[R] 3d cloud plot with point size reflecting variable value
Hello all, I'm using the cloud function to plot the iris data as per the document: http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/stats/fichiers/_gallery.pdf I'd like to change the point size to reflect a fourth variable, as done here http://www.cis.hut.fi/projects/somtoolbox/download/pics2/shotvs2_origdata.png Does anybody know how to do this? There doesn't seem to be an option in cloud() Thanks, Richie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error in storage when attempting to run GLM
Hello, I'd be very grateful for help with the following. I attempt to run a basic GLM as follows: basic_model=glm(factor(A$b) ~ factor(A$c) ) variables b and c are text values and their class is factor. they have no missing values. I get the error: Error: NA/NaN/Inf in foreign function call (arg4) In addition: warning messages: 1: Ops.factor(y,mu) : - not meaningful for factors 2: Ops.factor(eta, offset) : - not meaningful for factors etc What does this mean? R [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] barplot() x axes are not updated after removal of categories from the dataframe
Hi all, I'd be grateful for your help. I am a new user struggling with a barplot issue. I am plotting categories (X axis) and their mean count (Y axies) with barplot(). The first call to barplot works fine. I remove records from the dataframe using final=[!final$varname == "some value",] I echo the dataframe and the records are no longer in the dataframe. When I call plot again however, the X axis still contains the removed category values albeit with a count of 0. How can I stop the removed categories appearing in the barplot? Are they stored globally after the first barplot call? thanks in advance for your help. R [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to obtain p values from an ANOVA result
Hi all, I'm tryint to turn my ANOVA result from anova(model) in to p values. The default output is: term ; Df ; Deviance ; resid Df; Resid. Dev Is there a way to add p values to this output so the significance of the terms can be easily determined? Thanks in advance. Richie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multiple levels of nesting with trellis plots
Hi guys, I have a tricky problem that I'd appreciate your help with. I have two categorical variables, say varA and varB and an associated frequency Freq for combinations of the levels of varA and varB. This was created with a table() call. I'd now like to make panel plots of the frequency. I can do a panel plot by varA: barchart(data$Freq ~ data$varB | data$varA) How do I achieve two levels of nesting for say a third categorical variable varC? That is, how do I specify 2 'given's in the the panel plot, and preferably arranged the panels vertically within the 'inner' panel/ thanks very much, Richie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] vertically aligned X axis labels disappear off R Graphics window
Hi guys, I'm evaluating R for basic data exploration. I produce a bar plot of the data, with the x axis labels aligned vertically. However, the start of labels longer than about 10 characters are cut off by the bottom of the graphics window. I'd appreciate your help in properly spacing the space around a plot reserved for labels so that this problem can be avoided. Thanks, Richie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] barplot with specific order of x axis labels
Hi all, I'd appreciate your help with this problem. I need to plot a barplot with the categories in a specific order. My data might be: hours Freq AN 10 MO 14 LU 30 I need the categories to be in the order: MO LU AN Is there some way to pass sort the dataset into this order so that it plots correctly when passed to barplot()? Thanks very much, Richie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] including tabular information with a plot in R Graphics
Hi all, I have a presentation problem that I cannot find a solution to in the documetnation. I have a nice barplot. Below this I would also like a table with some information relating to the plot. My idea was to have the plot and table on the same graphics window so I can output them as an image file for a report. Does anybody know how to include tabular information from a dataset or table into the graphics device? Is there a better/more correct way to output tables and graphics to a single file? Thanks very much, Richie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] including tabular information with a plot in R Graphics
Hi all, Thanks very much for the suggestions. My experience for the benefit of others is: - use addtable2plot if you want a fancier legend or small table *within* a plot area - use textplot if you want combinations of tables and text listings in the graphics device. The help for textplot gives a very good example Thanks again, Richie 2009/3/5 Eik Vettorazzi > Hi Richie, > have a look at textplot() from the gplots-package. > hope, it helps! > > R User R User schrieb: > >> Hi all, >> I have a presentation problem that I cannot find a solution to in the >> documetnation. >> I have a nice barplot. Below this I would also like a table with some >> information relating to the plot. >> My idea was to have the plot and table on the same graphics window so I >> can >> output them as an image file for a report. >> >> Does anybody know how to include tabular information from a dataset or >> table >> into the graphics device? >> Is there a better/more correct way to output tables and graphics to a >> single >> file? >> >> Thanks very much, >> Richie >> >>[[alternative HTML version deleted]] >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > > -- > Eik Vettorazzi > Institut für Medizinische Biometrie und Epidemiologie > Universitätsklinikum Hamburg-Eppendorf > > Martinistr. 52 > 20246 Hamburg > > T ++49/40/42803-8243 > F ++49/40/42803-7790 > > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] svydesign syntax
This message is for those familiar with the survey package. I need to fit a weighted Cox model to accommodate the sampling weights as I have a case-control study with controls sampled at random from a database in a ratio 2:1 to cases (whom were all sampled). I want to make sure I am using the right svydesign syntax to specify this sampling design. Can anyone please check if the statement below is appropriate for my design? #group represents the case (total of 132) vs control (253 out of the total of 853 controls) groups; prob is 1 for cases and 253/853 for controls and ssize=132 for cases and 853 otherwise; dstr=svydesign(id=~1, strata=~group, prob=~prob, fpc=~ssize, data=noNA) -- View this message in context: http://r.789695.n4.nabble.com/svydesign-syntax-tp2298793p2298793.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Calibration and validation for svycoxph
Hello, This post is for Dr. Thomas Lumley or anybody familiar with the survey package. I am estimating a proportional hazards model with weights using svycoxph. Are there functions already built in the survey package that allow me to do validation and calibration of the model? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Calibration-and-validation-for-svycoxph-tp2249004p2249004.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] calibration and validation for svycoxph
Hello, This post is for Dr. Thomas Lumley or anybody familiar with the survey package. I am estimating a proportional hazards model with weights using svycoxph. Are there functions already built in the survey package that allow me to do validation and calibration of the model? Thanks -- View this message in context: http://r.789695.n4.nabble.com/calibration-and-validation-for-svycoxph-tp2249118p2249118.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calibration and validation for svycoxph
Hi Dr. Lumley, Sorry about the succession of the 2 messages. It wasn't intended. This is my first post to the forum and I first signed up to Nabble and submitted the post and later got the message from Nabble that the post has not been accepted by the R forum and that I need separate subscription for the R forum. So I signed up for the R forum and resubmitted the post and both messages ended up being posted. Yes, I was looking for similar functions to those in the Design package to build a calibration plot (Design, calibrate function) and to do bootstrap validation of the model (Design, validate function). I will check the options of the functions you mentioned to see if I can easily get those. Could you please advise on what measure should I use to quantify the optimism of fit (the way c-index was used for Cox models)? If you have existent code that you used for these purposes that would be great. Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/calibration-and-validation-for-svycoxph-tp2249118p2250730.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help on computing Geary's C statistic to test for Spatial Autocorrelation
Dear Users: I have been trying to use the geary.test() function in *R*, but am having slight difficulty understanding how I am to apply it in my context. I have 2 matrices: 1) *n x p* matrix of *n* observations with *p* measurements each. It may be noted that this matrix has a spatial dimension to it, as the *n*observations are at different geographical locations on a map. 2) *n x n* spatial weights matrix (symmetric) with each matrix element being an inter-locality weight. Using the above 2 matrices, I am trying to compute the Geary's *C* statistic for each of the *p* dimensions and also obtain corresponding *p*-values to determine its statistical significance for spatial autocorrelation. I will appreciate any help you could provide me in helping me compute the same. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R2wd
Hi all,
I'm currently trying to get accustomed to R and some of its packages, thus
need some help for a package called R2wd. As I am trying to use the wdGET()
function I'm getting the following message:
Error in if (!(tmp[["ActiveDocument"]][["Name"]] == filename))
tmp$Open(paste("path", :
argument is of length zero
Does anybody know what that means?
Best,
--
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