Re: [R] how can I plot the histogram like this using R?
Aer you asking how to have more bars on the axis ? That can be controlled using: barplot(stuff, br = 50) # br can be other numbers according to needs. The vertical line can be done with: abline(v=20) # You may change 20 There are other elements to the plot to reproduce, but is this enough for your needs? Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Apr 14, 2010 at 7:45 AM, bbslover dlu...@yeah.net wrote: I want to get the plot like this, http://n4.nabble.com/file/n1839303/%25E9%25A2%2591%25E7%258E%2587%25E5%2588%2586%25E5%25B8%2583%25E5%259B%25BE%25E6%25A0%2587%25E5%2587%2586.jpg %E9%A2%91%E7%8E%87%E5%88%86%E5%B8%83%E5%9B%BE%E6%A0%87%E5%87%86.jpg not this, http://n4.nabble.com/file/n1839303/R.jpg R.jpg and the data here, thank you! http://n4.nabble.com/file/n1839303/y1.txt y1.txt can R deal with this problem? how can I do? -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p1839303.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. [[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] maptools-export owin as shapefile, error message
Hello R users, I am trying to export an object of class owin from the Spatstat package to an ESRI shapefile using the package Maptools. I am using the function writePolyShape; pointsp is an object of class ppp, ripras is a function in SpatStat that creates a polygon around points. I have tried with several different owin objects and each time I get the same error, as follows. x=ripras(pointsp,shape=convex) xpoly=as(x,SpatialPolygons) xpolyframe=as(xpoly,SpatialPolygonsDataFrame) class(xpolyframe) [1] SpatialPolygonsDataFrame attr(,package) [1] sp writePolyShape(xpolyframe,pgon) Error in write.polylistShape(pls, df, file = fn, factor2char = factor2char, : different number of rows in polylist and data frame thanks for any help, Tom Elliott, Central Washington University [[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] WinBUGS Question
Or even easier: Use BRugs which has a considerably cleaner interface and
does not need to restart the WinBUGS executable again and again.
Uwe Ligges
On 13.04.2010 22:45, Yihui Xie wrote:
If you are using R2WinBUGS, I guess you may put them in a loop like:
# models
...
data_i[j]~dnorm(...)
...
# save them in a sequence of files with names like 'model_i.bug'
# write.model() might help?
# then call bugs()
for(i in names.of.your.100.datasets){
bugs(data=i,...,model.file='model_i.bug',...)
}
The above code might need paste() here and there, e.g. paste('data_',
i, sep='').
I don't know if WinBUGS itself supports such a loop.
Regards,
Yihui
--
Yihui Xiexieyi...@gmail.com
Phone: 515-294-6609 Web: http://yihui.name
Department of Statistics, Iowa State University
3211 Snedecor Hall, Ames, IA
On Tue, Apr 13, 2010 at 1:48 PM, Anamika Chaudhuricanam...@gmail.com wrote:
Hi:
Is there a way we can set up WINBUGS to run 100 simulated datasets on the
same model and output results? Or do we have to call in each dataset at a
time and repeat the process 100 times manually?
Thanks
Anamika
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[R] Problem trying to plot Vennerable object
Hi, I'm new to the list so apologies if this has been asked before. I couldn't find any refs in google. I recently installed the Vennerable library from Rforge, this required an upgrade of R to 2.10.0 by the 'pylr' dependency. However, a very simple command fails: Vcomb - Venn(SetNames= c(EOCT, EOCM), Weight=c(0, 11841, 24084, 24660)) plot(Vcomb) with this error: Error in do.call(c, lapply(.faceNames(new1), .faceEdgeNames, drawing = new1)) : 'what' must be a character string or a function What's frustrating is that a colleague with different versions of R (2.8.x) and some of the libraries gets the above function to work fine. I have no idea how to debug this error. Any help would be much appreciated. Chris __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0
Dear colleagues, in the help archive there was a previous person who encountered a problem with the recode command in the car library. I'm not sure if that was solved, there was no posting to that effect, but I'm having the same problem. I'm trying to recode a numeric variable with values from 0-100 into a binary variable with values (0,1). The following command: recode(green_2004_2$french, c(50:100)=0; c(0:49.99)=1) gets the following error message Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 I tried it with a second numerical variable in the same data set, but get precisely the same error at precisely the same location in the command, i.e. the second colon. As far as I can tell I have the most up-to-date version of car installed. Any suggestions? Yours, Simon Kiss * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] creating a new corClass for lme()
No idea if this helps, but if the optimizer (nlminb) is giving you problems,
you could try switching to another optimizer (nlm) with:
control=list(opt=nlm)
Best,
--
Wolfgang Viechtbauerhttp://www.wvbauer.com/
Department of Methodology and StatisticsTel: +31 (43) 388-2277
School for Public Health and Primary Care Office Location:
Maastricht University, P.O. Box 616 Room B2.01 (second floor)
6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck)
Original Message
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Michael Steven
Rooney Sent: Wednesday, April 14, 2010 07:07 To: r-help@r-project.org
Subject: [R] creating a new corClass for lme()
Hi,
I have been using the function lme() of the package nlme to model
grouped data that is auto-correlated in time and in space (the data
was collected on different days via a moving monitor). I am aware
that I can use the correlation classes corCAR1 and corExp (among
other options) to model the temporal and spatial components of the
auto-correlation. However, as far as I can tell, I can only model
using one correlation class or the other. I would like my model to
account for both temporal and spatial autocorrelation simultaneously.
The ?corClasses help page provides some advice on how to create your
own correlation class. I was able to create a new class that I called
corSPT: I add the spatial and temporal autocorrelation matrices to
produce the corSPT correlation matrix. The code for this is pasted
below:
## BEGIN ###
# Create some data
N - 100
x - round(sin(rep(1:23/2,length.out=N)),digits=2)+1:N*2/N
y - round(cos(rep(1:23/2,length.out=N)),digits=2)+1:N*2/N
g - rep(1:5,each=N/5)
a - round(runif(N,0,10))
t - 1:N
r - runif(N,0,5)
e - 5*sin(4*x) +
5*cos(4*y) +
5*sin(t) +
2*g +
a +
r
e - round(e)
df - data.frame(x,y,g,a,t,r,e)
library(nlme)
# Define constructor function and methods
corSPT - function(a,b) {
object - list(time=a,space=b)
class(object) - c(corSPT,corStruct)
return(object)
}
coef.corSPT - function(object,...) {
c(coef(object[[time]],...)[1],coef(object[[space]],...))
}
coef-.corSPT - function(object,...,value) {
coef(object[[time]]) - value[1]
coef(object[[space]]) - value[2:3]
class(object) - c(corSPT,corStruct)
return(object)
}
Initialize.corSPT - function(object,...) {
object -
list(time=Initialize(object[[time]],...),space=Initialize(object[[space]],...))
class(object) - c(corSPT,corStruct)
return(object)
}
corMatrix.corSPT - function(object,covariate = NULL, ...) {
a -
corMatrix(object[[time]],covariate=getCovariate(object[[time]]),...)
b -
corMatrix(object[[space]],covariate=getCovariate(object[[space]]),...)
lapply(seq(length(a)),function(n) pmax(-1,pmin(1,a[[n]]+b[[n]]))) }
formula.corSPT - function(object,...) {
a - as.character(formula(object[[time]]))
b - as.character(formula(object[[space]]))
a - strsplit(a[2],split=|,fixed=TRUE)[[1]]
b - strsplit(b[2],split=|,fixed=TRUE)[[1]]
as.formula(paste(~,a[1],+,b[1],|,a[2]))
}
Dim.corSPT - function(object,...) {
Dim(object[[time]],...)
}
END ###
When I run this model on:
mymodel - lme(fixed = e ~ a,random= ~ 1 |
g,data=df,correlation=corSPT(corCAR1(.2,form = ~ t |
g),corExp(c(1,.5),form= ~ x + y | g,
nugget=TRUE)),control=list(msVerbose=TRUE))
I get sensible results. However if I change the way the temporal data
is
modeled:
mymodel - lme(fixed = e ~ a,random= ~ 1 |
g,data=df,correlation=corSPT(corExp(.2,form = ~ t |
g),corExp(c(1,.5),form= ~ x + y | g,
nugget=TRUE)),control=list(msVerbose=TRUE))
I get a C runtime error. I have been trying to track this down using
browser() and debug(), but all I have been able to tell is that the
problem arises during
.Call(R_port_nlminb,obj,grad,hess,rho,low,upp,d=rep(as.double(scale),length.out=length(par)),iv,v)
in the nlminb() function.
Please let me know if you know what might be going on. I am using R
version 2.7.2 on Windows XP.
Thanks,
Mike
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[R] GAMM : how to use a smoother for some levels of a variable, and a linear effect for other levels?
Hi, I was reading the book on Mixed Effects Models and Extensions in Ecology with R by Zuur et al. In Section 6.2, an example is discussed where a gamm-model is fitted, with a smoother for time, which differs for each value of ID (4 different bird species). In earlier versions of R, the following code was used BM2-gamm(Birds~Rain+ID+ s(Time,by=as.numeric(ID==Stilt.Oahu))+ s(Time,by=as.numeric(ID==Stilt.Maui))+ s(Time,by=as.numeric(ID==Coot.Oahu))+ s(Time,by=as.numeric(ID==Coot.Maui)), correlation=corAR1(form=~Time |ID ), weights=varIdent(form=~1|ID)) However, in the current version of R, this does not work anymore, and should be changed into BM2-gamm(Birds~Rain+ID+ s(Time,by=ID), correlation=corAR1(form=~Time |ID ), weights=varIdent(form=~1|ID)) It turns out that 2 of the 4 smoothers have estimated degrees of freedom of 1, so a linear effect would be sufficient. Now my question is how I need to change the code in order to have a time smoother for ID=Coot.Oahu and ID=Coot.Maui, and a linear time effect for ID=Stilt.Oahu and ID=Stilt.Maui. With the old R-code, this seems trivial, but I don't have any idea how to do it in the newest R-version (interactions with a dummy variable do not work in gamm). Thanks, Ivy Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] sum specific rows in a data frame
I have a data frame called pose: DESCRIPTION QUANITY CLOSING.PRICE 1 WHEAT May/101467.75 2 WHEAT May/102467.75 3 WHEAT May/101467.75 4 WHEAT May/101467.75 5 COTTON NO.2 May/101 78.13 6 COTTON NO.2 May/103 78.13 7 COTTON NO.2 May/101 78.13 I would like to sum the quantity for each category (i.e WHEAT and COTTON),but I have no idea how to write it in a simple manner. The number or rows will change every day. TY for any help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bayesian bootstrap with boot
Hi, I wonder about whether it is possible to perform a Bayesian bootstrap using the boot package. The documentation isn't very detailed and I don't have the associated book. So I would be glad, if someone could help me. If it isn't possible: Which package / which function can I use instead? I'm rather new to R, so I don't have much knowledge about writing programs and it would be nice, if there exists an easy to use package. Thanks! Hans-Peter Hafner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] sum specific rows in a data frame
Hi Arnaud, Try aggregate function regards M arnaud Gaboury a écrit : I have a data frame called pose: DESCRIPTION QUANITY CLOSING.PRICE 1 WHEAT May/101467.75 2 WHEAT May/102467.75 3 WHEAT May/101467.75 4 WHEAT May/101467.75 5 COTTON NO.2 May/101 78.13 6 COTTON NO.2 May/103 78.13 7 COTTON NO.2 May/101 78.13 I would like to sum the quantity for each category (i.e WHEAT and COTTON),but I have no idea how to write it in a simple manner. The number or rows will change every day. TY for any help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mohamed Lajnef,IE INSERM U955 eq 15 Pôle de Psychiatrie Hôpital CHENEVIER 40, rue Mesly 94010 CRETEIL Cedex FRANCE mohamed.laj...@inserm.fr tel : 01 49 81 31 31 (poste 18470) Sec : 01 49 81 32 90 fax : 01 49 81 30 99 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0
Get rid of the unnecessary c(...) construction: recode(green_2004_2$french, 50:100=0; 0:49.99=1) -Peter Ehlers On 2010-04-14 1:56, Simon Kiss wrote: Dear colleagues, in the help archive there was a previous person who encountered a problem with the recode command in the car library. I'm not sure if that was solved, there was no posting to that effect, but I'm having the same problem. I'm trying to recode a numeric variable with values from 0-100 into a binary variable with values (0,1). The following command: recode(green_2004_2$french, c(50:100)=0; c(0:49.99)=1) gets the following error message Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 I tried it with a second numerical variable in the same data set, but get precisely the same error at precisely the same location in the command, i.e. the second colon. As far as I can tell I have the most up-to-date version of car installed. Any suggestions? Yours, Simon Kiss * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem trying to plot Vennerable object
On 2010-04-14 1:54, Chris Cole wrote:
Hi,
I'm new to the list so apologies if this has been asked before. I
couldn't find any refs in google.
I recently installed the Vennerable library from Rforge, this required
an upgrade of R to 2.10.0 by the 'pylr' dependency.
However, a very simple command fails:
Vcomb - Venn(SetNames= c(EOCT, EOCM), Weight=c(0, 11841, 24084,
24660))
plot(Vcomb)
with this error:
Error in do.call(c, lapply(.faceNames(new1), .faceEdgeNames, drawing =
new1)) :
'what' must be a character string or a function
I don't know the Vennerable *package*, but does this tell you
anything:
do.call(c, list('a', 'b'))
[1] a b
c - 3
do.call(c, list('a', 'b'))
Then try
rm(c)
and run your Venn code again.
-Peter Ehlers
What's frustrating is that a colleague with different versions of R
(2.8.x) and some of the libraries gets the above function to work fine.
I have no idea how to debug this error. Any help would be much appreciated.
Chris
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--
Peter Ehlers
University of Calgary
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[R] MiscPsycho - incorrect levenshtein distance?
For some strings I get a wrong (MiscPsycho) Levenstein distance: stringMatch(abc, ab, normalize=NO) [1] 1 stringMatch(abc, bc, normalize=NO) [1] 2 I think the lines d - matrix(0, nrow = n + 1, ncol = m + 1) d[, 1] - 1:(n + 1) d[1, ] - 1:(m + 1) d[1, 1] - 0 should be changed to d - matrix(0, nrow = n + 1, ncol = m + 1) d[, 1] - 0:n d[1, ] - 0:m __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R package documentation
Dear R users, I am currently writing the documentation for my first package. I have created a short user manual using sweave/pdflatex which is distinct from the manual/summary-of-package-functions created by R CMD CHECK. I was wondering how could I seamlessly combine both documents. Thanks for your help Sebastien [[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: could not find function tsts tradesys package
Did you load tradesys after you installed it? library(tradesys) That seems to be a common beginner problem. Sarah On Tue, Apr 13, 2010 at 9:56 PM, dbonneau daronnebonn...@gmail.com wrote: Hi, I am pretty new to R and would like to follow the code in the paper below, tradesys package. but I am stuck at the 2nd page where x-tsts(spx) is written. Could anyopne help me why I am getting an Error :could not find function tsts . I guess I need function call tsts. where can I find that function ? I installed tradesys, zoo, RUnit packages but I don't know why it gives me error. Thanks http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/*checkout*/pkg/inst/doc/tradesys.pdf?rev=19root=tradesys -- View this message in context: http://n4.nabble.com/Error-could-not-find-function-tsts-tradesys-package-tp1839233p1839233.html Sent from the R help mailing list archive at Nabble.com. _ -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package documentation
Hi Sébastien, Sébastien Bihorel wrote: I am currently writing the documentation for my first package. I have created a short user manual using sweave/pdflatex which is distinct from the manual/summary-of-package-functions created by R CMD CHECK. I was wondering how could I seamlessly combine both documents. It is common to have - technical documentation in your .Rd files (in the man/ directory of your package) - functional documentation as a so-called vignette (Sweave file documenting concrete use of your package) in the inst/doc directory of your package. http://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes Combining both documents into one file is not common. I hope this helps, Tobias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package documentation
Hi Tobias, The .R files that I have created for all my functions are somehow used to generate a package manual pdf when I used R CMD CHECK. This is what I'd like to add in my vignette. It might be uncommon, but I saw this was done for several package documentations (e.g. PBS collections) and I kind of like this combination. Sebastien On Wed, Apr 14, 2010 at 6:52 AM, Tobias Verbeke tobias.verb...@openanalytics.eu wrote: Hi Sébastien, Sébastien Bihorel wrote: I am currently writing the documentation for my first package. I have created a short user manual using sweave/pdflatex which is distinct from the manual/summary-of-package-functions created by R CMD CHECK. I was wondering how could I seamlessly combine both documents. It is common to have - technical documentation in your .Rd files (in the man/ directory of your package) - functional documentation as a so-called vignette (Sweave file documenting concrete use of your package) in the inst/doc directory of your package. http://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes Combining both documents into one file is not common. I hope this helps, Tobias [[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 can I plot the histogram like this using R?
thanks for your help. I can have a try. -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p1839534.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] Problems getting symbols() to show table data
Hello, I am trying to create a graphic to help me visualise data. A (very simplified) sample of the data is http://n4.nabble.com/file/n1839676/circle_data.txt circle_data.txt : Aug-07 Nov-07 Feb-08 data1 1 1.5 -1 data2 1 1.2 1.6 data3 1.31.41.8 data4 1.3 -1.21 What I am trying to achieve is: * Circles representing each item of data, * The circle size represents the number, * The data is arranged in rows and columns, similar to the table layout (i.e. dates along the top or bottom), * Positive numbers are blue circles, negative red circles. I have used info from lots of previous posts on symbols() to get me some of the way, but I am still far off getting it to actually work, with the result that I think I may be heading in completely the wrong direction. I can create a grid of circles with the right number of dimensions: Read_data=read.table(C:/files/circle_data.txt, head = T) number_rows = nrow(Read_data) number_cols = ncol(Read_data) xaxis = rep(seq(1,ncol(Read_data),1),nrow(Read_data)) yaxis = rep(seq(1,nrow(Read_data),1),ncol(Read_data)) zvalues = rep(0.1,(number_rows*number_cols))#This is just a dummy vector symbols(xaxis, yaxis, circles = zvalues, inches = FALSE, xlab=, ylab=) axis(2, at=c(1:number_rows), rownames(Read_data), las = 1) axis(1, at=c(1:number_cols), colnames(Read_data)) BUT... this only uses dummy values - I can't think how to get the table into a form the symbols() function can use. I tried as.vector() unsuccessfully. Also, this code simply overwrites the x and y-axis labels, which looks terrible: again, I can't think how to get this right from the start. On getting positive values to be blue and negative red, I had assumed I could just split the data into two and plot separately: Data_positive = replace(Read_data, Read_data0,0) Data_negative = -replace(Read_data, Read_data0,0) However, this quick trial below gives little dots for zero values, so it is not a perfect result: zvalues_pos = rep(c(0.1,0.2,0), 4) #Dummy vector for positives zvalues_neg = rep(c(0,0,0.3), 4)#Dummy vector for negatives symbols(xaxis, yaxis, circles = zvalues_pos, inches = FALSE, xlab=, ylab=, bg=blue) symbols(xaxis, yaxis, circles = zvalues_neg, inches = FALSE, xlab=, ylab=, bg=red, add=TRUE) [Incidentally, I have tried to work through this example ( http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=152 http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=152 ) but I am out of my depth in making sense of the code.] Any help would be gratefully received. Thanks, Guy -- View this message in context: http://n4.nabble.com/Problems-getting-symbols-to-show-table-data-tp1839676p1839676.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] how can I plot the histogram like this using R?
thank you, I will try this function barplot. -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p1839541.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] Running cumulative sums in matrices
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as possible. Can
someone think how I can compute the result in the following example (that uses
a for-loop) using some version of apply instead (or any other similarly
super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column containing the cumulative
sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package documentation
Hi Sébastien, Sébastien Bihorel wrote: The .R files that I have created for all my functions are somehow used to generate a package manual pdf when I used R CMD CHECK. This is what I'd like to add in my vignette. It might be uncommon, but I saw this was done for several package documentations (e.g. PBS collections) and I kind of like this combination. I now understand what you mean. The PBS documentation you refer to seems a mere (manual) concatenation of a (non-LaTeX based) pdf document and the reference manual pdf which is not generated from a Sweave file. Such manipulations can be done using e.g. the pdfjam toolbox by David Firth. http://go.warwick.ac.uk/pdfjam Best, Tobias On Wed, Apr 14, 2010 at 6:52 AM, Tobias Verbeke tobias.verb...@openanalytics.eu mailto:tobias.verb...@openanalytics.eu wrote: Hi Sébastien, Sébastien Bihorel wrote: I am currently writing the documentation for my first package. I have created a short user manual using sweave/pdflatex which is distinct from the manual/summary-of-package-functions created by R CMD CHECK. I was wondering how could I seamlessly combine both documents. It is common to have - technical documentation in your .Rd files (in the man/ directory of your package) - functional documentation as a so-called vignette (Sweave file documenting concrete use of your package) in the inst/doc directory of your package. http://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes Combining both documents into one file is not common. I hope this helps, Tobias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Running cumulative sums in matrices
Hi:
Is this what you want?
m1=cbind(1:5,1:5,1:5)
apply(m1, 1, cumsum)
[,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]2468 10
[3,]369 12 15
HTH,
Dennis
On Wed, Apr 14, 2010 at 5:18 AM, Eleni Rapsomaniki
er...@medschl.cam.ac.ukwrote:
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as possible. Can
someone think how I can compute the result in the following example (that
uses a for-loop) using some version of apply instead (or any other similarly
super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column containing the
cumulative sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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]]
__
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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] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0
Dear Simon, The problem is that the recode specification is incorrect: In recode(), colons mean ranges, and shouldn't appear within c(), which is used to list values. See ?recode, and the following example: (green_2004_2 - data.frame(french=runif(10, 0, 100))) french 1 42.693517 2 18.063822 3 21.046906 4 17.045596 5 9.308359 6 30.018840 7 53.598261 8 17.739567 9 65.836818 10 37.727236 recode(green_2004_2$french, 50:100=0; 0:49.99=1) [1] 1 1 1 1 1 1 0 1 0 1 BTW, 50:100=0; 0:50=1 will produce the same result -- again see ?recode. Finally, it's generally a good idea to send a small reproducible example with a question like this. What if there were really a data-dependent bug in recode()? I hope this helps, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Simon Kiss Sent: April-14-10 3:56 AM To: r-help@r-project.org Subject: [R] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 Dear colleagues, in the help archive there was a previous person who encountered a problem with the recode command in the car library. I'm not sure if that was solved, there was no posting to that effect, but I'm having the same problem. I'm trying to recode a numeric variable with values from 0-100 into a binary variable with values (0,1). The following command: recode(green_2004_2$french, c(50:100)=0; c(0:49.99)=1) gets the following error message Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 I tried it with a second numerical variable in the same data set, but get precisely the same error at precisely the same location in the command, i.e. the second colon. As far as I can tell I have the most up-to-date version of car installed. Any suggestions? Yours, Simon Kiss * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Running cumulative sums in matrices
?cumsum can help you
m1 - cbind(1:5,1:5,1:5)
m2 - m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m3 - t(apply(m1, 1, cumsum))
all.equal(m2, m3)
HTH,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] Namens Eleni Rapsomaniki
Verzonden: woensdag 14 april 2010 14:18
Aan: r-help@r-project.org
Onderwerp: [R] Running cumulative sums in matrices
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as
possible. Can someone think how I can compute the result in
the following example (that uses a for-loop) using some
version of apply instead (or any other similarly
super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column
containing the cumulative sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care University of Cambridge
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in this message
and any annex are purely those of the writer and may not be regarded as stating
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] how can I plot the histogram like this using R?
Hi, My bid - do all that I wrote with hist instead of barplot Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Apr 14, 2010 at 12:46 PM, bbslover dlu...@yeah.net wrote: thank you, I will try this function barplot. -- View this message in context: http://n4.nabble.com/how-can-I-plot-the-histogram-like-this-using-R-tp1839303p1839541.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. [[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] can not execute two functions - env() and profile()
Hi, I had the same problem on windows with same R version... With the package lme4a (from R-forge), I can use the env() function. However, I am still unable to use the profile function (in the aim of establishing confidence interval for the std devaition of random effect). any help will be greatly appreciated!! pierre -- View this message in context: http://n4.nabble.com/can-not-execute-two-functions-env-and-profile-tp1836709p1839737.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0
On Apr 14, 2010, at 2:56 AM, Simon Kiss wrote: Dear colleagues, in the help archive there was a previous person who encountered a problem with the recode command in the car library. I'm not sure if that was solved, there was no posting to that effect, but I'm having the same problem. I'm trying to recode a numeric variable with values from 0-100 into a binary variable with values (0,1). The following command: recode(green_2004_2$french, c(50:100)=0; c(0:49.99)=1) Look at the last example in the recode help page: recode(x, 1:2='A'; 3='B') ## [1] A A B A A B A A B It appears to me that the c() function around your sequences may be part of the problem and I further wondered whether 0:49.99 can succeed. Generally the : operator expects integer arguments, but the help page is not clear in this area and it appears that recode has a different interpretation. require(car) recode(x, -Inf:0=-1; 0.01:Inf=1) # succeeds -- David gets the following error message Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 I tried it with a second numerical variable in the same data set, but get precisely the same error at precisely the same location in the command, i.e. the second colon. As far as I can tell I have the most up-to-date version of car installed. Any suggestions? Yours, Simon Kiss * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Running cumulative sums in matrices
you can even use a simple for-loop, e.g.,
m1 - cbind(1:5,1:5,1:5)
out - m1
for(i in 1:nrow(out))
out[i, ] - cumsum(out[i, ])
which seems to be faster than apply(m1, 1, cumsum), i.e.,
m1 - m1[rep(1:5, each = 1e04), ]
library(rbenchmark)
benchmark(
apply = apply(m1, 1, cumsum),
for = {out - m1; for(i in 1:nrow(out)) out[i, ] - cumsum(out[i,
])},
replications = 50, order = relative
)
I hope it helps.
Best,
Dimitris
On 4/14/2010 2:18 PM, Eleni Rapsomaniki wrote:
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as possible. Can
someone think how I can compute the result in the following example (that uses
a for-loop) using some version of apply instead (or any other similarly
super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column containing the cumulative
sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
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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] Problems getting symbols() to show table data
Try this: library(gplots) m - matrix(c(1, 2, -3, -6, 5, 4), 3) tm - t(m) balloonplot(row(tm), col(tm), abs(tm), dotcolor = c(blue, red)[(c(tm) 0) + 1], show.margins = FALSE, cum.margins = FALSE, xlab = Cols, ylab = Rows, main = m) On Wed, Apr 14, 2010 at 7:58 AM, Guy Green guygr...@netvigator.com wrote: Hello, I am trying to create a graphic to help me visualise data. A (very simplified) sample of the data is http://n4.nabble.com/file/n1839676/circle_data.txt circle_data.txt : Aug-07 Nov-07 Feb-08 data1 1 1.5 -1 data2 1 1.2 1.6 data3 1.3 1.4 1.8 data4 1.3 -1.2 1 What I am trying to achieve is: * Circles representing each item of data, * The circle size represents the number, * The data is arranged in rows and columns, similar to the table layout (i.e. dates along the top or bottom), * Positive numbers are blue circles, negative red circles. I have used info from lots of previous posts on symbols() to get me some of the way, but I am still far off getting it to actually work, with the result that I think I may be heading in completely the wrong direction. I can create a grid of circles with the right number of dimensions: Read_data=read.table(C:/files/circle_data.txt, head = T) number_rows = nrow(Read_data) number_cols = ncol(Read_data) xaxis = rep(seq(1,ncol(Read_data),1),nrow(Read_data)) yaxis = rep(seq(1,nrow(Read_data),1),ncol(Read_data)) zvalues = rep(0.1,(number_rows*number_cols)) #This is just a dummy vector symbols(xaxis, yaxis, circles = zvalues, inches = FALSE, xlab=, ylab=) axis(2, at=c(1:number_rows), rownames(Read_data), las = 1) axis(1, at=c(1:number_cols), colnames(Read_data)) BUT... this only uses dummy values - I can't think how to get the table into a form the symbols() function can use. I tried as.vector() unsuccessfully. Also, this code simply overwrites the x and y-axis labels, which looks terrible: again, I can't think how to get this right from the start. On getting positive values to be blue and negative red, I had assumed I could just split the data into two and plot separately: Data_positive = replace(Read_data, Read_data0,0) Data_negative = -replace(Read_data, Read_data0,0) However, this quick trial below gives little dots for zero values, so it is not a perfect result: zvalues_pos = rep(c(0.1,0.2,0), 4) #Dummy vector for positives zvalues_neg = rep(c(0,0,0.3), 4) #Dummy vector for negatives symbols(xaxis, yaxis, circles = zvalues_pos, inches = FALSE, xlab=, ylab=, bg=blue) symbols(xaxis, yaxis, circles = zvalues_neg, inches = FALSE, xlab=, ylab=, bg=red, add=TRUE) [Incidentally, I have tried to work through this example ( http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=152 http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=152 ) but I am out of my depth in making sense of the code.] Any help would be gratefully received. Thanks, Guy -- View this message in context: http://n4.nabble.com/Problems-getting-symbols-to-show-table-data-tp1839676p1839676.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.
Re: [R] MiscPsycho - incorrect levenshtein distance?
Generally bug reports should go the the package emaintainer. On Apr 14, 2010, at 5:08 AM, Ben Meijering wrote: For some strings I get a wrong (MiscPsycho) Levenstein distance: I see you spelled it correctly in your subject line. stringMatch(abc, ab, normalize=NO) [1] 1 stringMatch(abc, bc, normalize=NO) [1] 2 I think the lines d - matrix(0, nrow = n + 1, ncol = m + 1) d[, 1] - 1:(n + 1) d[1, ] - 1:(m + 1) d[1, 1] - 0 should be changed to d - matrix(0, nrow = n + 1, ncol = m + 1) d[, 1] - 0:n d[1, ] - 0:m __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] R package documentation
Thanks Tobias, If there is no automated way to combine both documents, I will stack them manually... that will likely cause some problems with page numbering tough. Sebastien On Wed, Apr 14, 2010 at 8:18 AM, Tobias Verbeke tobias.verb...@openanalytics.eu wrote: Hi Sébastien, Sébastien Bihorel wrote: The .R files that I have created for all my functions are somehow used to generate a package manual pdf when I used R CMD CHECK. This is what I'd like to add in my vignette. It might be uncommon, but I saw this was done for several package documentations (e.g. PBS collections) and I kind of like this combination. I now understand what you mean. The PBS documentation you refer to seems a mere (manual) concatenation of a (non-LaTeX based) pdf document and the reference manual pdf which is not generated from a Sweave file. Such manipulations can be done using e.g. the pdfjam toolbox by David Firth. http://go.warwick.ac.uk/pdfjam Best, Tobias On Wed, Apr 14, 2010 at 6:52 AM, Tobias Verbeke tobias.verb...@openanalytics.eu mailto:tobias.verb...@openanalytics.eu wrote: Hi Sébastien, Sébastien Bihorel wrote: I am currently writing the documentation for my first package. I have created a short user manual using sweave/pdflatex which is distinct from the manual/summary-of-package-functions created by R CMD CHECK. I was wondering how could I seamlessly combine both documents. It is common to have - technical documentation in your .Rd files (in the man/ directory of your package) - functional documentation as a so-called vignette (Sweave file documenting concrete use of your package) in the inst/doc directory of your package. http://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes Combining both documents into one file is not common. I hope this helps, Tobias [[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] Running cumulative sums in matrices
That's really interesting... I have always assumed that for-loops take
longer than apply. Perhaps it depends on the application. I'll try both
in my code and see.
Thank you!
Eleni Rapsomaniki
Research Associate
Tel: +44 (0) 1223 740273
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
-Original Message-
From: Dimitris Rizopoulos [mailto:d.rizopou...@erasmusmc.nl]
Sent: 14 April 2010 13:47
To: Eleni Rapsomaniki
Cc: r-help@r-project.org
Subject: Re: [R] Running cumulative sums in matrices
you can even use a simple for-loop, e.g.,
m1 - cbind(1:5,1:5,1:5)
out - m1
for(i in 1:nrow(out))
out[i, ] - cumsum(out[i, ])
which seems to be faster than apply(m1, 1, cumsum), i.e.,
m1 - m1[rep(1:5, each = 1e04), ]
library(rbenchmark)
benchmark(
apply = apply(m1, 1, cumsum),
for = {out - m1; for(i in 1:nrow(out)) out[i, ] - cumsum(out[i,
])},
replications = 50, order = relative
)
I hope it helps.
Best,
Dimitris
On 4/14/2010 2:18 PM, Eleni Rapsomaniki wrote:
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as possible.
Can someone think how I can compute the result in the following example
(that uses a for-loop) using some version of apply instead (or any other
similarly super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column containing the
cumulative sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
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Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
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Re: [R] env() for lme4
Hi, using lme4a, and the dystuff data, I call profile and get: profile(fm1ML) Error in UseMethod(profile) : no applicable method for 'profile' applied to an object of class lmer any solutions? -- View this message in context: http://n4.nabble.com/env-for-lme4-tp1565045p1839791.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] Third and fourth order of derivative in smooth.lf function from locfit package
Dear All, Could someone please advice me the way to define the derivative of the local polynomial regression in third and fourth order from the smooth.lf function? Thank you Fir [[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] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0
Dear David, Thank you for addressing this question, but I answered Simon's question in an email I sent to the R help list a while ago: You can't mix : and c() in a recode specification; : isn't the sequence operator in a recode specification but rather represents a continuous range of values. Thus, something like 0:49.99=1 is perfectly line, but c(0:49.99)=1 isn't. Regards, John -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: April-14-10 8:45 AM To: Simon Kiss Cc: r-help@r-project.org Subject: Re: [R] Problem with recode -Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 On Apr 14, 2010, at 2:56 AM, Simon Kiss wrote: Dear colleagues, in the help archive there was a previous person who encountered a problem with the recode command in the car library. I'm not sure if that was solved, there was no posting to that effect, but I'm having the same problem. I'm trying to recode a numeric variable with values from 0-100 into a binary variable with values (0,1). The following command: recode(green_2004_2$french, c(50:100)=0; c(0:49.99)=1) Look at the last example in the recode help page: recode(x, 1:2='A'; 3='B') ## [1] A A B A A B A A B It appears to me that the c() function around your sequences may be part of the problem and I further wondered whether 0:49.99 can succeed. Generally the : operator expects integer arguments, but the help page is not clear in this area and it appears that recode has a different interpretation. require(car) recode(x, -Inf:0=-1; 0.01:Inf=1) # succeeds -- David gets the following error message Error in parse(text = range[[1]][1]) : unexpected end of input in c(0 I tried it with a second numerical variable in the same data set, but get precisely the same error at precisely the same location in the command, i.e. the second colon. As far as I can tell I have the most up-to-date version of car installed. Any suggestions? Yours, Simon Kiss * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MiscPsycho - incorrect levenshtein distance?
Thanks for pointing this out, it is indeed a bug. I have a few things on my plate today but will try and revise and place a new version on CRAN soon. -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Wednesday, April 14, 2010 9:06 AM To: Ben Meijering Cc: r help; Doran, Harold Subject: Re: [R] MiscPsycho - incorrect levenshtein distance? Generally bug reports should go the the package emaintainer. On Apr 14, 2010, at 5:08 AM, Ben Meijering wrote: For some strings I get a wrong (MiscPsycho) Levenstein distance: I see you spelled it correctly in your subject line. stringMatch(abc, ab, normalize=NO) [1] 1 stringMatch(abc, bc, normalize=NO) [1] 2 I think the lines d - matrix(0, nrow = n + 1, ncol = m + 1) d[, 1] - 1:(n + 1) d[1, ] - 1:(m + 1) d[1, 1] - 0 should be changed to d - matrix(0, nrow = n + 1, ncol = m + 1) d[, 1] - 0:n d[1, ] - 0:m __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] import file formatted RFC-822
Barry, thank you so much! It's work. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] total. factor. prodctvty. help!!
Dear all, I have a basic(!) econometric question which i couldnt find the way to do it in R. Well this could be also because of my wrong interpretation of the econometric process that i am trying to implemet.so here i wanna ask if am doing a logical mistake!!! so here is the question with the explanation of the process, hope there will be someone who can help me! suppose i have a basic Cobb-Douglas production function, ( i am not gonna give many information about the R commands or about the data since my questionn is rather theoric) and i run this model with OLS as following; mdl1 = lm(lnQ~lnC+lnL+lnM+lnE,data=newdata) than in the second step, i need to get the predicted residual as a mesure of total factor productivity == epsilon(hat)it= lnQit-lnQ(hat)it and i get the residual by typing; residuals(mdl1) == do i make mistake here or should i write another command get the epsilon(hat), suppose i typed the correct command than i save the residuals as a vector with resid-mdl1$residuals supposing that epsilon(hat) measures the TFP (TFPit=epsilon(it)), i need to regress knowledge variables on it, such as eco and RD and i want to use panel-data techniques in order to get the effect of eco and RD net of unobserved heterogeneity. so the theortically the model that i want to estimate is TFPit=alpha0+alpha1(eco)+alpha2(RD)+Ui+Vt+Wit so i run this command; mdl2-plm(resid~eco+RD, data=newdata) then there is an error Error in model.frame.default(formula = resid ~ eco + RD, data = ds, drop.unused.levels = TRUE) : variable lengths differ (found for 'eco') well here in fact, probably i am doing a econometrical mistake that might be quite easy for somepeople, think that it is a silly question, but i need help in this situation... if someone knows about Total Factor Productivity and willing to help i would be greatful cheers [[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] svm of e1071 package
Hi Shyama, On Tue, Apr 13, 2010 at 10:40 AM, Shyamasree Saha [shs] s...@aber.ac.uk wrote: Dear Steve, We have finally managed to run our code. Sparse matrix is helping a lot (I should say without matrix.csr, we would not be able to do it). This time it is taking very small amount of memory while running svm, but we could not use as.matrix.csr directly on our huge data. we had to divide the data in small chunk. we created matrix.csr from those small chunk, removed our original object, loaded next chunk and used rbind to put all of them together. we need to be very careful how much data we load at a time. Thanks again for you kind help. This is great news :-) So, just to recap -- is the only thing that you did to get this to work is to convert your input matrix to a sparse matrix (via SparseM)? No parameter tweaking necessary? Would an alternative approach to creating the sparse matrix be more helpful? You can, for instance, create the entire sparse matrix in one shot, like: R m - as.matrix.csr(0, nrow=10, ncol=10) (with appropriate numbers for your nrow,ncol params) Then you can load subsets of your data into it and skipping the chunked-`rbing` strategy .. is that easier? Also, the e1071 package has read.matrix.csr and write.matrix.csr functinos that might help facilitate loading/saving your data matrices in the future. -steve Regards Shyama From: Steve Lianoglou [mailinglist.honey...@gmail.com] Sent: Wednesday, April 07, 2010 4:00 PM To: Shyamasree Saha [shs] Cc: r help Subject: Re: [R] svm of e1071 package Hi, On Tue, Apr 6, 2010 at 7:16 PM, Shyamasree Saha [shs] s...@aber.ac.uk wrote: Dear Steve, Thanks again for your help and reply. your help was very useful and gave us some options. We will follow your suggestions and let you know about it. No problem ... yeah, please write back when you figure out what's up (or hit more roadblocks), I'd be curious to know what the solution is. Thanks, -steve Regards, shyama From: Steve Lianoglou [mailinglist.honey...@gmail.com] Sent: Tuesday, April 06, 2010 9:40 PM To: Shyamasree Saha [shs] Cc: r help Subject: Re: [R] svm of e1071 package Hi Shyama, Don't forget to CC the r-help list in your discussions so that there are more eyes on this problem, and others might potentially benefit from discussion. Comments in line. On Tue, Apr 6, 2010 at 4:06 PM, Shyamasree Saha [shs] s...@aber.ac.uk wrote: Dear Steve, Thanks a lot for your reply. As you have suggested kernlab and SparseM packages, we have now installed it and reading about these packages. I am trying to answer your questions. I have also added a bit of code. Please let me know whether you need to know more and what is your suggestions. Thanks again for your help. Regards, Shyamasree R .Machine$sizeof.pointer ## it should be 8 Yes, it is indeed 8. OK * What type of kernel are you using? Have you tried different ones? Just tried the linear kernel, haven't tried with other kernels. OK, let's stick with that for now. * Are you doing classification or regression? We are doing multi-class classification. There are 11 classes. Is it any better if you just do 1-vs-all? Also (from your code at the end of the email) what if you train the model with `probability=FALSE`? * Is your data/feature matrix sparse? If so, are you passing libsvm a SparseM matrix? Yes, the feature matrix is indeed very sparse. Just passing a matrix at the moment. Not sure how to define it as SparseM matrix. R library(SparseM) R ?as.matrix.csr * Have you tried playing with some of the params in the svm call, like the values for tolerance, epsilon, cost/nu/etc. No, have not played with these at all. What do you recommend? Try to increase (I think (maybe decrease??)) the tolerance from its default value. Moving this in one direction or the other allows the solver to converge to a less-precise solution -- haven't read the source in a while, though, so test it. * Try an even smaller subset of your data ( 1.4 GB) It works fine with a much smaller subset but have not tried with intermediate sizes. OK Can you give an idea of how long it takes for your call to `svm` to return with different data sizes? How does its memory stats look like? * What is the dimensionality of your X matrix -- how many examples, and how many features does each example have X matrix dimensionality: 35,500 rows x 52,058 cols . All features are binary. I think that's quite large. This might be a good reason to try liblinear as it is more appropriate for large feature spaces and is made by the same libsvm folks: http://www.csie.ntu.edu.tw/~cjlin/liblinear/ http://www.csie.ntu.edu.tw/~cjlin/papers/liblinear.pdf * Include sessionInfo() -- we don't know what version of R/e1071 etc. R version 2.10.1 (2009-12-14) e1071 1.5-23 running on Linux version
Re: [R] env() for lme4
Pierre, This question is better asked on R-sig-ME. I updated below call to 'profile(fm...@env)' Regards, Rob On Apr 14, 2010, at 6:28 AM, pnouvellet wrote: Hi, using lme4a, and the dystuff data, I call profile and get: profile(fm1ML) Error in UseMethod(profile) : no applicable method for 'profile' applied to an object of class lmer any solutions? -- View this message in context: http://n4.nabble.com/env-for-lme4-tp1565045p1839791.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. [[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] how to delete columns with NA values?
Hi everyone: I have a dataset: tm1 col1 col2 [1,]1 NA [2,]11 [3,]22 [4,]11 [5,]22 [6,]1 NA I need to delete entire column 2 that has NA in it(not all of them are NAs), and the result I want is tm1 col1 [1,]1 [2,]1 [3,]2 [4,]1 [5,]2 [6,]1 what should I do? I search a lot, all I found is how to delete column with all NA values.. Thanks a lot muting -- View this message in context: http://n4.nabble.com/how-to-delete-columns-with-NA-values-tp1839902p1839902.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] how to delete columns with NA values?
Hello, muting wrote: Hi everyone: I have a dataset: This looks like a matrix. To perform functions on each row or column of a matrix, use the apply function. If you had a data.frame, you could perform a function on each column using sapply or lapply. tm1 col1 col2 [1,]1 NA [2,]11 [3,]22 [4,]11 [5,]22 [6,]1 NA I need to delete entire column 2 that has NA in it(not all of them are NAs), and the result I want is tm1 col1 [1,]1 [2,]1 [3,]2 [4,]1 [5,]2 [6,]1 what should I do? ## for a data.frame x x - data.frame(a = 1:10, b = c(2:10, NA), c = 2:11) x[sapply(x, function(x) !any(is.na(x)))] ## for a matrix y y - matrix(1:30, ncol = 3) y[20] - NA y[, apply(y, 2, function(x) !any(is.na(x)))] ## or maybe even simply... y[,complete.cases(t(y))] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 delete columns with NA values?
On 4/14/2010 10:56 AM, muting wrote: Hi everyone: I have a dataset: tm1 col1 col2 [1,]1 NA [2,]11 [3,]22 [4,]11 [5,]22 [6,]1 NA I need to delete entire column 2 that has NA in it(not all of them are NAs), and the result I want is tm1 col1 [1,]1 [2,]1 [3,]2 [4,]1 [5,]2 [6,]1 what should I do? subset(tm1, select=colMeans(is.na(tm1)) == 0) OR tm1[,colMeans(is.na(tm1)) == 0] I search a lot, all I found is how to delete column with all NA values.. Thanks a lot muting -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Roxygen - basic usage uncertain
I am trying to make a package consisting of a single function with auto-documentation assistance from 'roxygen' but am uncertain of the correct procedure. My version of 'R' is 2.10.1. I followed the following steps: 1) Get an existing function (un-commented) as an '.R' file. 2) Add formal comments (e.g. owner) above that function's code using the [#' @] syntax. 3) Create a further '.R' file to contain formal comments relating to the package as a whole. This file contains no meaningful 'R' code but must at least have an NA at the end to ensure it gets parsed. 4) Use 'package.skeleton' to turn these two files into a basic package (folder structure etc.) 5) The '.Rd' files so-produced to have empty titles. Empty titles would give rise to error message when installing. However 'roxygenize' (next step) will replace these '.Rd' files with its own generated ones having non-empty titles. To avoid clutter and confusion (e.g. if package name not identical in formal comments), the existing '.Rd' files are best deleted. 6) From 'R', apply 'roxygenize' to the basic package. Must make the target directory the same as the source directory otherwise no '.R' files will be present (that's what I observe - does it indicate some problem with my procedure or is that to be expected?). So make a safe copy of the source directory first. 7) R CMD check mypackage 8) R CMD INSTALL mypackage Is that a reasonable process? Please, I'm really needing baby-steps here. -- View this message in context: http://n4.nabble.com/Roxygen-basic-usage-uncertain-tp1839933p1839933.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package documentation
pomchip wrote:
Dear R users,
I am currently writing the documentation for my first package. I have
created a short user manual using sweave/pdflatex which is distinct from
the
manual/summary-of-package-functions created by R CMD CHECK. I was
wondering
how could I seamlessly combine both documents.
Thanks for your help
Sebastien
The .Rd files are normally kept separate from the vignette- this is because
Rd files have to be translated into several different formats such as html,
man pages and pdf. The vignette allows for a more free-form discussion as
it does not have the rigid structure that allows .Rd files to be translated.
That being said, you could add the contents of .Rd files to something like
an appendix in your vignette by converting the .Rd files to .tex and
including them in your Sweave source. Something like the following would
convert each .Rd file and append it to a single .tex file (on UNIX/Linux
systems):
cd yourPackage/man
ls *.Rd | xargs -I % R CMD Rdconv -t latex % manPages.tex
You could then move manPages.tex to yourPackage/inst/doc and include int in
your Sweave source via \input{}. You will need to ensure
$R_HOME/share/texmf is on your tex search path as the LaTeX compiler will
need Rd.sty to define some of the macros in the code produced by R CMD
Rdconv.
Hope this helps!
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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[R] fitting a quadratic function - poly?
Hi List, I can not get my head around the following problem. I want to fit a quadratic function to some data and stumbled across poly(). What exactly does it, i.e. why are there different results for fit1 and fit2? x = seq(-10, 10) y = x^2 fit1 = lm(y ~ x + I(x^2)) fit2 = lm(y ~ poly(x, 2)) plot(x,y) lines(x, fit1$fitted.values, col = 2) lines(x, fit2$fitted.values, col = 3) round(fit1$coefficients, 2) round(fit2$coefficients, 2) Thanks in advance, 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] how to delete columns with NA values?
Thank you all! It works well now -- View this message in context: http://n4.nabble.com/how-to-delete-columns-with-NA-values-tp1839902p1839953.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] how to delete columns with NA values?
Hi muting, # your data muting - data.frame(col1 = c(1,1,2,1,2,1), col2=c(NA,1,2,1,2,NA)) # 1. finding rows with NA is.na(muting) # 2. counting the NAs per column colSums(is.na(muting)) # 3. keeping only the ones without NAs muting[,colSums(is.na(muting)) == 0] Regards, Stefan schrieb muting, Am 14.04.2010 16:56: Hi everyone: I have a dataset: tm1 col1 col2 [1,]1 NA [2,]11 [3,]22 [4,]11 [5,]22 [6,]1 NA I need to delete entire column 2 that has NA in it(not all of them are NAs), and the result I want is tm1 col1 [1,]1 [2,]1 [3,]2 [4,]1 [5,]2 [6,]1 what should I do? I search a lot, all I found is how to delete column with all NA values.. Thanks a lot muting __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] fitting a quadratic function - poly?
On 14/04/2010 11:12 AM, Stefan Uhmann wrote: Hi List, I can not get my head around the following problem. I want to fit a quadratic function to some data and stumbled across poly(). What exactly does it, i.e. why are there different results for fit1 and fit2? x = seq(-10, 10) y = x^2 fit1 = lm(y ~ x + I(x^2)) fit2 = lm(y ~ poly(x, 2)) plot(x,y) lines(x, fit1$fitted.values, col = 2) lines(x, fit2$fitted.values, col = 3) These look the same to me. round(fit1$coefficients, 2) round(fit2$coefficients, 2) These look different, because poly uses orthogonal polynomials, a different parametrization. You can see the difference if you ask for model.matrix(fit1) and model.matrix(fit2). (You can plot these using matplot(model.matrix(fit1)), etc.) Duncan Murdoch Thanks in advance, 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] sum specific rows in a data frame
Thank you for your help. The best I have found is to use the ddply function. pose DESCRIPTION QUANITY CLOSING.PRICE 1 WHEAT May/101467.75 2 WHEAT May/101467.75 3 WHEAT May/101467.75 4 WHEAT May/101467.75 5 COTTON NO.2 May/101 78.13 6 COTTON NO.2 May/101 78.13 7 COTTON NO.2 May/101 78.13 library(plyr) op=ddply(pose, c(DESCRIPTION,CLOSING.PRICE),summarise, POSITION= sum(QUANITY)) op DESCRIPTION CLOSING.PRICE POSITION 1 COTTON NO.2 May/10 78.133 2 WHEAT May/10 467.754 Op is a data.frame object.The trick is done! *** Arnaud Gaboury Mobile: +41 79 392 79 56 BBM: 255B488F __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Network Analysis
Does anyone have any thoughts on this? I would really appreciate any insights/suggestions that the group could provide. -- View this message in context: http://n4.nabble.com/Network-Analysis-tp1838902p1839992.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] Running cumulative sums in matrices
Eleni et. al.:
Perhaps it's worth noting that there is generally NO reason to prefer
apply-family code to explicit for-loops for execution speed. Apply-type
statments **are** essentially disguised loops -- that is, they execute the
loop code repeatedly at the R interpreter level. They do employ some
efficiency tricks to try to do so as fast as possible; but as posts in this
thread have already noted, whether they run faster or slower than explicit
loops is generally code and problem specific. Sometimes yes; sometimes no;
often about the same.
So, for example,
myfun - function(x){...}
z - somelist
ans -lapply(z,myfun)
## and
ans - vector(list,10)
for(i in seq_len(length(z)))ans[[i]] - myfun(z[[i]])
should take about the same time.
The main reason to prefer the former instead of the latter is that the
former conforms to R's functional programming paradigm and tends to produce
cleaner, more debuggable, more maintainable code (I realize that this is a
subjective preference with which many may disagree).
When speedup is desired, the key is to move the loop from the interpreted to
the compiled code level via vectorization, either by making use of R's
built-in compiled functions (like cumsum), which are generally .Internal or
.Primitive, or to write and call your own compiled code, e.g.via .Call. This
often can make things orders of magnitude faster.
I hope this provides some clarification about an issue that many seem
confused about. If anything I have said is misstated or requires further
clarification, I would appreciate corrections.
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Eleni Rapsomaniki
Sent: Wednesday, April 14, 2010 5:18 AM
To: r-help@r-project.org
Subject: [R] Running cumulative sums in matrices
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as possible. Can
someone think how I can compute the result in the following example (that
uses a for-loop) using some version of apply instead (or any other similarly
super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column containing the
cumulative sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
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Re: [R] - how/when/why do you use it?
The - assignment operator is very powerful, but can be dangerous as well. When tempted to use it, look for alternatives first, there may be a better way. But having said that, I am one of the more guilty people for using it (quite a few of the functions in the TeachingDemos package use -). The main use that I see is when you are using a function written by someone else that takes one of your functions as an argument and you want to save information from your function that is not being passed back through the calling function. For example you may want to trace the calls to your function that is being called by optim, just define your function A which defines within it function B which is to be optimized, A also contains an empty vector to store results in, then A calls optim passing B to it, B uses - to update the vector in A every time that it is called, now A has the results of optim and also a trace of info on all the calls to B. - can also be used for package local variables (less evil than globals) where within a package you can call one function to set some things up, then other functions in the package can refer to the variable created to see the setup as well as modifying options local to the package. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Tal Galili Sent: Tuesday, April 13, 2010 8:03 AM To: r-help@r-project.org Subject: [R] - how/when/why do you use it? Hi all, Today I came across scoping in the R introhttp://cran.r-project.org/doc/manuals/R-intro.html#Scope (after reading Robert Gentleman fortunehttp://rfortunes.posterous.com/im-always-thrilled-when-people- discover-what on lexical scooping) , and am very curious about the - assignment. The manual showed one (very interesting) example for -, which I feel I understood. What I am still missing is the context of when this can be useful. So what I would love to read from you are examples (or links to examples) on when using - can be interesting/useful. What might be the dangers of using it (it looks easy to loose track of), and any tips you might feel like sharing. Thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) --- --- [[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] Odp: fitting a quadratic function - poly?
Hi r-help-boun...@r-project.org napsal dne 14.04.2010 17:12:51: Hi List, I can not get my head around the following problem. I want to fit a quadratic function to some data and stumbled across poly(). What exactly does it, i.e. why are there different results for fit1 and fit2? x = seq(-10, 10) y = x^2 fit1 = lm(y ~ x + I(x^2)) fit2 = lm(y ~ poly(x, 2)) plot(x,y) lines(x, fit1$fitted.values, col = 2) lines(x, fit2$fitted.values, col = 3) round(fitted(fit1)-fitted(fit2),5) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 results are same. round(fit1$coefficients, 2) round(fit2$coefficients, 2) Coefficients are different as you fit different values. See ?poly poly(-10:10,2) I believe that others give you better explanation. So you can not use coefficients evaluated by lm(.~poly(...)) directly. Regards Petr Thanks in advance, 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] Odp: fitting a quadratic function - poly?
Below. -- Bert Bert Gunter Genentech Nonclinical Statistics Coefficients are different as you fit different values. See ?poly poly(-10:10,2) I believe that others give you better explanation. So you can not use coefficients evaluated by lm(.~poly(...)) directly. -- Well, it depends what you mean by use...directly. But I think the answer is, yes you can. See ?SafePrediction for details. -- Bert Regards Petr Thanks in advance, 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Odp: fitting a quadratic function - poly?
Hi Bert Gunter gunter.ber...@gene.com napsal dne 14.04.2010 18:01:52: Below. -- Bert Bert Gunter Genentech Nonclinical Statistics Coefficients are different as you fit different values. See ?poly poly(-10:10,2) I believe that others give you better explanation. So you can not use coefficients evaluated by lm(.~poly(...)) directly. -- Well, it depends what you mean by use...directly. But I think the I mean that you can use fit- lm(y~x+I(x^2)) coef(fit)[1] + coef(fit)[2]*x + coef(fit)[3]*x^2 but you can not use fit- lm(y~poly(x,2)) coef(fit)[1] + coef(fit)[2]*x + coef(fit)[3]*x^2 to compute y. Regards Petr answer is, yes you can. See ?SafePrediction for details. -- Bert Regards Petr Thanks in advance, 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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/when/why do you use it?
I love Patrick Burns' comment on the - operator in R Inferno:
If you think you need '-', think again. If on reflection you still
think you need '-', think again.
Is this in package::fortunes?
John
John Szumiloski, Ph.D.
Senior Biometrician
Biometrics Research
WP53B-120
Merck Research Laboratories
P.O. Box 0004
West Point, PA 19486-0004
(215) 652-7346 (PH)
(215) 993-1835 (FAX)
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Greg Snow
Sent: Wednesday, 14 April, 2010 11:43 AM
To: Tal Galili; r-help@r-project.org
Subject: Re: [R] - how/when/why do you use it?
The - assignment operator is very powerful, but can be dangerous as
well. When tempted to use it, look for alternatives first, there may be
a better way. But having said that, I am one of the more guilty people
for using it (quite a few of the functions in the TeachingDemos package
use -).
The main use that I see is when you are using a function written by
someone else that takes one of your functions as an argument and you
want to save information from your function that is not being passed
back through the calling function. For example you may want to trace
the calls to your function that is being called by optim, just define
your function A which defines within it function B which is to be
optimized, A also contains an empty vector to store results in, then A
calls optim passing B to it, B uses - to update the vector in A every
time that it is called, now A has the results of optim and also a trace
of info on all the calls to B.
- can also be used for package local variables (less evil than
globals) where within a package you can call one function to set some
things up, then other functions in the package can refer to the variable
created to see the setup as well as modifying options local to the
package.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Tal Galili
Sent: Tuesday, April 13, 2010 8:03 AM
To: r-help@r-project.org
Subject: [R] - how/when/why do you use it?
Hi all,
Today I came across scoping in the R
introhttp://cran.r-project.org/doc/manuals/R-intro.html#Scope (after
reading Robert Gentleman
fortunehttp://rfortunes.posterous.com/im-always-thrilled-when-people-
discover-what
on
lexical scooping) , and am very curious about the - assignment.
The manual showed one (very interesting) example for -, which I
feel I
understood. What I am still missing is the context of when this can be
useful.
So what I would love to read from you are examples (or links to
examples) on
when using - can be interesting/useful. What might be the dangers
of
using it (it looks easy to loose track of), and any tips you might
feel
like
sharing.
Thanks,
Tal
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew)
|
www.r-statistics.com (English)
---
---
[[alternative HTML version deleted]]
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guide.html
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[R] array manipulation
Hello listeRs, I'm trying to make a square radius around a given reference point. So given the following array, how can I manipulate it so that x0 - array(1,dim=c(5,5)) x0 1 1 1 1 1 1 1 1 1 1 1 1 *1* 1 1 1 1 1 1 1 1 1 1 1 1 becomes into 3 3 3 3 3 3 2 2 2 3 3 2 *1* 2 3 3 2 2 2 3 3 3 3 3 3 Thanks. Muhammad __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] memory failure in adonis function (permanova)
On Tue, 2010-03-16 at 17:12 +0100, Paloma Ruiz wrote: Dear all, I am trying to get a PERMANOVA with quite large data set. I am reading a lot about this question, but I do not get the answer about it. Although I know that the R function is adonis () (vegan package), it does not work: adonis(Pha.env~SPha, data=Pha, permutations=10) The error message: Error: cannot allocate vector of size 334.2 Mb In addition: Warning messages: 1: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 2: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 3: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) 4: In vegdist(lhs, method = method, ...) : Reached total allocation of 1535Mb: see help(memory.size) When I have received this message from R usually it is due to an incorrect introduction of the function elements (i.e., memory message errors). However, I've just checked my matrix (Pha.env is a data.frame with num or int variables, and, Pha is a data.frame with factor variables) and the length of matrices is the same. I know that I'm wrong somewhere specifying the matrices in adonis(), but I can't fix it. That error is coming from the calculation of the dissimilarity matrix and you've exhausted the 1.5GB of (allocated) RAM on your system. How many samples (rows) are you trying that on? G Thanks in advance, Paloma [[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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Gaussian Quadrature Numerical Integration In R
Just do a variable transformation. If your function is f(x), your new function would be: f'(x) = sigma * f(sigma * x + mu). You can integrate f'(x) using the Hermite quadrature. Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ines Azaiez Sent: Tuesday, April 13, 2010 9:25 PM To: r-help-boun...@stat.math.ethz.ch; r-help@r-project.org Subject: [R] Gaussian Quadrature Numerical Integration In R Hi All, I am trying to use A Gaussian quadrature over the interval (-infty,infty) with weighting function W(x)=exp(-(x-mu)^2/sigma) to estimate an integral. Is there a way to do it in R? Is there a function already implemented which uses such weighting function. I have been searching in the statmode package and I found the function gauss.quad(100, kind=hermite) which uses the weighting function W(x)=exp(-x^2). Is there a more general version of this weighting function (using mu and sigma)? Thanks for your help Iazaiez __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Odp: fitting a quadratic function - poly?
Petr Pikal wrote: ... I mean that you can use fit- lm(y~x+I(x^2)) coef(fit)[1] + coef(fit)[2]*x + coef(fit)[3]*x^2 but you can not use fit- lm(y~poly(x,2)) coef(fit)[1] + coef(fit)[2]*x + coef(fit)[3]*x^2 (to get the fits for any x vector) -- But you **can** use ypred - predict(fit,data.frame(x = x)) -- in **both** cases. Which is, I think, how it should be done. Cheers, Bert Bert Gunter Genentech Nonclinical Statistics answer is, yes you can. See ?SafePrediction for details. -- Bert Regards Petr Thanks in advance, 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Import ASCII data using a .sas program
Good Day, I have several ASCII data files that I would like to import into R. They all have a SAS import file which is used to bring the data into SAS and I am hoping to use this to bring the data into R. There are lots of variables involved and the ASCII data file is 2308 columns long so I would certainly prefer to figure out a smart way of converting the data to R. The ASCII data is a long stream of numbers (no field separators or delimiters) while the SAS import file looks like: libname mine 'c:\'; data mine.fh4; infile 'd:\fh4.txt' lrecl=2309; input perstat1 $1-2 linenum $3-4 I_wave1 $5-5 bnocost1 $6-10 bnosta1 $11-12 So SAS uses the position of the ASCII character to determine what variable the data should be in while the SCAN or the READ. FWF function of R uses the width of the column. Does anyway have a smart and/or automated way of moving my ASCII data into R using this .SAS program ? -- -Don Don Catanzaro, PhD Landscape Ecologist dgcatanz...@gmail.com 16144 Sigmond Lane Lowell, AR 72745 479-751-3616 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Simulation problem.
This looks like homework. If it is, you should really tell us along with what
your teacher's policy is on getting help over the internet is (and note that
many teachers monitor this list and can see if you are getting help).
You have done the first part yourself, much better than some who have tried to
get us to do the whole thing for them, so a possible hint: the new problem
really has 3 groups, never sick, currently sick, and healed. Just modify your
current code to allow for people to move from the currently sick to the healed
group.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Piotr Arendarski
Sent: Tuesday, April 13, 2010 4:27 PM
To: r-help@r-project.org
Subject: [R] Simulation problem.
Hi,
I have problem with simulating.
This is my task...
Suppose that there are N persons some of whom are sick with influenza.
The
following assumptions are made:
* when a sick person meets a healthy one, the chance is á that the
latter
will be infected
* all encounters are between two persons
Write a function which simulates this model for various values of
N (say, 10 000) and á (say, between 0.001 and 0.1). Monitor the
history of this process, assuming that one individual is infected at
the beginning.
The code is:
*
simulation - function(number, prob){
cumulative.time - 0
current.time - 0
number.sick - 1
while(number.sicknumber){
current.time - current.time + 1
meetings - rhyper(nn=1, m=number.sick, n=number-number.sick, k=2)
if(meetings==1){
one.sick - rbinom(n=1, size=1, prob)
if(one.sick==1){
cumulative.time - c(cumulative.time, current.time)
number.sick - number.sick + 1
}}}
cumulative.time
}
number - 1000
prob - .05
model - simulate(number, prob)*
But than add the assumption that *each infected person has a 0.01
chance
of recovering at each time unit* Do you have idea how to modify the
code
?
Piotr Arendarski
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Re: [R] array manipulation
1+pmax(abs(row(z)-3),abs(col(z)-3)) ?row ?col ?pmax for details. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Muhammad Rahiz Sent: Wednesday, April 14, 2010 9:44 AM To: r-help@r-project.org Subject: [R] array manipulation Hello listeRs, I'm trying to make a square radius around a given reference point. So given the following array, how can I manipulate it so that x0 - array(1,dim=c(5,5)) x0 1 1 1 1 1 1 1 1 1 1 1 1 *1* 1 1 1 1 1 1 1 1 1 1 1 1 becomes into 3 3 3 3 3 3 2 2 2 3 3 2 *1* 2 3 3 2 2 2 3 3 3 3 3 3 Thanks. Muhammad __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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/when/why do you use it?
If you use '-' remember that you are going to get into trouble and it will be a challange to debug your script. Only use it if you have a real good understanding of the scoping rules in R and have exhausted all the other avenues. I, like Greg, am guilty of using it because I still keep some of my old habits (like COMMON in FORTRAN) and every so often do have the need for a global variable I can change in a lower level routine without returning a value (and am willing to suffer the consequences of side effects). And make sure that you always use the - when referring to that object so that you do not create a local copy in some subroutine and really get messed up. So as the answer to when, I typically says never. On Wed, Apr 14, 2010 at 11:42 AM, Greg Snow greg.s...@imail.org wrote: The - assignment operator is very powerful, but can be dangerous as well. When tempted to use it, look for alternatives first, there may be a better way. But having said that, I am one of the more guilty people for using it (quite a few of the functions in the TeachingDemos package use -). The main use that I see is when you are using a function written by someone else that takes one of your functions as an argument and you want to save information from your function that is not being passed back through the calling function. For example you may want to trace the calls to your function that is being called by optim, just define your function A which defines within it function B which is to be optimized, A also contains an empty vector to store results in, then A calls optim passing B to it, B uses - to update the vector in A every time that it is called, now A has the results of optim and also a trace of info on all the calls to B. - can also be used for package local variables (less evil than globals) where within a package you can call one function to set some things up, then other functions in the package can refer to the variable created to see the setup as well as modifying options local to the package. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Tal Galili Sent: Tuesday, April 13, 2010 8:03 AM To: r-help@r-project.org Subject: [R] - how/when/why do you use it? Hi all, Today I came across scoping in the R introhttp://cran.r-project.org/doc/manuals/R-intro.html#Scope (after reading Robert Gentleman fortunehttp://rfortunes.posterous.com/im-always-thrilled-when-people- discover-what on lexical scooping) , and am very curious about the - assignment. The manual showed one (very interesting) example for -, which I feel I understood. What I am still missing is the context of when this can be useful. So what I would love to read from you are examples (or links to examples) on when using - can be interesting/useful. What might be the dangers of using it (it looks easy to loose track of), and any tips you might feel like sharing. Thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) --- --- [[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-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.htmlhttp://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? [[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] what is the intercept of a two-way anova model without interaction term?
Dear list, I have a question regarding the meaning of intercept term in a two-way anova model without interaction term. for example (let's assume there is no interaction between factor1 and factor2) : df        val       factor1 factor2 1 48.61533      A     t1 2 171.13535      B     t1 3 65.96884      C     t1 4 63.71222      A     t2 5 80.22049      B     t2 6 96.95929      C     t2 7 38.70078      A     t3 8 99.44787      B     t3 9 36.58818      C     t3 the summary of regression : summary(m) Call: lm(formula = val ~ factor1 + factor2, data = df) Residuals:      1      2      3      4      5      6      7      8      9 -19.040 36.889 -17.849 11.000 -39.084 28.084  8.040  2.195 -10.235 Coefficients:            Estimate Std. Error t value Pr(|t|) (Intercept)   67.66     25.42  2.661  0.0563 . factor1B      66.59     27.85  2.391  0.0751 . factor1C      16.16     27.85  0.580  0.5928 factor2t2    -14.94     27.85 -0.537  0.6200 factor2t3    -36.99     27.85 -1.328  0.2548 --- Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1 Residual standard error: 34.11 on 4 degrees of freedom Multiple R-squared: 0.6669,    Adjusted R-squared: 0.3338 F-statistic: 2.002 on 4 and 4 DF, p-value: 0.2589 This is contrast treatment, and my question is what the intercept (here is 67.66) represent for? Thank you. Xiaokuan [[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] Network Analysis
On Wed, Apr 14, 2010 at 07:44:23AM -0800, bchaney wrote: Does anyone have any thoughts on this? I would really appreciate any insights/suggestions that the group could provide. I did not do sophisticated analyzes, but my opinion is that igraph is easier to use and more versatile than statnet. It is also more capable of dealing with big networks. The only issue with igraph functions is that we have to remember that the indexes start at 0 and not 1 as all other R functions. The default igraph plots are very simple, but it is easy to add attributes to an igraph object to make nice graphics. -- Jakson A. Aquino Federal Uni. of Ceara www.lepem.ufc.br - Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 can I plot the histogram like this using R?
There are several ways in which the picture you show is uglier than the histogram produced by R. Which of these do you want to accomplish and why? -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of bbslover Sent: Tuesday, April 13, 2010 10:46 PM To: r-help@r-project.org Subject: [R] how can I plot the histogram like this using R? I want to get the plot like this, http://n4.nabble.com/file/n1839303/%25E9%25A2%2591%25E7%258E%2587%25E5% 2588%2586%25E5%25B8%2583%25E5%259B%25BE%25E6%25A0%2587%25E5%2587%2586.j pg %E9%A2%91%E7%8E%87%E5%88%86%E5%B8%83%E5%9B%BE%E6%A0%87%E5%87%86.jpg not this, http://n4.nabble.com/file/n1839303/R.jpg R.jpg and the data here, thank you! http://n4.nabble.com/file/n1839303/y1.txt y1.txt can R deal with this problem? how can I do? -- View this message in context: http://n4.nabble.com/how-can-I-plot-the- histogram-like-this-using-R-tp1839303p1839303.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.
Re: [R] Getting Started with Bayesian MCMC
The purpose of the task view is to answer questions like this. I for one would not be able to give a better answer than what is there. My suggestion would be to pull out your Bayesian textbook (or get one, or use online notes from a class, etc.) and look through the homework problems and examples for things that may be similar to what you may be doing in the future. Then try doing those problems/examples using a few of the different tools recommended in the task view (start with simple things even if they are not the types of problems you will do for real, just to get a feel for the different packages). This will help you decide which packages work best for you and which interfaces you prefer. Then when you have real problems to solve, you will have the knowledge of which tools to use and how to use them. You should also consider contributing what you learn back to the task view for others. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Ben Sent: Tuesday, April 13, 2010 5:50 PM To: r-help@r-project.org Subject: [R] Getting Started with Bayesian MCMC Hi all, I would like to start to use R's MCMC abilities to compute answers in Bayesian statistics. I don't have any specific problems in mind yet, but I would like to be able to compute/sample posterior probabilities for low-dimensional custom models, as well as handle standard Bayesian cases like linear regression and hierarchical models. R clearly has a lot of abilities in this area: http://cran.r-project.org/web/views/Bayesian.html --enough to be confusing! For instance, there are apparently three separate interfaces to JAGS, and I'm not even sure I want/need to interface to JAGS at all. Can someone please get me started? Are there a handful of must-have packages and software that everyone (who uses MCMC regularly) uses? Any responses are appreciated, -- Ben __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] import file formatted RFC-822
I have a problem, In a few cases robot-exclusion-useragent have 2 or more values, is there a manner to fix it? For example, robot askjeeves has three names. 2010/4/13 Barry Rowlingson b.rowling...@lancaster.ac.uk: On Tue, Apr 13, 2010 at 6:26 PM, Sebastian Kruk residuo.so...@gmail.com wrote: Dear R-list users: I would like to import a database of web robots, http://www.robotstxt.org/db/all.txt, it´s formatted RFC-822, ¿how can I do it? RFC822 looks very much like R's package DESCRIPTION files, and they are read in using read.dcf because they are conformant to 'Debian Control File' format. So I tried read.dcf on it: robots = read.dcf(all.txt) dim(robots) [1] 298 38 so that's a matrix: dimnames(robots) [[1]] NULL [[2]] [1] robot-id robot-name [3] robot-cover-url robot-details-url [5] robot-owner-name robot-owner-url [7] robot-owner-email robot-status [9] robot-purpose robot-type [11] robot-platform robot-availability [13] robot-exclusion robot-exclusion-useragent [15] robot-noindex robot-host [17] robot-from robot-useragent [19] robot-language robot-description [21] robot-history robot-environment [23] modified-date modified-by [25] robot-nofollow robot-owner-name2 [27] robot-owner-url2 robot-owner-email2 [29] robot-owner-name3 robot-owner-name4 [31] robot-environment1 robot-environment2 [33] robot-purpose1 robot-purpose2 [35] robot-purpose3 robot-platform1 [37] robot-description1 robot-description2 and I guess it pads out the columns so every row has every possible variable value even if it doesn't exist in the record for that robot. Sorted? 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] import file formatted RFC-822
On Wed, Apr 14, 2010 at 6:20 PM, Sebastian Kruk residuo.so...@gmail.com wrote: I have a problem, In a few cases robot-exclusion-useragent have 2 or more values, is there a manner to fix it? For example, robot askjeeves has three names. use 'all=TRUE'? test data: foo: 1 bar: 2 foo: 1 foo: 2 bar: 4 baz: 7 read.dcf(simple.txt,all=TRUE) foo bar baz 11 2 NA 2 1, 2 47 note that $foo is a *list* in order to handle multiple values in its elements: m=read.dcf(simple.txt,all=TRUE) m$foo [[1]] [1] 1 [[2]] [1] 1 2 whereas $bar is a simple vector: m$bar [1] 2 4 as is $baz (with NA where no baz record exists) m$baz [1] NA 7 sorted? 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] - how/when/why do you use it?
x - will usually wind up assigning into the parent or global environment but since it depends on what is already there the following are safer: e - environment() parent.env(e)$x - 1 globalenv()$x - 2 Typically in cases like this the function that contains the assignment can be regarded as a method of the object containing x so an OO approach can be taken such as facilitated by the proto package. Here p is defined to be a proto object with method square.x and property x. library(proto) p - proto(x = 2, square.x = function(.) .$x - .$x^2) p$x [1] 2 p$square.x() p$x [1] 4 On Wed, Apr 14, 2010 at 11:42 AM, Greg Snow greg.s...@imail.org wrote: The - assignment operator is very powerful, but can be dangerous as well. When tempted to use it, look for alternatives first, there may be a better way. But having said that, I am one of the more guilty people for using it (quite a few of the functions in the TeachingDemos package use -). The main use that I see is when you are using a function written by someone else that takes one of your functions as an argument and you want to save information from your function that is not being passed back through the calling function. For example you may want to trace the calls to your function that is being called by optim, just define your function A which defines within it function B which is to be optimized, A also contains an empty vector to store results in, then A calls optim passing B to it, B uses - to update the vector in A every time that it is called, now A has the results of optim and also a trace of info on all the calls to B. - can also be used for package local variables (less evil than globals) where within a package you can call one function to set some things up, then other functions in the package can refer to the variable created to see the setup as well as modifying options local to the package. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Tal Galili Sent: Tuesday, April 13, 2010 8:03 AM To: r-help@r-project.org Subject: [R] - how/when/why do you use it? Hi all, Today I came across scoping in the R introhttp://cran.r-project.org/doc/manuals/R-intro.html#Scope (after reading Robert Gentleman fortunehttp://rfortunes.posterous.com/im-always-thrilled-when-people- discover-what on lexical scooping) , and am very curious about the - assignment. The manual showed one (very interesting) example for -, which I feel I understood. What I am still missing is the context of when this can be useful. So what I would love to read from you are examples (or links to examples) on when using - can be interesting/useful. What might be the dangers of using it (it looks easy to loose track of), and any tips you might feel like sharing. Thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) --- --- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] - how/when/why do you use it?
If you think you need '-', think again. If on reflection you still think you need '-', think again. Is this in package::fortunes? +1 for adding that to fortunes ... I remember reading through The R Inferno and getting a good laugh from several such one liners ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Factor variables with GAM models
On Fri, 2010-03-19 at 20:37 -0700, Steven McKinney wrote:
Hi Noah
GAM models were developed to assess the functional form
of the relationship of continuous predictor variables to the
response, so weren't really meant to handle factor variables
as predictor variables. GAMs are of the form
E(Y | X1, X2, ...) = So + S(X1) + S(X2) + ...
where S(X) is a smooth function of X.
But there is absolutely nothing wrong with including factors in
mgcv::gam - they get expanded into the usually dummy variables depending
on the current contrasts as part of the model set-up routines just like
they do in lm(). Perhaps semiparametric might be a better description of
such a model but at least one implementation of GAMs in R can certainly
handle factors.
I haven't used gam::gam so can't comment on that and the OP doesn't say
which gam he is using.
HTH
G
Hence you might want to rethink why you'd want a
factor variable as a predictor variable in a GAM.
This is why the gam machinery doesn't just do the
factor conversion to indicator variables as is done in
lm.
HTH
Steven McKinney
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf
Of Noah Silverman [n...@smartmediacorp.com]
Sent: March 19, 2010 12:54 PM
To: r-help@r-project.org
Subject: [R] Factor variables with GAM models
I'm just starting to learn about GAM models.
When using the lm function in R, any factors I have in my data set are
automatically converted into a series of binomial variables.
For example, if I have a data.frame with a column named color and values
red, green, blue. The lm function automatically replaces it with
3 variables colorred, colorgreen, colorblue which are binomial {0,1}
When I use the gam function, R doesn't do this so I get an error.
1) Is there a way to ask the gam function to do this conversion for me?
2) If not, is there some other tool or utility to make this data
transformation easy?
3) Last option - can I use lm to transform the data and then extract it
into a new data.frame to then pass to gam?
Thanks!!!
__
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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[R] ur.df ADF Unit Root Test: what is the meaning of phi1 and phi2 test statistic?
Hello,
I am using the ur.df function from the {arca} package to run the augmented
Dickey-Fuller unit root test on several time series. However; I do not
understand the econometric interpretation of the the phi1 and phi2
test-statisitc which are output if you choose a trend or drift model. I
looked at the source code for the function but I do not quite understand the
code (which I have included below). Any help would be much appreciate.
Thanks,
Max
if (type == drift) {
result - lm(z.diff ~ z.lag.1 + 1)
phi1.reg - lm(z.diff ~ -1)
phi1 - anova(phi1.reg, result)$F[2]
tau - coef(summary(result))[2, 3]
teststat - as.matrix(t(c(tau, phi1)))
colnames(teststat) - c(tau2, phi1)
}
if (type == trend) {
result - lm(z.diff ~ z.lag.1 + 1 + tt)
phi2.reg - lm(z.diff ~ -1)
phi3.reg - lm(z.diff ~ 1)
phi2 - anova(phi2.reg, result)$F[2]
phi3 - anova(phi3.reg, result)$F[2]
tau - coef(summary(result))[2, 3]
teststat - as.matrix(t(c(tau, phi2, phi3)))
colnames(teststat) - c(tau3, phi2, phi3)
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and provide commented, minimal, self-contained, reproducible code.
[R] Sig differences in Loglinear Models for Three-Way Tables
Hi all, I've been running loglinear models for three-way tables: one of the variables having three levels, and the other two having two levels each. An example looks like below: yes.no - c(Yes,No) switch - c(On,Off) att - c(BB,AA,CC) L - gl(2,1,12,yes.no) T - gl(2,2,12,switch) A - gl(3,4,12,att) n - c(1136,4998,25,339,305,2752,31,692,251,1677,17,557) d.table - data.frame(A,T,L,n) d.table A T Ln 1 BB On Yes 1136 2 BB On No 4998 3 BB Off Yes 25 4 BB Off No 339 5 AA On Yes 305 6 AA On No 2752 7 AA Off Yes 31 8 AA Off No 692 9 CC On Yes 251 10 CC On No 1677 11 CC Off Yes 17 12 CC Off No 557 First, I run the independence model and found a poor fit: library(MASS) loglm(n~A+T+L) Call: loglm(formula = n ~ A + T + L) Statistics: X^2 df P( X^2) Likelihood Ratio 1001.431 70 Pearson 1006.287 70 Thus, I went on and run the two-way association model and found a good fit: loglm(n~A:T+A:L+T:L) Call: loglm(formula = n ~ A:T + A:L + T:L) Statistics: X^2 df P( X^2) Likelihood Ratio 4.827261 2 0.08948981 Pearson 4.680124 2 0.09632168 I compared the independence model (Model1), two-way association model (Model 2), and three-way interaction model (Saturated), and found that the two-way association model was the most parsimonious one: ind - loglm(n~A+T+L) twoway - loglm(n~A:T+A:L+T:L) anova(ind,twoway) LR tests for hierarchical log-linear models Model 1: n ~ T + A + L Model 2: n ~ A:L + A:T + T:L Deviance df Delta(Dev) Delta(df) P( Delta(Dev) Model 1 1001.430955 7 Model 2 4.827261 2 996.603694 50.0 Saturated0.00 0 4.827261 20.08949 By running a Chi-square test, I found that all of the three two-way associations are significant. drop1(twoway,test=Chisq) Single term deletions Model: n ~ A:T + A:L + T:L DfAICLRT Pr(Chi) none 24.83 A:T 2 645.91 625.08 2.2e-16 *** A:L 2 152.93 132.10 2.2e-16 *** T:L 1 143.60 120.77 2.2e-16 *** --- Signif. codes: 0 ¡***¢ 0.001 ¡**¢ 0.01 ¡*¢ 0.05 ¡.¢ 0.1 ¡ ¢ 1 Then, I got the coefficients: coef(twoway) $`(Intercept)` [1] 5.866527 $A BB AA CC 0.27277069 -0.01475892 -0.25801177 $T On Off 1.156143 -1.156143 $L YesNo -1.225228 1.225228 $A.T T AOnOff BB 0.4809533 -0.4809533 AA -0.1783651 0.1783651 CC -0.3025882 0.3025882 $A.L L AYes No BB 0.19166429 -0.19166429 AA -0.15632604 0.15632604 CC -0.03533825 0.03533825 $T.L L TYes No On 0.2933774 -0.2933774 Off -0.2933774 0.2933774 I, then, hand-calculated odds ratio for A x T, A x L, and T x L. T x L: *èTL *=* e4(.293) *= 3.23 A x L: *èAL(BB vs. AA) *= *e 2(.19166) + 2(.1563) = *2.01 *èAL(BB vs. CC) *= *e 2(.19166) + 2(.03533) = *1.57 A x T: *èAT(BB vs. AA) *= *e 2(.48095) + 2(.17837) = 3.74* * * *èAT(BB vs. CC) = e 2(.48095) + 2(.30259) = 4.79 * Now, I'd like to know if BB and AA (or BB and CC) are significantly different from each other (i.e., the odds of BB to be 2.01 times larger than AA is significant) and the differences between BB and CC are significant (i.e., the odds of BB to be 1.6 times bigger is significant) etc. I'd really appreciate if someone can answer this question! Thank you, Sachi [[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] Running cumulative sums in matrices
Does this do what you want?
m1 - cbind(1:5,1:5,1:5)
m2 - m1
for(i in 2:ncol(m1)){
m2[,i] - apply(m1[,1:i],1,sum)
}
m2
ut - diag( ncol(m1) )
ut[upper.tri(ut)] - 1
m3 - m1 %*% ut
m3
all.equal(m2,m3)
hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Eleni Rapsomaniki
Sent: Wednesday, April 14, 2010 6:18 AM
To: r-help@r-project.org
Subject: [R] Running cumulative sums in matrices
Dear R-helpers,
I have a huge data-set so need to avoid for loops as much as possible.
Can someone think how I can compute the result in the following example
(that uses a for-loop) using some version of apply instead (or any
other similarly super-efficient function)?
example:
#Suppose a matrix:
m1=cbind(1:5,1:5,1:5)
#The aim is to create a new matrix with every column containing the
cumulative sum of all previous columns.
m2=m1
for(i in 2:ncol(m1)){
m2[,i]=apply(m1[,1:i],1,sum)
}
m2
Many thanks in advance
Eleni Rapsomaniki
Research Associate
Strangeways Research Laboratory
Department of Public Health and Primary Care
University of Cambridge
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Re: [R] NMDS Ordination Graphics Problem
On Mon, 2010-04-05 at 09:58 -0800, Trey wrote: Dr. Stevens, Hmm, did you get the wrong address there ;-) As Michael Denslow has mentioned, the way to handle this sort of customised plotting at the moment in vegan is to build the plot up by hand. Michael's response earlier showed you how to do it with the in-built data set. Here's how I'd do it (essentially the same thing), using Stephen Sefick's conveniently dput()ed version of your example data: ## something to hold the data dat - (structure(list(a = c(1L, 12L, 2L, 0L, 0L, 13L), b = c(4L, 17L, 5L, 2L, 1L, 15L), c = c(7L, 6L, 8L, 4L, 4L, 19L), d = c(9L, 2L, 1L, 7L, 6L, 10L), e = c(2L, 3L, 3L, 2L, 9L, 8L), f = c(5L, 7L, 2L, 1L, 10L, 9L)), .Names = c(a, b, c, d, e, f), class = data.frame, row.names = c(1i, 2i, 3i, 1c, 2c, 3c))) ## to hold the factor for whether a site is infested or control tlabs - c(infested,control) treat - factor(rep(tlabs, each = 3), levels = tlabs) ## setting the levels explicitly insures R doesn't reorder them alphabetically ## sanity check: all.equal(length(treat), nrow(dat)) ## do the analysis p - metaMDS(x) ## set-up the plotting region: plot(p, display = sites, type = n) ## now add the points, coding the infested/control by colour and pch ## this is where I differ slightly from the example Michael gave ## as here the user can specify the cols, pchs etc required cols - c(red,navy) ## chose what you want pchs - c(3,16) ## ditto choose what you want points(p, display = sites, pch = pchs[treat], col = cols[treat]) ## add a legend: legend(topleft, legend = levels(treat), pch = pchs, col = cols, bty = n) Notice how I've done the indexing there. Remember treat is a factor with more than two observations in it. In the points call above we rely on the factor being coded internally as 1,2,3,...,k for the k levels in the factor. To see what is actually being passed to col in the above call, do: cols[treat] So we've only specified our two colours and then used the treatment variable created earlier to do the right thing for us. If you have more toruble with vegan, try posting on the R SIG Ecology list (as that's where Jari Oksanen tends to hang out rather than R-Help) or on the R-Forge forum for Vegan: http://r-forge.r-project.org/forum/forum.php?forum_id=194 HTH G Hi, my name is Trey Scott, and I'm a grad student of Brian McCarthy's. He referred me to you because of your expertise in handling complex R problems. We were hoping you could help us solve a nagging problem that is prohibiting me from producing graphicl output. Here is a simple mock-up of the matrix I'm using a b c d e f 1i 1 4 7 9 2 5 2i 12 176 2 3 7 3i 25 8 1 3 2 1c 02 4 7 2 1 2c 01 4 6 9 10 3c 13 15 19 108 9 Where: 1i-3i are infested sites, and 1c-3c are control sites. A-F are species found at each site. I have several of these ordinations to perform on different variables (BA, density, RIV, cover, etc..., all in different matrices). I'm running NMDS (metaMDS) ordinations on each matrices, and producing ordination graphs for each cloud of points. The problem I have is that I cannot devise a way to split the cloud of points into infested and control so that I can deduce any significant groupings. A simple difference in symbols/color (Ex. gray triangles for infested, black circles for control) would do. Also, I understand the use of pch/col/cex, I just need to apply them to the split. So: + How would I split these out in R after I run the metaMDS in vegan? + What code would be necessary to bring this about? McCarthy and I are at the end of our preoverbial rope on this; nothing has worked. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] vegan (ordisurf): R² for smoothed surf aces
On Tue, 2010-04-13 at 15:02 +0200, Kim Vanselow wrote:
Dear r-helpers,
I just read in an article by Virtanen et al. (2006) where
vegetation-environment relationships are studied by fitting smoothed
surfaces on an NMDS ordination using GAMs (Wood 2000). The authors
describe, that they used R² as goodness-of-fit statistic, which they
compare to the R² of fitted vectors. Calculations were carried out
using the package vegan (Oksanen).
I know that I can fit vectors onto ordinations with the function
envfit. The R² is listed in the output table. I also know that GAMs
are implemented in vegan by the function ordisurf. But how can I get
an R² from this function.
?ordisurf and see the Value section. ordisurf returns the mgcv::gam
object describing the model fit. If you assign the object returned by
ordisurf and run summary on it (as you would any other mgcv::gam model),
you'll get the R^2(adj). Here's an example:
data(varespec)
data(varechem)
library(MASS)
vare.dist - vegdist(varespec)
vare.mds - isoMDS(vare.dist)
## capture return value
mod - with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5))
## summary
summary(mod)
You can then pull apart the returned object ('mod') if you need to get
at the R^2 for subsequent computations, storage etc rather than just
display it.
HTH
G
Thanks in advance,
Kim
--
GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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Re: [R] GAMM : how to use a smoother for some levels of a variable, and a linear effect for other levels?
On Wed, 2010-04-14 at 10:03 +0200, JANSEN, Ivy wrote: Hi, I was reading the book on Mixed Effects Models and Extensions in Ecology with R by Zuur et al. In Section 6.2, an example is discussed where a gamm-model is fitted, with a smoother for time, which differs for each value of ID (4 different bird species). In earlier versions of R, the following code was used BM2-gamm(Birds~Rain+ID+ s(Time,by=as.numeric(ID==Stilt.Oahu))+ s(Time,by=as.numeric(ID==Stilt.Maui))+ s(Time,by=as.numeric(ID==Coot.Oahu))+ s(Time,by=as.numeric(ID==Coot.Maui)), correlation=corAR1(form=~Time |ID ), weights=varIdent(form=~1|ID)) However, in the current version of R, this does not work anymore, and should be changed into BM2-gamm(Birds~Rain+ID+ s(Time,by=ID), correlation=corAR1(form=~Time |ID ), weights=varIdent(form=~1|ID)) It turns out that 2 of the 4 smoothers have estimated degrees of freedom of 1, so a linear effect would be sufficient. Now my question is how I need to change the code in order to have a time smoother for ID=Coot.Oahu and ID=Coot.Maui, and a linear time effect for ID=Stilt.Oahu and ID=Stilt.Maui. With the old R-code, this seems trivial, but I don't have any idea how to do it in the newest R-version (interactions with a dummy variable do not work in gamm). Isn't a smooth that uses 1 df == to a linear function? So doesn't the current model already do what you want? You don't need to refit it with two smooths and two linear parametric terms as the two models should be effectively equivalent anyway. Or have I misunderstood your question? HTH G Thanks, Ivy Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] what is the intercept of a two-way anova model without interaction term?
Hi: Perhaps this will clarify some things: model.matrix(m) (Intercept) factor1B factor1C factor2t2 factor2t3 1 100 0 0 2 110 0 0 3 101 0 0 4 100 1 0 5 110 1 0 6 101 1 0 7 100 0 1 8 110 0 1 9 101 0 1 Now tack on the predicted values from the model: cbind(model.matrix(m), predict(m)) (Intercept) factor1B factor1C factor2t2 factor2t3 1 100 0 0 67.65502 2 110 0 0 134.24682 3 101 0 0 83.81768 4 100 1 0 52.71252 5 110 1 0 119.30431 6 101 1 0 68.87518 7 100 0 1 30.66079 8 110 0 1 97.25259 9 101 0 1 46.82345 In the first row, the subject is neither at levels B nor C of factor1, nor at level t2 of factor2. At what levels of factor1 and factor2 must this subject be? You'll see a pattern in how the predicted values are obtained from the level combinations in each observation, the model and its estimated coefficients. In the process, you'll learn how treatment contrasts work. Since I smell homework, this is as far as I'll go. HTH, Dennis On Wed, Apr 14, 2010 at 10:13 AM, Xiaokuan Wei weixiaok...@yahoo.comwrote: Dear list, I have a question regarding the meaning of intercept term in a two-way anova model without interaction term. for example (let's assume there is no interaction between factor1 and factor2) : df valfactor1 factor2 1 48.61533 A t1 2 171.13535 B t1 3 65.96884 C t1 4 63.71222 A t2 5 80.22049 B t2 6 96.95929 C t2 7 38.70078 A t3 8 99.44787 B t3 9 36.58818 C t3 the summary of regression : summary(m) Call: lm(formula = val ~ factor1 + factor2, data = df) Residuals: 1 2 3 4 5 6 7 8 9 -19.040 36.889 -17.849 11.000 -39.084 28.084 8.040 2.195 -10.235 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept)67.66 25.42 2.661 0.0563 . factor1B 66.59 27.85 2.391 0.0751 . factor1C 16.16 27.85 0.580 0.5928 factor2t2 -14.94 27.85 -0.537 0.6200 factor2t3 -36.99 27.85 -1.328 0.2548 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 34.11 on 4 degrees of freedom Multiple R-squared: 0.6669, Adjusted R-squared: 0.3338 F-statistic: 2.002 on 4 and 4 DF, p-value: 0.2589 This is contrast treatment, and my question is what the intercept (here is 67.66) represent for? Thank you. Xiaokuan [[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] Import ASCII data using a .sas program
Dear Don, What read.fwf() needs are the field widths. I think that the following will do what you want: strings - scan(what=) 1: perstat1 $1-2 3: linenum $3-4 5: I_wave1 $5-5 7: bnocost1 $6-10 9: bnosta1 $11-12 11: Read 10 items (fields - matrix(as.numeric(unlist(strsplit( + gsub(\\$, , grep(^\\$, strings, value=TRUE)), -))), + ncol=2, byrow=TRUE)) [,1] [,2] [1,]12 [2,]34 [3,]55 [4,]6 10 [5,] 11 12 (widths - fields[,2] - fields[,1] + 1) [1] 2 2 1 5 2 I hope this helps, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Donald Catanzaro, PhD Sent: April-14-10 1:02 PM To: r-help@r-project.org Subject: Re: [R] Import ASCII data using a .sas program Good Day, I have several ASCII data files that I would like to import into R. They all have a SAS import file which is used to bring the data into SAS and I am hoping to use this to bring the data into R. There are lots of variables involved and the ASCII data file is 2308 columns long so I would certainly prefer to figure out a smart way of converting the data to R. The ASCII data is a long stream of numbers (no field separators or delimiters) while the SAS import file looks like: libname mine 'c:\'; data mine.fh4; infile 'd:\fh4.txt' lrecl=2309; input perstat1 $1-2 linenum $3-4 I_wave1 $5-5 bnocost1 $6-10 bnosta1 $11-12 So SAS uses the position of the ASCII character to determine what variable the data should be in while the SCAN or the READ. FWF function of R uses the width of the column. Does anyway have a smart and/or automated way of moving my ASCII data into R using this .SAS program ? -- -Don Don Catanzaro, PhD Landscape Ecologist dgcatanz...@gmail.com 16144 Sigmond Lane Lowell, AR 72745 479-751-3616 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Error: could not find function tsts tradesys package
Thank you so much for your reply. On the first page of the paper, there are logics which I typed library(tradesys) library(TTR) data(spx) tail(spx) ,and it runs smoothly. But it gives me an error at x - tsts(spx) Thanks, db -- View this message in context: http://n4.nabble.com/Error-could-not-find-function-tsts-tradesys-package-tp1839233p1840069.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] svm of e1071 package
Hello Steve, Thanks for your reply. yes, i converted input matrix to a sparse matrix (via SparseMatrix). rbind is fine for our case as anyway we have to do it. So, instead of using rbind on dense matrix and convert the whole matrix at the end, we take convert each chunk and add it to the big one. No parameter tweaking was necessary. But as you have mentioned, I will like to try read.matrix.csr and write.matrix.csr . this can save lot of our time and resources. Thanks again for your help. Regards Shyama From: Steve Lianoglou [mailinglist.honey...@gmail.com] Sent: Wednesday, April 14, 2010 2:49 PM To: Shyamasree Saha [shs] Cc: r help Subject: Re: [R] svm of e1071 package Hi Shyama, On Tue, Apr 13, 2010 at 10:40 AM, Shyamasree Saha [shs] s...@aber.ac.uk wrote: Dear Steve, We have finally managed to run our code. Sparse matrix is helping a lot (I should say without matrix.csr, we would not be able to do it). This time it is taking very small amount of memory while running svm, but we could not use as.matrix.csr directly on our huge data. we had to divide the data in small chunk. we created matrix.csr from those small chunk, removed our original object, loaded next chunk and used rbind to put all of them together. we need to be very careful how much data we load at a time. Thanks again for you kind help. This is great news :-) So, just to recap -- is the only thing that you did to get this to work is to convert your input matrix to a sparse matrix (via SparseM)? No parameter tweaking necessary? Would an alternative approach to creating the sparse matrix be more helpful? You can, for instance, create the entire sparse matrix in one shot, like: R m - as.matrix.csr(0, nrow=10, ncol=10) (with appropriate numbers for your nrow,ncol params) Then you can load subsets of your data into it and skipping the chunked-`rbing` strategy .. is that easier? Also, the e1071 package has read.matrix.csr and write.matrix.csr functinos that might help facilitate loading/saving your data matrices in the future. -steve Regards Shyama From: Steve Lianoglou [mailinglist.honey...@gmail.com] Sent: Wednesday, April 07, 2010 4:00 PM To: Shyamasree Saha [shs] Cc: r help Subject: Re: [R] svm of e1071 package Hi, On Tue, Apr 6, 2010 at 7:16 PM, Shyamasree Saha [shs] s...@aber.ac.uk wrote: Dear Steve, Thanks again for your help and reply. your help was very useful and gave us some options. We will follow your suggestions and let you know about it. No problem ... yeah, please write back when you figure out what's up (or hit more roadblocks), I'd be curious to know what the solution is. Thanks, -steve Regards, shyama From: Steve Lianoglou [mailinglist.honey...@gmail.com] Sent: Tuesday, April 06, 2010 9:40 PM To: Shyamasree Saha [shs] Cc: r help Subject: Re: [R] svm of e1071 package Hi Shyama, Don't forget to CC the r-help list in your discussions so that there are more eyes on this problem, and others might potentially benefit from discussion. Comments in line. On Tue, Apr 6, 2010 at 4:06 PM, Shyamasree Saha [shs] s...@aber.ac.uk wrote: Dear Steve, Thanks a lot for your reply. As you have suggested kernlab and SparseM packages, we have now installed it and reading about these packages. I am trying to answer your questions. I have also added a bit of code. Please let me know whether you need to know more and what is your suggestions. Thanks again for your help. Regards, Shyamasree R .Machine$sizeof.pointer ## it should be 8 Yes, it is indeed 8. OK * What type of kernel are you using? Have you tried different ones? Just tried the linear kernel, haven't tried with other kernels. OK, let's stick with that for now. * Are you doing classification or regression? We are doing multi-class classification. There are 11 classes. Is it any better if you just do 1-vs-all? Also (from your code at the end of the email) what if you train the model with `probability=FALSE`? * Is your data/feature matrix sparse? If so, are you passing libsvm a SparseM matrix? Yes, the feature matrix is indeed very sparse. Just passing a matrix at the moment. Not sure how to define it as SparseM matrix. R library(SparseM) R ?as.matrix.csr * Have you tried playing with some of the params in the svm call, like the values for tolerance, epsilon, cost/nu/etc. No, have not played with these at all. What do you recommend? Try to increase (I think (maybe decrease??)) the tolerance from its default value. Moving this in one direction or the other allows the solver to converge to a less-precise solution -- haven't read the source in a while, though, so test it. * Try an even smaller subset of your data ( 1.4 GB) It works fine with a much smaller subset but have not tried with intermediate sizes. OK Can you give an idea of
[R] Selecting derivative order penalty for thin plate spline regression (GAM - mgcv)
Hi, I am using GAMs (package mgcv) to smooth event rates in a penalized regression setting and I was wondering if/how one can select the order of the derivative penalty. For my particular problem the order of the penalty (parameter m inside the s terms of the formula argument) appears to have a larger effect on the AIC/deviance of the estimated model than the number (or even the location!) of the knots for the covariate of interest. In particular, the estimated smooth changes shape from a linear (default m (=2) value for a TP smooth or a P-spline smooth) with a edf of 2.06 to a non-linear one with a edf of 4.8-5.1 when the m is raised to 3. There are no changes in the estimate shape of the smooth when I tried higher values of m and different bases (thin plate, p-spline). The overall significance of the smooth term changes, but is 0.05 in both cases, however the interpretation afforded by the shapes of the smooths are different. Smoothing the same dataset with a different approach to GAMs (BayesX) results in shapes that are more like the ones I have been getting with m=3 rather than m=2 (I have not tried the conditional autoregressive regressions of WinBUGS yet). Any suggestion on how to proceed to test the optimal order of the penalty would be appreciated. The 2 approaches I am thinking of trying are: a) use un-penalized smoothing regressions and comparing the 2 models with ANOVA b) First, fit the m=2 model and extract the smoothing parameters of all other smooth terms from that model. Second, fit a model in which the smooth of the covariate of interest is set to m=3 , fixing the parameters of all other smooth terms appearing in the model statement to the values estimated in the first step. Then I could compare the (m=2) v.s. (m=3) models with ANOVA as the 2 models are properly nested within each other. Any other ideas? Sincerely, Christos Argyropoulos University of Pittsburgh _ Hotmail: Trusted email with powerful SPAM protection. [[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] how to draw multiple vertical bands
hi R gurus I saw some graphs with vertical band like this one: http://pragcap.com/wp-content/uploads/2010/04/GS.png how to draw the blue band in R, can't find any clue to do this,any ideas? thanks in advance [[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] envelope in spatstat
Hi R users,
This query is regarding the use of the 'envelope' function in Spatstat.
My data can be represented as a point process with CONTINUOUS marks:
points - ppp(x=x,y=y, marks=m, window= wind)
However the marks are alignments (lines), and so have to be treated
differently to normal scalar marks. Hence to create a mcf object with the
appropriate test function for alignment marks, I input 'func' (below)
suggested by Stoyan Penttinen (1989):
func - function(m1,m2) { sin(abs(m1-m2))^2}
mcf - markcorr(points, func, normalise = TRUE, method=density)
So far, so good. However, usinf 'envelope' and 'rlabel' I would like to
check if the pattern in the data is lost when randomly relabeling the mark
for each point. If the test function, 'func' were the usual G(m1,m2)=m1*m2,
then the following would work:
E - envelope(points, markcorr, nsim=20,
simulate=expression(rlabel(points)))
Howeve, in the above 'markcorr' calculates G(m1,m2)=m1*m2 by default. So
need to specify the test function to be G(m1,m2)= sin(abs(m1-m2))^2.
According to the spatstat manual (p177), I may need to 'cook up' a specific
function, like this:
Kdif = function(X, ..., i) {
Kidot = Kdot(X, ..., i = i)
K = Kest(X, ...)
dif = eval.fv(Kidot - K)
return(dif)
}
E = envelope(lansing, Kdif, i='blackoak',
simulate=expression(rlabel(lansing)))
So how do I tell 'envelope' that I want to specify the mark correlation
test function ??
Many thanks in advance!
T
---
Dept. of Maths and Stats, UWE and Ant Lab, Bristol
Room B79.
SoBS, Woodland Rd. BS8 1UG.
+44 (0)117 928 8443
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[R] Conflict plot.circular and layout() using different column width of the layout matrix
Hi I am trying to make a figure with several subfigure using the layout(). The subfigures include circular plots (package:circular). When I use different widths of the columns (layout(matrix(1:6, 2,3), width=c(1,1.5,1))) the circular plots in the first row have an elliptic and unpredictible shape but are normal in the second row. When the widths of the columns are equal the problem does not occur. The same problems occurs when the heights of the subfigure rows are different. Is this a bug? Any suggestions how to solve the problem? Below is an example to outline the problem. Many thanks, Daniela library(circular) layout(matrix(1:6, 2,3), width=c(1,1.5,1)) layout.show(6) angles - circular(pi) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) Without different column widths there it works fine. library(circular) layout(matrix(1:6, 2,3)) layout.show(6) angles - circular(pi) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) plot(angles, stack=T, bins=360, col=green, xlim=c(-1,1), ylim=c(-1,1)) -- Sicherer, schneller und einfacher. Die aktuellen Internet-Browser - jetzt kostenlos herunterladen! http://portal.gmx.net/de/go/chbrowser __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: could not find function tsts tradesys package
You need to take this up with the package authors. After I install tradesys, and type vignette(tradesys), I get a PDF that no longer contains the example in the PDF you reference from the web. That particular version of the PDF that you reference is probably no longer relevant to the package. Those functions are no longer distributed with tradesys, it appears. dbonneau wrote: Thank you so much for your reply. On the first page of the paper, there are logics which I typed library(tradesys) library(TTR) data(spx) tail(spx) ,and it runs smoothly. But it gives me an error at x - tsts(spx) Thanks, db __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: could not find function tsts tradesys package
I think that this package is very much in the early stages of development. It may be that the tsts function is still just a gleam in the eyes of the developers. The paper that you cite may be ahead of code development. -Peter Ehlers On 2010-04-14 10:20, dbonneau wrote: Thank you so much for your reply. On the first page of the paper, there are logics which I typed library(tradesys) library(TTR) data(spx) tail(spx) ,and it runs smoothly. But it gives me an error at x- tsts(spx) Thanks, db -- Peter Ehlers University of Calgary __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: could not find function tsts tradesys package
Peter Ehlers wrote: I think that this package is very much in the early stages of development. It may be that the tsts function is still just a gleam in the eyes of the developers. The paper that you cite may be ahead of code development. Yes, in my reply I assumed behind, but 'ahead' is certainly possible, too! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] curve
Dear R users, How can I use curve with a function of two variables ? Thank you very much, Dwayne [[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] liner regression for multiple keys
newbie_2010 girishbogu at gmail.com writes:
a1 is the first key in input. second column is x-axis and 3rd is y-axis and
4th is its corresponding key.
Now for every key in 1st column I would like to calculate LR that gives p
value. I tried to manage with a single key. But my problem is that How could
I manage multiple keys in input.
Thanx in advance
something like:
library(nlme)
fm - lmList(y~x|key,data=...)
get.pval - function(z) {
x - summary(z)
pf(x$fstatistic[1L],
x$fstatistic[2L], x$fstatistic[3L], lower.tail = FALSE)
}
sapply(fm,get.pval)
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Re: [R] curve
Dwayne Blind dwayneblind at gmail.com writes: How can I use curve with a function of two variables ? see curve3d in the emdbook package. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Sig differences in Loglinear Models for Three-Way Tables
See comments in line. On Wed, 14 Apr 2010, Sachi Ito wrote: Hi all, I've been running loglinear models for three-way tables: one of the variables having three levels, and the other two having two levels each. An example looks like below: yes.no - c(Yes,No) switch - c(On,Off) att - c(BB,AA,CC) L - gl(2,1,12,yes.no) T - gl(2,2,12,switch) A - gl(3,4,12,att) n - c(1136,4998,25,339,305,2752,31,692,251,1677,17,557) d.table - data.frame(A,T,L,n) d.table A T Ln 1 BB On Yes 1136 2 BB On No 4998 3 BB Off Yes 25 4 BB Off No 339 5 AA On Yes 305 6 AA On No 2752 7 AA Off Yes 31 8 AA Off No 692 9 CC On Yes 251 10 CC On No 1677 11 CC Off Yes 17 12 CC Off No 557 First, I run the independence model and found a poor fit: library(MASS) loglm(n~A+T+L) Call: loglm(formula = n ~ A + T + L) Statistics: X^2 df P( X^2) Likelihood Ratio 1001.431 70 Pearson 1006.287 70 Thus, I went on and run the two-way association model and found a good fit: loglm(n~A:T+A:L+T:L) Call: loglm(formula = n ~ A:T + A:L + T:L) Statistics: X^2 df P( X^2) Likelihood Ratio 4.827261 2 0.08948981 Pearson 4.680124 2 0.09632168 I compared the independence model (Model1), two-way association model (Model 2), and three-way interaction model (Saturated), and found that the two-way association model was the most parsimonious one: ind - loglm(n~A+T+L) twoway - loglm(n~A:T+A:L+T:L) anova(ind,twoway) LR tests for hierarchical log-linear models Model 1: n ~ T + A + L Model 2: n ~ A:L + A:T + T:L Deviance df Delta(Dev) Delta(df) P( Delta(Dev) Model 1 1001.430955 7 Model 2 4.827261 2 996.603694 50.0 Saturated0.00 0 4.827261 20.08949 By running a Chi-square test, I found that all of the three two-way associations are significant. drop1(twoway,test=Chisq) Single term deletions Model: n ~ A:T + A:L + T:L DfAICLRT Pr(Chi) none 24.83 A:T 2 645.91 625.08 2.2e-16 *** A:L 2 152.93 132.10 2.2e-16 *** T:L 1 143.60 120.77 2.2e-16 *** --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 Then, I got the coefficients: coef(twoway) $`(Intercept)` [1] 5.866527 $A BB AA CC 0.27277069 -0.01475892 -0.25801177 $T On Off 1.156143 -1.156143 $L YesNo -1.225228 1.225228 $A.T T AOnOff BB 0.4809533 -0.4809533 AA -0.1783651 0.1783651 CC -0.3025882 0.3025882 $A.L L AYes No BB 0.19166429 -0.19166429 AA -0.15632604 0.15632604 CC -0.03533825 0.03533825 $T.L L TYes No On 0.2933774 -0.2933774 Off -0.2933774 0.2933774 I, then, hand-calculated odds ratio for A x T, A x L, and T x L. T x L: *?TL *=* e4(.293) *= 3.23 A x L: *?AL(BB vs. AA) *= *e 2(.19166) + 2(.1563) = *2.01 *?AL(BB vs. CC) *= *e 2(.19166) + 2(.03533) = *1.57 A x T: *?AT(BB vs. AA) *= *e 2(.48095) + 2(.17837) = 3.74* * * *?AT(BB vs. CC) = e 2(.48095) + 2(.30259) = 4.79 * Now, I'd like to know if BB and AA (or BB and CC) are significantly different from each other (i.e., the odds of BB to be 2.01 times larger than AA is significant) and the differences between BB and CC are significant (i.e., the odds of BB to be 1.6 times bigger is significant) etc. It will be easier to answer this if you formulate the problem as a surrogate Poisson regression via glm(). The relationship between the surrogate Poisson and the loglinear model is well known. See VR or McCullagh and Nelder, for example. Then the hypotheses about odds ratios become hypotheses about coefficients, which you can test via summary(), or linear combinations of coefficients, which you can test with the pieces that vcov() and coef() provide. HTH, Chuck I'd really appreciate if someone can answer this question! Thank you, Sachi [[alternative HTML version deleted]] Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu 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.
Re: [R] R package documentation
Sébastien Bihorel wrote: Thanks Tobias, If there is no automated way to combine both documents, I will stack them manually... that will likely cause some problems with page numbering tough. Sebastien There was a thread a while back (this year) about someone who wanted to incorporate his package manual in his thesis. A solution was offered to this as I recall and it seems like the same problem to me. What you need is the LaTeX that comes out of the package check. Just add it to your vignette LaTeX and that should do the trick. David _ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018 Director of Consulting, Department of Statistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Ranking correlation with R
Hello Guys, thank you all very much for the help! Sorry for my total lack of knowledge in R... so I did the correlation.. and got these results: cor(A, C, method = spearman) [1] 0.4922165 cor(B, C, method = spearman) [1] 0.1922412 cor(A, B, method = spearman) [1] -0.00889328 I don't know how to interpret them... so the correlation is good when it is really close to 1 or to 0? What about negative correlation?? Cheers, -- David Nemer On Sat, Apr 10, 2010 at 2:58 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: Try this: A - c(file1.java, file3.java, file2.java) B - c(file2.java, file4.java, file1.java) cor(A, B, method = spearman) [1] 0.5 On Fri, Apr 9, 2010 at 11:22 AM, David Nemer davidne...@gmail.com wrote: Hey Everyone, Im fresh new in R, and Im supposed to write a code to give me a correlation between two rankings. So I have two ranking lists, which contain file names, e.g.: Ranking list 1: file1.java file3.java file2.java Ranking list 2: fiile2.java file4.java file1.java I need to see how much are these two ranking lists are alike, get a correlation between them. I dont even know where to start. Can anyone bring me some light or tips? Thank you in advance. Cheers, -- David Nemer [[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] how to draw multiple vertical bands
?rect On Wed, Apr 14, 2010 at 10:36 AM, senne wase...@gmail.com wrote: hi R gurus I saw some graphs with vertical band like this one: http://pragcap.com/wp-content/uploads/2010/04/GS.png how to draw the blue band in R, can't find any clue to do this,any ideas? thanks in advance [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] filled.contour ON TOP of a base map
Anyone? [[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.
