Re: [R] Table and ftable
There might be simpler ways, but you can certainly do this with the reshape package, like this: library(reshape) dta - read.table(clipboard,header=TRUE) sic level area 1 a 211 2.4 2 b 311 2.3 3 b 322 0.2 4 b 322 0.5 5 c 100 3.0 6 c 100 1.5 7 c 242 1.5 8 d 222 0.2 mlt.dta - melt(dta) cst.dta - cast(mlt.dta,sic~level,sum) sic 100 211 222 242 311 322 1 a NA 2.4 NA NA NA NA 2 b NA NA NA NA 2.3 0.7 3 c 4.5 NA NA 1.5 NA NA 4 d NA NA 0.2 NA NA NA Then just replace the NAs with 0s. HTH. David Barron On 9/4/07, Giulia Bennati [EMAIL PROTECTED] wrote: Dear listmembers, I have a little question: I have my data organized as follow sic level area a2112.4 b3112.3 b3220.2 b3220.5 c1003.0 c1001.5 c2421.5 d2220.2 where levels and sics are factors. I'm trying to obtain a matrix like this: level 211311322 100242 222 sic a2.4 0 0 0 00 b 0 2.30.7 0 00 c 00 0 4.5 1.5 0 d 00 00 0 0.2 I tryed with table function as table(sic,level) but i obteined only a contingency table. Have you any suggestions? Thank you very much, Giulia __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to fit an linear model withou intercept
A number of alternatives, such as: lm(y ~ 0 + x) lm(y ~ x -1) See ?formula On 8/23/07, Michal Kneifl [EMAIL PROTECTED] wrote: Please could anyone help me? How can I fit a linear model where an intercept has no sense? Thanks in advance.. Michael __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regression with Missing values. na.action?
na.exclude should give the same results as na.omit, which is the default na.action. Is the number of complete cases the same in these two regressions? On 26/07/07, Vaibhav Gathibandhe [EMAIL PROTECTED] wrote: Hi all, Can you please tell me what is the problem here. My regression eq is y = B0 + B1X1 +B2X2 +e And i am interested in coefficient B1 I am doing regression with two cases: 1) reg-lm(y ~ X1 + X2, sam) where sam is the data 2) reg-lm(y ~ X1 + X2, sam, na.action= na.exclude) . I have missing values in X1 but the values of coefficient is not consistent in two cases. Actually B1 in case one sould be smaller than B1 in case 2. But sometimes it comes greater. I can't figure it out. Is there some problem with *na.action ? *My sample size is 100 *Regards,* *Vaibhav* [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] standardization
Try having a look at the scale and sweep functions. David On 13/07/07, Amir_17 [EMAIL PROTECTED] wrote: Hi I have dataframe which contain 5 columns and 1000 records. I want standard each cell. I want range each column between 0 and 1 . I think i must use loop? could you help me? - Moody friends. Drama queens. Your life? Nope! - their life, your story. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Standard Probability Distributions.
Have a look in the stats package for the distributions that come with base R. There is a package called SuppDists that has some others, and no doubt there are others. Try RSiteSearch to look for specific distributions. On 30/06/07, Marcus Vinicius [EMAIL PROTECTED] wrote: Dear all, What are the standard probability distributions available in R? I need some as Normal-Truncated, Half-Normal, Gamma, Chi-squared, Wishard, etc. Thanks. Marcus Vinicius [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transposing data.frames
t(KK) will transpose your data frame On 25/06/07, Christoph Heibl [EMAIL PROTECTED] wrote: Hello, This must be simple... Thanks a lot - Christoph # Imagine you have a list, e.g: K - list(1:10, 2:11, 9:18) K # Transforming to dataframe... KK - as.data.frame(K) # ... one obtaines the list elements as column. KK # But I need the list elements as rows # How can I achieve this? Is there a simple way to transpose data.frames? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Highliting a text in a plot
How about this:
hilight - function(x,y,s, bg=yellow) {
text.width - strwidth(s)
text.height - strheight(s)
rect(x,y,x+text.width,y+text.height,col=bg,border=NA)
text(x,y,s,adj=c(0,0))
}
plot(1:10,1:10,type=b)
hilight(4,4,Point)
On 23/06/07, Maja Schröter [EMAIL PROTECTED] wrote:
Hi everyone,
I want to highlight something in a plot.
So I want to write a text with a yellow background.
I tried to make use of text(x,y,hallo,bg=yellow)
but that does not work.
I know I am a handful. Sorry!
Maja!
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=
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University of Oxford
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Oxford OX1 1HP
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Re: [R] Could not find lmer function in {Matrix} package
It's now in the lme4 package.
On 19/06/07, Steve Brady [EMAIL PROTECTED] wrote:
I am having trouble calling the lmer function in the {Matrix}
package. I first installed and loaded {Matrix} as follows:
install.packages(Matrix)
library(Matrix)
The package loaded successfully, however when I attempted to call
lmer, I received the following message:
Error: could not find function lmer
I also tried:
?lmer
which produced no search results.
I have attempted these actions in both MacOSx R Versions 2.4.1 and
2.5.0. I have also tried this in Version 2.5.1. beta on a Windows
machine.
Thanks in advance for any suggestions.
Steve
Steven P. Brady, M.E.Sc (2007)
School of Forestry Environmental Studies
Yale University
http://www.cbc.yale.edu/people/skelly/steveb.html
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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.
--
=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
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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] Histogram
I expect there's a more elegant way of doing this, but this should work: set.seed(101) x - rnorm(500,sd=.03) hist (x, seq(-0.1,0.1,0.01),freq = FALSE) d - density(x,bw=SJ) lowt - d$x -.05 upt - d$x .05 lines (d$x[lowt],d$y[lowt], col = red) lines(d$x[upt],d$y[upt], col = red) On 19/06/07, livia [EMAIL PROTECTED] wrote: Hello, I am using the following codes to plot a histogram and density line for x. For the density line, I just want it to show the two tails, eg, for x larger than 0.05 ans smaller than -0.05 hist (x, seq(-0.1,0.1,0.01),freq = FALSE) lines (density(x,bw=SJ), x 0.05 x (-0.05), col = red) But is does not work, can anyone give me some advice? -- View this message in context: http://www.nabble.com/Histogram-tf3947281.html#a11197644 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Storing output vector form a loop as a matrix
I'm not sure I've completely understood this, but would this do what you want:
for (i in 1:N){
aa - sample(a, replace=TRUE)
c -data.frame(b,aa)
output - by(c, aa, function(x) sum(x$b))
output.matrix[,i] - as.vector(output)
}
On 17/06/07, Economics Guy [EMAIL PROTECTED] wrote:
Based on help files and searching the archives and help from the listserv I
have managed to build my monte carlo program.
However I cannot get the proper syntax for running the loop and storing the
output of each loop (which is a vector) into a matrix.
I took out some of the crazy code I was writing, but here is what I have:
rm(list = ls(all = TRUE))
# removes everything
a -c(A,C,B,A,B,C)
b -c(10,20,30,40,50,60)
c -data.frame(a,b)
N=10 #Number of Loops
output.matrix - matrix(0.0,3,N)
#I need to START LOOP HERE
a - sample(a, replace=TRUE)
c -data.frame(b,a)
output.vector - by(c, a, function(x) sum(x$b))
output.vector - as.vector(output)
output.vector - data.frame(output)
#END LOOP here
--
What I would like to have at the end is the output.matrix contain as a
column the output.vector from each iteration. The actual data frame I
will be running has 60,000 observations and I am going to run 2
iterations so speed is important too.
Thanks so much
EG
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=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
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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] Recoding
I've used the one in car with no problems. For grouping a continuous variable you might also consider cut. On 11/06/07, David Scott [EMAIL PROTECTED] wrote: I want to do some recoding of variables: code Age into groups and recode a factor into a smaller number of levels. There are a couple of options for recode functions, in the car package and in memisc, and I think in gmisc. Does anyone have any opinions on the the easiest, most reliable approach for these problems? David Scott _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000 Email: [EMAIL PROTECTED] Graduate Officer, Department of Statistics Director of Consulting, Department of Statistics __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to plot vertical line
abline(v=c(intercept1,intercept2,intercept3)) On 09/06/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi,I have a result from polr which I fit a univariate variable (of ordinal data) with probit function. What I would like to do is to overlay the plot of my fitted values with the different intercept for each level in my ordinal data. I can do something like:lines(rep(intercept1, 1000), seq(from=0,to=max(fit),by=max(fit)/1000))where my intercept1 is, for example, the intercept that breaks between y=1 and y=2 labels and the max(fit) is the maximum of overall fitted values or maximum of all ordinal y labels. I'm wondering if there is better way to do this? If you could let me know, I would really appreciated. Thank you.- adschai [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] comparison of two logistic regression models
You could use lmer in the lme4 package to fit the logistic regression with random effect as it does report the AIC. On 07/06/07, Anna-Maria Tyriseva [EMAIL PROTECTED] wrote: Dear list members! Could you help me? I would like to compare two models: a) logistic regression model, 3 factors as independents b) logistic regression model, 3 factors and one random effect as independents (function glmmPQL). AIC are not available with PQL and model comparison using ANOVA is not possible. What should I do? Thanks in advance. Anna-Maria __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] list
There's no special method, just create a list in the usual way. For example: l1-list(a=letters[1:5],b=letters[6:10]) l1 $a [1] a b c d e $b [1] f g h i j l2-list(c=LETTERS[1:5],d=LETTERS[6:10]) l2 $c [1] A B C D E $d [1] F G H I J l3-list(l1,l2) l3 [[1]] [[1]]$a [1] a b c d e [[1]]$b [1] f g h i j [[2]] [[2]]$c [1] A B C D E [[2]]$d [1] F G H I J On 06/06/07, elyakhlifi mustapha [EMAIL PROTECTED] wrote: hello, I wanna know how to create a list of list if it's possible and if it isn't possible how to do without. thanks. _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using cut
You can split a vector into groups with equal numbers using the quantcut function in the gtools package. For example, to split into two groups, use: c - quantcut(y,c(0,.5,1)) On 26/05/07, J. Scott Olsson [EMAIL PROTECTED] wrote: Suppose I have some data x - rnorm(1000); y - x*x; then try to cut it into 2 chunks, c - cut(y, breaks=2); summary(y) Min. 1st Qu.Median Mean 3rd Qu. Max. 6.879e-06 9.911e-02 3.823e-01 9.499e-01 1.297e+00 8.342e+00 summary(c) (-0.00833,4.17] (4.17,8.35] 958 42 Is that the correct behavior? Why is the left hand side of the interval negative? How would I split a data vector into groups/intervals such that each interval contained the same number of points? Thanks much! Scott [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] impossible to open SPSS file
Have a look at FAQ 2.16 in the R for Windows FAQ. On 29/04/07, Frank Thomas [EMAIL PROTECTED] wrote: Hi, I try to import a SPSS file with foreign but don't succeed. I looked into the help pages but find no answer. The file has been produced with SPSS 15 but I got the same error with a file in SPSS portable format. mydata-read.spss(C:\Rdata\ESS1_ICT.SAV) Erreur dans read.spss(C:RdataESS1_ICT.SAV) : impossible d'ouvrir le fichier I guess the error is evident for everyone else, but I don't see it. Thanks Frank Thomas -- .. Dr. Frank Thomas FTR Internet Research 93110 Rosny-sous-Bois France __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] No fit statistics for some models using sem
It's not the correlation as such that is the problem; it's because you only have 10 degrees of freedom available with four observed variables, and you are estimating 10 parameters, which is why you get a chi square of zero. When you remove any one free parameter (such as the correlation), the model becomes identified. On 07/03/07, Ista Zahn [EMAIL PROTECTED] wrote: Hi, New to both R and SEM, so this may be a very simple question. I am trying to run a very simple path analysis using the sem package. There are 2 exogenous (FARSCH, LOCUS10) and 2 endogenous (T_ATTENT, RMTEST) observed variables in the model. The idea is that T_ATTENT mediates the effect of FARSCH and LOCUS10 on RMTEST. The RAM specification I used is FARSCH - T_ATTENT, y1x1, NA LOCUS10 - T_ATTENT, y1x2, NA FARSCH - RMTEST10, y2x1, NA LOCUS10 - RMTEST10, y2x2, NA T_ATTENT - RMTEST10, y2y1, NA FARSCH - FARSCH, x1x1, NA LOCUS10 - LOCUS10, x2x2, NA T_ATTENT - T_ATTENT, y1y1, NA RMTEST10 - RMTEST10, y2y2, NA LOCUS10 - FARSCH, x2x1, NA This model runs, but using the summary function does not return the usual model fit statistics, only the following: Model Chisquare = 0 Df = 0 Pr(Chisq) = NA Chisquare (null model) = 8526.8 Df = 6 Goodness-of-fit index = 1 BIC = 0 If I omit the last line from the RAM specification(i.e., delete LOCUS10 - FARSCH, x2x1, NA), I DO get all the usual statistics: Model Chisquare = 1303.7 Df = 1 Pr(Chisq) = 0 Chisquare (null model) = 8526.8 Df = 6 Goodness-of-fit index = 0.95864 Adjusted goodness-of-fit index = 0.58639 RMSEA index = 0.30029 90% CI: (NA, NA) Bentler-Bonnett NFI = 0.84711 Tucker-Lewis NNFI = 0.082726 Bentler CFI = 0.84712 BIC = 1294.1 My understanding is the you should always put in the correlation between exogenous predictors, but when I do this I don't get fit statistics. Can anyone help me understand what is happening here? Thank you, Ista __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dispersion_parameter_GLMM's
That amount of overdispersion would make the use of a poisson model very questionable, and will very likely result in estimated standard errors that are too low, hence the change in statistical significance when you switch to quasipoisson. On 06/03/07, Cristina Gomes [EMAIL PROTECTED] wrote: Hi all, I was wondering if somebody could give me advice regarding the dispersion parameter in GLMM's. I'm a beginner in R and basically in GLMM's. I've ran a GLMM with a poisson family and got really nice results that conform with theory, as well with results that I've obtained previously with other analysis and that others have obtained in similar studies. But the dispersion parameter is too large (25 compared to 1). So I ran a quasipoisson that allows for overdispersion and all of the significant results fell out. My question is, how much does overdispersion invalidate ones results when using a poisson family? What could the reason be for having non significant results with a quasipoisson distribution? If anybody could give me some help with this or/and recommend me literature that is somewhat comprehensible to lay people (i.e. non statisticians) that would be great. Thanks in advance, Cristina. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Identifying points in a plot that have duplicate values
Have a look at ?sunflowerplot, which not only produces a scatterplot showing multiple points with the same coordinates using special symbols, but will also produce a list showing the number of points at each coordinate as well. On 05/03/07, David Lloyd [EMAIL PROTECTED] wrote: I have code like this: - #--- -- x=scan() 0 0 0 0 0 1 2 3 4 y=scan() 1 1 1 2 2 1 3 4 5 plot(x,y) identify(0,1,3) #Allows me to select manually to identify co-ordinate (0,1) as being duplicated 3 times identify(0,2,2) #Allows me to select manually to identify co-ordinate (0,2) as being duplicated 2 times #--- -- Is there not a way I can automatically display if points are duplicated and by how many times? I thought if I 'jittered' the points ever so slightly I could get an idea of how many duplicates there are but with 100 points the graph looks very messy. Regards DaveL Click for free info on getting an MBA and make $200K/ year Need cash? Click to get a payday loan http://tagline.bidsystem.com/fc/CAaCDCZ60nyjrrOboFeUJgRjigwgNftK/ span id=m2wTlpfont face=Arial, Helvetica, sans-serif size=2 style=font-size:13.5px___BRGet the Free email that has everyone talking at a href=http://www.mail2world.com target=newhttp://www.mail2world.com/abr font color=#99Unlimited Email Storage #150; POP3 #150; Calendar #150; SMS #150; Translator #150; Much More!/font/font/span [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rbind with data frames -- column names question
I don't know if this is the right way, but I think this would work (I'm assuming you want the result to be a data frame): data.frame(rbind(as.matrix(A),B)) You might get a warning about row names, but I think it works OK. On 05/03/07, Gregg Lind [EMAIL PROTECTED] wrote: As part of my work, I am trying to append matrices onto data frames. Naively I assumed that when rbinding a data.frame and matrix, the matrix would be coerced and appended, keeping the names from the data frame. Clearly, I am not fully understanding the process by which rbind works. Example code: A-data.frame(1,1,1); names(A)=letters[1:3] ; B-matrix(0,2,3) rbind(A,B) Error in match.names(clabs, names(xi)) : names do not match previous names: V1, V2, V3 rbind(A,as.data.frame(B)) Error in match.names(clabs, names(xi)) : names do not match previous names: V1, V2, V3 Is there a right way to combine the two such that the both end up having the same column names? I have tried to understand the deparse.level argument of rbind, but it doesn't seem to do what I'm asking. Thank you for any help you can give. Gregg -- Gregg Lind, M.S. Division of Epidemiology and Community Health School of Public Health University of Minnesota, United States __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Chi Square with two tab-delimited text files
It's a bit difficult to advise without knowing what the rows and columns represent, but why not just calculate the statistic yourself, given that you already have observed and expected values? For example: chi2 - sum((y-x)^2/x) On 26/02/07, Carina Brehony [EMAIL PROTECTED] wrote: Yes, I would like to do a goodness-of-fit test. -Original Message- From: Petr Klasterecky [mailto:[EMAIL PROTECTED] Sent: 26 February 2007 11:50 To: Carina Brehony Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Chi Square with two tab-delimited text files Carina Brehony napsal(a): Hi, I want to do a chi square test and I have two tab delimited text files with Expected and Observed values to compare. Each file contains only the values snip There are a lot of chi^2 tests, most of them compare OE quantities and it is not clear which one you want to use. I'd guess a goodness of fit test, but who knows? See ?chisq.test and the examples given there. It also tells you that the y-argument is ignored if x is a matrix (that's probably the reason why you get different results using read.table and scan). Petr -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Chi Square with two tab-delimited text files
In that case, you can just ignore the expected values and use the observed values in the chisq.test. The reason you got a p value of 1 before is because the second argument was ignored, and so you did a chi square test on the expected values alone. If you have loaded the obseved values into a matrix y using read.table as in your first example, then just use chisq.test(y). But you should notice that you have a lot of zero cells and so probably lots of small expected values, which is a problem for the chi square test. On 26/02/07, Carina Brehony [EMAIL PROTECTED] wrote: Hi, The files look like below and the rows and columns are numbers of genetic types e.g. row1 is type 4; column1 is type A. So for, row1:column1 cell there are 78 type 4/type A combinations. I hope this makes sense! 78 500 18 6 0 4 0 1 6 1 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 2 1 0 0 0 1 0 0 0 0 23 0 0 0 7 0 0 7 0 0 0 6 0 8 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 45 0 0 0 0 0 0 0 0 0 0 0 0 3 0 40 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 8 4 0 0 0 0 0 0 etc... -Original Message- From: David Barron [mailto:[EMAIL PROTECTED] Sent: 26 February 2007 12:12 To: Carina Brehony; r-help Subject: Re: [R] Chi Square with two tab-delimited text files It's a bit difficult to advise without knowing what the rows and columns represent, but why not just calculate the statistic yourself, given that you already have observed and expected values? For example: chi2 - sum((y-x)^2/x) On 26/02/07, Carina Brehony [EMAIL PROTECTED] wrote: Yes, I would like to do a goodness-of-fit test. -Original Message- From: Petr Klasterecky [mailto:[EMAIL PROTECTED] Sent: 26 February 2007 11:50 To: Carina Brehony Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Chi Square with two tab-delimited text files Carina Brehony napsal(a): Hi, I want to do a chi square test and I have two tab delimited text files with Expected and Observed values to compare. Each file contains only the values snip There are a lot of chi^2 tests, most of them compare OE quantities and it is not clear which one you want to use. I'd guess a goodness of fit test, but who knows? See ?chisq.test and the examples given there. It also tells you that the y-argument is ignored if x is a matrix (that's probably the reason why you get different results using read.table and scan). Petr -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sorting rows of a binary matrix
I'm sure there are more elegant ways, but this should work: ix-order(mat[,1],mat[,2],mat[,3]) ix [1] 1 5 3 7 2 6 4 8 mat[ix,] Var1 Var2 Var3 1000 5001 3010 7011 2100 6101 4110 8111 On 22/02/07, Serguei Kaniovski [EMAIL PROTECTED] wrote: Hallo, The command: x - 3 mat - as.matrix(expand.grid(rep(list(0:1), x))) generates a matrix with 2^x columns containing the binary representations of the decimals from 0 to (2^x-1), here from 0 to 7. But the rows are not sorted in this order. How can sort the rows the ascending order of the decimals they represent, preferably without a function which converts binaries to decimals (which I have)? Alternatively, generate a matrix that has the rows sorted that way? Thanks, Serguei [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] residuals and glm
You really need to look at ?glm and ?residuals.glm. resfit$residuals are the *working* residuals, which are not typically very useful in themselves. Far better to use the extractor function. This enables you to obtain a number of different types of residuals, but the default (and therefore the type you have obtained) are deviance residuals. You can also specify other types, such as pearson residuals. Hope this helps. David On 22/02/07, Martin Olivier [EMAIL PROTECTED] wrote: Hi all, I have some problems to compute the residuals from a glm model with binomial distribution. Suppose I have the following result : resfit-glm(y~x1+x2,weights=we,family=binomial(link=logit)) Now I would like to obtain the residuals . the command residuals(resfit) and the vector resfit$residuals give different results, and they do not correspond to residuals E(yi)-yi (that is resfit$fitted-resfit$y) so, I would like to know what formula is applied to compute these residuals. And moreover, if I want to compute the standardized residuals, what is the right command from the glmfit result. Is it (resfit$fitted-resfit$y)/sqrt(1/resfit$prior*resfit$fitt*(1-resfit$fitt)) ?? Thanks for your help, Olivier. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data frame: how to create list of row max?
Try do.call(pmax,c(dataframe[,intensityindices],na.rm=TRUE))
This is like the second example in the help page for do.call
On 19/02/07, Johannes Graumann [EMAIL PROTECTED] wrote:
On Monday 19 February 2007 11:53, Prof Brian Ripley wrote:
do.call(pmax, dataframe[,intensityindeces])
Thank you very much for your help!
Any idea why do.call(pmax,list(na.rm=TRUE),dataframe[,intensityindeces])
would give me
Error in if (quote) { : argument is not interpretable as logical
In addition: Warning message:
the condition has length 1 and only the first element will be used in: if
(quote) {
?
Thanks, Joh
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=
David Barron
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University of Oxford
Park End Street
Oxford OX1 1HP
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Advice on visual graph packages
You might also want to look at the network package, which includes a plot method for network objects that is pretty flexible. It also enables you to convert a network object into various different matrix reprentations. On 13/02/07, Jarrett Byrnes [EMAIL PROTECTED] wrote: Hey, all. I'm looking for packages that are good at two things 1) Drawing directed graphs (i.e nodes and edges), both with single and double headed arrows, as well as allowing for differences in line width and solid versus dashed. Note: I've tried Rgraphviz here, but have run into some problems (which seem fixable and I may go with it in the end), and it doesn't satisfy need # 2 (which would be ideal if there is a package that does both). 2) Allowing a user to create a directed graph, and have some text object created that can be reprocessed easily reprocessed into a matrix representation, or other representation of my choosing. I've tried dynamicGraph, but it seems buggy, and continually either crashes, behaves very erratically (nodes disappearing when I modify edges), nor is it clear from the UI how one outputs a new graph, nor how one even accesses many graph attributes. This may be my own ignorance on the latter. Do you have any suggestions? Thanks! -Jarrett -- A Quick and (Very) Dirty Guide to Stats in R http://didemnid.ucdavis.edu/rtutorial.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] extract submatrix with unique names
This should do it, assuming you data is in a data frame called dat: sel - unique(dat$V1) ix - match(sel,dat$V1) dat[ix,] On 09/02/07, Glazko, Galina [EMAIL PROTECTED] wrote: Dear list, I have a table where first 3 columns are identical if the name in the first column is the same, and the number in N4 is slightly different for all identical names, like this: --- 29Mm.1_at 3 + 93649936 30Mm.1_at 3 + 93649990 31Mm.1_at 3 + 93649993 32Mm.1_at 3 + 93650001 33Mm.1_at 3 + 93650010 34 Mm.10_at 4 + 147438101 35 Mm.10_at 4 + 147438192 36 Mm.10_at 4 + 147438214 37 Mm.100043_at 5 + 31602952 38 Mm.100043_at 5 + 31602982 39 Mm.100043_at 5 + 31603000 --- I need to select unique identifiers in column N 1, without paying attention to what is in column N4, taking the first number in N4 corresponding to first unique ID in N1, like this: 29Mm.1_at 3 + 93649936 34 Mm.10_at 4 + 147438101 37 Mm.100043_at 5 + 31602952 Could someone tell me how to do it without FOR cycle over all IDs in N1? Thank you! Best regards Galina [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Zeta and Zipf distribution
Does the zipf function in the VGAM package do what you want? On 08/02/07, Mauro Rossi [EMAIL PROTECTED] wrote: Dear R user, I want to estimate the parameter of ZETA or/and ZIPF distributions using R, given a series of integer values. Do you know a package (similar to MASS) or a function (similar to fitdistr) I can use to estimate the parameter of these distributions using MLE method? Otherwise do you know a function (which use MLE method to estimate distribution parameters) that allow me to specify a PDF or PMF? Thanks, Regards Mauro Rossi -- Mauro Rossi Istituto di Ricerca per la Protezione Idrogeologica Consiglio Nazionale delle Ricerche Via della Madonna Alta, 126 06128 Perugia Italia Tel. +39 075 5014421 Fax +39 075 5014420 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Zeta and Zipf distribution
I don't claim to be a huge expert on this, but I think you are mistaken about what you are getting when you use the zipf family with the vglm function. From what I can tell from the documentation, this does indeed give you an estimate of the parameter of the zipf distribution. I've tried to test this using some random numbers (probably not strictly correct procedure, but I think it's a reasonable approximation): set.seed(1234) N - 5 y - (1:N) alpha - 2.5 # this is the parameter of the zipf distribution p - 1/(y^alpha) ; p - p/sum(p) n - 10 x - sample (y, n, replace=TRUE, prob=p) w - as.vector(table(x)) fit = vglm (y ~ 1, zipf(link=identity, init=2), tra=TRUE, weight=w) Coef(fit) s 2.501086 Is this not what you need? On 08/02/07, Mauro Rossi [EMAIL PROTECTED] wrote: Dear David, thank you for your reply. I tried to use the package VGAM, the function zipf and also the function zetaff, but these functions don't allow me to estimate parameters directly, I have to use a Gerneralized Linear Model or a Generalized Additive Model (vgam or vglm functions) and I don't want to use those. Don't you know a way to apply these tools to my data? At the end my PMF has to be Y=f(X) where f(X) is a zeta or a zipf distribution, while using VGAM the PMF is Y = b0 + b1*f(X1)+ ... +bn*f(Xn). Do you know how I can write the script using the VGAM function for the PMF I need? Thank you in advance, Mauro Rossi David Barron ha scritto: Does the zipf function in the VGAM package do what you want? On 08/02/07, *Mauro Rossi* [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Dear R user, I want to estimate the parameter of ZETA or/and ZIPF distributions using R, given a series of integer values. Do you know a package (similar to MASS) or a function (similar to fitdistr) I can use to estimate the parameter of these distributions using MLE method? Otherwise do you know a function (which use MLE method to estimate distribution parameters) that allow me to specify a PDF or PMF? Thanks, Regards Mauro Rossi -- Mauro Rossi Istituto di Ricerca per la Protezione Idrogeologica Consiglio Nazionale delle Ricerche Via della Madonna Alta, 126 06128 Perugia Italia Tel. +39 075 5014421 Fax +39 075 5014420 __ R-help@stat.math.ethz.ch mailto:R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP -- Mauro Rossi Istituto di Ricerca per la Protezione Idrogeologica Consiglio Nazionale delle Ricerche Via della Madonna Alta, 126 06128 Perugia Italia Tel. +39 075 5014421 Fax +39 075 5014420 -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] remove component from list or data frame
The first example you provide is a vector, not a list. You can remove the third element with: lst[-3] [1] 5 6 8 9 The same thing works for rows of data frames: frame[-3,] lst1 lst2 116 227 449 55 10 On 08/02/07, Jason Horn [EMAIL PROTECTED] wrote: Sorry to ask such a simple question, but I can't find the answer after extensive searching the docs and the web. How do you remove a component from a list? For example say you have: lst-c(5,6,7,8,9) How do you remove, for example, the third component in the list? lst[[3]]]-NULL generates an error: Error: more elements supplied than there are to replace Also, how do you remove a row from a data frame? For example, say you have: lst1-c(1,2,3,4,5) lst2-c(6,7,8,9,10) frame-data.frame(lst1,lst2) How do you remove, for example, the second row of frame? Thanks, - Jason __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Beginner Question on Persp()
read.delim creates a data frame (which is a type of list), whereas persp requires that the z argument be a matrix. These are different classes of object in R -- you might want to read the Introduction to R that ships with the programme. Try persp(x,y,as.matrix(z)) On 05/02/07, Tom H. [EMAIL PROTECTED] wrote: I recently downloaded R for Windows, running on Win XP. I'm trying to create a perspective plot but not having any luck after reading the R manual and several examples found on the Internet. I have a 100 x 100 matrix of Z data as a tab-delimited text file exported from Minitab. I read this in to R using read.delim; this seemed to go ok. I created X and Y using seq() to get 100 divisions for the X and Y axes. Again, everything looked good, when I typed X or Y I got a string of 100 numbers. However, when I try to do persp(x,y,z) I get an error something like: (list) cannot be coerced to double. I know the basic data (matrix of z values) is ok (no hidden non-numeric values) because Minitab will graph it just fine. Any suggestions on how to proceed? Thanks in advanced for your help. -- View this message in context: http://www.nabble.com/Beginner-Question-on-Persp%28%29-tf3174399.html#a8806483 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] indexing without looping
One way would be to use merge, like this: merge(assignation,data.frame(class=x),all.y=TRUE) There might well be better ways... On 01/02/07, javier garcia-pintado [EMAIL PROTECTED] wrote: Hello, I've got a data.frame like this: assignation - data.frame(value=c(6.5,7.5,8.5,12.0),class=c(1,3,5,2)) assignation value class 1 6.5 1 2 7.5 3 3 8.5 5 4 12.0 2 and a long vector of classes like this: x - c(1,1,2,7,6,5,4,3,2,2,2...) And would like to obtain a vector of length = length(x), with the corresponding values extracted from assignation table. Like this: x.value [1] 6.5 6.5 12.0 NA NA 8.5 NA 7.5 12.0 12.0 12.0 Could you help me with an elegant way to do this ? (I just can do it with looping for each class in the assignation table, what a think is not perfect in R's sense) Wishes, Javier -- Javier García-Pintado Institute of Earth Sciences Jaume Almera (CSIC) Lluis Sole Sabaris s/n, 08028 Barcelona Phone: +34 934095410 Fax: +34 934110012 e-mail:[EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] solving a structural equation model using sem or other package
This is an extract from the sem help page, which deals with your situation: S covariance matrix among observed variables; may be input as a symmetric matrix, or as a lower- or upper-triangular matrix. S may also be a raw (i.e., ``uncorrected'') moment matrix — that is, a sum-of-squares-and-products matrix divided by N. This form of input is useful for fitting models with intercepts, in which case the moment matrix should include the mean square and cross-products for a unit variable all of whose entries are 1; of course, the raw mean square for the unit variable is 1. Raw-moment matrices may be computed by raw.moments. On 24/01/07, Daniel Nordlund [EMAIL PROTECTED] wrote: I am trying to work my way through the book Singer, JD and Willett, JB, Applied Longitudinal Data Analysis. Oxford University Press, 2003 using R. I have the SAS code and S-Plus code from the UCLA site (doesn't include chapter 8 or later problems). In chapter 8, there is a structural equation/path model which can be specified for the sem package as follows S - cov(al2) #al2 contains the variables alc1, alc2, alc3, and cons N - 1122 modelA.ram - specify.model() f1- alc1, NA, 1 f1- alc2, NA, 1 f1- alc3, NA, 1 f2- alc1, NA, 0 f2- alc2, NA, .75 f2- alc3, NA, 1.75 cons - f1,p0, 1 cons - f2,p1, 1 alc1 - alc1, u1, 1 alc2 - alc2, u2, 1 alc3 - alc3, u3, 1 cons - cons, u4, 1 f1 - f1,s1, 1 f2 - f2,s2, 1 f1 - f2,s3, 1 modelA - sem(modelA.ram, S, N, analytic.gradient=FALSE) An equivalent specification in SAS produces the solution presented in the book. The variable cons is a constant vector of 1's. The problem with the sem package is that the covariance matrix which includes the variable cons is singular and sem says so and will not continue. Is there an alternative way to specify this problem for sem to obtain a solution? If not, is there another package that would produce a solution? Thanks, Dan Nordlund Bothell, WA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Scatterplot help
The following three lines will do what you want. You will probably want to change some of the default behaviour; just look at the relevant help pages. plot(x,y) text(x,y,ID) grid(2) On 21/01/07, gnv shqp [EMAIL PROTECTED] wrote: Hi my friends, I'm trying to make a scatterplot like this. 1) I have a 3-variable dataset. They are ID, x, and y. 2) x is for the X-axis, y for the Y-axis, and ID is used to label all the cases in the scatterplot. 3) After creating the scatterplot, I need to add both a X-axis reference line and a Y-axis reference line. The X-axis reference line is a vertical line starting from the center of the X-axis. The Y-axis reference line is a horizontal line starting from the center of the Y-axis. In other words, by creating the two reference lines, the scatterplot is divided into 4 quadrants. Please help me figure out how to do that in R. Many thanks in advance! Feng [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combination of variables
You don't say what model you want to do. It isn't necessary to store each combination of predictors in a separate matrix unless you really need to do this for some other reason, in which case I imagine you could adopt this idea. I dare say there are better ways, but this should work (assuming you want a linear model): x-matrix(runif(30*6),ncol=6) y - rnorm(30) cmbs - list() for (i in 1:6) cmbs - c(cmbs,combn(6,i,simplify=FALSE)) for (i in 1:length(cmbs)) print(summary(lm(y ~ x[,cmbs[[i]]]))) On 22 Jan 2007 08:51:22 -, anil kumar rohilla [EMAIL PROTECTED] wrote: Hi, List , i have 6 predictor variables and i want to make possible combinations of these 6 predictors ,all the data is in matrix form , if i am having 6 predictors than possible combination of sets are 64 2 power 6, or 63 ,whatever it may be i want to store the result in another variable to each combination and that i want to put in some model , i want to put every combination in some model ,please help me how to find suitable combinations of these variables i was not able to do this . Any package is there in R which can help me in this regards any help . thanks in Advance ANIL KUMAR( METEOROLOGIST) LRF SECTION NATIONAL CLIMATE CENTER ADGM(RESEARCH) INDIA METEOROLOGICAL DEPARTMENT SHIVIJI NAGAR PUNE-411005 INDIA MOBILE +919422023277 [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Insert R logo
I expect you could do something with the addlogo function in the pixmap package. On 20/01/07, Arun Kumar Saha [EMAIL PROTECTED] wrote: Dear all R users, I want to insert the R logo in every graphic that I made in my Statistical analysis using R. Can anyone tell me whether is it possible or not and if possible how to do this? your help will be highly appreciated. Thanks and Regards, Arun [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Insert R logo
Something like this: library(pixmap) # From the addlogo example x - read.pnm(system.file(pictures/logo.ppm, package=pixmap)[1]) fg - matrix(c(0,1,0,1,0,.05,0,.05), ncol=4, byrow=TRUE) split.screen(fg) screen(1) plot(rnorm(100)) screen(2) addlogo(x,c(0,1),c(0,1)) On 20/01/07, Arun Kumar Saha [EMAIL PROTECTED] wrote: Dear all R users, I want to insert the R logo in every graphic that I made in my Statistical analysis using R. Can anyone tell me whether is it possible or not and if possible how to do this? your help will be highly appreciated. Thanks and Regards, Arun [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selecting rows for inclusion in lm
Why not use the subset option? Something like:
lm(diff ~ Age + Race, data=data, subset=data$Meno==PRE)
should do the trick, and be much easier to read!
On 18/01/07, John Sorkin [EMAIL PROTECTED] wrote:
I am having trouble selecting rows of a dataframe that will be included
in a regression. I am trying to select those rows for which the variable
Meno equals PRE. I have used the code below:
difffitPre-lm(data[,diff]~data[,Age]+data[,Race],data=data[data[,Meno]==PRE,])
summary(difffitPre)
The output from the summary indicates that more than 76 rows are
included in the regression:
Residual standard error: 2.828 on 76 degrees of freedom
where in fact only 22 rows should be included as can be seen from the
following:
print(data[length(data[,Meno]==PRE,Meno]))
[1] 22
I would appreciate any help in modifying the data= parameter of the lm
so that I include only those subjects for which Meno=PRE.
R 2.3.1
Windows XP
Thanks,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC,
University of Maryland School of Medicine Claude D. Pepper OAIC,
University of Maryland Clinical Nutrition Research Unit, and
Baltimore VA Center Stroke of Excellence
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
[EMAIL PROTECTED]
Confidentiality Statement:
This email message, including any attachments, is for the so...{{dropped}}
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Re: [R] logistic regression packages
1. multinom is is the nnet package 2. There is a polyclass function in package polspline On 10/01/07, Feng Qiu [EMAIL PROTECTED] wrote: Hi All: I'm testing a set of data classification algorithms in this paper (www.stat.wisc.edu/~loh/treeprogs/quest1.7/mach1317.pdf ) I couldn't find such algorithms in R packages: 1. LOG: polytomous logistic regression (there was one in MASS library: multinom. But after I update MASS library, multinom was lost.) 2. POL: POLYCLASS algorithm. There is a S-Plus package(polyclass library) for this algorithm, so there should be a corresponding package in R, but I haven't found it so far. Any advice is appreciated. Best, Feng __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] loop is going to take 26 hours - needs to be quicker!
What about
gpcc.array - array(gpcc.data2[,5], dim=c(144,72,46))
On 14/12/06, Rainer M Krug [EMAIL PROTECTED] wrote:
Jenny Barnes wrote:
Dear R-help,
I have a loop, which is set to take about 26 hours to run at the rate it's
going
- this is ridiculous and I really need your help to find a more efficient
way of
loading up my array gpcc.array:
#My data is stored in a table format with all the data in one long column
#running though every longitute, for every latitude, for every year. The
#original data is sotred as gpcc.data2 where dim(gpcc.data2) = [476928,5]
where
#the 5th column is the data:
#make the array in the format I need [longitude,latitude,years]
gpcc.array - array(NA, c(144,72,46))
n=0
for(k in 1:46){
for(j in 1:72){
for(i in 1:144){
n - n+1
gpcc.array[i,j,k] - gpcc.data2[n,5]
print(j)
}
}
}
I don't know if it is faster - but adding three columns to qpcc.data,
one for longitude, one for lattitude and one for year (using rep() as
they are in sequence) and the using reshape() might be faster?
So it runs through all the longs for every lat for every year - which is the
order the data is running down the column in gpcc.data2 so n increses by 1
each
time and each data point is pulled off
It needs to be a lot quicker, I'd appreciate any ideas!
Many thanks for taking time to read this,
Jenny Barnes
~~
Jennifer Barnes
PhD student - long range drought prediction
Climate Extremes
Department of Space and Climate Physics
University College London
Holmbury St Mary, Dorking
Surrey
RH5 6NT
01483 204149
07916 139187
Web: http://climate.mssl.ucl.ac.uk
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--
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology and Entomology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)86 516 2782
Fax:+27 - (0)21 808 3304 (w)
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email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
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Re: [R] Switch and integer
From the help entry for switch: If the value of EXPR is an integer between 1 and nargs()-1 then the corresponding element of ... is evaluated and the result returned. So, for integers you don't give names to the elements in ... This should work: test=c(3,9,3,9,3,9,8,9,8,9,8,9,3,9,3,9,5,9,3,9,1,2,7,9,3,9,1,1,2,2,3,9,2,1,2,5,9,8,9,1,2) count1 - 0 for (i in 1:length(test)) switch(EXPR=test[i], NULL, NULL, NULL, count1 - count1 +1, count1 - count1 +1, count1 - count1 +1, count1 - count1 +1, count1 - count1 +1, NULL ) count1 On 11/12/06, Knut Krueger [EMAIL PROTECTED] wrote: I searched the help list and the manual, but I do not find my mistake. Switch is working with character , with integer, but not in the third example Regards Knut count1 - 0 test =c(3,9,3,9,3,9,8,9,8,9,8,9,3,9,3,9,5,9,3,9,1,2,7,9,3,9,1,1,2,2,3,9,2,1,2,5,9,8,9,1,2) count1 - 0 for (i in 1:length(test)) switch (EXPR=test[i], 5 = print(test[i]), 6 = print(test[i]), 7 = print(test[i]), 8 = print(test[i]), 9 = print(test[i]) ) count1 # example from helpfile for(i in c(-1:3,9)) print(switch(i, 1,2,3,4)) # not working test =c(3,9,3,9,3,9,8,9,8,9,8,9,3,9,3,9,5,9,3,9,1,2,7,9,3,9,1,1,2,2,3,9,2,1,2,5,9,8,9,1,2) count1 - 0 for (i in 1:length(test)) switch (EXPR=test[i], 4 = count1 - count1 +1, 5 = count1 - count1 +1, 6 = count1 - count1 +1, 7 = count1 - count1 +1, 8 = count1 - count1 +1 ) count1 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A smal fitting problem...
b = mean(y) On 08/12/06, Kåre Edvardsen [EMAIL PROTECTED] wrote: Dear R-helpers, I'm for sure not familiar with R, but it seem like a nice sofware tool, so I've decided to try using it. Here is my problem I just can't figure out: I'd like to do least square fit of a straight horizontal (a = 0) line y = ax + b through some data points x = (3,4,5,6,7,8) y = (0.62, 0.99, 0.83, 0.69, 0.76, 0.82) How would i find b? All the best, Ked [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] incidence and adjacency matrix conversion
I think you can do this using the network package. Look at the as.network.matrix and as.matrix.network functions, for example. On 05/12/06, Philip Leifeld [EMAIL PROTECTED] wrote: Dear all, how can I convert an m x n incidence matrix into an m x m adjacency matrix or an n x n adjacency matrix? The current matrix contains binary data, hence the new matrix would contain counts of common occurrences. Thank you for your help. Phil __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dummies multiplied with other variable
I'm not sure if this will help, but it's worth a try. Do the regression as I suggested before, extract the model matrix and remove the offending column. I'm assuming you don't know in advance how many levels there are in the factor. Then use this to perform the regression. Something like this: m1 - lm(x ~ fd:y + fd) mm - model.matrix(m1) nl - length(levels(fd)) newdat - mm[,-c(1,nl)] lm(x ~ newdat) On 30/11/06, Andreas Goesele [EMAIL PROTECTED] wrote: David Barron [EMAIL PROTECTED] writes: I'm not sure that's possible, given that you would effectively be fitting a different model to those cases with fd==1, wouldn't you? This was what I was afraid of. But your argument I don't understand completely. Do you want to say, that the *model* x = a + b1*fd2 + b2*fd3 + c1*fd2*y + c1*fd3*y doesn't make sense as fd2 together with fd3 doesn't cover all cases? And that because the model doesn't make sense it is not easily implemented in R? My problem is that I have to estimate a model of this kind whether it makes sense or not. So I still would be happy to find an easy and elegant way... On 29/11/06, Andreas Goesele [EMAIL PROTECTED] wrote: David Barron [EMAIL PROTECTED] writes: Is this what you want? lm(y ~ fd + fd:y) Thanks for you fast reply. But it's not what I wanted. To make it clearer I have to correct the first part of what I wrote: On 29/11/06, Andreas Goesele [EMAIL PROTECTED] wrote: I would like to estimate something like y = a + b*d2*y + c*d3*y where the dummies are created from some vector d with three (actually many more) levels using factor(). But either there is included the variable y or d1*y. How could I get rid of these? This should have been something like: x = a + b1*d2 + b2*d3 + c1*d2*y + c1*d3*y When I change your suggestion to lm(x ~ fd + fd:y) I get the same as for lm(x ~ fd*y - y), namely: Coefficients: (Intercept) fd2 fd3 fd1:y fd2:y fd3:y 2.4231 9.5769 6.1822 -0.1154 -1. -0.4474 What I want is: Coefficients: (Intercept) fd2 fd3 fd2:y fd3:y Thanks a lot again! Andreas Goesele -- Andreas Gösele Omnis enim res, quae dando non deficit, Inst. f. Gesellschaftspolitikdum habetur et non datur, Kaulbachstr. 31a, 80539 München nondum habetur, quomodo habenda est. E-mail: [EMAIL PROTECTED] (Augustinus) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP -- Andreas Gösele Omnis enim res, quae dando non deficit, Inst. f. Gesellschaftspolitikdum habetur et non datur, Kaulbachstr. 31a, 80539 München nondum habetur, quomodo habenda est. E-mail: [EMAIL PROTECTED] (Augustinus) -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] need help with barplot
You need the transpose of the matrix (or create it differently in the first place!). Changing the last line to barplot(t(b),beside=T,col=(c(red,orange,yellow))) should do the trick. On 29/11/06, Robertas Kavaliūnas [EMAIL PROTECTED] wrote: Hello, I do this a=c(10.2,0.4,0.2,5.2,8.6,1.6,0.0,1.0,6.3,1.4,0.4,0.2) b=matrix(a,nrow=4) rownames(b)=c(20/04/2002,21/04/2002,22/04/2002,23/04/2002) colnames(b)=c(p1,p2,p3) barplot(b,beside=T,col=(c(red,orange,yellow))) then I have http://www.mif.vu.lt/~roka5178/barplot1.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot1.JPG but I need to have http://www.mif.vu.lt/~roka5178/barplot.JPGhttp://www.mif.vu.lt/%7Eroka5178/barplot.JPG how can i do this? i need to to change axis x whit y -- Robertas [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dummies multiplied with other variable
Is this what you want? lm(y ~ fd + fd:y) On 29/11/06, Andreas Goesele [EMAIL PROTECTED] wrote: Hi, I would like to estimate something like y = a + b*d2*y + c*d3*y where the dummies are created from some vector d with three (actually many more) levels using factor(). But either there is included the variable y or d1*y. How could I get rid of these? Example: x = c(1,2,3,4,5,6,7,8) y = c(3,6,2,8,7,6,2,4) d = c(1,1,1,2,3,2,3,3) fd = factor(d) lm(x ~ fd*y) gives: Coefficients: (Intercept) fd2 fd3 y fd2:y fd3:y 2.4231 9.5769 6.1822 -0.1154 -0.8846 -0.3320 lm(x ~ fd*y - y) gives: Coefficients: (Intercept) fd2 fd3 fd1:y fd2:y fd3:y 2.4231 9.5769 6.1822 -0.1154 -1. -0.4474 What I would like to get is: Coefficients: (Intercept) fd2 fd3 fd2:y fd3:y Is there an easy way to achieve this? Maybe it's obvious how to do it, but I'm new to R did quite some searching without finding the solution. Thanks a lot in advance! Andreas Goesele -- Andreas Gösele __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Predicted values in lmer modeling
The fitted values for m5 must be logits. On 28/11/06, Aimin Yan [EMAIL PROTECTED] wrote: m3 is a logistic regression model without random effect fitted by glm m5 is a logistic regression model with random effect fitted by lmer why the range for the fitted value for m5 is not between 0 and 1. thanks, Aimin range(fitted(m3)) [1] 0.1630141 0.9903415 range(fitted(m5)) [1] -1.515915 4.576576 At 07:53 AM 11/28/2006, Douglas Bates wrote: fitted(model) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot p(Y=1) vs as
I'd recommend having a look at the lrm function in the Design package. Looking at the examples should show you how you can product this type of plot using some of the other components of this package. On 26/11/06, Aimin Yan [EMAIL PROTECTED] wrote: I am trying to fit a logistic regression model for this data set. Firstly, I want to plot P(Y=1) vs As and P(Y=1) vs Aa. Does any body know how to do these in R. Thanks, Aimin p5 - read.csv(http://www.public.iastate.edu/~aiminy/data/p_5_2.csv;) str(p5) 'data.frame': 1030 obs. of 6 variables: $ P : Factor w/ 5 levels 821p,8ABP,..: 1 1 1 1 1 1 1 1 1 1 ... $ Aa : Factor w/ 19 levels ALA,ARG,ASN,..: 12 16 7 18 11 10 19 19 19 1 ... $ As : num 126.9 64.1 82.7 7.6 42.0 ... $ Ms : num 92.4 50.7 75.3 17.2 57.7 ... $ Cur: num -0.1320 -0.0977 -0.0182 0.2368 0.1306 ... $ Y : int 0 0 1 1 0 0 1 0 1 1 ... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Questions about generating samples in R
?sample should tell you what you need to know. On 26/11/06, Alexander Geisler [EMAIL PROTECTED] wrote: Hello! I have a data set with 8 columns and in about 5000 rows. What I want to do is to generate samples of this data set. Samples of a special size, as example 200. What is the easiest way to do this? No special things are needed, only the random selection of 200 rows of the data set. Thanks Alex -- Alexander Geisler * Kaltenbach 151 * A-6272 Kaltenbach email: [EMAIL PROTECTED] | [EMAIL PROTECTED] phone: +43 650 / 811 61 90 | skpye: al1405ex __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot with two seperate y axis
Assuming the data are in a data frame called dt, this should work: plot(dt$Wk,dt$Para1,type=h) par(new=TRUE) plot(dt$Wk,dt$Para2,yaxt=n) axis(4,at=97:100) On 24/11/06, Thorsten Muehge [EMAIL PROTECTED] wrote: Hello, I would like to plot the following matrix: Wk=x achsis. Para 1 = left y-axis as a barplot para 2 right y-axis as a normal scatter plat. I could not find such a solution in any of my documentation. Can someone help me? Thanks a lot Thorsten WkPara 1 Para 2 312000 99.8 322005 99.0 332002 98.0 341090 98.5 352001 99.1 362010 97.0 372010 98.8 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using roman and italic fonts in an xlab expression for a plot
Something like: xlab=expression(paste(The excess level is,italic( M))) in your plot command should do the trick. See ?plotmath. On 23/11/06, Philip Boland [EMAIL PROTECTED] wrote: Just wondering if it is possible to put something like The excess level is M in the xlab position of a plot but where the M is in italic font and the rest in ordinary (or Roman) font. Thanks - Phil Boland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (no subject)
I'm not sure what the last line is trying to achieve, but this might be what you want: i - ifelse(m==0, l/ky, l/ky + 1) j - ifelse(m==0,ky, l %% ky) On 18/11/06, Céline Henzelin [EMAIL PROTECTED] wrote: Hello, I need help to understand my error in this code... I would like to make a direct sampler... thanks Celine p-matrix(c(1,2,3,2,1,4),3,2,byrow=T) p-p/sum(p) ky-ncol(p) kx-nrow(p) p.vec-as.vector(t(p)) l-rmultinom(1,1,p) l-(t(l)) m-(l%%ky) ifelse (m==0, i-l/ky (j-ky), i-((l/ky)+1) (j-(l %% ky) _ Faites de MSN Search votre page d'accueil: Toutes les réponses en un clic! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating a table
addmargins(table(df)) On 14/11/06, Michael Graber [EMAIL PROTECTED] wrote: Dear R List, I am a new to R, so my question may be easy to answer for you: I have a dataframe, for example: df-data.frame(loc=c(A,B,A,A,A), year=as.numeric(c(1970,1970,1970,1976,1980))) and I want to create the following table without using loops: 1970-74 ; 1975-79 ; 1980-85; rowsum A 2 1 1 4 B 1 00 1 colsum 31 15 so that the frequencies of df$loc are shown in the table for different time intervals. Thanks in advance for any hint, Michael Graber __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
d - read.table(lahore.txt, header=TRUE) On 11/11/06, amna khan [EMAIL PROTECTED] wrote: Respected Sir I request you to please fill the following read.table function and read.csvfor my understanding by assuming my data attached with this maiL, because I am fail to run these functions using manual guidlines. read.table(file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = !stringsAsFactors, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors()) read.csv(file, header = TRUE, sep = ,, quote=\, dec=., fill = TRUE, comment.char=, ...) read.delim(file, header = TRUE, sep = \t, quote=\, dec=., fill = TRUE, comment.char=, ...) I shall be really thankful to you. REGARDS -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] neg-bin clustered analysis in R?
I'm not certain, but I think you should be able to use the robcov function in the Design package in conjunction with glm.nb, perhaps with a bit of tweaking. Another alternative might be to use the quasi family in lmer. On 06/11/06, Lutz Ph. Breitling [EMAIL PROTECTED] wrote: Dear All, I'm analysing a negative binomial dataset from a population-based study. Many covariates were determined on household level, so all members of a household have the same value for those covariates. In STATA, there seems to be an option for 'clustered analysis' for neg-bin regression. Does an equivalent exist for R(MASS)'s glm.nb or a comparable function? Many thanks for all help! Lutz -- Lutz Ph. Breitling, Marie Curie EST Research Fellow Integrative Comparative Biology (Irene Manton 8.93e) University of Leeds, LS2 9JT Leeds/UK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grep searching for sequence of 3 consecutive upper case letters
Try
str[grep('[[:upper:]]{3}',str)]
On 06/11/06, Lapointe, Pierre [EMAIL PROTECTED] wrote:
Hello,
I need to identify all elements which have a sequence of 3 consecutive upper
case letters, anywhere in the string.
I tested my grep expression on this site: http://regexlib.com/RETester.aspx
But when I try it in R, it does not filter anything.
str -c(AGH, this WOUld be good, Not Good at All)
str[grep('[A-Z]{3}',str)] #looking for a sequence of 3 consecutive upper
case letters
[1] AGHthis WOUld be good Not Good at All
Any idea?
Pierre
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University of Oxford
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Re: [R] information about sna packages
I don't think so, but you should email the package's author, Carter Butts for help on this package. His email is [EMAIL PROTECTED] On 31/10/06, Bagatti Davide [EMAIL PROTECTED] wrote: Hello, I'm a student who want to use the R social network analysis package. I have a question: can this package analyse dynamical networks (network changing over time)? I didn't find this functionality in the package's user manual. Thank you Davide [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Put a normal curve on plot
Something like this?
library(MASS)
mu - c(0,1)
Sigma - matrix(c(1,.8,.8,1), ncol=2)
set.seed(123)
x - mvrnorm(50,mu,Sigma)
dta - data.frame(x=x[,1],y=x[,2])
plot(x)
fit - lm(y~x, data=dta)
sfit - summary(fit)
se - sfit$sigma
abline(fit)
yhat - predict(fit,data.frame(x=c(-1,0,1)),se.fit=TRUE)
x1 - seq(-2,0,length=50)
x2 - x1 + 1
x3 - x2 + 1
lines(x1,yhat$fit[1]+dnorm(x1,-1,se))
lines(x2,yhat$fit[2]+dnorm(x2,0,se))
lines(x3,yhat$fit[3]+dnorm(x3,1,se))
On 31/10/06, Doran, Harold [EMAIL PROTECTED] wrote:
I would like to be able to place a normal distribution surrounding the
predicted values at various places on a plot. Below is some toy code
that creates a scatterplot and plots a regression line through the data.
library(MASS)
mu - c(0,1)
Sigma - matrix(c(1,.8,.8,1), ncol=2)
set.seed(123)
x - mvrnorm(50,mu,Sigma)
plot(x)
abline(lm(x[,2] ~ x[,1]))
Say I want to add a normal distribution surrounding the predicted values
at the x-values of -1, 0, and 1. That is, at the points
\hat{y} = \mu + \beta_1(-1)
\hat{y} = \mu + \beta_1(0)
\hat{y} = \mu + \beta_1(1)
How might I go about doing this?
Harold
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
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University of Oxford
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Re: [R] for importing data
Most likely the file lahore.txt isn't in the current working directory, which is where R will be looking for it as you don't specify a path (I'm assuming that you are working in Windows). If so, you have three options. 1) Move lahore.txt to the current working directory (you can find with directory that is using the function getwd()). 2) Specify the full path in read.delim (e.g., read.delim(c:/my documents/data/lahore.txt). 3) Change the working directory to the one in which lahore.txt is located using the function setwd(). Hope this helps. David On 30/10/06, amna khan [EMAIL PROTECTED] wrote: *I am a very new user of R. I've spent several hours trying to import data, so I feel okay asking the list for help. * *I had an Excel file, then I turned it into a tab-delimited file, as instructed by directions My filename is lahore.txt I amusing the following commands for read.delim but i am getting following mesages. Sir i am sending you my excel data file i request you to please write the right read.delim function for importing data file after transforming it into a tab-delimited form.* lahore-read.delim(lahore.txt) Error in file(file, r) : unable to open connection In addition: Warning message: cannot open file 'lahore.txt', reason 'No such file or directory' Regards AMINA SHAHZADI*.* Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] correlation structure in lme without random effect
You haven't specified a random equation. Try: fit-lme(fixed=y~g,random=~1|g,correlation=corAR1(0,~1|g)) On 30/10/06, Benjamin Tyner [EMAIL PROTECTED] wrote: I was hoping to fit along the lines of g-gl(20,5) y-runif(100) fit-lme(fixed=y~g,correlation=corAR1(0,~1|g)) But I get the error Incompatible formulas for groups in random and correlation Any help would be greatly appreciated. Ben __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot history
Are you working in Windows? If so, you can turn on recording either
in the History menu on the active graphics device window, or by using
windows(record=TRUE) to open a new device.
On 30/10/06, Rohini Mulford [EMAIL PROTECTED] wrote:
___
Hi,
When I create multiple graphs subsequent graphs overwrite previous
graphs. How do I keep all my graphs in the current workspace (but not
all on the same page) so I can scroll through them?
thanks,
Rohini
Rohini Mulford
Senior Research Analyst
Technical Research
Research Development
Insurance Australia Group(IAG)
ph (02) 9292 1560
fax (02) 9292 1509
email: [EMAIL PROTECTED]
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[R] legends in ggplot
Is it possible to change the legend title in ggplot that is generated by a colour (other than by changing the name of the variable)? For example, this produces a legend title, tip/total_bill. How can that title be changed? ggpoint(ggplot(tips,aesthetics=list(y=tip,x=total_bill,colour=tip/total_bill)) ) Thanks. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] distance between legend title and legend box
I don't know if there is a nice, easy way of doing this, but this method will work: with(iris, plot(Sepal.Length, Sepal.Width, pch=as.numeric(Species), cex=1.2)) lg-legend(6.5, 4.2, c(setosa, versicolor, virginica), cex=1, pch=1:3, title=expression(kg/km^2), bty=n) x1 - lg$rect$left y1 - lg$rect$top - lg$rect$h x2 - x1 + lg$rect$w y2 - lg$rect$top + .1 # change the .1 to get more or less space rect(x1,y1,x2,y2) On 26/10/06, Denis Chabot [EMAIL PROTECTED] wrote: Hi, I've looked at the parameters available for the legend function and cannot find a way to change the distance between the top of the box surrounding a legend and the legend's title. I have a math expression that raises the height of my title. If you don't mind the non-sensical title I give to the legend for this plot (Figure 3.20 in R Graphics): with(iris, plot(Sepal.Length, Sepal.Width, pch=as.numeric(Species), cex=1.2)) legend(6.5, 4.2, c(setosa, versicolor, virginica), cex=1, pch=1:3, title=expression(kg/km^2)) The result depends on the device, but I think any device will show the box needs to be raised a bit (in quartz, the top of the box passes in the middle of the 2, in pdf it is acceptable, but just (the top of the box lightly touches the top of the 2). Sincerely, Denis Chabot __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] To big characters in barplot
Use the option cex.names. For example: tN - table(Ni - rpois(100, lambda=5)) barplot(tN, col=rainbow(20)) barplot(tN, col=rainbow(20), cex.names=.6) On 24/10/06, David Graf [EMAIL PROTECTED] wrote: Hi everybody! The characters under the bars in my barplot are to big, so I can't see them all. How can I make them smaller? Thanks! David GRaf -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] colinearity?
There are functions to calculate variance inflation factors in various packages, e.g. car and Design. I believe these work with generalized linear models. On 24/10/06, Chris Linton [EMAIL PROTECTED] wrote: I'm sorry to all those who are tired of seeing my email appear in need of help. But, I've never coded in any program before, so this has been a difficult process for me. Is there a simple function to test for colinearity in R? I'm running a logistic regression and a linear regression. Thanks for the help! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] colinearity?
Also, have a look at the perturb package which has a couple of functions for collinearity diagnosis. On 24/10/06, Chris Linton [EMAIL PROTECTED] wrote: I'm sorry to all those who are tired of seeing my email appear in need of help. But, I've never coded in any program before, so this has been a difficult process for me. Is there a simple function to test for colinearity in R? I'm running a logistic regression and a linear regression. Thanks for the help! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with understanding [[]] [] array, list, matrix referencing
Have you tried help([), which gives a good explanation.
On 24/10/06, Joe W. Byers [EMAIL PROTECTED] wrote:
Hi all,
I would greatly appreciate some help understanding how R references
arrays, matrices, lists, and objects using [[]] and []. I have read the
R guides and several tutorials but I am not the fastest kid on the block
so I am still having difficulty understanding this. For examples the
following code produces a 5 element list of 2X5 random numbers that I
then convert to a 2X5X5 matrix.
cov-matrix(c(.4,-.1,-.1,.3),nrow=2,ncol=2)
rnds-NULL;
for (i in 1:5){
t1-rnorm(5,cov)
t2-rnorm(5,cov)
t3-rbind(t1,t2)
rnds[i]-list(t3)
}
rnds.matrix-array(unlist(rnds),dim=c(2,5,5));
To access the matrix rnds.matrix I use rnds.matrix[x,y,z]. This I
understand.
To access the list I user [[z]][x,y]. This I do not understand. I
found by chance this reference notation in an old mailing list that
helped me.
I could use some help in knowing when to use [[]] referencing and when
to use [] referencing. If there is a really good book, webpage, or link
with explanation and examples I would appreciate you forwarding the the
citation.
Thank you
Joe
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Re: [R] Help with understanding [[]] [] array, list, matrix referencing
Well, as I understand it, with a list [] doesn't return the actual
contents of that element of the list, whereas [[]] does. Compare, for
example rnds[1] + 1 with rnds[[1]] + 1. So, with a list you have to
use the double bracket notation to get to the actual contents of that
element of the list, as opposed to a pointer to the element. With a
vector or a matrix, [[]] doesn't seem to have much use, though you can
use it with a single number, in which case you will get the same
result as [].
There is a separate method for data frames, in which [[]] will give
you a column. So, I think that data[[1]] is the same as data[,1].
Anyway, these rules have always worked for me, though I'm sure others
can give a more sophisticated answer!
On 24/10/06, Joe Byers [EMAIL PROTECTED] wrote:
David,
Yes, I did. I just still do not get it. That is why I ask here.
Hoping someone knew a step by step guide that I could look at. My trial
and error approach takes me hours some days. I currently move most
things in and out of data.frames where I can name the columns and
reference with the $ and a subsetting function, but that is not always
efficient. If I could understand the [ referencing better, my code
would be more efficient and I think faster. Part of my problem is my
SAS background where everything is a flat table and coding is really
sloppy. A data step with a bunch of if-then-else to perform the
calculation where as in matrix format like in R you do things more
compactly. Not always easy to read but efficient and fast.
I appreciate you help.
Thank you
Joe
David Barron wrote:
Have you tried help([), which gives a good explanation.
On 24/10/06, Joe W. Byers [EMAIL PROTECTED] wrote:
Hi all,
I would greatly appreciate some help understanding how R references
arrays, matrices, lists, and objects using [[]] and []. I have read the
R guides and several tutorials but I am not the fastest kid on the block
so I am still having difficulty understanding this. For examples the
following code produces a 5 element list of 2X5 random numbers that I
then convert to a 2X5X5 matrix.
cov-matrix(c(.4,-.1,-.1,.3),nrow=2,ncol=2)
rnds-NULL;
for (i in 1:5){
t1-rnorm(5,cov)
t2-rnorm(5,cov)
t3-rbind(t1,t2)
rnds[i]-list(t3)
}
rnds.matrix-array(unlist(rnds),dim=c(2,5,5));
To access the matrix rnds.matrix I use rnds.matrix[x,y,z]. This I
understand.
To access the list I user [[z]][x,y]. This I do not understand. I
found by chance this reference notation in an old mailing list that
helped me.
I could use some help in knowing when to use [[]] referencing and when
to use [] referencing. If there is a really good book, webpage, or link
with explanation and examples I would appreciate you forwarding the the
citation.
Thank you
Joe
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Re: [R] Plotting Text on a graph
Have you thought of using split.screen instead?
Something like might work for you:
split.screen(c(1,1))
split.screen(c(3,4), 1)
for (i in 1:12) {
screen(i+1)
par(mar=c(2,2,4,2))
plot(1:20,rnorm(20),xlab=,ylab=)
}
screen(1)
title(Overall title)
On 23/10/06, Dan Chan [EMAIL PROTECTED] wrote:
Hi,
I plotted 12 graphs on a page and output to a png file. I wanted to
have an overall title for all 12 graphs. What command can I use to do
this? Below is the code that plotted the 12 graphs in one page.
# FM10 by Month/ Export the plot to Wash2005FM10.png
png(file=Wash2005FM10.png,bg=white)
par(mfrow = c(3,4))
# Plot 12 Month of OFM10, FFM10
for(i in 1:12) {
Temp - subset (Wash2005, MM == i)
plot (Temp$FM10.1,
Temp$FM10,main=month.name[i],xlim=c(5,25),ylim=c(5,25))
}
text(10,10, Overall Title) 'This will plot Overall Title at
coordinate (10,10) on the last graph, and so it is not what I want.
dev.off()
Thank you.
Daniel Chan
Meteorologist
Georgia Forestry Commission
P O Box 819
Macon, GA
31202
Tel: 478-751-3508
Fax: 478-751-3465
[[alternative HTML version deleted]]
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Re: [R] extract arguments from a list
First, that isn't what is called a list in R, it is a character vector. Second, to get what you want, try sort(unique(x)) [1] Atrazine Atrazine desethyl Bentazone [4] Epoxiconazol Fenpropimorph Metolachlor [7] Simazine On 19/10/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi, I would like to know how to extract the arguments from a list : For example, I have a list of charchacter x x- c(Bentazone,Atrazine,Epoxiconazol,Metolachlor,Epoxiconazol,Atrazine desethyl,Fenpropimorph,Epoxiconazol,Metolachlor,Simazine,Atrazine desethyl,Epoxiconazol,Atrazine desethyl,Atrazine,Epoxiconazol,Metolachlor,Epoxiconazol,Atrazine desethyl,Fenpropimorph,Epoxiconazol,Metolachlor,Simazine) and I am searching for a (basic) function which would return arguments of the list x, aphabeticaly reordered like this : (Atrazine,Atrazine desethyl,Bentazone,Epoxiconazol,Fenpropimorph,Metolachlor,Simazine). Can anyone help me ? Thanks by advance Jessica [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Labels for Points- 2 character labels?
Is this what you want?
plot(e,n)
text(e,n,labels=e_order,pos=4)
On 18/10/06, ableape [EMAIL PROTECTED] wrote:
I would like to be able to label each point in a scatter plot with
the numeric order of that point. for example, I create the following plot:
plot(e,n)
#
# now I go back and create my labels
#
for(i in 1:length(e)) {# lets say e 10
pc - as.character(e_order[i]) # e_order has an
integer array 1,4,3,2... which is the order of e
points(e15[i], n15[i],pch=pc)# this will plot
0-9 as data labels
}
#
The above works for single characters. Now if the length of e[] is
greater than 9, the character string converted by as.character will
yield more than one digit. At this point, my labeling trick fails:-(
1) is there a way to create two character labels for a plot?
2) Or even better, is there a way to do what I am trying to
do. Label each point by its numeric order?
Thanks for your help.
Renaldo
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Re: [R] How to get multiple Correlation Coefficients
Oh, and of course you need to use an explicit print inside a for loop.
So, the line would be:
print( polychor(sdi[,i], sdi[,j]))
On 19/10/06, David Barron [EMAIL PROTECTED] wrote:
The problem is that in the expression polychor(vars[i], vars[j]),
vars[i] and vars[j] refer to the names of the variables, not the
variables themselves. So, use sdi[,i] and sdi[,j] instead.
On 19/10/06, Kum-Hoe Hwang [EMAIL PROTECTED] wrote:
Hi
I have used a polycor package for categorical correlation coefficients.
I run the following script. But there were no results.
Could you tell me how to correct the script?
Thanks in advance,
vars - names(sdi)
for (i in 1:length(vars)) {
for (j in 1:length(vars)) {
paste(vars[i], and , vars[j])
polychor(vars[i], vars[j])
# corr
}
}
--
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--
=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
--
=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to get multiple Correlation Coefficients
The problem is that in the expression polychor(vars[i], vars[j]),
vars[i] and vars[j] refer to the names of the variables, not the
variables themselves. So, use sdi[,i] and sdi[,j] instead.
On 19/10/06, Kum-Hoe Hwang [EMAIL PROTECTED] wrote:
Hi
I have used a polycor package for categorical correlation coefficients.
I run the following script. But there were no results.
Could you tell me how to correct the script?
Thanks in advance,
vars - names(sdi)
for (i in 1:length(vars)) {
for (j in 1:length(vars)) {
paste(vars[i], and , vars[j])
polychor(vars[i], vars[j])
# corr
}
}
--
Kum-Hoe Hwang, Ph.D.Phone : 82-31-250-3516Email : [EMAIL PROTECTED]
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Oxford OX1 1HP
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Re: [R] Multiple histograms in one plot
I suspect that mar doesn't work with split.screen. You could try using mfrow instead: par(mar=c(1,1,1,1),mfrow=c(5,4)) for (i in 1:20) hist(rnorm(100),main=,cex.axis=.8) With margins this small, though, you won't be able to see the axis annotation for the left axes of the left column or the bottom axis of the bottom row. On 18/10/06, Johann Hibschman [EMAIL PROTECTED] wrote: Hi all, I'm trying to plot multiple histograms in one plot (cross-validation values of model parameters), but I cannot seem to reduce the margins enough to fit as many of them in as I would like. I'm using split.screen to divide the window into a 5x4 grid, then plotting with hist. I've tried explicitly reducing the margins with par(mar=c(1,1,1,1)), but it doesn't seem to have any effect. Visually, there is a lot of whitespace and very little histogram in my results. Can anyone suggest either a better method to visualize these results, a better way to plot histograms, or a way to actually reduce the margins used? The intent is to give a sense of how well-constrained the various model parameters are. Thanks, Johann __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Variance of fitted value in lm
You can get these via the predict function. On 17/10/06, Li Zhang [EMAIL PROTECTED] wrote: Hi, I am wondering if a linear model lm(y~ x1+x2) calculates the variance of a fitted value. Thank you Li __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fill a matrix with vectors of different lengths
for (i in 1:length(v)) {
bi - binc(v[1:i])
mat[1:length(bi),i]=mat[1:length(bi),i]+bi
}
On 16/10/06, Serguei Kaniovski [EMAIL PROTECTED] wrote:
Hello,
how can I best fill a (fixed) matrix with vectors of varying lengths by
column, setting the superfluous elements to zero? Here is my code:
v-(1,1,2,3,4,6)
binc-function(x){
l-sum(x)+1
y-c(1,rep(0,l-1))
for (i in x) y-y+c(rep(0,i),y)[1:l]
}
mat-matrix(0, nrow=sum(v)+1, ncol=length(v))
for (i in 1:length(v)) mat[,i]=mat[,i]+binc(v[1:i])
the expression in the for-loop produces an error since mat[,i] and
binc(v[1:i]) are of unequal lengths, except on the last iteration.
Thanks in advance,
Serguei
--
___
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Name: Serguei Kaniovski P.O.Box 91
Tel.: +43-1-7982601-231 Arsenal Objekt 20
Fax: +43-1-7989386 1103 Vienna, Austria
Mail: [EMAIL PROTECTED]
http://www.wifo.ac.at/Serguei.Kaniovski
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Re: [R] set linetype with plotCI
You could look at the plotCI function in the plotrix package, which has a separate parameter for setting the linetype of the error bars. (An additional benefit is that it works with R 2.4.0 -- gplots seems not to have been updated, or at least the windows binary hasn't, and still includes a now defunct feature.) On 16/10/06, JeeBee [EMAIL PROTECTED] wrote: Sorry, the plot_linetypes[1] is a debugging leftover. It's plot_linetypes[graph_idx] in my actual code ... And plot_linetypes is just the sequence 1,2,3,4... etc plotCI( x = xvals.f[sorted], y = yvals.f[sorted], xlim = c(xmin, xmax), ylim = c(ymin, ymax), pch = plot_symbols[graph_idx], type = b, lty = plot_linetypes[1], col = plot_colors[graph_idx], barcol = plot_colors[graph_idx], uiw = NA, xlab = , ylab = , add = (plot_cnt 0) ) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] set linetype with plotCI
Looking at the source code for plotCI, I see that it calls plot with type specified as n when the error bars are not being added to an existing plot, so you cannot use the type argument in a call to plotCI. If you want to add lines as well as points, I think you will have to use lines(x,y,type=b,lty = plot_linetypes[graph_idx]) in addition to plotCI, or amend the plotCI function to your own specifications. On 16/10/06, JeeBee [EMAIL PROTECTED] wrote: Thanks, I tried using plotCI in the plotrix library. This, however, gives me the below error. CODE:: cat(x = ); print(xvals.f[sorted]) cat(y = ); print(yvals.f[sorted]) cat(pch = ); print(plot_symbols[graph_idx]) cat(lty = ); print(plot_linetypes[graph_idx]) cat(col = ); print(plot_colors[graph_idx]) print(paste(graph_idx =, graph_idx, and plot_cnt =, plot_cnt)) plotCI( x = xvals.f[sorted], y = yvals.f[sorted], xlim = c(xmin, xmax), ylim = c(ymin, ymax), pch = plot_symbols[graph_idx], type = b, lty = plot_linetypes[graph_idx], col = plot_colors[graph_idx], barcol = plot_colors[graph_idx], uiw = NA, xlab = , ylab = , add = (plot_cnt 0) ) print(plotCI succeeeded...) OUTPUT:: x = [1] 160 160 160 160 160 160 160 160 160 160 320 320 320 320 320 320 320 320 320 [20] 480 480 480 480 480 480 480 480 480 640 640 640 640 640 640 640 640 800 800 [39] 800 800 800 800 800 800 800 960 960 960 960 960 960 960 960 960 y = [1] 0.062263829 0.062263829 0.062263829 0.062263829 0.062263829 0.062263829 [7] 0.062263829 0.062263829 0.062263829 0.062263829 0.029483948 0.029483948 [13] 0.029483948 0.029483948 0.029483948 0.029483948 0.029483948 0.029483948 [19] 0.029483948 0.018035707 0.018035707 0.018035707 0.018035707 0.018035707 [25] 0.018035707 0.018035707 0.018035707 0.018035707 0.009895540 0.009895540 [31] 0.009895540 0.009895540 0.009895540 0.009895540 0.009895540 0.009895540 [37] 0.008534913 0.008534913 0.008534913 0.008534913 0.008534913 0.008534913 [43] 0.008534913 0.008534913 0.008534913 0.007301515 0.007301515 0.007301515 [49] 0.007301515 0.007301515 0.007301515 0.007301515 0.007301515 0.007301515 pch = [1] 0 lty = [1] 1 col = [1] #FF [1] graph_idx = 1 and plot_cnt = 0 Error in plot.default(c(160, 160, 160, 160, 160, 160, 160, 160, 160, 160, : formal argument type matched by multiple actual arguments __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with plot()
It's possible the problem is with your data; could you provide some sample data with which we can reproduce the error? On 16/10/06, tom soyer [EMAIL PROTECTED] wrote: Hi, I am new to R and I have been trying it out. I ran into a problem with the plot() function. Below is my code: d - read.table(c:/test/sp.txt,header=0) spval - d[,2] plot(spval,type=l) Warning messages: 1: graphical parameter type is obsolete in: plot.window(xlim, ylim, log, asp, ...) 2: graphical parameter type is obsolete in: axis(side, at, labels, tick, line, pos, outer, font, lty, lwd, 3: graphical parameter type is obsolete in: title(main, sub, xlab, ylab, line, outer, ...) 4: graphical parameter type is obsolete in: axis(side, at, labels, tick, line, pos, outer, font, lty, lwd, I tried to plot a line graph from a text file with two columns. Some how R won't plot the data as lines, and it kept giving me the same warning: type is obsolete. What does this mean? Am I doing something wrong, or is the parameter really obsolete, or do I need install some package? Thanks, Tom [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] BarPlot
Specify margins using par(mar=c(5,1,4,2)) before the call to barplot.
You won't be able to see the vertical axis labels with those settings,
though.
On 16/10/06, Mohsen Jafarikia [EMAIL PROTECTED] wrote:
Hello everyone:
I am using the following code to draw my barplot but it has two problems.
BL-c(1.97,8.04,2.54,10.53,4.85,1.73)
LR-c(0.85,0.86,8.33,04.18,6.26,2.40)
Q-c(0.00,0.00,1.92,01.92,4.48,0.00)
cols - ifelse(Q!=0, orange, green)
Graph- barplot(LR, main='LR Value',col=cols, border='black', space=0.05,
width=(BL), xlab='Length', ylab='LR block',mar=c(5,1,4,2))
axis(1, at=Graph, sprintf('%0.2f',BL))
mtext(1, at=Graph, text=ifelse(Q!=0, sprintf('%0.2f',Q), ), line=2)
mtext(1, at=par('usr')[1], text='BL', line=1)
mtext(1, at=par('usr')[1], text='Var', line=2)
abline(h=3.84,col='blue')
abline(h=6.64,col='red')
text(31,3.84,expression(paste(alpha==5,%)),pos=3)
text(31,6.64,expression(paste(alpha==1,%)),pos=3)
1) I don't know how to specify the margins. I have written it in the
code but it is not working.
2) I want the value of alph=5% at the right end of the line but it is
almost in the left side and sometimes in the right side when I use the same
code for drawing another barplot.
I appreciate any comments about these problems.
Thanks,
Mohsen
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Re: [R] BarPlot
Try adding
text(31,3.8,expression(paste(alpha==5,%)),pos=3)
On 15/10/06, Mohsen Jafarikia [EMAIL PROTECTED] wrote:
Hello again,
Thanks for answering my questions.
If my program is now:
pdf('Test.pdf')
BL-c(1.97,8.04,2.54,10.53,4.85,1.73)
LR-c(0.85,0.86,8.33,04.18,6.26,2.40)
Q-c(0.00,0.00,1.92,01.92,4.48,0.00)
cols - ifelse(Q!=0, orange, green)
Graph- barplot(LR, main='LR Value',col=cols, border='black', space=0.05,
width=(BL), xlab='Length', ylab='LR block')
axis(1, at=Graph, sprintf('%0.2f',BL))
mtext(1, at=Graph, text=ifelse(Q!=0, sprintf('%0.2f',Q), ), line=2)
mtext(1, at=par('usr')[1], text='BL', line=1)
mtext(1, at=par('usr')[1], text='Var', line=2)
abline(h=3.8, col='blue')I want to add alpha=5% at the end
of this line
And now I want to write alpha=5% at the end of the line that I have on my
graph.
Thanks,
Mohsen
On 10/15/06, Marc Schwartz [EMAIL PROTECTED] wrote:
On Sat, 2006-10-14 at 23:52 -0400, Mohsen Jafarikia wrote:
Hello everyone,
I have the following program to draw a barplot.
MP-read.table(file='AR.out')
names(MP)-c('BN','BL','LR','Q')
Graph- barplot(MP$LR, main='LR Value', col='orange', border='black',
space=
0.05, width=(MP$BL), xlab='Length', ylab='LR each')
axis(1, at=Graph, sprintf('%0.2f',MP$BL))
mtext(1, at=Graph, text=sprintf('%0.2f',MP$Q), line=2)
mtext(1, at=par('usr')[1], text='BL', line=1)
mtext(1, at=par('usr')[1], text='Var', line=2)
abline(h= 3.841,col='blue')
abline(h=6.635,col='red')
I have two more questions about the graph that I have:
1) I want to write the 'Q' only when it is not equal to zero.
2) I would like to change the bars when 'Q' is not zero. For example,
from
orange to green.
I would appreciate your input to this question.
Thanks,
Mohsen
It would be helpful to have the data that you are working with so that
we can provide each other a working example.
However, here are some hints:
1.
mtext(1, at = Graph,
text = ifelse(MP$Q != 0, sprintf('%0.2f',MP$Q), ),
line=2)
2.
cols - ifelse(MP$Q != 0, orange, green)
barplot(..., col = cols, ...)
See ?ifelse
HTH,
Marc Schwartz
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Re: [R] Need help with barplots
First, produce two barplots for comparison: par(mfrow=c(2,1) ) barplot(VADeaths,beside=TRUE) barplot(VADeaths) The same information is in both plots; in the top, it is displayed as 5 separate bars for each group, and in the stacked plot it is shown as 5 separate regions in each of the four bars. The hight of each of these regions is the same as the hight of the corresponding bar in the side-by-side plot. The stacked plot enables you to see overall differences more easily (easier to see that the death rate is highest for Urban Males), but it is harder to compare the sizes of the categories. On 13/10/06, laba diena [EMAIL PROTECTED] wrote: I`ve read all the manuals and still couln`t find what is the difference between the stacked and side-by-side barplots ? Could you explain me ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need help with tables
I'm not quite sure what you mean, but if you are wanting to select columns of a data frame, have a look at help([) David On 13/10/06, laba diena [EMAIL PROTECTED] wrote: I have a data file with 3 columns and I need to take only 2, how to do that ? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] for loop not working in function
I'd suggest looking at the boxcox function in the MASS package, which might
show you how to change your code.
It would be easier to diagnose the problem if you included a small example
showing the errors. Some possibilities are that if x is a vector, nrow(x)
will return NULL, that you are using lambda as the index variable in the
for loop, so the sequence generated in the second line is getting
overwritten, and the for loop isn't enclosed in braces, so only the first
line will be counted as being in the loop.
HTH,
David
On 11/10/06, Dale Steele [EMAIL PROTECTED] wrote:
I'm trying to write a small function (below) to compute Box Cox
transformations of x for arbitrary values of lambda. I'd like to
specify a range of values for lamba (min,max,step) and am having trouble
getting the for loop to work. Suggestions?
Any pointers to resources for learning to write functions in R for
neophyte programmers? Thanks. --Dale
boxcox - function(x,min,max,step) {
lambda - seq(min,max,step)
s - length(lambda)
for (lambda in 1:s)
n - nrow(x)
if(lambda ==0) xL - log(x) else
xL - ((x^lambda) - 1)/lambda
xLbar - mean(xL)
t1 - (-n/2)* log((1/n)*sum((xL - xLbar)^2))
t2 - (lambda - 1)*sum(log(x))
l= t1 + t2
l
}
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Re: [R] samples to dataframes
I'm not familiar with seewave package, but I imagine what you have to do is extract the sound component of the sample object and convert that to a data frame. waveLeft - 2*((seq(0,80,length=88200)%%1^2)-.5) s - as.Sample(waveLeft,44100,16) ds - data.frame(s$sound) is.data.frame(ds) [1] TRUE On 11/10/06, randy zelick [EMAIL PROTECTED] wrote: Hello all, I'll bet this is not complicated, but I really did hunt for information on it, and tried some ideas without success. Running Windows XP and R 2.3.1 I am using the Sound package to read in .wav files, and this works fine. The R object produced is of class sample. I want to use some of the functions in the package Seewave to do further analysis, but this package wants data objects to be dataframes. So I tried various ways to coerce samples to dataframes, but was not successful. Does anyone have a hint/solution? Thanks much, =Randy= -- Randy Zelickemail: [EMAIL PROTECTED] Department of Biology voice: 503-725-3086 Portland State University fax: 503-725-3888 mailing: P.O. Box 751 Portland, OR 97207 shipping: 1719 SW 10th Ave, Room 246 Portland, OR 97201 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rank Function
y-round(c(0.68,0.95,b,c,d),2) rank(y) [1] 3.5 5.0 1.0 2.0 3.5 On 10/10/06, Li Zhang [EMAIL PROTECTED] wrote: Does anyone know why the two rank functions gives different results? I need to use the rank function in a for loop, so the sequence to be ranked is given values in the form of part (1). How can I use assignment like in part (1) to get correct ranks as in part (2)? Thank You Part (1) i-1.94 b-0.95-i c-1.73-i d-2.62-i y-c(0.68,0.95,b,c,d) y 0.68 0.95 -0.99 -0.21 0.68 rank(y) 3 5 1 2 4 Part(2) rank(c(0.68,0.95,-0.99,-0.21,0.68)) 3.5 5.0 1.0 2.0 3.5 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] hist plot
This is taken from the help for the hist function: Typical plots with vertical bars are not histograms. Consider barplot or plot(*, type = h) for such bar plots. For example: x - rchisq(100, df = 4) op-hist(x, freq = FALSE, ylim = c(0, 0.2)) plot(op$mids,op$counts,type=h) On 06/10/06, Baoqiang Cao [EMAIL PROTECTED] wrote: Hi there, I really couldn't find out how to plot histogram with point/line instead of rectangle for each bin? Any help please? Thanks! Best, -Cao __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Partition into quantiles
You might also want to look at the function quantcut in the gtools package (part of the gregmisc bundle). On 05/10/06, Alberto Monteiro [EMAIL PROTECTED] wrote: Is there any function that divides a sample into N quantiles? For example, for N = 2, this would be the solution: x - rnorm(100) m - median(x) q - ifelse(x = median, 1, 2) Alberto Monteiro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] xyplot
If you include a conditioning factor (here it is the variable
groups) you will get more than one panel. To get loess curves for
the two groups, the easiest way is to use the type argument:
xyplot(y ~ time, groups=group,data=df,type=c(p,smooth))
On 05/10/06, Osman Al-Radi [EMAIL PROTECTED] wrote:
Hello,
Thanks for your answer, however, the resulting graph has two panels with a
loess curve per subject. I need a single panel with a loess curve per
group..
Osman
On 10/5/06, Sundar Dorai-Raj [EMAIL PROTECTED] wrote:
Osman Al-Radi said the following on 10/5/2006 3:43 PM:
Hi,
for the data below:
time-c(rep(1:10,5))
y-time+rnorm(50,5,2)
subject-c(rep('a',10),rep('b',10),rep('c',10),rep('d',10),rep('e',10))
group-c(rep('A',30),rep('B',20))
df-data.frame(subject,group,time,y)
I'd like to produce a plot with a single pannel with two loess curves
one
for each group. the code below does that but on two different pannels,
I'd
like to have both curves on the same pannel with different colors.
xyplot(y~time|group, groups=subject,
panel=function(...){
panel.loess(...)
}
,data=df)
Simple:
xyplot(y ~ time | group, data = df, groups = subject,
panel = function(...) {
panel.superpose(...)
panel.superpose(panel.groups = panel.loess, ...)
})
HTH,
--sundar
--
Osman O. Al-Radi, MD, MSc, FRCSC
Fellow, Cardiovascular Surgery
The Hospital for Sick Children
University of Toronto, Canada
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Re: [R] convert vector to matrix
cbind always produces a matrix or data frame. What the FAQ says is that a subsetting operation *on* a matrix will result in redundant dimensions being dropped, not that you can't get a matrix with a redundant dimension as a result of a function. So, vec-1:10 vec [1] 1 2 3 4 5 6 7 8 9 10 cbind(vec) vec [1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6 [7,] 7 [8,] 8 [9,] 9 [10,] 10 mat-cbind(vec) dim(mat) [1] 10 1 mat[,1] [1] 1 2 3 4 5 6 7 8 9 10 takes us back to a vector again. On 04/10/06, Alberto Monteiro [EMAIL PROTECTED] wrote: Gavin Simpson wrote: Did you even try to use cbind on your vector? I guess not as, vec - 1:10 mat - cbind(vec) mat Why does mat remain a matrix instead of losing one dimension? I am reading the FAQ at... http://cran.us.r-project.org/doc/FAQ/R-FAQ.html#Why-do-my-matrices-lose- dimensions_003f ... and it seems that anything you do to mat should turn it back into a one-dimensional vector. Alberto Monteiro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] bar chart with several lines
This should be enough to show how to do it: dta - read.table(clipboard,dec=,,row.names=NULL) r - barplot(dta$use,ylim=c(-80,60)) lines(r,dta$x1,type=b,col=red,pch=20) lines(r,dta$x2,type=b,col=blue,pch=21) On 01/10/06, Marko Ekqvist [EMAIL PROTECTED] wrote: Hi, I have been some problems with producing bar graph with r. Here is my example data (link) and picture but I am not able to do that with r. Please any kind of help is welcome http://www.pasilankaista.com/~ekqvistmt/r/Page001.html Kind Regards, Marko __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] finding correlation between two matrices
Have you looked at the function mantel.rtest in the ade4 package? On 02/10/06, sima fakheran [EMAIL PROTECTED] wrote: Dear all, I would like to compare two distance matrices to find the correlation between those and create a XY plot.could you please kindly help me and let me know how I can do that using R.(Mantel test?). Your help is very much appreciated!! Many thanks! Regards, Sima Fakheran ... Sima Fakheran Esfahani PhD Student Institute of Environmental Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland Tel: +41 1 635 61 18 Fax:+41 1 635 57 11 email:[EMAIL PROTECTED] http://www.uwinst.unizh.ch www.uwinst.unizh.ch [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] line plot through NA
I assume you mean that you want the first point to be connected by a straight line to the third, etc. because fisrt and sixth points are shown on the plot. If so, you can use the approx function: plot(approx(Day,V,n=length(Day)), type=l) points(Day,V) On 02 Oct 2006 15:31:59 +0100, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear R-help list, I hope I did not miss something obvious, because my question seems very simple, but I couln't figure out how to do it. If I have the following data: Day-c(1,2,3,4,5,6,7) V-c(5,NA,10,30,45,NA,10) than the line in plot plot(V~Day, type=b) will start with the 3rd value and stop stop at the 5th value because all NA are omitted. Is there now a parameter which can be added to the plot function so the line will start with with the first value and skip the NA values and can this than applied to xyplots. Many thanks __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Setting NA
Would using the subset argument that is available in many functions (eg lm) achieve what you want? On 30/09/06, Anupam Tyagi [EMAIL PROTECTED] wrote: Is there a way to set NA values in R, without changing the dataframe? I would like to use different combinations of non-response values, as if they were NA for some of the computations. I don't want to change the dataframe each time I have to do this? Anupam. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inner product
For inner product see ?%*%. There is a norm function in the Matrix package. On 30/09/06, Sonal Darbari [EMAIL PROTECTED] wrote: Hi, How do we find out the inner product norm of eigen vectors in R? Lets say we have eigen vectors : x1 = 1,2,3 and x2 = 2,-3,4 are there any functions buit in R which directly calculate the inner product norm of vectors? Thanks, Sonal. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Any hot-deck imputation packages?
I'm not sure if this is exactly what you're after, but it might be worth looking at aregImpute in the Hmisc package. On 27/09/06, Eleni Rapsomaniki [EMAIL PROTECTED] wrote: Hi I found on google that there is an implementation of hot-deck imputation in SAS: http://ideas.repec.org/c/boc/bocode/s366901.html Is there anything similar in R? Many Thanks Eleni Rapsomaniki __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Constrained OLS regression
Have a look at the linear.hypothesis function in the car package. For example: mod.duncan - lm(prestige ~ income + education, data=Duncan) linear.hypothesis(mod.duncan, income + education = 1) Linear hypothesis test Hypothesis: income + education = 1 Model 1: prestige ~ income + education Model 2: restricted model Res.DfRSS Df Sum of Sq F Pr(F) 1 42 7506.7 2 43 8045.2 -1-538.5 3.0129 0.08994 . --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 On 27/09/06, Mesomeris, Spyros [CIR] [EMAIL PROTECTED] wrote: Hello R helpers, I am trying to do a linear OLS regression of y on two variables x1 and x2. I want to constrain the coefficients of x1 and x2 to sum up to 1. and therefore run a constrained OLS. Can anybody help with this? (I have seen some answers to similar questions but it was not clear to me what I need to do) - I have tried the lm function with offset but I must not have used it properly. Thanks, Spyros __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Searching for keyword values in a text (configuration) file
Something like this? library(Hmisc) t - readLines(clipboard) t [1] DEVICE = 'PC' CPU_SPEED = '1999', '233' ix - grep(CPU_SPEED,t) loc - substring.location(t[ix],,) cpu - substring(t[ix],loc$first+2) cpu [1] '233' On 27/09/06, Andre Jung [EMAIL PROTECTED] wrote: Hi, I would like to read values from an ASCII text file that contains information in the following format: DEVICE = 'PC' CPU_SPEED = '1999', '233' ... It's like a config file. How can I e.g. get R to read the 2nd value of CPU_SPEED? How do I go through text files and search for keywords and their values? Thanks a lot, Andre __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting text to numbers
Then, I tried to convert them to numbers using the following. Sample1$FCT2 - as.numeric(Sample1$FCT2) Sample1$OBS2 - as.numeric(Sample1$OBS2) This is actually an FAQ. Do the following and it should be fine: Sample1$FCT2 - as.numeric(as.character(Sample1$FCT2)) Sample1$OBS2 - as.numeric(as.character(Sample1$OBS2)) -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] printing a variable name in a for loop
This would do it:
v1 - 5
v2 - 6
v3 - 7
vns - paste(v,1:3,sep=)
for (i in 1:length(vns)) cat(Hello, vns[i], get(vns[i]), World\n, sep=,)
Hello,v1,5,World
Hello,v2,6,World
Hello,v3,7,World
On 24/09/06, Suzi Fei [EMAIL PROTECTED] wrote:
Hello,
How do you print a variable name in a for loop?
I'm trying to construct a csv file that looks like this:
Hello, variable1, value_of_variable1, World,
Hello, variable2, value_of_variable2, World,
Hello, variable3, value_of_variable3, World,
Using this:
for (variable in list(variable1, variable2, variable3)){
cat(Hello,, ???variable???, variable, , World,)
}
This works fine if I'm trying to print the VALUE of variable, but I want to
print the NAME of variable as well.
Thanks,
Suzi
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--
=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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