[R] Problem
Hi, I am a Equity Research Analyst i have a task to do. Ranking of Pair Trades i.e.i have so many parameters like share price, Technical indicators(like Stochastic Indicator, Relative Strength Index, Directional Movement Indicator, Moving Acerage Convergence Divergence) and so on. Now i am looking for the trading opportunities in pair on the basis of all the above parameters. I want to give ranks to all the pairs to get in which pair i have more opportunity to play and earn... I have already started with using Principal Component Analysis(PCA) basically to reduce the dimension of the parameters on the basis of which i have to give the rank to the pairs. And after that i will go for the skewness in all the pair with respect to the reduced parameters.Where the skewness is more that will be rank 1 pair so on.Because where the skewness is more there we will have more opportunities to play. But i am not confident with this appraoch. So, can you please help me with some other good method to solve this problem Thanks in Advance Regards, Ramesh [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Discriminant analysis
Hi, I'm a newbie in R and don't much aobut all the modules and their capabilities, but I'm interested in solving a problem about a discriminant analysis done with SPSS tool. The thing is that I would like to make a discrimant analysis similar to the one done with SPSS, but I can't find the way to solve it. I've been playing with R and I can handle more or less my data, the point is that I need to know what kind of discriminant analysis should I use to obtain the same results as I obtain with SPSS. Should I use qda or lda?? If not, what else could I use?? Can anybody help me to find out a light in my way? I've been searching all over the web to fetch any help or example but I couldn't get anything. I would apreciate any help greatly. Thanks Carlos Niharra López Software Engineer Madrid (Spain) __ Nuevos servicios, más seguridad __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Discriminant analysis
C NL wrote: Hi, I'm a newbie in R and don't much aobut all the modules and their capabilities, but I'm interested in solving a problem about a discriminant analysis done with SPSS tool. The thing is that I would like to make a discrimant analysis similar to the one done with SPSS, but I can't find the way to solve it. I've been playing with R and I can handle more or less my data, the point is that I need to know what kind of discriminant analysis should I use to obtain the same results as I obtain with SPSS. Should I use qda or lda?? If not, what else could I use?? Well, what about asking SPSS what it does, at first? What assumptions have you had re. the covariance matrix? I guess the default will be a linear discriminant analysis, but I do not know SPSS. And *you* should know whether the analysis you did with SPSS made sense or not for your data (hence also which models/methods you applied). Uwe Ligges Can anybody help me to find out a light in my way? I've been searching all over the web to fetch any help or example but I couldn't get anything. I would apreciate any help greatly. Thanks Carlos Niharra López Software Engineer Madrid (Spain) __ Nuevos servicios, más seguridad __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Where the error message comes from?
Mohammad A. Chaudhary wrote:
Hi all:
I get the following error message that I am not able to resolve.
Error in if (const(t, min(1e-08, mean(t)/1e+06))) { :
missing value where TRUE/FALSE needed
That means that for some value of t,
const(t, min(1e-08, mean(t)/1e+06))
gives NA or NaN rather than something that could be interpreted as TRUE
or FALSE.
What is const, BTW?
It appears right before the last data.frame statement.
Below is the program that simulates data from one way random effects
model and then computes normality and bootstrap confidence interval for
Cost-Effectiveness Ratio.
I have pasted the message in blue.
No, we do not want html mail (and the html version got deleted, see
below), hence nothing is blue (although we statisticians do like sort of
BLUEs, of course).
Uwe Ligges
I appreciate any guidance in figuring it out.
Ashraf
SIMULATING DATA #
SimClust - function(k,m,mu,sb2,sw2,r,z) {
#set.seed(1234)
# k = Number of groups
# m = Group size
# mu = Group mean, same for all groups
# sb2 = Between group variance
# sw2 = Within group variance
# r = Corelation coefficient
# z = standard normal variate cutoff value for binomial rv
# Simulate the random effects
A = rnorm(n=k, mean=0, sd=sqrt(sb2))
# Work out the mean of each group of data
means = matrix(mu, nrow=k,ncol=1)
for(row in 1:k){
means[row] = means[row,1] + A[row]}
# Initializing the data vectors
g=c=c1=mu1=numeric(k*m)
# Now generate the data one group at a time.
ind=0
for(u in 1:k){
for(replicate in 1:m){
ind = ind + 1
x=rnorm(1);y=rnorm(1)
c[ind] = sqrt(sw2)*x+means[u]
c1[ind] - sqrt(sw2)*(x*r+y*sqrt(1-r**2))+means[u]
g[ind] = u
mu1[ind] =means[u]
}}
data.frame(g=factor(g),c,e=(c1 mean(c1)+z*sd(c1))+0)
}
#
sk1=sk2=sk11=sk21=skR=k1=m1=R2=R1=n10=f10=nb10=b10=s10=p10=bca10=NULL
n.cp=f.cp=nb.cp=b.cp=s.cp=p.cp=bca.cp=NULL
for (k in c(12,24,48)) {
for (m in c(25,50,100)) {
for (j in 1:1000) {
PREPARING CLUSTER LEVEL DATA ##
d1=SimClust(k,m,mu=30,sb2=25,sw2=75,r=0.5,z=0.841621) # for p=0.2
d2=SimClust(k,m,mu=20,sb2=25,sw2=75,r=0.5,z=1.281552) # for p=0.1
## TREATMENT ##
r1 - cor(d1[,2:3])[1,2]
# COST #
ac1 - anova(lm(c~g,d1))
rc1 - (ac1[1,3]-ac1[2,3])/(ac1[1,3]+(m-1)*ac1[2,3])
if (rc1 0) rc1 - 0
vc1 - var(d1[,2])
mc1 - as.vector(by(d1[,2],as.numeric(d1[,1]),mean))
vc1m - vc1*(1+(m-1)*rc1)/(k*m)
# EFFECT #
ae1 - anova(lm(e~g,d1))
re1 - (ae1[1,3]-ae1[2,3])/(ae1[1,3]+(m-1)*ae1[2,3])
if (re1 0) re1 - 0
ve1 - var(d1[,3])
me1 - as.vector(by(d1[,3],as.numeric(d1[,1]),mean))
re1p - 1- m*sum(me1*(1-me1))/(k*(m-1)*mean(me1)*(1-mean(me1)))
ve1m - ve1*(1+(m-1)*re1)/(k*m)
## CONTROL ##
r2 - cor(d2[,2:3])[1,2]
# COST #
ac2 - anova(lm(c~g,d2))
rc2 - (ac2[1,3]-ac2[2,3])/(ac2[1,3]+(m-1)*ac2[2,3])
if (rc2 0) rc2 - 0
vc2 - var(d2[,2])
mc2 - as.vector(by(d2[,2],as.numeric(d2[,1]),mean))
vc2m - vc2*(1+(m-1)*rc2)/(k*m)
# EFECT #
ae2 - anova(lm(e~g,d2))
re2 - (ae2[1,3]-ae2[2,3])/(ae2[1,3]+(m-1)*ae2[2,3])
if (re2 0) re2 - 0
ve2 - var(d2[,3])
me2 - as.vector(by(d2[,3],as.numeric(d2[,1]),mean))
re2p - 1- m*sum(me2*(1-me2))/(k*(m-1)*mean(me2)*(1-mean(me2)))
ve2m - ve2*(1+(m-1)*re2)/(k*m)
## Combining and Computing ICER ##
d - data.frame(s = c(rep(1,k),rep(2,k)),
i = c(1:k,1:k), n =rep(m,2*k),
mc=c(mc1,mc2),me=c(me1,me2))
mmc1 - mean(d[1:k,4])
mmc2 - mean(d[(k+1):(2*k),4])
mme1 - mean(d[1:k,5])
mme2 - mean(d[(k+1):(2*k),5])
cnn - (vc1m+vc2m)/(mmc1-mmc2)^2
cdd - (ve1m+ve2m)/(mme1-mme2)^2
cnd -
(r1*(vc1m*ve1m)^0.5+r2*(vc2m*ve2m)^0.5)/((mmc1-mmc2)*(mme1-mme2))
R - (mmc1-mmc2)/(mme1-mme2)
seR - R*(cnn+cdd-2*cnd)^0.5
f1 -
R*((1-3.8416*cnd)-1.96*((cnn+cdd-2*cnd)-3.8416*(cnn*cdd-cnd^2))^0.5)/(1-
3.8416*cdd)
f2 -
R*((1-3.8416*cnd)+1.96*((cnn+cdd-2*cnd)-3.8416*(cnn*cdd-cnd^2))^0.5)/(1-
3.8416*cdd)
BOOTSTRAPPING AND PRINTING ##
icer-function(d0,f) {
mmc1 - mean(d0[1:k,4]*f[1:k])
mmc2 - mean(d0[(k+1):(2*k),4]*f[(k+1):(2*k)])
mme1 - mean(d0[1:k,5]*f[1:k])
mme2 - mean(d0[(k+1):(2*k),5]*f[(k+1):(2*k)])
c((mmc1-mmc2)/(mme1-mme2),seR^2)
}
bout - boot(d,icer, R=999, stype=f, strata=d[,1])
bci - boot.ci(bout, conf = 0.95, type =
c(norm,basic,stud,perc,bca))
sk1[j] - 3*(mean(d1[,2])-median(d1[,2]))/sd(d1[,2])
sk2[j] - 3*(mean(d2[,2])-median(d2[,2]))/sd(d2[,2])
R2[j] - R
n10[j] -
Re: [R] clara - memory limit
ReidH == Huntsinger, Reid [EMAIL PROTECTED] on Wed, 3 Aug 2005 13:21:45 -0400 writes: ReidH I thought setting keep.data=FALSE might help, but ReidH running this on a 32-bit Linux machine, the R process ReidH seems to use 1.2 GB until just before clara returns, ReidH when it increases to 1.9 GB, regardless of whether ReidH keep.data=FALSE or TRUE. Possibly it's the overhead ReidH of the .C() interface, but that's mostly an ReidH uninformed guess. not only; I've found at least one place to save more memory for 'keep.data = FALSE', thanks to your careful observation, Reid! This, together, with another small change, will lead to a new release of the cluster package, soon. Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Installation problem on SGI IRIX6.5
Hi, all, I'm a newbie to R. I came across a problem when I tried to install R on an SGI machine which is running IRIX64 6.5. I have successfully run configure, but when I tried to run make(or gmake), errors came out. Following is the error message. Does someone has experiences in the R's installation on IRIX ? Any hints will be greatly appreciated ! Thanks in advance! Error Message: cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include -I../../src/include -I/user_data2/jfxiao/local/include -DHAVE_CONFIG_H -OPT:IEEE_NaN_inf=ON -g -c character.c -o character.o cc-1185 cc: WARNING File = character.c, Line = 714 An enumerated type is mixed with another type. warn = warn | !utf8strIsASCII(CHAR(STRING_ELT(CAR(args), i))); ^ cc-1552 cc: WARNING File = character.c, Line = 698 The variable uclass is set but never used. int i, len, minlen, uclass; ^ cc-1020 cc: ERROR File = character.c, Line = 1300 The identifier wctrans_t is undefined. wctrans_t tr = wctrans(ul ? toupper : tolower); ^ cc-1185 cc: WARNING File = character.c, Line = 1733 An enumerated type is mixed with another type. Rboolean warn = !utf8strIsASCII(CHAR(STRING_ELT(pat, 0))); ^ cc-1185 cc: WARNING File = character.c, Line = 1926 An enumerated type is mixed with another type. useRaw = strcmp(CHAR(STRING_ELT(stype, 0)), integer); ^ 1 error detected in the compilation of character.c. gmake[3]: *** [character.o] Error 2 gmake[3]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src/main' gmake[2]: *** [R] Error 2 gmake[2]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src/main' gmake[1]: *** [R] Error 1 gmake[1]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src' gmake: *** [R] Error 1 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to set the floating point precision beyond e-22?
We have a problem inverting a matrix which has the following eigenvalues: eigen(tcross, only.values=TRUE) $values [1] 7.917775e+20 2.130980e+16 7.961620e+13 8.241041e+12 2.258325e+12 [6] 3.869428e+11 6.791041e+10 2.485352e+09 9.863098e+08 9.819373e+05 [11] 3.263408e+05 2.929853e+05 2.920419e+05 2.714355e+05 8.733435e+04 [16] 8.127136e+04 6.543883e+04 5.335074e+04 3.773311e+04 2.904373e+04 [21] 2.418297e+04 1.387422e+04 8.925090e+03 5.538344e+03 4.831908e+03 [26] 1.133571e+03 9.882477e+02 7.725812e+02 5.081682e+02 3.010545e+02 [31] 1.801611e+02 1.319787e+02 1.050521e+02 7.096471e+01 5.576549e+01 [36] 4.192645e+01 3.549810e+01 2.638731e+01 2.29e+01 1.735139e+01 [41] 1.058796e+01 7.425778e+00 7.209576e+00 4.689665e+00 3.181650e+00 [46] 3.002956e+00 1.959247e+00 1.551665e+00 1.079589e+00 1.064981e+00 [51] 5.409617e-01 4.076501e-01 2.010129e-01 1.302394e-01 4.029787e-02 [56] 2.599448e-02 1.061294e-02 1.634286e-03 4.095303e-09 1.021885e-10 [61] 2.124763e-11 6.906665e-12 2.850103e-12 9.440867e-13 6.269723e-13 [66] 1.043794e-13 -1.300171e-13 -7.220665e-13 -4.166945e-12 -6.145350e-12 [71] -2.776804e-11 -5.269669e-11 -7.154246e-10 -1.490515e-09 -1.294256e-08 [76] -1.224821e-02 -3.278657e+00 -4.620100e+01 -9.781843e+02 -1.303929e+04 [81] -5.545949e+04 -8.077540e+04 -8.577861e+04 -1.329961e+05 -1.450908e+05 [86] -3.022353e+05 -4.015776e+05 As yout can see, the eigenvalues spread very much (between e+20 and e-13). We presume, that it has something to do with R's floating point precision, which I read is about 22-digits in mantissa as default. Can this precision be set to values above 22? The problem occurs especially when trying to perform 2SLS with the 'systemfit' package. There appears always an error message like the following from the inverting routine: solve(tcross) Error in solve.default(tcross) : Lapack routine dgesv: system is exactly singular Or is there another source of error? We would like to embed R-routines in a non-commercial web application for which we need to employ 'systemfit' together with individual, user-submitted data. So the problem needs a general solution and not a special one for this particular matrix. Thanks in advance Roy PS: The 'gmp' package is definitely not the solution. I already tried it. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to set the floating point precision beyond e-22?
-Ursprüngliche Nachricht- Von: Roy Nitze [mailto:[EMAIL PROTECTED] Gesendet: Freitag, 5. August 2005 10:38 An: 'r-help@stat.math.ethz.ch' Betreff: How to set the floating point precision beyond e-22? We have a problem inverting a matrix which has the following eigenvalues: eigen(tcross, only.values=TRUE) $values [1] 7.917775e+20 2.130980e+16 7.961620e+13 8.241041e+12 2.258325e+12 [6] 3.869428e+11 6.791041e+10 2.485352e+09 9.863098e+08 9.819373e+05 [11] 3.263408e+05 2.929853e+05 2.920419e+05 2.714355e+05 8.733435e+04 [16] 8.127136e+04 6.543883e+04 5.335074e+04 3.773311e+04 2.904373e+04 [21] 2.418297e+04 1.387422e+04 8.925090e+03 5.538344e+03 4.831908e+03 [26] 1.133571e+03 9.882477e+02 7.725812e+02 5.081682e+02 3.010545e+02 [31] 1.801611e+02 1.319787e+02 1.050521e+02 7.096471e+01 5.576549e+01 [36] 4.192645e+01 3.549810e+01 2.638731e+01 2.29e+01 1.735139e+01 [41] 1.058796e+01 7.425778e+00 7.209576e+00 4.689665e+00 3.181650e+00 [46] 3.002956e+00 1.959247e+00 1.551665e+00 1.079589e+00 1.064981e+00 [51] 5.409617e-01 4.076501e-01 2.010129e-01 1.302394e-01 4.029787e-02 [56] 2.599448e-02 1.061294e-02 1.634286e-03 4.095303e-09 1.021885e-10 [61] 2.124763e-11 6.906665e-12 2.850103e-12 9.440867e-13 6.269723e-13 [66] 1.043794e-13 -1.300171e-13 -7.220665e-13 -4.166945e-12 -6.145350e-12 [71] -2.776804e-11 -5.269669e-11 -7.154246e-10 -1.490515e-09 -1.294256e-08 [76] -1.224821e-02 -3.278657e+00 -4.620100e+01 -9.781843e+02 -1.303929e+04 [81] -5.545949e+04 -8.077540e+04 -8.577861e+04 -1.329961e+05 -1.450908e+05 [86] -3.022353e+05 -4.015776e+05 As yout can see, the eigenvalues spread very much (between e+20 and e-13). We presume, that it has something to do with R's floating point precision, which I read is about 22-digits in mantissa as default. Can this precision be set to values above 22? The problem occurs especially when trying to perform 2SLS with the 'systemfit' package. There appears always an error message like the following from the inverting routine: solve(tcross) Error in solve.default(tcross) : Lapack routine dgesv: system is exactly singular Or is there another source of error? We would like to embed R-routines in a non-commercial web application for which we need to employ 'systemfit' together with individual, user-submitted data. So the problem needs a general solution and not a special one for this particular matrix. Thanks in advance Roy PS: The 'gmp' package is definitely not the solution. I already tried it. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] using for loop
Hi everybody, how can I create a loop for plotting parameters for each level of a variable, for example: NAME temperature depth aaa 23 -1 aaa 22 -2 aaa 24 -1 bbb 23 -4 bbb 23 -1 aaa 22 -1 bbb 220 I mean, I would like R to plot temperature vs depth for aaa, then another plot for bbb, and so on. Is it for loop ok? Thanks __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] using for loop
alessandro carletti a écrit : Hi everybody, how can I create a loop for plotting parameters for each level of a variable, for example: NAME temperature depth aaa 23 -1 aaa 22 -2 aaa 24 -1 bbb 23 -4 bbb 23 -1 aaa 22 -1 bbb 220 I mean, I would like R to plot temperature vs depth for aaa, then another plot for bbb, and so on. Is it for loop ok? Thanks Package lattice is your friend. Using your example: Data - read.table(file = clipboard, header = TRUE) library(lattice) xyplot(temperature ~ depth | NAME, data = Data) Best, Renaud -- Dr Renaud Lancelot, vétérinaire Projet FSP régional épidémiologie vétérinaire C/0 Ambassade de France - SCAC BP 834 Antananarivo 101 - Madagascar e-mail: [EMAIL PROTECTED] tel.: +261 32 40 165 53 (cell) +261 20 22 665 36 ext. 225 (work) +261 20 22 494 37 (home) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] kappa-accuracy and test for signifcance
Dear list, I calculated the kappa-accuracy for two differnt classifications. How can I test now the two kappa-value for significance? thanks, Mark . Markus Schwarz Wissenschaftliche Mitarbeiterin Eidg. Forschungsanstalt WSL Forschungsprogramm Musterland Zürcherstrasse 111 CH-8903 Birmensdorf Telefon +41-44-739 22 87 Fax +41-44-739 22 15 [EMAIL PROTECTED] http://www.wsl.ch/staff/markus.schwarz/ . __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] kappa-accuracy and test for signifcance
On 08/05/05 11:24, Markus Schwarz wrote: Dear list, I calculated the kappa-accuracy for two differnt classifications. How can I test now the two kappa-value for significance? If you search the functions in http://finzi.psych.upenn.edu/nmz.html or just use RSiteSearch(kappa,restrict=functions) then you will find several ways to compute kappa (assuming that it is the same kappa we're talking about). The first one I looked at (kappa2 in irr) yields a p value. I'm not sure that this is what you are asking, though. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to set the floating point precision beyond e-22?
Roy Nitze wrote: We have a problem inverting a matrix which has the following eigenvalues: eigen(tcross, only.values=TRUE) $values [1] 7.917775e+20 2.130980e+16 7.961620e+13 8.241041e+12 2.258325e+12 [6] 3.869428e+11 6.791041e+10 2.485352e+09 9.863098e+08 9.819373e+05 [11] 3.263408e+05 2.929853e+05 2.920419e+05 2.714355e+05 8.733435e+04 [16] 8.127136e+04 6.543883e+04 5.335074e+04 3.773311e+04 2.904373e+04 [21] 2.418297e+04 1.387422e+04 8.925090e+03 5.538344e+03 4.831908e+03 [26] 1.133571e+03 9.882477e+02 7.725812e+02 5.081682e+02 3.010545e+02 [31] 1.801611e+02 1.319787e+02 1.050521e+02 7.096471e+01 5.576549e+01 [36] 4.192645e+01 3.549810e+01 2.638731e+01 2.29e+01 1.735139e+01 [41] 1.058796e+01 7.425778e+00 7.209576e+00 4.689665e+00 3.181650e+00 [46] 3.002956e+00 1.959247e+00 1.551665e+00 1.079589e+00 1.064981e+00 [51] 5.409617e-01 4.076501e-01 2.010129e-01 1.302394e-01 4.029787e-02 [56] 2.599448e-02 1.061294e-02 1.634286e-03 4.095303e-09 1.021885e-10 [61] 2.124763e-11 6.906665e-12 2.850103e-12 9.440867e-13 6.269723e-13 [66] 1.043794e-13 -1.300171e-13 -7.220665e-13 -4.166945e-12 -6.145350e-12 [71] -2.776804e-11 -5.269669e-11 -7.154246e-10 -1.490515e-09 -1.294256e-08 [76] -1.224821e-02 -3.278657e+00 -4.620100e+01 -9.781843e+02 -1.303929e+04 [81] -5.545949e+04 -8.077540e+04 -8.577861e+04 -1.329961e+05 -1.450908e+05 [86] -3.022353e+05 -4.015776e+05 As yout can see, the eigenvalues spread very much (between e+20 and e-13). We presume, that it has something to do with R's floating point precision, which I read is about 22-digits in mantissa as default. Less than that. It depends a bit on the platform and the exact calculation, but you can't count on more than 15-16 decimal digits precision. Can this precision be set to values above 22? No. R generally uses the floating point hardware type double precision, and it's a fixed size. The problem occurs especially when trying to perform 2SLS with the 'systemfit' package. There appears always an error message like the following from the inverting routine: solve(tcross) Error in solve.default(tcross) : Lapack routine dgesv: system is exactly singular You will have to find a different solution to the problem. To machine precision, that matrix looks singular. This usually indicates that it's not the right matrix to try to invert. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to set the floating point precision beyond e-22?
Duncan Murdoch [EMAIL PROTECTED] writes: You will have to find a different solution to the problem. To machine precision, that matrix looks singular. This usually indicates that it's not the right matrix to try to invert. It might be a scaling issue though: If you're measuring age in days and hormone concentrations in Molar, then you'll get that sort of eigenvalue ratios in a fairly benign way. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Documenting data sets with many variables
Hi,
I extended the data set Blanciforti86 that is included in my R package
micEcon. For instance, I added consumer prices, annual consumption
expenditures and expenditure shares of eleven aggregate commodity groups.
The corresponding variables in the data frame are called pAgg1,
pAgg2, ..., pAgg11, xAgg1, xAgg2, ..., xAgg11, wAgg1,
wAgg2, ..., wAgg11. To avoid to describe all 33 items in the \format
section of the documentation (.Rd file) I wrote something like
\format{
This data frame contains the following columns:
\describe{
[ . . . ]
\item{xAggX}{Expenditure on the aggregate commodity group X
(in Millions of US-Dollars).}
\item{pAggX}{Price index for the aggregate commodity group X
(1972 = 100).}
\item{wAggX}{Expenditure share of the aggregate commodity group X.}
[ . . . ]
}
}
and explained the 11 aggregate commodity groups only once in a different
section (1=food, 2=clothing, ... ). However, R CMD check now complains
about data codoc mismatches, e.g.
Code: [...] pAgg1pAgg2 pAgg3 [...]
Docs: [...] pAggX [...]
Is there a way to avoid the description of all 33 items without getting a
complaint from R CMD check?
Thanks,
Arne
--
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
[EMAIL PROTECTED]
http://www.uni-kiel.de/agrarpol/ahenningsen/
__
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[R] Help, my RGui is speaking French!
Dear R-helpers, First of all I have nothing against the French language! But now my problem, yesterday I installed R 2.1.1 and I had to experience that my RGui is speaking French. My windows locals is French (Switzerland). I'm used to English and I want to reset my RGui to English. I was seeking for the solution in the archives, however not successfully. By the way the searchable archives via: http://www.r-project.org/, Mailing Lists, R-help, web-interface, searchable achieves, did not work: http://maths.newcastle.edu.au/~rking/R/ Also I was seeking in the FAQ's http://cran.r-project.org/doc/FAQ/R-FAQ.html and http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html and could not find the solution. I'm sure that lots of people have queried already and that the solution is already written down somewhere. However I cant find it. Could somebody give me a hint? Kind regards, Dominik My system: platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor1.1 year 2005 month06 day 20 language R [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to set the floating point precision beyond e-22?
You will have to find a different solution to the problem. To machine precision, that matrix looks singular. This usually indicates that it's not the right matrix to try to invert. It might be a scaling issue though: If you're measuring age in days and hormone concentrations in Molar, then you'll get that sort of eigenvalue ratios in a fairly benign way. I'm quite aware of that problem, but we have to deal with certain economic variables which are usually given in a certain dimension. So it is difficult to force all values to a certain order. The other thing is, that i.e. EViews is able to perform 2SLS in the same regression setup. Don't they have to invert the same matrices? If so, how do they do it and how can we mimic their proceeding in R? Scaling and Rescaling? What about the interpretation of the coefficients computed on a scaled basis and given in the context of re-/unscaled data? I'm not quite clear about it. Thanks to all of you. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] interpolation function
Hi, I have a sparse matrix.I want to fill values into the entries whose value is 0.The new generated values should come from the interpolation of the values have existed.Does R provide such interpolation functions which operate on Matrix, for example ,such a matrix below 0 0 0 0 2.3 0 0 0 0 0 0 3.1 0 0 0 0 1.4 0 0 0 0 0 0 0 0 0 0 1.1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 3 0 0 0 0 6 0 0 0 0 0 0 9 0 0 0 0 thanks a lot hao wu __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to set the floating point precision beyond e-22?
Peter Dalgaard wrote: Duncan Murdoch [EMAIL PROTECTED] writes: You will have to find a different solution to the problem. To machine precision, that matrix looks singular. This usually indicates that it's not the right matrix to try to invert. It might be a scaling issue though: If you're measuring age in days and hormone concentrations in Molar, then you'll get that sort of eigenvalue ratios in a fairly benign way. Remember the old joke. The patient to his doctor: It hurts when I do this. The doctor: So don't do that. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help, my RGui is speaking French!
Grathwohl, Dominik, LAUSANNE, NRC-BAS wrote: Dear R-helpers, First of all I have nothing against the French language! But now my problem, yesterday I installed R 2.1.1 and I had to experience that my RGui is speaking French. My windows locals is French (Switzerland). I'm used to English and I want to reset my RGui to English. I was seeking for the solution in the archives, however not successfully. By the way the searchable archives via: http://www.r-project.org/, Mailing Lists, R-help, web-interface, searchable achieves, did not work: http://maths.newcastle.edu.au/~rking/R/ Also I was seeking in the FAQ's http://cran.r-project.org/doc/FAQ/R-FAQ.html and http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html and could not find the solution. I'm sure that lots of people have queried already and that the solution is already written down somewhere. However I cant find it. Could somebody give me a hint? For example, read the most recent R Newsletter on localization of R. As one solution, set the environment variable LANGUAGE=en Uwe Ligges Kind regards, Dominik My system: platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor1.1 year 2005 month06 day 20 language R [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interpolation function
What you intend strikes me as being pretty silly. Do not expect R to work magic for you. Even if there were such a function as you desire in R, the results it would give would be effectively meaningless for data such as you exhibited. cheers, Rolf Turner [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to set the floating point precision beyond e-22?
You will have to find a different solution to the problem. To machine precision, that matrix looks singular. This usually indicates that it's not the right matrix to try to invert. It might be a scaling issue though: If you're measuring age in days and hormone concentrations in Molar, then you'll get that sort of eigenvalue ratios in a fairly benign way. I'm quite aware of that problem, but we have to deal with certain economic variables which are usually given in a certain dimension. So it is difficult to force all values to a certain order. The other thing is, that i.e. EViews is able to perform 2SLS in the same regression setup. Don't they have to invert the same matrices? If so, how do they do it and how can we mimic their proceeding in R? Scaling and Rescaling? What about the interpretation of the coefficients computed on a scaled basis and given in the context of re-/unscaled data? I'm not quite clear about it. Thanks to all of you. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help, my RGui is speaking French!
Grathwohl, Dominik, LAUSANNE, NRC-BAS [EMAIL PROTECTED] writes: Dear R-helpers, First of all I have nothing against the French language! But now my problem, yesterday I installed R 2.1.1 and I had to experience that my RGui is speaking French. My windows locals is French (Switzerland). I'm used to English and I want to reset my RGui to English. I was seeking for the solution in the archives, however not successfully. By the way the searchable archives via: http://www.r-project.org/, Mailing Lists, R-help, web-interface, searchable achieves, did not work: http://maths.newcastle.edu.au/~rking/R/ Also I was seeking in the FAQ's http://cran.r-project.org/doc/FAQ/R-FAQ.html and http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html and could not find the solution. I'm sure that lots of people have queried already and that the solution is already written down somewhere. However I cant find it. Could somebody give me a hint? Make sure that the environment variable LANGUAGE is set to en. I think the consensus is that putting it into HOME/.Renviron is the most practical way. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interpolation function
I do not understand your question. If this was not a sparse matrix, then I would have asked you refer into the missing value literature. Even there, people generally remove any columns/rows that have too many missing values to avoid unreliable results. And since this is a sparse matrix, you are going to have too many missing values on all rows and columns. I could be wrong but if I am, someone will tell me that soon enough. Regards, Adai On Fri, 2005-08-05 at 12:12 +, 吴 昊 wrote: Hi, I have a sparse matrix.I want to fill values into the entries whose value is 0.The new generated values should come from the interpolation of the values have existed.Does R provide such interpolation functions which operate on Matrix, for example ,such a matrix below 0 0 0 0 2.3 0 0 0 0 0 0 3.1 0 0 0 0 1.4 0 0 0 0 0 0 0 0 0 0 1.1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 3 0 0 0 0 6 0 0 0 0 0 0 9 0 0 0 0 thanks a lot hao wu __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to set the floating point precision beyond e-22?
On 8/5/05, Roy Nitze [EMAIL PROTECTED] wrote: We have a problem inverting a matrix which has the following eigenvalues: eigen(tcross, only.values=TRUE) $values [1] 7.917775e+20 2.130980e+16 7.961620e+13 8.241041e+12 2.258325e+12 [6] 3.869428e+11 6.791041e+10 2.485352e+09 9.863098e+08 9.819373e+05 [11] 3.263408e+05 2.929853e+05 2.920419e+05 2.714355e+05 8.733435e+04 [16] 8.127136e+04 6.543883e+04 5.335074e+04 3.773311e+04 2.904373e+04 [21] 2.418297e+04 1.387422e+04 8.925090e+03 5.538344e+03 4.831908e+03 [26] 1.133571e+03 9.882477e+02 7.725812e+02 5.081682e+02 3.010545e+02 [31] 1.801611e+02 1.319787e+02 1.050521e+02 7.096471e+01 5.576549e+01 [36] 4.192645e+01 3.549810e+01 2.638731e+01 2.29e+01 1.735139e+01 [41] 1.058796e+01 7.425778e+00 7.209576e+00 4.689665e+00 3.181650e+00 [46] 3.002956e+00 1.959247e+00 1.551665e+00 1.079589e+00 1.064981e+00 [51] 5.409617e-01 4.076501e-01 2.010129e-01 1.302394e-01 4.029787e-02 [56] 2.599448e-02 1.061294e-02 1.634286e-03 4.095303e-09 1.021885e-10 [61] 2.124763e-11 6.906665e-12 2.850103e-12 9.440867e-13 6.269723e-13 [66] 1.043794e-13 -1.300171e-13 -7.220665e-13 -4.166945e-12 -6.145350e-12 [71] -2.776804e-11 -5.269669e-11 -7.154246e-10 -1.490515e-09 -1.294256e-08 [76] -1.224821e-02 -3.278657e+00 -4.620100e+01 -9.781843e+02 -1.303929e+04 [81] -5.545949e+04 -8.077540e+04 -8.577861e+04 -1.329961e+05 -1.450908e+05 [86] -3.022353e+05 -4.015776e+05 As yout can see, the eigenvalues spread very much (between e+20 and e-13). We presume, that it has something to do with R's floating point precision, which I read is about 22-digits in mantissa as default. Can this precision be set to values above 22? The problem occurs especially when trying to perform 2SLS with the 'systemfit' package. There appears always an error message like the following from the inverting routine: solve(tcross) Error in solve.default(tcross) : Lapack routine dgesv: system is exactly singular Or is there another source of error? We would like to embed R-routines in a non-commercial web application for which we need to employ 'systemfit' together with individual, user-submitted data. So the problem needs a general solution and not a special one for this particular matrix. It appears that you are using the crossproduct but not taking advantage of the symmetry. The condition number of the crossproduct is the square of the condition number of the original matrix so you are making your conditioning problems much worse by taking the crossproduct. I suggest that you use a QR or SVD decomposition of the original model matrix instead. You will still end up with a very ill-conditioned problem but now quite as bad as the one you have now. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem configuring R-patched
Sorry to chime in a bit late here.. Kevin == Kevin E Thorpe [EMAIL PROTECTED] on Thu, 04 Aug 2005 22:13:05 -0400 writes: Kevin Duncan Murdoch wrote: Kevin E. Thorpe wrote: Gavin Simpson wrote: On Thu, 2005-08-04 at 14:57 -0400, Kevin E. Thorpe wrote: I downloaded R-patched (2005-08-04) from CRAN today. I ran ./configure --enable-R-shlib I received the error message: checking for recommended packages... no configure: error: Some of the recommended packages are missing Use --without-recommended-packages if this was intentional ^^ So was this intentional? No, it wasn't. I built a previous version of R-patched successfully on my system which is running the SuSE 9,2 Pro Linux distribution. I untarred the tar ball into the same directory I did my last build on in case that's important. The only other differences between this attempt and my successful build are: 1. I did not use --enable-R-shlib last time. 2. I found and installed the blas libraries for this build. Have I messed up or made an erroneous assumption along the way? Yes and No. You obviously haven't compiled R recently. If you haven't got the recommended packages in the source you are compiling, configure now gives an error, which quite clearly states (and you've quoted it in your email!) that it cannot find (some of) the recommended packages. Actually, I compiled it about a week ago. Here is my current version. version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status Patched major 2 minor 1.1 year 2005 month 07 day 28 language R When I compiled that version, I did my tar xzf to a clean directory and did not receive that error. A solution - again given by the error message you quote! - is: ./configure --enable-R-shlib --without-recommended-packages ^ That should clear things up. I realise that would clear it up. I was puzzled why I got this message in the first place, given I didn't get it last week. I believe there are two kinds of tar files. The daily snapshots don't include the recommended packages, the releases do. eeehm, no: The daily snapshots do contain the recommended packages, and have for quite a while now. Or perhaps the test is a recent addition. only for a pretty generous definition of recent. To be honest, I don't know what Kevin's problem could be. The daily snapshots are really produced here at ETH Zurich and daily mirrored from here to CRAN. I can see that the R-patched_2005-08-04.tar.gz does contain the recommended packages. Maybe your download wasn't completed; your disk full; or you have a gnome in your computer who occasionally deletes some of your files? I've had similar feelings a few times in the past... Kevin Both versions were R-patched.tar.gz as opposed to the Kevin devel sets which looks like it's actually a link to Kevin the most recent. Maybe I incorrectly assumed that Kevin Maybe I incorrectly assumed that the patched tarballs Kevin contained the recommended packages. actually that was a correct assumption. Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] High resolution plots
Gabor Grothendieck schrieb: On 7/13/05, Luis Tercero [EMAIL PROTECTED] wrote: Dear R-help community, would any of you have a (preferably simple) example of a presentation-quality .png plot, i.e. one that looks like the .eps plots generated by R? I am working with R 2.0.1 in WindowsXP and am having similar problems as Knut Krueger in printing high-quality plots. I have looked at the help file and examples therein as well as others I have been able to find online but to no avail. After many many tries I have to concede I cannot figure it out. I would be very grateful for your help. If you want the highest resolution use a vector format, not a bitmapped format such as png. See: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html The link is now broken, and I did not copy the hints. Does anybody knows if it its available at any other location? And I tried to find Thanks for the pointer! .wmf is far superior, I was just in the dark about the format and R's ability to produce it (An Introduction to R Device drivers does not mention it and I had obviously missed the deciding last two words in ?device 'windows') the wmf command but there is nothing to find with help.search(wmf) with regards Knut Krueger [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to set the floating point precision beyond e-22?
And don't forget to rescale first, as Peter Dalgaard suggested. I've been giving this lecture for over 20 years, and I got caught by it myself a few years ago. I computed the crossproduct matrix, as Doug said, and had no end of trouble because it was numerically singular. I rescaled each column by subtracting some number roughly close to the mean or median and dividing by something close to the standard deviation, and the problem went away. spencer graves Douglas Bates wrote: On 8/5/05, Roy Nitze [EMAIL PROTECTED] wrote: We have a problem inverting a matrix which has the following eigenvalues: eigen(tcross, only.values=TRUE) $values [1] 7.917775e+20 2.130980e+16 7.961620e+13 8.241041e+12 2.258325e+12 [6] 3.869428e+11 6.791041e+10 2.485352e+09 9.863098e+08 9.819373e+05 [11] 3.263408e+05 2.929853e+05 2.920419e+05 2.714355e+05 8.733435e+04 [16] 8.127136e+04 6.543883e+04 5.335074e+04 3.773311e+04 2.904373e+04 [21] 2.418297e+04 1.387422e+04 8.925090e+03 5.538344e+03 4.831908e+03 [26] 1.133571e+03 9.882477e+02 7.725812e+02 5.081682e+02 3.010545e+02 [31] 1.801611e+02 1.319787e+02 1.050521e+02 7.096471e+01 5.576549e+01 [36] 4.192645e+01 3.549810e+01 2.638731e+01 2.29e+01 1.735139e+01 [41] 1.058796e+01 7.425778e+00 7.209576e+00 4.689665e+00 3.181650e+00 [46] 3.002956e+00 1.959247e+00 1.551665e+00 1.079589e+00 1.064981e+00 [51] 5.409617e-01 4.076501e-01 2.010129e-01 1.302394e-01 4.029787e-02 [56] 2.599448e-02 1.061294e-02 1.634286e-03 4.095303e-09 1.021885e-10 [61] 2.124763e-11 6.906665e-12 2.850103e-12 9.440867e-13 6.269723e-13 [66] 1.043794e-13 -1.300171e-13 -7.220665e-13 -4.166945e-12 -6.145350e-12 [71] -2.776804e-11 -5.269669e-11 -7.154246e-10 -1.490515e-09 -1.294256e-08 [76] -1.224821e-02 -3.278657e+00 -4.620100e+01 -9.781843e+02 -1.303929e+04 [81] -5.545949e+04 -8.077540e+04 -8.577861e+04 -1.329961e+05 -1.450908e+05 [86] -3.022353e+05 -4.015776e+05 As yout can see, the eigenvalues spread very much (between e+20 and e-13). We presume, that it has something to do with R's floating point precision, which I read is about 22-digits in mantissa as default. Can this precision be set to values above 22? The problem occurs especially when trying to perform 2SLS with the 'systemfit' package. There appears always an error message like the following from the inverting routine: solve(tcross) Error in solve.default(tcross) : Lapack routine dgesv: system is exactly singular Or is there another source of error? We would like to embed R-routines in a non-commercial web application for which we need to employ 'systemfit' together with individual, user-submitted data. So the problem needs a general solution and not a special one for this particular matrix. It appears that you are using the crossproduct but not taking advantage of the symmetry. The condition number of the crossproduct is the square of the condition number of the original matrix so you are making your conditioning problems much worse by taking the crossproduct. I suggest that you use a QR or SVD decomposition of the original model matrix instead. You will still end up with a very ill-conditioned problem but now quite as bad as the one you have now. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] High resolution plots
Knut Krueger wrote: Gabor Grothendieck schrieb: On 7/13/05, Luis Tercero [EMAIL PROTECTED] wrote: Dear R-help community, would any of you have a (preferably simple) example of a presentation-quality .png plot, i.e. one that looks like the .eps plots generated by R? I am working with R 2.0.1 in WindowsXP and am having similar problems as Knut Krueger in printing high-quality plots. I have looked at the help file and examples therein as well as others I have been able to find online but to no avail. After many many tries I have to concede I cannot figure it out. I would be very grateful for your help. If you want the highest resolution use a vector format, not a bitmapped format such as png. See: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html The link is now broken, and I did not copy the hints. Does anybody knows if it its available at any other location? And I tried to find Thanks for the pointer! .wmf is far superior, I was just in the dark about the format and R's ability to produce it (An Introduction to R Device drivers does not mention it and I had obviously missed the deciding last two words in ?device 'windows') the wmf command but there is nothing to find with help.search(wmf) See ?win.metafile Uwe Ligges with regards Knut Krueger [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interpolation function
I hope you don't take offense at anything said on this list. My philosophy about this is summarized in something I wrote last December that has since been immoratlized in the fortunes package: library(fortunes) fortune(Spencer Graves) Our great-great grandchilren as yet unborn may read some of the stupid questions and/or answers that I and perhaps others give from time to time. I'd rather get flamed for saying something stupid in public on this list than to continue to provide substandard service to the people with whom I work because I perpetrated the same mistake in an environment in which no one questioned so effectively my errors. -- Spencer Graves (in a discussion on whether answers on R-help should be more polite) R-help (December 2004) Best Wishes, spencer graves Rolf Turner wrote: What you intend strikes me as being pretty silly. Do not expect R to work magic for you. Even if there were such a function as you desire in R, the results it would give would be effectively meaningless for data such as you exhibited. cheers, Rolf Turner [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help, my RGui is speaking French!
On Fri, 5 Aug 2005, Peter Dalgaard wrote:
Grathwohl, Dominik, LAUSANNE, NRC-BAS [EMAIL PROTECTED] writes:
Dear R-helpers,
First of all I have nothing against the French language!
But now my problem, yesterday I installed R 2.1.1
and I had to experience that my RGui is speaking French.
My windows locals is French (Switzerland).
I'm used to English and I want to reset my RGui to English.
I was seeking for the solution in the archives,
however not successfully.
Well, did you try the `R Installation and Administration Manual'? That
does sound appropriate and it is covered there.
By the way the searchable archives via:
http://www.r-project.org/, Mailing Lists, R-help, web-interface, searchable
achieves,
did not work: http://maths.newcastle.edu.au/~rking/R/
Also I was seeking in the FAQ's
http://cran.r-project.org/doc/FAQ/R-FAQ.html
and
http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html
and could not find the solution.
I'm sure that lots of people have queried already
and that the solution is already written down somewhere.
However I cant find it.
Could somebody give me a hint?
Make sure that the environment variable LANGUAGE is set to en. I
think the consensus is that putting it into HOME/.Renviron is the most
practical way.
The rw-FAQ recommends a different way, though.
This is a new topic in the next release of the rw-FAQ (to go with the next
release of R) since it has recently been fairly frequently asked. To wit
I selected English for Installation but R runs in Chinese!
Precisely, you selected English @strong{for installation}! The language
of the installer has nothing to do with the language used to run R: this
is completely standard Windows practice (and necessary as different
users of the computer may use different languages).
The language R uses for menus and messages is determined by the
@emph{locale}: please read the appropriate manual (the @emph{R
Installation and Administration Manual}) for the details. You can
ensure that R uses English messages by appending @code{LANGUAGE=en} to
the shortcut you use to start R.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] Installation problem on SGI IRIX6.5
[EMAIL PROTECTED] wrote: Hi, all, I'm a newbie to R. I came across a problem when I tried to install R on an SGI machine which is running IRIX64 6.5. I have successfully run configure, but when I tried to run make(or gmake), errors came out. Following is the error message. Does someone has experiences in the R's installation on IRIX ? Any hints will be greatly appreciated ! Thanks in advance! Error Message: cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include -I../../src/include -I/user_data2/jfxiao/local/include -DHAVE_CONFIG_H -OPT:IEEE_NaN_inf=ON -g -c character.c -o character.o cc-1185 cc: WARNING File = character.c, Line = 714 An enumerated type is mixed with another type. warn = warn | !utf8strIsASCII(CHAR(STRING_ELT(CAR(args), i))); ^ cc-1552 cc: WARNING File = character.c, Line = 698 The variable uclass is set but never used. int i, len, minlen, uclass; ^ cc-1020 cc: ERROR File = character.c, Line = 1300 The identifier wctrans_t is undefined. wctrans_t tr = wctrans(ul ? toupper : tolower); ^ I think the problem is here. In the GNU C Library, wctrans_t is defined in wctype.h, but on my system, wctrans_t is not defined in /usr/include/wctype.h Does anybody has successfully installed R 2.1.1 on IRIX 6.5 ? I have spent all day surfing on the net but find no helpful information. Thanks again ! 1 error detected in the compilation of character.c. gmake[3]: *** [character.o] Error 2 gmake[3]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src/main' gmake[2]: *** [R] Error 2 gmake[2]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src/main' gmake[1]: *** [R] Error 1 gmake[1]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src' gmake: *** [R] Error 1 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] High resolution plots
On Fri, 5 Aug 2005, Knut Krueger wrote: Gabor Grothendieck schrieb: On 7/13/05, Luis Tercero [EMAIL PROTECTED] wrote: Dear R-help community, would any of you have a (preferably simple) example of a presentation-quality .png plot, i.e. one that looks like the .eps plots generated by R? I am working with R 2.0.1 in WindowsXP and am having similar problems as Knut Krueger in printing high-quality plots. I have looked at the help file and examples therein as well as others I have been able to find online but to no avail. After many many tries I have to concede I cannot figure it out. I would be very grateful for your help. If you want the highest resolution use a vector format, not a bitmapped format such as png. See: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html The link is now broken, and I did not copy the hints. Does anybody knows if it its available at any other location? And I tried to find Thanks for the pointer! .wmf is far superior, I was just in the dark about the format and R's ability to produce it (An Introduction to R Device drivers does not mention it and I had obviously missed the deciding last two words in ?device 'windows') the wmf command but there is nothing to find with help.search(wmf) Searching for acronyms is not usually a good idea. Searching for `metafile' should work (on Windows). Note that R can produce Windows metafiles only on Windows, which is why it is not in `An Introduction to R'. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Discriminant analysis
At 11:59 PM 8/4/2005, C NL wrote: Hi, I'm a newbie in R and don't much aobut all the modules and their capabilities, but I'm interested in solving a problem about a discriminant analysis done with SPSS tool. The thing is that I would like to make a discrimant analysis similar to the one done with SPSS, but I can't find the way to solve it. I've been playing with R and I can handle more or less my data, the point is that I need to know what kind of discriminant analysis should I use to obtain the same results as I obtain with SPSS. Should I use qda or lda?? If not, what else could I use?? Can anybody help me to find out a light in my way? I've been searching all over the web to fetch any help or example but I couldn't get anything. I would apreciate any help greatly. If you're using R, you are not going to get SPSS results using lda or qda. You will get results comparable to SPSS, but not all the extra output. Virtually all the extra output can be obtained by taking advantage of the programming tools available to you in R. What you should do is to learn what lda is capable of doing -- read the help files in particular, read the book(s) on which lda is based (MASS - Modern Applied Statistics with S by Venables and Ripley, as well as Ripley's Pattern Recognition and Neural Networks. ) Both books - coupled with the help files and the examples - give you a pretty good sense of what you can do with lda. Study the output of an lda object to see what is in there. If you understand discriminant analysis and the computations involved, R provides all the tools to go from the lda object to most of the information that you want. However, if you are looking for statistics at the push of a button, then I suggest you stick with SPSS or SAS (or as an alternative, the commercial version of S - SPlus, which does have a very powerful discriminant routine built on the top of lda). Hope this helps. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interpolation function
On Fri, 2005-05-08 at 12:12 +, 吴 昊 wrote:
Hi,
I have a sparse matrix.I want to fill values into the entries whose value
is 0.The new generated values should come from the interpolation of the
values have existed.Does R provide such interpolation functions which
operate on Matrix, for example ,such a matrix below
0 0 0 0 2.3 0 0 0 0
0 0 3.1 0 0 0 0 1.4 0
0 0 0 0 0 0 0 0 0
1.1 0 0 0 0 0 0 0 0
0 0 0 4 0 0 0 0 6
0 0 0 0 0 0 0 0 0
0 0 0 0 0 7 0 0 0
0 3 0 0 0 0 6 0 0
0 0 0 0 9 0 0 0 0
thanks a lot
hao wu
Does this look like an answer? If anyone knows a better way please tell
me.
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==0]-mean(d.mat[,i][d.mat[,i]0])
+ }
Thanks
Tom
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Re: [R] High resolution plots
On 8/5/05, Knut Krueger [EMAIL PROTECTED] wrote: Gabor Grothendieck schrieb: On 7/13/05, Luis Tercero [EMAIL PROTECTED] wrote: Dear R-help community, would any of you have a (preferably simple) example of a presentation-quality .png plot, i.e. one that looks like the .eps plots generated by R? I am working with R 2.0.1 in WindowsXP and am having similar problems as Knut Krueger in printing high-quality plots. I have looked at the help file and examples therein as well as others I have been able to find online but to no avail. After many many tries I have to concede I cannot figure it out. I would be very grateful for your help. If you want the highest resolution use a vector format, not a bitmapped format such as png. See: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html The link is now broken, and I did not copy the hints. Does anybody knows if it its available at any other location? And I tried to find Thanks for the pointer! .wmf is far superior, I was just in the dark about the format and R's ability to produce it (An Introduction to R Device drivers does not mention it and I had obviously missed the deciding last two words in ?device 'windows') the wmf command but there is nothing to find with help.search(wmf) It seems that the links have changed so that the part of the url that reads: http:maths.newcastle.edu.au/~rking needs to be replaced with: http://tolstoy.newcastle.edu.au That is, the link has changed from: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html to: http://tolstoy.newcastle.edu.au/R/help/04/02/1168.html Alternately google for the message id, which is: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] SJava linux installation problems
Hi: I am extremely new to linux so bare with the questions. I am trying to install the SJava package for R on linux (debian). I issue the R CMD INSTALL SJava_0.68-0.tar.gz and get the following error Cannot find Java. Please set your path to include the directory in which the java executable resides, or set the environment variable JAVA_HOME before this configure script is run. I have j2sdk1.4.2_08 installed and I am assuming that the I need to set the environment variable JAVA_HOME to its path, so I did the following export JAVA_HOME=/usr/local/j2sdk1.4.2/j2sdk1.4.2_08/bin/ I get the same error as before. Can someone please help me if I am missing something? Your help will be greatly appreciated. -Dhiren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interpolation function
I don't know if what Hao wanted to do is to hang himself, but if so, perhaps here is one possible rope: idx - which(m 0, arr.ind=TRUE) m.nz - m[idx] library(akima) (m.int - interp.new(idx[,1], idx[,2], m.nz, xo=1:9, yo=1:9, extrap=TRUE)) $x [1] 1 2 3 4 5 6 7 8 9 $y [1] 1 2 3 4 5 6 7 8 9 $z [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 57.1356740 55.18522 38.413800 18.086957 2.30 0.737908 22. 544616 [2,] 18.8241001 19.35348 3.10 -20.355403 -41.610566 -51.308028 -40. 090327 [3,]3.2234619 8.63630 -5.312670 -29.221287 -53.732091 -69.487619 -67. 130408 [4,]1.100 13.75521 4.290890 -17.935507 -43.566514 -63.244671 -67. 612515 [5,]3.2013295 25.25298 22.408739 4.00 -20.615776 -42.081126 -51. 038588 [6,]0.2005624 33.62766 39.538938 27.083292 5.618185 -15.498922 -26. 910566 [7,] -17.2478151 29.37731 46.179546 41.812431 25.633428 7.00 -4. 730390 [8,] -58.4893169 3.0 32.828625 38.685475 29.928013 15.913700 6. 00 [9,] -130.5161684 -53.43667 -9.550716 8.258617 9.00 1.817369 -3. 604296 [,8] [,9] [1,] 76.7287988 170.407375 [2,] 1.400 80.913745 [3,] -37.3029968 28.876027 [4,] -47.3125835 6.953079 [5,] -38.1307000 6.00 [6,] -19.2592860 16.750369 [7,] -0.2080329 29.451691 [8,] 9.3350825 34.229953 [9,] 0.8303142 21.211142 Note how wild the interpolated/extrapolated values can be... Andy From: Adaikalavan Ramasamy I do not understand your question. If this was not a sparse matrix, then I would have asked you refer into the missing value literature. Even there, people generally remove any columns/rows that have too many missing values to avoid unreliable results. And since this is a sparse matrix, you are going to have too many missing values on all rows and columns. I could be wrong but if I am, someone will tell me that soon enough. Regards, Adai On Fri, 2005-08-05 at 12:12 +, 吴 昊 wrote: Hi, I have a sparse matrix.I want to fill values into the entries whose value is 0.The new generated values should come from the interpolation of the values have existed.Does R provide such interpolation functions which operate on Matrix, for example ,such a matrix below 0 0 0 0 2.3 0 0 0 0 0 0 3.1 0 0 0 0 1.4 0 0 0 0 0 0 0 0 0 0 1.1 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 3 0 0 0 0 6 0 0 0 0 0 0 9 0 0 0 0 thanks a lot hao wu __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] use of NA's
with NAs it's always safest to use the construction
if(is.na(foo))
rather than
if(foo==NA)
cheers Bob Kinley
tom wright [EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
05/08/2005 12:30
To
r-help@stat.math.ethz.ch
cc
Subject
[R] use of NA's
Can someone please explain why this works:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==0]-mean(d.mat[,i][d.mat[,i]0])
+ }
Whereas:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
d.mat[d.mat==0]-NA
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==NA]-mean(d.mat[,i],na.rm=TRUE)
+ }
dosnt
Thanks
Tom
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[[alternative HTML version deleted]]
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[R] use of NA's
Can someone please explain why this works:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==0]-mean(d.mat[,i][d.mat[,i]0])
+ }
Whereas:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
d.mat[d.mat==0]-NA
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==NA]-mean(d.mat[,i],na.rm=TRUE)
+ }
dosnt
Thanks
Tom
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Re: [R] use of NA's
To test for 'NA' you shouldn't use '=='. Use 'is.na()' instead.
-roger
tom wright wrote:
Can someone please explain why this works:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==0]-mean(d.mat[,i][d.mat[,i]0])
+ }
Whereas:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
d.mat[d.mat==0]-NA
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==NA]-mean(d.mat[,i],na.rm=TRUE)
+ }
dosnt
Thanks
Tom
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Re: [R] use of NA's
tom wright wrote:
Can someone please explain why this works:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==0]-mean(d.mat[,i][d.mat[,i]0])
+ }
Whereas:
d-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
d.mat[d.mat==0]-NA
for(i in 1:length(d.mat[1,])){
+ d.mat[,i][d.mat[,i]==NA]-mean(d.mat[,i],na.rm=TRUE)
+ }
dosnt
Thanks
Tom
d.mat[,i] == NA returns NA. You want ?is.na to test for missing values.
--sundar
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[R] Help, my RGui is speaking French!
Dear R-helpers, Thank you very much! Now my RGui shortcut calls R according: N:\BioAnalyticalScience\8940_InVivoEvaluation\Statistics\R\rw2011\bin\Rgui.exe --internet2 LANGUAGE=en Have a nice weekend, Dominik [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] High resolution plots
On Fri, 5 Aug 2005 22:38, Prof Brian Ripley wrote: On Fri, 5 Aug 2005, Knut Krueger wrote: Gabor Grothendieck schrieb: On 7/13/05, Luis Tercero [EMAIL PROTECTED] wrote: Dear R-help community, would any of you have a (preferably simple) example of a presentation-quality .png plot, i.e. one that looks like the .eps plots generated by R? I am working with R 2.0.1 in WindowsXP and am having similar problems as Knut Krueger in printing high-quality plots. I have looked at the help file and examples therein as well as others I have been able to find online but to no avail. After many many tries I have to concede I cannot figure it out. I would be very grateful for your help. If you want the highest resolution use a vector format, not a bitmapped format such as png. See: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html The link is now broken, and I did not copy the hints. Does anybody knows if it its available at any other location? And I tried to find Thanks for the pointer! .wmf is far superior, I was just in the dark about the format and R's ability to produce it (An Introduction to R Device drivers does not mention it and I had obviously missed the deciding last two words in ?device 'windows') the wmf command but there is nothing to find with help.search(wmf) Searching for acronyms is not usually a good idea. Searching for `metafile' should work (on Windows). Note that R can produce Windows metafiles only on Windows, which is why it is not in `An Introduction to R'. As I mentioned last month (https://stat.ethz.ch/pipermail/r-help/2005-July/074591.html) I've been able to run R under Wine and use it to produce windows metafiles. -- Cheers, RJ Cunningham __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] prediction from glm
Hugues Santin-Janin hsantin-janin at gct.org.uk writes: I try to fit birds counts over years using glm. I have done (with Estate and year as factors): Model1 - glm(Females~Estate+Year+offset = log(area)), family = quasipoisson(link = log), na.action = na.exclude) .. Pred1 - predict(Model1, type = response, na.action = na.exclude) My question is: How can I obtain predictions for Females in each year that are standardized by averaging over the levels of Estate? You should use the newdata argument in predict.glm to construct the should-be data set. The example on the page ?predict.glm creates budworm-data on the fly, but it's probably easier to understand if you create a separate data frame myfemales first, the do predict(Model1, newdata=myfemales,..) in a separate step. Dieter Menne __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] lda discriminant functions
Hi list, I'm looking about lda function. I'd like to know how calcolate the value of the discriminant functions for the original datas. I see that in the result object lda there is $scaling a matrix which transforms observations to discriminant functions, normalized so that within groups covariance matrix is spherical. I'd like to have the value of the discriminant function not normalized. Best regards Leonardo -- Leonardo Lami [EMAIL PROTECTED]www.faunalia.it Via Colombo 3 - 51010 Massa e Cozzile (PT), Italy Tel: (+39)349-1310164 GPG key @: hkp://wwwkeys.pgp.net http://www.pgp.net/wwwkeys.html https://www.biglumber.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installation problem on SGI IRIX6.5
Please do try reading the R-admin manual (as the INSTALL file asks you to:
it does not ask you to `surf on the net').
The following section may help you:
To enable UTF-8 support, configure with default @option{--enable-mbcs}.
This will check for a large number of features, notably support for the
C99/UNIX98 wide character functions and for UTF-8 or MBCS support in
X11. If enough of these are found, @code{MBCS} will be listed as one
of the ``Additional capabilities''
so try --disable-mbcs if your OS has broken header files. (It apparently
does have wctrans, but not the type it returns.)
Now we know of the existence of such an OS, we can add a check. Are
wctrans and wctrans_t defined anywhere else?
On Fri, 5 Aug 2005, Xiao Jianfeng wrote:
[EMAIL PROTECTED] wrote:
Hi, all,
I'm a newbie to R. I came across a problem when I tried to install R on
an SGI machine which is running IRIX64 6.5.
I have successfully run configure, but when I tried to run make(or
gmake), errors came out. Following is the error message.
Does someone has experiences in the R's installation on IRIX ? Any hints
will be greatly appreciated !
Thanks in advance!
Error Message:
cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre
-I. -I../../src/include -I../../src/include
-I/user_data2/jfxiao/local/include -DHAVE_CONFIG_H -OPT:IEEE_NaN_inf=ON
-g -c character.c -o character.o
cc-1185 cc: WARNING File = character.c, Line = 714
An enumerated type is mixed with another type.
warn = warn | !utf8strIsASCII(CHAR(STRING_ELT(CAR(args), i)));
^
cc-1552 cc: WARNING File = character.c, Line = 698
The variable uclass is set but never used.
int i, len, minlen, uclass;
^
cc-1020 cc: ERROR File = character.c, Line = 1300
The identifier wctrans_t is undefined.
wctrans_t tr = wctrans(ul ? toupper : tolower);
^
I think the problem is here.
In the GNU C Library, wctrans_t is defined in wctype.h, but on
my system,
wctrans_t is not defined in /usr/include/wctype.h
Does anybody has successfully installed R 2.1.1 on IRIX 6.5 ? I have
spent all
day surfing on the net but find no helpful information.
Thanks again !
1 error detected in the compilation of character.c.
gmake[3]: *** [character.o] Error 2
gmake[3]: Leaving directory
`/user_data2/jfxiao/local/source/R/R-2.1.1/src/main'
gmake[2]: *** [R] Error 2
gmake[2]: Leaving directory
`/user_data2/jfxiao/local/source/R/R-2.1.1/src/main'
gmake[1]: *** [R] Error 1
gmake[1]: Leaving directory `/user_data2/jfxiao/local/source/R/R-2.1.1/src'
gmake: *** [R] Error 1
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] lda discriminant functions
--- Leonardo Lami [EMAIL PROTECTED] wrote: Hi list, I'm looking about lda function. I'd like to know how calcolate the value of the discriminant functions for the original datas. I see that in the result object lda there is $scaling a matrix which transforms observations to discriminant functions, normalized so that within groups covariance matrix is spherical. I'd like to have the value of the discriminant function not normalized. The information you need to do this is already there, but you need to understand how to manipulate your raw data in conjunction with the lda object to calculate the result you want. If you don't understand the matrix math involved and the statistics necessary, you probably won't be successful. Suggest you read ?lda, followed by MASS, followed by Professor Ripley's Pattern Recognition and Neural Networks, followed by a any good book that shows you the matrix algebra for doing the discriminant calculations. It isn't hard to do. If you understand the math to get the individual scores, normalized or unnormalized, but just do not understand the R-way of doing things, check back again. Dr. Marc R Feldesman Professor Chair Emeritus Department of Anthropology Portland State University Portland, OR 97207 Please respond to all emails at: [EMAIL PROTECTED] Some people live and die by actuarial tables Groundhog Day __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Computing sums of the columns of an array
Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? Thanks, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
See ?colSums. Andy From: Martin C. Martin Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? Thanks, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
colSums() is a lot faster. Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin C. Martin Sent: Friday, August 05, 2005 12:17 PM To: r-help@stat.math.ethz.ch Subject: [R] Computing sums of the columns of an array Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? Thanks, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] fit non linear model using weighted least squares
Di Tanna Gian Luca GDiTanna at Regione.Emilia-Romagna.it writes: I'd like to fit a non linear model using weighted least squares. I am using the gnls function but I don't know how to perform a weighted least squares (my weights are a simple colum of data). In your case it probably would be easier to use nls (in stats) instead of gnls. There is an example using weighting on the help-page. Dieter Menne __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
Martin C. Martin wrote: Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) colSums(A) Uwe Ligges But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? Thanks, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
On 8/5/2005 12:16 PM, Martin C. Martin wrote: Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? You'd probably do better with matrix multiplication: rep(1, nrow(A)) %*% A Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SJava linux installation problems
On Fri, 5 Aug 2005, Dhiren DSouza wrote: I am extremely new to linux so bare with the questions. I am trying to install the SJava package for R on linux (debian). I issue the R CMD INSTALL SJava_0.68-0.tar.gz and get the following error Cannot find Java. Please set your path to include the directory in which the java executable resides, or set the environment variable JAVA_HOME before this configure script is run. I have j2sdk1.4.2_08 installed and I am assuming that the I need to set the environment variable JAVA_HOME to its path, so I did the following export JAVA_HOME=/usr/local/j2sdk1.4.2/j2sdk1.4.2_08/bin/ Remove '/bin/' from the environment variable path as JAVA_HOME should point to the directory containing the 'bin' subdirectory. Best practice is NOT to include the trailing slash of directory name in the value for an environment variable. -- SIGSIG -- signature too long (core dumped) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] log-logistic distribution
Hi, I need to get quantile function for log-logistic distribution. How can I do it? Thanks a lot Pete __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
On Fri, 2005-08-05 at 12:16 -0400, Martin C. Martin wrote: Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? Yes, colSums() e.g.: set.seed(1234) dat - matrix(runif(5*731), ncol = 731) system.time(for(i in 1:1000) apply(dat, 2, sum), gcFirst = TRUE) [1] 8.05 0.00 9.89 0.00 0.00 system.time(for(i in 1:1000) colSums(dat), gcFirst = TRUE) [1] 0.09 0.01 0.09 0.00 0.00 But neither is that slow on my system. What is A? HTH Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk 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. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem configuring R-patched
Martin Maechler wrote: Duncan I believe there are two kinds of tar files. The daily Duncan snapshots don't include the recommended packages, the Duncan releases do. eeehm, no: The daily snapshots do contain the recommended packages, and have for quite a while now. Duncan Or perhaps the test is a recent addition. only for a pretty generous definition of recent. To be honest, I don't know what Kevin's problem could be. The daily snapshots are really produced here at ETH Zurich and daily mirrored from here to CRAN. I can see that the R-patched_2005-08-04.tar.gz does contain the recommended packages. Maybe your download wasn't completed; your disk full; or you have a gnome in your computer who occasionally deletes some of your files? I've had similar feelings a few times in the past... Kevin Both versions were R-patched.tar.gz as opposed to the Kevin devel sets which looks like it's actually a link to Kevin the most recent. Maybe I incorrectly assumed that Kevin Maybe I incorrectly assumed that the patched tarballs Kevin contained the recommended packages. actually that was a correct assumption. Martin Maechler, ETH Zurich I still don't know why it didn't work observe (sorry for the wrapping): [EMAIL PROTECTED]:/home/src tar tvzf R-patched.tar.gz | grep Recommended drwxr-xr-x local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/ -rw-r--r-- local/local2394 2005-04-18 08:51:32 R-patched/src/library/Recommended/Makefile.in -rw-r--r-- local/local 20 2005-04-18 08:51:32 R-patched/src/library/Recommended/.cvsignore -rw-r--r-- local/local 25656 2005-04-18 08:58:17 R-patched/src/library/Recommended/KernSmooth_2.22-15.tar.gz -rw-r--r-- local/local 465529 2005-07-28 11:45:14 R-patched/src/library/Recommended/VR_7.2-17.tar.gz -rw-r--r-- local/local 179895 2005-07-28 11:45:14 R-patched/src/library/Recommended/boot_1.2-23.tar.gz -rw-r--r-- local/local 190975 2005-07-03 11:45:11 R-patched/src/library/Recommended/cluster_1.10.1.tar.gz -rw-r--r-- local/local 273520 2005-07-14 11:45:08 R-patched/src/library/Recommended/foreign_0.8-9.tar.gz -rw-r--r-- local/local 205131 2005-07-27 11:45:14 R-patched/src/library/Recommended/lattice_0.12-1.tar.gz -rw-r--r-- local/local 240276 2005-07-12 11:46:13 R-patched/src/library/Recommended/mgcv_1.3-4.tar.gz -rw-r--r-- local/local 662143 2005-07-26 11:45:13 R-patched/src/library/Recommended/nlme_3.1-62.tar.gz -rw-r--r-- local/local 110072 2005-04-19 11:45:20 R-patched/src/library/Recommended/rpart_3.1-23.tar.gz -rw-r--r-- local/local 846737 2005-06-10 11:45:23 R-patched/src/library/Recommended/survival_2.18.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/VR.tgz - VR_7.2-17.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/boot.tgz - boot_1.2-23.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/cluster.tgz - cluster_1.10.1.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/foreign.tgz - foreign_0.8-9.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/KernSmooth.tgz - KernSmooth_2.22-15.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/lattice.tgz - lattice_0.12-1.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/nlme.tgz - nlme_3.1-62.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/mgcv.tgz - mgcv_1.3-4.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/rpart.tgz - rpart_3.1-23.tar.gz lrwxrwxrwx local/local 0 2005-08-03 20:45:50 R-patched/src/library/Recommended/survival.tgz - survival_2.18.tar.gz It appears to me that the recommended packages were in the tarball. I suppose it is largely immaterial now given I have successfully re-built R. Thanks your help. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Department of Public Health Sciences Faculty of Medicine, University of Toronto email: [EMAIL PROTECTED] Tel: 416.946.8081 Fax: 416.971.2462 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
Duncan Murdoch wrote: On 8/5/2005 12:16 PM, Martin C. Martin wrote: Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? You'd probably do better with matrix multiplication: rep(1, nrow(A)) %*% A No, better use colSums(), which has been optimized for this purpose: A - matrix(seq(1, 1000), ncol=1) system.time(colSums(A)) # ~ 0.1 sec. system.time(rep(1, nrow(A)) %*% A) # ~ 0.5 sec. Uwe Ligges Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] log-logistic distribution
On Fri, 5 Aug 2005, Petr Mandys wrote: I need to get quantile function for log-logistic distribution. How can I do it? From the quantile function qlogis for the logistic: X is log-logistic iff log(X) is logistic. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] heatmap row names as char vector?
Hi All, Could anyone help me on how to output the row names of a heatmap as a character vector? I'm looking for a way to have the names in a list (or similar) in the same order as they appear in the clustering of the heatmap. Thanks in advance, Jake __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] contrast {Design} question
All, I have been trying to get the following code to work: A.quantiles - quantile(foo.frame$A, probs = seq(from = 0.05, to = 0.95, by = 0.05)) base.quantiles - quantile(Efficacy205$BASELINE_RANK, probs = seq(from = 0.05, to = 0.95, by = 0.05)) gender - levels(Efficacy205$GENDER) contrast.1 - contrast(Model.1, list(TPCODE= 'A', AGE = age.quantiles, BASELINE_RANK = base.quantiles, GENDER = gender), list(TPCODE = 'D', AGE = age.quantiles, BASELINE_RANK = base.quantiles, GENDER = gender), type = 'average', weights = table(gender)) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] contrast {Design} question
Sorry about the previous email, hadn't finished editing yet Here is some code that I have been trying to get to work: A.quant - quantile(foo.frame$A, probs=seq(from=0.05, to=0.95, by=0.05)) B.quant - quantile(foo.frame$B, probs=seq(from=0.05, to=0.95, by=0.05)) gender - levels(foo.frame$GENDER) contrast.1 - contrast(Model.1, list(TREAT= 'A', A= A.quant, B = B.quant, GENDER = gender), list(TREAT= 'D', A= A.quant, B = B.quant, GENDER = gender), type = 'average', weights = table(gender)) My goal is to obtain a set of average Type II contrasts over the levels of GENDER, but not over the levels of A and B. R keeps telling me that weights needs to be 722 elements, but this is the total number of contrasts over all levels of A, B, and GENDER Any suggestions would be greatly appreciated, Greg __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] calculate likelihood based on logit regression
Hi, I just ran the following logit regression. But can anyone tell me how to calculate how much more likely males (Male=1) could show such symptom than females(Male=0)? I know it must be simple to get once I have the coefficients, but I just don't recall. Thank you very much! Call: glm(formula = Symptoms ~ 1 + Male, family = binomial(link = logit), data = HA) Deviance Residuals: Min 1Q Median 3Q Max -6.038e+03 -2.067e-06 0.000e+00 0.000e+00 6.720e+03 Coefficients: Estimate Std. Errorz value Pr(|z|) (Intercept) 5.711e+00 8.466e-02 6.746e+01 2e-16 *** Male-6.493e+00 8.540e-02 -7.603e+01 2e-16 *** Best, Ed __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
Thanks everyone. Gavin Simpson wrote: But neither is that slow on my system. What is A? It's in the middle of a loop. I'm doing some maximum likelihood estimation, and having to evaluate my model over and over again for different parameter values. Thanks, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Computing sums of the columns of an array
Duncan Murdoch wrote: On 8/5/2005 12:43 PM, Uwe Ligges wrote: Duncan Murdoch wrote: On 8/5/2005 12:16 PM, Martin C. Martin wrote: Hi, I have a 5x731 array A, and I want to compute the sums of the columns. Currently I do: apply(A, 2, sum) But it turns out, this is slow: 70% of my CPU time is spent here, even though there are many complicated steps in my computation. Is there a faster way? You'd probably do better with matrix multiplication: rep(1, nrow(A)) %*% A No, better use colSums(), which has been optimized for this purpose: A - matrix(seq(1, 1000), ncol=1) system.time(colSums(A)) # ~ 0.1 sec. system.time(rep(1, nrow(A)) %*% A) # ~ 0.5 sec. I didn't claim my solution was the best, only better. :-) One point of interest: I think your example exaggerates the difference by using a matrix of integers. On my machine I get a ratio something like yours with the same example A - matrix(seq(1, 1000), ncol=1) system.time(colSums(A)) [1] 0.08 0.00 0.08 NA NA system.time(rep(1, nrow(A)) %*% A) [1] 0.25 0.01 0.23 NA NA but if I make A floating point, there's much less difference: A - matrix(as.numeric(seq(1, 1000)), ncol=1) system.time(colSums(A)) [1] 0.09 0.00 0.09 NA NA On my machine: [1] 0.12 0.00 0.12 NA NA system.time(rep(1, nrow(A)) %*% A) [1] 0.11 0.00 0.12 NA NA On my machine: [1] 0.32 0.00 0.32 NA NA Hence still a bigger factor both with R-2.1.1 release (standard BLAS; gcc-3.4.2, WinNT4.0, Athlon XP with real freq. of 1667MHz, 1Gb). And still a bigger factor (0.09 vs. 0.21) on a Xeon 3.06Ghz with 2Gb. Are you using Goto's BLAS (for me, your performance is still not achievable with ATLAS)? Best, Uwe Still, colSums is the winner in both cases. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Explaining timings (was Computing sums of the columns of an array)
On Fri, 5 Aug 2005, Liaw, Andy wrote: A - matrix(runif(5 * 731), 5) system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 5.28 0.13 5.46 NA NA system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 1.99 0.20 2.22 NA NA system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 1.97 0.25 2.28 NA NA system.time(replicate(1e4, rep(1, nrow(A)) %*% A), gcFirst=TRUE) [1] 1.90 0.20 2.16 NA NA system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.53 0.22 1.75 NA NA system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.53 0.19 1.72 NA NA system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.51 0.19 1.70 NA NA system.time(replicate(1e4, colSums(A)), gcFirst=TRUE) [1] 1.49 0.25 1.79 NA NA However, I don't understand why the first try took so much longer. I've explained that to someone else earlier in the week. You need to get R's internal gc limits tuned up to match the task in hand, and on the first run it will often gc frequently. I got 90 GCs the first time, 9 the second and eventually about 7. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] calculate likelihood based on logit regression
I think males are z times more likely to show such symptom, where: z=(1+exp(6.493-5.711))/(1+exp(-5.711)) Is this right? Thanks! Ed. --- Haibo Huang [EMAIL PROTECTED] wrote: Hi, I just ran the following logit regression. But can anyone tell me how to calculate how much more likely males (Male=1) could show such symptom than females(Male=0)? I know it must be simple to get once I have the coefficients, but I just don't recall. Thank you very much! Call: glm(formula = Symptoms ~ 1 + Male, family = binomial(link = logit), data = HA) Deviance Residuals: Min 1Q Median 3Q Max -6.038e+03 -2.067e-06 0.000e+00 0.000e+00 6.720e+03 Coefficients: Estimate Std. Errorz value Pr(|z|) (Intercept) 5.711e+00 8.466e-02 6.746e+01 2e-16 *** Male-6.493e+00 8.540e-02 -7.603e+01 2e-16 *** Best, Ed __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Technical Support Engineer for R/S and Bioconductor
__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Technical Support Engineer for R/S and Bioconductor
__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Statistical significance of a classifier
From: Martin C. Martin Hi, I have a bunch of data points x from two classes A B, and I'm creating a classifier. So I have a function f(x) which estimates the probability that x is in class A. (I have an equal number of examples of each, so p(class) = 0.5.) One way of seeing how well this does is to compute the error rate on the test set, i.e. if f(x)0.5 call it A, and see how many times I misclassify an item. That's what MASS does. But we should Surely you mean `99% of dataminers/machine learners' rather than `MASS'? be able to do better: misclassifying should be more of a problem if the regression is confident then if it isn't. How can I show that my f(x) = P(x is in class A) does better than chance? It depends on what you mean by `better'. For some problem, people are perfectly happy with misclassifcation rate. For others, the estimated probabilities count a lot more. One possibility is to look at the ROC curve. Another possibility is to look at the calibration curve (see MASS the book). Andy Thanks, Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] question regarding logit regression using glm
I got the following warning messages when I did a binomial logit regression using glm(): Warning messages: 1: Algorithm did not converge in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, 2: fitted probabilities numerically 0 or 1 occurred in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, Can some one share your thoughts on how to solve this problem? Please read the following for details. Thank you very much! Best, Ed Lease=read.csv(lease.csv, header=TRUE) Lease$ET = factor(Lease$EarlyTermination) SICCode=factor(Lease$SIC.Code) TO=factor(Lease$TenantHasOption) LO=factor(Lease$LandlordHasOption) TEO=factor(Lease$TenantExercisedOption) RegA=glm(ET~1+MSA, + family=binomial(link=logit), data=Lease, weights=Origil.SQFT) Warning messages: 1: Algorithm did not converge in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, 2: fitted probabilities numerically 0 or 1 occurred in: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart, summary(RegA) Call: glm(formula = ET ~ 1 + MSA, family = binomial(link = logit), data = Lease, weights = Origil.SQFT) Deviance Residuals: Min 1Q Median 3Q Max -6.038e+03 -2.066e-06 0.000e+00 0.000e+00 6.720e+03 Coefficients: Estimate Std. Errorz value Pr(|z|) (Intercept) 5.711e+00 8.466e-02 6.745e+01 2e-16 *** MSAAnchorage-6.493e+00 8.541e-02 -7.602e+01 2e-16 *** MSAAtlanta 6.894e+14 2.310e+04 2.985e+10 2e-16 *** MSAAustin -9.362e+14 4.954e+04 -1.890e+10 2e-16 *** MSABoston -2.474e+15 2.151e+04 -1.150e+11 2e-16 *** MSACharlotte-2.150e+15 7.265e+04 -2.960e+10 2e-16 *** MSAChicago -1.174e+15 2.057e+04 -5.707e+10 2e-16 *** MSACleveland-7.607e+14 7.046e+04 -1.080e+10 2e-16 *** MSAColumbus -2.768e+15 1.685e+05 -1.642e+10 2e-16 *** MSADallas2.061e+14 3.261e+04 6.321e+09 2e-16 *** MSADenver5.470e+14 3.366e+04 1.625e+10 2e-16 *** MSAEast Bay -6.191e+01 1.344e+05 -4.61e-04 1 MSAFt. Worth-6.565e+00 8.483e-02 -7.739e+01 2e-16 *** MSAHouston -2.735e+15 3.576e+04 -7.648e+10 2e-16 *** MSAIndianapolis -7.483e+14 6.588e+04 -1.136e+10 2e-16 *** MSALos Angeles -1.388e+15 2.887e+04 -4.809e+10 2e-16 *** MSAMinneapolis -1.011e+15 2.731e+04 -3.702e+10 2e-16 *** MSANashville 2.143e+01 9.395e+04 2.28e-04 1 MSANew Orleans -3.370e+15 5.038e+04 -6.689e+10 2e-16 *** MSANew York -2.526e+15 2.969e+04 -8.507e+10 2e-16 *** MSANorfolk -5.614e+01 2.020e+06 -2.78e-05 1 MSAOakland-East Bay -2.272e+15 3.642e+04 -6.239e+10 2e-16 *** MSAOrange County-5.165e+14 2.428e+04 -2.128e+10 2e-16 *** MSAOrlando -3.215e+15 1.096e+05 -2.933e+10 2e-16 *** MSAPhiladelphia -8.871e+14 4.948e+04 -1.793e+10 2e-16 *** MSAPhoenix -1.156e+01 8.807e-02 -1.313e+02 2e-16 *** MSAPortland 7.604e+14 3.841e+04 1.980e+10 2e-16 *** MSARaleigh-Durham -4.312e+01 1.294e+05 -3.33e-04 1 MSARiverside 1.626e+15 4.645e+05 3.500e+09 2e-16 *** MSASacramento -9.873e+14 5.345e+04 -1.847e+10 2e-16 *** MSASalt Lake City1.793e+15 2.029e+05 8.839e+09 2e-16 *** MSASan Antonio 9.451e+14 9.473e+04 9.977e+09 2e-16 *** MSASan Diego-3.740e+15 6.651e+04 -5.623e+10 2e-16 *** MSASan Francisco 3.109e+14 2.394e+04 1.299e+10 2e-16 *** MSASan Jose 7.392e+14 2.961e+04 2.497e+10 2e-16 *** MSASeattle -2.250e+15 1.581e+04 -1.423e+11 2e-16 *** MSASt. Louis-2.606e+15 1.801e+05 -1.447e+10 2e-16 *** MSAStamford -6.592e+00 8.469e-02 -7.784e+01 2e-16 *** MSAWashington DC 8.460e+13 3.319e+04 2.549e+09 2e-16 *** MSAWest Palm Beach -3.924e+01 2.308e+05 -1.70e-04 1 --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 123111026 on 9302 degrees of freedom Residual deviance: 3028559052 on 9263 degrees of freedom AIC: 3028559132 Number of Fisher Scoring iterations: 25 anova(RegA) Analysis of Deviance Table Model: binomial, link: logit Response: ET Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev NULL 9302 123111026 MSA39 0 9263 3028559052 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] make error: X11/Intrinsic.h: No such,,,
I had the same problem with my ubuntu machine. A search for a Debian package that includes the header file Intrinsic.h at http://www.debian.org/distrib/packages (with stable distribution and Intel x86 architecture) turned up libdevel/libxt-dev package. I installed libxt-dev package (with the synaptic package manager) and was able to compile. Hope this helps. tak __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] code for gap statistic
Hi, Can anyone point me to code for the gap statistic? Many thanks and best wishes! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] make error: X11/Intrinsic.h: No such,,,
Thanks for the help -- this morning someone (on the Ubuntu boards) was kind enough to point this out to me. Now if there were only a decent Linux front end/gui for R... Thanks, Jake On Fri, 2005-08-05 at 13:17 -0700, Tak Ishikida wrote: I had the same problem with my ubuntu machine. A search for a Debian package that includes the header file Intrinsic.h at http://www.debian.org/distrib/packages (with stable distribution and Intel x86 architecture) turned up libdevel/libxt-dev package. I installed libxt-dev package (with the synaptic package manager) and was able to compile. Hope this helps. tak __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] use of color for hclust
Hi, I have a grouping of some observations. I want to cluster them using hierarchical clustering and compare how the hierarchical clustering shows up vis-a-vis the groupings. Is it possible to do this in color? I guess what I am looking for is a way to color the labels of a hierarchical clustering plot using different colors according to the original grouping. Any suggestions? Many thanks and best wishes! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Statistical significance of a classifier
Liaw, Andy wrote: From: Martin C. Martin Hi, I have a bunch of data points x from two classes A B, and I'm creating a classifier. So I have a function f(x) which estimates the probability that x is in class A. (I have an equal number of examples of each, so p(class) = 0.5.) One way of seeing how well this does is to compute the error rate on the test set, i.e. if f(x)0.5 call it A, and see how many times I misclassify an item. That's what MASS does. But we should Surely you mean `99% of dataminers/machine learners' rather than `MASS'? That was my impression, but I didn't want to presume to speak for most dataminers/machine learners. be able to do better: misclassifying should be more of a problem if the regression is confident then if it isn't. How can I show that my f(x) = P(x is in class A) does better than chance? It depends on what you mean by `better'. For some problem, people are perfectly happy with misclassifcation rate. For others, the estimated probabilities count a lot more. One possibility is to look at the ROC curve. Another possibility is to look at the calibration curve (see MASS the book). Thanks, those are getting closer to what I want. I think the bottom line is that I can't really assign a p-value the way I want to, since the problem I'm thinking of is ill-posed. Thanks, Martin [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] GAP pointer
I am trying to do a simple segregation analysis using the GAP package. I have the documentation for pointer but I desperately need an example so that I can see how to format the datfile and the jobfile. For each individual, I have FamilyId, SubjectId, FatherId, MotherId, and AffectedStatus (0/1). I would like to obtain the likelihood ratio statistic for transmission. I would greatly appreciate any help on this subject. Best to all, Julia Reid __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Latex error with Sweave example
I created a tex file following the example in the Sweave help which
produced the following files in my working directory.
Sweave-test-1-006.eps
Sweave-test-1-006.pdf
Sweave-test-1-007.eps
Sweave-test-1-007.pdf
Sweave-test-1.tex
When I run latex on this, I get a latex error, log file below. I am
running R 2.1.1 on Windows XP. I have installed small MiKTeX and I
have added C:\Program Files\R\rw2011\share\texmf to the roots of
MiKTex. The MiKTeX test ran fine after I installed it.
Any tips would be most appreciated.
This is e-TeX, Version 3.141592-2.2 (MiKTeX 2.4) (preloaded format=latex
2005.8.5) 6 AUG 2005 09:28
entering extended mode
**Sweave-test-1
(Sweave-test-1.tex
LaTeX2e 2003/12/01
Babel v3.8a and hyphenation patterns for english, french, german,
ngerman, du
mylang, nohyphenation, loaded.
(C:\usr\texmf\tex\latex\base\article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(C:\usr\texmf\tex\latex\base\size10.clo
File: size10.clo 2004/02/16 v1.4f Standard LaTeX file (size option)
)
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(C:\usr\texmf\tex\latex\ltxmisc\a4wide.sty
Package: a4wide 1994/08/30
(C:\usr\texmf\tex\latex\ntgclass\a4.sty
Package: a4 1999/03/03 v1.2f A4 based page layout
))
! Missing \endcsname inserted.
to be read again
\protect
l.11 \begin
{document}
?
! Emergency stop.
to be read again
\protect
l.11 \begin
{document}
End of file on the terminal!
Here is how much of TeX's memory you used:
223 strings out of 95898
2212 string characters out of 1195177
46816 words of memory out of 1050593
3336 multiletter control sequences out of 35000
3640 words of font info for 14 fonts, out of 50 for 1000
14 hyphenation exceptions out of 607
23i,0n,17p,117b,36s stack positions out of 1500i,500n,5000p,20b,32768s
No pages of output.
\documentclass[a4paper]{article}
\title{A Test File}
\author{Friedrich Leisch}
\usepackage{a4wide}
\usepackage{C:/PROGRA~1/R/rw2011/share/texmf/Sweave}
\begin{document}
\maketitle
A simple example that will run in any S engine: The integers from 1 to
10 are
\begin{Schunk}
\begin{Soutput}
[1] 1 2 3 4 5 6 7 8 9 10
\end{Soutput}
\end{Schunk}
We can also emulate a simple calculator:
\begin{Schunk}
\begin{Sinput}
1 + 1
\end{Sinput}
\begin{Soutput}
[1] 2
\end{Soutput}
\begin{Sinput}
1 + pi
\end{Sinput}
\begin{Soutput}
[1] 4.141593
\end{Soutput}
\begin{Sinput}
sin(pi/2)
\end{Sinput}
\begin{Soutput}
[1] 1
\end{Soutput}
\end{Schunk}
Now we look at Gaussian data:
\begin{Schunk}
\begin{Soutput}
[1] 1.0549825921 1.0338743287 1.3960748544 0.8442504660 -1.3844903806
[6] -0.1132289262 0.0340332855 0.0002775862 -1.0397650922 0.4255640780
[11] -0.0101131650 -0.9338368343 -0.8404841222 0.1815343256 -0.0655929025
[16] -0.6401327742 0.2787653149 -0.0940385332 -0.6531716561 -0.8501837369
\end{Soutput}
\begin{Soutput}
One Sample t-test
data: x
t = -0.4006, df = 19, p-value = 0.6932
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
-0.4281708 0.2906027
sample estimates:
mean of x
-0.06878406
\end{Soutput}
\end{Schunk}
Note that we can easily integrate some numbers into standard text: The
third element of vector \texttt{x} is 1.39607485443702, the
$p$-value of the test is 0.69319. % $
Now we look at a summary of the famous iris data set, and we want to
see the commands in the code chunks. Note that the summary needs to
be \texttt{print()}ed explicitly, because eval would discard it otherwise. I
consider this a feature, because it allows for much finer control on
what gets into the final report.
% the following code is R-specific, as data(iris) will not run in Splus.
% Hence, we mark it as R code.
\begin{Schunk}
\begin{Sinput}
data(iris)
print(summary(iris))
\end{Sinput}
\begin{Soutput}
Sepal.LengthSepal.Width Petal.LengthPetal.Width
Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100
1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300
Median :5.800 Median :3.000 Median :4.350 Median :1.300
Mean :5.843 Mean :3.057 Mean :3.758 Mean :1.199
3rd Qu.:6.400 3rd Qu.:3.300 3rd Qu.:5.100 3rd Qu.:1.800
Max. :7.900 Max. :4.400 Max. :6.900 Max. :2.500
Species
setosa:50
versicolor:50
virginica :50
\end{Soutput}
\end{Schunk}
\begin{figure}[htbp]
\begin{center}
\begin{Schunk}
\begin{Sinput}
library(graphics)
pairs(iris)
\end{Sinput}
\end{Schunk}
\includegraphics{Sweave-test-1-006}
\caption{Pairs plot of the iris data.}
\end{center}
\end{figure}
\begin{figure}[htbp]
\begin{center}
\begin{Schunk}
\begin{Sinput}
boxplot(Sepal.Length ~ Species, data = iris)
\end{Sinput}
\end{Schunk}
[R] code for metric / nonmetric MDS
This does metric/nonmetric weighted least squares multidimensional scaling using the smacof algorithm (deleeuw, 1977, in barra et al (eds), recent developments in statistics; or deleeuw and heiser, 1980, in krishnaiah (ed), multivariate analysis V). Uses a dist object for both dissimilarities and weights, which should both be non-negative for convergence. Fits euclidean distances only. Monotone regression is done by pool-adjacent-violators, implemented in pava.R. The pava function can actually do monotone regression using weighted means, medians, or p-fractiles -- although for mds only means are used. Somebody asked for this and it may be useful to others. It is not written for efficiency, but the flexibility of allowing weights can be handy. By using relaxed smacof updates (see deleeuw and heiser or the book by borg and groenen) we can make this about twice as fast -- but that will come later. Feel free to tinker away. == Jan de Leeuw, 11667 Steinhoff Rd, Frazier Park, CA 93225, 661-245-1725 == Und die Einen sind im Dunkeln Und die Andern sind im Licht Und man siehe die im Lichte Die im Dunklen sieht man nicht Brecht __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
This does metric/nonmetric weighted least squares multidimensional scaling using the smacof algorithm (deleeuw, 1977, in barra et al (eds), recent developments in statistics; or deleeuw and heiser, 1980, in krishnaiah (ed), multivariate analysis V). Uses a dist object for both dissimilarities and weights, which should both be non-negative for convergence. Fits euclidean distances only. Monotone regression is done by pool-adjacent-violators, implemented in pava.R. The pava function can actually do monotone regression using weighted means, medians, or p-fractiles -- although for mds only means are used. Somebody asked for this and it may be useful to others. It is not written for efficiency, but the flexibility of allowing weights can be handy. By using relaxed smacof updates (see deleeuw and heiser or the book by borg and groenen) we can make this about twice as fast -- but that will come later. Feel free to tinker away. === Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: [EMAIL PROTECTED] .mac: jdeleeuw ++ aim: deleeuwjan ++ skype: j_deleeuw homepages: http://gifi.stat.ucla.edu ++ http://www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au - __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Latex error with Sweave example
sosman wrote:
I created a tex file following the example in the Sweave help which
produced the following files in my working directory.
Sweave-test-1-006.eps
Sweave-test-1-006.pdf
Sweave-test-1-007.eps
Sweave-test-1-007.pdf
Sweave-test-1.tex
When I run latex on this, I get a latex error, log file below. I am
running R 2.1.1 on Windows XP. I have installed small MiKTeX and I
have added C:\Program Files\R\rw2011\share\texmf to the roots of
MiKTex. The MiKTeX test ran fine after I installed it.
Any tips would be most appreciated.
I think you need to ask on one of the Miktex lists. My guess would be
that your problem is caused by using e-TeX, but I couldn't say for sure.
Certainly the error is occurring entirely within MikTeX packages; you
haven't got to the R stuff yet.
My web page
http://www.murdoch-sutherland.com/Rtools/miktex.html
is getting kind of old, but it does tell you how to avoid using e-TeX.
Duncan Murdoch
This is e-TeX, Version 3.141592-2.2 (MiKTeX 2.4) (preloaded format=latex
2005.8.5) 6 AUG 2005 09:28
entering extended mode
**Sweave-test-1
(Sweave-test-1.tex
LaTeX2e 2003/12/01
Babel v3.8a and hyphenation patterns for english, french, german,
ngerman, du
mylang, nohyphenation, loaded.
(C:\usr\texmf\tex\latex\base\article.cls
Document Class: article 2004/02/16 v1.4f Standard LaTeX document class
(C:\usr\texmf\tex\latex\base\size10.clo
File: size10.clo 2004/02/16 v1.4f Standard LaTeX file (size option)
)
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
)
(C:\usr\texmf\tex\latex\ltxmisc\a4wide.sty
Package: a4wide 1994/08/30
(C:\usr\texmf\tex\latex\ntgclass\a4.sty
Package: a4 1999/03/03 v1.2f A4 based page layout
))
! Missing \endcsname inserted.
to be read again
\protect
l.11 \begin
{document}
?
! Emergency stop.
to be read again
\protect
l.11 \begin
{document}
End of file on the terminal!
Here is how much of TeX's memory you used:
223 strings out of 95898
2212 string characters out of 1195177
46816 words of memory out of 1050593
3336 multiletter control sequences out of 35000
3640 words of font info for 14 fonts, out of 50 for 1000
14 hyphenation exceptions out of 607
23i,0n,17p,117b,36s stack positions out of 1500i,500n,5000p,20b,32768s
No pages of output.
\documentclass[a4paper]{article}
\title{A Test File}
\author{Friedrich Leisch}
\usepackage{a4wide}
\usepackage{C:/PROGRA~1/R/rw2011/share/texmf/Sweave}
\begin{document}
\maketitle
A simple example that will run in any S engine: The integers from 1 to
10 are
\begin{Schunk}
\begin{Soutput}
[1] 1 2 3 4 5 6 7 8 9 10
\end{Soutput}
\end{Schunk}
We can also emulate a simple calculator:
\begin{Schunk}
\begin{Sinput}
1 + 1
\end{Sinput}
\begin{Soutput}
[1] 2
\end{Soutput}
\begin{Sinput}
1 + pi
\end{Sinput}
\begin{Soutput}
[1] 4.141593
\end{Soutput}
\begin{Sinput}
sin(pi/2)
\end{Sinput}
\begin{Soutput}
[1] 1
\end{Soutput}
\end{Schunk}
Now we look at Gaussian data:
\begin{Schunk}
\begin{Soutput}
[1] 1.0549825921 1.0338743287 1.3960748544 0.8442504660 -1.3844903806
[6] -0.1132289262 0.0340332855 0.0002775862 -1.0397650922 0.4255640780
[11] -0.0101131650 -0.9338368343 -0.8404841222 0.1815343256 -0.0655929025
[16] -0.6401327742 0.2787653149 -0.0940385332 -0.6531716561 -0.8501837369
\end{Soutput}
\begin{Soutput}
One Sample t-test
data: x
t = -0.4006, df = 19, p-value = 0.6932
alternative hypothesis: true mean is not equal to 0
95 percent confidence interval:
-0.4281708 0.2906027
sample estimates:
mean of x
-0.06878406
\end{Soutput}
\end{Schunk}
Note that we can easily integrate some numbers into standard text: The
third element of vector \texttt{x} is 1.39607485443702, the
$p$-value of the test is 0.69319. % $
Now we look at a summary of the famous iris data set, and we want to
see the commands in the code chunks. Note that the summary needs to
be \texttt{print()}ed explicitly, because eval would discard it otherwise. I
consider this a feature, because it allows for much finer control on
what gets into the final report.
% the following code is R-specific, as data(iris) will not run in Splus.
% Hence, we mark it as R code.
\begin{Schunk}
\begin{Sinput}
data(iris)
print(summary(iris))
\end{Sinput}
\begin{Soutput}
Sepal.LengthSepal.Width Petal.LengthPetal.Width
Min. :4.300 Min. :2.000 Min. :1.000 Min. :0.100
1st Qu.:5.100 1st Qu.:2.800 1st Qu.:1.600 1st Qu.:0.300
Median :5.800 Median :3.000 Median :4.350 Median :1.300
Mean
[R] [R-pkgs] new version of lattice
[This is more a warning than an announcement] A new version of lattice should be soon on CRAN. From this version onwards, all high-level lattice functions are (S3) generic. All of them have formula methods, some have other methods as well, formalizing the various non-formula uses which used to be handled by clumsy hacks in the past. There's also a new table method for barchart. Ideally, this change should be completely transparent to the user and no existing code should break (except undocumented and inappropriate examples like dotplot( x | a ) which used to work like dotplot(~x | a) before). However, Murphy's law usually prevails, so... Deepayan ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] oldClass vs. class
Hi,When I read the source of str,i find these code - ## Show further classes // Assume that they do NOT have an own Method -- ## not quite perfect ! (.Class = 'remaining classes', starting with current) cl - oldClass(object); cl - cl[cl != data.frame] #- not THIS class - so I use ?oldClass to try to learn more about oldClass.But after I have reading all the help page ,I still have no idea the diiference between oldClass and class. Anynone can help me ? 2005-08-06 -- Deparment of Sociology Fudan University Blog:http://sociology.yculblog.com __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] High resolution plots
On 8/5/05, Gabor Grothendieck [EMAIL PROTECTED] wrote: On 8/5/05, Knut Krueger [EMAIL PROTECTED] wrote: Gabor Grothendieck schrieb: On 7/13/05, Luis Tercero [EMAIL PROTECTED] wrote: Dear R-help community, would any of you have a (preferably simple) example of a presentation-quality .png plot, i.e. one that looks like the .eps plots generated by R? I am working with R 2.0.1 in WindowsXP and am having similar problems as Knut Krueger in printing high-quality plots. I have looked at the help file and examples therein as well as others I have been able to find online but to no avail. After many many tries I have to concede I cannot figure it out. I would be very grateful for your help. If you want the highest resolution use a vector format, not a bitmapped format such as png. See: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html The link is now broken, and I did not copy the hints. Does anybody knows if it its available at any other location? And I tried to find Thanks for the pointer! .wmf is far superior, I was just in the dark about the format and R's ability to produce it (An Introduction to R Device drivers does not mention it and I had obviously missed the deciding last two words in ?device 'windows') the wmf command but there is nothing to find with help.search(wmf) It seems that the links have changed so that the part of the url that reads: http:maths.newcastle.edu.au/~rking needs to be replaced with: http://tolstoy.newcastle.edu.au That is, the link has changed from: http://maths.newcastle.edu.au/~rking/R/help/04/02/1168.html to: http://tolstoy.newcastle.edu.au/R/help/04/02/1168.html Alternately google for the message id, which is: [EMAIL PROTECTED] There is a useful summary of differences between bitmapped and vector graphics at: http://www.stc-saz.org/resources/0203_graphics.pdf __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
