Re: [R] Error producing density curve
2008/8/27 Nicky Chorley [EMAIL PROTECTED]: 2008/8/27 rr400 [EMAIL PROTECTED]: Hi, i have never really used R before and i need to produce a density curve for use in an assignment. Following the instructions in the manual provided with my course i keep getting this error message: Error in plot.xy(xy, type, ...) : invalid plot type '1' The commands i have entered are: x=seq(0, 1800, 10) x f=dnorm(x, 1454.190, 162.6301) f plot(x,f,type='1') It's probably a lowercase L, not a 1 (to plot lines rather than points). For more information about plot, see the man page: ? plot Regards, Nicky Chorley __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting 1-D array to vector
You were very close to an answer : as.vector(unlist(df[1,])) Nael On Wed, Aug 27, 2008 at 7:53 AM, Ronnen Levinson [EMAIL PROTECTED] wrote: Hi. How do I convert a one-dimensional array of characters to a character vector? In the example below I am trying to get the result c(a,d). The function as.vector() returns the same one-dimensional array, and unlist() returns something more complicated than I seek. Yours truly, Ronnen. P.S. E-mailed CCs of posted replies appreciated. df=data.frame(x=letters[1:3],y=letters[4:6]) df x y 1 a d 2 b e 3 c f df[1,] x y 1 a d as.vector(df[1,]) x y 1 a d unlist(df[1,]) x y a d Levels: a b c d e f c(a,d) # desired result [1] a d version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 7.0 year 2008 month 04 day22 svn rev45424 language R version.string R version 2.7.0 (2008-04-22) -- Ronnen Levinson, Ph.D. scientist, Lawrence Berkeley National Lab The Onion horoscope: Libra September 23 - October 23 Your tactics of overwhelming your opposition with spectacular shows of force and choking the roads with fleeing refugees will be seen as inappropriate by the other electronics wholesalers. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] loop with splitted data -solved
Thank you for the hints, finally I was looking for the substitution of splitted$2 to splitted[[as.character(counter)]] I did not know that I can substitute f.e the $2 with [[2]] or/and $y (second column) with [[2]] Knut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Variance-covariance matrix
Hi all, Sorry to ask again but I'm still not sure how to get the full variance-covariance matrix. Peter suggested a three-level treatment factor. However, I thought that the censoring variable could only take values 0 or 1 so how do you programme such a factor. Alternatively, is there another way to produce the required covariance? Thank you, Laura On Tue, Aug 26, 2008 at 11:37 AM, Laura Bonnett [EMAIL PROTECTED]wrote: The standard treatment is the same in both comparison. How do you do a three-level treatment factor? I thought you had to have a censoring indicator which took values 0 or 1 not 1, 2 or 3? Thanks, Laura On Tue, Aug 26, 2008 at 11:05 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Laura Bonnett wrote: Dear R help forum, I am using the function 'coxph' to obtain hazard ratios for the comparison of a standard treatment to new treatments. This is easily obtained by fitting the relevant model and then calling exp(coef(fit1)) say. I now want to obtain the hazard ratio for the comparison of two non-standard treatments. From a statistical point of view, this can be achieved by dividing the exponentiated coefficients of 2 comparisions. E.g. to compared new treatment 1 (nt1) to new treatment 2 (nt2) we can fit 2 models: fit1 = standard treatment vs nt1 fit2 = standard treatment vs nt2. The required hazard ratio is therefore exp(coef(fit1))/exp(coef(fit2)) In order to obtain an associated confidence interval for this I require the covariance of this comparison. I know that R gives the variance-covariance matrix by the command 'fit$var'. However, this only gives the covariance matrix for non standard drugs and not the full covariance matrix. Can anyone tell me how to obtain the full covariance matrix? What kind of data do you have? Is the standard treatment group the same in both comparisons? If so, why not just have a three-level treatment factor and compare nt1 to nt2 directly. If the control groups are completely separate, then the covariance between fits made on independent data is of course zero. Thank you, Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error producing density curve
This was exactly the problem. It has worked a treat this time around. Thank you so much! -- View this message in context: http://www.nabble.com/Error-producing-density-curve-tp19173403p19176280.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] three character vi commands to edit R commands
As ``vi'' user I remarked a while ago, that - after calling ``R'' - three character commands like ``ctX'' will beep and do not work whereas two character commands like ``fX'' work as expected. Is there some help? Best regards - Wolfram __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding a probability
Thank you so much, at least i got that part right. But what is the meaning of the e-11 at the end?? Thanks again You commands are correct and the interpretation is that the probability that a normal random variable with mean 1454.190 and standard deviation 162.6301 achieves a value of 417 or less is 8.99413e-11 -- View this message in context: http://www.nabble.com/Finding-a-probability-tp19173491p19176249.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting 1-D array to vector
N. Lapidus wrote: You were very close to an answer : as.vector(unlist(df[1,])) I'd use as.character() there, for clarity. It's not easy to remember what as.vector on a factor variable does. Also notice that the original post has serious confusion about what the data structures are: df is data frame, not a matrix df[1,] is a one-row data frame, not a 1-d vector the components of df are factors, not character vectors A data frame is a kind of list, and lists are a kind of vector, hence as.vector does nothing to df[,1]. The unlist() function applied to factors will take the union of their level sets and concatenate the values. An alternative way is to make sure that you have a character matrix to begin with: as.matrix(df) x y [1,] a d [2,] b e [3,] c f as.matrix(df)[1,] x y a d (but beware the rather surprising as.character(df) [1] 1:3 1:3 !!!) Nael On Wed, Aug 27, 2008 at 7:53 AM, Ronnen Levinson [EMAIL PROTECTED] wrote: Hi. How do I convert a one-dimensional array of characters to a character vector? In the example below I am trying to get the result c(a,d). The function as.vector() returns the same one-dimensional array, and unlist() returns something more complicated than I seek. Yours truly, Ronnen. P.S. E-mailed CCs of posted replies appreciated. df=data.frame(x=letters[1:3],y=letters[4:6]) df x y 1 a d 2 b e 3 c f df[1,] x y 1 a d as.vector(df[1,]) x y 1 a d unlist(df[1,]) x y a d Levels: a b c d e f c(a,d) # desired result [1] a d -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding a probability
2008/8/27 rr400 [EMAIL PROTECTED]: Thank you so much, at least i got that part right. But what is the meaning of the e-11 at the end?? Exponential notation. It means 10^-11. Regards, Nicky Chorley __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Variance-covariance matrix
Laura Bonnett wrote: Hi all, Sorry to ask again but I'm still not sure how to get the full variance-covariance matrix. Peter suggested a three-level treatment factor. However, I thought that the censoring variable could only take values 0 or 1 so how do you programme such a factor. Well, not to put it too diplomatically: If you can confuse the treatment factor and the censoring indicator, there might be more wrong with your analysis than we originally assumed, so how about showing us a bit more of what you actually did? Alternatively, is there another way to produce the required covariance? Thank you, Laura On Tue, Aug 26, 2008 at 11:37 AM, Laura Bonnett [EMAIL PROTECTED]wrote: The standard treatment is the same in both comparison. How do you do a three-level treatment factor? I thought you had to have a censoring indicator which took values 0 or 1 not 1, 2 or 3? Thanks, Laura On Tue, Aug 26, 2008 at 11:05 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Laura Bonnett wrote: Dear R help forum, I am using the function 'coxph' to obtain hazard ratios for the comparison of a standard treatment to new treatments. This is easily obtained by fitting the relevant model and then calling exp(coef(fit1)) say. I now want to obtain the hazard ratio for the comparison of two non-standard treatments. From a statistical point of view, this can be achieved by dividing the exponentiated coefficients of 2 comparisions. E.g. to compared new treatment 1 (nt1) to new treatment 2 (nt2) we can fit 2 models: fit1 = standard treatment vs nt1 fit2 = standard treatment vs nt2. The required hazard ratio is therefore exp(coef(fit1))/exp(coef(fit2)) In order to obtain an associated confidence interval for this I require the covariance of this comparison. I know that R gives the variance-covariance matrix by the command 'fit$var'. However, this only gives the covariance matrix for non standard drugs and not the full covariance matrix. Can anyone tell me how to obtain the full covariance matrix? What kind of data do you have? Is the standard treatment group the same in both comparisons? If so, why not just have a three-level treatment factor and compare nt1 to nt2 directly. If the control groups are completely separate, then the covariance between fits made on independent data is of course zero. Thank you, Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard �ster 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] juxtaposed and stacked bars in one barplot?
Hi, anybody any hints how to get a barplot with both juxtaposed and stacked bars? /Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Variance-covariance matrix
Here is the exact code I have written which does the standard vs nt1 and
standard vs nt2 and also gives me the hazard ratio for nt1 vs nt2.
with - read.table(allwiths.txt,header=TRUE)
fix(arm)
function (data)
{
dummy - rep(0,2437)
for(i in 1:2437){
if(data$Arm[i]==CBZ)
dummy[i] - i
}
return(data[-dummy,])
}
fix(x1)
function (data)
{
x1 - rep(0,716)
for(i in 1:716){
if(data$Treat[i]==TPM)
x1[i] - 0
if(data$Treat[i]==VPS)
x1[i] - 0
if(data$Treat[i]==LTG)
x1[i] - 1
}
return(x1)
}
fix(x2)
function (data)
{
x2 - rep(0,716)
for(i in 1:716){
if(data$Treat[i]==TPM)
x2[i] - 1
if(data$Treat[i]==VPS)
x2[i] - 0
if(data$Treat[i]==LTG)
x2[i] - 0
}
return(x2)
}
fit1 = coxph(Surv(Withtime,Wcens)~x1(armb),data=armb,method=breslow)
exp(fit1$coefficients)
exp(confint(fit1))
fit2 = coxph(Surv(Withtime,Wcens)~x2(armb),data=armb,method=breslow)
exp(fit2$coefficients)
exp(confint(fit2))
exp(fit2$coefficients)/exp(fit1$coefficients)
From that, how do I get the necessary variance-covaraince matrix.
Sorry if I appear dense. It really isn't my intention.
Laura
On Wed, Aug 27, 2008 at 10:36 AM, Peter Dalgaard
[EMAIL PROTECTED]wrote:
Laura Bonnett wrote:
Hi all,
Sorry to ask again but I'm still not sure how to get the full
variance-covariance matrix. Peter suggested a three-level treatment
factor. However, I thought that the censoring variable could only take
values 0 or 1 so how do you programme such a factor.
Well, not to put it too diplomatically: If you can confuse the treatment
factor and the censoring indicator, there might be more wrong with your
analysis than we originally assumed, so how about showing us a bit more
of what you actually did?
Alternatively, is there another way to produce the required covariance?
Thank you,
Laura
On Tue, Aug 26, 2008 at 11:37 AM, Laura Bonnett
[EMAIL PROTECTED]wrote:
The standard treatment is the same in both comparison.
How do you do a three-level treatment factor?
I thought you had to have a censoring indicator which took values 0 or 1
not 1, 2 or 3?
Thanks,
Laura
On Tue, Aug 26, 2008 at 11:05 AM, Peter Dalgaard
[EMAIL PROTECTED]
wrote:
Laura Bonnett wrote:
Dear R help forum,
I am using the function 'coxph' to obtain hazard ratios for the
comparison
of a standard treatment to new treatments. This is easily obtained by
fitting the relevant model and then calling exp(coef(fit1)) say.
I now want to obtain the hazard ratio for the comparison of two
non-standard
treatments.
From a statistical point of view, this can be achieved by dividing
the
exponentiated coefficients of 2 comparisions. E.g. to compared new
treatment
1 (nt1) to new treatment 2 (nt2) we can fit 2 models:
fit1 = standard treatment vs nt1
fit2 = standard treatment vs nt2.
The required hazard ratio is therefore exp(coef(fit1))/exp(coef(fit2))
In order to obtain an associated confidence interval for this I
require
the
covariance of this comparison. I know that R gives the
variance-covariance
matrix by the command 'fit$var'. However, this only gives the
covariance
matrix for non standard drugs and not the full covariance matrix.
Can anyone tell me how to obtain the full covariance matrix?
What kind of data do you have? Is the standard treatment group the
same in both comparisons? If so, why not just have a three-level
treatment factor and compare nt1 to nt2 directly. If the control groups
are completely separate, then the covariance between fits made on
independent data is of course zero.
Thank you,
Laura
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
O__ Peter Dalgaard �ster 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
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
O__ Peter Dalgaard Ãster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of
[R] Odp: more dot plots on 1 page
Hi
[EMAIL PROTECTED] napsal dne 26.08.2008 17:06:27:
Hi,
I would like to have six dot plots on one page. I make the plots in a
'for loop' because it is six times the same graph but for different
subjects (species).
I tried it with par(mfrow=c(3,2), oma=c(3,3,2,0), mar=c(2,2,2,2)); but
this does not work for dot plots apparently.
You mix standard and grid graphics which I would not recommend without
detailed knowledge of both. From what you write I presume that you want 6
panels on one page. Maybe you could try to put discriminating variable to
dotplot directly?
Something like
dotplot(XX7$BG_dry~XX7$stress|inputdot$sp)
Regards
Petr
Then I tried with print(). But then I had to give the dot plots names.
This also does not work.
Any one who has some more ideas? What do I do wrong?
species.vector-c(Lp,Pp,Pl,Ra,Lc,Ml)
for(i in 1:6){
- inputdot[inputdot$sp_==species.vector[i],]
str()
XX7-subset(,chamber==7)
XX8-subset(,chamber==8)
XX9-subset(,chamber==9)
XX10-subset(,chamber==10)
species.vector[i] -
dotplot(XX7$BG_dry~XX7$stress,ylim=c(0,20),ylab=biomass,scales=list(ti
ck.number=10),
panel = function (x, y) {
panel.abline(v=c(1:8),lty=2,col=gray)
panel.xyplot(x, y, pch = 1, col = blue, cex = .75)
panel.xyplot(XX8$stress,XX8$BG_dry, pch = 16, col = red, cex = .6)
panel.xyplot(XX9$stress,XX9$BG_dry, pch = 2, col = blue, cex = .6)
panel.xyplot(XX10$stress,XX10$BG_dry, pch = 17, col = red, cex = .6)
},
key = list(text = list(c(ch7, ch8,ch9,ch10), cex = .75),
points = list(pch = c(1, 16,2,17), col = c(blue,red,blue,red),
cex = .75),
space = bottom, border = T),main=species.vector[i]) )
}
print(Lp, split=c(1,1,2,3), more=TRUE)
print(Pp, split=c(2,1,2,3), more=TRUE)
print(Pl, split=c(1,2,2,3), more=TRUE)
print(Ra, split=c(2,2,2,3), more=TRUE)
print(Lc, split=c(1,3,2,3), more=TRUE)
print(Ml, split=c(2,3,2,3))
Thanks a lot!
Joke
Joke Van den Berge, PhDs
University of Antwerp, Campus Drie Eiken
Department of Biology
Research Group of Plant and Vegetation Ecology
Universiteitsplein 1
B-2610 Wilrijk, Belgium
email: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
tel: +32 3 820 22 72 fax: +32 3 820 22 71
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] A Tip: lm, glm, and retained cases
Marc Schwartz wrote: on 08/26/2008 07:31 PM (Ted Harding) wrote: On 26-Aug-08 23:49:37, hadley wickham wrote: On Tue, Aug 26, 2008 at 6:45 PM, Ted Harding [EMAIL PROTECTED] wrote: Hi Folks, This tip is probably lurking somewhere already, but I've just discovered it the hard way, so it is probably worth passing on for the benefit of those who might otherwise hack their way along the same path. Say (for example) you want to do a logistic regression of a binary response Y on variables X1, X2, X3, X4: GLM - glm(Y ~ X1 + X2 + X3 + X4) Say there are 1000 cases in the data. Because of missing values (NAs) in the variables, the number of complete cases retained for the regression is, say, 600. glm() does this automatically. QUESTION: Which cases are they? You can of course find out by hand on the lines of ix - which( (!is.na(Y))(!is.na(X1))...(!is.na(X4)) ) but one feels that GLM already knows -- so how to get it to talk? ANSWER: (e.g.) ix - as.integer(names(GLM$fit)) Alternatively, you can use: attr(GLM$model, na.action) Hadley Thanks! I can see that it works -- though understanding how requires a deeper knowledge of R internals. However, since you've approached it from that direction, simply GLM$model is a dataframe of the retained cases (with corresponding row-names), all variables at once, and that is possibly an even simpler approach! Or just use: model.frame(ModelObject) as the extractor function... :-) Another 'a priori' approach would be to use na.omit() or one of its brethren on the data frame before creating the model. Which function is used depends upon how 'na.action' is set. The returned value, or more specifically the 'na.action' attribute as appropriate, would yield information similar to Hadley's approach relative to which records were excluded. For example, using the simple data frame in ?na.omit: DF - data.frame(x = c(1, 2, 3), y = c(0, 10, NA)) DF x y 1 1 0 2 2 10 3 3 NA DF.na - na.omit(DF) DF.na x y 1 1 0 2 2 10 attr(DF.na, na.action) 3 3 attr(,class) [1] omit So you can see that record 3 was removed from the original data frame due to the NA for 'y'. Also notice the possibility of (g)lm(., na.action=na.exclude) as in library(ISwR); attach(thuesen) fit - lm(short.velocity ~ blood.glucose, na.action=na.exclude) which(is.na(fitted(fit))) # 16 This is often recommendable anyway, e.g. in case you want to plot residuals against original predictors. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Variance-covariance matrix
Laura Bonnett wrote:
Here is the exact code I have written which does the standard vs nt1
and standard vs nt2 and also gives me the hazard ratio for nt1 vs nt2.
with - read.table(allwiths.txt,
header=TRUE)
fix(arm)
function (data)
{
dummy - rep(0,2437)
for(i in 1:2437){
if(data$Arm[i]==CBZ)
dummy[i] - i
}
return(data[-dummy,])
}
fix(x1)
function (data)
{
x1 - rep(0,716)
for(i in 1:716){
if(data$Treat[i]==TPM)
x1[i] - 0
if(data$Treat[i]==VPS)
x1[i] - 0
if(data$Treat[i]==LTG)
x1[i] - 1
}
return(x1)
}
fix(x2)
function (data)
{
x2 - rep(0,716)
for(i in 1:716){
if(data$Treat[i]==TPM)
x2[i] - 1
if(data$Treat[i]==VPS)
x2[i] - 0
if(data$Treat[i]==LTG)
x2[i] - 0
}
return(x2)
}
fit1 = coxph(Surv(Withtime,Wcens)~x1(armb),data=armb,method=breslow)
exp(fit1$coefficients)
exp(confint(fit1))
fit2 = coxph(Surv(Withtime,Wcens)~x2(armb),data=armb,method=breslow)
exp(fit2$coefficients)
exp(confint(fit2))
exp(fit2$coefficients)/exp(fit1$coefficients)
From that, how do I get the necessary variance-covaraince matrix.
Sorry if I appear dense. It really isn't my intention.
You need to read up on vectorized arithmetic, (and don't use fix() to
define functions, x1 - function() {} will do, and what's with
the unused arm() function??).
However, if I get your data structure correctly, what I meant was that
you could just look at
fit3 - coxph(Surv(Withtime,Wcens)~Treat, data=armb,method=breslow)
(possibly factor(Treat) instead). If VPS is your control, I think you'll
even get the desired coefficient directly from the output because the
group comparisons will be against LTG.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
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[R] random error with lme for repeated measures anova
Hi, what is the appropriate syntax to get the random error correct when performing repeated measures anova with 'lme'. let's say i have 3 independent variables, with 'aov', i would write something like: aov(dep_var~(indep_var1*indep_var2*indep_var3) + Error(subject/(indep_var1*indep_var2*indep_var3)). With 'lme' however, i can't find the right formula. i tried things like: lme(dep_var~(indep_var1*indep_var2*indep_var3), random = ~1|subject) or nesting my independent variables in 'subject', but those are obviously wrong with my design. i'm quite clueless (and i haven't found any convincing piece of information about how to correctly use 'lme' or 'lmer'). So, any advice along that line is more than welcome. JP -- View this message in context: http://www.nabble.com/random-error-with-lme-for-repeated-measures-anova-tp19178239p19178239.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random error with lme for repeated measures anova
Hi JP, I suggest that you read the literature cited in the help file, most particularly Pinheiro, J.C., and Bates, D.M. (2000) Mixed-Effects Models in S and S-PLUS, Springer. MASS (Modern Applied Statistics in S) also has some useful things in it. Cheers Andrew On Wed, Aug 27, 2008 at 03:23:58AM -0700, Jean-Pierre Bresciani wrote: Hi, what is the appropriate syntax to get the random error correct when performing repeated measures anova with 'lme'. let's say i have 3 independent variables, with 'aov', i would write something like: aov(dep_var~(indep_var1*indep_var2*indep_var3) + Error(subject/(indep_var1*indep_var2*indep_var3)). With 'lme' however, i can't find the right formula. i tried things like: lme(dep_var~(indep_var1*indep_var2*indep_var3), random = ~1|subject) or nesting my independent variables in 'subject', but those are obviously wrong with my design. i'm quite clueless (and i haven't found any convincing piece of information about how to correctly use 'lme' or 'lmer'). So, any advice along that line is more than welcome. JP -- View this message in context: http://www.nabble.com/random-error-with-lme-for-repeated-measures-anova-tp19178239p19178239.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-6410 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] SparseM
Hello, I am trying to load the package SparseM. It seems that I have successfully installed SparseM (version 0.78), but I did not succeed in loading the SparseM package into R 2.7. Does anybody know a trick for loading SparseM? Thanks in advance, Heike library(SparseM,lib.loc=my.lib.loc) Error in packageDescription(pkg)$Version : $ operator is invalid for atomic vectors In addition: Warning message: In packageDescription(pkg) : no package 'SparseM' was found Error : .onLoad failed in 'loadNamespace' for 'SparseM' Error: package/namespace load failed for 'SparseM' sessionInfo() R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 [4] GO_2.0.1Biobase_2.0.1 graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.10 tcltk_2.7.0 -- Dr. Heike Pospisil | [EMAIL PROTECTED] University of Hamburg | Center for Bioinformatics Bundesstrasse 43| 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using interactive plots to get information about data points
I have been experimenting with interactive packages such iplots and playwith. Consider the following sample dataset: A B C D 1 5 5 9 3 2 8 4 1 7 3 0 7 2 2 6 Let's say I make a plot of variable A. I would like to be able to click on a data point (e.g. 3) and have a pop-up window tell me the corresponding value for variable D (e.g. 4). You're right that iplots can't do that (it's on the wishlist), but it offers alternatives. As a multiwindowing package, it is natural to have graphics displays open for all variables of current interest. This means that selecting a point highlights it in all displays and you can see or query the corresponding values. Antony Unwin Professor of Computer-Oriented Statistics and Data Analysis, Mathematics Institute, University of Augsburg, 86135 Augsburg, Germany Tel: + 49 821 5982218 [EMAIL PROTECTED] http://stats.math.uni-augsburg.de/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fw: How to learn R language?
--- On Wed, 27/8/08, saggak [EMAIL PROTECTED] wrote: From: saggak [EMAIL PROTECTED] Subject: How to learn R language? To: r-help@r-project.org Date: Wednesday, 27 August, 2008, 3:37 PM Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K Unlimited freedom, unlimited storage. Get it now Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Two envelopes problem
Duncan Murdoch wrote: On 26/08/2008 7:54 AM, Jim Lemon wrote: Hi again, Oops, I meant the expected value of the swap is: 5*0.5 + 20*0.5 = 12.5 Too late, must get to bed. But that is still wrong. You want a conditional expectation, conditional on the observed value (10 in this case). The answer depends on the distribution of the amount X, where the envelopes contain X and 2X. For example, if you knew that X was at most 5, you would know you had just observed 2X, and switching would be a bad idea. Yes, I used the example values. If you want an algebraic expression: 0.5x*0.5 + 2x*0.5 = 1.25x where x is the value of the opened envelope. The paradox arises because people want to put a nonsensical Unif(0, infinity) distribution on X. The Wikipedia article points out that it can also arise in cases where the distribution on X has infinite mean: a mathematically valid but still nonsensical possibility. Okay, I read the Wikipedia article, and now realize that the envelope isn't opened in the first version _and_ that it looks like a one trial problem. If the envelope isn't opened, let's call the two envelopes on offer A and B as in the explanation given. If we simultaneously perform the calculation on the two envelopes without knowledge of their contents, we find that the swaps for both have the same expected value: 0.5xB*0.5 + 2xB*0.5 = 1.25xA (if A is chosen) BUT 0.5xA*0.5 + 2xA*0.5 = 1.25xB (if B is chosen) By reductio ad absurdum (two things cannot both be larger than the other) we can say that it makes no sense to swap. It is only when the operations are applied to each envelope in sequence that the apparent paradox arises in this case. In the single trial, no data case, it doesn't make sense to swap in the first place. In a multiple trial situation, if A and B are constant, the optimal solution is known after the first trial. If A and B can vary on each trial, applying the above reasoning, it still doesn't make sense to swap. In the second version of the problem, the value of A is known. The twin isn't really necessary, for if the person making the choice performs the above operation with constants rather than unknowns, the same outcome emerges. I think (but I don't really have the time right now to follow it through) that the third version can be shown to have the same solution. This seems logically equivalent to the solution at the bottom proposed by James Chase, except that I have used the rather pedestrian method of formal logic. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fw: How to learn R language?
I am sure that there are as many ways as people, but this is what I did. MASS 4, Simple R (internet), and this list. I taught myself and it may have been easier to have a guide as this would have cut the learning curve down, but this is not essential. Find out what you need to do, do the examples or vigenettes that come along with the function you would like to use, cuss a lot, and repeat. I am a biologist and never thought I would be programing, but I am now literate enough to solve the problems that present themselves. good luck and welcome Stephen On Wed, Aug 27, 2008 at 7:27 AM, saggak [EMAIL PROTECTED] wrote: --- On Wed, 27/8/08, saggak [EMAIL PROTECTED] wrote: From: saggak [EMAIL PROTECTED] Subject: How to learn R language? To: r-help@r-project.org Date: Wednesday, 27 August, 2008, 3:37 PM Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K Unlimited freedom, unlimited storage. Get it now Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to print out console output
Dear R-helpers, I am desperately looking for a solution for how to print out the console output to a standard printer. For example, I would like to print out the summary.lm() output, the output of different ftable-functions etc. I use R on a linux machine. The only ways so far have been to copy-paste the output into an external editor or to use sink() to redirect the output into a text file and then use shell commands to print out the file. Both ways work but are a bit laborious :) Many thanks in advance for Your help! Kind regards, Kimmo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to print out console output
?capture.output ?sink x - capture.output(runif(20)) x [1] [1] 0.2730090246 0.4462614490 0.2382041477 0.9826505063 0.1556554718 0.3746872961 [2] [7] 0.6108254879 0.6617410595 0.6694177436 0.4650380281 0.0414420397 0.2307212995 [3] [13] 0.5338913775 0.9186298891 0.0006410333 0.8046684864 0.6205502201 0.5352788521 [4] [19] 0.4255279053 0.7711444888 cat(x, sep=\n) [1] 0.2730090246 0.4462614490 0.2382041477 0.9826505063 0.1556554718 0.3746872961 [7] 0.6108254879 0.6617410595 0.6694177436 0.4650380281 0.0414420397 0.2307212995 [13] 0.5338913775 0.9186298891 0.0006410333 0.8046684864 0.6205502201 0.5352788521 [19] 0.4255279053 0.7711444888 On Wed, Aug 27, 2008 at 7:44 AM, K. Elo [EMAIL PROTECTED] wrote: Dear R-helpers, I am desperately looking for a solution for how to print out the console output to a standard printer. For example, I would like to print out the summary.lm() output, the output of different ftable-functions etc. I use R on a linux machine. The only ways so far have been to copy-paste the output into an external editor or to use sink() to redirect the output into a text file and then use shell commands to print out the file. Both ways work but are a bit laborious :) Many thanks in advance for Your help! Kind regards, Kimmo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to print out console output
Hi! Thanks, Jim, for Your quick answer. But my question was how to (re)direct the output to a printer. Kind regards, Kimmo jim holtman wrote: ?capture.output ?sink x - capture.output(runif(20)) x [1] [1] 0.2730090246 0.4462614490 0.2382041477 0.9826505063 0.1556554718 0.3746872961 [2] [7] 0.6108254879 0.6617410595 0.6694177436 0.4650380281 0.0414420397 0.2307212995 [3] [13] 0.5338913775 0.9186298891 0.0006410333 0.8046684864 0.6205502201 0.5352788521 [4] [19] 0.4255279053 0.7711444888 cat(x, sep=\n) [1] 0.2730090246 0.4462614490 0.2382041477 0.9826505063 0.1556554718 0.3746872961 [7] 0.6108254879 0.6617410595 0.6694177436 0.4650380281 0.0414420397 0.2307212995 [13] 0.5338913775 0.9186298891 0.0006410333 0.8046684864 0.6205502201 0.5352788521 [19] 0.4255279053 0.7711444888 On Wed, Aug 27, 2008 at 7:44 AM, K. Elo [EMAIL PROTECTED] wrote: Dear R-helpers, I am desperately looking for a solution for how to print out the console output to a standard printer. For example, I would like to print out the summary.lm() output, the output of different ftable-functions etc. I use R on a linux machine. The only ways so far have been to copy-paste the output into an external editor or to use sink() to redirect the output into a text file and then use shell commands to print out the file. Both ways work but are a bit laborious :) Many thanks in advance for Your help! Kind regards, Kimmo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] warning message while using mice Multivariate Imputation by Chained Equations
Hi there, I am a beginner with R. Anyone could help to explain me what the following warning msg means? Warning messages: 1: In any(predictorMatrix[j, ]) : coercing argument of type 'double' to logical Got 6 of it...although further calculations were done. Because of this warning I am not sure if they are reliable since have no idea what exactly the warning is about. Could anyone please help with the explanation? I used mice Multivariate Imputation by Chained Equations (belonging to mice package) - the default version - predictive mean matching imp-mice(file) By using the command mice it is instead of using default version (which I was using in this case and got the warning msg) possible to create your own function which tells how the imputation data should be created. I would like to create that function saying that Bayes bootstrap of the known data should be imputed for those missing data. Any idea how that could be done?? Ana [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fw: How to learn R language?
saggak wrote: Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K It depends on your starting point, of course. Whether you have a background with other statistical packages and/or with programming languages like C, etc. Quite a few people have started from the intro manual that ships with R (and its predecessor for S-PLUS). There are quite a few books out, see for instance http://www.r-project.org/doc/bib/R-books.html (thanks for reminding me that the info for my own book needs to be updated for the 2nd ed., by the way...), and freely available documents in http://cran.r-project.org/other-docs.html. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to learn R language?
Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K Did you know? You can CHAT without downloading messenger. Go to http://in.webmessenger.yahoo.com/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odd behavior in histogram breaks?
I am looking at histogram breaks, and notice something odd: foo - hist(runif(1),breaks=20) length(foo$breaks) [1] 21 This makes sense to me. foo - hist(runif(1),breaks=200) length(foo$breaks) [1] 201 This also makes sense. BUT foo - hist(runif(1),breaks=250) length(foo$breaks) [1] 201 foo - hist(runif(10),breaks=250) length(foo$breaks) [1] 201 Why only 201 breaks? Where did the other 50 go? -- Here miracles become marvels, and marvels recurring wonders. -- William Beebe Dr. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Seksjon Vinderen PB 85 Vinderen 0319 Oslo http://folk.uio.no/davidgl [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] coding rules
Dear all, I am organizing a set of specific R code as package (to ease the documentation and deployment of it to users). Before doing so, I would like to know if there are written coding rules for R (with functions, objects naming convention for example). Thanks a lot, Thomas -- - Thomas LOUBRIEU IFREMER IDM/ISI BP70 29280 Plouzane FRANCE email: [EMAIL PROTECTED] WWW : http://www.coriolis.eu.org/cdc Tel.: (+33) (0)2 98 22 48 53 Fax: (+33) (0)2 98 22 46 44 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] coding rules
See http://www1.maths.lth.se/help/R/RCC/ On Wed, Aug 27, 2008 at 9:36 AM, Thomas LOUBRIEU [EMAIL PROTECTED] wrote: Dear all, I am organizing a set of specific R code as package (to ease the documentation and deployment of it to users). Before doing so, I would like to know if there are written coding rules for R (with functions, objects naming convention for example). Thanks a lot, Thomas -- - Thomas LOUBRIEU IFREMER IDM/ISI BP70 29280 Plouzane FRANCE email: [EMAIL PROTECTED] WWW : http://www.coriolis.eu.org/cdc Tel.: (+33) (0)2 98 22 48 53 Fax: (+33) (0)2 98 22 46 44 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] speeding up multiple kriging predictions using fields package
Sorry for the double post - I accidentially hit my the send button...
We want to build a global optimizer for extremely expensive noisy objective
functions based
on physical measurements.
Our approach is based on optimizing kriging response surfaces surface models.
(as seen in www.cs.ubc.ca/~hutter/earg/stack/taxonomy-global_optimization.pdf)
In each iteration, we
- model the response surface based on the measurements done so far
using Krig
from fields.
- find a parameter set that maximizes the probability of improvement on
this model
using constrOptim from multiple starting points.
- measure the parameter set that maximizes the probability of
improvement
My problem:
Unfortunately, the optimizations are extremely slow (~30s per iteration of the
algorithm)
despite not making excessive numbers of objective function evaluations (~1000
per
iteration).
I suspect this is because the many calls of predict.Krig and predict.se.Krig
made by optim
are slow, compared to a single call with many x values:
##example code:
library(fields)
fun-function(x){return(sin(x*9)*1/((x)^2+0.02))}
#make some kriging model of a nasty objective function
x=matrix(seq(-1,1,0.5),ncol=1)
y=apply(x,2,fun)
kfit=Krig(x,y,cov.function=Exp.cov,p=2,theta=0.2)
#this is fast:
xp=matrix(seq(-1,1,0.001),ncol=1)
yp=predict.se(kfit,xp)
#this is _very_ slow:
for(i in 1:nrow(xp)){
yp[i]=predict.se(kfit,xp[i,])
}
##end example code
My question:
how can I speed up the many single predictions so they can be used efficiently
in an
objective-function in an optimization?
thanks!
Felix Bonowski
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to learn R language?
Dear Sagga, How give a look at the introduction material on Help / Manual (in pdf) / An introduction to R HTH miltinho astronauta brazil On 8/27/08, saggak [EMAIL PROTECTED] wrote: Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K Did you know? You can CHAT without downloading messenger. Go to http://in.webmessenger.yahoo.com/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random error with lme for repeated measures anova
Hi Jean-Pierre, A general comment is that I think you need to think more carefully about what you are trying to get out of your analysis. The random effects structure you are aiming for could be stretching your data a little thin. It might be a good idea to read through the archives of the R-sig-mixed-models mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models This should give you a better idea of some of the issues involved. If you can't source the source (PB) then there are other documents that might help. You could begin by locationing the directory where nlme package is installed and looking at the scripts in the scripts subdirectory. These are from PB. Baayen has the following draft document on his website. Though DRAFT'ed all over the place, it is well worth a read, even if you are not interested in linguistic analysis. I think it has now been published by Cambridge UP. http://www.ualberta.ca/~baayen/publications/baayenCUPstats.pdf Paul Bliese's document (Multilevel Modeling in R) also has some useful sections (find it under the contributed documents section on CRAN). HTH, Mark. Jean-Pierre Bresciani wrote: Hi, what is the appropriate syntax to get the random error correct when performing repeated measures anova with 'lme'. let's say i have 3 independent variables, with 'aov', i would write something like: aov(dep_var~(indep_var1*indep_var2*indep_var3) + Error(subject/(indep_var1*indep_var2*indep_var3)). With 'lme' however, i can't find the right formula. i tried things like: lme(dep_var~(indep_var1*indep_var2*indep_var3), random = ~1|subject) or nesting my independent variables in 'subject', but those are obviously wrong with my design. i'm quite clueless (and i haven't found any convincing piece of information about how to correctly use 'lme' or 'lmer'). So, any advice along that line is more than welcome. JP -- View this message in context: http://www.nabble.com/random-error-with-lme-for-repeated-measures-anova-tp19178239p19180027.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Com Object mystake
Hi, I've some problem to close a com Object that I've open. example : I create the Com Object Excel : fxl = comCreateObject(Excel.Application) To close I normally used gc(verbose = FALSE) - silent This is ok with my first Pc, the Com Object Excel is kill, but for my second computer this do nothing ... ? I've you an idea of the reason why the gc(verbose = FALSE) - silent don't close my com object ? Thanks -- View this message in context: http://www.nabble.com/Com-Object-mystake-tp19180043p19180043.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Basic question about X11()
Hello, I have a basic question about the display() function, but I can't find the answer easily. I am running R 2.7.16.0 on Suse linux 11.0 with KDE 4.0 I have several desktops, that I use at the same time, called Desktop 1, Desktop 2, etc. I want to open a X11() window in another desktop than the one I'm working from. I tried to do this by using: X11(display=Desktop 1); However, this results in an error: Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, : unable to start device X11cairo In addition: Warning message: In X11(display = Desktop 1) : unable to open connection to X11 display 'Desktop 1' If I make a window with just x11() and than move the window manually to another desktop, It works fine, i.e. I can draw a plot in that window. I am probably just missing some basic syntax rules here. What should I do to get my X11 window to be generated on another desktop than the one i was working from? Thanks in advance, Mathijs Groeneweg [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Closest value
Hello, I have this command: x.axis - seq(from=0.5, to=4.5, length.out=13112) How can I which of the x.axis components is the closest to a given value, for example 3.2? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behavior in histogram breaks?
I think the answer is in this line in hist.default():
breaks - pretty(range(x), n = breaks, min.n = 1)
length(pretty(c(1:1000), 100))
[1] 101
length(pretty(c(1:1000), 200))
[1] 201
length(pretty(c(1:1000), 250))
[1] 201
length(pretty(c(1:1000), 300))
[1] 201
length(pretty(c(1:1000), 500))
[1] 501
Rory Winston
RBS Global Banking Markets
Office: +44 20 7085 4476
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Glenn Lawyer
Sent: 27 August 2008 13:27
To: r-help@r-project.org
Subject: [R] Odd behavior in histogram breaks?
I am looking at histogram breaks, and notice something odd:
foo - hist(runif(1),breaks=20)
length(foo$breaks)
[1] 21
This makes sense to me.
foo - hist(runif(1),breaks=200)
length(foo$breaks)
[1] 201
This also makes sense.
BUT
foo - hist(runif(1),breaks=250)
length(foo$breaks)
[1] 201
foo - hist(runif(10),breaks=250)
length(foo$breaks)
[1] 201
Why only 201 breaks? Where did the other 50 go?
--
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marvels recurring wonders.
-- William Beebe
Dr. Glenn Lawyer
+352 661 967 244
Instituttgruppe for psykiatri
Seksjon Vinderen
PB 85 Vinderen
0319 Oslo
http://folk.uio.no/davidgl
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Re: [R] Closest value
Try this: x.axis[which.min(abs(x.axis - 3.2))] On Wed, Aug 27, 2008 at 10:12 AM, Dani Valverde [EMAIL PROTECTED] wrote: Hello, I have this command: x.axis - seq(from=0.5, to=4.5, length.out=13112) How can I which of the x.axis components is the closest to a given value, for example 3.2? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Closest value
Maybe this which.min(abs(x.axis-3.2)) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dani Valverde Sent: Wednesday, August 27, 2008 9:13 AM To: R Help Subject: [R] Closest value Hello, I have this command: x.axis - seq(from=0.5, to=4.5, length.out=13112) How can I which of the x.axis components is the closest to a given value, for example 3.2? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Closest value
Hi [EMAIL PROTECTED] napsal dne 27.08.2008 15:12:58: Hello, I have this command: x.axis - seq(from=0.5, to=4.5, length.out=13112) How can I which of the x.axis components is the closest to a given value, for example 3.2 E.g. which.min((x.axis-3.2)^2) Regards Petr Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Seeking Code for Chaid or Similar
Quick disclaimer: I'm new to the list and I'm not sure if I'm sending this to the correct forum. If there is a better place for this questions, please let me know! Dear R List, I'm interested in modifying a regression tree algorithm to use the difference between a control and a dosed sample as its dependent variable. I was wondering if anyone knew where I could find code to implement a basic chaid algorithm. Is it possible to access the code inside of R? Is there another place I can find the basic algorithm already coded. I'd prefer a chaid-like algorithm over a crt like algorithm, as my sample is small. I'm a reasonably good programmer, a background in C++ and experience in many different languages. I'd very much appreciate any thoughts. Thank you! David Cobey PS. Of course, if this has been done before, I'd be very grateful for the opportunity to save myself the trouble of reprogramming it myself! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to print out console output
What type of system are you running on? You can create a textConnection and maybe 'pipe' the output to 'lpr' if you are running on UNIX. On Windows there is probably a way of connecting to a printer; you can save the file and then execute the PRINT command. On Wed, Aug 27, 2008 at 7:51 AM, K. Elo [EMAIL PROTECTED] wrote: Hi! Thanks, Jim, for Your quick answer. But my question was how to (re)direct the output to a printer. Kind regards, Kimmo jim holtman wrote: ?capture.output ?sink x - capture.output(runif(20)) x [1] [1] 0.2730090246 0.4462614490 0.2382041477 0.9826505063 0.1556554718 0.3746872961 [2] [7] 0.6108254879 0.6617410595 0.6694177436 0.4650380281 0.0414420397 0.2307212995 [3] [13] 0.5338913775 0.9186298891 0.0006410333 0.8046684864 0.6205502201 0.5352788521 [4] [19] 0.4255279053 0.7711444888 cat(x, sep=\n) [1] 0.2730090246 0.4462614490 0.2382041477 0.9826505063 0.1556554718 0.3746872961 [7] 0.6108254879 0.6617410595 0.6694177436 0.4650380281 0.0414420397 0.2307212995 [13] 0.5338913775 0.9186298891 0.0006410333 0.8046684864 0.6205502201 0.5352788521 [19] 0.4255279053 0.7711444888 On Wed, Aug 27, 2008 at 7:44 AM, K. Elo [EMAIL PROTECTED] wrote: Dear R-helpers, I am desperately looking for a solution for how to print out the console output to a standard printer. For example, I would like to print out the summary.lm() output, the output of different ftable-functions etc. I use R on a linux machine. The only ways so far have been to copy-paste the output into an external editor or to use sink() to redirect the output into a text file and then use shell commands to print out the file. Both ways work but are a bit laborious :) Many thanks in advance for Your help! Kind regards, Kimmo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R for reliability engineering?
Hello, I was wondering whether anyone's using R for reliability (RAMS/LCC) engineering? Sincerely, Wolfgang Keller __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] juxtaposed and stacked bars in one barplot?
Hi Stefan, Could you be a bit more explicit? Do you have an example dataset that you are trying to visualise? Hadley On Wed, Aug 27, 2008 at 4:38 AM, Stefan Uhmann [EMAIL PROTECTED] wrote: Hi, anybody any hints how to get a barplot with both juxtaposed and stacked bars? /Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fw: How to learn R language?
I'm not a statistician so my approach may not make sense for you but I'd suggests having a look at Bob Muenchen's R for SAS and SPSS users in pdf form (very useful) or his new book with the same title (which I have not seen yet) for a start. http://rforsasandspssusers.com/ If you want some very, very basic things I'd suggest having a look at the tutorial at http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html After that there are any number of useful references and on-line materials available through the R site. Have a look at Books and Other on the left hand side of the page. If you can get them, I'd suggest having a look at Peter Dalgaard's Introductory Statistics with R or John Verzani's Simple R. The stats may be simple for you but the organized treatment of how to use these stats in R is very valuable. The Introduction to R is very good but, at the risk of being accused of heresy, I'd suggest that it is much better if you read it after you get a feeling for the language. It also should be downloaded and read in the PDF format. Read the FAQ carefully, especially Section 7. Section 7 highlights a lot of little things that can confuse a new user and reading it can save you hours of pounding your head against the wall. From: saggak [EMAIL PROTECTED] Subject: How to learn R language? To: r-help@r-project.org Date: Wednesday, 27 August, 2008, 3:37 PM Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K __ [[elided Yahoo spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to learn R language?
There are many books, but if I had to choose one that teaches R and teaches statistics at the same time (Yes, you already know stats, so it will be that much easier) I'd choose Peter Dalgaard's book, Introductory Statistics with R. It's exceptionally well written, easy to follow, and will systematically teach you R. It's paperback, not too expensive and available at Amazon. Start at the front, work all the way through it and you will be delighted with the results. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of saggak Sent: Wednesday, August 27, 2008 6:07 AM To: r-help@r-project.org Subject: [R] How to learn R language? Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K Did you know? You can CHAT without downloading messenger. Go to http://in.webmessenger.yahoo.com/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Integrate a 1-variable function with 1 parameter (Jose L. Romero)
Hey fellas:
I would like to integrate the following function:
integrand - function (x,t) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
with respect to the t variable, from 0 to 10.
The variable x here works as a parameter: I would like to integrate the said
function for each value of x in 0,1,..,44.
I have tried Vectorize to no avail.
Thanks in advance,
jose romero
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Seeking Code for Chaid or Similar
On Wed, 27 Aug 2008, David Cobey wrote: Quick disclaimer: I'm new to the list and I'm not sure if I'm sending this to the correct forum. If there is a better place for this questions, please let me know! Dear R List, I'm interested in modifying a regression tree algorithm to use the difference between a control and a dosed sample as its dependent variable. I was wondering if anyone knew where I could find code to implement a basic chaid algorithm. Is it possible to access the code inside of R? Is there another place I can find the basic algorithm already coded. I'd prefer a chaid-like algorithm over a crt like algorithm, as my sample is small. I'm a reasonably good programmer, a background in C++ and experience in many different languages. I'd very much appreciate any thoughts. ctree() in package party implements in inference-based tree algorithm. It's based on conditional inference, but not unsimilar to CHAID in the case of categorical variables. See its references and vignette for more details. Torsten and I are also working on some basic tree infrastructure which could/should eventually also be used for implementing classical CHAID but that will take some more time. hth, Z Thank you! David Cobey PS. Of course, if this has been done before, I'd be very grateful for the opportunity to save myself the trouble of reprogramming it myself! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integrate a 1-variable function with 1 parameter (Jose L. Romero)
jose romero wrote:
Hey fellas:
I would like to integrate the following function:
integrand - function (x,t) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
with respect to the t variable, from 0 to 10.
The variable x here works as a parameter: I would like to integrate the said
function for each value of x in 0,1,..,44.
I have tried Vectorize to no avail.
Will this do?
sapply(0:44,function(x)integrate(integrand,x=x, lower=0, upper=10)$value
--
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c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] Integrate a 1-variable function with 1 parameter (Jose L. Romero)
Here is one way:
integrand - function (t, x) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
x - 0:44
ans - sapply(x, function(x) integrate(integrand, lower=0, upper=10, x=x))
cbind(x=x, integral=unlist(ans[1,]), abs.error=unlist(ans[2,]))
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of jose romero
Sent: Wednesday, August 27, 2008 10:24 AM
To: r-help@r-project.org
Subject: [R] Integrate a 1-variable function with 1 parameter (Jose L.
Romero)
Hey fellas:
I would like to integrate the following function:
integrand - function (x,t) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
with respect to the t variable, from 0 to 10.
The variable x here works as a parameter: I would like to integrate the said
function for each value of x in 0,1,..,44.
I have tried Vectorize to no avail.
Thanks in advance,
jose romero
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integrate a 1-variable function with 1 parameter (Jose L. Romero)
Peter Dalgaard wrote:
jose romero wrote:
Hey fellas:
I would like to integrate the following function:
integrand - function (x,t) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
with respect to the t variable, from 0 to 10.
The variable x here works as a parameter: I would like to integrate the said
function for each value of x in 0,1,..,44.
I have tried Vectorize to no avail.
Will this do?
sapply(0:44,function(x)integrate(integrand,x=x, lower=0, upper=10)$value
Oops. Forgot this:
)
--
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c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
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[R] convert princomp output to equation for plane?
I want to fit something like: z = b0 + b1*x + b2*y Since x, y,and z all have measurement errors attached, the proper way to do the fit is with principal components analysis, and to use the first component (called loadings in princomp output). My dumb question is: how do I convert the princomp output to equation coefficients in the format above? I guess another dumb question would be: how about getting the standard deviations of b0, b1, b2? Thanks very much for any help. Bill __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SparseM
Hi Heike library(SparseM,lib.loc=my.lib.loc) Error in packageDescription(pkg)$Version : $ operator is invalid for atomic vectors In addition: Warning message: In packageDescription(pkg) : no package 'SparseM' was found Error : .onLoad failed in 'loadNamespace' for 'SparseM' Error: package/namespace load failed for 'SparseM' Maybe omitting 'lib.loc=my.lib.loc' will do the job. Regards, Sam __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Seeking Code for Chaid or Similar
Quick disclaimer: I'm new to the list and I'm not sure if I'm sending this to the correct forum. If there is a better place for questions like these, please let me know! Dear R List, I'm interested in modifying a regression tree algorithm to use the difference between a control and a dosed sample as its dependent variable. I was wondering if anyone knew where I could find code to implement a basic chaid algorithm. Is it possible to access the code inside of R? Is there another place I can find the basic algorithm already coded. I'd prefer a chaid-like algorithm over a crt like algorithm, as my sample is small. I'm a reasonably good programmer, a background in C++ and experience in many different languages. I'd very much appreciate any thoughts. Thank you! David Cobey PS. Of course, if this has been done before, I'd be very grateful for the opportunity to save myself the trouble of reprogramming it myself! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] averaging pairs of columns in a dataframe
Dear all, I have a dataframe with 132 columns and 100 rows. Every 2nd column is a repeat measurement so that the columns could be titled, a a b b c c d d etc. I would like to average the repeats such that I am left with a data frame of 66 columns (of means) and 100 rows. I have been trying to use rowMeans but have not been able to average the pairs of columns, only the whole dataframe. Any help would be appreciated, I am new to R. Thanks in advance, Jon. -- View this message in context: http://www.nabble.com/averaging-pairs-of-columns-in-a-dataframe-tp19181319p19181319.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Ratio of gammas
hello, gamma(a) works fine for a173, but gamma(173) returns [1] Inf Warning message: value out of range in 'gammafn' What I really need is the ratio gamma(nu/2) / gamma((nu+1)/2) is anyone aware of a way to re-express this in a form that pushes the threshold past which a warning message is generated? thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fw: How to learn R language?
- go with Bob and Peter's book. Too many sources can be confusing. - Join the list, create filters for keywords of your specialty (like from R -Help ) contains regression. - Try use it for a live project . Let the R begin Ajay On Wed, Aug 27, 2008 at 7:46 PM, John Kane [EMAIL PROTECTED] wrote: I'm not a statistician so my approach may not make sense for you but I'd suggests having a look at Bob Muenchen's R for SAS and SPSS users in pdf form (very useful) or his new book with the same title (which I have not seen yet) for a start. http://rforsasandspssusers.com/ If you want some very, very basic things I'd suggest having a look at the tutorial at http://www.math.ilstu.edu/dhkim/Rstuff/Rtutor.html After that there are any number of useful references and on-line materials available through the R site. Have a look at Books and Other on the left hand side of the page. If you can get them, I'd suggest having a look at Peter Dalgaard's Introductory Statistics with R or John Verzani's Simple R. The stats may be simple for you but the organized treatment of how to use these stats in R is very valuable. The Introduction to R is very good but, at the risk of being accused of heresy, I'd suggest that it is much better if you read it after you get a feeling for the language. It also should be downloaded and read in the PDF format. Read the FAQ carefully, especially Section 7. Section 7 highlights a lot of little things that can confuse a new user and reading it can save you hours of pounding your head against the wall. From: saggak [EMAIL PROTECTED] Subject: How to learn R language? To: r-help@r-project.org Date: Wednesday, 27 August, 2008, 3:37 PM Hi! I am a post graduate in Statistics. I want to learn R language, but am very confused as to how to begin systematically. I need to learn R language from Statistics point of view e.g. I need to fit distributions to data or run regression analysis etc. No doubt there are so many articles available on internet. But can someone guide me as to how do I begin and go on improving myself SYSTEMATICALLY? Hence, please guide me as to how should I start learning R language? What should I read first etc. Thanks in advance, Sagga K __ [[elided Yahoo spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Regards, Ajay Ohri http://tinyurl.com/liajayohri [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SparseM
Hi Sam, thank your for your reply. The lib location statement is correct. I have installed SparseM locally because I do not have su rights. Best, Heike (BTW: An installation by our systems administrator into the R directory did not work, too.) On Wednesday 27 August 2008 19:00, Samuel Bächler wrote: Hi Heike library(SparseM,lib.loc=my.lib.loc) Error in packageDescription(pkg)$Version : $ operator is invalid for atomic vectors In addition: Warning message: In packageDescription(pkg) : no package 'SparseM' was found Error : .onLoad failed in 'loadNamespace' for 'SparseM' Error: package/namespace load failed for 'SparseM' Maybe omitting 'lib.loc=my.lib.loc' will do the job. Regards, Sam __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Heike Pospisil | [EMAIL PROTECTED] University of Hamburg | Center for Bioinformatics Bundesstrasse 43| 20146 Hamburg, Germany phone:+49-40-42838-7303 | fax: +49-40-42838-7312 = __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting 1-D array to vector
c(as.matrix(df[1,])) will also work in your case. Gasper Cankar -Original Message- From: N. Lapidus [mailto:[EMAIL PROTECTED] Sent: Wednesday, August 27, 2008 9:06 AM To: r-help@r-project.org Subject: Re: [R] Converting 1-D array to vector You were very close to an answer : as.vector(unlist(df[1,])) Nael On Wed, Aug 27, 2008 at 7:53 AM, Ronnen Levinson [EMAIL PROTECTED] wrote: Hi. How do I convert a one-dimensional array of characters to a character vector? In the example below I am trying to get the result c(a,d). The function as.vector() returns the same one-dimensional array, and unlist() returns something more complicated than I seek. Yours truly, Ronnen. P.S. E-mailed CCs of posted replies appreciated. df=data.frame(x=letters[1:3],y=letters[4:6]) df x y 1 a d 2 b e 3 c f df[1,] x y 1 a d as.vector(df[1,]) x y 1 a d unlist(df[1,]) x y a d Levels: a b c d e f c(a,d) # desired result [1] a d version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 7.0 year 2008 month 04 day22 svn rev45424 language R version.string R version 2.7.0 (2008-04-22) -- Ronnen Levinson, Ph.D. scientist, Lawrence Berkeley National Lab The Onion horoscope: Libra September 23 - October 23 Your tactics of overwhelming your opposition with spectacular shows of force and choking the roads with fleeing refugees will be seen as inappropriate by the other electronics wholesalers. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] juxtaposed and stacked bars in one barplot?
You can simply do a - c(2,4,3,4,5) b - c(4,3,4,5,2) barplot(cbind(a,b)) or you can put a and b in matrix as help suggests. Gasper Cankar -Original Message- From: Stefan Uhmann [mailto:[EMAIL PROTECTED] Sent: Wednesday, August 27, 2008 11:39 AM To: r-help@r-project.org Subject: [R] juxtaposed and stacked bars in one barplot? Hi, anybody any hints how to get a barplot with both juxtaposed and stacked bars? /Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to learn R language?
On 27-Aug-08 14:24:31, Charles Annis, P.E. wrote: There are many books, but if I had to choose one that teaches R and teaches statistics at the same time (Yes, you already know stats, so it will be that much easier) I'd choose Peter Dalgaard's book, Introductory Statistics with R. It's exceptionally well written, easy to follow, and will systematically teach you R. It's paperback, not too expensive and available at Amazon. Start at the front, work all the way through it and you will be delighted with the results. Charles Annis, P.E. I have to agree with that (especially the well written part). Especially, Sagga, already knowing statistics, you will be familiar with what Peter Dalgaard is doing, tatistically, at any point and will therefore be able to follow him easily as he works out how to do it in R; and then you will appreciate the result. The book has a clear divide between the two viewpoints: the view of a person applying statistical procedures (for which brief basic outline descriptions are given), and the point of view of someone who wants to implement these in a programming language. The explanations of how the latter is achieved in R are clear and thorough (for a basic example, see the dicussion of Factors in the first Chapter). Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 27-Aug-08 Time: 16:31:03 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ratio of gammas
On 8/27/2008 11:14 AM, [EMAIL PROTECTED] wrote: hello, gamma(a) works fine for a173, but gamma(173) returns [1] Inf Warning message: value out of range in 'gammafn' What I really need is the ratio gamma(nu/2) / gamma((nu+1)/2) is anyone aware of a way to re-express this in a form that pushes the threshold past which a warning message is generated? Use logs: exp( lgamma(nu/2) - lgamma((nu+1)/2) ) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] averaging pairs of columns in a dataframe
Try this: # test data DF - data.frame(a = 1:9, a = 21:29, b = 31:39, b = 41:49, check.names = FALSE) t(apply(DF, 1, tapply, names(DF), mean)) It gives a matrix so use as.data.frame on that if you need a data frame On Wed, Aug 27, 2008 at 9:47 AM, JonD [EMAIL PROTECTED] wrote: Dear all, I have a dataframe with 132 columns and 100 rows. Every 2nd column is a repeat measurement so that the columns could be titled, a a b b c c d d etc. I would like to average the repeats such that I am left with a data frame of 66 columns (of means) and 100 rows. I have been trying to use rowMeans but have not been able to average the pairs of columns, only the whole dataframe. Any help would be appreciated, I am new to R. Thanks in advance, Jon. -- View this message in context: http://www.nabble.com/averaging-pairs-of-columns-in-a-dataframe-tp19181319p19181319.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Significant digits for checking values of variable?
All, I'm witnessing some strange behavior when checking the values of one of my variables. My guess is that it has something to do with the number of significant digits being represented, but perhaps not as my variable was created from other variables that only had one decimal place. See below. I'm sure this is something basic, any suggestions much appreciated. Cheers, David visit.2.SEK.delta.baseline [1] 0.1 -0.7 0.8 -0.1 -0.5 0.8 0.7 0.2 0.4 0.3 0.6 0.6 0.3 0.8 0.8 0.3 0.4 0.8 visit.2.SEK.delta.baseline 0 [1] TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE visit.2.SEK.delta.baseline == .8 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE ### but some of the values are equal to .8 ## here it is okay when I try to reproduce junk = c(0.1, -0.7,0.8, -0.1, -0.5, 0.8, 0.7, 0.2, 0.4, 0.3, 0.6, 0.6, 0.3, 0.8, 0.8, 0.3, 0.4, 0.8 ) junk == .8 [1] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ratio of gammas
This will work: exp( lgamma(nu/2) - lgamma((nu+1)/2) ) Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, August 27, 2008 11:14 AM To: r-help@r-project.org Subject: [R] Ratio of gammas hello, gamma(a) works fine for a173, but gamma(173) returns [1] Inf Warning message: value out of range in 'gammafn' What I really need is the ratio gamma(nu/2) / gamma((nu+1)/2) is anyone aware of a way to re-express this in a form that pushes the threshold past which a warning message is generated? thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A manipulation problem for a large data set in R
I have two questions for the group. One is very concrete, and is dangerously close to a please do my homework posting. The second follows from the first one but is more general. I would welcome the advice of experienced R users. As for the first one: I have a data frame with two variables X Y A, chris D, chris B, chris B, chris C, andrew E, andrew C, andrew B, beth D, chris D, beth C, beth D, beth D, beth A, andrew A, andrew A, andrew C, chris B, beth D, chris E, andrew D, chris D, beth D, chris A, andrew A, chris Cchris Achris Bchris Cbeth Achris I would like to produce a table, with one row for every level of the factor X, and multiple columns, filled with the observed levels of the factor Y that are observed jointly with X. Hence: X Z1 Z2 Z3 A, andrew, chris B, chris beth, chris C, andrew, beth, chris D, chris, beth E, andrew A solution would be to something like temp = tapply(Y, X, function(a) levels(a[,drop=TRUE]))) and then putting the output in an appropriately sized data frame. The issue I have with this is that it is inelegant and rather slow for my typical data set (~200K rows). So I was wondering if a more efficient, nicer solution exists. This leads me to a second question. Maybe out of laziness, maybe because R is good enough, I tend to do all my local data manipulations in R. This includes de-duping records, joining tables, and grouping observations. I do this also for larger data sets (say, dense tables with 100M+ elements). Is this current practice among R users? If so, is there a tutorial, or an R view on it? If not, what do you use? Thanks in advance, -gappy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Significant digits for checking values of variable?
FAQ 7.31 On Wed, Aug 27, 2008 at 11:51 AM, David Afshartous [EMAIL PROTECTED] wrote: All, I'm witnessing some strange behavior when checking the values of one of my variables. My guess is that it has something to do with the number of significant digits being represented, but perhaps not as my variable was created from other variables that only had one decimal place. See below. I'm sure this is something basic, any suggestions much appreciated. Cheers, David visit.2.SEK.delta.baseline [1] 0.1 -0.7 0.8 -0.1 -0.5 0.8 0.7 0.2 0.4 0.3 0.6 0.6 0.3 0.8 0.8 0.3 0.4 0.8 visit.2.SEK.delta.baseline 0 [1] TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE visit.2.SEK.delta.baseline == .8 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE ### but some of the values are equal to .8 ## here it is okay when I try to reproduce junk = c(0.1, -0.7,0.8, -0.1, -0.5, 0.8, 0.7, 0.2, 0.4, 0.3, 0.6, 0.6, 0.3, 0.8, 0.8, 0.3, 0.4, 0.8 ) junk == .8 [1] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A manipulation problem for a large data set in R
On Wed, 27 Aug 2008, Giuseppe Paleologo wrote: I have two questions for the group. One is very concrete, and is dangerously close to a please do my homework posting. The second follows from the first one but is more general. I would welcome the advice of experienced R users. As for the first one: I have a data frame with two variables X Y A, chris D, chris B, chris B, chris C, andrew E, andrew C, andrew B, beth D, chris D, beth C, beth D, beth D, beth A, andrew A, andrew A, andrew C, chris B, beth D, chris E, andrew D, chris D, beth D, chris A, andrew A, chris Cchris Achris Bchris Cbeth Achris I would like to produce a table, with one row for every level of the factor X, and multiple columns, filled with the observed levels of the factor Y that are observed jointly with X. Hence: X Z1 Z2 Z3 A, andrew, chris B, chris beth, chris C, andrew, beth, chris D, chris, beth E, andrew A solution would be to something like temp = tapply(Y, X, function(a) levels(a[,drop=TRUE]))) lapply( split(Y,X), unique ) or lapply( split(Y,X), function(x) as.character(unique(x))) HTH, Chuck and then putting the output in an appropriately sized data frame. The issue I have with this is that it is inelegant and rather slow for my typical data set (~200K rows). So I was wondering if a more efficient, nicer solution exists. This leads me to a second question. Maybe out of laziness, maybe because R is good enough, I tend to do all my local data manipulations in R. This includes de-duping records, joining tables, and grouping observations. I do this also for larger data sets (say, dense tables with 100M+ elements). Is this current practice among R users? If so, is there a tutorial, or an R view on it? If not, what do you use? Thanks in advance, -gappy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2: problem with large fonts and overlapping labels
Hi, I am using ggplot2 to generate graphs for a paper I am writing in two column format. When I shrink the graphs to fit in a single column, the graph is clear but the axis and tick labels are way too small. I have increased the font sizes by manipulating the grid. However, when I do this the tick labels and axis labels get very close or even overlap, especially on the y-axis. Is there a way to increase the margin between tick labels and axis labels with ggplot or by manipulating the grid? Regards, Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to calculate cumulative values for a simple Bernoulli's distribution?
Hi there, I have two questions and believe that there is an extremely easy solution. Being a beginner with R makes thinks a bit more complicated. This is the code: rpois(15,3) n-15 DATA-cbind(D,rpois(15,3)) data-as.data.frame(DATA) colnames(data)-c(D,X) *# 1. question: is it possible to put the following creation of x in a nicer form?* x-c(sum(D0),sum(D0),sum(D0),sum(D0),sum(D0),sum(D0),sum(D0),sum(D0),sum(D0),sum(D0)) p1-seq(0, 1, 0.1) # Posterior Bernoulli distribution Bn1-(p1^x*(1-p1)^(n-x))*choose(n,x) bn1-as.data.frame(Bn1) # Normalized posterior Bernoulli distribution f1-1/sum(bn1) nbn1-bn1*f1 nbn1 # Control check that sum is equal to 1 sum(nbn1) *# 2. question: how can I calculate cumulative values for nbn1 distribution? Was looking for the answer on-line but couldn't find anything.* Your help will be greatly appreciated!! Good day to all of you Ana [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Seeking Code for Chaid or Similar
on 08/27/2008 09:26 AM David Cobey said the following: I'm interested in modifying a regression tree algorithm to use the difference between a control and a dosed sample as its dependent variable. I was wondering if anyone knew where I could find code to implement a basic chaid algorithm. Is it possible to access the code inside of R? Is there another place I can find the basic algorithm already coded. don't know about your specific target, but as a general question of seeing the code: to see a function's code in R, just type its name at the prompt without parentheses - that will show the code, rather than invoke the function. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Significant digits for checking values of variable?
Thanks. Is there simple way around this for simple checking of single values? The all.equal() mentioned in the FAQ doesn't seem appropriate. X = c(1.2, 2) X.new = X -1 X == 1.2 [1] TRUE FALSE X.new == .2 [1] FALSE FALSE On 8/27/08 11:47 AM, jim holtman [EMAIL PROTECTED] wrote: FAQ 7.31 On Wed, Aug 27, 2008 at 11:51 AM, David Afshartous [EMAIL PROTECTED] wrote: All, I'm witnessing some strange behavior when checking the values of one of my variables. My guess is that it has something to do with the number of significant digits being represented, but perhaps not as my variable was created from other variables that only had one decimal place. See below. I'm sure this is something basic, any suggestions much appreciated. Cheers, David visit.2.SEK.delta.baseline [1] 0.1 -0.7 0.8 -0.1 -0.5 0.8 0.7 0.2 0.4 0.3 0.6 0.6 0.3 0.8 0.8 0.3 0.4 0.8 visit.2.SEK.delta.baseline 0 [1] TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE visit.2.SEK.delta.baseline == .8 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE ### but some of the values are equal to .8 ## here it is okay when I try to reproduce junk = c(0.1, -0.7,0.8, -0.1, -0.5, 0.8, 0.7, 0.2, 0.4, 0.3, 0.6, 0.6, 0.3, 0.8, 0.8, 0.3, 0.4, 0.8 ) junk == .8 [1] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] averaging pairs of columns in a dataframe
That's great, thanks! Jon Gabor Grothendieck wrote: Try this: # test data DF - data.frame(a = 1:9, a = 21:29, b = 31:39, b = 41:49, check.names = FALSE) t(apply(DF, 1, tapply, names(DF), mean)) It gives a matrix so use as.data.frame on that if you need a data frame -- View this message in context: http://www.nabble.com/averaging-pairs-of-columns-in-a-dataframe-tp19181319p19184350.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Significant digits for checking values of variable?
Try this using 'sapply' sapply(X.new, all.equal, .2) == TRUE [1] TRUE FALSE On Wed, Aug 27, 2008 at 12:13 PM, David Afshartous [EMAIL PROTECTED] wrote: Thanks. Is there simple way around this for simple checking of single values? The all.equal() mentioned in the FAQ doesn't seem appropriate. X = c(1.2, 2) X.new = X -1 X == 1.2 [1] TRUE FALSE X.new == .2 [1] FALSE FALSE On 8/27/08 11:47 AM, jim holtman [EMAIL PROTECTED] wrote: FAQ 7.31 On Wed, Aug 27, 2008 at 11:51 AM, David Afshartous [EMAIL PROTECTED] wrote: All, I'm witnessing some strange behavior when checking the values of one of my variables. My guess is that it has something to do with the number of significant digits being represented, but perhaps not as my variable was created from other variables that only had one decimal place. See below. I'm sure this is something basic, any suggestions much appreciated. Cheers, David visit.2.SEK.delta.baseline [1] 0.1 -0.7 0.8 -0.1 -0.5 0.8 0.7 0.2 0.4 0.3 0.6 0.6 0.3 0.8 0.8 0.3 0.4 0.8 visit.2.SEK.delta.baseline 0 [1] TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE visit.2.SEK.delta.baseline == .8 [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE ### but some of the values are equal to .8 ## here it is okay when I try to reproduce junk = c(0.1, -0.7,0.8, -0.1, -0.5, 0.8, 0.7, 0.2, 0.4, 0.3, 0.6, 0.6, 0.3, 0.8, 0.8, 0.3, 0.4, 0.8 ) junk == .8 [1] FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fw: How to learn R language?
Ajay ohri wrote: - go with Bob and Peter's book. Too many sources can be confusing. - Join the list, create filters for keywords of your specialty (like from R -Help ) contains regression. - Try use it for a live project . I think this is really very good advice: - 2 books (I would recommend Peter Dalgaard's and Modern Applied Statistics by Venables/Ripley) - the R-help list is very, very valuable - most importantly: use it for some real project Please let me add two more things: - the road is long. Even after years using it exclusively as your statistical language/package of choice, there are still surprises around the corner (at least it happens to me, just discovered '.bquote' a few weeks ago) - have an open mind. For example, if you have a background in SPSS, Excel, ... but not in general purpose programming languages, you might be surprised that your data don't have to be in rectangular shape. In my experience this is one of the first obstacles for students with a social science background. - You get often world-class help and advice *for free* on the r-help list. So please read the posting guide before posting questions to the r-help list. This will save you some answer which might appear to be rude (but usually answer your question anyway). I hope this helps you further, Roland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Quantitative risk analysis with R
Recently a course with this title, from Vose consulting, was announced on the list. Does anyone know of any books/websites/downloadable tutorials etc that cover the same ground. ie not just quantitative risk analysis, but specifically on using R for risk analysis and as an alternative to @Risk/Crystal Ball. Many thanks, Graham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RCurl: using netrc with curlPerform
Thanks Martin! Valerie Martin Morgan wrote: Hi Valerie -- curlPerform is expecting the url to be an option that is named, i.e., myopts -curlOptions(netrc=1) url - http://www.omegahat.org/RCurl/testPassword/index.html; cat(curlPerform(url=url, .opts=myopts)) !DOCTYPE HTML PUBLIC -//IETF//DTD HTML//EN html head titleBasic Password Test/title /head body h1Basic Password Test/h1 This is a test page. If you can read it, you have correctly supplied the password. hr addressa href=http://stat.ucdavis.edu/~duncan;Duncan Temple Lang/a a href=mailto:[EMAIL PROTECTED]lt;[EMAIL PROTECTED]gt;/a/address !-- hhmts start -- Last modified: Sun Aug 1 13:57:44 PDT 2004 !-- hhmts end -- /body /html (also curlPerform(url=url, netrc=1)) Martin Valerie Obenchain [EMAIL PROTECTED] writes: Hello, I am having trouble getting the curlPerform function to authenticate using the .netrc file. From the documentation I've read it certainly seems as though this function should be able to authenticate via the .netrc file. The example I am using here comes from the R as a Web Client- the RCurl package paper and demonstrates using the .netrc file to access the www.omegahat.org page. Authentication takes place by RCurl (curl) reading the username and password out of the .netrc file in the user's home directory. For this example the username is bob and password is welcome. The .netrc file in the user's home directory contains the following information: machine www.omegahat.org login bob password welcome I can successfully use the .netrc file with the getURL function: getURL(http://www.omegahat.org/RCurl/testPassword/index.html;, netrc=1) [1] !DOCTYPE HTML PUBLIC \-//IETF//DTD HTML//EN\\nhtml head\ntitleBasic Password Test/title\n/head\n\nbody\nh1Basic Password Test/h1\nThis is a test page.\nIf you can read it, you have correctly supplied\nthe password.\n\n\nhr\naddressa href=\http://stat.ucdavis.edu/~duncan\;Duncan Temple Lang/a\na href=mailto:[EMAIL PROTECTED]lt;[EMAIL PROTECTED]gt;/a/address\n!-- hhmts start --\nLast modified: Sun Aug 1 13:57:44 PDT 2004\n!-- hhmts end --\n/body /html\n When I try to do the same with the curlPerform function I get an error saying that the curl option is not recognized. I have tried 3 different ways of instructing the curlPerform function to use the .netrc file (in the .opts, curl handle and the ... argument) but got the same error message each time. # Failed attempt using .opts construct myopts -curlOptions(netrc=1) curlPerform(http://www.omegahat.org/RCurl/testPassword/index.html;, .opts=myopts) # Failed attempt using curl handle handle - getCurlHandle(netrc=1) curlPerform(http://www.omegahat.org/RCurl/testPassword/index.html;, curl=handle) # Failed attempt using ... construct curlPerform(http://www.omegahat.org/RCurl/testPassword/index.html;, netrc=1) Common error message for all failed attempts: Error in mapCurlOptNames(names(.els), asNames = TRUE) : Unrecognized CURL options: Valid curl option names are listed by typing listCurlOptions() and netrc is one of the options. The mapCurlOptNames code is not available for the user to view so I'm not able to deduce anything more from the error message. Thanks, Valerie __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] accessing sd and var functions in embedded app
I am able to call R functions like min, mean, and mad from from a C/C++ embedded application, but when I try to get the standard deviation or variance (sd, var) R segfaults. Can someone suggest how to resolve this? Thanks and best regards, EBo -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Simple programming problem with 'with' or 'data ='
Hello
I wrote a simple program to modify a boxplot:
gdsbox - function(indvar){
boxplot(indvar~gds3lev,
main = paste('Boxplot of', substitute(indvar), for GDS groups),
names = c('1', '3', '4, 5, 6'))
}
If I attach the dataframe gdsgraph, this works fine. However, I've been warned
against attach. When I tried to run this program using 'with', it did not work.
e.g.
with(gdsgraph, gdsbox(BReT3T5T))
produced an error that gds3level was not found
but if I try
with(gdsgraph, boxplot(BReT3T5T~gds3lev))
it works fine.
Similar problems occurred when I tried to use data =
What am I missing?
Thanks
Peter
Peter L. Flom, PhD
Brainscope, Inc.
212 263 7863 (MTW)
917 488 7176 (ThF)
[[alternative HTML version deleted]]
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Re: [R] Calculating total observations based on combinations of variable values
On Wednesday 27 August 2008, Josip Dasovic wrote: Hello: As someone making the move from STATA to R, I'm finding it difficult at times to perform basic tasks in R, so forgive me if I've missed an obvious and easily obtained solution to my problem. I've searched the help guides and the archives and have not been able to find a solution that works. I have a data frame with thousands of observations that looks something like this: YEAR MONTH DAY COUNTRY REGION PROVINCE CITY 1994 1 22 Sri Lanka South Asia Northern (Province) Pungudutivu 1994 1 25 Sri Lanka South AsiaCentral (Province) Kandy 1994 2 26 Sri Lanka South Asia Central (Province) Kandy 1994 2 28 Sri Lanka South AsiaEastern (Province) Wakianeri 1994 6 28 Sri Lanka South AsiaEastern (Province)Valachenai 1994 6 31 Sri Lanka South AsiaCentral (Province) Kandy 1995 3 1 Sri Lanka South Asia North (Province) Kilinochchi 1995 3 6 Sri Lanka South AsiaWestern (Province) Colombo 1995 7 15 Sri Lanka South Asia Northern (Province) Mankulam 1995 7 23 Sri Lanka South Asia Northern (Province) Point Pedro 1995 9 25 Sri Lanka South Asia Northern (Province)Kilali ... What I would like to do is to calculate the total number of observations by unique combinations of the values of (some of the) variables above. For example, I would like to know how many observations (i.e. rows) have the values YEAR==1994 and MONTH==1. In the end, I'd like a table that looks like this: YEAR MONTH #OBS 1994 1 2 1994 2 2 1994 3 0 1994 4 0 1994 5 0 1994 6 2 1994 7 0 1994 8 0 1994 9 0 1994 10 0 1994 11 0 1994 12 0 1995 1 0 1995 2 0 1995 3 2 1995 4 0 ... I do need to fill out the table with all the possible combinations, even where there are no observations with that combination in the data set. At first, it seemed like this would not be think that aggregate is probably the way to go, but there doesn't seem to be an appropriate summary function (FUN) available. Thanks in advance for any help in this matter, Josip ?table ?xtabs -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calculating total observations based on combinations of variable values
Try this: merge(aggregate(x$DAY, x[, c(YEAR, MONTH)], length), data.frame(YEAR = unique(x$YEAR), MONTH = 1:12), all = T) On Wed, Aug 27, 2008 at 2:11 PM, Josip Dasovic [EMAIL PROTECTED] wrote: Hello: As someone making the move from STATA to R, I'm finding it difficult at times to perform basic tasks in R, so forgive me if I've missed an obvious and easily obtained solution to my problem. I've searched the help guides and the archives and have not been able to find a solution that works. I have a data frame with thousands of observations that looks something like this: YEAR MONTH DAY COUNTRY REGION PROVINCE CITY 1994 1 22 Sri Lanka South Asia Northern (Province) Pungudutivu 1994 1 25 Sri Lanka South AsiaCentral (Province) Kandy 1994 2 26 Sri Lanka South AsiaCentral (Province) Kandy 1994 2 28 Sri Lanka South AsiaEastern (Province) Wakianeri 1994 6 28 Sri Lanka South AsiaEastern (Province) Valachenai 1994 6 31 Sri Lanka South AsiaCentral (Province) Kandy 1995 3 1 Sri Lanka South Asia North (Province) Kilinochchi 1995 3 6 Sri Lanka South AsiaWestern (Province) Colombo 1995 7 15 Sri Lanka South Asia Northern (Province) Mankulam 1995 7 23 Sri Lanka South Asia Northern (Province) Point Pedro 1995 9 25 Sri Lanka South Asia Northern (Province) Kilali ... What I would like to do is to calculate the total number of observations by unique combinations of the values of (some of the) variables above. For example, I would like to know how many observations (i.e. rows) have the values YEAR==1994 and MONTH==1. In the end, I'd like a table that looks like this: YEAR MONTH #OBS 1994 1 2 1994 2 2 1994 3 0 1994 4 0 1994 5 0 1994 6 2 1994 7 0 1994 8 0 1994 9 0 1994 10 0 1994 11 0 1994 12 0 1995 1 0 1995 2 0 1995 3 2 1995 4 0 ... I do need to fill out the table with all the possible combinations, even where there are no observations with that combination in the data set. At first, it seemed like this would not be think that aggregate is probably the way to go, but there doesn't seem to be an appropriate summary function (FUN) available. Thanks in advance for any help in this matter, Josip __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Two envelopes problem
The reason that taking the log fixes things is because log( 2 ) = -log( 1/2 ), so log takes us to an additive difference. I think the use of log(utility) is actually based on experiments where people were asked what they were willing to risk for various potential gains and the results were more similar to the log than any other simple function (plus it makes sense based on the above). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Leeds Sent: Tuesday, August 26, 2008 9:44 AM To: 'Duncan Murdoch' Cc: r-help@r-project.org Subject: Re: [R] Two envelopes problem Hi Duncan: I think I get you. Once one takes expectations, there is an underlying assumption about the distribution of X and , in this problem, we don't have one so taking expectations has no meaning. If the log utility fixing the problem is purely just a coincidence, then it's surely an odd one because log(utility) is often used in economics for expressing how investors view the notion of accumulating capital versus the risk of losing it. I'm not a economist but it's common for them to use log utility to prove theorems about optimal consumption etc. Thanks because I think I see it now by your example below. Mark -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: Tuesday, August 26, 2008 11:26 AM To: Mark Leeds Cc: r-help@r-project.org Subject: Re: [R] Two envelopes problem On 8/26/2008 9:51 AM, Mark Leeds wrote: Duncan: I think I see what you're saying but the strange thing is that if you use the utility function log(x) rather than x, then the expected values are equal. I think that's more or less a coincidence. If I tell you that the two envelopes contain X and 2X, and I also tell you that X is 1,2,3,4, or 5, and you open one and observe 10, then you know that X=5 is the content of the other envelope. The expected utility of switching is negative using any increasing utility function. On the other hand, if we know X is one of 6,7,8,9,10, and you observe a 10, then you know that you got X, so the other envelope contains 2X = 20, and the expected utility is positive. As Heinz says, the problem does not give enough information to come to a decision. The decision *must* depend on the assumed distribution of X, and the problem statement gives no basis for choosing one. There are probably some subjective Bayesians who would assume a particular default prior in a situation like that, but I wouldn't. Duncan Murdoch Somehow, if you are correct and I think you are, then taking the log , fixes the distribution of x which is kind of odd to me. I'm sorry to belabor this non R related discussion and I won't say anything more about it but I worked/talked on this with someone for about a month a few years ago and we gave up so it's interesting for me to see this again. Mark -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Duncan Murdoch Sent: Tuesday, August 26, 2008 8:15 AM To: Jim Lemon Cc: r-help@r-project.org; Mario Subject: Re: [R] Two envelopes problem On 26/08/2008 7:54 AM, Jim Lemon wrote: Hi again, Oops, I meant the expected value of the swap is: 5*0.5 + 20*0.5 = 12.5 Too late, must get to bed. But that is still wrong. You want a conditional expectation, conditional on the observed value (10 in this case). The answer depends on the distribution of the amount X, where the envelopes contain X and 2X. For example, if you knew that X was at most 5, you would know you had just observed 2X, and switching would be a bad idea. The paradox arises because people want to put a nonsensical Unif(0, infinity) distribution on X. The Wikipedia article points out that it can also arise in cases where the distribution on X has infinite mean: a mathematically valid but still nonsensical possibility. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented,
Re: [R] Integrate a 1-variable function with 1 parameter (Jose L. Romero)
To Ravi Varadhan and Peter Dalgaard:
Infinite thanks for your help and suggestions- they were very instructive, as i
have still to learn on the appropriate use of the apply family of functions.
jlrp
--- On Wed, 8/27/08, Ravi Varadhan [EMAIL PROTECTED] wrote:
From: Ravi Varadhan [EMAIL PROTECTED]
Subject: RE: [R] Integrate a 1-variable function with 1 parameter (Jose L.
Romero)
To: [EMAIL PROTECTED], r-help@r-project.org
Date: Wednesday, August 27, 2008, 2:42 PM
Here is one way:
integrand - function (t, x) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
x - 0:44
ans - sapply(x, function(x) integrate(integrand,
lower=0, upper=10, x=x))
cbind(x=x, integral=unlist(ans[1,]),
abs.error=unlist(ans[2,]))
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On
Behalf Of jose romero
Sent: Wednesday, August 27, 2008 10:24 AM
To: r-help@r-project.org
Subject: [R] Integrate a 1-variable function with 1
parameter (Jose L.
Romero)
Hey fellas:
I would like to integrate the following function:
integrand - function (x,t) {
exp(-2*t)*(2*t)^x/(10*factorial(x))
}
with respect to the t variable, from 0 to 10.
The variable x here works as a parameter: I would like to
integrate the said
function for each value of x in 0,1,..,44.
I have tried Vectorize to no avail.
Thanks in advance,
jose romero
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[R] Combine x-axis labels size
Hello, I would like to combine different label sizes in the same x-axis, for example 1 2 3 4 5 6 7 8 9 How can I do it? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simple programming problem with 'with' or 'data ='
On 8/27/2008 1:15 PM, Peter Flom wrote:
Hello
I wrote a simple program to modify a boxplot:
gdsbox - function(indvar){
boxplot(indvar~gds3lev,
main = paste('Boxplot of', substitute(indvar), for GDS groups),
names = c('1', '3', '4, 5, 6'))
}
If I attach the dataframe gdsgraph, this works fine. However, I've been warned
against attach. When I tried to run this program using 'with', it did not work.
e.g.
with(gdsgraph, gdsbox(BReT3T5T))
produced an error that gds3level was not found
but if I try
with(gdsgraph, boxplot(BReT3T5T~gds3lev))
it works fine.
Similar problems occurred when I tried to use data =
What am I missing?
You defined your gdsbox function in the global environment, which means
it will go looking for non-local variables there. It doesn't matter
where you call it from, R uses lexical scoping.
To get what you want, you could define your function within the with, i.e.
with(gdsgraph, {
gdsbox - function(indvar){
boxplot(indvar~gds3lev,
main = paste('Boxplot of', substitute(indvar), for GDS groups),
names = c('1', '3', '4, 5, 6'))
}
gdsbox(BReT3T5T)
})
but this misses the point of defining gdsbox once, and using it in many
places. So I'd say the best thing to do is to change the definition of
it to use the data argument, i.e.
gdsbox - function(indvar, data) {
boxplot(indvar~gds3lev,
main = paste('Boxplot of', substitute(indvar), for GDS groups),
names = c('1', '3', '4, 5, 6'), data=data)
}
and call it as
gdsbox(BReT3T5T, gdsgraph)
There are ways to make your function act as though it doesn't use
lexical scoping (parent.env, etc.), but they are ugly, and I don't think
they're necessary here.
Duncan Murdoch
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combine x-axis labels size
Hi, I'm not sure I understand what you want, but perhaps: x - 1:9 y - x plot(x, y, ann=F, xaxt=n) axis(1, lab=F) - positions mtext(paste(positions), side = 1, line = 1, outer = F, at = test, cex=1:length(positions)) HTH, baptiste On 27 Aug 2008, at 18:36, Dani Valverde wrote: Hello, I would like to combine different label sizes in the same x-axis, for example 1 2 3 4 5 6 7 8 9 How can I do it? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combine x-axis labels size
Whoops, typo in my previous post: x - 1:10 y - x plot(x, y, ann=F, xaxt=n) axis(1, lab=F) - positions mtext(paste(positions), side = 1, line = 1, outer = F, at = positions, cex=seq(1, 9, length=length(positions))) Is this what you mean by label sizes? On 27 Aug 2008, at 18:51, baptiste auguie wrote: Hi, I'm not sure I understand what you want, but perhaps: x - 1:9 y - x plot(x, y, ann=F, xaxt=n) axis(1, lab=F) - positions mtext(paste(positions), side = 1, line = 1, outer = F, at = test, cex=1:length(positions)) HTH, baptiste On 27 Aug 2008, at 18:36, Dani Valverde wrote: Hello, I would like to combine different label sizes in the same x-axis, for example 1 2 3 4 5 6 7 8 9 How can I do it? Best, Dani -- Daniel Valverde Saubí Grup de Biologia Molecular de Llevats Facultat de Veterinària de la Universitat Autònoma de Barcelona Edifici V, Campus UAB 08193 Cerdanyola del Vallès- SPAIN Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN) Grup d'Aplicacions Biomèdiques de la RMN Facultat de Biociències Universitat Autònoma de Barcelona Edifici Cs, Campus UAB 08193 Cerdanyola del Vallès- SPAIN +34 93 5814126 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Two envelopes problem
-Original Message-
From: Mario [mailto:[EMAIL PROTECTED]
Sent: Monday, August 25, 2008 5:41 PM
To: Greg Snow
Cc: r-help@r-project.org
Subject: Re: [R] Two envelopes problem
Dear Greg,
The problem is that in your code you are creating a
distribution where there are only 5-10 and 10-20 pairs. Yes,
if I knew that there are only those two types of pairs, and
if I new that the probability of each pair was .50, .50, then
it is advantageous to switch, but that is because I have a
priori information on the distribution of the pairs. Now lets
assume, I opened the envelope, and I see £20, should I
switch? Well, now it depends. Are you going to rewrite the
simulation so that line 1 within tmpfun reads x -
sample(c(10,20), 1)? otherwise is not going to work. The
question is, if I see £20, according to my friend's argument,
I should switch, since there is a 50% chance of seeing 40 and
a 50% chance of seeing 10. However, in your simulation, £40's
are never seen, so under your simulator, switching every time
you see a £20 is a sure loss. You see, that's the problem.
You don't know the distribution of pairs, the fact that
you've got a tenner note, does not give you any additional
information. By the way, you could run your example with my
own code (which is faster as I'm not using sample for the
creation of the env pairs), just define the function
r5.10 - function(n) return (sample(c(5,10), n, rep=T))
and now:
env - generateenv(r=2, r5.10, n=1e6)
i10 - which(env[,1]==10)
mean(env[i10,1]) # Exactly 10
mean(env[i10,2]) # ~ 12.50 you do get a definite advantage
when switching
But this is an example that was tailored to work with the
actual value of £10.
Yes, conditional on you seeing 10, the only posibilities for x is 5 or 10. If
you want a more general approach, try this:
generateenv - function (r, rdist, n, ...) {
+ env - matrix(0, ncol=2, nrow=n)
+ env[,1] - rdist(n, ...) # first envelope has `x'
+ env[,2] - r*env[,1] # second envelope has `r*x'
+
+ # randomize de envelopes, so we don't know which one from
+ # the pair has `x' or `r*x'
+ i - as.logical(rbinom(n, 1, 0.5))
+ renv - env
+ renv[i,1] - env[i,2]
+ renv[i,2] - env[i,1]
+
+ return(renv) # return the randomized envelopes
+ }
TeachingDemos::char2seed('envelope')
# same as
# set.seed(5190728)
env - generateenv(r=2, rpois, n=1e6, lambda=10)
# keep envelope # 1 strategy (no conditioning)
mean(env[,1])
[1] 15.00811
# given envelope #1 == 10, expected value of switching
mean( env[ env[,1]==10, 2] )
[1] 16.54452
I generate data using your function and low and behold, given that the 1st
envelope is 10, the switching strategy is the winner. However this is
dependent on the distribution of x, change the distribution and the expected
gain can either increase or decrease.
But the original puzzle does not say anything about the distribution of x (or
implies uniform on 0,Infinity like Duncan mentions).
If you want this to work for any possible value of the 1st envelope, then the
distribution of x needs to be the improper infinite uniform, but once you give
a specific value to condition on, then the distribution of x only needs to be
relatively flat in the region of the value of the 1st envelope and half that
value (10 and 5 in this case):
env - generateenv(r=2, function(n,...) sample(3:52,n,replace=TRUE), n=1e6)
mean( env[ env[,1]==10, 2] )
[1] 12.55169
(expected value still greater than 10)
Your original post says that you told your friend that he was talking nonsense,
the real case is that you are working from a different set of assumptions than
your friend, and answering a different question. So in a sense you were both
correct, just working from different sets of assumptions of what was beyond the
stated question. My intent (beyond continuing the discussion/contriversy) was
to show that you were answering a different question than your friend and that
your answer to the different question does not make your friend's answer to his
question wrong.
One correction, in my prior post I talked about the n-envelope problem. The
strategy that I mentioned maximizes the probability of getting the envelope
with the highest value, not the expected value, any strategy for expected value
would depend on the distribution of the values which is not known in that
problem. Similar but different.
Is the idea that whichever envelope you choose, the strategy should be to
switch is really that unbelievable? Just ask anyone with at least 2 children,
more often than not when you give them something, they will all be convinced
that someone else received more/better. My daughters once even counted the
number of beans I put on their plate (their utility was the less was better),
then the one with fewer pointed out that her beans were longer (I put a stop to
it before they got out a ruler).
system.time(env - generateenv(r=2, r5.10, n=1e6)) # 0.500 0.020
[R] problems formating scientific collaboration data
Hello all and thanks in advance for any help or direction. I have co-authorship data that looks like: PaperAuthor Year 1 SmithKK JonesSD 2008 2 WallaceAR DarwinCA 1999 3 HawkingS2003 I would like: Paper Author Year 1 SmithKK 2008 1 JonesSD 2008 2 WallaceAR 1999 2 DarwinCA1999 3 HawkingS2003 Thanks for your patience with what is likely an easy question r-help@r-project.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problems formating scientific collaboration data
Hi, name of the data.frame is assumed to be dt. cnt.tmp - strsplit(dt$Author, ) cnt - sapply(cnt.tmp, length) paper.cnt - dt$Paper[cnt] author - unlist(cnt.tmp) year - dt$Year[cnt] dt.new - data.frame(Paper = paper.cnt, Author = author, Year = year) HTH, Dong-hyun Oh On Aug 27, 2008, at 9:27 PM, Grant Gillis wrote: Hello all and thanks in advance for any help or direction. I have co-authorship data that looks like: PaperAuthor Year 1 SmithKK JonesSD 2008 2 WallaceAR DarwinCA 1999 3 HawkingS2003 I would like: Paper Author Year 1 SmithKK 2008 1 JonesSD 2008 2 WallaceAR 1999 2 DarwinCA1999 3 HawkingS2003 Thanks for your patience with what is likely an easy question r-help@r-project.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lattice: plotting an arbitrary number of panels, defining arbitrary groups
On Tue, Aug 26, 2008 at 6:56 PM, Alex Karner [EMAIL PROTECTED] wrote: Thanks Deepayan, works like a charm. A followup question though--I'd like to produce the same data on four panels with the final two zoomed in, i.e. plotted with shorter x and y axes. Since I can't access panel.number in the prepanel function, and since updating the plot with lists of the new x and y axis ranges via xlim and ylim doesn't work (I think since I only actually have one repeated panel), There is no simple way to do this. The lattice model associates axis limits with packets (data subsets that go in panels) and not panels (i.e., if two or more panels display the same packet, they will also have the same limits). One way to work around this is to override the default axis annotation. The easier solution is to make a second copy of your data. E.g., dataSet2 - make.groups(full = dataSet, sub = subset(dataSet, Value y1 Value y2 Detector x1 Detector x2)) p - xyplot(Value ~ Detector | which, dataSet2, scales = free) and then proceed as before. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problems formating scientific collaboration data
Dear Grant, Try this: x=Paper,Author, Year 1,SmithKK JonesSD, 2008 2,WallaceAR DarwinCA, 1999 3,HawkingS, 2003 X=read.delim2(textConnection(x),sep=,,header=TRUE) closeAllConnections() author= strsplit(as.character(X$Author), ) l=lapply(author,length) P=rep(X$Paper,l) Y=P=rep(X$Year,l) X.new=data.frame(Paper=P,Authore=unlist(author),Year=Y) X.new HTH, Jorge On Wed, Aug 27, 2008 at 3:27 PM, Grant Gillis [EMAIL PROTECTED]wrote: Hello all and thanks in advance for any help or direction. I have co-authorship data that looks like: PaperAuthor Year 1 SmithKK JonesSD 2008 2 WallaceAR DarwinCA 1999 3 HawkingS2003 I would like: Paper Author Year 1 SmithKK 2008 1 JonesSD 2008 2 WallaceAR 1999 2 DarwinCA1999 3 HawkingS2003 Thanks for your patience with what is likely an easy question r-help@r-project.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problems formating scientific collaboration data
I'm sorry Grant, my bad. To reproduce what you'd like to do, my previous code should be: x=Paper,Author, Year 1,SmithKK JonesSD, 2008 2,WallaceAR DarwinCA, 1999 3,HawkingS, 2003 X=read.delim2(textConnection(x),sep=,,header=TRUE) closeAllConnections() author= strsplit(as.character(X$Author), ) l=lapply(author,length) P=rep(X$Paper,l) Y=rep(X$Year,l) X.new=data.frame(Paper=P,Author=unlist(author),Year=Y) X.new HTH, Jorge On Wed, Aug 27, 2008 at 3:59 PM, Jorge Ivan Velez [EMAIL PROTECTED]wrote: Dear Grant, Try this: x=Paper,Author, Year 1,SmithKK JonesSD, 2008 2,WallaceAR DarwinCA, 1999 3,HawkingS, 2003 X=read.delim2(textConnection(x),sep=,,header=TRUE) closeAllConnections() author= strsplit(as.character(X$Author), ) l=lapply(author,length) P=rep(X$Paper,l) Y=P=rep(X$Year,l) X.new=data.frame(Paper=P,Authore=unlist(author),Year=Y) X.new HTH, Jorge On Wed, Aug 27, 2008 at 3:27 PM, Grant Gillis [EMAIL PROTECTED]wrote: Hello all and thanks in advance for any help or direction. I have co-authorship data that looks like: PaperAuthor Year 1 SmithKK JonesSD 2008 2 WallaceAR DarwinCA 1999 3 HawkingS2003 I would like: Paper Author Year 1 SmithKK 2008 1 JonesSD 2008 2 WallaceAR 1999 2 DarwinCA1999 3 HawkingS2003 Thanks for your patience with what is likely an easy question r-help@r-project.org [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] r function for calculating extreme spread in group
I'm trying to figure out how to write a r function that will calculate
the extreme spread of a group of points given their (x,y)
coordinates. Extreme Spread is the maximal Euclidean distance between
two points in a group
ex.spread = max{ sqrt [ (xi-xj)^2 - (yi-yj)^2 ] } for i not equal to j
I have 60 levels to apply this to.
There is the combination function in the dprep package but I wasn't
sure how to use this or apply an index the points in each group.
Any ideas?
Steve
Steven Matthew Anderson
[EMAIL PROTECTED]
Ad Astra per Aspera
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Re: [R] Basic question about X11()
On Wed, 27-Aug-2008 at 02:42PM +0200, Groeneweg M (GEN) wrote:
| Hello,
|
| I have a basic question about the display() function, but I can't find the
answer easily.
|
| I am running R 2.7.16.0 on Suse linux 11.0
Are you sure of that? R-2.7.2 is the most recent.
| with KDE 4.0
Your question is one relating to your window manager. The display
parameter for x11() does not relate to desktops. All the desktops are
part of the same display. Some very clever R-devel people might be
able to think of a way of making a specific X call to achieve what you
want, but it seems unlikely to me that it could be make to work with
more than one window manager.
It's very simple in KDE to set up keyboard shortcuts to move a window
to a specific desktop.
HTH
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] conversion of data structure between R and Perl
Dear R users,
I am trying to call a Perl subroutine from R . The subroutine returns an
arrray contaning three elements wihch are all strings. But the calling in R
return an integer which is 0. I have no idea how this could happen. Maybe
becasue I shouldn't use system() in R or I should load a particular package
for my R in windows. Please help
---
the perl subroutine in presentPerformance.pl
sub findAccuracy{
while(defined($filename=glob(*.log))){
open(WORDLIST , $filename)||die(can't open the file!);
while($line=WORDLIST){
if ($line=~m/accuracy/){
$line=~s/-accuracy://;
@temp=split( ,$line);
$temp[0]=~s/\%//;
$temp[2]=~s/\%//;
@accInfoList=($temp[0],$temp[2],$filename);
}
}
}
return(@accInfoList)
}
findAccuracy();
The R code
class(system(perl presentPerformance.pl))
[1] integer
regard,
Shu-Kai Chang
--
View this message in context:
http://www.nabble.com/conversion-of-data-structure-between-R-and-Perl-tp19189221p19189221.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] conversion of data structure between R and Perl
You need to do:
system(perl presentPerformance.pl,intern=TRUE)
It does pay to read the help, you know.
cheers,
Rolf Turner
On 28/08/2008, at 8:36 AM, kevinchang wrote:
Dear R users,
I am trying to call a Perl subroutine from R . The subroutine
returns an
arrray contaning three elements wihch are all strings. But the
calling in R
return an integer which is 0. I have no idea how this could happen.
Maybe
becasue I shouldn't use system() in R or I should load a particular
package
for my R in windows. Please help
---
the perl subroutine in presentPerformance.pl
sub findAccuracy{
while(defined($filename=glob(*.log))){
open(WORDLIST , $filename)||die(can't open the file!);
while($line=WORDLIST){
if ($line=~m/accuracy/){
$line=~s/-accuracy://;
@temp=split( ,$line);
$temp[0]=~s/\%//;
$temp[2]=~s/\%//;
@accInfoList=($temp[0],$temp[2],$filename);
}
}
}
return(@accInfoList)
}
findAccuracy();
--
--
The R code
class(system(perl presentPerformance.pl))
[1] integer
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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Re: [R] Basic question about X11()
2008/8/27 Patrick Connolly [EMAIL PROTECTED]: Your question is one relating to your window manager. The display parameter for x11() does not relate to desktops. All the desktops are part of the same display. Some very clever R-devel people might be able to think of a way of making a specific X call to achieve what you want, but it seems unlikely to me that it could be make to work with more than one window manager. It's very simple in KDE to set up keyboard shortcuts to move a window to a specific desktop. There's some X11 command utilities to muck with window placements: devilspie: this runs in the background and watches for windows being created. If any match the rules given in a file then a function is applied, so for example any window with 'R' in the title can be moved to Workspace 2. You can set the title on an X11 window with X11(title=WS2). (The config files (.ds files) are written in a lisp-like language but there's plenty of help on the web) wmctrl: this is a shell command that moves (and otherwise plays with) existing windows. For example if you do: wmctrl -r R Graphics -t 2 it will move the window with title R Graphics to workspace 2. You could run this in R after doing X11() with the R function call system(wmctrl ...etc...) Both these methods will cause the window to briefly flash in the current workspace before moving. Some window managers have the facility to place specific windows in specific workspaces by putting them in config files if you don't want the window to flash up in front of the user. Good luck with that then... Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] r function for calculating extreme spread in group
Steven Matthew Anderson adastra69 at mac.com writes:
I'm trying to figure out how to write a r function that will calculate
the extreme spread of a group of points given their (x,y)
coordinates. Extreme Spread is the maximal Euclidean distance between
two points in a group
ex.spread = max{ sqrt [ (xi-xj)^2 - (yi-yj)^2 ] } for i not equal to j
I have 60 levels to apply this to.
how about something like
max(dist(cbind(x,y)) ... ???
(or to do this in a data frame d with columns x, y, and g (group),
sapply(split(d,d$g),function(Z)max(dist(Z[,c(x,y)])))
Ben Bolker
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