gmane.comp.lang.r.general

Non-interactive passing of quoted variables (ggplot, plyr, subset, transform, etc)

Vitalie Spinu — 2008-12-01T17:06:15

Hello Everyone, May be a silly question. How to pass programmatically variables which are not known in advance and are quoted? Variables are quoted implicitly in functions like "subset" and "transform" and explicitly in ggplot and plyr. For instance I would like to have something like this: myfunc<-functon(mydata,X) subset(mydata,X>4) myfunc<-function(mydata,X,Y) {ggplot(mydata,aes(x=X,y=Y))+geom_points()} this does not work since X and Y are not in mydata. Many, many thanks, Vitalie. ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Parameters of exponential power density

Schacka24 — 2008-12-01T16:12:22

Hello! I must estimate the parameters of a exponential power density. There is the normalp package, but this works only for a shape parameter bigger than 1. But what should i do if the shape parameter is less than 1? (Sorry for my english) Thank you very much for help!

Error: "subscript out of bounds"

Alex99 — 2008-12-01T15:05:50

Hi All, I am trying to replace the "NA" values in a matrix by using the following function: it gets a "name" of the matrix or list or vector and turns it to a matrix called "m". then checks the elements of the matrix and if any of them is "NA" replace them with "0". rep=function(name){ m=as.matrix(name) for(i in 1:length(m)){ for(j in 1:length(m)){ if(is.na(m[i,j])){ m[i,j]=0 }}}} when I use the function with the following matrix: X1 X2 X3 X5 X1 1.00 NA NA -0.25 X2 NA 1 NA NA X3 NA NA 1 NA X5 -0.25 NA NA 1.00 I get this error: "subscript out of bounds". I used debug on "rep" function and it seems it works for i=1 and j=1&2&3&4&5 after that, when it's suppose to go to i=2 I get the error. any idea why and how to fix it? Thanks

Spatstat - K2 index

Gough Lauren — 2008-12-01T15:30:13

Hi all, I'm using spatstat to investigate the spatial structure of an arid shrub population. The first-order intensity of my data does not appear to be homogenous, so I would like to use inhomogeneous techniques. I realise there is a inhomogeneous K-function available in spatstat, but there doesn't not appear to be one for the pair-correlation function (O-ring statistic). As such I was planning to use a new technique (the K2 index) as described in Schiffers et al. (2008) [Ecography, 31:545-555]. The following website has more detail [http://www.oikos.ekol.lu.se/appendixdown/E5374-example.R]. Despite this I cannot get the function to run! I am not very familiar with R so it is likely my problem is simple. Does anyone have any experience with the K2-index who can give me some pointers? Many thanks Lauren This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. E

align two lattice plots with grid

baptiste auguie — 2008-12-01T16:13:50

Dear list, I need to align two plots on top of each other for comparison (they only have the x-axis in common). When the y-labels have a different extent, I cannot find a way to align the x-axes, as illustrated below, Any help would be greatly appreciated! baptiste _____________________________ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

gee + rcs

Heymans, M.W. — 2008-12-01T14:50:40

Hi all, I have fitted a gee model with the gee package and included restricted cubic spline functions. Here is the model: chol.g <- gee(SKIN ~ rcs(CHOLT, 3), id=ID, data=chol, family=binomial(link="logit"), corstr="exchangeable") To extract the log odds I use: predict.glm(chol.g, type = "link") Now I want to compute the logg odds for specific CHOLT values (the dependent variable) that I want to choose myself (i.e. that are not available in the dataset). Is there a way to get the linear predictor of the gee model including all separate spline functions and related coefficients? Latex from the Design package does not work here. Thanks for your help! kind regards, Martijn W Heymans Faculty of Earth and Life Sciences Institute of Health Sciences Department of Methodology and Applied Biostatistics VU University Amsterdam, the Netherlands [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinf

Question about the rgroup option in Hmisc latex function

Ista Zahn — 2008-12-01T12:24:09

Is there a way to use the rgroup option without creating horizontal rules separating the groups? For example, say I have the following matrix containing sample sizes, means, and standard deviations, for three groups of male and female participants: n Mean SD Male "2" "0.703" "-0.809" Female "3" "0.533" "-0.376" Male "2" "2.097" "-0.534" Female "3" "0.843" " 0.966" Male "2" "0.350" " 0.149" Female "3" "0.685" " 0.600" I try typesetting the table with which results in \ctable[ caption={Means and standard deviations by condition and sex}, label=tab:descript, pos=!tbp, ]{llll} {} {\FL\multicolumn{1}{l}{Condition}& \multicolumn{1}{c}{n}& \multicolumn{1}{c}{Mean}& \multicolumn{1}{c}{SD} \ML {\bfseries One}&&&\NN ~~Male&2&0.703&-0.809\NN ~~Female&3&0.533&-0.376 \ML {\bfseries Two}&&&\NN ~~Male&2&2.097&-0.534\NN ~~Female&3&0.843& 0.966 \ML {\bfseries Three}&&&\NN ~~Male&2&0.350& 0.149\NN ~~Female&3&0.685& 0.600 \LL } but I want \ctable[ caption={Means and standard deviations by condition an

Coercing a list of variables in a function call

Philip Whittall — 2008-12-01T12:09:41

This is hopefully a trivial problem for list subscribers, but I am very new to writing R functions. I wish to call an R function written by myself from another program to fit a model. I need to tell it which of the independent variables are factors. I need to do this in a generic way, so that when the list is passed, R will work through the variables in the data frame and coerce them into being factors. This is what I tried ... # Fictitious data for illustration y<-c(1,2.1,3.3,4.3,5,6.5) x1<-c(1,1,1,2,2,2) x2<-c(1,2,3,1,2,3) x3<-c(1,3,2,4,2,4) d<-as.data.frame(cbind(y,x1,x2,x3)) #Function definition model_it=function(data=" ", model=" ", factors=list()){ attach(d) #Attach the data formula<-as.formula(model) #Set up the model #Identify the factors if (length(factors)>0) for(i in 1:length(factors)){ factors[i]<-as.factor(factors[i]) } #Fit the model glm(formula, data=data) } #Function call attempted mod

2D density tophat

Aaron Robotham — 2008-12-01T11:46:05

Hello R users, I have successfully created a square (or more generally, rectangular) tophat smoothing routine based on altering the already available KDE2D. I would be keen to implement a circular tophat routine also, however this appears to be much more difficult to write efficiently (I have a routine, but it's very slow). I tried to create one based on using crossdist (in spatstat) to create a distance matrix between my data and the sampling grid, but it doesn't take a particularly large amount of data (or hi-res grid) for memory to be a big problem. The 2D density routines I have been able to find either don't support a simple tophat, or don't use the absolute distances between the sampling grid and the data. Should anyone know of more general 2D density routines that might support circular tophats, or know of a simple and efficient method for creating them, I would be very grateful. Thanks for your time, Aaron PS: I tried sending this on Friday originally, but as far as I know

request: how to assign alphabets to integer values

Muhammad Azam — 2008-12-01T09:35:01

Dear R community I am trying to assign alphabets to integer values 1, 2, 3 etc. in y given below. Can any body suggest some simple way to do the same job? ds=iris; dl=nrow(ds) c1=ds[,1]; c2=ds[,2]; c3=ds[,3]; c4=ds[,4]; c5=ds[,5]; iris=cbind(c1,c2,c3,c4,c5) y=iris[,5] y1=which(y==1); y[y1] <- c("a"); y2=which(y==2); y[y2] <- c("b"); y3=which(y==3); y[y3] <- c("c"); iris=cbind(c1,c2,c3,c4,y) Thnks and best regards M. Azam [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

how to ignore errors

Jiang Peng — 2008-12-01T08:17:26

Dear listers, Hi . I googled before I ask this question in case to avoid violating the "list law". The question was proposed by somebody else but nobody gives a proper solution. How to ignore errors in a R loop? I have a R source file ,namely, test.r. I ran a loop in a command line > for(i in 1 : 100 ) {source("test.r",echo =T ) } and I found that when test.r have some error the loop will stop, but test.r is just stochastically wrong,i.e., sometimes it works well if no bad values return. I want to know how to ignore such errors and let the loop continue. thanks in advance. _______________________ Jiang Peng, Ph.D. Candidate Department of Mathematics & Antai college of Economics and Management Shanghai Jiao Tong University Address: Room 431, #3 Building, Xuhui Campus E-mail: jp021 at sjtu.edu.cn jp021 at 126.com MSN: jp021 at hotmail.com iChat: mathfrog at mac.com Mobile: +86-138 168 780 95 ______________________________________________ R-help< at >r-project.org mail

factanal question

Don McNeil — 2008-12-01T04:38:44

Dear R users: I'm wondering if it's possible to get the residual correlation matrix when using factanal. Since factanal assumes that the errors are normally distributed and independent (provided the factor model fits the data) this would be useful. Of course you would need to submit the data to the function to get the residuals (not just their correlation matrix), but it should be possible to get the residual correlation matrix if only the data correlation matrix is provided. Don McNeil ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Attempting to get a STELLA model into R

Gibson, Tyler F — 2008-12-01T01:02:37

To whomever may be of help, I am a student in a graduate modeling class at the University of North Carolina at Wilmington. I am trying to get a STELLA model converted into R. I am in the process of trying to 're-write' the script into R, but I seem to be missing pieces (i.e. parm values) that are keeping me from being able to replicate this model into R. Does anyone have an idea of a possible solution to my problem? Are there conversion programs or packages available that can convert STELLA models into R format? Thank you very much for you time, and I hope to hear back from you soon. -Tyler Gibson tfg5854< at >uncw.edu ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

How to make a banner table.

Andrew Choens — 2008-12-01T03:41:11

I have a dataframe with the following variables: idnumareagenderraceetc. I would like to make a table that looks like areagenderrace M FB W A 14 53 5 1 26 7 4 6 3 etc. Basically, I want to make a single broad table with a number of sub-set tables. I have tried: cbind(table(area, gender), table(area, race)) But, when I do this, I lose the labels gender / race. This makes it a lot harder to understand my factor labels. when I use cbind, I get this: M F B W A 1 4 5 3 5 1 2 6 7 4 6 3 Although, it is technically correct, I really want to keep my factor labels. I also tried this with xtabs and get the same results. Any ideas? I saw a relatively recent thread asking a similar question, but the proposed solution did not work for me, so I thought I would ask the questions again. If I am missing someting terribly obvious, I apologize. thanks.

explaining a model with rcs() terms

Dylan Beaudette — 2008-12-01T03:23:54

Hi, I am using the rcs() function in the Design library to model non-linearity that is not well characterized by an otherwise mechanistic function. I am able to make the model 'available' to others through the excellent nomogram() function and the set of tables that it can create. However, I would like to present the model in an 'expanded' format-- probably what rcspline.restate() or latex.Design() produce on a model fit object. Here is how the model was fit: fit.ols <- ols( log(k) ~ (rcs(activity) * (log(conc) + sar)) + (rcs(sand) * (log(conc) + sar)), data=sm.clean, x=TRUE, y=TRUE) Here is how I am accessing the 'expanded' format of the model structure: options(digits=3) latex(fit.ols, file='fit_rcs.tex') The output contains several notation elements that I am not familiar with: 1. x_{+} --> it seems that this represent a term that should be set to 0, when x is 0? i.e. the entire expression −453(activity − 0.842)_{+}^{3} = 0 when 'activity' = 0 ?? 2. the '!x' found in : +log(conc) [ −0.0

Rserve and creating a list of lists

Saptarshi Guha — 2008-11-30T22:53:09

Hello, I have some code which generates lattice objects. The function recieves serialized forms of the lattice objects which it then unserializes and then adds to an ArrayList. REXPRaw rser = new REXPRaw( target ); //target contains the raw serialized forms of lattice objects rconn.assign("temp",rser); REXP ret = rconn.eval("invisible(unserialize(temp))"); (1) rexpArr.add(ret); RList rlist = new RList(rexpArr); REXPList rl = new REXPList(rlist); The problem is when I do an assign rconn.assign("finalresult",rl); whence I get *** REXPFactory unable to interpret org.rosuda.REngine.REXPUnknown< at >1629ce8c[4] * ** REXPFactory unable to interpret org.rosuda.REngine.REXPUnknown< at >1629ce8c[4] *** REXPFactory unable to interpret org.rosuda.REngine.REXPUnknown< at >1629ce8c[4] *** REXPFactory unable to interpret org.rosuda.REngine.REXPUnknown< at >1629ce8c[4] *** REXPFactory unable to interpret org.rosuda.REngine.REXPUnknown< at >1629ce8c[4] * ** REXPFactory unable to interpret org.rosuda.REn

controlling the number of times a script is repeated in a loop

Salas, Andria Kay — 2008-11-30T18:21:00

I am running a large for loop and at the end of each iteration a matrix is produced. The program changes the columns in the matrix, and each time a column is added the name of that column is "y". All original columns have no column name. Due to the nature of the program, all original columns will eventually be replaced with new columns each with the column name "y". It is at this point that I want the program to stop running the for loop (right now I just have it running for 20 iterations resulting in a matrix with a mix of old and new columns). I was thinking maybe I could do something with an if else statement and the command colnames. For example: If(colnames all are "y") (stop) else (run the program again) Not entirely sure how to go about this though, or if I am even on the right track. Maybe I need to get rid of the master for loop as perhaps for loops are more constraining in the number of times the program is run? The number of runs to get all original columns replaced with new ones will nev

how to select cases based on value of one or more variables

Simone Gabbriellini — 2008-11-30T20:36:53

dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Randomization of a two-way ANOVA?

Joe Ratster — 2008-11-30T20:22:01

Hello list, I wish to perform a randomization test on the F-statistics of a 2 way ANOVA but have not been able to find out how to do so - is there a package / function that can perform this that I am unaware of? FactorA has 6 levels (0,1,2,3,4,5) whereas FactorB has 3 (1,2,3). A sample: Resp.FactorAFactorB 202 312 122 032 042 052 401 611 121 031 141 051 202 312 122 232 142 052 301 311 121 031 041 713 223 033 143 053 103 Also, is the F-statistic an appropriate test-statistic for the randomization test when it is computed using non-normal data? Any insight into this issue would be much appreciated. Thanks.

using survey weights for correlations

Steve Powell — 2008-11-30T19:41:10

Dear list, I have a data file which includes, alongside various variables representing questionnaire scores, a variable for survey weights computed as the number of observations in the sample drawn from that group divided by the number of observations in the population in the group. I need to calculate a covariance matrix of the questionnaire scores for use in sem. How do I apply the weights? Thanks in advance, Steve Powell www.promente.org proMENTE social research Krančevićeva 35 71000 Sarajevo skype stevepowell99 mob. +387 61 215 997 tel. +387 33 556 865 fax. +387 33 556 866 ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Graphics for proportion within factor

Rob James — 2008-11-30T19:36:47

BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }I am looking to draw what I hoped was a simple plot of proportion WITHIN a strata, save % males by site. I seem to be able to get proportion of males, by site, where the proportion is across the whole dataset, but not the proportion within each site. thanks in advance, Rob [[alternative HTML version deleted]] ______________________________________________ R-help< at >r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.