Re: [R] Printing Lattice Graphs from Windows
On Sunday 06 June 2004 22:11, Charles and Kimberly Maner wrote:
Hi. This did not work for me per my R output/session below:
library(lattice)
win.metafile()
trellis.par.set('background', list('white'))
This doesn't make sense; the components need to be named. Should be
trellis.par.set('background', list(col = 'white'))
trellis.par.set('plot.symbol',list(cex=0.8, col=blue, font=1,
pch=1))
xyplot(1 ~ 1)
Error in unit(rep(1 * xaxis.cex[1], length(strbar)), strheight,
strbar) : x and units must have length 0
Looks like a completely unrelated bug, which I'll fix. Can be worked
around by starting the device with
trellis.device(win.metafile)
dev.off()
null device
1
When I pasted the result into MS Word, I got the same paste--blank.
Probably due to the error above and not the bug we have been discussing.
And, yes, another default bg color such as white or transparent
would be great as I am definitely not a fan of the standard gray
either. I researched how to default it to something else, but it
seems to have to be done manually when a lattice/trellis graph is
fired up. Strange, though, as the standard/base graph/plotting does
default to a white background.
Well, the idea is for screen devices to have grey backgrounds and
'print' devices white. Currently, only pdf, postscript and xfig are
considered print devices. If the general consensus is that win.metafile
should also be put into that category, I could probably make the
necessary changes easily enough.
That said, defaults are just that, and you can change them. In
particular, calling
lset(col.whitebg())
before the xyplot call should give a fairly robust scheme with a white
(or rather 'transparent') background.
Deepayan
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] contour lines on levelplot?
On Sunday 06 June 2004 20:40, Spencer Graves wrote: With image and contour, one can get both colors and lines to enhance the image of a contour plot. What's the best way to do this with Lattice graphics? The following is one ugly hack, producing the desired result after much trial and error (R 1.9.1 alpha under Windows 2000): # setup DF - expand.grid(x=1:3, y=1:3) DF$z - (DF$x+DF$y) # Traditional base graphics: image(x=1:3, y=1:3, z=array(DF$z, dim=c(3,3))) contour(x=1:3, y=1:3, z=array(DF$z, dim=c(3,3)), add=T) # Lattice hack: lvlplt - levelplot(z~x*y, DF) cont - contourplot(z~x*y, DF) print(lvlplt, more=T) print(cont, position=c(0, 0, 0.9055, 1)) ## By comparison, the same ugly hack in S-Plus required 0.952 instead of 0.955. Is this the best we can currently get with a modest effort? There's certainly much easier ways to do this, namely contourplot(z~x*y, DF, region = TRUE) or levelplot(z~x*y, DF, contour = TRUE) the only restriction being that you would need to use the same 'at' vector. If you want them to differ, you need to write a small panel function of your own that makes use of panel.levelplot(). Deepayan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Rmetrics - new Built 190.10054
* Rmetrics - new Built 190.10054 **Juni 7 , 2004 *The new built at www.rmetrics.org should now run out of the box under Windows and Linux. In addition new functionality has been added, and some fixes have been done. Many new example files have been added. Please inspect the CHANGES file. The user guides and reference guides are not yet updated, they have still the status of Version 181.100xx. Diethelm Wuertz ETH Zurich www.rmetrics.org [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MCLUST Covariance Parameterization.
I'm not going to directly answer your question but it seems to me that you want to fit a completely unconstrained Gaussian mixture model. This may not be the best thing to do as without constraints on the Sigma_k the model may have more parameters than it is reasonable to try to estimate with the available data. A preliminary fit of a mixture model, even if it does not have quite the covariance structure that you want gives a clustering of the data that you can use to explore the correlation structure of the components empirically: then you can revise the covariance structure and re-fit. I think that this sort of approach is likely to be more effective than fitting the fully unstructured model directly. Murray Jorgensen [EMAIL PROTECTED] wrote: Hello all (especially MCLUS users). I'm trying to make use of the MCLUST package by C. Fraley and A. Raftery. My problem is trying to figure out how the (model) identifier (e.g, EII, VII, VVI, etc.) relates to the covariance matrix. The parameterization of the covariance matrix makes use of the method of decomposition in Banfield and Rraftery (1993) and Fraley and Raftery (2002) where Sigma_k = lambda_k*D_k*A_k*D_k^' where Sigma_k is the covariance matrix for the kth (k=1,...,G), lambda_k is the kth groups constant of proportionality, D_k is the orthogonal matrix of eigenvectors for the kth group, and A_k is a diagonal matrix whose elements are proportional to the eigenvalues. The parameterization of the covariance matrix Sigma_k depends on the distribution (whether spherical, diagonal, or ellipsoidal), volume (equal or variable), shape (equal or variable), and orientation (coordinate axes, equal, or variable). The distribution, volume, shape and orientation are a function of lambda_k, D_k, and A_k. Thus, depending on whether or not these values are constant across class defines Sigma_k. What I'm trying to figure out is how the distribution, volume, shape, and orientation relate to Sigma_k. As far as the parameterization of Sigma_k, what do distribution, volume, shape, and orientation even mean. Does a table exist of how these values relate to the Sigma_k? I know a table exists in the MCLUST software manual on the MCLUST website, but this table doesn't relate the values of distribution, volume, shape, and orientation to Sigma_k directly, only to how Sigma_k would be parameterized (this isnt helpful unless you know what distribution, volume, shape and orientation mean in terms of the within class covariance matrix) So, just what do the distribution, volume, shape, and orientation mean in the context of Sigma_k? What do the distribution, volume, shape, and orientation mean for a Sigma_k=sigma^2*I where I is a p by p covariance matrix, sigma^2 is the constant variance and Sigma_1=Sigma_2==Sigma_G. What about when a Sigma_k=sigma^2_k*I, or when Sigma_1=Sigma_2==Sigma_G in situations where each element of the (constant across class) covariance matrix is different? I would say I have a pretty good understanding of finite mixture modeling, but nothing I've read (expect the works cited in the 2002 JASA paper) talks about parameterizing the Sigma_k matrix in such a way. It would be nice to specify a structure directly for Sigma_k (as most books talk about). Any help on this issue would be greatly appreciated. Thanks, Ken. __ [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Dr Murray Jorgensen http://www.stats.waikato.ac.nz/Staff/maj.html Department of Statistics, University of Waikato, Hamilton, New Zealand Email: [EMAIL PROTECTED]Fax 7 838 4155 Phone +64 7 838 4773 wk+64 7 849 6486 homeMobile 021 1395 862 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] dfs in lme
Dear R-mixed-effects-modelers,
I could not answer this questions with the book by Pinheiro Bates and did
not find anything appropriate in the archives, either ...
We are preparing a short lecture on degrees of freedom and would like to
show lme's as an example as we often need to work with these. I have a
problem in understanding how many dfs are needed if random terms are used
for explanatory variables in addition to the intercept (if I have understood
correctly that ist the same as saying that interactions between random and
fixed effects are considered). I tried the following code:
library ('nlme')
options (contrasts= c ('contr.treatment', 'contr.poly'))
# create fake data
data.df - data.frame (gruppe= rep (1:4, rep (20, 4)))
# create response variable
data.df$zv - rnorm (80, 2)
# create potential explanatory variables
data.df$explan - rnorm (80, 2)
data.df$treat - as.factor (sample (1:3, 80, T))
data.df$treat1 - as.factor (sample (1:4, 80, T))
data.df$treat2 - as.factor (sample (1:5, 80, T))
data.df$treat3 - as.factor (sample (1:6, 80, T))
# with each of the explanatory variables
withoutInt - lme (zv ~ explan, data= data.df, random= ~1 | gruppe)
withInt - lme (zv ~ explan, data= data.df, random= ~ explan | gruppe)
anova (withoutInt)
anova (withInt)
anova (withoutInt, withInt)
There are two main things that I wonder about:
(1) the two anova() commands on the single models have the same residual
degrees of freedom even though the model withInt has an additional
explanatory variable. Why are the residual dfs not reduced?
(2) In the model comparison, it becomes visible that the model with 'explan'
in the random effect does indeed use more dfs. But I cannot figure out where
that number of dfs comes from. I thought that basically for each of the
levels in the grouping variable additional parameters are estimated? Thus, I
would expect somethind like df(interaction)= df(explanatory
variable)*df(random effect), but what I find is:
explanatory variabledelta-dfs of the model comparison
(= dfs of the interaction of the explanatory
variable with the random effect 'gruppe',
which has 4 levels, 3 dfs)
continuous (1 df)2
3 levels (2 dfs) 5
4 levels (3 dfs) 9
5 levels (4 dfs)14
6 levels (5 dfs)20
Can anyone point me in the right direction on where and how to answer these
questions?
Many thanks and regards, Lorenz
-
Lorenz Gygax
Tel: +41 (0)52 368 33 84 / [EMAIL PROTECTED]
Center for proper housing of ruminants and pigs
Swiss Veterinary Office
agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland
Fax : +41 (0)52 365 11 90 / Tel: +41 (0)52 368 31 31
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MCLUST Covariance Parameterization.
Dear Ken, in principle you have all relevant informations already in your mail. As far as I know, the parameterization of Fraley and Raftery is the most intuitive one. I don't know for which kind of application you need direct parameterization, but in my experience the parameters volume, shape and orientation are more interesting in most applications than the direct values of Sigma_k. However, not all possible structures seem to be implemented. Your examples are not, I suspect: What do the distribution, volume, shape, and orientation mean for a Sigma_k=sigma^2*I where I is a p by p covariance matrix, sigma^2 is the constant variance and Sigma_1=Sigma_2= =Sigma_G. This would be VEE. If you assume det(Sigma_1)=1 (which is necessary for your parameterization to be identified), then sigma^2 is lambda, i.e., the volume parameter, and Sigma_1 would be the remaining matrix product. However, VEE is not implemented. You may mail to Chris Fraley and ask why... You see that the problem is not the parameterization, but the fact that VEE is missing in mclust. (It is somewhat confusing the you use I for the covariance matrix, because emclust uses this letter for a covariance matrix, which is the identity matrix.) What about when a Sigma_k=sigma^2_k*I, or when Sigma_1=Sigma_2= =Sigma_G in situations where each element of the (constant across class) covariance matrix is different? I do not really understand this. Do you want to assume that the elements of Sigma_1 should be pairwise different? Why do you need such an assumption? That's not a very favourable choice for estimation, I think, and it would be estimated by VEE as well (which would yield such a solution with probability 1), if it would be implemented. Best, Christian *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Average R-squared of model1 to model n
Hi, We got a question about interpretating R-suqared. The actual outputs for a test dataset is X=(x1,x2, ..., xn). model 1 predicted the outputs as Y1=(y11,y12,..., y1n) model n predicted the outputs as Y2=(y21,y22,..., y2n) ... model m predicted the outputs as Ym=(ym1,ym2,..., ymn) Now we have two ways to calculate R squared to evaluate the average performance of committee model. (a) Calculate R squared between (X, Y1), (X, Y2), ..., (X,Ym), and then averaging the R squared (b) Calculate average Y=(Y1+Y2, + ... Ym)/m, and then calculate the R squared between (X, Y). We found it seemed that R squared calculated in (b) is 'always' higher than that in (a). Does this result depends on the test dataset or this happened by chance?Can you advise me any reference for this issue? Many thanks in advance! Kan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Aggregate rows to see the number of occurences
Hi, I have a set of data like the following: [,1] [,2] [1,] 102 [2,]70 [3,]10 [4,]10 [5,] 150 [6,] 174 [7,]40 [8,] 198 [9,] 102 [10,] 195 I'd like to aggregate it in order to obtain the frequency (the number of occurences) for each couple of values (e.g.: (10,2) appears twice, (7,0) appears once). Something cool would be to have this value in a third column... I've been looking at aggregate() but either I couldn't get the right parameters, or this is not the right tool to use... Thank's for any help ! -- Nicolas STRANSKY Équipe Oncologie Moléculaire Institut Curie - UMR 144 - CNRS Tel : +33 1 42 34 63 40 26, rue d'Ulm - 75248 Paris Cedex 5 - FRANCEFax : +33 1 42 34 63 49 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] question
Hello,
I'd like to know if I can modify a constant value with a function.
Example :
a=4
f1-function()
{a=3}
Of course, after the function f1() is executed , the value of a is
always 4.
I'd like the value returned is 3, like it is possible in C by doing *a=3
Thank you
nicolas
[[alternative HTML version deleted]]
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Aggregate rows to see the number of occurences
Hallo On 7 Jun 2004 at 12:18, Nicolas STRANSKY wrote: Hi, I have a set of data like the following: [,1] [,2] [1,] 102 [2,]70 [3,]10 [4,]10 [5,] 150 [6,] 174 [7,]40 [8,] 198 [9,] 102 [10,] 195 Maybe it can be done more elegantly but table and match can probably do what you want. tab V2 V3 1 10 2 2 7 0 3 1 0 4 1 0 5 15 0 6 17 4 7 4 0 8 19 8 9 10 2 10 19 5 counts-table(tab[,1]) count.no-as.numeric(names(counts)) selection-match(tab[,1],count.no) cbind(tab,no=as.numeric(counts[selection])) V2 V3 no 1 10 2 2 2 7 0 1 3 1 0 2 4 1 0 2 5 15 0 1 6 17 4 1 7 4 0 1 8 19 8 2 9 10 2 2 10 19 5 2 Is this what you want? Cheers Petr I'd like to aggregate it in order to obtain the frequency (the number of occurences) for each couple of values (e.g.: (10,2) appears twice, (7,0) appears once). Something cool would be to have this value in a third column... I've been looking at aggregate() but either I couldn't get the right parameters, or this is not the right tool to use... Thank's for any help ! -- Nicolas STRANSKY quipe Oncologie Molculaire Institut Curie - UMR 144 - CNRS Tel : +33 1 42 34 63 40 26, rue d'Ulm - 75248 Paris Cedex 5 - FRANCEFax : +33 1 42 34 63 49 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question
Hi
On 7 Jun 2004 at 12:57, zze-PELAY Nicolas FTRD/DMR/BE
wrote:
Hello,
I'd like to know if I can modify a constant value with a function.
Example :
a=4
f1-function()
{a=3}
Simply use - in the function. But I am not sure if this is
recommendable way of items manipulating in R.
f1-function() a-3
f1()
a-4
a
[1] 4
f1()
a
[1] 3
Cheers
Petr
BTW using informative subject is preferable to plain question
statement. :-)
Of course, after the function f1() is executed , the value of a is
always 4. I'd like the value returned is 3, like it is possible in C
by doing *a=3
Thank you
nicolas
[[alternative HTML version deleted]]
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
Petr Pikal
[EMAIL PROTECTED]
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Aggregate rows to see the number of occurences
Oops, you wanted to count number of pairs, this modification should work int-interaction(tab[,1],tab[,2]) counts-table(int) count.no-names(counts) selection-match(int,count.no) cbind(tab,no=as.numeric(counts[selection])) Cheers Petr On 7 Jun 2004 at 13:05, Petr Pikal wrote: Hallo On 7 Jun 2004 at 12:18, Nicolas STRANSKY wrote: Hi, I have a set of data like the following: [,1] [,2] [1,] 102 [2,]70 [3,]10 [4,]10 [5,] 150 [6,] 174 [7,]40 [8,] 198 [9,] 102 [10,] 195 Maybe it can be done more elegantly but table and match can probably do what you want. tab V2 V3 1 10 2 2 7 0 3 1 0 4 1 0 5 15 0 6 17 4 7 4 0 8 19 8 9 10 2 10 19 5 counts-table(tab[,1]) count.no-as.numeric(names(counts)) selection-match(tab[,1],count.no) cbind(tab,no=as.numeric(counts[selection])) V2 V3 no 1 10 2 2 2 7 0 1 3 1 0 2 4 1 0 2 5 15 0 1 6 17 4 1 7 4 0 1 8 19 8 2 9 10 2 2 10 19 5 2 Is this what you want? Cheers Petr I'd like to aggregate it in order to obtain the frequency (the number of occurences) for each couple of values (e.g.: (10,2) appears twice, (7,0) appears once). Something cool would be to have this value in a third column... I've been looking at aggregate() but either I couldn't get the right parameters, or this is not the right tool to use... Thank's for any help ! -- Nicolas STRANSKY quipe Oncologie Molculaire Institut Curie - UMR 144 - CNRS Tel : +33 1 42 34 63 40 26, rue d'Ulm - 75248 Paris Cedex 5 - FRANCEFax : +33 1 42 34 63 49 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Petr Pikal [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] filled.contour - color palette so z=0 ONLY is blue
I am trying to create a topographic map of an island - the filled.contour function works fine except i am experiencing difficulty trying to represent the sea properly. Basically I want the default colour blue for any instance where z=0, if I simply use the default topo.color I get shades of blue for z values up to 220 metres. Is there a way in which I can specify terrain.color for all values of z0 but blue for z=0 - or is there another way of acheiving this simply? Thanks, Laura __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Confidence intervals for predicted values in nls
Cristina Silva wrote:
Dear all
I have tried to estimate the confidence intervals for predicted values of a
nonlinear model fitted with nls. The function predict gives the predicted
values and the lower and upper limits of the prediction, when the class of
the object is lm or glm. When the object is derived from nls, the function
predict (or predict.nls) gives only the predicted values. The se.fit and
interval aguments are just ignored.
Could anybody tell me how to estimate the confidence intervals for the
predicted values (not the model parameters), using an object of class nls?
Regards,
Cristina
--
Cristina Silva
IPIMAR - Departamento de Recursos Marinhos
Av. de Brasília, 1449-006 Lisboa
Portugal
Tel.: 351 21 3027096
Fax: 351 21 3015948
[EMAIL PROTECTED]
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
maybe this example helps:
==cut here===
#define a model formula (a and b are the parameters, f is x):
frml - k1 ~ f*(1-a*exp(-b/f))
#simulate some data:
a0 - .6
b0 - 1.2
f - seq(0.01,4,length=20)
k1true- f*(1-a0*exp(-b0/f))
#include some noise
amp - .1
k1 - rnorm(k1true,k1true,amp*k1true)
#fit:
fifu - deriv(frml,c(a,b),function(a,b,x){})
rr-nls(k1~fifu(a,b,f),start=list(a=.5,b=1))
#the derivatives and variance/covariance matrix:
#(derivs could be extracted from fifu, too)
dk1.da - D(frml[[3]],'a')
dk1.db - D(frml[[3]],'b')
covar - vcov(rr)
#gaussian error propagation:
a - coef(rr)['a']
b - coef(rr)['b']
vark1 -
eval(dk1.da)^2*covar[1,1]+
eval(dk1.db)^2*covar[2,2]+
2*eval(dk1.da)*eval(dk1.db)*covar[1,2]
errk1 - sqrt(vark1)
lower.bound - fitted(rr)-2*errk1 #two sigma !
upper.bound - fitted(rr)+2*errk1 #dito
plot(f,k1,pch=1)
ff - outer(c(1,1),f)
kk - outer(c(1,1),k1)*c(1-amp,1+amp)
matlines(ff,kk,lty=3,col=1)
matlines(f,cbind(k1true,fitted(rr),lower.bound,upper.bound),col=c(1,2,3,3),lty=c(1,1,2,2))
xylim - par('usr')
xpos - .1*(xylim[2]-xylim[1])+xylim[1]
ypos - xylim[4] - .1*(xylim[4]-xylim[3])
legend(xpos,ypos,
c(
'data',
'true',
'fit',
'confidence'
),
pch=c(1,-1,-1,-1),
lty=c(0,1,1,2),
col=c(1,1,2,3)
)
==cut here===
if you put this in a file and source it a few times from within R you'll
get an impression how often the fit deviates from the 'true' curve more
than expected from
the shown confidence limits.
I believe this approach is 'nearly' valid as long as gaussian error
probagation is valid (i.e. only to first order in covar and therefore
for not too large std. errors, am I right?).
to my simple physicist's mind this should suffice to get 'reasonable'
(probably, in strict sense, not completely correct?) confidence
intervals for the fit/the prediction.
If somebody objects, please let me know!
joerg
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Aggregate rows to see the number of occurences
I have a set of data like the following: [,1] [,2] [1,] 102 ... [10,] 195 I'd like to aggregate it in order to obtain the frequency (the number of occurences) for each couple of values (e.g.: (10,2) appears twice, (7,0) appears once). Something cool would be to have this value in a third column... I've been looking at aggregate() but either I couldn't get the right parameters, or this is not the right tool to use... You can use: x=paste(a[,1],a[,2],sep=,) table(x) then, if you need to have the count for each line from the original table: table(x)[x] Or you could indeed use the 'aggregate' function: aggregate(a[,1],list(a[,1],a[,2]),length) This yields one line per unique value (but that may be what you want...) Christophe Pallier www.pallier.org __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] filled.contour - color palette so z=0 ONLY is blue
Laura Quinn [EMAIL PROTECTED] writes: I am trying to create a topographic map of an island - the filled.contour function works fine except i am experiencing difficulty trying to represent the sea properly. Basically I want the default colour blue for any instance where z=0, if I simply use the default topo.color I get shades of blue for z values up to 220 metres. Is there a way in which I can specify terrain.color for all values of z0 but blue for z=0 - or is there another way of acheiving this simply? my.colors - function(n)c(blue,terrain.colors(n-1)) data(volcano) filled.contour(volcano, color = my.colors, asp = 1) You'll probably need to diddle the levels= setting too. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question
Hello,
I'd like to know if I can modify a constant value with a function.
Example :
a=4
f1-function()
{a=3}
Of course, after the function f1() is executed , the value of
a is always 4. I'd like the value returned is 3, like it is
possible in C by doing *a=3
Use return:
f1 - function()
{a=3; return(a)}
Matthias
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Average R-squared of model1 to model n
The Y1, Y2, etc. that Kan mentioned are predicted values of a test set data from models that supposedly were fitted to the same (or similar) data. It's hard for me to imagine the outcome would be as `severe' as Y1 = -Y2. That said, I do not think that the R-squared (or q-squared as some call it) of the aggregate model is necessarily larger or equal to the average R-squared of the component models. It obviously depends on how the component models are generated. As a hypothetical example (because I haven't acutally tried it, just speculating): Suppose the data are generated from a step function, the sort that would be perfect for regression trees. If one grows several well-pruned trees, I'd guess that the average R-squared of the individual trees has a chance of being larger than the R-squared of the averaged model. Best, Andy From: Gabor Grothendieck Suppose m=2, Y1=Y and Y2= -Y. Then (b) is zero so (a) must be greater or equal to (b). Thus (b) is not necessarily greater than (a). kan Liu kan_liu1 at yahoo.com writes: : : Hi, : : We got a question about interpretating R-suqared. : : The actual outputs for a test dataset is X=(x1,x2, ..., xn). : model 1 predicted the outputs as Y1=(y11,y12,..., y1n) : model n predicted the outputs as Y2=(y21,y22,..., y2n) : : ... : model m predicted the outputs as Ym=(ym1,ym2,..., ymn) : : Now we have two ways to calculate R squared to evaluate the average performance of committee model. : : (a) Calculate R squared between (X, Y1), (X, Y2), ..., (X,Ym), and then averaging the R squared : (b) Calculate average Y=(Y1+Y2, + ... Ym)/m, and then calculate the R squared between (X, Y). : : We found it seemed that R squared calculated in (b) is 'always' higher than that in (a). : : Does this result depends on the test dataset or this happened by chance?Can you advise me any reference for : this issue? : : Many thanks in advance! : : Kan : : : : - : : [[alternative HTML version deleted]] : : __ : R-help at stat.math.ethz.ch mailing list : https://www.stat.math.ethz.ch/mailman/listinfo/r-help : PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html : : __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Lazy Evaluation?
Hello,
I've stumbled upon following problem, when trying to overload the methods
for group Math for an S4-class which contains functions as slots.
setClass(NumFunction, representation = list(fun = function))
NumFunction - function(f) new(NumFunction, fun = f)
square - function(x) x^2
NF - NumFunction(square)
setMethod(Math,
NumFunction,
function(x){
nfun - function(n) callGeneric([EMAIL PROTECTED](n))
tmp - function(n) nfun(n)
NumFunction(tmp)
})
sinNF - sin(NF)
[EMAIL PROTECTED](sqrt(pi/2))
# works as expected, returns 1
# now a slightly different version of setMethod(Math, NumFunction,
# ...), which dispenses the unnecessary wrapper function tmp()
setMethod(Math,
NumFunction,
function(x){
nfun - function(n) callGeneric([EMAIL PROTECTED](n))
return(NumFunction(nfun))
})
sinNF - sin(NF)
[EMAIL PROTECTED](sqrt(pi/2))
# produces an error, namely:
# Error in typeof(fdef) : evaluation nested too deeply: infinite
# recursion / options(expression=)?
Replacing the generating function NumFunction() with corresponding
new(..) calls doesn't change the outcome.
When I call the newly defined functions nfun resp. tmp from within the
function body of setMethod(), e.g.
setMethod(Math,
NumFunction,
function(x){
nfun - function(n) callGeneric([EMAIL PROTECTED](n))
cat(nfun(1))
NumFunction(nfun)
})
by tmp(1) resp. nfun(1), both versions cat correct output when called by
sin(NF).
If I don't return NumFunction(tmp) resp. NumFunction(nfun) but tmp resp.
nfun, both versions work just fine, i.e. sin(NF)(sqrt(pi/2)) returns 1.
Would someone explain me this behavior? (R Version 1.9.0)
Best regards,
Thomas Stabla
Sourcecode can be found at:
http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/NumFun.R
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Aggregate rows to see the number of occurences
Petr Pikal wrote: Oops, you wanted to count number of pairs, this modification should work int-interaction(tab[,1],tab[,2]) counts-table(int) count.no-names(counts) selection-match(int,count.no) cbind(tab,no=as.numeric(counts[selection])) Yes, thank's for all your answers. This is a way to do what I wanted to. I have to also say that there is a one-liner to do it :) (hint by P. Hup). x - cbind(c(10,7,1,1,15,17,4,19,10,19,10), c(2,0,0,0,0,4,0,8,2,5,2)) aggregate(x, list(a=x[,1],b=x[,2]),NROW) -- Nicolas STRANSKY quipe Oncologie Molculaire Institut Curie - UMR 144 - CNRS Tel : +33 1 42 34 63 40 26, rue d'Ulm - 75248 Paris Cedex 5 - FRANCEFax : +33 1 42 34 63 49 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Xtable giving an interesting problem
I'm using the current version of xtable for 1.9.0 and I have an interesting error: Error in match.names(clabs, names(xi)) : names don't match previous names: F value, Pr(F) In addition: Warning message: longer object length is not a multiple of shorter object length in: clabs == nmi This is produced in the following manner: data.trans - data.frame(ref=rep(c(3.995,20.003),2), actual=c(.1,100.3,.1,100.3), level=gl(2,1)) parameters - data.frame(trans.range=c(0,100), trans.output=c(4,20), ref.error=c(.0074)) a - lm(trans.range~trans.output,data=parameters) pred - data.frame(trans.output=data.trans$actual) data.trans$cor - predict(a,pred) fit.trans - lm(cor~ref,data.trans) fit.trans.aov - aov(cor~ref+Error(level),data.trans) fit.trans Call: lm(formula = cor ~ ref, data = data.trans) Coefficients: (Intercept) ref -180.6639.12 fit.trans.aov Call: aov(formula = cor ~ ref + Error(level), data = data.trans) Grand Mean: 288.75 Stratum 1: level Terms: ref Sum of Squares 392189.1 Deg. of Freedom1 Estimated effects are balanced Stratum 2: Within Terms: Residuals Sum of Squares 1.074245e-27 Deg. of Freedom2 Residual standard error: 2.317591e-14 summary(fit.trans.aov) Error: level Df Sum Sq Mean Sq ref 1 392189 392189 Error: Within Df Sum SqMean Sq F value Pr(F) Residuals 2 1.0742e-27 5.3712e-28 library(xtable) xtable(fit.trans.aov) Error in match.names(clabs, names(xi)) : names don't match previous names: F value, Pr(F) In addition: Warning message: longer object length is not a multiple of shorter object length in: clabs == nmi Any ideas? Everything should made as simple as possible, but not simpler. -Albert Einstein Shawn Way, PE Tanox, Inc. 10301 Stella Link Houston, TX 77025 Engineering Manager Sway[at]tanox.com Note: Any use, dissemination, forwarding, printing or copying of this e-mail without consent of Tanox, Inc. is not authorized. Further, this communication may contain confidential information intended only for the person to whom it is addressed, and any use, dissemination, forwarding, printing or copying of such confidential information without the express consent of Tanox or in violation of any agreements to which the recipient is subject is prohibited. If you have received this e-mail in error, please immediately notify the sender and delete the original and all copies. Any views or opinions expressed may be solely those of the author and do not necessarily represent the views or opinions of Tanox, Inc. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Xtable giving an interesting problem
Did you try dump.frames/debugger? Or even traceback()? debugger() Message: Error in match.names(clabs, names(xi)) : names don't match previous names: F value, Pr(F) Available environments had calls: 1: xtable(fit.trans.aov) 2: xtable.aovlist(fit.trans.aov) 3: xtable.summary.aovlist(summary(x), caption = caption, label = label, align = ali 4: rbind(result, xtable.anova(x[[i]][[1]], caption = caption, label = label, align 5: rbind(...) 6: match.names(clabs, names(xi)) 7: stop(paste(names don't match previous names:\n\t, paste(nmi[nii == 0], collaps and if you look in xtable.summary.aovlist you will see it is trying to rbind a dataframe with 5 columns to one with three columns. That's not surprising given the print output for summary(fit.trans.aov) and is a design error in the xtable package that should be reported to the maintainer. However, is this model really `interesting'? I cannot see what you hoped to learn by fitting it. On Mon, 7 Jun 2004, Shawn Way wrote: I'm using the current version of xtable for 1.9.0 and I have an interesting error: Error in match.names(clabs, names(xi)) : names don't match previous names: F value, Pr(F) In addition: Warning message: longer object length is not a multiple of shorter object length in: clabs == nmi This is produced in the following manner: data.trans - data.frame(ref=rep(c(3.995,20.003),2), actual=c(.1,100.3,.1,100.3), level=gl(2,1)) parameters - data.frame(trans.range=c(0,100), trans.output=c(4,20), ref.error=c(.0074)) a - lm(trans.range~trans.output,data=parameters) pred - data.frame(trans.output=data.trans$actual) data.trans$cor - predict(a,pred) fit.trans - lm(cor~ref,data.trans) fit.trans.aov - aov(cor~ref+Error(level),data.trans) fit.trans Call: lm(formula = cor ~ ref, data = data.trans) Coefficients: (Intercept) ref -180.6639.12 fit.trans.aov Call: aov(formula = cor ~ ref + Error(level), data = data.trans) Grand Mean: 288.75 Stratum 1: level Terms: ref Sum of Squares 392189.1 Deg. of Freedom1 Estimated effects are balanced Stratum 2: Within Terms: Residuals Sum of Squares 1.074245e-27 Deg. of Freedom2 Residual standard error: 2.317591e-14 summary(fit.trans.aov) Error: level Df Sum Sq Mean Sq ref 1 392189 392189 Error: Within Df Sum SqMean Sq F value Pr(F) Residuals 2 1.0742e-27 5.3712e-28 library(xtable) xtable(fit.trans.aov) Error in match.names(clabs, names(xi)) : names don't match previous names: F value, Pr(F) In addition: Warning message: longer object length is not a multiple of shorter object length in: clabs == nmi Any ideas? Everything should made as simple as possible, but not simpler. -Albert Einstein Shawn Way, PE Tanox, Inc. 10301 Stella Link Houston, TX 77025 Engineering Manager Sway[at]tanox.com Note: Any use, dissemination, forwarding, printing or copying of this e-mail without consent of Tanox, Inc. is not authorized. Further, this communication may contain confidential information intended only for the person to whom it is addressed, and any use, dissemination, forwarding, printing or copying of such confidential information without the express consent of Tanox or in violation of any agreements to which the recipient is subject is prohibited. If you have received this e-mail in error, please immediately notify the sender and delete the original and all copies. Any views or opinions expressed may be solely those of the author and do not necessarily represent the views or opinions of Tanox, Inc. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question
Petr == Petr Pikal [EMAIL PROTECTED]
on Mon, 07 Jun 2004 13:12:07 +0200 writes:
Petr Hi On 7 Jun 2004 at 12:57, zze-PELAY Nicolas
Petr FTRD/DMR/BE wrote:
Hello,
I'd like to know if I can modify a constant value with a
function.
Example :
a=4
f1-function() {a=3}
Petr Simply use - in the function.
yes.
Petr But I am not sure if this is recommendable way of
Petr items manipulating in R.
Thank you, Petr. Indeed, I am even sure that it *is* not recommended:
Very much recommended is to write a function such that
1) it only uses its arguments (and no global variables) as input
2) provides all its results as return() value, often a list().
There are exceptions to these rules, e.g. for plot()
functions, 2) will often not be true [and for print.*() methods,
the unwritten R standard asks for print.*(x, ) to return(invisible(x))]
1) {and sometimes 2) as well} will be violated for UI (not only GUI)
functions.
When working very large objects, it can make sense to
violate both 1) and 2).. -- but that's really for more
advanced programming.
Martin Maechler
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MCLUST Covariance Parameterization.
Hi Christian and thanks for your message. From reading standard mixture model books, I don't recall any of them talking directly about shape, orientation, and volume. So, in the finite mixture context I'm not exactly sure what these terms even mean as they relate to the covariance matrix. Maybe I'm missing something but it seems that the Fraley and Raftery framework is different than any mixture approach I've read about. I have a three dimensional model. Thus, the covariance matrix will be 3 by 3 for each of the G classes. I want the covariance matrix to be unrestricted (i.e., each of the 6 elements free to be estimated), yet for each of the G classes to share a common covariance matrix. That is, Sigma_1=Sigma_2=...=Sigma_G, where the elements are themselves unrestricted. My problem is translating the structure of the covariance matrix to the Fraley and Raftery framework. Reading their work I kept thanking they would have a table that translated the structure of the covariance matrix to their method of parameterization. You mention that it is the most intuitive framework, and I would agree if what was interested was the volume, shape, orientation, and distribution. My impression though is that people think in terms of the covariance structure. Where are these terms even defined? Anyway, thanks for your help. Any insight would be greatly appreciated. Ken Christian Hennig [EMAIL PROTECTED] wrote: Dear Ken, in principle you have all relevant informations already in your mail. As far as I know, the parameterization of Fraley and Raftery is the most intuitive one. I don't know for which kind of application you need direct parameterization, but in my experience the parameters volume, shape and orientation are more interesting in most applications than the direct values of Sigma_k. However, not all possible structures seem to be implemented. Your examples are not, I suspect: What do the distribution, volume, shape, and orientation mean for a Sigma_k=sigma^2*I where I is a p by p covariance matrix, sigma^2 is the constant variance and Sigma_1=Sigma_2= =Sigma_G. This would be VEE. If you assume det(Sigma_1)=1 (which is necessary for your parameterization to be identified), then sigma^2 is lambda, i.e., the volume parameter, and Sigma_1 would be the remaining matrix product. However, VEE is not implemented. You may mail to Chris Fraley and ask why... You see that the problem is not the parameterization, but the fact that VEE is missing in mclust. (It is somewhat confusing the you use I for the covariance matrix, because emclust uses this letter for a covariance matrix, which is the identity matrix.) What about when a Sigma_k=sigma^2_k*I, or when Sigma_1=Sigma_2= =Sigma_G in situations where each element of the (constant across class) covariance matrix is different? I do not really understand this. Do you want to assume that the elements of Sigma_1 should be pairwise different? Why do you need such an assumption? That's not a very favourable choice for estimation, I think, and it would be estimated by VEE as well (which would yield such a solution with probability 1), if it would be implemented. Best, Christian *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Precision for a former question*
I got many answers to the question I asked below , and I thank you all.
Several of you told me to use - but told also that it is not a
recommendable way of items manipulating in R.
I don't really understand what it exactly means :
1) does it mean it's not a very good way of programming , a
dangerous way of programming because the variable a can be modified ? ,
etc
Or 2) does it mean that R is not done to manipulate the operation
- in a function in a safe way , that there can be some mistakes, that
the memory allocation is not forseen for this case?
I indeed saw in the archive the function f - function(x) { g -
function() x[1] - x[1]+1; g() } # g nested , which is an exemple of
function where x (of the global environnement) won't be modified when
doing f(x) , but I'm not in the case of complicated programmes such as
f.
I am just carefull because in my programmes, I use arrays with important
datas , and it would better for my programmes to be able to modify some
variables (of the global environnement) directly in my function by using
-. Consequently, I just want to be sure that I will note have false
results , and that i won't have problems I can't deal with (such as
allocation memory).
So , is it 1) or 2) ?
Thank you
Nicolas
--
* Former question :
I'd like to know if I can modify a constant value with a function.
Example :
a=4
f1-function()
{a=3}
Of course, after the function f1() is executed , the value of a is
always 4.
I'd like the value returned is 3, like it is possible in C by doing *a=3
[[alternative HTML version deleted]]
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MCLUST Covariance Parameterization.
Hi Ken, it seems that you want equal covariance matrices, which means equal, but free volume, orientation and shape. That's EEE, and it *is* implemented. I still do not really understand your translation problem. All information is in the formula which appeared in your first posting: Sigma_k = lambda_k*D_k*A_k*D_k^' That is, if you have lambda (volume0), D (orientation, orthogonal) and A (shape, diagonal0), you can compute Sigma and if you have Sigma, you can compute lambda, A, and D by spectral decomposition. Hope this helps, Christian On Mon, 7 Jun 2004, [EMAIL PROTECTED] wrote: Hi Christian and thanks for your message. From reading standard mixture model books, I don't recall any of them talking directly about shape, orientation, and volume. So, in the finite mixture context I'm not exactly sure what these terms even mean as they relate to the covariance matrix. Maybe I'm missing something but it seems that the Fraley and Raftery framework is different than any mixture approach I've read about. I have a three dimensional model. Thus, the covariance matrix will be 3 by 3 for each of the G classes. I want the covariance matrix to be unrestricted (i.e., each of the 6 elements free to be estimated), yet for each of the G classes to share a common covariance matrix. That is, Sigma_1=Sigma_2=...=Sigma_G, where the elements are themselves unrestricted. My problem is translating the structure of the covariance matrix to the Fraley and Raftery framework. Reading their work I kept thanking they would have a table that translated the structure of the covariance matrix to their method of parameterization. You mention that it is the most intuitive framework, and I would agree if what was interested was the volume, shape, orientation, and distribution. My impression though is that people think in terms of the covariance structure. Where are these terms even defined? Anyway, thanks for your help. Any insight would be greatly appreciated. Ken Christian Hennig [EMAIL PROTECTED] wrote: Dear Ken, in principle you have all relevant informations already in your mail. As far as I know, the parameterization of Fraley and Raftery is the most intuitive one. I don't know for which kind of application you need direct parameterization, but in my experience the parameters volume, shape and orientation are more interesting in most applications than the direct values of Sigma_k. However, not all possible structures seem to be implemented. Your examples are not, I suspect: What do the distribution, volume, shape, and orientation mean for a Sigma_k=sigma^2*I where I is a p by p covariance matrix, sigma^2 is the constant variance and Sigma_1=Sigma_2= =Sigma_G. This would be VEE. If you assume det(Sigma_1)=1 (which is necessary for your parameterization to be identified), then sigma^2 is lambda, i.e., the volume parameter, and Sigma_1 would be the remaining matrix product. However, VEE is not implemented. You may mail to Chris Fraley and ask why... You see that the problem is not the parameterization, but the fact that VEE is missing in mclust. (It is somewhat confusing the you use I for the covariance matrix, because emclust uses this letter for a covariance matrix, which is the identity matrix.) What about when a Sigma_k=sigma^2_k*I, or when Sigma_1=Sigma_2= =Sigma_G in situations where each element of the (constant across class) covariance matrix is different? I do not really understand this. Do you want to assume that the elements of Sigma_1 should be pairwise different? Why do you need such an assumption? That's not a very favourable choice for estimation, I think, and it would be estimated by VEE as well (which would yield such a solution with probability 1), if it would be implemented. Best, Christian *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!
Re: [R] contour lines on levelplot?
Thanks very much. spencer graves Deepayan Sarkar wrote: On Sunday 06 June 2004 20:40, Spencer Graves wrote: With image and contour, one can get both colors and lines to enhance the image of a contour plot. What's the best way to do this with Lattice graphics? The following is one ugly hack, producing the desired result after much trial and error (R 1.9.1 alpha under Windows 2000): # setup DF - expand.grid(x=1:3, y=1:3) DF$z - (DF$x+DF$y) # Traditional base graphics: image(x=1:3, y=1:3, z=array(DF$z, dim=c(3,3))) contour(x=1:3, y=1:3, z=array(DF$z, dim=c(3,3)), add=T) # Lattice hack: lvlplt - levelplot(z~x*y, DF) cont - contourplot(z~x*y, DF) print(lvlplt, more=T) print(cont, position=c(0, 0, 0.9055, 1)) ## By comparison, the same ugly hack in S-Plus required 0.952 instead of 0.955. Is this the best we can currently get with a modest effort? There's certainly much easier ways to do this, namely contourplot(z~x*y, DF, region = TRUE) or levelplot(z~x*y, DF, contour = TRUE) the only restriction being that you would need to use the same 'at' vector. If you want them to differ, you need to write a small panel function of your own that makes use of panel.levelplot(). Deepayan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Vectors of years, months, and days to dates?
The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. I am quite sure there is much better solution for it. What is it? Thanks. Daehyok Shin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] models for compositional data by J. Aitchison
Hi, is there any R software for model building with data of the compositional data type: The statistical analysis of compositional data by J. Aitchison. thanks *** Matthias Schmidt Forstliche Versuchs- und Forschungsanstalt Baden-Württemberg (FVA) Abteilung Biometrie und Informatik Wonnhaldestr. 4 79100 Freiburg i. Br Tel.: + 49 (0)761 / 4018 -187 Fax: + 49 (0)761 / 4018 - 333 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vectors of years, months, and days to dates?
On Mon, 7 Jun 2004, Shin, Daehyok wrote: The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. Really? You have measured the loss? A million causes no problem for example, and what are you going to do with a million dates that is instantaneous and worthwhile? And a million dates are hardly going to be unique so you only need to convert the unique values. I am quite sure there is much better solution for it. What is it? Write your own C code, or make a POSIXlt object directly from the numbers and convert that. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vectors of years, months, and days to dates?
On Mon, 7 Jun 2004, Daehyok Shin wrote: How can I create POSIXlt directly from the numbers? I failed to find the solution from help documents. ?POSIXlt ?as.POSIXlt: res - as.POSIXlt(paste(years, months, days, sep=-)) str(res) `POSIXlt', format: chr [1:2] 1991-01-01 1992-10-02 res$year [1] 91 92 Daehyok --On Monday, June 07, 2004 4:44 PM +0100 Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 7 Jun 2004, Shin, Daehyok wrote: The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. Really? You have measured the loss? A million causes no problem for example, and what are you going to do with a million dates that is instantaneous and worthwhile? And a million dates are hardly going to be unique so you only need to convert the unique values. I am quite sure there is much better solution for it. What is it? Write your own C code, or make a POSIXlt object directly from the numbers and convert that. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Precision for a former question*
On Mon, 7 Jun 2004 16:08:58 +0200, zze-PELAY Nicolas FTRD/DMR/BEL [EMAIL PROTECTED] wrote : I got many answers to the question I asked below , and I thank you all. Several of you told me to use - but told also that it is not a recommendable way of items manipulating in R. I don't really understand what it exactly means : 1) does it mean it's not a very good way of programming , a dangerous way of programming because the variable a can be modified ? , etc Or 2) does it mean that R is not done to manipulate the operation - in a function in a safe way , that there can be some mistakes, that the memory allocation is not forseen for this case? I think it's dangerous in the first sense. It's best to try to contain the effects of functions as much as possible, avoiding side effects like a change to a variable outside the function. Something else that hasn't been mentioned is that - is different in R and S-PLUS, so it may come to haunt you if you ever try to port your code there. Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
res - as.POSIXlt(paste(years, months, days, sep=-)) This command still convert numbers to a character vector, right? Daehyok Shin (Peter) Terrestrial Hydrological Ecosystem Modellers Geography Department University of North Carolina-Chapel Hill [EMAIL PROTECTED] We can do no great things, only small things with great love. - Mother Teresa -Original Message- From: Roger Bivand [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 PM 12:20 To: Daehyok Shin Cc: R, Help Subject: Re: [R] Vectors of years, months, and days to dates? On Mon, 7 Jun 2004, Daehyok Shin wrote: How can I create POSIXlt directly from the numbers? I failed to find the solution from help documents. ?POSIXlt ?as.POSIXlt: res - as.POSIXlt(paste(years, months, days, sep=-)) str(res) `POSIXlt', format: chr [1:2] 1991-01-01 1992-10-02 res$year [1] 91 92 Daehyok --On Monday, June 07, 2004 4:44 PM +0100 Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 7 Jun 2004, Shin, Daehyok wrote: The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. Really? You have measured the loss? A million causes no problem for example, and what are you going to do with a million dates that is instantaneous and worthwhile? And a million dates are hardly going to be unique so you only need to convert the unique values. I am quite sure there is much better solution for it. What is it? Write your own C code, or make a POSIXlt object directly from the numbers and convert that. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
Thanks, but, what I want is to convert three vectors of years, months, and days directly into POSIXlt or Date objects without creating character vectors. Daehyok Shin (Peter) Terrestrial Hydrological Ecosystem Modellers Geography Department University of North Carolina-Chapel Hill [EMAIL PROTECTED] We can do no great things, only small things with great love. - Mother Teresa -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 PM 12:15 To: [EMAIL PROTECTED] Subject: Re: [R] Vectors of years, months, and days to dates? If you 'unclass' dates you will get a numeric vector that just has the days since the epoch. Is this what you want? years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) dates [1] 1991-01-01 1992-10-02 str(dates) Class 'Date' num [1:2] 7670 8310 unclass(dates) [1] 7670 8310 __ James HoltmanWhat is the problem you are trying to solve? Executive Technical Consultant -- Office of Technology, Convergys [EMAIL PROTECTED] +1 (513) 723-2929 Shin, Daehyok [EMAIL PROTECTED]To: R, Help [EMAIL PROTECTED] cc: Sent by: Subject: [R] Vectors of years, months, and days to dates? [EMAIL PROTECTED] ath.ethz.ch 06/07/2004 11:16 Please respond to sdhyok The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. I am quite sure there is much better solution for it. What is it? Thanks. Daehyok Shin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vectors of years, months, and days to dates?
Prof Brian Ripley [EMAIL PROTECTED] writes: On Mon, 7 Jun 2004, Shin, Daehyok wrote: The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. Really? You have measured the loss? A million causes no problem for example, and what are you going to do with a million dates that is instantaneous and worthwhile? And a million dates are hardly going to be unique so you only need to convert the unique values. However, considering what goes on in ISOdatetime, one might as well do as.Date(paste(years, months, days, sep=-)) -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error message
I received the below error using UNIX R. Could someone instruct me on helpful batch options to avoid this please? ERROR: cannot allocate vector of size 32kb __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
On Mon, 7 Jun 2004, Shin, Daehyok wrote: res - as.POSIXlt(paste(years, months, days, sep=-)) This command still convert numbers to a character vector, right? Yes, as Prof. Ripley said, the overhead of conversion to character and using carefully crafted R functions is much less, for reasonable numbers of dates, than inserting all the appropriate values into the POSIXlt class object, since you need, in addition to years (since 1900), checked month-days (31 February?), and months, week-days, year days, daylight savings time flag, and seconds, minutes and hours. I would also be interested to know whether you can demonstrate (system.time()) that anything reliable is faster than as.POSIXlt() for fewer than millions of dates (and would you trust it on 29 February even if it was faster?). Using base classes and functions is in general much more robust than rolling your own, simply because many more people use them - they have much more data run through them, and the time you might save trying to avoid integer to character conversion will/should be eaten up by debugging. Daehyok Shin (Peter) Terrestrial Hydrological Ecosystem Modellers Geography Department University of North Carolina-Chapel Hill [EMAIL PROTECTED] We can do no great things, only small things with great love. - Mother Teresa -Original Message- From: Roger Bivand [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 PM 12:20 To: Daehyok Shin Cc: R, Help Subject: Re: [R] Vectors of years, months, and days to dates? On Mon, 7 Jun 2004, Daehyok Shin wrote: How can I create POSIXlt directly from the numbers? I failed to find the solution from help documents. ?POSIXlt ?as.POSIXlt: res - as.POSIXlt(paste(years, months, days, sep=-)) str(res) `POSIXlt', format: chr [1:2] 1991-01-01 1992-10-02 res$year [1] 91 92 Daehyok --On Monday, June 07, 2004 4:44 PM +0100 Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 7 Jun 2004, Shin, Daehyok wrote: The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. Really? You have measured the loss? A million causes no problem for example, and what are you going to do with a million dates that is instantaneous and worthwhile? And a million dates are hardly going to be unique so you only need to convert the unique values. I am quite sure there is much better solution for it. What is it? Write your own C code, or make a POSIXlt object directly from the numbers and convert that. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vectors of years, months, and days to dates?
Shin, Daehyok [EMAIL PROTECTED] writes: Thanks, but, what I want is to convert three vectors of years, months, and days directly into POSIXlt or Date objects without creating character vectors. Well, if you insist: x - as.POSIXlt(structure(rep(0,2),class=POSIXct)) x$year - years-1900 x$mon - months-1 x$mday - days as.Date(as.POSIXct(x)) This is definitely not kosher programming, and I doubt that it is the least bit faster than the other solutions, but there's no character vectors in there... -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vectors of years, months, and days to dates?
Shin, Daehyok sdhyok at email.unc.edu writes: Thanks, but, what I want is to convert three vectors of years, months, and days directly into POSIXlt or Date objects without creating character vectors. I would probably just convert it to character using paste and from that to Date as others have already suggested but if it is really important to you for some reason not to use character variables as intermediates try this: require(chron) z - structure(julian(months, days, years), class=Date) Note that when you print it out it may look like its character but its not.Try class(z) is.character(z) str(z) dput(z) to convince yourself. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] error message
The message says at some point in the calculation, R tries to get about 312MB of memory and was not able to. Maybe try increasing the amount of virtual (or physical) memory in your system? Andy From: Tim York I received the below error using UNIX R. Could someone instruct me on helpful batch options to avoid this please? ERROR: cannot allocate vector of size 32kb __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (low level) profiling of code
Dear R-help, Can some one tell me how to profile compiled code dynamically loaded into R? Here's what I tried on our dual Opteron running SUSE Linux Enterprise Server 8 (GCC 3.3): Start with R-patched dated 2004-06-07: (I also had MAIN_CFLAGS=-pg in config.site.) R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local C compiler:gcc -O2 -g -pg -march=k8 -msse2 -m64 C++ compiler: g++ -O2 -g -pg -march=k8 -msse2 -m64 Fortran compiler: g77 -O2 -g -pg -march=k8 -msse2 -m64 Interfaces supported: X11, tcltk External libraries:readline Additional capabilities: PNG, JPEG Options enabled: R profiling Recommended packages: no I then tried running /path/to/R-patched/bin/R CMD BATCH -q -slave myscript.R where inside myscript.R is call to R functions that calls .C(). However, this does not produce the gmon.out file. Can anyone tell me what I'm missing? Any help much appreciated! Best, Andy Andy Liaw, PhD Biometrics Research PO Box 2000, RY33-300 Merck Research Labs Rahway, NJ 07065 andy_liaw (at) merck.com732-594-0820 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (low level) profiling of code
You normally need to switch R profiling off, as that uses the same interrupts as low-level profiling. I would expect you to get gmon.out output from the the main R executable on any run, so the first question must be `does your OS support -pg?' I don't think dynamically loaded code is relevant (provided it is compiled with -pg). I am pretty sure I managed to profile some examples from the cluster package on RH8.0 Linux the other day. On Mon, 7 Jun 2004, Liaw, Andy wrote: Dear R-help, Can some one tell me how to profile compiled code dynamically loaded into R? Here's what I tried on our dual Opteron running SUSE Linux Enterprise Server 8 (GCC 3.3): Start with R-patched dated 2004-06-07: (I also had MAIN_CFLAGS=-pg in config.site.) R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local C compiler:gcc -O2 -g -pg -march=k8 -msse2 -m64 C++ compiler: g++ -O2 -g -pg -march=k8 -msse2 -m64 Fortran compiler: g77 -O2 -g -pg -march=k8 -msse2 -m64 Interfaces supported: X11, tcltk External libraries:readline Additional capabilities: PNG, JPEG Options enabled: R profiling Recommended packages: no I then tried running /path/to/R-patched/bin/R CMD BATCH -q -slave myscript.R where inside myscript.R is call to R functions that calls .C(). However, this does not produce the gmon.out file. Can anyone tell me what I'm missing? Any help much appreciated! -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ask for help
Hi Don! Welcome new R user. Just use one of the mailing list search interfaces which you can find browsing the www.r-project.org page. After you find the search interface just paste you error message in the search form. I ensure you you will find the a lot of e-mails wich will help you to solve your problem. Sincerely Eryk *** REPLY SEPARATOR *** On 6/7/2004 at 1:44 PM don wrote: Dear colleagues, I am a beginner of using R. I am involved in some microarray data analyses and found that R is the most common software in this area. I tried to install the free software today. It seemed to be successful in installing, but when I trigger the short-cut, I got a error massage saying 'Fetal error: invalid HOMEDRIVE'. I have no idea where the homedrive was defined (or implied) and how to solve the problem. I wonder if someone could help me to start the first step of this fancy trip. Many thanks! Don Li National Cancer Institute of Canada - Clinical Trials Group __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Dipl. bio-chem. Eryk Witold Wolski@MPI-Moleculare Genetic Ihnestrasse 63-73 14195 Berlin 'v' tel: 0049-30-83875219 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ask for help
The problem is probably a bug in your OS. You haven't even told us what that is, but I bet you have Windows XP with critical update KB835732 installed. If so, see http://www.murdoch-sutherland.com/HOMEPATH.html and the archives of this list. On Mon, 7 Jun 2004, don wrote: I am a beginner of using R. I am involved in some microarray data analyses and found that R is the most common software in this area. I tried to install the free software today. It seemed to be successful in installing, but when I trigger the short-cut, I got a error massage saying 'Fetal error: invalid HOMEDRIVE'. I have no idea where the homedrive was defined (or implied) and how to solve the problem. I wonder if someone could help me to start the first step of this fancy trip. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ask for help
Don Li wrote: I am a beginner of using R. I am involved in some microarray data analyses and found that R is the most common software in this area. I tried to install the free software today. It seemed to be successful in installing, but when I trigger the short-cut, I got a error massage saying 'Fetal error: . Shouldn't that be ``Foetal error''? :-) cheers, Rolf Turner [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
Is what I asked such an exceptional case? A lot of data I am dealing with (usually hydrologic data) are recorded with three columns of years, months, and days. In my opinion, the direct conversion from numeric vectors of years, months and days into some internal representation of date is widely supported in most matrix oriented languages (ex. datenum() in MATLAB). Am I really asking an odd operation for date conversion? For performance, you are right. The loss of performance is negligible when users call it directly. But, what happens when it is called in an iterative loop? How can we assume some functions are only called directly by users in an interactive shell? Please consider positively this kind of simple interface for as.Date. I am quite sure this operation will be used widely once implemented. as.Date(c(years, months, days)) Is there no one supporting my idea? Daehyok Shin (Peter) Terrestrial Hydrological Ecosystem Modellers Geography Department University of North Carolina-Chapel Hill [EMAIL PROTECTED] We can do no great things, only small things with great love. - Mother Teresa -Original Message- From: Roger Bivand [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 PM 1:02 To: Shin, Daehyok Cc: R, Help Subject: RE: [R] Vectors of years, months, and days to dates? On Mon, 7 Jun 2004, Shin, Daehyok wrote: res - as.POSIXlt(paste(years, months, days, sep=-)) This command still convert numbers to a character vector, right? Yes, as Prof. Ripley said, the overhead of conversion to character and using carefully crafted R functions is much less, for reasonable numbers of dates, than inserting all the appropriate values into the POSIXlt class object, since you need, in addition to years (since 1900), checked month-days (31 February?), and months, week-days, year days, daylight savings time flag, and seconds, minutes and hours. I would also be interested to know whether you can demonstrate (system.time()) that anything reliable is faster than as.POSIXlt() for fewer than millions of dates (and would you trust it on 29 February even if it was faster?). Using base classes and functions is in general much more robust than rolling your own, simply because many more people use them - they have much more data run through them, and the time you might save trying to avoid integer to character conversion will/should be eaten up by debugging. Daehyok Shin (Peter) Terrestrial Hydrological Ecosystem Modellers Geography Department University of North Carolina-Chapel Hill [EMAIL PROTECTED] We can do no great things, only small things with great love. - Mother Teresa -Original Message- From: Roger Bivand [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 PM 12:20 To: Daehyok Shin Cc: R, Help Subject: Re: [R] Vectors of years, months, and days to dates? On Mon, 7 Jun 2004, Daehyok Shin wrote: How can I create POSIXlt directly from the numbers? I failed to find the solution from help documents. ?POSIXlt ?as.POSIXlt: res - as.POSIXlt(paste(years, months, days, sep=-)) str(res) `POSIXlt', format: chr [1:2] 1991-01-01 1992-10-02 res$year [1] 91 92 Daehyok --On Monday, June 07, 2004 4:44 PM +0100 Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 7 Jun 2004, Shin, Daehyok wrote: The interface for dates in R is a little confusing to me. I want to create a vector of Date objects from vectors of years, months, and days. One solution I found is: years - c(1991, 1992) months - c(1, 10) days - c(1, 2) dates - as.Date(ISOdate(years, months, days)) But, in this solution the ISOdate function converts the vectors into characters, which can cause serious performance and memory loss when the vectors of years, months, and days are huge. Really? You have measured the loss? A million causes no problem for example, and what are you going to do with a million dates that is instantaneous and worthwhile? And a million dates are hardly going to be unique so you only need to convert the unique values. I am quite sure there is much better solution for it. What is it? Write your own C code, or make a POSIXlt object directly from the numbers and convert that. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting
RE: [R] Vectors of years, months, and days to dates?
Daehyok Shin (Peter) wrote: Is what I asked such an exceptional case? Apparently. A lot of data I am dealing with (usually hydrologic data) are recorded with three columns of years, months, and days. In my opinion, the direct conversion from numeric vectors of years, months and days into some internal representation of date is widely supported in most matrix oriented languages (ex. datenum() in MATLAB). Am I really asking an odd operation for date conversion? Apparently. You still haven't given any indication of what's wrong with the way R does things, which is perfectly transparent and user friendly. If other packages do things in a slightly different way, so what? For performance, you are right. The loss of performance is negligible when users call it directly. But, what happens when it is called in an iterative loop? How can we assume some functions are only called directly by users in an interactive shell? Have you ***any*** evidence that R's procedure degrades performance, under any circumstances? (Apparently not.) In that case why are you going on and on about it? Please consider positively this kind of simple interface for as.Date. [as.Date(c(years, months, days))] The standard response to this kind of request is ``R is a cooperative endeavour. Feel free to contribute.'' I am quite sure this operation will be used widely once implemented. Have you ***any*** evidence for this assertion? Is there no one supporting my idea? Apparently not. cheers, Rolf Turner [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] GLMM(..., family=binomial(link=cloglog))?
Thanks, Andy, Doug, Deepayan. I now have lme4 0.6-1 2004/05/31 installed for R 1.9.1 alpha under Windows 2000. When I tried the example below, GLMM ran, but the print method reported an error: Generalized Linear Mixed Model Fixed: immun ~ 1 Data: guImmun log-likelihood: -1440.052 Random effects: Groups NameVariance Std.Dev. comm (Intercept) 0.31686 0.5629 Estimated scale (compare to 1) 0.9717356 Error in cm[, 1] : incorrect number of dimensions The following is a possibly simpler example that returns the same error message: simDF - data.frame(yield=(1:4)/5, gp=factor(rep(1:2,2)), nobs=5) simFit - GLMM(yield~1, family=binomial, data=simDF, random=~1|gp, weights=nobs) Iteration 1 Termination Criterion: 2.206532e-08 Iteration 2 Termination Criterion: 8.659736e-16 simFit Generalized Linear Mixed Model Fixed: yield ~ 1 Data: simDF log-likelihood: -2.128803 Random effects: Groups NameVariance Std.Dev. gp (Intercept) 2.2065e-09 4.6974e-05 Estimated scale (compare to 1) 1 Error in cm[, 1] : incorrect number of dimensions Any suggestions on what I should try next? So far, I've only gotten this with an intercept-only model such as yield~1. When I added a term from the help file example making it, immun ~ kid2p, this error disappeared. Thanks, Spencer Graves Liaw, Andy wrote: As Doug said in his announcement, version 0.6-1 of lme4 (which is pure R code) depends on the Matrix package, version 0.8-7. AFAICT the Windows binary on CRAN for Matrix is version 0.8-6. Not sure if that will work with the current lme4... It's probably best to wait for the right versions of these packages to propagate to appropriate places on CRAN... Best, Andy From: Spencer Graves Hi, Deepayan: Thanks for your reply. How can I get the new release in a Windows 2000 format, downloaded and properly installed? I tried update.packages, but the new version has not yet migrated within reach of the default update.packages function call. I tried downloading lme4 0.6-0-2.tar.gz from http://www.stat.wisc.edu/%7Ebates/;, unzipping it and replacing the old \\R\rw1090pat\library\lme4 with the new. Unfortunately, when I then tried to start R, I got a fatal error message: Error in loadNamespace(i[[1]], c(lib.loc, libPaths()), keep.source): There is no package called 'Matrix'. Fortunately, I was able to restore R to apparently functioning order by merely restoring the old version. Is there something easy I can do to get lme4 0.6-0-2.tar.gz to install properly for me? Or do I need to wait until it migrates to my update.packages default (http://cran.r-project.org;) or some other designated CRAN mirror? Thanks for your excellent work in bringing this excellent software to its present state. Best Wishes, spencer graves Deepayan Sarkar wrote: On Tuesday 01 June 2004 17:25, Spencer Graves wrote: I'm having trouble using binomial(link=cloglog) with GLMM in lme4, Version: 0.5-2, Date: 2004/03/11. The example in the Help file works fine, even simplified as follows: fm0 - GLMM(immun~1, data=guImmun, family=binomial, random=~1|comm) However, for another application, I need binomial(link=cloglog), and this generates an error for me: fm0. - GLMM(immun~1, data=guImmun, family=binomial(link=cloglog), random=~1|comm) Error in getClass(thisClass) : family is not a defined class Error in GLMM(immun ~ 1, data = guImmun, family = binomial(link = cloglog), : S language method selection got an error when called from internal dispatch for function GLMM Any suggestions? This should work better in the new lme4 (0.6-x) announced earlier today on r-packages. There is still a bug with cases (like in your example) with only one fixed effect where the show and summary methods produce an error, but that should be fixed soon. Deepayan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
On Mon, 7 Jun 2004, Shin, Daehyok wrote:
Is what I asked such an exceptional case?
A lot of data I am dealing with (usually hydrologic data) are recorded with
three columns of years, months, and days.
In my opinion, the direct conversion from numeric vectors of years, months
and days into some internal representation of date
is widely supported in most matrix oriented languages (ex. datenum() in
MATLAB).
Am I really asking an odd operation for date conversion?
For performance, you are right. The loss of performance is negligible when
users call it directly.
But, what happens when it is called in an iterative loop?
How can we assume some functions are only called directly by users in an
interactive shell?
Please read the code inside the functions we have been discussing. You
will see that there is plenty of error checking, which is needed. In
addition, paste() is vectorised. Specifically:
years - sample(1900:2000, 10, replace=TRUE)
months - sample(1:12, 10, replace=TRUE)
days - sample(1:28, 10, replace=TRUE)
system.time(x - as.Date(as.POSIXlt(paste(years, months, days, sep=-
[1] 5.91 0.02 5.98 0.00 0.00
f - function(y, m, d) { # taken from Peter Dalgaard's reply
+ x - as.POSIXlt(structure(rep(0,length(y)),class=POSIXct))
+ x$year - y-1900
+ x$mon - m-1
+ x$mday - d
+ as.Date(as.POSIXct(x))
+ }
system.time(y - f(years, months, days))
[1] 2.76 0.01 2.78 0.00 0.00
identical(x, y)
[1] TRUE
So for 10 dates, the integer insertion is only about twice as fast,
but it took much longer than the difference to find that out.
Please consider positively this kind of simple interface for as.Date.
I am quite sure this operation will be used widely once implemented.
as.Date(c(years, months, days))
I have a feeling that won't do what you want, really. Looking at
as.POSIXlt, and as.Date, you could create a variant recognising an integer
matrix with your special class as having years in column 1, etc., but I
think that your implementation and support costs will outbalance the
saving you think you are making.
The most enjoyable fortunes package has a fitting opinion:
fortune(Fox)
I think that it's generally a good idea not to resist the most natural way of
programming in R.
-- John Fox
R-help (March 2004)
Is there no one supporting my idea?
Well, you are, so that's a start - contribute an as.Date.MatrixOfDates
method to dispatch on a MatrixOfDates class, and you may find others?
Daehyok Shin (Peter)
Terrestrial Hydrological Ecosystem Modellers
Geography Department
University of North Carolina-Chapel Hill
[EMAIL PROTECTED]
We can do no great things,
only small things with great love.
- Mother Teresa
-Original Message-
From: Roger Bivand [mailto:[EMAIL PROTECTED]
Sent: Monday, June 07, 2004 PM 1:02
To: Shin, Daehyok
Cc: R, Help
Subject: RE: [R] Vectors of years, months, and days to dates?
On Mon, 7 Jun 2004, Shin, Daehyok wrote:
res - as.POSIXlt(paste(years, months, days, sep=-))
This command still convert numbers to a character vector, right?
Yes, as Prof. Ripley said, the overhead of conversion to character and
using carefully crafted R functions is much less, for reasonable numbers
of dates, than inserting all the appropriate values into the POSIXlt class
object, since you need, in addition to years (since 1900), checked
month-days (31 February?), and months, week-days, year days, daylight
savings time flag, and seconds, minutes and hours.
I would also be interested to know whether you can demonstrate
(system.time()) that anything reliable is faster than as.POSIXlt() for
fewer than millions of dates (and would you trust it on 29 February even
if it was faster?). Using base classes and functions is in general much
more robust than rolling your own, simply because many more people use
them - they have much more data run through them, and the time you might
save trying to avoid integer to character conversion will/should be eaten
up by debugging.
Daehyok Shin (Peter)
Terrestrial Hydrological Ecosystem Modellers
Geography Department
University of North Carolina-Chapel Hill
[EMAIL PROTECTED]
We can do no great things,
only small things with great love.
- Mother Teresa
-Original Message-
From: Roger Bivand [mailto:[EMAIL PROTECTED]
Sent: Monday, June 07, 2004 PM 12:20
To: Daehyok Shin
Cc: R, Help
Subject: Re: [R] Vectors of years, months, and days to dates?
On Mon, 7 Jun 2004, Daehyok Shin wrote:
How can I create POSIXlt directly from the numbers?
I failed to find the solution from help documents.
?POSIXlt
?as.POSIXlt:
res - as.POSIXlt(paste(years, months, days, sep=-))
str(res)
`POSIXlt', format: chr [1:2] 1991-01-01 1992-10-02
res$year
[1] 91 92
Daehyok
--On
Re: [R] GLMM(..., family=binomial(link=cloglog))?
Spencer Graves [EMAIL PROTECTED] writes:
Thanks, Andy, Doug, Deepayan. I now have lme4 0.6-1 2004/05/31
installed for R 1.9.1 alpha under Windows 2000. When I tried the
example below, GLMM ran, but the print method reported an error:
Generalized Linear Mixed Model
As I write this I am uploading lme4_0.6-2 to the incoming area at
CRAN. This version fixes that bug (I neglected to add drop=FALSE in a
subsetting operation in the show method for the summary.ssclme class.)
You can see the details of the fix at
http://bates4.stat.wisc.edu:2180/cgi-bin/viewcvs.cgi/trunk/lme4/R/ssclme.R
or
/home/bates/src/Rlibs/lme4 $ svn diff -r 209 R/ssclme.R
Index: R/ssclme.R
===
--- R/ssclme.R (revision 209)
+++ R/ssclme.R (working copy)
@@ -205,7 +205,7 @@
cm = cbind(cm, stat, pval)
colnames(cm) = c(nms, t value, Pr(|t|))
} else {
- cm = cm[, 1:2]
+ cm = cm[, 1:2, drop = FALSE]
stat = cm[,1]/cm[,2]
pval = 2*pnorm(abs(stat), lower = FALSE)
nms = colnames(cm)
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] GLMM(..., family=binomial(link=cloglog))?
Hi, Doug:
Thanks. I ran 'tst - getMethod(show, summary.ssclme)', then
edited tst as you indicated and ran 'setMethod(show, summary.ssclme,
tst)', and it fixed the problem.
Best Wishes,
spencer graves
Douglas Bates wrote:
Spencer Graves [EMAIL PROTECTED] writes:
Thanks, Andy, Doug, Deepayan. I now have lme4 0.6-1 2004/05/31
installed for R 1.9.1 alpha under Windows 2000. When I tried the
example below, GLMM ran, but the print method reported an error:
Generalized Linear Mixed Model
As I write this I am uploading lme4_0.6-2 to the incoming area at
CRAN. This version fixes that bug (I neglected to add drop=FALSE in a
subsetting operation in the show method for the summary.ssclme class.)
You can see the details of the fix at
http://bates4.stat.wisc.edu:2180/cgi-bin/viewcvs.cgi/trunk/lme4/R/ssclme.R
or
/home/bates/src/Rlibs/lme4 $ svn diff -r 209 R/ssclme.R
Index: R/ssclme.R
===
--- R/ssclme.R (revision 209)
+++ R/ssclme.R (working copy)
@@ -205,7 +205,7 @@
cm = cbind(cm, stat, pval)
colnames(cm) = c(nms, t value, Pr(|t|))
} else {
- cm = cm[, 1:2]
+ cm = cm[, 1:2, drop = FALSE]
stat = cm[,1]/cm[,2]
pval = 2*pnorm(abs(stat), lower = FALSE)
nms = colnames(cm)
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error during make of R-patched on Fedora core 2
Dear list, I've just upgraded to Fedora Core 2 and seeing as there wasn't an rpm for this OS on CRAN yet I thought it was about time I had a go at compiling R myself. Having run into the X11 problem I switched to trying to install R-patched. I followed the instructions in the R Installation Admin manual to download the sources of the Recommended packages and place the files in R_HOME/src/library/Recommended. ./configure worked fine so I progressed to make, which has hit upon this error when the process arrived at the Recommended packages: make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' building/updating vignettes for package 'grid' ... make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: *** No rule to make target `survival.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make: *** [stamp-recommended] Error 2 Being a relative newbie to Linux I have no-idea how to continue to solve this issue :-( The only difference I can see between the /src/library/Recommended directories of R-1.9.0 and R-patched is that in R-1.9.0 it contains links to each of the tar.gz (excluding the version info) as well as the tar.gz themselves for each of the packages. Is this in some way related to my problem? If anyone can help me solve this issue I'd be most grateful. Thanks in advance, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error during make of R-patched on Fedora core 2
This feels like: After downloading the R sources you should also download the recommended packages by entering the R source tree and running tools/rsync-recommended from a shell command line. from the R Sources page on CRAN - could you try that (I guess rsync is installed on most Linux standard distributions)? On Mon, 7 Jun 2004, Gavin Simpson wrote: Dear list, I've just upgraded to Fedora Core 2 and seeing as there wasn't an rpm for this OS on CRAN yet I thought it was about time I had a go at compiling R myself. Having run into the X11 problem I switched to trying to install R-patched. I followed the instructions in the R Installation Admin manual to download the sources of the Recommended packages and place the files in R_HOME/src/library/Recommended. ./configure worked fine so I progressed to make, which has hit upon this error when the process arrived at the Recommended packages: make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' building/updating vignettes for package 'grid' ... make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: *** No rule to make target `survival.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make: *** [stamp-recommended] Error 2 Being a relative newbie to Linux I have no-idea how to continue to solve this issue :-( The only difference I can see between the /src/library/Recommended directories of R-1.9.0 and R-patched is that in R-1.9.0 it contains links to each of the tar.gz (excluding the version info) as well as the tar.gz themselves for each of the packages. Is this in some way related to my problem? If anyone can help me solve this issue I'd be most grateful. Thanks in advance, Gavin -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] latex function in Hmisc
Is there a way to prevent latex.default() from starting LaTeX and JUST create the file requested? I generate a number of LaTeX tables for inclusion in a document running R in batch, and I don't want a lot of calls to LaTeX. I cannot find any arguments for that task in the documentation. It seems a little clumsy to have to direct the output from a function with a file argument using sink() and 'file='. Bendix Carstensen -- Bendix Carstensen Senior Statistician Steno Diabetes Center Niels Steensens Vej 2 DK-2820 Gentofte Denmark tel: +45 44 43 87 38 mob: +45 30 75 87 38 fax: +45 44 43 07 06 [EMAIL PROTECTED] www.biostat.ku.dk/~bxc __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error during make of R-patched on Fedora core 2
On Mon, 2004-06-07 at 15:08, Gavin Simpson wrote: Dear list, I've just upgraded to Fedora Core 2 and seeing as there wasn't an rpm for this OS on CRAN yet I thought it was about time I had a go at compiling R myself. Having run into the X11 problem I switched to trying to install R-patched. I followed the instructions in the R Installation Admin manual to download the sources of the Recommended packages and place the files in R_HOME/src/library/Recommended. ./configure worked fine so I progressed to make, which has hit upon this error when the process arrived at the Recommended packages: make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' building/updating vignettes for package 'grid' ... make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: *** No rule to make target `survival.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make: *** [stamp-recommended] Error 2 Being a relative newbie to Linux I have no-idea how to continue to solve this issue :-( The only difference I can see between the /src/library/Recommended directories of R-1.9.0 and R-patched is that in R-1.9.0 it contains links to each of the tar.gz (excluding the version info) as well as the tar.gz themselves for each of the packages. Is this in some way related to my problem? If anyone can help me solve this issue I'd be most grateful. Thanks in advance, Gavin You might want to try the following commands using rsync as an alternative to downloading the tarball: rsync -rCv rsync.r-project.org::r-patched R-patched ./R-patched/tools/rsync-recommended cd R-patched ./configure make I actually have the above in a script file that I can just run quickly, when I want to update the code. I am now running FC2, so if you have any problems, drop me a line. Best regards, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error during make of R-patched on Fedora core 2
Roger Bivand wrote: This feels like: After downloading the R sources you should also download the recommended packages by entering the R source tree and running tools/rsync-recommended from a shell command line. from the R Sources page on CRAN - could you try that (I guess rsync is installed on most Linux standard distributions)? On Mon, 7 Jun 2004, Gavin Simpson wrote: snip Thanks Roger and Marc, for suggesting I use ./tools/rsync-recommended from within the R-patched directory. This seems to have done the trick as make completed without errors this time round. The Recommended directory also contained the links to the actual tar.gz files after doing the rsync command, so I guess this was the problem (or at least related to it.) I'm off home now with the laptop to see if I can finish make check-all and make install R. I have re-read the section describing the installation process for R-patched or R-devel in the R Installation and Administration manual (from R.1.9.0) just in case I missed something. Section 1.2 of this manual indicates that one can proceed *either* by downloading R-patched and then the Recommended packages from CRAN and placing the tar.gz files in R_HOME/src/library/Recommended, or by using rsync to download R-patched, and then to get the Recommended packages. The two are quite separately documented in the manual, and do seem to be in disagreement with the R-sources page on the CRAN website, which doesn't mention the manual download method (for Recommended) at all. Is there something wrong with the current Recommended files on CRAN, or is the section in the R Installation Admin manual out-of-date or in error, or am I missing something vital here? This isn't a complaint: I'm just pointing this out in case this is something that needs updating in the documentation. All the best, Gavin -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error during make of R-patched on Fedora core 2
Gavin Simpson [EMAIL PROTECTED] writes: Dear list, I've just upgraded to Fedora Core 2 and seeing as there wasn't an rpm for this OS on CRAN yet I thought it was about time I had a go at compiling R myself. Having run into the X11 problem I switched to trying to install R-patched. I followed the instructions in the R Installation Admin manual to download the sources of the Recommended packages and place the files in R_HOME/src/library/Recommended. ./configure worked fine so I progressed to make, which has hit upon this error when the process arrived at the Recommended packages: make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' building/updating vignettes for package 'grid' ... make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library' make[1]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: Entering directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[2]: *** No rule to make target `survival.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: Leaving directory `/home/gavin/tmp/R-patched/src/library/Recommended' make: *** [stamp-recommended] Error 2 Being a relative newbie to Linux I have no-idea how to continue to solve this issue :-( The only difference I can see between the /src/library/Recommended directories of R-1.9.0 and R-patched is that in R-1.9.0 it contains links to each of the tar.gz (excluding the version info) as well as the tar.gz themselves for each of the packages. Is this in some way related to my problem? If anyone can help me solve this issue I'd be most grateful. Thanks in advance, The easiest approach is to run ./tools/rsync-recommended from the top-level source directory for R. That uses rsync to downloads the sources for the recommended packages then creates the necessary links. (At least it works for R-devel and I believe it works for R-patched. There was a time when the links were not getting corrected properly.) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Load a dll
Hi folks, I have a question about how to load a dll. First, I use the command dyn.load(lassofu.dll); then, I got the message below NULL Warning message: DLL attempted to change FPU control word from 9001f to 90003; After I tried to use this dll in one of s functions, I got the message below Error in .Fortran(lasso, as.double(x), as.double(y), as.double(b), as.integer(n), : Fortran function name not in load table. BTW, my system is Windows98 + R1.9.0. Could anyone help me to solve this question? Thanks Rui Wang Phone: (403)220-4501 Email: [EMAIL PROTECTED] Department of Mathematics and Statistics University of Calgary [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error during make of R-patched on Fedora core 2
On Mon, 2004-06-07 at 15:51, Gavin Simpson wrote: snip Thanks Roger and Marc, for suggesting I use ./tools/rsync-recommended from within the R-patched directory. This seems to have done the trick as make completed without errors this time round. The Recommended directory also contained the links to the actual tar.gz files after doing the rsync command, so I guess this was the problem (or at least related to it.) I'm off home now with the laptop to see if I can finish make check-all and make install R. I have re-read the section describing the installation process for R-patched or R-devel in the R Installation and Administration manual (from R.1.9.0) just in case I missed something. Section 1.2 of this manual indicates that one can proceed *either* by downloading R-patched and then the Recommended packages from CRAN and placing the tar.gz files in R_HOME/src/library/Recommended, or by using rsync to download R-patched, and then to get the Recommended packages. The two are quite separately documented in the manual, and do seem to be in disagreement with the R-sources page on the CRAN website, which doesn't mention the manual download method (for Recommended) at all. Is there something wrong with the current Recommended files on CRAN, or is the section in the R Installation Admin manual out-of-date or in error, or am I missing something vital here? This isn't a complaint: I'm just pointing this out in case this is something that needs updating in the documentation. All the best, Gavin Perhaps I am being dense, but in reviewing the two documents (R Admin and the CRAN sources page), I think that the only thing lacking is a description on the CRAN page of the manual download option for the Rec packages. You would need to go here now for 1.9.1 Alpha/Beta which is where the current r-patched is: http://www.cran.mirrors.pair.com/src/contrib/1.9.1/Recommended/ The standard links on CRAN are for the current 'released' version, which is still 1.9.0 for the moment. Procedurally, I think that the rsync approach is substantially easier (one step instead of multiple downloads) and certainly less error prone. Also the ./tools/rsync-recommended script is set up to pick up the proper package versions, which also helps to avoid conflicts. HTH, Marc __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] msm capabilities
Hello, I'm wondering if anyone has used the msm package to compute the steady state probabilities for a Markov model? thanks, Russell __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] betareg
Hi, I try beta regression model using betareg. I have two questions: (i) The example data pratergrouped is not exist. pratergrouped [1] V11 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 0 rows (or 0-length row.names) (ii) In the description of betareg, it said variable, say y, is restricted in (0,1). Does this retriction be [0,1] (Kieschnick and McCullough, Statistical modeling 2003, 193-213)? Thanks for helps in advance. Cheers! Han __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] GLMM(..., family=binomial(link=cloglog))?
Another GLMM/glmm problem: I simulate rbinom(N, 100, pz), where
logit(pz) = rnorm(N). I'd like to estimate the mean and standard
deviation of logit(pz). I've tried GLMM{lme4}, glmmPQL{MASS}, and
glmm{Jim Lindsey's repeated}. In several replicates of this for N = 10,
100, 500, etc., my glmm call produced estimates of the standard
deviation of the random effect in the range of 0.6 to 0.8 (never as high
as the 1 simulated). Meanwhile, my calls to GLMM produced estimates
between 1e-12 and 1e-9, while the glmmPQL results tended to be closer to
0.001, though it gave one number as high as 0.7. (I'm running R 1.9.1
alpha, lme4 0.6-1 under Windows 2000)
Am I doing something wrong, or do these results suggest bugs in the
software or deficiencies in the theory or ... ?
Consider the following:
set.seed(1); N - 10
z - rnorm(N)
pz - inv.logit(z)
DF - data.frame(z=z, pz=pz, y=rbinom(N, 100, pz)/100, n=100,
smpl=factor(1:N))
GLMM(y~1, family=binomial, data=DF, random=~1|smpl, weights=n)
Generalized Linear Mixed Model
Fixed: y ~ 1
Data: DF
log-likelihood: -55.8861
Random effects:
Groups NameVariance Std.Dev.
smpl (Intercept) 1.7500e-12 1.3229e-06
Estimated scale (compare to 1) 3.280753
Fixed effects:
Estimate Std. Error z value Pr(|z|)
(Intercept) 0.148271 0.063419 2.3379 0.01939
Number of Observations: 10
Number of Groups: 10
library(repeated) # Jim Lindsey's repeated package
glmm(y~1, family=binomial, data=DF, weights=n, nest=smpl)
Warning messages:
1: non-integer #successes in a binomial glm! in: eval(expr, envir,
enclos) ...
Coefficients:
(Intercept) sd
0.1971 0.6909
Degrees of Freedom: 9 Total (i.e. Null); 8 Residual
Null Deviance: 111.8
Residual Deviance: 32.03AIC: 1305
Normal mixing variance: 0.4773187
glmmPQL(y~1, family=binomial, data=DF, random=~1|smpl, weights=n)
Linear mixed-effects model fit by maximum likelihood
Data: DF
Log-likelihood: -10.78933
Fixed: y ~ 1
(Intercept)
0.1622299
Random effects:
Formula: ~1 | smpl
(Intercept) Residual
StdDev: 0.7023349 0.5413203
Variance function:
Structure: fixed weights
Formula: ~invwt
Number of Observations: 10
Number of Groups: 10
Suggestions?
So far, the best tool I've got for this problem is a normal
probability plot of a transform of the binomial responses with Monte
Carlo confidence bands, as suggested by Venables and Ripley, S
Programming and Atkinson (1985). However, I ultimately need to estimate
these numbers.
Thanks,
spencer graves
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] (low level) profiling of code
Someone get out the whip... Apologies for wasting everyone's time. I missed setting MAIN_LDFLAGS=-pg in consig.site. Best, Andy From: Prof Brian Ripley You normally need to switch R profiling off, as that uses the same interrupts as low-level profiling. I would expect you to get gmon.out output from the the main R executable on any run, so the first question must be `does your OS support -pg?' I don't think dynamically loaded code is relevant (provided it is compiled with -pg). I am pretty sure I managed to profile some examples from the cluster package on RH8.0 Linux the other day. On Mon, 7 Jun 2004, Liaw, Andy wrote: Dear R-help, Can some one tell me how to profile compiled code dynamically loaded into R? Here's what I tried on our dual Opteron running SUSE Linux Enterprise Server 8 (GCC 3.3): Start with R-patched dated 2004-06-07: (I also had MAIN_CFLAGS=-pg in config.site.) R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local C compiler:gcc -O2 -g -pg -march=k8 -msse2 -m64 C++ compiler: g++ -O2 -g -pg -march=k8 -msse2 -m64 Fortran compiler: g77 -O2 -g -pg -march=k8 -msse2 -m64 Interfaces supported: X11, tcltk External libraries:readline Additional capabilities: PNG, JPEG Options enabled: R profiling Recommended packages: no I then tried running /path/to/R-patched/bin/R CMD BATCH -q -slave myscript.R where inside myscript.R is call to R functions that calls .C(). However, this does not produce the gmon.out file. Can anyone tell me what I'm missing? Any help much appreciated! -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] AR models
Dear R People: Is it possible to fit an AR model such as: y_t = fee_1 y_t-1 + fee_2 y_t-9 + a_t, please? I know that we can fit an AR(9) model, but I was wondering if we could do a partial as described. Thank you for your help. Sincerely, Laura Holt mailto: [EMAIL PROTECTED] _ Watch the online reality show Mixed Messages with a friend and enter to win a trip to NY http://www.msnmessenger-download.click-url.com/go/onm00200497ave/direct/01/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to Describe R to Finance People
Tamas Papp [EMAIL PROTECTED] wrote: I would emphasize the following: ... 2. The programming language is really friendly and convenient to work with. In finance, you often need to hack together special solutions for problems that are not conventional (especially in term structure models, but I think that the same applies to bi- and trinomial models and their ilk). As an R newbie, it took me an afternoon to implement a basic toolkit for the former, which I could use for interesting explorations. There are three perspectives on programming languages like the S/R family: (1) The programming language perspective. I am sorry to tell you that the only excuse for R is S. R is *weird*. It combines error-prone C-like syntax with data structures that are APL-like but not sufficiently* APL-like to have behaviour that is easy to reason about. The scope rules (certainly the scope rules for S) were obviously designed by someone who had a fanatical hatred of compilers and wanted to ensure that the language could never be usefully compiled. Thanks to 'with' the R scope rules are little better. The fact that (object)$name returns NULL instead of reporting an error when the object doesn't _have_ a $name property means that errors can be delayed to the point where debugging is harder than it needs to be. The existence of two largely unrelated object-oriented extensions further complicates the language. APL, Xerox's Interactive Data-analysis Language (an extension of Interlisp), and Lisp-Stat are *far* cleaner as programming languages. (2) The Excel perspective. Many people are using Excel as their statistics package. (One of my students persists in using it for making his graphs. I've talked another lecturer and his student into using R although it's too late for a paper they've published. Dark backgrounds for printed graphs don't work well. What persuaded them was a number of relevant things available out-of-the-box in R.) In Excel, there are at least three languages: - direct manipulation - the formula language - Visual Basic for Applications What R offers is a *single* language that's used uniformly, with a rich data model. (3) The statistics package perspective. I've used Minitab, GLIM, SPSS, Matlab, and Octave (and BASIS, if anyone remembers that). I've owned and read manuals for GENSTAT. Recently I had occasion to look at more SAS code than I ever wish to. (No, I didn't understand it.) Several of these packages share a common design feature: there is a language of built-in commands, perhaps a data transformation language, and a separate macro language. The macro language is typically very clumsy. What R offers is a *single* language that's used uniformly, with a rich data model. Analysis components you get off CRAN are accessed using the *same* syntax as 'built-in' analyses. R also offers something important for people who _do_ have the money to buy commercial packages, and who might be reluctant to trust open source: a very high degree of compatibility with an established commercial product. R could almost be seen as an indefinite lifetime 'evaluation' version of S-Plus. The fact that I can use 'contributed' code, or even my own code, exactly the same way as 'built-in' stuff, even including access to on-line documentation and examples, actually *improves* the learning curve for R compared with many packages. At least it did for me. In the words of an old Listerine commercial: 'I hate it. Twice a day.' __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [Q] raw - gpr in aroma package
Hi. Is it possible to make gpr from raw? library(aroma) #read gpr file gpr - GenePixData$read(gpr123.gpr, path=aroma$dataPath) # gpr - raw raw - as.RawData(gpr) # raw - ma ma - getSignal(raw, bgSubtract=FALSE) ma.norm - clone(ma) #normalization normalizeWithinSlide(ma.norm, s) #ma - raw raw2 - as.RawData(ma) I want to make gpr data from raw2 and then I want to write new gpr( write(gpr,¡±result.gpr¡±)). Is it possible? Can anyone help me with this? Thanks, Hee-Jeong Jin. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Recoding a multiple response question into a series of 1, 0 variables
Hello R folks. 1) The question that generated the data, which I call Qx: Which of the following 5 items have you performed in the past month? (multipe response) 2) How the data is coded in my current dataframe: The first item that a person selected is coded under a field called Qxfirst; the second selected under Qxsecond, etc. For the first Person, the NAs mean that that person only selected two of the five items. Hypothetical data is shown QxfirstQxsecondQxthirdQxfourthQxfifth Person142NANANA Person2134 5 NA Person332NANANA 3) How I want the data to be be coded: I want each field to be one of the five items and I want each field to contain a 1 or 0 code--1 if they mentioned the item, 0 otherwise. Given the above data, the new fields would look as follows: Item1Item2Item3Item4Item5 Person101 01 0 Person210 11 1 Person301 10 0 I know how to do this using brute force (by writing bunch of ifelse statements), but given I have quite a lot of data in the above format, I was hoping a function would streamline this--I have tried to create a function for this, but my efforts to date have turned up junk. Thanks Greg Blevins The Market Solutions Group [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Recoding a multiple response question into a series of 1, 0 variables
On 06/07/04 21:28, Greg Blevins wrote: Hello R folks. 1) The question that generated the data, which I call Qx: Which of the following 5 items have you performed in the past month? (multipe response) 2) How the data is coded in my current dataframe: The first item that a person selected is coded under a field called Qxfirst; the second selected under Qxsecond, etc. For the first Person, the NAs mean that that person only selected two of the five items. Hypothetical data is shown QxfirstQxsecondQxthirdQxfourthQxfifth Person142NANANA Person2134 5 NA Person332NANANA 3) How I want the data to be be coded: I want each field to be one of the five items and I want each field to contain a 1 or 0 code--1 if they mentioned the item, 0 otherwise. Given the above data, the new fields would look as follows: Item1Item2Item3Item4Item5 Person101 01 0 Person210 11 1 Person301 10 0 Here is an idea: X - c(4,5,NA,NA,NA) # one row Y - rep(NA,5) # an empty row Y[X] - 1 Y is now NA NA NA 1 1 which is what you want. So you need to do this on each row and then convert the NAs to 0s. So first create an empty data frame, the same size as your original one X, like my Y. Callit Y. Then a loop? (I can't think of a better way just now, like with mapply.) for (i in [whatever]) Y[i][X[i]] - 1 (Not tested.) Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page:http://www.sas.upenn.edu/~baron R search page:http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Recoding a multiple response question into a series of 1, 0 variables
On 06/07/04 22:45, Jonathan Baron should have written: for (i in [whatever]) Y[i,][X[i,]] - 1 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
Rolf Turner [EMAIL PROTECTED] attacked: Have you ***any*** evidence that R's procedure degrades performance, under any circumstances? (Apparently not.) In that case why are you going on and on about it? I did the following: library(chron) ymd.to.POSIXlt - function (y, m, d) as.POSIXlt(chron(julian(y=y, x=m, d=d))) n - 10 y - sample(1970:2004, n, replace=TRUE) m - sample(1:12, n, replace=TRUE) d - sample(1:28, n, replace=TRUE) system.time(ymd.to.POSIXlt(y, m, d)) [1] 8.78 0.10 31.76 0.00 0.00 system.time(as.POSIXlt(paste(y,m,d, sep=-))) [1] 14.64 0.13 53.30 0.00 0.00 This was on a 500MHz SunBlade100, a slow machine by today's standards, using R 1.9.0. There is all the evidence one could reasonably ask for that going through paste() instead of providing y, m, d as numeric vectors *does* degrade performance under at least some circumstances. The cost is less than a factor of 2, but not negligible either. The standard response to this kind of request is ``R is a cooperative endeavour. Feel free to contribute.'' Well, ymd.to.POSIXlt is my contribution. Is there no one supporting my idea? Apparently not. Wrong: the idea *is* already supported (all except for one trivial line of code) by the chron package. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] More than one series in a coplot
Hi
Matthew Walker wrote:
Hi!
I would like to know, how do you plot more than one data series when
using coplot?
I think I know the answer if plot is being used:
x - 1:10
y - 1:10
y2 - 1:10* 1.1
plot ( y ~ x, type=n )
points( y ~ x, type = b, col = red ) # plot the points and lines
for the first series
points( y2 ~ x, type = b, col = blue ) # plot the points and lines
for the second series
But how should it be done with coplot?
If I make my question more concrete:
df - data.frame( x=x, y=y, y2=y2, v=c(a,b)) # using the vectors above
coplot( df$y~df$x | df$v, type=b, col=red) # gives me a coplot of y
~ x
How do I now put points and lines for y2 on the same graphs?
Use the panel argument, as below ...
x - 1:10
y - 1:10
y2 - 1:10* 1.1
df - data.frame( x=x, y=y, y2=y2, v=c(a,b)) # using the vectors above
coplot( df$y~df$x | df$v, type=b, col=red,
subscripts=TRUE,
panel=function(x, y, subscripts, ...) {
points(x, y, ...)
points(x, y2[subscripts], ...)})
Paul
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Differential Equations
Hello! I would like to know if R can solve Differential Equations... I don't think so because, in my point, I see R like a Statistical System, not a Math System. Am I wrong? Thank you very much. Márcio de Medeiros Ribeiro Graduando em Ciência da Computação Departamento de Tecnologia da Informação - TCI Universidade Federal de Alagoas - UFAL Maceió - Alagoas - Brasil Projeto CoCADa __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Vectors of years, months, and days to dates?
Thanks, Richard. This is what I was looking for. As you said, the chron package seems so useful that I will use it a lot. I don't think the performance gain (53:31) is not what we can neglect. Still, I am wondering why this kind of intuitive interface is not supported through the base package. Daehyok Shin (Peter) -Original Message- From: Richard A. O'Keefe [mailto:[EMAIL PROTECTED] Sent: Monday, June 07, 2004 PM 10:50 To: [EMAIL PROTECTED] Subject: RE: [R] Vectors of years, months, and days to dates? as.Date(c(years, months, days)) That would put all the years, followed by all the months, followed by all the days, in one vector. Try the chron package, where you can use julian(y=years, x=months, d=days) # vectors = vector of day numbers (I really mean 'x', not 'm') chron(julian(...)) # vector of day numbers = vector of chron objects as.POSIXlt(chron(...)) # vector of chron objects = vector of POSIXlt objects So: ymd.to.POSIXlt - function (y, m, d) as.POSIXlt(chron(julian(y=y, x=m, d=d))) Now, n - 10 y - sample(1970:2004, n, replace=TRUE) m - sample(1:12, n, replace=TRUE) d - sample(1:28, n, replace=TRUE) system.time(ymd.to.POSIXlt(y, m, d)) [1] 8.78 0.10 31.76 0.00 0.00# user cpu, system cpu, elapsed system.time(as.POSIXlt(paste(y,m,d, sep=-))) [1] 14.64 0.13 53.30 0.00 0.00 This was on a 500MHz SunBlade100, a slow machine by today's standards. There *is* a time advantage for the approach you prefer, but it's less than a factor of 2. Is there no one supporting my idea? It _is_ supported, via the chron() package. Just add ymd.to.POSIXlt to your .Rprofile It may even be that chron objects do everything you need. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Vectors of years, months, and days to dates?
On Tue, 08-Jun-2004 at 02:57PM +1200, Richard A. O'Keefe wrote: | Rolf Turner [EMAIL PROTECTED] attacked: | Have you ***any*** evidence that R's procedure degrades | performance, under any circumstances? (Apparently not.) In | that case why are you going on and on about it? | | I did the following: | | library(chron) | ymd.to.POSIXlt - | function (y, m, d) as.POSIXlt(chron(julian(y=y, x=m, d=d))) | n - 10 | y - sample(1970:2004, n, replace=TRUE) | m - sample(1:12, n, replace=TRUE) | d - sample(1:28, n, replace=TRUE) | system.time(ymd.to.POSIXlt(y, m, d)) | [1] 8.78 0.10 31.76 0.00 0.00 | system.time(as.POSIXlt(paste(y,m,d, sep=-))) | [1] 14.64 0.13 53.30 0.00 0.00 | | This was on a 500MHz SunBlade100, a slow machine by today's standards, | using R 1.9.0. There is all the evidence one could reasonably ask for | that going through paste() instead of providing y, m, d as numeric | vectors *does* degrade performance under at least some circumstances. Ain't that just the darnest thing? I tried on a somewhat faster machine and got this: system.time(ymd.to.POSIXlt(y, m, d)) [1] 2.06 0.22 2.29 0.00 0.00 system.time(as.POSIXlt(paste(y,m,d, sep=-))) [1] 2.82 0.04 2.86 0.00 0.00 Negligible difference, I'd have thought, but I tried a few more times system.time(ymd.to.POSIXlt(y, m, d)) [1] 1.12 0.11 1.23 0.00 0.00 system.time(as.POSIXlt(paste(y,m,d, sep=-))) [1] 2.69 0.04 2.73 0.00 0.00 system.time(ymd.to.POSIXlt(y, m, d)) [1] 0.98 0.02 1.00 0.00 0.00 system.time(as.POSIXlt(paste(y,m,d, sep=-))) [1] 2.82 0.00 2.82 0.00 0.00 system.time(ymd.to.POSIXlt(y, m, d)) [1] 0.98 0.04 1.02 0.00 0.00 system.time(as.POSIXlt(paste(y,m,d, sep=-))) [1] 2.65 0.03 2.68 0.00 0.00 ymd.to.POSIXlt benefits from repeated, but the as.POSIXlt method doesn't. I even tried it again with a new R process and got the same sort of thing? What makes the difference? -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
