, with the same result. As I understand it, the multcomp package is new so maybe the method is not implemented for complex designs yet. Any suggestion will be appreciated (including such as "read the instructions" if they can point me to such instructions!). Thank you very much in advance and all the best Giuliano __ 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] test for a single variance
Dear R Gurus: Is there a test for a single variance available in R, please? Thanks, Edna Bell __ 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] "figure margins too large" issue
Hi everyone, I updated R from 2.6.2 to 2.7.2 recently but keep getting the error "figure margins too large" when plot pictures which never happened to me when using 2.6.2. After googling and searching the mailing list, I still have no idea how to optimize it. One of my packages fixed bugs in 2.7.2 version, so that I have to use it. Any suggestions are really appreciated!!! Best regards, Hui-Yi Chu [[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] Modality Test
Here is a function that tests for equality of however many distributions as
you like:
equaldist <- function(...){
## ... numeric sample vectors from the possibly different distributions to
be tested
## returns TRUE only if the distributions are the same
FALSE
}
;-)
-- Bert Gunter
Genentech
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Mark Difford
Sent: Tuesday, September 09, 2008 1:23 PM
To: r-help@r-project.org
Subject: Re: [R] Modality Test
Hi Amin,
And I have just remembered that there is a function called curveRep in Frank
Harrell's Hmisc package that might be useful, even if not quite in the
channel of your enquiry. curveRep was added to the package after my
struggles, so I never used it and so don't know how well it performs (quite
well, I would think).
Regards, Mark.
Amin W. Mugera wrote:
>
>
> Dear Readers:
>
> I have two issues in nonparametric statistical analysis that i need
> help:
>
> First, does R have a package that can implement the multimodality test,
> e.g., the Silverman test, DIP test, MAP test or Runt test. I have seen
> an earlier thread (sometime in 2003) where someone was trying to write
> a code for the Silverman test of multimodality. Is there any other
> tests that can enable me to know how many modes are in a distribution?
>
> Second, i would like to test whether two distributions are equal. Does R
> have a package than can implement the Li (1996) test of the equality
> of two distributions? Is there any other test i can use rather than the
> Li test?
>
> Thank you in advance for your help.
>
> Amin Mugera
> Graduate Student
> AgEcon Dept. Kansas State University
>
> __
> 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/Modality-Test-tp19396085p19400426.html
Sent from the R help mailing list archive at Nabble.com.
__
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[R] [R-pkgs] survey package
Version 3.9 of the survey package is now on CRAN. Since the last announcement (version 3.6-11, about a year ago) the main changes are - Database-backed survey objects: the data can live in a SQLite (or other DBI-compatible) database and be loaded as needed. - Ordinal logistic regression - Support for the 'mitools' package and multiply-imputed data - Conditioning plots, transparent scatterplots, survival and CDF plots. There is more information on the package web page at http://faculty.washington.edu/tlumley/survey/ -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] naive variance in GEE
Sorry, I misread your message. Prof Ripley is right, as usual -- the estimates use different stopping criteria and so are just numerically different. -thomas On Tue, 9 Sep 2008, Thomas Lumley wrote: On Mon, 8 Sep 2008, Qiong Yang wrote: Hi, The standard error from logistic regression is slightly different from the naive SE from GEE under independence working correlation structure. Yes Shouldn't they be identical? Anyone has insight about this? No, they shouldn't. They are different estimators of the same quantity, like the mean and median of a symmetric distribution. -thomas Thanks, Qiong a<-rbinom(1000,1) b<-rbinom(1000,2,0.1) c<-rbinom(1000,10,0.5) summary(gee(a~b, id=c,family="binomial",corstr="independence"))$coef summary(glm(a~b,family="binomial")) __ 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. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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] naive variance in GEE
On Mon, 8 Sep 2008, Qiong Yang wrote: Hi, The standard error from logistic regression is slightly different from the naive SE from GEE under independence working correlation structure. Yes Shouldn't they be identical? Anyone has insight about this? No, they shouldn't. They are different estimators of the same quantity, like the mean and median of a symmetric distribution. -thomas Thanks, Qiong a<-rbinom(1000,1) b<-rbinom(1000,2,0.1) c<-rbinom(1000,10,0.5) summary(gee(a~b, id=c,family="binomial",corstr="independence"))$coef summary(glm(a~b,family="binomial")) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Binning
This should do what you want.
#--x <- read.table('clipboard', header=TRUE, as.is=TRUE)
# convert dates
x$date <- as.POSIXct(strptime(x$SampleDate, "%m/%d/%Y"))
# put ForkLength into bins
x$bins <- cut(x$ForkLength, breaks=c(32, 34, 37, 40), include.lowest=TRUE)
# count the bins
tapply(x$Count, x$bins, sum)
# plot the data
plot(x$date, x$ForkLength, col=c('green', 'red', 'orange')[x$bins])
On Tue, Sep 9, 2008 at 3:12 PM, Felipe Carrillo
<[EMAIL PROTECTED]> wrote:
> Dear List:
> I have a dataset with over 5000 records and I would like to put the Count in
> bins
> based on the ForkLength. e.g.
> Forklength Count
> 32-34?
> 35-37?
> 38-40?
> and so on...
> and lastly I would like to plot (scatterplot) including the SampleDate
> along the X axis and ForkLength along the Y axis. I recently saw an
> example similar to this one here but I don't want a histogram I
> just want to see the ForkLength ranges with different colors. For example:
> ForkLength 32-34---green
> ForkLength 35-37---red
> ForkLength 38-40--Orange
> Thanks in advance
>
> SampleDate ForkLength Count
> 112/4/2007 32 2
> 212/6/2007 33 1
> 312/7/2007 33 2
> 412/7/2007 33 2
> 512/7/2007 34 1
> 612/9/2007 31 1
> 712/9/2007 33 2
> 8 12/10/2007 33 5
> 9 12/10/2007 34 1
> 10 12/11/2007 33 2
> 11 12/15/2007 34 1
> 12 12/16/2007 33 2
> 13 12/17/2007 35 1
> 14 12/19/2007 33 1
> 15 12/19/2007 35 1
> 16 12/20/2007 31 1
> 17 12/20/2007 32 1
> 18 12/20/2007 33 1
> 19 12/20/2007 34 3
> 20 12/21/2007 31 1
> 21 12/21/2007 32 3
> 22 12/21/2007 33 4
> 23 12/21/2007 3411
> 24 12/21/2007 3516
> 25 12/21/2007 36 3
> 26 12/21/2007 37 1
> 27 12/22/2007 32 1
> 28 12/22/2007 33 3
> 29 12/22/2007 34 1
> 30 12/22/2007 35 2
> 31 12/23/2007 32 1
> 32 12/23/2007 35 1
> 33 12/25/2007 32 1
> 34 12/25/2007 36 1
> 35 12/26/2007 34 1
> 36 12/26/2007 35 2
> 37 12/26/2007 36 1
> 38 12/27/2007 34 4
> 39 12/27/2007 35 2
> 40 12/27/2007 36 2
> 41 12/28/2007 32 1
> 42 12/28/2007 33 1
> 43 12/28/2007 34 1
> 44 12/28/2007 35 3
> 45 12/28/2007 36 4
> 46 12/28/2007 37 6
> 47 12/28/2007 38 2
> 48 12/28/2007 39 2
> 49 12/29/2007 34 1
> 50 12/29/2007 35 5
> 51 12/29/2007 36 2
> 52 12/29/2007 37 1
> 53 12/30/2007 33 3
> 54 12/30/2007 3410
> 55 12/30/2007 3510
> 56 12/30/2007 36 6
> 57 12/30/2007 3715
> 58 12/30/2007 38 3
> 59 12/31/2007 33 3
> 60 12/31/2007 34 8
> 61 12/31/2007 35 9
> 62 12/31/2007 36 6
> 63 12/31/2007 37 3
> 64 12/31/2007 38 1
> 651/1/2008 34 6
> 661/1/2008 35 6
> 671/1/2008 35 1
> 681/1/2008 36 6
> 691/1/2008 37 9
> 701/1/2008 38 1
> 711/2/2008 34 2
> 721/2/2008 34 1
> 731/2/2008 35 2
> 741/2/2008 36 2
> 751/2/2008 37 2
> 761/2/2008 39 1
> 771/3/2008 34 3
> 781/3/2008 35 3
> 791/3/2008 36 2
> 801/3/2008 37 3
> 811/8/2008 32 1
> 821/8/2008 33 7
> 831/8/2008 34 6
> 841/8/2008 3510
> 851/8/2008 3616
> 861/8/2008 37 7
> 871/8/2008 38 1
> 881/8/2008 39 1
> 891/9/2008 33 1
> 901/9/2008 3420
> 911/9/2008 3549
> 921/9/2008 3649
> 931/9/2008 3739
> 941/9/2008 37 1
> 951/9/2008 3818
> 961/9/2008 39 1
> 971/9/2008 40 1
> 98 1/10/2008 32 3
> 99 1/10/2008 3313
> 100 1/10/2008 3456
> 101 1/10/2008 3533
> 102 1/10/2008 3624
> 103 1/10/2008 3718
> 104 1/10/2008 39 1
> 105 1/11/2008 33 7
> 106 1/11/2008 3446
> 107 1/11/2008 3541
> 108 1/11/2008 3628
> 109 1/11/2008 3729
>
> Felipe D. Carrillo
> Supervisory Fishery Biologist
> Department of the Interior
> US Fish & Wildlife Service
> Cali
Re: [R] Help with 'spectrum'
This is why some help pages have references: please use them (Venables & Ripley explain the exact formulae used in R). On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: For the command 'spectrum' I read: The spectrum here is defined with scaling 1/frequency(x), following S-PLUS. This makes the spectral density a density over the range (-frequency(x)/2, +frequency(x)/2], whereas a more common scaling is 2π and range (-0.5, 0.5] (e.g., Bloomfield) or 1 and range (-π, π]. Forgive my ignorance but I am having a hard time interpreting this. Does this mean that in the spectrum output every element of the $spec array is scaled by 1/frequency(x)? I am having a hard time determing what is meant by 'frequency'. So please do look up the help for frequency(). Say I define a time series for a year with samples for every day. I input a 'frequency' of 365 (which in my mind is the period). The point is that your time unit is 1 year, and your measurements are every 1/365 year. That is unrelated to the 'period' (no one mentioned periodicity yet). On the output of 'spectrum' would this mean that every element of the $spec array is scaled by 1/365? There is a corresponding frequency array on the output from 'spectrum'. If the frequency is 365 and an element in the frequency array output from 'spectrum' is .1 am I to assume that the period is 36.5 and a corresponding sin wave would be sin(2 * pi * 36.5/365)? Hmm, you need a 't' in there (and a phase). The issue is the units for t. A frequency in the 'freq' element of the output of 0.1 corresponds to 10 cycles per unit of time, and in your example the unit of time is 365 observations. So the sine (sic) wave is sin(2*pi*0.1*t + phi), where the increments in 't' are 1/365: that gives 10 complete cycles in observations at, say, c(1990, 1) ... c(1990, 365), the days of 1990 (not a leap year). Thank you in advance for helping me clear up some confusion. Kevin -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] splitting time vector into days
Here is one way of doing it:
> x <- data.frame(dates=seq(as.POSIXct('2008-09-08'), by='7 hours', length=10),
+ values=1:10)
> # split into days
> x.s <- split(x, format(x$dates, "%Y%m%d"))
> x.s
$`20080908`
dates values
1 2008-09-08 00:00:00 1
2 2008-09-08 07:00:00 2
3 2008-09-08 14:00:00 3
4 2008-09-08 21:00:00 4
$`20080909`
dates values
5 2008-09-09 04:00:00 5
6 2008-09-09 11:00:00 6
7 2008-09-09 18:00:00 7
$`20080910`
dates values
8 2008-09-10 01:00:00 8
9 2008-09-10 08:00:00 9
10 2008-09-10 15:00:00 10
> lapply(x.s, function(.df) mean(.df$values))
$`20080908`
[1] 2.5
$`20080909`
[1] 6
$`20080910`
[1] 9
>
On Tue, Sep 9, 2008 at 3:25 PM, Alexy Khrabrov <[EMAIL PROTECTED]> wrote:
> Greetings -- I have a dataframe a with one element a vector, time, of
> POSIXct values. What's a good way to split the data frame into periods of
> a$time, e.g. days, and apply a function, e.g. mean, to some other column of
> the dataframe, e.g. a$value?
>
> Cheers,
> Alexy
>
> __
> 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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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[R] building a package that contains S4 classes and methods
Hello R users,
I am trying to make a my first package and I get an error that I can
understand. The package is build out of three files (one for functions, 1
for s4 classes and 1 for s4 methods).
Once I source them I run
package.skeleton( name="TDC" )
within a R session and I get
Creating directories ...
Creating DESCRIPTION ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './TDC/Read-and-delete-me'.
Warning messages:
1: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
2: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
3: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse of an S4 object will not be source()able
4: In dump(internalObjs, file = file.path(code_dir,
sprintf("%s-internal.R", :
deparse may be incomplete
I keep going in spite of the warnings with
R CMD check --no-examples TDC
and I get
* checking for working pdflatex ... OK
* using log directory
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck'
* using R version 2.7.1 (2008-06-23)
* using session charset: UTF-8
* checking for file 'TDC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TDC' version '1.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'TDC' can be installed ... ERROR
Installation failed.
The error file says:
* Installing *source* package 'TDC' ...
** R
** preparing package for lazy loading
Error in parse(n = -1, file = file) : unexpected '<' at
102: `.__C__BindArgs` <-
103: <
Calls: -> code2LazyLoadDB -> sys.source -> parse
Execution halted
ERROR: lazy loading failed for package 'TDC'
** Removing
'/home/mariepierre/Packages/PermAlgo/PermAlgo/PermAlgo2/TDC.Rcheck/TDC'
The problem is with my classes and methods. The respective files contain:
setClass("BindArgs", signature( "function" ))
setClass("BindArgs2", signature( "function" ))
and
setMethod("initialize", "BindArgs", function( .Object, f, ... )
callNextMethod( .Object, function( x ) f( x, ... ) ))
setMethod("initialize", "BindArgs2", function( .Object, f, ...)
callNextMethod( .Object, function( x, y ) f( x, y, ... ) ))
Everything works well within a R session but I can build the package.
If I look at the internal R file that this created I get
`.__C__BindArgs` <-
`.__C__BindArgs2` <-
`.__M__initialize:methods` <-
`.__T__initialize:methods` <-
Well, let just say that I am new to classes so this confuses me greatly. I
have checked the documentation and tried a few things but I reached my
personal limits!
I am using R 2.7.1 on Linux Fedora 8.
Any comments on what is happening and/or help would be greatly appreciated.
MP
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] NMDS and varimax rotation
have you looked at the vegan viginette- I know there is proscrutes rotation. On Tue, Sep 9, 2008 at 3:54 PM, Bernd Panassiti <[EMAIL PROTECTED]> wrote: > hello, > > subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is > it possible to > rotate the axis through a varimax-rotation? > > Thanks in advance. > > Bernd Panassiti > > __ > 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. > -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy 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 __ 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] splitting time vector into days
?aggregate ?window.zoo ?rollapply anyway have a look at package zoo On Tue, Sep 9, 2008 at 3:25 PM, Alexy Khrabrov <[EMAIL PROTECTED]> wrote: > Greetings -- I have a dataframe a with one element a vector, time, of > POSIXct values. What's a good way to split the data frame into periods of > a$time, e.g. days, and apply a function, e.g. mean, to some other column of > the dataframe, e.g. a$value? > > Cheers, > Alexy > > __ > 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. > -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy 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 __ 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] tsdiag error
Does anyone know why I get the following error when trying tsdiag?
Error in UseMethod("tsdiag") : no applicable method for "tsdiag"
I am invoking it as: tsdiag(mar).
Thank you.
Kevin
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[R] csaps in R?
Is there is function in R equivalent to Matlab's csaps? I need a spline function with the same calculation of the smoothing parameter in csaps to compare some results. AFAIK, the spar in smooth.spline is related but not the same. __ 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] NMDS and varimax rotation
hello, subsequently to a NMDS analysis (performed with metaMDS or isoMDS) is it possible to rotate the axis through a varimax-rotation? Thanks in advance. Bernd Panassiti __ 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] Modality Test
Hi Amin, And I have just remembered that there is a function called curveRep in Frank Harrell's Hmisc package that might be useful, even if not quite in the channel of your enquiry. curveRep was added to the package after my struggles, so I never used it and so don't know how well it performs (quite well, I would think). Regards, Mark. Amin W. Mugera wrote: > > > Dear Readers: > > I have two issues in nonparametric statistical analysis that i need > help: > > First, does R have a package that can implement the multimodality test, > e.g., the Silverman test, DIP test, MAP test or Runt test. I have seen > an earlier thread (sometime in 2003) where someone was trying to write > a code for the Silverman test of multimodality. Is there any other > tests that can enable me to know how many modes are in a distribution? > > Second, i would like to test whether two distributions are equal. Does R > have a package than can implement the Li (1996) test of the equality > of two distributions? Is there any other test i can use rather than the > Li test? > > Thank you in advance for your help. > > Amin Mugera > Graduate Student > AgEcon Dept. Kansas State University > > __ > 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/Modality-Test-tp19396085p19400426.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.
Re: [R] Information on the number of CPU's
The wmic command line utility can also be used to query this; on a dual-core Vista laptop I get C:\Users\luke>wmic cpu get NumberOfCores,NumberOfLogicalProcessors NumberOfCores NumberOfLogicalProcessors 2 2 luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: Many thanks, that's very helpful. Regards, Tolga - Original Message - From: Prof Brian Ripley [EMAIL PROTECTED] Sent: 09/09/2008 20:57 CET To: Tolga Uzuner Cc: r-help@r-project.org Subject: Re: [R] Information on the number of CPU's On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: Dear R Users, I am on Windows XP SP2 platform, using R version 2.7.2 . I was wondering if there is a way to find out, within R, the number of CPU's on my machine ? I would use this information to set the number of nodes in a cluster, depending on the machine. Sys.info() and .Platform do not carry this information. Correct, since a) R does not make use of more than 1. b) It is really not portable, and not even well-defined. (How many CPUs has a hyperthreaded dual Xeon? Some say 2, some say 4. Do you want CPUs or cores? If this is a virtualized OS, is the physical number or the logical number?) In the case of Windows, how depends on the Windows version. The w32api (XP or later) call GetNativeSystemInfo will tell you the number of CPUs, for some (unstated) definition of 'CPU'. Later versions have GetLogicalProcessorInformation, which can give the number of cores. Thanks in advance, Tolga Uzuner -- 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 Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase & Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. __ 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.
Re: [R] Modality Test
Whoops! I think that should be Stuetzle --- though I very much doubt that he reads the list. Mark Difford wrote: > > Hi Amin, > >>> First, does R have a package that can implement the multimodality test, >>> e.g., the Silverman test, DIP test, MAP test or Runt test. > > Jeremy Tantrum (a Ph.D. student of Werner Steutzle's, c. 2003/04) did some > work on this. There is some useful code on Steutzle's website: > > http://www.stat.washington.edu/wxs/Stat593-s03/Code/jeremy-unimodality.R > > I used it last year when I was trying to solve the problem of how best to > compare lots of density curves (age distributions of 3 spp. of tree > euphorbias from about very different 35 sites). In particular I had to > ensure that I wasn't creating spurious bimodality at a particular age > range when combining sites. > > You might find it useful. Feel free to contact me off list if the code has > gone, as I think I still have it (somewhere). > > Regards, Mark. > > > Amin W. Mugera wrote: >> >> >> Dear Readers: >> >> I have two issues in nonparametric statistical analysis that i need >> help: >> >> First, does R have a package that can implement the multimodality test, >> e.g., the Silverman test, DIP test, MAP test or Runt test. I have seen >> an earlier thread (sometime in 2003) where someone was trying to write >> a code for the Silverman test of multimodality. Is there any other >> tests that can enable me to know how many modes are in a distribution? >> >> Second, i would like to test whether two distributions are equal. Does R >> have a package than can implement the Li (1996) test of the equality >> of two distributions? Is there any other test i can use rather than the >> Li test? >> >> Thank you in advance for your help. >> >> Amin Mugera >> Graduate Student >> AgEcon Dept. Kansas State University >> >> __ >> 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/Modality-Test-tp19396085p19400138.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.
Re: [R] Modality Test
Hi Amin, >> First, does R have a package that can implement the multimodality test, >> e.g., the Silverman test, DIP test, MAP test or Runt test. Jeremy Tantrum (a Ph.D. student of Werner Steutzle's, c. 2003/04) did some work on this. There is some useful code on Steutzle's website: http://www.stat.washington.edu/wxs/Stat593-s03/Code/jeremy-unimodality.R I used it last year when I was trying to solve the problem of how best to compare lots of density curves (age distributions of 3 spp. of tree euphorbias from about very different 35 sites). In particular I had to ensure that I wasn't creating spurious bimodality at a particular age range when combining sites. You might find it useful. Feel free to contact me off list if the code has gone, as I think I still have it (somewhere). Regards, Mark. Amin W. Mugera wrote: > > > Dear Readers: > > I have two issues in nonparametric statistical analysis that i need > help: > > First, does R have a package that can implement the multimodality test, > e.g., the Silverman test, DIP test, MAP test or Runt test. I have seen > an earlier thread (sometime in 2003) where someone was trying to write > a code for the Silverman test of multimodality. Is there any other > tests that can enable me to know how many modes are in a distribution? > > Second, i would like to test whether two distributions are equal. Does R > have a package than can implement the Li (1996) test of the equality > of two distributions? Is there any other test i can use rather than the > Li test? > > Thank you in advance for your help. > > Amin Mugera > Graduate Student > AgEcon Dept. Kansas State University > > __ > 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/Modality-Test-tp19396085p19400095.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.
Re: [R] Information on the number of CPU's
Many thanks, that's very helpful. Regards, Tolga - Original Message - From: Prof Brian Ripley [EMAIL PROTECTED] Sent: 09/09/2008 20:57 CET To: Tolga Uzuner Cc: r-help@r-project.org Subject: Re: [R] Information on the number of CPU's On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: Dear R Users, I am on Windows XP SP2 platform, using R version 2.7.2 . I was wondering if there is a way to find out, within R, the number of CPU's on my machine ? I would use this information to set the number of nodes in a cluster, depending on the machine. Sys.info() and .Platform do not carry this information. Correct, since a) R does not make use of more than 1. b) It is really not portable, and not even well-defined. (How many CPUs has a hyperthreaded dual Xeon? Some say 2, some say 4. Do you want CPUs or cores? If this is a virtualized OS, is the physical number or the logical number?) In the case of Windows, how depends on the Windows version. The w32api (XP or later) call GetNativeSystemInfo will tell you the number of CPUs, for some (unstated) definition of 'CPU'. Later versions have GetLogicalProcessorInformation, which can give the number of cores. Thanks in advance, Tolga Uzuner -- 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 Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase & Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. __ 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] Information on the number of CPU's
On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: Dear R Users, I am on Windows XP SP2 platform, using R version 2.7.2 . I was wondering if there is a way to find out, within R, the number of CPU's on my machine ? I would use this information to set the number of nodes in a cluster, depending on the machine. Sys.info() and .Platform do not carry this information. Correct, since a) R does not make use of more than 1. b) It is really not portable, and not even well-defined. (How many CPUs has a hyperthreaded dual Xeon? Some say 2, some say 4. Do you want CPUs or cores? If this is a virtualized OS, is the physical number or the logical number?) In the case of Windows, how depends on the Windows version. The w32api (XP or later) call GetNativeSystemInfo will tell you the number of CPUs, for some (unstated) definition of 'CPU'. Later versions have GetLogicalProcessorInformation, which can give the number of cores. Thanks in advance, Tolga Uzuner -- 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 __ 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] cluster/snow question
Understood, that's what I'll do. I'm thinking of exporting the number of nodes to all nodes and passing in the node rank as 1:nonodes through clusterApply. Thanks all, Tolga Luke Tierney <[EMAIL PROTECTED]> 09/09/2008 20:11 To [EMAIL PROTECTED] cc [EMAIL PROTECTED], r-help@r-project.org Subject Re: [R] cluster/snow question On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: > Hi Markus, > > Many thanks. Is the "cluster" variable you mention below available in the > environment of the nodes ? Specifically, within that environment, how > could one identify the rank of that specific node ? No -- that isn't the way snow works. With snow the partitioning is done on the master. If you need a node to know how many other nodes there are or which index it represents in a clusterApply call then you need to pass that information in the arguments. luke > > My code would use that information to partition the problem. > > Thanks, > Tolga > > > > > Markus Schmidberger <[EMAIL PROTECTED]> > 09/09/2008 07:11 > Please respond to > [EMAIL PROTECTED] > > > To > [EMAIL PROTECTED] > cc > r-help@r-project.org > Subject > Re: [R] cluster/snow question > > > > > > > Hi Tolga, > > in SNOW you have to start a cluster with the command > > > library(snow) > > cluster <- makeCluster(#nodes) > > The object "cluster" is a list with an object for each node and each > object again is a list with all informations (rank, comm, tags) > The size of the cluster is the length of the list. > > > #nodes == length(cluster) > > E.g. the rank for node one you can get by > > cluster[[1]]$rank > > Best > Markus > > [EMAIL PROTECTED] schrieb: >> Dear R Users, >> >> I am attempting to use the snow package for clustering. Is there a way > to >> identfy, in the environment of each node, a rank for that node and also, > >> the total size of the cluster ? >> >> By way of analogy, I am looking for the functions in snow equivalent to >> mpi.comm.rank() and mpi.comm.size() from RMPI, in case that makes things > >> clearer. >> >> Thanks in advance, >> Tolga >> >> Generally, this communication is for informational purposes only >> and it is not intended as an offer or solicitation for the purchase >> or sale of any financial instrument or as an official confirmation >> of any transaction. In the event you are receiving the offering >> materials attached below related to your interest in hedge funds or >> private equity, this communication may be intended as an offer or >> solicitation for the purchase or sale of such fund(s). All market >> prices, data and other information are not warranted as to >> completeness or accuracy and are subject to change without notice. >> Any comments or statements made herein do not necessarily reflect >> those of JPMorgan Chase & Co., its subsidiaries and affiliates. >> >> This transmission may contain information that is privileged, >> confidential, legally privileged, and/or exempt from disclosure >> under applicable law. If you are not the intended recipient, you >> are hereby notified that any disclosure, copying, distribution, or >> use of the information contained herein (including any reliance >> thereon) is STRICTLY PROHIBITED. Although this transmission and any >> attachments are believed to be free of any virus or other defect >> that might affect any computer system into which it is received and >> opened, it is the responsibility of the recipient to ensure that it >> is virus free and no responsibility is accepted by JPMorgan Chase & >> Co., its subsidiaries and affiliates, as applicable, for any loss >> or damage arising in any way from its use. If you received this >> transmission in error, please immediately contact the sender and >> destroy the material in its entirety, whether in electronic or hard >> copy format. Thank you. >> Please refer to http://www.jpmorgan.com/pages/disclosures for >> disclosures relating to UK legal entities. >>[[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. >> > > > -- > Dipl.-Tech. Math. Markus Schmidberger > > Ludwig-Maximilians-Universit?? M??chen > IBE - Institut f?? medizinische Informationsverarbeitung, > Biometrie und Epidemiologie > Marchioninistr. 15, D-81377 Muenchen > URL: http://ibe.web.med.uni-muenchen.de > Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de > Tel: +49 (089) 7095 - 4599 > > > > > > Generally, this communication is for informational purposes only > and it is not intended as an offer or solicitation for the purchase > or sale of any financial instrument or as an official confirmation > of any transaction. In the event you are receiving the offering > materials attached below related to your interest in hedge funds or > private equity, this communicatio
[R] splitting time vector into days
Greetings -- I have a dataframe a with one element a vector, time, of POSIXct values. What's a good way to split the data frame into periods of a$time, e.g. days, and apply a function, e.g. mean, to some other column of the dataframe, e.g. a$value? Cheers, Alexy __ 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] Modality Test
the diptest package, perhaps? url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Sep 9, 2008, at 11:23 AM, Amin W. Mugera wrote: Dear Readers: I have two issues in nonparametric statistical analysis that i need help: First, does R have a package that can implement the multimodality test, e.g., the Silverman test, DIP test, MAP test or Runt test. I have seen an earlier thread (sometime in 2003) where someone was trying to write a code for the Silverman test of multimodality. Is there any other tests that can enable me to know how many modes are in a distribution? Second, i would like to test whether two distributions are equal. Does R have a package than can implement the Li (1996) test of the equality of two distributions? Is there any other test i can use rather than the Li test? Thank you in advance for your help. Amin Mugera Graduate Student AgEcon Dept. Kansas State University __ 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.
Re: [R] cluster/snow question
On Tue, 9 Sep 2008, [EMAIL PROTECTED] wrote: Hi Markus, Many thanks. Is the "cluster" variable you mention below available in the environment of the nodes ? Specifically, within that environment, how could one identify the rank of that specific node ? No -- that isn't the way snow works. With snow the partitioning is done on the master. If you need a node to know how many other nodes there are or which index it represents in a clusterApply call then you need to pass that information in the arguments. luke My code would use that information to partition the problem. Thanks, Tolga Markus Schmidberger <[EMAIL PROTECTED]> 09/09/2008 07:11 Please respond to [EMAIL PROTECTED] To [EMAIL PROTECTED] cc r-help@r-project.org Subject Re: [R] cluster/snow question Hi Tolga, in SNOW you have to start a cluster with the command > library(snow) > cluster <- makeCluster(#nodes) The object "cluster" is a list with an object for each node and each object again is a list with all informations (rank, comm, tags) The size of the cluster is the length of the list. > #nodes == length(cluster) E.g. the rank for node one you can get by > cluster[[1]]$rank Best Markus [EMAIL PROTECTED] schrieb: Dear R Users, I am attempting to use the snow package for clustering. Is there a way to identfy, in the environment of each node, a rank for that node and also, the total size of the cluster ? By way of analogy, I am looking for the functions in snow equivalent to mpi.comm.rank() and mpi.comm.size() from RMPI, in case that makes things clearer. Thanks in advance, Tolga Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase & Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. [[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. -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?? M??chen IBE - Institut f?? medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599 Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying,
[R] Binning
Dear List: I have a dataset with over 5000 records and I would like to put the Count in bins based on the ForkLength. e.g. Forklength Count 32-34? 35-37? 38-40? and so on... and lastly I would like to plot (scatterplot) including the SampleDate along the X axis and ForkLength along the Y axis. I recently saw an example similar to this one here but I don't want a histogram I just want to see the ForkLength ranges with different colors. For example: ForkLength 32-34---green ForkLength 35-37---red ForkLength 38-40--Orange Thanks in advance SampleDate ForkLength Count 112/4/2007 32 2 212/6/2007 33 1 312/7/2007 33 2 412/7/2007 33 2 512/7/2007 34 1 612/9/2007 31 1 712/9/2007 33 2 8 12/10/2007 33 5 9 12/10/2007 34 1 10 12/11/2007 33 2 11 12/15/2007 34 1 12 12/16/2007 33 2 13 12/17/2007 35 1 14 12/19/2007 33 1 15 12/19/2007 35 1 16 12/20/2007 31 1 17 12/20/2007 32 1 18 12/20/2007 33 1 19 12/20/2007 34 3 20 12/21/2007 31 1 21 12/21/2007 32 3 22 12/21/2007 33 4 23 12/21/2007 3411 24 12/21/2007 3516 25 12/21/2007 36 3 26 12/21/2007 37 1 27 12/22/2007 32 1 28 12/22/2007 33 3 29 12/22/2007 34 1 30 12/22/2007 35 2 31 12/23/2007 32 1 32 12/23/2007 35 1 33 12/25/2007 32 1 34 12/25/2007 36 1 35 12/26/2007 34 1 36 12/26/2007 35 2 37 12/26/2007 36 1 38 12/27/2007 34 4 39 12/27/2007 35 2 40 12/27/2007 36 2 41 12/28/2007 32 1 42 12/28/2007 33 1 43 12/28/2007 34 1 44 12/28/2007 35 3 45 12/28/2007 36 4 46 12/28/2007 37 6 47 12/28/2007 38 2 48 12/28/2007 39 2 49 12/29/2007 34 1 50 12/29/2007 35 5 51 12/29/2007 36 2 52 12/29/2007 37 1 53 12/30/2007 33 3 54 12/30/2007 3410 55 12/30/2007 3510 56 12/30/2007 36 6 57 12/30/2007 3715 58 12/30/2007 38 3 59 12/31/2007 33 3 60 12/31/2007 34 8 61 12/31/2007 35 9 62 12/31/2007 36 6 63 12/31/2007 37 3 64 12/31/2007 38 1 651/1/2008 34 6 661/1/2008 35 6 671/1/2008 35 1 681/1/2008 36 6 691/1/2008 37 9 701/1/2008 38 1 711/2/2008 34 2 721/2/2008 34 1 731/2/2008 35 2 741/2/2008 36 2 751/2/2008 37 2 761/2/2008 39 1 771/3/2008 34 3 781/3/2008 35 3 791/3/2008 36 2 801/3/2008 37 3 811/8/2008 32 1 821/8/2008 33 7 831/8/2008 34 6 841/8/2008 3510 851/8/2008 3616 861/8/2008 37 7 871/8/2008 38 1 881/8/2008 39 1 891/9/2008 33 1 901/9/2008 3420 911/9/2008 3549 921/9/2008 3649 931/9/2008 3739 941/9/2008 37 1 951/9/2008 3818 961/9/2008 39 1 971/9/2008 40 1 98 1/10/2008 32 3 99 1/10/2008 3313 100 1/10/2008 3456 101 1/10/2008 3533 102 1/10/2008 3624 103 1/10/2008 3718 104 1/10/2008 39 1 105 1/11/2008 33 7 106 1/11/2008 3446 107 1/11/2008 3541 108 1/11/2008 3628 109 1/11/2008 3729 Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish & Wildlife Service California, USA __ 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] : writeMat
Hi,
On Tue, Sep 9, 2008 at 9:53 AM, erola pairo <[EMAIL PROTECTED]> wrote:
> I write a .mat file using the writeMat() command, but when i try to load it
> in Matlab it says that file may be corrupt. I did it a month ago and it
> worked. It exists any option that I can change for making the file readable
> to Matlab?
>
>> A <- c(1:10)
>> dim(A) <- c(2,5)
>> library(R.matlab)
>> writeMat('A.mat', A=A)
>
> And what matlab say is:
> "file may be corrupt"
you need to provide much more information that this. Please see the
posting guides for the list (see footer), and provide sessionInfo() so
we know what version of R and R.matlab you are using. What version of
Matlab are you using? If it worked a month ago, what have you changed
since then?
Cheers
Henrik
(author of R.matlab)
>
> Regards
>
>[[alternative HTML version deleted]]
>
> __
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> and provide commented, minimal, self-contained, reproducible code.
>
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[R] Information on the number of CPU's
Dear R Users, I am on Windows XP SP2 platform, using R version 2.7.2 . I was wondering if there is a way to find out, within R, the number of CPU's on my machine ? I would use this information to set the number of nodes in a cluster, depending on the machine. Sys.info() and .Platform do not carry this information. Thanks in advance, Tolga Uzuner Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase & Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. [[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] cluster/snow question
Hi Markus, Many thanks. Is the "cluster" variable you mention below available in the environment of the nodes ? Specifically, within that environment, how could one identify the rank of that specific node ? My code would use that information to partition the problem. Thanks, Tolga Markus Schmidberger <[EMAIL PROTECTED]> 09/09/2008 07:11 Please respond to [EMAIL PROTECTED] To [EMAIL PROTECTED] cc r-help@r-project.org Subject Re: [R] cluster/snow question Hi Tolga, in SNOW you have to start a cluster with the command > library(snow) > cluster <- makeCluster(#nodes) The object "cluster" is a list with an object for each node and each object again is a list with all informations (rank, comm, tags) The size of the cluster is the length of the list. > #nodes == length(cluster) E.g. the rank for node one you can get by > cluster[[1]]$rank Best Markus [EMAIL PROTECTED] schrieb: > Dear R Users, > > I am attempting to use the snow package for clustering. Is there a way to > identfy, in the environment of each node, a rank for that node and also, > the total size of the cluster ? > > By way of analogy, I am looking for the functions in snow equivalent to > mpi.comm.rank() and mpi.comm.size() from RMPI, in case that makes things > clearer. > > Thanks in advance, > Tolga > > Generally, this communication is for informational purposes only > and it is not intended as an offer or solicitation for the purchase > or sale of any financial instrument or as an official confirmation > of any transaction. In the event you are receiving the offering > materials attached below related to your interest in hedge funds or > private equity, this communication may be intended as an offer or > solicitation for the purchase or sale of such fund(s). All market > prices, data and other information are not warranted as to > completeness or accuracy and are subject to change without notice. > Any comments or statements made herein do not necessarily reflect > those of JPMorgan Chase & Co., its subsidiaries and affiliates. > > This transmission may contain information that is privileged, > confidential, legally privileged, and/or exempt from disclosure > under applicable law. If you are not the intended recipient, you > are hereby notified that any disclosure, copying, distribution, or > use of the information contained herein (including any reliance > thereon) is STRICTLY PROHIBITED. Although this transmission and any > attachments are believed to be free of any virus or other defect > that might affect any computer system into which it is received and > opened, it is the responsibility of the recipient to ensure that it > is virus free and no responsibility is accepted by JPMorgan Chase & > Co., its subsidiaries and affiliates, as applicable, for any loss > or damage arising in any way from its use. If you received this > transmission in error, please immediately contact the sender and > destroy the material in its entirety, whether in electronic or hard > copy format. Thank you. > Please refer to http://www.jpmorgan.com/pages/disclosures for > disclosures relating to UK legal entities. >[[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. > -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universität München IBE - Institut für medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599 Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defec
Re: [R] Hardwarefor R cpu 64 vs 32, dual vs quad
On Tue, Sep 9, 2008 at 6:31 AM, Nic Larson <[EMAIL PROTECTED]> wrote: > Need to buy fast computer for running R on. Today we use 2,8 MHz intel D cpu > and the calculations takes around 15 days. Is it possible to get the same > calculations down to minutes/hours by only changing the hardware? > Should I go for an really fast dual 32 bit cpu and run R over linux or xp or > go for an quad core / 64 bit cpu? > Is it effective to run R on 64 bit (and problem free > (running/installing))??? > Have around 2000-3000 euro to spend Faster machines won't do that much. Without knowing what methods and algorithms you are running, I bet you a beer that it can be made twice as fast by just optimizing the code. My claim applies recursively. In other words, by optimizing the algorithms/code you can speed up things quite a bit. From experience, it is not unlikely to find bottlenecks in generic algorithms that can be made 10-100 times faster. Here is *one* example illustrating that even when you think the code is "fully optimized" you can still squeeze out more: http://wiki.r-project.org/rwiki/doku.php?id=tips:programming:code_optim2 So, start profiling your code to narrow down the parts that takes most of the CPU time. help(Rprof) is a start. There is also a Section 'Profiling R code for speed' in 'Writing R Extensions'. Good old verbose print out of system.time() also helps. My $.02 ...or 2000-3000USD if it was bounty?! ;) /Henrik > Thanx for any tip > >[[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] creating table of averages
Perfect! Thanks. On Tue, Sep 9, 2008 at 11:27 AM, Duncan Murdoch <[EMAIL PROTECTED]>wrote: > On 9/9/2008 2:12 PM, Adam D. I. Kramer wrote: > >> Maybe something like this: >> >> by(df[,c(77,81,86,90,94,98,101,106)],df$category,apply,2,mean) >> >> ...which would then need to be reformatted into a data frame (there is >> probably an easy way to do this which I don't know). >> > > sparseby() in the reshape package is more flexible than by(). If the > function returns a vector with a consistent length, you'll get a dataframe > with columns corresponding to its entries. > > Duncan Murdoch > > > >> aggregate seems like a more reasonable choice, but the function for >> aggregate must return scalars, not rows...tapply doesn't take data.frame >> inputs. Maybe someone else has a suggestion? >> >> --Adam >> >> On Tue, 9 Sep 2008, Lawrence Hanser wrote: >> >> Dear Colleagues, >>> >>> I have a dataframe with variables: >>> >>> [1] "ID" "category" "a11""a12" >>> "a13""a21" >>> [7] "a22""a23""a31""a32" >>> "b11""b12" >>> [13] "b13""b21""b31""b32" >>> "b33""b41" >>> [19] "b42""c11""c12""c21" >>> "c22""c23" >>> [25] "c31""c32""c33""d11" >>> "d12""d13" >>> [31] "d14""d21""d22""d23" >>> "d24""d25" >>> [37] "d31""d32""d33""e11" >>> "e12""e13" >>> [43] "e21""e22""e23""e31" >>> "e32""e33" >>> [49] "f11""f12""f13""f14" >>> "f21""f22" >>> [55] "f23""f24""g11""g12" >>> "g13""g14" >>> [61] "g21""g22""g23""g24" >>> "g31""g32" >>> [67] "g33""g41""g42""g43" >>> "h11""h12" >>> [73] "h13""h21""h22""h23" >>> "C1.Employ" "SC11.Ops" >>> [79] "SC12.Unit" "SC13.Nonadvers" "C2.Enterprise" "SC21.Structure" >>> "SC22.Gov" "SC23.Culture" >>> [85] "SC24.Stratcomm" "C3.Manage" "SC31.Resource" "SC32.Change" >>> "SC33.Continue" "C4.Stratthink" >>> [91] "SC41.Vision""SC42.Decision" "SC43.Adapt" "C5.Lead" >>> "SC51.Develop" "SC52.Care" >>> [97] "SC53.Diversity" "C6.Foster" "SC61.Teams" "SC62.Negotiate" >>> "C7.Embody" "SC71.Ethical" >>> [103] "SC72.Follower" "SC73.Warrior" "SC74.Develop" "C8.Comm" >>> "C81.Speak" "C82.Listen" >>> [109] "OverallImp" >>> >>> The variable "category" has four values: Regular, CCM, CFM, and Other >>> >>> I'd like to create a table like this to feed into barplot2: >>> >>> row.name C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead >>> C6.Foster C7.Embody C8.Comm >>> Regular 3.68 4.27 3.22 >>> etc.. >>> CCM 4.32 4.56 etc. >>> CFM etc. >>> Other etc. >>> >>> So far, I have been able to get this far: >>> >>> > >>> >>> mean(subset(impchiefs08,category=="Regular",select=c(C1.Employ,C2.Enterprise,C3.Manage,C4.Stratthink,C5.Lead,C6.Foster,C7.Embody,C8.Comm >>> ))) >>> C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead >>> C6.Foster C7.Embody C8.Comm >>>3.60 3.85 4.48 4.346667 4.608889 >>> 4.44 4.60 4.49 >>> >>> But I am stumped as to how to get what I want. >>> >>> Thanks in advance. >>> >>> Larry >>> >>>[[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-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. > [[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] creating table of averages
On 9/9/2008 2:12 PM, Adam D. I. Kramer wrote: Maybe something like this: by(df[,c(77,81,86,90,94,98,101,106)],df$category,apply,2,mean) ...which would then need to be reformatted into a data frame (there is probably an easy way to do this which I don't know). sparseby() in the reshape package is more flexible than by(). If the function returns a vector with a consistent length, you'll get a dataframe with columns corresponding to its entries. Duncan Murdoch aggregate seems like a more reasonable choice, but the function for aggregate must return scalars, not rows...tapply doesn't take data.frame inputs. Maybe someone else has a suggestion? --Adam On Tue, 9 Sep 2008, Lawrence Hanser wrote: Dear Colleagues, I have a dataframe with variables: [1] "ID" "category" "a11""a12" "a13""a21" [7] "a22""a23""a31""a32" "b11""b12" [13] "b13""b21""b31""b32" "b33""b41" [19] "b42""c11""c12""c21" "c22""c23" [25] "c31""c32""c33""d11" "d12""d13" [31] "d14""d21""d22""d23" "d24""d25" [37] "d31""d32""d33""e11" "e12""e13" [43] "e21""e22""e23""e31" "e32""e33" [49] "f11""f12""f13""f14" "f21""f22" [55] "f23""f24""g11""g12" "g13""g14" [61] "g21""g22""g23""g24" "g31""g32" [67] "g33""g41""g42""g43" "h11""h12" [73] "h13""h21""h22""h23" "C1.Employ" "SC11.Ops" [79] "SC12.Unit" "SC13.Nonadvers" "C2.Enterprise" "SC21.Structure" "SC22.Gov" "SC23.Culture" [85] "SC24.Stratcomm" "C3.Manage" "SC31.Resource" "SC32.Change" "SC33.Continue" "C4.Stratthink" [91] "SC41.Vision""SC42.Decision" "SC43.Adapt" "C5.Lead" "SC51.Develop" "SC52.Care" [97] "SC53.Diversity" "C6.Foster" "SC61.Teams" "SC62.Negotiate" "C7.Embody" "SC71.Ethical" [103] "SC72.Follower" "SC73.Warrior" "SC74.Develop" "C8.Comm" "C81.Speak" "C82.Listen" [109] "OverallImp" The variable "category" has four values: Regular, CCM, CFM, and Other I'd like to create a table like this to feed into barplot2: row.name C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead C6.Foster C7.Embody C8.Comm Regular 3.68 4.27 3.22 etc.. CCM 4.32 4.56 etc. CFM etc. Other etc. So far, I have been able to get this far: > mean(subset(impchiefs08,category=="Regular",select=c(C1.Employ,C2.Enterprise,C3.Manage,C4.Stratthink,C5.Lead,C6.Foster,C7.Embody,C8.Comm ))) C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead C6.Foster C7.Embody C8.Comm 3.60 3.85 4.48 4.346667 4.608889 4.44 4.60 4.49 But I am stumped as to how to get what I want. Thanks in advance. Larry [[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-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.
Re: [R] creating table of averages
Maybe something like this: by(df[,c(77,81,86,90,94,98,101,106)],df$category,apply,2,mean) ...which would then need to be reformatted into a data frame (there is probably an easy way to do this which I don't know). aggregate seems like a more reasonable choice, but the function for aggregate must return scalars, not rows...tapply doesn't take data.frame inputs. Maybe someone else has a suggestion? --Adam On Tue, 9 Sep 2008, Lawrence Hanser wrote: Dear Colleagues, I have a dataframe with variables: [1] "ID" "category" "a11""a12" "a13""a21" [7] "a22""a23""a31""a32" "b11""b12" [13] "b13""b21""b31""b32" "b33""b41" [19] "b42""c11""c12""c21" "c22""c23" [25] "c31""c32""c33""d11" "d12""d13" [31] "d14""d21""d22""d23" "d24""d25" [37] "d31""d32""d33""e11" "e12""e13" [43] "e21""e22""e23""e31" "e32""e33" [49] "f11""f12""f13""f14" "f21""f22" [55] "f23""f24""g11""g12" "g13""g14" [61] "g21""g22""g23""g24" "g31""g32" [67] "g33""g41""g42""g43" "h11""h12" [73] "h13""h21""h22""h23" "C1.Employ" "SC11.Ops" [79] "SC12.Unit" "SC13.Nonadvers" "C2.Enterprise" "SC21.Structure" "SC22.Gov" "SC23.Culture" [85] "SC24.Stratcomm" "C3.Manage" "SC31.Resource" "SC32.Change" "SC33.Continue" "C4.Stratthink" [91] "SC41.Vision""SC42.Decision" "SC43.Adapt" "C5.Lead" "SC51.Develop" "SC52.Care" [97] "SC53.Diversity" "C6.Foster" "SC61.Teams" "SC62.Negotiate" "C7.Embody" "SC71.Ethical" [103] "SC72.Follower" "SC73.Warrior" "SC74.Develop" "C8.Comm" "C81.Speak" "C82.Listen" [109] "OverallImp" The variable "category" has four values: Regular, CCM, CFM, and Other I'd like to create a table like this to feed into barplot2: row.name C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead C6.Foster C7.Embody C8.Comm Regular 3.68 4.27 3.22 etc.. CCM 4.32 4.56 etc. CFM etc. Other etc. So far, I have been able to get this far: > mean(subset(impchiefs08,category=="Regular",select=c(C1.Employ,C2.Enterprise,C3.Manage,C4.Stratthink,C5.Lead,C6.Foster,C7.Embody,C8.Comm ))) C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead C6.Foster C7.Embody C8.Comm 3.60 3.85 4.48 4.346667 4.608889 4.44 4.60 4.49 But I am stumped as to how to get what I want. Thanks in advance. Larry [[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-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] Compiling date
Is this Month-Day or Day-Month or a mixture of both?
I still think using the Format -> Cell -> Date will work
much better...
el
On 09 Sep 2008, at 11:21 , David Scott wrote:
On Mon, 8 Sep 2008, Megh Dal wrote:
Hi,
I have following kind of dataset (all are dates) in my Excel sheet.
09/08/08
09/05/08
09/04/08
09/02/08
09/01/08
29/08/2008
28/08/2008
27/08/2008
26/08/2008
25/08/2008
22/08/2008
21/08/2008
20/08/2008
18/08/2008
14/08/2008
13/08/2008
08/12/08
08/11/08
08/08/08
08/07/08
However I want to use R to compile those data to make all dates in
same format. Can anyone please tell me any automated way for doing
that?
Well you have to read them in as character first. Then use sub to
make the two digit years into four digits. The following could
probably be improved by a regular expression whiz, but works:
strngs <- c("06/05/08","23/11/2008")
sub("([0-9][0-9]/[0-9][0-9]/)([0-9][0-9]$)","\\120\\2",strngs)
[1] "06/05/2008" "23/11/2008"
David Scott
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[R] randomForest
I am combining many different random forest objects run on the same data set using the combine ( ) function. After combining the forests I am not sure whether the variable importance, local importance, and rsq predictors are recalculated for the new random forest object or are calculated individually for each tree ensemble? Is it possible to calculate these predictors for the new random forest object after calling the combine function? Any help would be greatly apprecaited. Thanks, Kate [[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] creating table of averages
Dear Colleagues, I have a dataframe with variables: [1] "ID" "category" "a11""a12" "a13""a21" [7] "a22""a23""a31""a32" "b11""b12" [13] "b13""b21""b31""b32" "b33""b41" [19] "b42""c11""c12""c21" "c22""c23" [25] "c31""c32""c33""d11" "d12""d13" [31] "d14""d21""d22""d23" "d24""d25" [37] "d31""d32""d33""e11" "e12""e13" [43] "e21""e22""e23""e31" "e32""e33" [49] "f11""f12""f13""f14" "f21""f22" [55] "f23""f24""g11""g12" "g13""g14" [61] "g21""g22""g23""g24" "g31""g32" [67] "g33""g41""g42""g43" "h11""h12" [73] "h13""h21""h22""h23" "C1.Employ" "SC11.Ops" [79] "SC12.Unit" "SC13.Nonadvers" "C2.Enterprise" "SC21.Structure" "SC22.Gov" "SC23.Culture" [85] "SC24.Stratcomm" "C3.Manage" "SC31.Resource" "SC32.Change" "SC33.Continue" "C4.Stratthink" [91] "SC41.Vision""SC42.Decision" "SC43.Adapt" "C5.Lead" "SC51.Develop" "SC52.Care" [97] "SC53.Diversity" "C6.Foster" "SC61.Teams" "SC62.Negotiate" "C7.Embody" "SC71.Ethical" [103] "SC72.Follower" "SC73.Warrior" "SC74.Develop" "C8.Comm" "C81.Speak" "C82.Listen" [109] "OverallImp" The variable "category" has four values: Regular, CCM, CFM, and Other I'd like to create a table like this to feed into barplot2: row.name C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead C6.Foster C7.Embody C8.Comm Regular 3.68 4.27 3.22 etc.. CCM 4.32 4.56 etc. CFM etc. Other etc. So far, I have been able to get this far: > mean(subset(impchiefs08,category=="Regular",select=c(C1.Employ,C2.Enterprise,C3.Manage,C4.Stratthink,C5.Lead,C6.Foster,C7.Embody,C8.Comm ))) C1.Employ C2.Enterprise C3.Manage C4.Stratthink C5.Lead C6.Foster C7.Embody C8.Comm 3.60 3.85 4.48 4.346667 4.608889 4.44 4.60 4.49 > But I am stumped as to how to get what I want. Thanks in advance. Larry [[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] help on wavelet
It depends on what you want to do. In wavelet speak frequency is scale. these are the libraries: wmtsa - wavCWT (make sure that you pick the wavelet. I suggest morlet because it is compactly supported (disappears to zero quickly)) I would also suggest the fields packages for the tim.colors function which produces the familiar red to blue color scheme. sowas- more complex stuff here take a look very interesting if you are trying to tell if two signals are coherent. hope this helps stephen On Tue, Sep 9, 2008 at 12:03 PM, giov <[EMAIL PROTECTED]> wrote: > > Hi, > I have little experience using wavelet and I would like to know if it is > possible,using R wavelet package, to have a plot of frequency versus time. > > thank you > > giov > -- > View this message in context: > http://www.nabble.com/help-on-wavelet-tp19395583p19395583.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. > -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy 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 __ 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] printing all rows
options("max.print")
$max.print
[1] 9
options(max.print=10)
options("max.print")
$max.print
[1] 1e+05
...so check what your max.print is, and figure out whether you need to
set it to nrow, ncol, or nrow*ncol of your data frame...then do so...though
of course, this is a global variable, so everything you print from then on
will just keep printing and printing.
Really, though, you might get more utility out of write.table and then using
a word processor to read the data in your table.
--Adam
On Tue, 9 Sep 2008, ANJAN PURKAYASTHA wrote:
Hi,
my data table has 38939 rows. R prints the first 1 columns and then
prints an error message:[ reached getOption("max.print") -- omitted 27821
rows ]].
is it possible to set the maxprint parameter so that R prints all the rows?
tia,
anjan
--
=
anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142
purkayas [at] wi [dot] mit [dot] edu
703.740.6939
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[R] binomial(link="inverse")
this may be a better question for r-devel, but ... Is there a particular reason (and if so, what is it) that the inverse link is not in the list of allowable link functions for the binomial family? I initially thought this might have something to do with the properties of canonical vs non-canonical link functions, but since other link functions (probit, cloglog, cauchit, log) are allowed, I can't think of any good reason. In fact, it's sort of a mystery to me why the sets of link functions for each family are restricted. Is this from painful experience that some link functions just don't work well? I can go ahead and hack my own version that allows inverse link, but it would be nice to know if I'm doing something dumb. (The reason I want to do this is that the inverse link linearizes the Michaelis-Menten function, y = a*x/(b+x) ...) cheers Ben Bolker signature.asc Description: OpenPGP digital signature __ 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 on wavelet
Hi, I have little experience using wavelet and I would like to know if it is possible,using R wavelet package, to have a plot of frequency versus time. thank you giov -- View this message in context: http://www.nabble.com/help-on-wavelet-tp19395583p19395583.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] : writeMat
I write a .mat file using the writeMat() command, but when i try to load it
in Matlab it says that file may be corrupt. I did it a month ago and it
worked. It exists any option that I can change for making the file readable
to Matlab?
> A <- c(1:10)
> dim(A) <- c(2,5)
> library(R.matlab)
> writeMat('A.mat', A=A)
And what matlab say is:
"file may be corrupt"
Regards
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Re: [R] puzzle about contrasts
Peter Dalgaard skrev: > Prof Brian Ripley skrev: > >> -0.5*(A+B) is not a contrast, which is the seat of your puzzlement. >> >> All you can get from y ~ x is an intercept (a column of ones) and a >> single 'contrast' column for 'x'. >> >> If you use y ~ 0+x you can get two columns for 'x', but R does not >> give you an option of what columns in the case: see the source of >> contrasts(). So you would need to replace contrasts(), which I think >> will be hard as model.matrix.default will look in the 'stats' >> namespace. It would probably be easier to create the model matrix >> yourself. >> >> > Or accept the default and do the parameter transformations yourself. > > l <- lm(y~x) > T <- rbind( > c(-1,-.5), > c(0,1)) > > c2 <- T%*%coef(l) > V2 <- T%*%vcov(l) %*% t(T) > > cbind(coef=c(c2), s.e.=sqrt(diag(V2))) > I forgot: Also have a look at estimable() from the gmodels packages. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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 with 'spectrum'
For the command 'spectrum' I read: The spectrum here is defined with scaling 1/frequency(x), following S-PLUS. This makes the spectral density a density over the range (-frequency(x)/2, +frequency(x)/2], whereas a more common scaling is 2π and range (-0.5, 0.5] (e.g., Bloomfield) or 1 and range (-π, π]. Forgive my ignorance but I am having a hard time interpreting this. Does this mean that in the spectrum output every element of the $spec array is scaled by 1/frequency(x)? I am having a hard time determing what is meant by 'frequency'.Say I define a time series for a year with samples for every day. I input a 'frequency' of 365 (which in my mind is the period). On the output of 'spectrum' would this mean that every element of the $spec array is scaled by 1/365? There is a corresponding frequency array on the output from 'spectrum'. If the frequency is 365 and an element in the frequency array output from 'spectrum' is .1 am I to assume that the period is 36.5 and a corresponding sin wave would be sin(2 * pi * 36.5/365)? Thank you in advance for helping me clear up some confusion. Kevin __ 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] puzzle about contrasts
Prof Brian Ripley skrev: > -0.5*(A+B) is not a contrast, which is the seat of your puzzlement. > > All you can get from y ~ x is an intercept (a column of ones) and a > single 'contrast' column for 'x'. > > If you use y ~ 0+x you can get two columns for 'x', but R does not > give you an option of what columns in the case: see the source of > contrasts(). So you would need to replace contrasts(), which I think > will be hard as model.matrix.default will look in the 'stats' > namespace. It would probably be easier to create the model matrix > yourself. > Or accept the default and do the parameter transformations yourself. l <- lm(y~x) T <- rbind( c(-1,-.5), c(0,1)) c2 <- T%*%coef(l) V2 <- T%*%vcov(l) %*% t(T) cbind(coef=c(c2), s.e.=sqrt(diag(V2))) > On Tue, 9 Sep 2008, Kenneth Knoblauch wrote: > >> Hi, >> >> I'm trying to redefine the contrasts for a linear model. >> With a 2 level factor, x, with levels A and B, a two level >> factor outputs A and B - A from an lm fit, say >> lm(y ~ x). I would like to set the contrasts so that >> the coefficients output are -0.5 (A + B) and B - A, >> but I can't get the sign correct for the first coefficient >> (Intercept). >> >> Here is a toy example, >> >> set.seed(12161952) >> y <- rnorm(10) >> x <- factor(rep(letters[1:2], each = 5)) >> ## so A and B = >> tapply(y, x, mean) >> >> a b >> -0.719 0.8323837 >> >> ## and with treatment contrasts >> coef(lm(y ~ x)) ## A and B - A >> >> (Intercept) xb >> -0.719 1.5522724 >> >> Then, I try to redefine the contrasts >> >> ### would like contrasts: -0.5 (A + B) and B - A >> D1 <- matrix( c(-0.5, -0.5, >> -1, 1), >> 2, 2, byrow = TRUE) >> C1 <- solve(D1) >> Cnt <- C1[, -1] >> contrasts(x) <- Cnt >> coef(lm(y ~ x)) >> >> (Intercept) x1 >> 0.05624745 1.55227241 >> >> but note that the desired value is >> -0.5 * sum(tapply(y, x, mean)) >> >> [1] -0.05624745 >> >> I note that the first column of C1 is -1's not +1's >> and that working by hand, if I tamper with the model matrix >> >> mm <- model.matrix(y ~ x) >> mm[, 1] <- -1 >> >> mm >> (Intercept) x1 >> 1 -1 -0.5 >> 2 -1 -0.5 >> 3 -1 -0.5 >> 4 -1 -0.5 >> 5 -1 -0.5 >> 6 -1 0.5 >> 7 -1 0.5 >> 8 -1 0.5 >> 9 -1 0.5 >> 10 -1 0.5 >> attr(,"assign") >> [1] 0 1 >> attr(,"contrasts") >> attr(,"contrasts")$x >> [,1] >> a -0.5 >> b 0.5 >> >> solve(t(mm) %*% mm) %*% t(mm) %*% y ##Yes, I know. Use QR >> [,1] >> (Intercept) -0.05624745 >> x1 1.55227241 >> >> gives the correct sign. >> >> So, I guess my question reduces to how one would set the >> contrasts for the model.matrix to be correct >> for this to work out correctly? >> >> Thank you. >> >> Ken >> >> >> -- >> Ken Knoblauch >> Inserm U846 >> Institut Cellule Souche et Cerveau >> Département Neurosciences Intégratives >> 18 avenue du Doyen Lépine >> 69500 Bron >> France >> tel: +33 (0)4 72 91 34 77 >> fax: +33 (0)4 72 91 34 61 >> portable: +33 (0)6 84 10 64 10 >> http://www.sbri.fr >> >> __ >> 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. > -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Linear Modeling the best alternative
stephen sefick gmail.com> writes: > > I have a data set of mean velocity, discharge, and mean depth. I need > to find out which model best fits them out of log linear, linear, some > other kind of model... Using excel I have found that linear is not > that bad and log10(discharge) vs. the other two variables (I am trying > to predict velocity and depth from discharge) is not that bad either. > How do I test and see which one of these models is better... better > R-squared... I know this is a stats question and not particularly an > R question, but I will use R for the models vetting process. > any ideas would be greatly appreciated, AIC is not bad, but see http://www.unc.edu/courses/2006spring/ecol/145/001/docs/lectures/lecture18.htm for computing AIC to compare models where some have transformed response variables ... Ben Bolker __ 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] passing graph image data from remote Rserve
I believe I have found my solution, so please disregard. Thanks [[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] Modality Test
Dear Readers: I have two issues in nonparametric statistical analysis that i need help: First, does R have a package that can implement the multimodality test, e.g., the Silverman test, DIP test, MAP test or Runt test. I have seen an earlier thread (sometime in 2003) where someone was trying to write a code for the Silverman test of multimodality. Is there any other tests that can enable me to know how many modes are in a distribution? Second, i would like to test whether two distributions are equal. Does R have a package than can implement the Li (1996) test of the equality of two distributions? Is there any other test i can use rather than the Li test? Thank you in advance for your help. Amin Mugera Graduate Student AgEcon Dept. Kansas State University __ 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] passing graph image data from remote Rserve
Hello, I am using Rserve to create a dedicated computational back-engine. I generate and pass an array of data to a java application on a separate server. I was wondering if the same is possible for an image. I believe that Rserve supports passing certain R objects and JRclient can cast these objects into their Java counterparts. If I generate a barplot in R (remotely), can I pass the graph image back to the Java application for display? Currently, I am reduced to saving the graph as a .pdf locally, passing the .pdf's filepath to the Java application and allowing the application access to the file, which is not an ideal structure. Thanks for your help, Prasad [[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] puzzle about contrasts
-0.5*(A+B) is not a contrast, which is the seat of your puzzlement. All you can get from y ~ x is an intercept (a column of ones) and a single 'contrast' column for 'x'. If you use y ~ 0+x you can get two columns for 'x', but R does not give you an option of what columns in the case: see the source of contrasts(). So you would need to replace contrasts(), which I think will be hard as model.matrix.default will look in the 'stats' namespace. It would probably be easier to create the model matrix yourself. On Tue, 9 Sep 2008, Kenneth Knoblauch wrote: Hi, I'm trying to redefine the contrasts for a linear model. With a 2 level factor, x, with levels A and B, a two level factor outputs A and B - A from an lm fit, say lm(y ~ x). I would like to set the contrasts so that the coefficients output are -0.5 (A + B) and B - A, but I can't get the sign correct for the first coefficient (Intercept). Here is a toy example, set.seed(12161952) y <- rnorm(10) x <- factor(rep(letters[1:2], each = 5)) ## so A and B = tapply(y, x, mean) a b -0.719 0.8323837 ## and with treatment contrasts coef(lm(y ~ x)) ## A and B - A (Intercept) xb -0.719 1.5522724 Then, I try to redefine the contrasts ### would like contrasts: -0.5 (A + B) and B - A D1 <- matrix( c(-0.5, -0.5, -1, 1), 2, 2, byrow = TRUE) C1 <- solve(D1) Cnt <- C1[, -1] contrasts(x) <- Cnt coef(lm(y ~ x)) (Intercept) x1 0.05624745 1.55227241 but note that the desired value is -0.5 * sum(tapply(y, x, mean)) [1] -0.05624745 I note that the first column of C1 is -1's not +1's and that working by hand, if I tamper with the model matrix mm <- model.matrix(y ~ x) mm[, 1] <- -1 mm (Intercept) x1 1 -1 -0.5 2 -1 -0.5 3 -1 -0.5 4 -1 -0.5 5 -1 -0.5 6 -1 0.5 7 -1 0.5 8 -1 0.5 9 -1 0.5 10 -1 0.5 attr(,"assign") [1] 0 1 attr(,"contrasts") attr(,"contrasts")$x [,1] a -0.5 b 0.5 solve(t(mm) %*% mm) %*% t(mm) %*% y ##Yes, I know. Use QR [,1] (Intercept) -0.05624745 x1 1.55227241 gives the correct sign. So, I guess my question reduces to how one would set the contrasts for the model.matrix to be correct for this to work out correctly? Thank you. Ken -- Ken Knoblauch Inserm U846 Institut Cellule Souche et Cerveau Département Neurosciences Intégratives 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http://www.sbri.fr __ 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. -- 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__ 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] Linear Modeling the best alternative
I have a data set of mean velocity, discharge, and mean depth. I need to find out which model best fits them out of log linear, linear, some other kind of model... Using excel I have found that linear is not that bad and log10(discharge) vs. the other two variables (I am trying to predict velocity and depth from discharge) is not that bad either. How do I test and see which one of these models is better... better R-squared... I know this is a stats question and not particularly an R question, but I will use R for the models vetting process. any ideas would be greatly appreciated, -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy 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 __ 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] PCA and % variance explained
I did PCA stuff years there is a thing that is called a scree score
Which will give an indication of the number of PCA's and the variance
explained.
Might want to web search on scree score and PCA.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of pgseye
Sent: Tuesday, September 09, 2008 5:39 AM
To: r-help@r-project.org
Subject: [R] PCA and % variance explained
After doing a PCA using princomp, how do you view how much each
component contributes to variance in the dataset. I'm still quite new to
the theory of PCA - I have a little idea about eigenvectors and
eigenvalues (these determine the variance explained?). Are the
eigenvalues related to loadings in R?
Thanks,
Paul
--
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tml
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Re: [R] exporting tapply objects to csv-files
On Tue, Sep 9, 2008 at 3:48 AM, Kunzler, Andreas <[EMAIL PROTECTED]> wrote: > Dear Everyone, > > I try to create a cvs-file with different results form the table function. > > Imagine a data-frame with two vectors a and b where b is of the class factor. > > I use the tapply function to count a for the different values of b. > > tapply(a,b,table) > > and I use the table function to have a look of the frequencies as a total > > table(a) > > I would like to put both results together in one txt or csv file that I can > import to e.g. Excel. > > The export file should have a layout like > > 1,2,3,4,5,6,7 (possible values of a) > 3,6,7,8,8,8,1 (Counts of a total) > 1,2,3,4,5,3,0 (Counts of a where b==A) > 2,4,4,4,3,5,1 (Counts of a where b==B) > > I tried to change the class of the table result to a matrix but I could not > find a way to use the results of tapply. I use tapply because b has 15 > different values. An alternative would be to use reshape (http://had.co.nz/reshape): mydf <- data.frame( a = sample(7, 100, rep = T), b = sample(letters[1:15], 100, rep = T)) library(reshape) mydf$value <- 1 cast(mydf, b ~ a, sum, margins="row.major", fill = 0) Regards, Hadley -- http://had.co.nz/ __ 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] puzzle about contrasts
Hi, I'm trying to redefine the contrasts for a linear model. With a 2 level factor, x, with levels A and B, a two level factor outputs A and B - A from an lm fit, say lm(y ~ x). I would like to set the contrasts so that the coefficients output are -0.5 (A + B) and B - A, but I can't get the sign correct for the first coefficient (Intercept). Here is a toy example, set.seed(12161952) y <- rnorm(10) x <- factor(rep(letters[1:2], each = 5)) ## so A and B = tapply(y, x, mean) a b -0.719 0.8323837 ## and with treatment contrasts coef(lm(y ~ x)) ## A and B - A (Intercept) xb -0.719 1.5522724 Then, I try to redefine the contrasts ### would like contrasts: -0.5 (A + B) and B - A D1 <- matrix( c(-0.5, -0.5, -1, 1), 2, 2, byrow = TRUE) C1 <- solve(D1) Cnt <- C1[, -1] contrasts(x) <- Cnt coef(lm(y ~ x)) (Intercept) x1 0.05624745 1.55227241 but note that the desired value is -0.5 * sum(tapply(y, x, mean)) [1] -0.05624745 I note that the first column of C1 is -1's not +1's and that working by hand, if I tamper with the model matrix mm <- model.matrix(y ~ x) mm[, 1] <- -1 mm (Intercept) x1 1 -1 -0.5 2 -1 -0.5 3 -1 -0.5 4 -1 -0.5 5 -1 -0.5 6 -1 0.5 7 -1 0.5 8 -1 0.5 9 -1 0.5 10 -1 0.5 attr(,"assign") [1] 0 1 attr(,"contrasts") attr(,"contrasts")$x [,1] a -0.5 b 0.5 solve(t(mm) %*% mm) %*% t(mm) %*% y ##Yes, I know. Use QR [,1] (Intercept) -0.05624745 x1 1.55227241 gives the correct sign. So, I guess my question reduces to how one would set the contrasts for the model.matrix to be correct for this to work out correctly? Thank you. Ken -- Ken Knoblauch Inserm U846 Institut Cellule Souche et Cerveau Département Neurosciences Intégratives 18 avenue du Doyen Lépine 69500 Bron France tel: +33 (0)4 72 91 34 77 fax: +33 (0)4 72 91 34 61 portable: +33 (0)6 84 10 64 10 http://www.sbri.fr __ 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] Hardwarefor R cpu 64 vs 32, dual vs quad
On Tue, 9 Sep 2008, Nic Larson wrote: Need to buy fast computer for running R on. Today we use 2,8 MHz intel D cpu and the calculations takes around 15 days. Is it possible to get the same calculations down to minutes/hours by only changing the hardware? No: you would need to arrange to parallelize the computations. I'd be surprised if you got a computer within your budget that was 3x faster on a single CPU than your current one, and R will only use (unaided) one CPU for most tasks (the exception being some matrix algebra). Should I go for an really fast dual 32 bit cpu and run R over linux or xp or go for an quad core / 64 bit cpu? Is it effective to run R on 64 bit (and problem free (running/installing))??? All answered in the R-admin manual, so please RTFM. Have around 2000-3000 euro to spend Thanx for any tip [[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. -- 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 __ 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] printing all rows
Hi,
my data table has 38939 rows. R prints the first 1 columns and then
prints an error message:[ reached getOption("max.print") -- omitted 27821
rows ]].
is it possible to set the maxprint parameter so that R prints all the rows?
tia,
anjan
--
=
anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142
purkayas [at] wi [dot] mit [dot] edu
703.740.6939
[[alternative HTML version deleted]]
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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.
Re: [R] How does predict.lm work?
on 09/09/2008 09:59 AM Williams, Robin wrote: > Hi, > Please could someone explain how this element of predict.lm works? >>From the help file > ` > newdata > An optional data frame in which to look for variables with which to > predict. If omitted, the fitted values are used. > ' > Does this dataframe (newdata) need to have the same variable names as > was used in the original data frame used to fit the model? Yes. Also, see the Note in ?predict.lm: "Variables are first looked for in newdata and then searched for in the usual way (which will include the environment of the formula used in the fit). A warning will be given if the variables found are not of the same length as those in newdata if it was supplied." It also says "Variables", not columns. > Or will R > just look across consecutive columns of newdata, and apply them to the > call as appropriate? No. > For example, if I have fitted a model with four variables > (x1,x2,x3,x4) in my original dataframe, and then have a second dataframe > which I want to supply to the newdata argument in predict.lm with > variable names (x5, x6, x7, x8), do I need to change the variable names > in my newdata dataframe to match those of the original dataframe? Yes. > Or > will R treat x5 as x1, x6 as x2, etc, when using predict.lm? > I would like to know so that I can design the structure of some > somewhat larger dataframes in a manner which will make using predict.lm > straight forward and quick. > Hope this makes sense. > Many thanks for any help. HTH, Marc Schwartz __ 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] How does predict.lm work?
Just try it: > BOD # built in data frame Time demand 118.3 22 10.3 33 19.0 44 16.0 55 15.6 67 19.8 > BOD.lm <- lm(demand ~ Time, BOD) > predict(BOD.lm, list(Time = 10)) 1 25.73571 > predict(BOD.lm, list(10)) Error in eval(expr, envir, enclos) : object "Time" not found On Tue, Sep 9, 2008 at 10:59 AM, Williams, Robin <[EMAIL PROTECTED]> wrote: > Hi, > Please could someone explain how this element of predict.lm works? > >From the help file > ` > newdata > An optional data frame in which to look for variables with which to > predict. If omitted, the fitted values are used. > ' > Does this dataframe (newdata) need to have the same variable names as > was used in the original data frame used to fit the model? Or will R > just look across consecutive columns of newdata, and apply them to the > call as appropriate? > For example, if I have fitted a model with four variables > (x1,x2,x3,x4) in my original dataframe, and then have a second dataframe > which I want to supply to the newdata argument in predict.lm with > variable names (x5, x6, x7, x8), do I need to change the variable names > in my newdata dataframe to match those of the original dataframe? Or > will R treat x5 as x1, x6 as x2, etc, when using predict.lm? > I would like to know so that I can design the structure of some > somewhat larger dataframes in a manner which will make using predict.lm > straight forward and quick. > Hope this makes sense. > Many thanks for any help. > Robin Williams > Met Office summer intern - Health Forecasting > [EMAIL PROTECTED] > > >[[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-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] How does predict.lm work?
Hi, Please could someone explain how this element of predict.lm works? >From the help file ` newdata An optional data frame in which to look for variables with which to predict. If omitted, the fitted values are used. ' Does this dataframe (newdata) need to have the same variable names as was used in the original data frame used to fit the model? Or will R just look across consecutive columns of newdata, and apply them to the call as appropriate? For example, if I have fitted a model with four variables (x1,x2,x3,x4) in my original dataframe, and then have a second dataframe which I want to supply to the newdata argument in predict.lm with variable names (x5, x6, x7, x8), do I need to change the variable names in my newdata dataframe to match those of the original dataframe? Or will R treat x5 as x1, x6 as x2, etc, when using predict.lm? I would like to know so that I can design the structure of some somewhat larger dataframes in a manner which will make using predict.lm straight forward and quick. Hope this makes sense. Many thanks for any help. Robin Williams Met Office summer intern - Health Forecasting [EMAIL PROTECTED] [[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] Gumbell distribution - minimum case
If you mean you want an EVD with a fat left tail (instead of a fat
right tail), then can;t you just multiply all the values by -1 to
"reverse" the distribution? A new location parameter could then shift
the distribution wherever you want along the number line ...
-Aaron
On Mon, Sep 8, 2008 at 5:22 PM, Richard Gwozdz <[EMAIL PROTECTED]> wrote:
> Hello,
>
> I would like to sample from a Gumbell (minimum) distribution. I have
> installed package {evd} but the Gumbell functions there appear to refer to
> the maximum case. Unfortunately, setting the scale parameter negative does
> not appear to work.
>
> Is there a separate package for the Gumbell minimum?
>
>
> --
> _
> Rich Gwozdz
> Fire and Mountain Ecology Lab
> College of Forest Resources
> University of Washington
> cell: 206-769-6808 office: 206-543-9138
> [EMAIL PROTECTED]
>
> __
> 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.
>
__
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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.
Re: [R] R_USER - in which file should I include it?
Many thanks. I shall look at it. In case I run into trouble again, I'll try
to clarify the "the same".
Ed
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Tuesday, September 09, 2008 10:46 AM
To: Eduardo M. A. M.Mendes
Cc: r-help@r-project.org
Subject: Re: [R] R_USER - in which file should I include it?
You might look at ?.libPaths
(note the dot) and play around with adding a .libPaths command
to your Rprofile.site and again you may need Administrator rights
when editing it. If that does not help then you can try clarifying
the problem. In particular what "the same" refers to and what
is happening now and what you want to happen.
On Tue, Sep 9, 2008 at 9:14 AM, Eduardo M. A. M.Mendes
<[EMAIL PROTECTED]> wrote:
> Hello
>
> Many thanks. It works just fine.
>
> How about the packages issue? That is, same thing for the installation
> path.
>
> Cheers
>
> Ed
>
>
> -Original Message-
> From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
> Sent: Monday, September 08, 2008 10:01 PM
> To: Eduardo M. A. M.Mendes
> Cc: r-help@r-project.org
> Subject: Re: [R] R_USER - in which file should I include it?
>
> Try adding this at the end of your etc/Rprofile.site file. That file
> should already be there so you don't have to create it,
> just edit it.
>
> cat("Hello from Rprofile.site\n")
> setwd("C:/Users/eduardo/Documents")
>
> You may need to edit it as Administrator. You should
> see the Hello message in which case you will know that the
> Rprofile.site file is being run.
>
> That should work unless Tinn-R runs R in such a way as to
> ignore Rprofile.site.
>
> On Mon, Sep 8, 2008 at 8:11 PM, Eduardo M. A. M.Mendes
> <[EMAIL PROTECTED]> wrote:
>> Hello
>>
>> I am not sure whether R starts from the same dir. For instance:
>>
>> a) if I double-click on R-2.7.2 icon and then issue the command getwd(),
> the
>> result is:
>>
>>> getwd()
>> [1] "C:/Users/eduardo/Documents"
>>
>> b) If R starts from within Tinn-R, the result is:
>>
>> getwd()
>> [1] "C:/Program Files/R/R-2/bin"
>>
>> I want that no matter which calling R method I am using if I issue the
>> command getwd() (first command) the result is:
>>
>> "C:/Users/eduardo/Documents/R"
>>
>>
>> Moreover all new packages go to
"C:/Users/eduardo/Documents/R/win-library"
>>
>>
>> Thanks
>>
>> Ed
>>
>> -Original Message-
>> From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
>> Sent: Monday, September 08, 2008 8:57 PM
>> To: Eduardo M. A. M.Mendes
>> Cc: r-help@r-project.org
>> Subject: Re: [R] R_USER - in which file should I include it?
>>
>> Could you explain more clearly what you mean by "the same"?
>> Do you mean that each time you click on R 2.7.2 icon on your
>> desktop that running this from the R console:
>>
>> getwd()
>>
>> is the same directory on each startup? Isn't that already the case?
>> I don't think you need to set any environment variables at all. If
>> you don't set
>> any environment variables then what specifically is happening that
>> you don't want to happen?
>>
>> On Mon, Sep 8, 2008 at 7:10 PM, Eduardo M. A. M.Mendes
>> <[EMAIL PROTECTED]> wrote:
>>> Hello
>>>
>>> I am a newbie. I had my R upgraded from 2.7.1 to 2.7.2 and in doing so
I
>>> decided to install all 2.7 versions under c:\program files\R\2.7 from
now
>>> on (2.7.1 is located under .\2.7.1)
>>>
>>> Although I don't like the idea (I am running Vista), I have edited
>>> etc\Renviron.site to contain:
>>>
>>>
>>> R_USER=c:/Users/eduardo/Documents/R
>>> R_LIBS_USER=c:/Users/eduardo/Documents/R/win-library/2.7
>>>
>>> As far as R starting always from the same location, that is,
>>> c:/Users/eduardo/Documents/R, etc\Renviron.site didn't help. So I
wonder
>>> whether someone from the list could help me to:
>>>
>>> a) force R to start always from the same location
>>> b) force R to install all new packages in the same location
>>>
>>>
>>> Many thanks
>>>
>>> Ed
>>>
>>> PS. Before sending this email, I read windows FAQ and browsed the
> archives
>>> (too many posts in the subject!).
>>>
>>> __
>>> 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] Question
Hi, I'm trying to verify the assumption of homogeneity of variance of residuals in an ANOVA with levene.test. I don't know how to define the groups. I have 3 factors : A, B and C(AxB). What do I have to change or to add in the command to set that I'm working with the residuals and to set the groups? library(car) attach(anova.sns2) levene.test(residuals ~ ???) [[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] Vorticity and Divergence
Both vorticity and divergence are defined in terms of partial derivatives.
You can compute these derivatives using the `grad' function in "numDeriv"
package.
U <- function(X) { your U function}
V <- function(X) { your V function}
# where X = c(x,y)
library(numDeriv)
grU <- function(X) grad(X, func=U)
grV <- function(X) grad(X, func=V)
# For a 2-dimensional vector field
vortivcity <- function(X) grV(X)[2] - grU(X)[1]
divergence <- function(X) grU(X)[1] + grV(X)[2]
# Here is an example:
U <- function(X) X[1]^2 + X[1] * X[2]
V <- function(X) X[2]^2 - X[1] * X[2]
> vorticity(c(2,1))
[1] -5
> divergence(c(2,1))
[1] 5
>
Does this help?
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Igor Oliveira
Sent: Monday, September 08, 2008 11:37 AM
To: r-help@r-project.org
Subject: [R] Vorticity and Divergence
Hi all,
I have some wind data (U and V components) and I would like to compute
Vorticity and Divergence of these fields. Is there any R function that can
easily do that?
Thanks in advance for any help
Igor Oliveira
CSAG, Dept. Environmental & Geographical Science, University of Cape Town,
Private Bag X3, Rondebosch 7701. Tel.: +27 (0)21 650 5774
South Africa Fax: +27 (0)21 650 5773
http:///www.csag.uct.ac.za/~igor
__
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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.
__
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] plotting group means
On Tue, Sep 9, 2008 at 8:38 AM, Erich Studerus <[EMAIL PROTECTED]> wrote: > Thanks for all the suggestions, but it seems, that all these functions need > a rearrangement of my data, since in my case, the dependent variables are in > different columns. The error.bars.by-function seems to be the only plotting > function, that does not need a rearrangement. Are there other functions, > which can do that or is there an easy way to rearrange the columns into one? Try: library(reshape) melt(x) Hadley -- http://had.co.nz/ __ 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] PCA and % variance explained
After doing a PCA using princomp, how do you view how much each component contributes to variance in the dataset. I'm still quite new to the theory of PCA - I have a little idea about eigenvectors and eigenvalues (these determine the variance explained?). Are the eigenvalues related to loadings in R? Thanks, Paul -- View this message in context: http://www.nabble.com/PCA-and---variance-explained-tp19388970p19388970.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.
Re: [R] R_USER - in which file should I include it?
You might look at ?.libPaths
(note the dot) and play around with adding a .libPaths command
to your Rprofile.site and again you may need Administrator rights
when editing it. If that does not help then you can try clarifying
the problem. In particular what "the same" refers to and what
is happening now and what you want to happen.
On Tue, Sep 9, 2008 at 9:14 AM, Eduardo M. A. M.Mendes
<[EMAIL PROTECTED]> wrote:
> Hello
>
> Many thanks. It works just fine.
>
> How about the packages issue? That is, same thing for the installation
> path.
>
> Cheers
>
> Ed
>
>
> -Original Message-
> From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
> Sent: Monday, September 08, 2008 10:01 PM
> To: Eduardo M. A. M.Mendes
> Cc: r-help@r-project.org
> Subject: Re: [R] R_USER - in which file should I include it?
>
> Try adding this at the end of your etc/Rprofile.site file. That file
> should already be there so you don't have to create it,
> just edit it.
>
> cat("Hello from Rprofile.site\n")
> setwd("C:/Users/eduardo/Documents")
>
> You may need to edit it as Administrator. You should
> see the Hello message in which case you will know that the
> Rprofile.site file is being run.
>
> That should work unless Tinn-R runs R in such a way as to
> ignore Rprofile.site.
>
> On Mon, Sep 8, 2008 at 8:11 PM, Eduardo M. A. M.Mendes
> <[EMAIL PROTECTED]> wrote:
>> Hello
>>
>> I am not sure whether R starts from the same dir. For instance:
>>
>> a) if I double-click on R-2.7.2 icon and then issue the command getwd(),
> the
>> result is:
>>
>>> getwd()
>> [1] "C:/Users/eduardo/Documents"
>>
>> b) If R starts from within Tinn-R, the result is:
>>
>> getwd()
>> [1] "C:/Program Files/R/R-2/bin"
>>
>> I want that no matter which calling R method I am using if I issue the
>> command getwd() (first command) the result is:
>>
>> "C:/Users/eduardo/Documents/R"
>>
>>
>> Moreover all new packages go to "C:/Users/eduardo/Documents/R/win-library"
>>
>>
>> Thanks
>>
>> Ed
>>
>> -Original Message-
>> From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
>> Sent: Monday, September 08, 2008 8:57 PM
>> To: Eduardo M. A. M.Mendes
>> Cc: r-help@r-project.org
>> Subject: Re: [R] R_USER - in which file should I include it?
>>
>> Could you explain more clearly what you mean by "the same"?
>> Do you mean that each time you click on R 2.7.2 icon on your
>> desktop that running this from the R console:
>>
>> getwd()
>>
>> is the same directory on each startup? Isn't that already the case?
>> I don't think you need to set any environment variables at all. If
>> you don't set
>> any environment variables then what specifically is happening that
>> you don't want to happen?
>>
>> On Mon, Sep 8, 2008 at 7:10 PM, Eduardo M. A. M.Mendes
>> <[EMAIL PROTECTED]> wrote:
>>> Hello
>>>
>>> I am a newbie. I had my R upgraded from 2.7.1 to 2.7.2 and in doing so I
>>> decided to install all 2.7 versions under c:\program files\R\2.7 from now
>>> on (2.7.1 is located under .\2.7.1)
>>>
>>> Although I don't like the idea (I am running Vista), I have edited
>>> etc\Renviron.site to contain:
>>>
>>>
>>> R_USER=c:/Users/eduardo/Documents/R
>>> R_LIBS_USER=c:/Users/eduardo/Documents/R/win-library/2.7
>>>
>>> As far as R starting always from the same location, that is,
>>> c:/Users/eduardo/Documents/R, etc\Renviron.site didn't help. So I wonder
>>> whether someone from the list could help me to:
>>>
>>> a) force R to start always from the same location
>>> b) force R to install all new packages in the same location
>>>
>>>
>>> Many thanks
>>>
>>> Ed
>>>
>>> PS. Before sending this email, I read windows FAQ and browsed the
> archives
>>> (too many posts in the subject!).
>>>
>>> __
>>> 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.
>>>
>>
>>
>
>
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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.
Re: [R] plotting group means
Thanks for all the suggestions, but it seems, that all these functions need a rearrangement of my data, since in my case, the dependent variables are in different columns. The error.bars.by-function seems to be the only plotting function, that does not need a rearrangement. Are there other functions, which can do that or is there an easy way to rearrange the columns into one? Thanks Erich -Ursprüngliche Nachricht- Von: hadley wickham [mailto:[EMAIL PROTECTED] Gesendet: Dienstag, 9. September 2008 15:02 An: ONKELINX, Thierry Cc: Erich Studerus; r-help@r-project.org Betreff: Re: [R] plotting group means On Tue, Sep 9, 2008 at 6:56 AM, ONKELINX, Thierry <[EMAIL PROTECTED]> wrote: > Dear Erich, > > Have a look at ggplot2 > > library(ggplot2) > dataset <- expand.grid(x = 1:20, y = factor(LETTERS[1:4]), value = 1:10) > dataset$value <- rnorm(nrow(dataset), sd = 0.5) + as.numeric(dataset$y) Or with stat_summary: qplot(x, value, data=dataset, colour=y, group = y) + stat_summary(geom="line", fun="mean",size=2) -- http://had.co.nz/ __ 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] Hardwarefor R cpu 64 vs 32, dual vs quad
Need to buy fast computer for running R on. Today we use 2,8 MHz intel D cpu and the calculations takes around 15 days. Is it possible to get the same calculations down to minutes/hours by only changing the hardware? Should I go for an really fast dual 32 bit cpu and run R over linux or xp or go for an quad core / 64 bit cpu? Is it effective to run R on 64 bit (and problem free (running/installing))??? Have around 2000-3000 euro to spend Thanx for any tip [[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_USER - in which file should I include it?
Hello
Many thanks. It works just fine.
How about the packages issue? That is, same thing for the installation
path.
Cheers
Ed
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Monday, September 08, 2008 10:01 PM
To: Eduardo M. A. M.Mendes
Cc: r-help@r-project.org
Subject: Re: [R] R_USER - in which file should I include it?
Try adding this at the end of your etc/Rprofile.site file. That file
should already be there so you don't have to create it,
just edit it.
cat("Hello from Rprofile.site\n")
setwd("C:/Users/eduardo/Documents")
You may need to edit it as Administrator. You should
see the Hello message in which case you will know that the
Rprofile.site file is being run.
That should work unless Tinn-R runs R in such a way as to
ignore Rprofile.site.
On Mon, Sep 8, 2008 at 8:11 PM, Eduardo M. A. M.Mendes
<[EMAIL PROTECTED]> wrote:
> Hello
>
> I am not sure whether R starts from the same dir. For instance:
>
> a) if I double-click on R-2.7.2 icon and then issue the command getwd(),
the
> result is:
>
>> getwd()
> [1] "C:/Users/eduardo/Documents"
>
> b) If R starts from within Tinn-R, the result is:
>
> getwd()
> [1] "C:/Program Files/R/R-2/bin"
>
> I want that no matter which calling R method I am using if I issue the
> command getwd() (first command) the result is:
>
> "C:/Users/eduardo/Documents/R"
>
>
> Moreover all new packages go to "C:/Users/eduardo/Documents/R/win-library"
>
>
> Thanks
>
> Ed
>
> -Original Message-
> From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
> Sent: Monday, September 08, 2008 8:57 PM
> To: Eduardo M. A. M.Mendes
> Cc: r-help@r-project.org
> Subject: Re: [R] R_USER - in which file should I include it?
>
> Could you explain more clearly what you mean by "the same"?
> Do you mean that each time you click on R 2.7.2 icon on your
> desktop that running this from the R console:
>
> getwd()
>
> is the same directory on each startup? Isn't that already the case?
> I don't think you need to set any environment variables at all. If
> you don't set
> any environment variables then what specifically is happening that
> you don't want to happen?
>
> On Mon, Sep 8, 2008 at 7:10 PM, Eduardo M. A. M.Mendes
> <[EMAIL PROTECTED]> wrote:
>> Hello
>>
>> I am a newbie. I had my R upgraded from 2.7.1 to 2.7.2 and in doing so I
>> decided to install all 2.7 versions under c:\program files\R\2.7 from now
>> on (2.7.1 is located under .\2.7.1)
>>
>> Although I don't like the idea (I am running Vista), I have edited
>> etc\Renviron.site to contain:
>>
>>
>> R_USER=c:/Users/eduardo/Documents/R
>> R_LIBS_USER=c:/Users/eduardo/Documents/R/win-library/2.7
>>
>> As far as R starting always from the same location, that is,
>> c:/Users/eduardo/Documents/R, etc\Renviron.site didn't help. So I wonder
>> whether someone from the list could help me to:
>>
>> a) force R to start always from the same location
>> b) force R to install all new packages in the same location
>>
>>
>> Many thanks
>>
>> Ed
>>
>> PS. Before sending this email, I read windows FAQ and browsed the
archives
>> (too many posts in the subject!).
>>
>> __
>> 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.
>>
>
>
__
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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.
Re: [R] plotting group means
On Tue, Sep 9, 2008 at 6:56 AM, ONKELINX, Thierry <[EMAIL PROTECTED]> wrote: > Dear Erich, > > Have a look at ggplot2 > > library(ggplot2) > dataset <- expand.grid(x = 1:20, y = factor(LETTERS[1:4]), value = 1:10) > dataset$value <- rnorm(nrow(dataset), sd = 0.5) + as.numeric(dataset$y) Or with stat_summary: qplot(x, value, data=dataset, colour=y, group = y) + stat_summary(geom="line", fun="mean",size=2) -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting group means
Hi Erich, Have a look at brkdn.plot in the plotrix package. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] PCA and % variance explained
Hi Paul, >> how do you view how much each component contributes to variance in the >> dataset ... It helps to read the help: ?princomp ?prcomp Contributions to inertia or variance are reported as standard deviations (princomp.obj$sdev). So square these values to get the variance accounted for by each component. For the rest, see loadings sub Value in the help file. Regards, Mark. pgseye wrote: > > After doing a PCA using princomp, how do you view how much each component > contributes to variance in the dataset. I'm still quite new to the theory > of PCA - I have a little idea about eigenvectors and eigenvalues (these > determine the variance explained?). Are the eigenvalues related to > loadings in R? > > Thanks, > > Paul > -- View this message in context: http://www.nabble.com/PCA-and---variance-explained-tp19388970p19391466.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.
Re: [R] Compiling date
this is day month year? look at chron or maybe the easiest is to use excel to change the format On Tue, Sep 9, 2008 at 7:12 AM, Dr Eberhard Lisse <[EMAIL PROTECTED]> wrote: > Why not Format -> Cell in Excell? > > el > > on 9/9/08 1:03 PM Henrique Dallazuanna said the following: >> Try this: >> >> strptime(x, ifelse(nchar(x) == 8, '%d/%m/%y', '%d/%m/%Y')) >> >> On Tue, Sep 9, 2008 at 3:48 AM, Megh Dal <[EMAIL PROTECTED]> wrote: >> >>> Hi, >>> >>> I have following kind of dataset (all are dates) in my Excel sheet. >>> >>> 09/08/08 >>> 09/05/08 >>> 09/04/08 >>> 09/02/08 >>> 09/01/08 >>> 29/08/2008 >>> 28/08/2008 >>> 27/08/2008 >>> 26/08/2008 >>> 25/08/2008 >>> 22/08/2008 >>> 21/08/2008 >>> 20/08/2008 >>> 18/08/2008 >>> 14/08/2008 >>> 13/08/2008 >>> 08/12/08 >>> 08/11/08 >>> 08/08/08 >>> 08/07/08 >>> >>> However I want to use R to compile those data to make all dates in same >>> format. Can anyone please tell me any automated way for doing that? > > __ > 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. > -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy 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 __ 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] write dataframes
Hi, Just a thought. You wrote: ob1<-object1$ORF ob2<-object2$ORF and then use cbind like, HG<-cbind(on1,ob2) but there is an error. Is there any other function I can use? If you copied and pasted this from R, then your problem is Hg <- cbind(on1,ob2) You mean Hg <- cbind(ob1,ob2) So perhaps just a typo. HTH, Robin Williams Met Office summer intern - Health Forecasting [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Roberto Olivares-Hernández Sent: Tuesday, September 09, 2008 12:47 PM To: r-help@r-project.org Subject: [R] write dataframes Hi, After manipulate my data I have ended up with 5 different data frames with different number of observations but the same number of variables (columns) An example, if I write str(object1), I see this, data.frame': 47 obs. of 3 variables: $ ORF: Factor w/ 245 levels "YAL038W","YAL054C",..: 10 19 38 39 44 45 50 51 59 60 ... $ mRNA : num 0.891 1.148 1.202 1.479 1.445 ... $ Protein: num 1.230 1.288 1.175 0.724 0.851 .. str(object2) 'data.frame': 21 obs. of 3 variables: $ ORF: Factor w/ 245 levels "YAL038W","YAL054C",..: 11 25 40 55 66 78 104 119 141 153 ... $ mRNA : num 0.794 0.741 0.676 1.047 0.912 ... $ Protein: num 0.427 0.363 0.468 0.501 0.661 ... using the column $ORF from each object , how can I compose/write the results in a file that contains columns with different length ? I have tried to generate objects like ob1<-object1$ORF ob2<-object2$ORF and then use cbind like, HG<-cbind(on1,ob2) but there is an error. Is there any other function I can use? Thanks for the help Roberto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting group means
Dear Erich, Have a look at ggplot2 library(ggplot2) dataset <- expand.grid(x = 1:20, y = factor(LETTERS[1:4]), value = 1:10) dataset$value <- rnorm(nrow(dataset), sd = 0.5) + as.numeric(dataset$y) plotdata <- aggregate(dataset$value, list(x = dataset$x, y = dataset$y), mean) plotdata <- merge(plotdata, aggregate(dataset$value, list(x = dataset$x, y = dataset$y), sd)) plotdata$min <- plotdata$x.x - plotdata$x.y plotdata$max <- plotdata$x.x + plotdata$x.y ggplot(plotdata, aes(x = x, y = x.x, colour = y, min = min, max = max)) + geom_pointrange() + geom_line() + geom_point() HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Erich Studerus Verzonden: dinsdag 9 september 2008 12:49 Aan: r-help@r-project.org Onderwerp: [R] plotting group means Hi all, I want to plot the grouped means of some variables. The dependent variables and the grouping factor are stored in different columns. I want to draw a simple line-plot of means, in which the x-axis represents the variables and y-axis represents the means. The means of the groups should be connected by lines. So far, the only function that I could find comes closest to what I'm looking for, is the error.bars.by-function in the psych-package. To know, what I'm looking for, just type: library(psych) x <- matrix(rnorm(500),ncol=20) y <- sample(4,25 ,replace=TRUE) x <- x+y error.bars.by(x,y,ci=0) Now, I want to put a legend for the grouping factor of this graph. I also would like to manipulate the linetypes and colors of the lines. I've read the documentation, but it was not clear to me, how to do this. Are there other plotting functions in R, which can do the same? Erich Erich Studerus Lic. Phil. Klinische Psychologie Psychiatric University Hospital Zurich Division of Clinical Research Lenggstr. 31 CH-8008 Zurich Switzerland Mail: [EMAIL PROTECTED] Office: +41 44 384 26 66 Mobile: +41 76 563 31 54 [[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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] plotting group means
On 9/9/2008 6:49 AM, Erich Studerus wrote:
> Hi all,
>
>
>
> I want to plot the grouped means of some variables. The dependent variables
> and the grouping factor are stored in different columns. I want to draw a
> simple line-plot of means, in which the x-axis represents the variables and
> y-axis represents the means. The means of the groups should be connected by
> lines. So far, the only function that I could find comes closest to what I'm
> looking for, is the error.bars.by-function in the psych-package. To know,
> what I'm looking for, just type:
>
>
>
> library(psych)
> x <- matrix(rnorm(500),ncol=20)
> y <- sample(4,25 ,replace=TRUE)
> x <- x+y
> error.bars.by(x,y,ci=0)
>
>
>
> Now, I want to put a legend for the grouping factor of this graph. I also
> would like to manipulate the linetypes and colors of the lines. I've read
> the documentation, but it was not clear to me, how to do this. Are there
> other plotting functions in R, which can do the same?
Here is an approach which uses xyplot() in the lattice package and
shows how to control line types and colors:
mydf <- data.frame(x=rep(paste("Group", 1:4, sep=""), 6),
v=rep(paste("Variable", 1:6, sep=""), each=4),
y=runif(24))
library(lattice)
xyplot(y ~ v, groups = x, data = mydf, type="b",
xlab="Dependent Variables", ylab="Mean",
auto.key=list(lines=TRUE, points=TRUE, space="right"),
par.settings = list(superpose.symbol =
list(pch=c(16,8,1,5),
col=c("black","red","green","blue"),
lty=c(1,2,3,4)),
superpose.line =
list(col=c("black","red","green","blue"),
lty=c(1,2,3,4
> Erich
>
>
>
>
>
> Erich Studerus
> Lic. Phil. Klinische Psychologie
> Psychiatric University Hospital Zurich
> Division of Clinical Research
> Lenggstr. 31
> CH-8008 Zurich
> Switzerland
> Mail: [EMAIL PROTECTED]
> Office: +41 44 384 26 66
> Mobile: +41 76 563 31 54
>
>
>
>
>
> [[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.
--
Chuck Cleland, Ph.D.
NDRI, Inc. (www.ndri.org)
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
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