Re: [R] Plot map Brazil and documentation

2010-06-30 Thread Allan Engelhardt
On 01/07/10 05:43, Pablo Cerdeira wrote: [...] *My doubt is: what it means with see the package index? It is cryptic statistician speak for help(package = "maps") Should I find a Brazilian map on the index?* No. * *If not, can someone help me to find some brazilian map (with state

Re: [R] Help installing R commander in Fedora 13...

2010-06-30 Thread Allan Engelhardt
On 30/06/10 22:14, Carlo Tambuatco wrote: [...] Also, references to /usr/lib/libfontconfig.so.1, : undefined symbol: FT_Select_Size. No idea what this is or how to fix it. But it is the reason that R_X11.so is not being loaded. There's obviously something missing that I need to compile and insta

Re: [R] plain text in Chinese can not be set

2010-06-30 Thread Jinsong Zhao
Hi there, The following code can produce the correct type face, however, the Latin character are displayed in GB1 font. pdf("test_1.pdf", family = c("GB1")) plot(1:10) text(5,1, "\u4F60\u597D", font = 1) text(5,2, "\u4F60\u597D", font = 2) text(5,3, "\u4F60\u597D", font = 3) text(5,4, "\u4F60\

[R] Plot map Brazil and documentation

2010-06-30 Thread Pablo Cerdeira
Dear all, I'm trying to plot some data over a geographic map. I'm reading the documentation (?map)... The problem is here: *map(database = "world", regions = ".", exact = FALSE, boundary = TRUE,* * interior = TRUE, projection = "", parameters = NULL, orientation = NULL,* * fill = FALSE, col =

[R] vi readline key bindings -- some work, some don't

2010-06-30 Thread Mark Ebbert
Dear R Gurus, I have spent some time in the R mail archive and only found one thread that mentions key binding (http://tolstoy.newcastle.edu.au/R/help/06/03/22481.html). I use R (2.9.2) from the command line using OS X's (10.6.4) Terminal.app. I have spent a fair amount of time trying to unders

Re: [R] Note on PCA (not directly with R)

2010-06-30 Thread Jeremy Miles
See if you can track down Thurstone's box problem dataset. It comes (I believe) on a CD with Loehlin's book 'latent variable models', but I'd be surprised if you couldn't find it elsewhere. Thurstone measured boxes, and using EFA (rather than PCA, but they might be similar enough to start off with

Re: [R] Index of Character

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 10:48 PM, harsh yadav wrote: Hi, I am a newbie to R and this may be too simple to ask. I am trying to find out a string function in R that returns the index of a character. For e.g. indexOf("Test1234", '4') would return 8. ?grep ?strsplit > grep("4", strsplit("Test1

Re: [R] Index of Character

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 10:48 PM, harsh yadav wrote: Hi, I am a newbie to R and this may be too simple to ask. I am trying to find out a string function in R that returns the index of a character. For e.g. indexOf("Test1234", '4') would return 8. Is there a similar function in R. I tried sea

[R] Mac OS X R.app has trouble rendering certain fonts.

2010-06-30 Thread Carlo Tambuatco
I noticed this running a few graphics demos the other day. In particular the plotmath and the persp graphics demos, certain fonts don't seem to render on the demos. The plotmath demo displays certain math equations on a quartz window that don't render properly, and the persp demo displays a 3D mo

Re: [R] Index of Character

2010-06-30 Thread Joshua Wiley
Hello, This does what you are looking for: > regexpr("4", "Test1234") [1] 8 attr(,"match.length") [1] 1 see ?regexpr also ?regexp for more details on regular expressions in R. HTH, Josh On Wed, Jun 30, 2010 at 7:48 PM, harsh yadav wrote: > Hi, > > I am a newbie to R and this may be too simp

Re: [R] Index of Character

2010-06-30 Thread Erik Iverson
harsh yadav wrote: Hi, I am a newbie to R and this may be too simple to ask. I am trying to find out a string function in R that returns the index of a character. For e.g. indexOf("Test1234", '4') would return 8. > regexpr("4", "Test1234") [1] 8 attr(,"match.length") [1] 1 _

Re: [R] Note on PCA (not directly with R)

2010-06-30 Thread Nikos Alexandris
Christofer Bogaso wrote: > Dear all, I am looking for some interactive study materials on Principal > component analysis. Basically I would like to know what we are actually > doing with PCA? Having in mind the eigenvalue decomposition and a bivariate data set, the sum- it-all in a few sentences I

[R] Index of Character

2010-06-30 Thread harsh yadav
Hi, I am a newbie to R and this may be too simple to ask. I am trying to find out a string function in R that returns the index of a character. For e.g. indexOf("Test1234", '4') would return 8. Is there a similar function in R. I tried searching the documentation and could find other useful str

Re: [R] Coloring axis labels on Lattice xyplot.

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 7:38 PM, Andrew Liu wrote: Hello, I am trying to color particular labels on my lattice xyplot. For example: library(lattice) z = data.frame(x = 1:5) xyplot(x~x, z) Is there any way for me to make the "4" on the y-axis blue? xyplot(x~x, z, scales=list(x=list(col=c("bla

Re: [R] plot focus - another issue (ylim)

2010-06-30 Thread pdb
Thanks Henrique, that appeared to work, but now I have another issue. If I add a ylim to the plot then when I plot another line it gets plotted on the wrong scale. #this works as expected plot(iris[,1],col="red",ylim=c(-10,10)) #plot1 lines(iris[,4],col="black") #this does not par(mfrow=c(2,1

Re: [R] Multiline and grouping in R

2010-06-30 Thread Pablo Cerdeira
Oh thanks Thierry, the ggplot produces very nice graphics. Really amazing. I'll read more about it. Thanks, best regards On Wed, Jun 30, 2010 at 8:56 AM, ONKELINX, Thierry wrote: > Or you could use ggplot2 > > library(ggplot2) > Dataset <- read.csv("file.csv", header=TRUE) > ggplot(Dataset, ae

Re: [R] Factor Loadings in Vegan's PCA

2010-06-30 Thread Nikos Alexandris
On Wednesday 30 of June 2010 23:02:09 afso...@unisinos.br wrote: > Hi all, > >I am using the vegan package to run a prcincipal components analysis > on forest structural variables (tree density, basal area, average > height, regeneration density) in R. > >However, I could not find out ho

Re: [R] Interpretation of gam intercept parameter

2010-06-30 Thread Lidia Dobria
Gavin, Thank you for your clear explanation. I'm just learning R, hence my not knowing how to dummy code a variable using R. Your example was very useful! Thank you again. Lidia > Subject: Re: [R] Interpretation of gam intercept parameter > From: gavin

[R] plain text in Chinese can not be set

2010-06-30 Thread Jinsong Zhao
Hi there, According to ?par, 'font' is an integer which specifies which font to use for text, that 1 corresponds to plain text (the default), 2 to bold face, 3 to italic and 4 to bold italic. When I test Chinese character in pdf(), I found that 1 to bold face, 2 to italic, 3 to bold italic, 4 t

Re: [R] Correctly plotting bar and scatter chart on 2-y axis plot with par(new=T)

2010-06-30 Thread Greg Snow
For 1 you can just reverse one of the y ranges, e.g.: updateusr(1:2, range(0,y1), 1:2, rev(range(y2)) ) on my computer for some reason the axis command needs you to explicitly set the at points, but then it works properly. For 2, are the axes on all the plots the same? If so you can put all th

[R] question regarding panel data analysis

2010-06-30 Thread amatoallah ouchen
Good day R-users, So if the question may seem easy to many of you but this present a serious issue for me . I'm currently running a panel data analysis i've used the plm package to perform the Tests of poolability as results intercepts and coefficients are assumed different. so my question is sho

Re: [R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-06-30 Thread jim holtman
Use "Rprof" to determine where time is being spent. This might point out some problems in the code. On Wed, Jun 30, 2010 at 7:53 PM, Mike Williamson wrote: > Hi all, > >    I am using the package "random forest" for random forest predictions.  I > like the package.  However, I have fairly large

[R] question regarding panel data analysis

2010-06-30 Thread amatoallah ouchen
Good day R-users, So if the question may seem easy to many of you but this present a serious issue for me . I'm currently running a panel data analysis i've used the plm package to perform the Tests of poolability as results intercepts and coefficients are assumed different. so my question is sho

[R] anyone know why package "RandomForest" na.roughfix is so slow??

2010-06-30 Thread Mike Williamson
Hi all, I am using the package "random forest" for random forest predictions. I like the package. However, I have fairly large data sets, and it can often take *hours* just to go through the "na.roughfix" call, which simply goes through and cleans up any NA values to either the median (numer

[R] Coloring axis labels on Lattice xyplot.

2010-06-30 Thread Andrew Liu
Hello, I am trying to color particular labels on my lattice xyplot. For example: library(lattice) z = data.frame(x = 1:5) xyplot(x~x, z) Is there any way for me to make the "4" on the y-axis blue? Thanks, Andy __ R-help@r-project.org mailing list h

Re: [R] problem with rbind on data.frames that contain data.frames

2010-06-30 Thread Michael Lachmann
On 30 Jun 2010, at 22:55, Allan Engelhardt wrote: >> > a$z=z > You are (kind of) assigning *two* columns from the data frame "z" to > the name 'z' in "a" which is probably not going to work as you > expect. R tries to be clever which may or may not be a Good Thing. > Try > > a$z1 <- z[,1]

Re: [R] Axes intercept

2010-06-30 Thread Bert Gunter
I nominate the below for a Fortune. -- Bert Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of R. A. Bilonick Sent: Wednesday, June 30, 2010 3:16 PM To: r-help@r-project.org Subject:

Re: [R] What is wrong with this code?

2010-06-30 Thread Peter Ehlers
On 2010-06-30 15:56, Cable, Samuel B Civ USAF AFMC AFRL/RVBXI wrote: Okay, here is a reproducible example of a possible solution (actually it probably does not do what you want but it's a start for discussion. Note it is actual code and data which is what is needed. =

Re: [R] Axes intercept

2010-06-30 Thread R. A. Bilonick
On Mon, 2010-06-28 at 10:48 -0400, Robert Baer wrote: > y=rnorm(100) > x=abs(y) > plot(x, y, axes=FALSE) > axis(1, pos=0) > axis(2) > box() It's nice to know that R tends to make nice graphics by default. But you can have R do not so great graphics (like Excel and other programs that make really

Re: [R] What is wrong with this code?

2010-06-30 Thread Cable, Samuel B Civ USAF AFMC AFRL/RVBXI
> Okay, here is a reproducible example of a possible solution (actually > it > probably does not do what you want but it's a start for discussion. > Note it is actual code and data which is what is needed. > === > str1 <- "abc" > str2 <- "abcd" >

Re: [R] Embed function strips out date index

2010-06-30 Thread Gabor Grothendieck
On Wed, Jun 30, 2010 at 4:32 PM, Manussawee Sukunta wrote: > Hi, > > I'm having especially hard time today and couldn't find any > clue/answer through the internet.  I hope you can help. > > I'm in a process of writing a script to estimate error correction > model, and I was following an example i

Re: [R] plot focus

2010-06-30 Thread Henrique Dallazuanna
Try this: par(mfg = c(1, 1)) lines(iris[,4],col="black") On Wed, Jun 30, 2010 at 7:26 AM, pdb wrote: > > I am doing calculations in a loop and then plotting the results by adding a > point to each of 2 charts at the end of the loop. Its very informative as > you can see the progression through

Re: [R] plot focus

2010-06-30 Thread Greg Snow
I would generally write a function to create the entire first plot, then the entire 2nd plot based on data or other arguments passed in, then in your loop or whatever call the function with the different steps. This will recreate the plots from scratch at each step rather than adding to the exis

[R] I need guidance on better data management in preparation for time series analysis

2010-06-30 Thread Ted Byers
OK, I have managed to use some of the basic processes of getting data from my DB, passing it as a whole to something like fitdistr, &c. I know I can implement most of what I need using a brute force algorithm based on a series of nested loops. I also know I can handle some of this logic in a brut

Re: [R] Embed function strips out date index

2010-06-30 Thread Manussawee Sukunta
Sorry - I actually thought about it after I'd sent out the first message. When I did >attributes(series) I saw that series$class is 'xts' 'zoo'. I just want to keep some sort of indexing so that I can keep track of what is going on... a sanity check. My database can get quite large. I will try

Re: [R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread Ted Harding
I think this has reached the point where it is absolutely necessary for Asha Sharma to state *exactly* what is meant by a "linear lower envelope" of a set of points. There are too many possibilities for the problem as stated so far. For instance (possibilities which have not been considered so far)

Re: [R] string question

2010-06-30 Thread Henrique Dallazuanna
You can try noquote also: noquote(paste('abc', '"xyz"', sep = "")) On Wed, Jun 30, 2010 at 3:31 PM, Paul Evans wrote: > Hi, > > How can I get double quotes embedded in the string? > > Example: > > -- > str1 <- '"xyz"' > > ## desired output > # abc"xyz" > > qr2 <- paste('abc',str1,s

[R] Building Distance Matrix

2010-06-30 Thread cs
Dear All, I tried to build a distance matrix. The following example is using dis fucntion: a<- 1:100 grid <- as.matrix(expand.grid(a,a)) dis<-as.matrix(dist(grid)) This can create a 1 x 1 distance matrix, and the object size is about 764Mb. However, the actual usage of this operation is

Re: [R] Help installing R commander in Fedora 13...

2010-06-30 Thread Carlo Tambuatco
Yes. I've got the R-core, and R-devel packages both installed and updated. Also have tcl and tcl-devel installed and updated and also fontconfig-devel. For some reason, though the reason that Rcmdr fails to compile and be stored in the library is because its dependencies fail to compile and be lo

Re: [R] Embed function strips out date index

2010-06-30 Thread Peter Ehlers
On 2010-06-30 14:32, Manussawee Sukunta wrote: Hi, I'm having especially hard time today and couldn't find any clue/answer through the internet. I hope you can help. I'm in a process of writing a script to estimate error correction model, and I was following an example in Bernhard Pfaff's Anal

[R] Factor Loadings in Vegan's PCA

2010-06-30 Thread afsouza
Hi all, I am using the vegan package to run a prcincipal components analysis on forest structural variables (tree density, basal area, average height, regeneration density) in R. However, I could not find out how to extract factor loadings (correlations of each variable with each pca axis)

Re: [R] string question

2010-06-30 Thread Peter Ehlers
cat() is probably what you want, but note that print() has a 'quote=' argument that you could set to FALSE: print(qr2, quote = FALSE) See ?print.default -Peter Ehlers On 2010-06-30 13:16, Phil Spector wrote: Paul - When you print a string, it escapes the quotes with a backslash. That's a

[R] Factor Loadings in Vegan's PCA

2010-06-30 Thread afsouza
Hi all, I am using the vegan package to run a prcincipal components analysis on forest structural variables (tree density, basal area, average height, regeneration density) in R. However, I could not find out how to extract factor loadings (correlations of each variable with each pca axis)

Re: [R] merging and adding time series

2010-06-30 Thread Gabor Grothendieck
On Wed, Jun 30, 2010 at 4:02 PM, skan wrote: > > Hello > > I have two series (that can have with different frequencies or with missing > values). > I merge them and use na.locf, getting a zoo objet with a common index and > two core columns. > How can I add this columns getting a new zoo series? >

Re: [R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 4:02 PM, Asha Sharma wrote: Hi, Thanks to both of you for taking the time to answer my question. I was maybe not very clear in the way I framed my question. By plot, I meant an x-y plot with a cloud of points which should have a linear lower envelope. Is there a way t

Re: [R] What is wrong with this code?

2010-06-30 Thread Stephan Kolassa
Hi, your problem is called "string matching". Search for that term on rseek.org, there are a couple of functions and packages. And Wikipedia can tell you everything you ever wanted to know about string matching (and more). HTH, Stephan Cable, Samuel B Civ USAF AFMC AFRL/RVBXI schrieb: A

Re: [R] problem with rbind on data.frames that contain data.frames

2010-06-30 Thread Allan Engelhardt
On 30/06/10 20:46, Michael Lachmann wrote: It took me some time to find this bug in my code. Is this a feature of R? Am I doing something wrong? > a=data.frame(x=1:10,y=1:10) > b=data.frame(x=11:20,y=11:20) > z=data.frame(1:10,11:20) > a$z=z You are (kind of) assigning *two* columns from the d

Re: [R] Embed function strips out date index

2010-06-30 Thread Jonathan Christensen
Manussawee, What type of object is series? We could help you better if we could reproduce exactly what you are trying to do, which requires more information (you made a good start by including data and code, though). The output of diff is a vector (time series, ...) with length one less than the

Re: [R] merging and adding time series

2010-06-30 Thread skan
If I just add them (without merging) I get only the common elements. rowsum doesn't work for me -- View this message in context: http://r.789695.n4.nabble.com/merging-and-adding-time-series-tp2274125p2274131.html Sent from the R help mailing list archive at Nabble.com. _

Re: [R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread Asha Sharma
Hi, Thanks to both of you for taking the time to answer my question. I was maybe not very clear in the way I framed my question. By plot, I meant an x-y plot with a cloud of points which should have a linear lower envelope. Is there a way to both plot as well as get the parameters of the lowe

[R] merging and adding time series

2010-06-30 Thread skan
Hello I have two series (that can have with different frequencies or with missing values). I merge them and use na.locf, getting a zoo objet with a common index and two core columns. How can I add this columns getting a new zoo series? Any other way of adding two asynchronou series? regards --

[R] Help installing R commander in Fedora 13...

2010-06-30 Thread piscesboy
I did a standard install of R on Fedora 13 using yum as root, which I assumed installed both the base packages and the devel packages needed to install R Commander (there weren't any optional packages listed on the yum info page). My version of R is updated to the latest 2.11 version. But, running

Re: [R] merging/intersecting 2 data frames

2010-06-30 Thread John Kane
Have you changed the values in b.df? My reading of the original b.df in Erin's post was that there were no common values in PATIENT_ID and ID. --- On Tue, 6/29/10, jim holtman wrote: > From: jim holtman > Subject: Re: [R] merging/intersecting 2 data frames > To: "Erin Hodgess" > Cc: "R help

Re: [R] vlmc - "In vlmc(traffic.clusters.stationary, cutoff = i) : alphabet with >1-letter strings; trying to abbreviate"

2010-06-30 Thread Constantinos Antoniou
Dear Martin, Thank you very much for the (reassuring and helpful) response. Best regards, Costas On Jun 30, 2010, at 3:58 PM, Martin Maechler wrote: >> "CA" == Constantinos Antoniou >>on Wed, 30 Jun 2010 12:07:16 +0300 writes: >> "CA" == Constantinos Antoniou >>on Wed

Re: [R] What is wrong with this code?

2010-06-30 Thread Peter Ehlers
On 2010-06-30 14:28, Erik Iverson wrote: Cable, Samuel B Civ USAF AFMC AFRL/RVBXI wrote: Anyway, I still wouldn't mind some advice on character matching. Thanks. If so we need a reproducible example of what you are doing. OK, let's say I have three strings. Str1="abc". Str2="abcd". Str3

Re: [R] The R Journal, Vol.2 Issue 1

2010-06-30 Thread Peter Dalgaard
Peter Dalgaard wrote: > The first issue of the second volume of The R Journal will shortly be > available at jour...@r-project.org/current.html. Thanks to everyone As no less than 16 people has informed me, that of course wants to be http://journal.r-project.org/current.html (That's what you get

Re: [R] What is wrong with this code?

2010-06-30 Thread John Kane
Okay, here is a reproducible example of a possible solution (actually it probably does not do what you want but it's a start for discussion. Note it is actual code and data which is what is needed. === str1 <- "abc" str2 <- "abcd" str3 <- "ef

[R] longitudinal tobit regression in R

2010-06-30 Thread Biau David
Hi, I am trying to model a score over time. This score shows a ceiling effect. I was willing to use a longitudinal tobit model, such as the one described by Twisk et al. (Twisk_Longitudinal tobit regression: A new approach to analyze outcome variables with floor or ceiling effects_JCE_2009) b

[R] Embed function strips out date index

2010-06-30 Thread Manussawee Sukunta
Hi, I'm having especially hard time today and couldn't find any clue/answer through the internet.  I hope you can help. I'm in a process of writing a script to estimate error correction model, and I was following an example in Bernhard Pfaff's Analysis of Integrated and Cointegrated Time Series w

Re: [R] What is wrong with this code?

2010-06-30 Thread Henrique Dallazuanna
Try this: lapply(list(Str2, Str3), grepl, pattern = Str1) On Wed, Jun 30, 2010 at 5:22 PM, Cable, Samuel B Civ USAF AFMC AFRL/RVBXI < samuel.ca...@hanscom.af.mil> wrote: > > > > > Anyway, I still wouldn't mind some advice on character > > > matching. > > > Thanks. > > > > > If so we need a repr

Re: [R] What is wrong with this code?

2010-06-30 Thread Erik Iverson
Cable, Samuel B Civ USAF AFMC AFRL/RVBXI wrote: Anyway, I still wouldn't mind some advice on character matching. Thanks. If so we need a reproducible example of what you are doing. OK, let's say I have three strings. Str1="abc". Str2="abcd". Str3="efgh". I want to compare Str1 and Str2

Re: [R] What is wrong with this code?

2010-06-30 Thread Cable, Samuel B Civ USAF AFMC AFRL/RVBXI
> > Anyway, I still wouldn't mind some advice on character > > matching. > > Thanks. > > > If so we need a reproducible example of what you are doing. OK, let's say I have three strings. Str1="abc". Str2="abcd". Str3="efgh". I want to compare Str1 and Str2 in such a way that R detects that St

Re: [R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread Stephan Kolassa
Hi, To be honest, what you mean by "a (linear) lower envelope" becomes less and less clear to me. Take any cloud of 2-d points. The convex hull consists of a number of these points - or alternatively, of a number of line segments between successive ones of these points. Thus, every one of the

Re: [R] Why the variation when creating .pdf file output for my plots?

2010-06-30 Thread Jonathan Christensen
Karl, dev2bitmap runs its output through Ghostscript, and I assume that the difference is somehow due to that. I can't say whether Ghostscript is decreasing the file quality or just doing something clever, though. Jonathan On Wed, Jun 30, 2010 at 10:30 AM, Karl Brand wrote: > Thank you Erik!

Re: [R] What is wrong with this code?

2010-06-30 Thread John Kane
--- On Wed, 6/30/10, Cable, Samuel B Civ USAF AFMC AFRL/RVBXI wrote: > From: Cable, Samuel B Civ USAF AFMC AFRL/RVBXI > Subject: Re: [R] What is wrong with this code? > To: r-help@r-project.org > Received: Wednesday, June 30, 2010, 3:41 PM > OK, let me wipe the egg off of my > face The p

Re: [R] ggplot qplot bar removing bars when truncating scale

2010-06-30 Thread Jonathan Christensen
Matthew, The ggplot documentation pages (http://had.co.nz/ggplot2) have the following to say under geom_bar: "A bar chart maps the height of the bar to a variable, and so the base of the bar must always been shown to produce a valid visual comparison." Thus, I suspect what you are trying to do m

Re: [R] Help installing R commander in Fedora 13...

2010-06-30 Thread Allan Engelhardt
There is a Fedora mailing list for R which might be better, but some suggestions: On 30/06/10 20:18, Carlo Tambuatco wrote: I did a standard install of R on Fedora 13 using yum as root, which I assumed installed both the base packages and the devel packages needed If you want the developer

Re: [R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread Stephan Kolassa
Hi, one possibility would be to calculate the convex hull using chull(). I believe that the hull points are returned by chull() in a clockwise order (?), so the points between the rightmost and the leftmost point in the chull() result are the lower half of the convex hull. Remove these points

[R] problem with rbind on data.frames that contain data.frames

2010-06-30 Thread Michael Lachmann
It took me some time to find this bug in my code. Is this a feature of R? Am I doing something wrong? > a=data.frame(x=1:10,y=1:10) > b=data.frame(x=11:20,y=11:20) > z=data.frame(1:10,11:20) > a$z=z > b$z=z > rbind(a,b) Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "2", "3", "4

Re: [R] how to tabulate the prediction value using table function for naive baiyes in R

2010-06-30 Thread Steve Lianoglou
Hi, On Wed, Jun 30, 2010 at 11:44 AM, Aadhithya wrote: > > Hi, > I have written a code in R for classifying microarray data using naive > bayes, the code is given below: > library(e1071) > train<-read.table("Z:/Documents/train.txt",header=T); > test<-read.table("Z:/Documents/test.txt",header=T);

Re: [R] What is wrong with this code?

2010-06-30 Thread Cable, Samuel B Civ USAF AFMC AFRL/RVBXI
OK, let me wipe the egg off of my face The problem wasn't with the break statement, it was with how I had included my functions in the "input.list" list. I promise, I pounded on this for hours and saw the problem five minutes after I sent off the e-mail. Anybody else ever have this happen?

Re: [R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 2:05 PM, Asha Sharma wrote: Hi, I am looking for a way to find the lower envelope of points on a plot, preferably specifying what percentage of points should be allowed to lie outside the envelope. There must be a straightforward way to do this, but I do not seem to b

[R] Help installing R commander in Fedora 13...

2010-06-30 Thread Carlo Tambuatco
I did a standard install of R on Fedora 13 using yum as root, which I assumed installed both the base packages and the devel packages needed to install R Commander (there weren't any optional packages listed on the yum info page). My version of R is updated to the latest 2.11 version. But, running

Re: [R] string question

2010-06-30 Thread Phil Spector
Paul - When you print a string, it escapes the quotes with a backslash. That's a property of the print() function, not the string itself. If you want to see the string, use cat(). The nchar() function is also useful: str1 <- '"xyz"' qr2 <- paste('abc',str1,sep='') print(qr2) [1] "abc\

Re: [R] backslash escape characters in JSON strings

2010-06-30 Thread Dário Abdulrehman
Hi Erik, The reported problem is with the rjson package. Then I tried with RJSONIO, which worked fine and aparently is faster. Thanks. On Wed, Jun 30, 2010 at 4:05 PM, Erik Iverson wrote: > You don't say what package fromJSON is in, or give us the ability to > reproduce the error, since we do

Re: [R] Correctly plotting bar and scatter chart on 2-y axis plot with par(new=T)

2010-06-30 Thread dan.weavesham
Jim, Thanks for the reply and your help on this. In short, it's close but not quite there. In the plot you've produced, I'm looking to get the trinagular points plotted over the top of the bar chart. Does that make sense? Just so you know, there are 2 other considerations: - 1/ ideally, I'd l

[R] parameterization of glm nested design

2010-06-30 Thread Huso, Manuela
Dear R community, I am new to R, a reforming SAS user :) I am running R 2.10.1 on a Windows XP machine. I would like to write linear functions of my coefficient parameter estimates from a glm, but am having a difficult time understanding the parameterization R uses. In the toy example belo

[R] string question

2010-06-30 Thread Paul Evans
Hi, How can I get double quotes embedded in the string? Example: -- str1 <- '"xyz"' ## desired output # abc"xyz" qr2 <- paste('abc',str1,sep='') print(qr2) - Actual output: > [1] "abc\"str\"" I also tried putting an escape sequence before the quote, but couldn'

[R] how to tabulate the prediction value using table function for naive baiyes in R

2010-06-30 Thread Aadhithya
Hi, I have written a code in R for classifying microarray data using naive bayes, the code is given below: library(e1071) train<-read.table("Z:/Documents/train.txt",header=T); test<-read.table("Z:/Documents/test.txt",header=T); cl <- c(c(rep("ALL",10), rep("AML",10))); cl <- factor(cl) mode

[R] ggplot qplot bar removing bars when truncating scale

2010-06-30 Thread ml692787
I'm having problems with this example, it is posted with reproduceable code below, both with the normal 0-6 scale and the desired 3-6 scale (with bars removed). How can I get the graph to have the desired 3-6 scale without removing the bars. Thanks! #Data mean=as.numeric(c(5.117647059,5,4.9473684

Re: [R] Correctly plotting bar and scatter chart on 2-y axis plot with par(new=T)

2010-06-30 Thread dan.weavesham
Greg, Just a quick one to say thanks for helping me out with my 2-y axis query -- your solution works a treat. However, 2 extension points I was wondering if you could help with: - 1/ Is there any way to invert the 2nd y axis -- i.e. highest entry at the bottom of the axis? I can see that the

[R] Finding Lower Envelope of Points on a Plot?

2010-06-30 Thread Asha Sharma
Hi, I am looking for a way to find the lower envelope of points on a plot, preferably specifying what percentage of points should be allowed to lie outside the envelope. There must be a straightforward way to do this, but I do not seem to be able to find it. I would greatly appreciate any hel

Re: [R] merge.zoo and fill

2010-06-30 Thread Gabor Grothendieck
On Wed, Jun 30, 2010 at 10:05 AM, Research wrote: > Hello again, > > I merge different zoo time series with prices at different dates. This > returns a multivariate zoo object with NA's at various points i.e., > > 2010-02-28     NA     NA      NA       NA   850.2  2444.4     NA      NA >  NA      

Re: [R] Why software fails in scientific research

2010-06-30 Thread Bert Gunter
Just one small additional note below ... Bert Gunter Genentech Nonclinical Biostatistics "But a lot of academics are not going to "waste" their time documenting code properly, so others can reap the benefits of it. They would rather get on with the next project, to get the next paper. " --

Re: [R] Why software fails in scientific research

2010-06-30 Thread Dr. David Kirkby
On 03/ 1/10 12:23 AM, Sharpie wrote: John Maindonald wrote: I came across this notice of an upcoming webinar. The issues identified in the first paragraph below seem to me exactly those that the R project is designed to address. The claim that "most research software is barely fit for purp

Re: [R] plot focus

2010-06-30 Thread Peter Ehlers
On 2010-06-30 8:38, Tal Galili wrote: Good question pdb, I would suggest you to use: par(bg = "white") In the beginning of the code, But it doesn't solve the general problem of how to get the "lines" to be properly aligned. I am curious for the answer from betteR people. Best, Tal Instead

Re: [R] Assigning entries to category

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 12:27 PM, Charles C. Berry wrote: see ?cut ?interaction I had been thinking that findInterval or expand.grid might also be useful, but was really waiting for a test data preparation to emerge. -- David. HTH, Chuck On Wed, 30 Jun 2010, LogLord wro

Re: [R] Why the variation when creating .pdf file output for my plots?

2010-06-30 Thread Karl Brand
Thank you Erik! That works nicely now. The file size in (in kilobytes) is equal to the "File>Save As>PDF" method. Still curious why the file sizes (in Kb), differ by a factor of ~2 between the two methods: pdf() dev2bitmap(method = "pdf") I'm just *assuming* here that file size is inidcati

Re: [R] Assigning entries to category

2010-06-30 Thread Charles C. Berry
see ?cut ?interaction HTH, Chuck On Wed, 30 Jun 2010, LogLord wrote: Hi, I have the following problem: I have a large dataframe where each row is specified by two numerical value (one 1:25 and the other one large specific number (e.g. 203043)). I have a list of 60 categor

Re: [R] All possible permutations of letter A with other letters

2010-06-30 Thread Ted Harding
On 30-Jun-10 15:48:39, Barry Rowlingson wrote: > On Wed, Jun 30, 2010 at 11:57 AM, Yen Ngo wrote: >> Dear list, >> I have a vector of letter strings as follow: >> >>> LETTERS[c(1:7,9,15,18:25)] >> _[1] "A" "B" "C" "D" "E" "F" "G" "I" "O" "R" "S" "T" "U" "V" "W" "X" >> "Y" >> >> I need to find sequ

Re: [R] help on naivebayes function in R

2010-06-30 Thread Max Kuhn
So... You really should give the results of sessionInfo(). There are (at least) two naive Bayes functions. I'm assuming that you are using the one in klaR. Look at the manual page ? predict.NaiveBayes: the output is "A list with the conditional a-posterior probabilities for each class and the es

Re: [R] All possible permutations of letter A with other letters

2010-06-30 Thread Barry Rowlingson
On Wed, Jun 30, 2010 at 11:57 AM, Yen Ngo wrote: > Dear list, > > I have a vector of letter strings as follow: > > >> LETTERS[c(1:7,9,15,18:25)] >  [1] "A" "B" "C" "D" "E" "F" "G" "I" "O" "R" "S" "T" "U" "V" "W" "X" "Y" > > I need to find sequences of length 11, which are made from  all possible

Re: [R] Solution to differential equation for nls function

2010-06-30 Thread Ravi Varadhan
Yes, there is an analytical solution. Here is how you do it: bernoulli_anal <- function(t, R0, Rmax, a, b) { # Note: a, b, R0, Rmax all have to be positive (strictly > 0) R1 <- R0 / Rmax k <- R1^b / (1 - R1^b) R <- Rmax / (1 + exp(-a*b*t)/k)^(1/b) return(R) } R0 <- 1 Rmax <- 2 a <- 0.5 b <- 1.0

Re: [R] Threshold Cointegration test

2010-06-30 Thread David Winsemius
Read the Posting Guide. Your attachment apparently did not meet the requirements therein. On Jun 30, 2010, at 10:52 AM, Setlhare Lekgatlhamang wrote: Dear R Users (particularly tsDyn package users), I am very new in the use of R and the contributed packages in need of urgent assistance (see

Re: [R] run R

2010-06-30 Thread Erik Iverson
Please follow the posting guide and tell us minimally what your operating system is. You might find: http://cran.r-project.org/doc/manuals/R-intro.html#Scripting-with-R or http://code.google.com/p/batchfiles/#PROGRAM_LIST useful. jorge.conr...@cptec.inpe.br wrote: Hi, I'm s

Re: [R] run R

2010-06-30 Thread David Winsemius
On Jun 30, 2010, at 9:08 AM, jorge.conr...@cptec.inpe.br wrote: Hi, I'm starting use the R Package and I have some .R scripts. How can I run these .R scripts. ?source ... and re-read "Introduction to R". Conrado __ R-hel

Re: [R] run R

2010-06-30 Thread Joris Meys
Welcome to a new world. You're using the _programming language_ R with thousands of packages, and first of all you should be reading the introduction material thoroughly : http://cran.r-project.org/doc/manuals/R-intro.pdf http://cran.r-project.org/doc/contrib/Owen-TheRGuide.pdf Regarding your que

Re: [R] backslash escape characters in JSON strings

2010-06-30 Thread Erik Iverson
You don't say what package fromJSON is in, or give us the ability to reproduce the error, since we don't know what 's' is. If those two pieces of information are possible to give to the list, it will be much easier to help. dabd wrote: Hi, I am trying to consume a web service that returns a

Re: [R] Why the variation when creating .pdf file output for my plots?

2010-06-30 Thread Erik Iverson
Method 3: > pdf(file="my_plot.pdf", paper="a4") > dev.off() The `pdf` function opens a *new* graphics device, you then send output to the device before calling dev.off(), e.g., pdf(file = my_plot.pdf") plot(1:10, 1:10) dev.off() -yields a .pdf file of 1kb (same plot example) and retu

[R] Threshold Cointegration test

2010-06-30 Thread Setlhare Lekgatlhamang
Dear R Users (particularly tsDyn package users), I am very new in the use of R and the contributed packages in need of urgent assistance (see attachment for the explanation of the problem). Could someone assist me on conducting threshold cointegration test in R using the tsDyn package. I have gon

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