Re: [R] how to order each element according to alphabet

2011-07-14 Thread onthetopo
> dd [,1] [,2] [1,] "OP" "SU" [2,] "XA" "YQ" sapply( lapply( + strsplit(dd, split=""), sort), + paste, collapse="") [1] "OP" "AX" "SU" "QY" The result is not what I intended since it is a single line. It should be: [,1] [,2] [1,] "OP" "SU" [2,] "AX" "QY" -- View this message in conte

[R] combining elements in a data frame

2011-07-14 Thread Lee Averell
Hi all, I have 2 data frames the first contains a list with repeats of words and an associated response time (RT) measure for each word. The second is a tabulation of each unique word and other information such as the amount and of responses for each word. I need to determine the mean RT

Re: [R] how to order each element according to alphabet

2011-07-14 Thread onthetopo
dd=rbind(c("OP", "SU"),c("XA", "YQ")) -- View this message in context: http://r.789695.n4.nabble.com/how-to-order-each-element-according-to-alphabet-tp3668997p3669194.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org

Re: [R] how to order each element according to alphabet

2011-07-14 Thread David Winsemius
On Jul 14, 2011, at 11:56 PM, onthetopo wrote: Thank you very much for your reply doctor. I tried to apply your command to my table but couldn't Would you please enlighten me on how to do this when 'lets2' is a 4X4 matrix for example. The message doesn't seem to be getting through. Let's s

Re: [R] how to order each element according to alphabet

2011-07-14 Thread onthetopo
Thank you very much for your reply doctor. I tried to apply your command to my table but couldn't Would you please enlighten me on how to do this when 'lets2' is a 4X4 matrix for example. -- View this message in context: http://r.789695.n4.nabble.com/how-to-order-each-element-according-to-alpha

[R] Bar chart in ascending order for each level of X

2011-07-14 Thread Muhuri, Pradip (SAMHSA/CBHSQ)
Hello List, The question is how to plot a bar chart in which bars are sorted in ascending order for each level of X. I would appreciate receiving your advice and help. Thanks, Pradip Muhuri ** The following codes work when producing the chart in which bars are NOT sorted. Please see

Re: [R] how to order each element according to alphabet

2011-07-14 Thread David Winsemius
On Jul 14, 2011, at 11:19 PM, onthetopo wrote: Hi, There are many more patterns than VL to LV. In fact, too many to be listed manually. For example ML should be ordered as LM, QL should be ordered as LQ. The order is according to the alphabet. A more complete (reproducible) answer woul

Re: [R] how to order each element according to alphabet

2011-07-14 Thread onthetopo
Hi, There are many more patterns than VL to LV. In fact, too many to be listed manually. For example ML should be ordered as LM, QL should be ordered as LQ. The order is according to the alphabet. -- View this message in context: http://r.789695.n4.nabble.com/how-to-order-each-element-ac

Re: [R] how to order each element according to alphabet

2011-07-14 Thread David Winsemius
On Jul 14, 2011, at 9:18 PM, onthetopo wrote: Hi there, I have a large amino acid csv file like this: input.txt: P,LV,Q,Z P,VL,Q,Z P,ML,QL,Z Are you also asking how to read a comma separated file? ? read.csv # and read more introductory material There is a problem with this file, sin

[R] Calculate Az (A sub z) with R?

2011-07-14 Thread dd2es
I am looking for (or interested in writing) a function that calculates Az, an alternative measure of discriminability from SDT (alternative to d', Az). I have written my own functions for d', A', B"d, and am aware of the 'sdtalt' package, but I have yet to find a way to calculate Az, since it requi

[R] Export Unicode characters from R

2011-07-14 Thread Sverre Stausland
Dear helpers, I am not able to export Unicode characters from R. Below is an example where the Unicode character is correctly rendered as long as I am stay within R. When I export it, the character appears only with its basic code, and the same happens when I import it back into R . I'm using R 2.

[R] how to order each element according to alphabet

2011-07-14 Thread onthetopo
Hi there, I have a large amino acid csv file like this: input.txt: P,LV,Q,Z P,VL,Q,Z P,ML,QL,Z There is a problem with this file, since LV and VL are in fact the same thing. How do I order each element according to alphabetical order so that the desired output would look like: output.txt:

[R] Non-negative least squares for sparse matrix

2011-07-14 Thread Erik Wright
Hello, I am attempting to solve the least squares problem Ax = b in R, where A and b are known and x is unknown. It is simple to solve for x using one of a variety of methods outlined here: http://cran.r-project.org/web/packages/Matrix/vignettes/Comparisons.pdf As far as I can tell, none of th

Re: [R] computing functions with Euler's number (e^n)

2011-07-14 Thread warmstron1
R 2.11.1 on Mac OS X. I didn't see the Note. -- View this message in context: http://r.789695.n4.nabble.com/computing-functions-with-Euler-s-number-e-n-tp3655205p3668849.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project

Re: [R] validate survival with val.surv

2011-07-14 Thread Frank Harrell
The documentation for val.surv tried to be clear about that. Note that val.surv is only for the case where the predictions were developed on a separate dataset, i.e., that the validation is truly 'external'. Frank yz wrote: > > Dear R users: > > I want to externally validate a model with val.su

[R] validate survival with val.surv

2011-07-14 Thread zhu yao
Dear R users: I want to externally validate a model with val.surv. Can I use only calculated survival (at 1 year) and actual survival? Or I needed the survival function and actual survival. Thanks *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China*

Re: [R] Add coordinates at specific points...

2011-07-14 Thread Greg Snow
To add to what David and Duncan wrote: If you want to plot something at a point where the x coordinate is in user coordinates, but the y-coordinate is something like the middle of the plot, or 1/5th of the way from the top then you can use the grconvertY function along with the text function. I

Re: [R] Splitting one column value into multiple rows

2011-07-14 Thread David Winsemius
On Jul 14, 2011, at 6:47 PM, Madana_Babu wrote: Hi i have the data in the following format: rent,100,1,common,674 pipe,200,0,usual,864 car,300,1,uncommon,392:jump,700,0,common,664 car,200,1,uncommon,864:snap,900,1,usual,746 stint,600,1,uncommon,257 pull,800,0,usual,594 where as i want the abo

Re: [R] (no subject)

2011-07-14 Thread David Winsemius
On Jul 14, 2011, at 6:15 PM, Tyler Rinker wrote: Good Afternoon R Community, I often work with very large data bases and want to search for select cases by a particular word or numeric value. I created the following simple function to do just that. It searchs a particular column for

[R] Font problem

2011-07-14 Thread Noah Silverman
Hi, I'm running Redhat Linux (I believe it is Fedora 13 or 14) With the latest version of R Everything works nicely, except for the fonts on some plots. I see small empty boxes instead of the number. It seems as if this is only the case when the fonts are small. I've installed all of the f

Re: [R] recursive function - finding connections

2011-07-14 Thread Peter Langfelder
One more thing - for large data sets, the packages flashClust and fastcluster provide much faster hierarchical clustering that (at least for flashClust which I'm the maintainer of) give the exact same results. Simply insert a library(flashClust) before you call the function and your code will run

Re: [R] recursive function - finding connections

2011-07-14 Thread Peter Langfelder
Hi Paul, I assume you are using the argument cutoff to specify the p-value below which nodes are considered connected and above which they are not connected. I would use single linkage hierarchical clustering. If you have two groups of nodes and any two nodes between the groups are connected (i.e

Re: [R] SQldf with sqlite and H2

2011-07-14 Thread Mandans
Thanks a lot Gabor. It helped a lot. Appreciate your time and effort. Thanks --- On Thu, 7/14/11, Gabor Grothendieck wrote: > From: Gabor Grothendieck > Subject: Re: [R] SQldf with sqlite and H2 > To: "Mandans" > Cc: r-help@r-project.org > Date: Thursday, July 14, 2011, 2:22 PM > On Thu, Jul

Re: [R] recursive function - finding connections

2011-07-14 Thread Benton, Paul
Sorry bad example. My data is undirected. It's a correlation matrix so probably better to look at something like: foomat<-cor(matrix(rnorm(100), ncol=10)) foomat mine are pvalues from the correlation but same idea. On 14 Jul 2011, at 11:23, Erich Neuwirth wrote: > cliques only works for undir

[R] Splitting one column value into multiple rows

2011-07-14 Thread Madana_Babu
Hi i have the data in the following format: rent,100,1,common,674 pipe,200,0,usual,864 car,300,1,uncommon,392:jump,700,0,common,664 car,200,1,uncommon,864:snap,900,1,usual,746 stint,600,1,uncommon,257 pull,800,0,usual,594 where as i want the above 6 lines data into 8 lines as below (Spliting row

[R] (no subject)

2011-07-14 Thread Tyler Rinker
Good Afternoon R Community, I often work with very large data bases and want to search for select cases by a particular word or numeric value. I created the following simple function to do just that. It searchs a particular column for the phrase and returns a data frame with the rows that

[R] Cost-sensitive classification

2011-07-14 Thread snassimr
Hi , everybody !!! I want to perform a cost-sensitive classification using the rpart as a base classifier . Is it possible ? Nissim -- View this message in context: http://r.789695.n4.nabble.com/Cost-sensitive-classification-tp3668749p3668749.html Sent from the R help mailing list archive at N

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread Dennis Murphy
Hi: I think Bill's got the right idea for your problem, but for the fun of it, here's how Bert's suggestion would play out: # Kind of works, but only for the first variable in myvars... > aggregate(get(myvars) ~ group + mydate, FUN = sum, data = example) group mydate get(myvars) 1 group1 2

[R] Correct behavior of Hmisc::capitalize()?

2011-07-14 Thread Henrik Bengtsson
Hi, from example(capitalize) of the Hmisc package (v 0.8.3) you get: > capitalize(c("Hello", "bob", "daN")) [1] "Hello" "Bob" "daN" Is that "daN" correct? If so, then this behavior that only *all lowercase strings*, which the code indicates, will be capitalized is not documented. > Hmisc::c

Re: [R] Very slow optim(): solved

2011-07-14 Thread Mike Marchywka
> Date: Thu, 14 Jul 2011 12:44:18 -0800 > From: toshihide.hamaz...@alaska.gov > To: r-h...@stat.math.ethz.ch > Subject: Re: [R] Very slow optim(): solved > > After Googling and trial and errors, the major cause of optimization was not > functions, but d

[R] Error: "non-numeric argument to binary operator"

2011-07-14 Thread Anil acharya
Hi I am posting in the topic related to the "non-numeric argument to binary operator" as I got similar problem while running the netcdf code. I have attached the file with this post. It is a climate data from NOAA site. The code follows as: library(survival) library(RNetCDF) library(ncdf)

Re: [R] random selection of elements from a matrix

2011-07-14 Thread anaraster
ups...already found the solution matrix2 <- matrix1[sample(samplenumber,replace=F),] -- View this message in context: http://r.789695.n4.nabble.com/random-selection-of-elements-from-a-matrix-tp3668574p3668594.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread William Dunlap
You may find it easier to use the data.frame method for aggregate instead of the formula method when you are using vectors of column names. E.g., responseVars <- c("mpg", "wt") byVars <- c("cyl", "gear") aggregate(mtcars[responseVars], by=mtcars[byVars], FUN=median) gives the same result

[R] random selection of elements from a matrix

2011-07-14 Thread anaraster
Hi! How can I make a random selection of "n" row elements from a matrix. The matrix was previously created from a table with different rows and columns. However I want to keep all the information (columns), I just want to reduce the number of observations. Thanks, Ana -- View this message in co

[R] nlme gls errors

2011-07-14 Thread Roland Sookias
Hi I keep getting an error like this: Error in `coef<-.corARMA`(`*tmp*`, value = c(18.3113452983211, -1.56626248550284, : Coefficient matrix not invertible or like this: Error in gls(archlogfl ~ co2, correlation = corARMA(p = 3)) : false convergence (8) with the gls function in nlme. The f

Re: [R] plotting date data over couple of months

2011-07-14 Thread vamshi999
thank you for your reply.. As i have told you earlier... i want to plot the total no.of birds counted for each day and plot total no.of birds for each day.. one level for each day .. i wanted to normalize the data.. since i don't have the data for equal no.of hours for all days.. for example o

Re: [R] LME and overall treatment effects

2011-07-14 Thread Mark Bilton
Ok...lets try again with some code... --- Hello fellow R users, I am having a problem finding the estimates for some overall treatment effects for my mixed models using 'lme' (package nlme). I hope someone can help. Fi

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread Dimitri Liakhovitski
David - I tried exactly the thing you did (and after that asked my question to the forum): > form <- as.formula(paste( > "cbind(", > paste( myvars, collapse=","), > ") ~ group+mydate", > sep=" ") ) And it did not wo

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread Dimitri Liakhovitski
Thanks a lot! actually, what I tried to do is very simple - just passing tons of variable names into the formula. Maybe that "get" thing suggested by Bert would work... Dimitri On Thu, Jul 14, 2011 at 4:01 PM, David Winsemius wrote: > Dmitri: > > as.matrix makes a matrix out of the dataframe t

Re: [R] Very slow optim(): solved

2011-07-14 Thread Hamazaki, Hamachan (DFG)
After Googling and trial and errors, the major cause of optimization was not functions, but data setting. Originally, I was using data.frame for likelihood calculation. Then, I changed data.frame to vector and matrix for the same likelihood calculation. Now convergence takes ~ 14 sec instead o

[R] WLS regression, lm() with weights as a matrix

2011-07-14 Thread Victor11
Dear All, I've been trying to run a Weighted Least Squares (WLS) regression: Dependent variables: a 60*200 matrix (*Rit*) with 200 companies and 60 dates for each company Independent variables: a 60*4 matrix (*Ft*) with 4 factors and 60 dates for each factor Weights: a 60*200 matrix (*Wit*) with

Re: [R] Repating a loop of lm function with different columns of database

2011-07-14 Thread Weidong Gu
If I understood your question x<-data.frame(matrix(rnorm(2000,10,10),ncol=50)) sapply(1:5,function(i) summary(lm(x[,i]~x[,i+10]+x[,50]))) Weidong Gu On Thu, Jul 14, 2011 at 2:27 PM, Jon Toledo wrote: > > Hi, > First let me thank you for the incredible help and resource that this forum > is. >

Re: [R] Sum weights of independent variables across models (AIC)

2011-07-14 Thread Frank Harrell
Why go to so much trouble? Why not fit a single full model and use it? Even better why not use a quadratic penalty on the full model to get optimum cross-validation? Frank nofunsally wrote: > > Hello, > I'd like to sum the weights of each independent variable across linear > models that have be

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread David Winsemius
Dmitri: as.matrix makes a matrix out of the dataframe that is passed to it. As a further note I attempted and failed for reasons that are unclear to me to construct a formula that would (I hoped) preserve the column names which are being mangle in the posted effort: form <- as.formula(past

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread Bert Gunter
Dmitri: Look at my vars from myvars<-c("value1","value2") It's just a character vector of length 2! You can't cbind a character vector of length 2! These are not references/pointers. It's not at all clear to me what you ultimately want to do, but IF it's: pass a character vector of names to be u

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread Dimitri Liakhovitski
Thank you, David, it does work. Could you please explain why? What exactly does changing it to "as matrix" do? Thank you! Dimitri On Thu, Jul 14, 2011 at 3:25 PM, David Winsemius wrote: > > On Jul 14, 2011, at 3:05 PM, Dimitri Liakhovitski wrote: > >> Hello! >> >> I am aggregating using a formula

Re: [R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread David Winsemius
On Jul 14, 2011, at 3:05 PM, Dimitri Liakhovitski wrote: Hello! I am aggregating using a formula in aggregate - of the type: aggregate(cbind(var1,var2,var3)~factor1+factor2,sum,data=mydata) However, I actually have an object (vector of my variables to be aggregated): myvars<-c("var1","var2

[R] cbind in aggregate formula - based on an existing object (vector)

2011-07-14 Thread Dimitri Liakhovitski
Hello! I am aggregating using a formula in aggregate - of the type: aggregate(cbind(var1,var2,var3)~factor1+factor2,sum,data=mydata) However, I actually have an object (vector of my variables to be aggregated): myvars<-c("var1","var2","var3") I'd like my aggregate formula (its "cbind" part) to b

Re: [R] LME and overall treatment effects

2011-07-14 Thread Bert Gunter
Probably no hope of help until you do as the posting guide asks: > __ > 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 comm

[R] Repating a loop of lm function with different columns of database

2011-07-14 Thread Jon Toledo
Hi, First let me thank you for the incredible help and resource that this forum is. I am trying to compare the repeated measurement of more than 100 analytes that have been take in 70 subjects at 2 time points adjusted for the time difference of sample times(TimeDifferenceDays), therefore I wan

Re: [R] rgl: reproduce final state of interactive plot?

2011-07-14 Thread Ben Bolker
sjaffe riskspan.com> writes: [snip snip] > This can also be used to 'snap' the current view during an interactive > session and restore it later during that same session, which could be quite > useful. > > To save typing, a (trivial) pair of functions to encapsulate this: > > snap.view<- f

Re: [R] Writing Complex Formulas

2011-07-14 Thread Duncan Murdoch
On 14/07/2011 12:46 PM, warmstron1 wrote: I resolved this issue. It appears that "^" won't work for this case, but "**" worked. I can't find any reference to this, but where "^" seems to be used to raise a value to a numerical function, "**" is used for a y raised to the power of x where x it a

[R] Amelia_Multiple_Imputation_with_observational_priors_noms

2011-07-14 Thread Eric Miner
I am fairly new at using R/programming in general so I apologize if I am leaving crucial parts of the puzzle out, but here goes. First and foremost this is the error I am receiving: Error in muPriors[priors[, 1:2]] <- priors[, 3] : NAs are not allowed in subscripted assignments This occ

[R] LME and overall treatment effects

2011-07-14 Thread Mark Bilton
Hello fellow R users, I am having a problem finding the estimates for some overall treatment effects for my mixed models using 'lme' (package nlme). I hope someone can help. Firstly then, the model: The data: Plant biomass (log transformed) Fixed Factors: Treatment(x3 Dry, Wet, Control) Yea

[R] Simple clustering help

2011-07-14 Thread donvolencia
Hi all, I have just begun to use R and am hoping to receive some advice about the problem I need to solve. I have a file containing xy points that I need to find all significant clusters and write each of their xy coordinates to file(total points ~ 75000 and sig. cluster = 2500 points. I want t

Re: [R] SQldf with sqlite and H2

2011-07-14 Thread Gabor Grothendieck
On Thu, Jul 14, 2011 at 10:33 AM, Mandans wrote: > SQldf with sqlite and H2 > > I have a large csv file (about 2GB) and wanted to import the file into R and > do some filtering and analysis. Came across sqldf ( a great idea and product) > and was trying to play around to see what would be the be

Re: [R] rgl: reproduce final state of interactive plot?

2011-07-14 Thread sjaffe
Terrific! This is great to know. I first tried saving and restoring the entire set from par3d but this produced some changes (eg bg) and also one must call par3d with no.readonly=TRUE. Clearly this is the way to go if one has changed a variety of rgl properties. But if one has only used the mouse

Re: [R] Adding rows based on column value

2011-07-14 Thread Bert Gunter
Yes, because from your previous posts, you appeared to have read in the data as "character": file=read.table("file.txt",fill=T,colClasses = "character",header=T) But, of course, without a reproducible example, one cannot be sure. -- Bert On Thu, Jul 14, 2011 at 10:46 AM, Bansal, Vikas wrote:

Re: [R] Adding rows based on column value

2011-07-14 Thread Ben Bolker
On 07/14/2011 01:46 PM, Bansal, Vikas wrote: > I have tried that also.But it is showing this error- > > aggregate(file[,3:6], by = list(file[,2]), FUN = sum) > > Error in FUN(X[[1L]], ...) : invalid 'type' (character) of argument > > Farther down in your previous e-mail you state that you re

Re: [R] computing functions with Euler's number (e^n)

2011-07-14 Thread Berend Hasselman
warmstron1 wrote: > > I solved this in two ways: > 1. "**" was necessary to raise (-dummy + 1) to the power of B. "^" > doesn't work here, for some reason. > ... > Using which version R on which platform? Most strange. The help page for "Arithmetic operators" clearly states in a Note that "*

Re: [R] Adding rows based on column value

2011-07-14 Thread Bansal, Vikas
I have tried that also.But it is showing this error- aggregate(file[,3:6], by = list(file[,2]), FUN = sum) Error in FUN(X[[1L]], ...) : invalid 'type' (character) of argument Thanking you, Warm Regards Vikas Bansal Msc Bioinformatics Kings College London __

Re: [R] Adding rows based on column value

2011-07-14 Thread Ben Bolker
Bansal, Vikas kcl.ac.uk> writes: > I am using this- > > aggregate(x = file[,3:6], by = list(file[,2]), FUN = "sum") > Better, although still not reproducible (please *do* read the posting guide -- it is listed at the bottom of every R list post and is the *first* google hit for "posting guid

Re: [R] computing functions with Euler's number (e^n)

2011-07-14 Thread warmstron1
I solved this in two ways: 1. "**" was necessary to raise (-dummy + 1) to the power of B. "^" doesn't work here, for some reason. 2. I needed to use "as.complex" which greatly simplified my code and produces the correct response. (I had to revisit math that I had not used in many years.) W

Re: [R] Writing Complex Formulas

2011-07-14 Thread warmstron1
I resolved this issue. It appears that "^" won't work for this case, but "**" worked. I can't find any reference to this, but where "^" seems to be used to raise a value to a numerical function, "**" is used for a y raised to the power of x where x it a computation. -- View this message in co

Re: [R] Adding rows based on column value

2011-07-14 Thread Bansal, Vikas
Thanking you, Warm Regards Vikas Bansal Msc Bioinformatics Kings College London From: Bansal, Vikas Sent: Thursday, July 14, 2011 6:07 PM To: Bert Gunter Subject: RE: [R] Adding rows based on column value Yes sir.I am trying. I am using this- aggregate(x

Re: [R] R package: pbatR

2011-07-14 Thread Lisa
Thanks. I have installed PBAT on my computer. -- View this message in context: http://r.789695.n4.nabble.com/R-package-pbatR-tp3667844p3667907.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://st

Re: [R] Adding rows based on column value

2011-07-14 Thread Bansal, Vikas
I have checked it but did not get any results.Is there a way I can do it?I will be very thankful to you. Thanking you, Warm Regards Vikas Bansal Msc Bioinformatics Kings College London From: Bert Gunter [gunter.ber...@gene.com] Sent: Thursday, July 14, 201

Re: [R] rgl: reproduce final state of interactive plot?

2011-07-14 Thread Duncan Murdoch
On 14/07/2011 11:12 AM, sjaffe wrote: After interacting with a 3d plot (eg plot3d, persp3d), is there a way to capture the final settings of view angles, etc, so that the final plot could be easily reproduced? The plot functions themselves just return a vector of 'ids'. Yes, saving the result

Re: [R] question on formula and terms.formula()

2011-07-14 Thread Pang Du
Points taken and terms(formula) is used now. Thanks. -Original Message- From: William Dunlap [mailto:wdun...@tibco.com] Sent: Thursday, July 14, 2011 11:56 AM To: Pang Du; r-help@r-project.org Subject: RE: [R] question on formula and terms.formula() I think you should replace terms.fo

Re: [R] question on formula and terms.formula()

2011-07-14 Thread Pang Du
Thank you so much for your suggestion, Bill. The R program I try to modify needs match.call() for something else. But the problem does seem to be caused by this statement as you suggested. Following this clue, I find out that terms.formula(formula) does essentially what I want for "terms.formul

[R] rgl: reproduce final state of interactive plot?

2011-07-14 Thread sjaffe
After interacting with a 3d plot (eg plot3d, persp3d), is there a way to capture the final settings of view angles, etc, so that the final plot could be easily reproduced? The plot functions themselves just return a vector of 'ids'. -- View this message in context: http://r.789695.n4.nabble.com/r

Re: [R] question on formula and terms.formula()

2011-07-14 Thread William Dunlap
I think you should replace terms.formula(formula) by terms(formula) When terms() is given a formula object it will execute terms.formula but for other classes of inputs it will invoke the appropriate method. E.g., your formula may already be a terms object, in which case terms.formula(formula

Re: [R] Adding rows based on column value

2011-07-14 Thread Bert Gunter
?tapply (in base R) ?aggregate ?by (wrapper for tapply) ?ave (in base R -- based on tapply) Also package plyr (and several others, undoubtedly). Also google on "R summarize data by groups" or similar gets many relevant hits. -- Bert 2011/7/14 Bansal, Vikas : > Dear all, > > I have one prob

[R] Adding rows based on column value

2011-07-14 Thread Bansal, Vikas
Dear all, I have one problem and did not find any solution.(I have also attached the problem in text file because sometimes column spacing is not good in mail) I have a file(file.txt) attached with this mail.I am reading it using this code to make a data frame (file)- file=read.table("file.txt

Re: [R] calculating distance inland from coastline

2011-07-14 Thread Francois Rousseu
Hi Simon A combination of functions gDistance, gBuffer and gIntersects from package rgeos should do the job. Also, have a look at www.naturalearthdata.com. They have various shapefiles with coastlines and land polygons, though I don't know how the resolution compares with the worldHires datab

Re: [R] R package: pbatR

2011-07-14 Thread David Winsemius
I am guessing (from other evidence of lapses in attention to documentation) that you failed to pay attention when you encountered these sentences on the page you offered a link to: "For analysis, this package provides a frontend to the PBAT software" "For analysis, users must download PBAT

[R] R package: pbatR

2011-07-14 Thread Lisa
Dear All, Does anybody have experience with R package pbatR (http://cran.r-project.org/web/packages/pbatR/index.html)? I am trying to use it to analyze the family-based case-control data, but the package totally doesn’t work on my computer. I contacted the authors of the package, but I haven’t hea

[R] calculating distance inland from coastline

2011-07-14 Thread Simon Goodman
Hi All, Does anybody know of any existing functions that will calculate distance inland from a coastline? It's possible to test if a lon,lat location is land or sea using map.where(), but I need to add a buffer to this of say 2km, to allow for points that are just on the coast, and below the res

Re: [R] glm() scale parameters and predicted Values

2011-07-14 Thread Ben Bolker
Peter Maclean yahoo.com> writes: > > In glm() you can use the summary() function to recover > the shape parameter (the reciprocal of the > dispersion parameter). How do you recover the scale parameter? > Also, in the given example, how I estimate > and save the geometric mean of the predicted v

[R] plotting x y z data from an irregular grid

2011-07-14 Thread erika
Hi, I'm trying to plot some data (z) that is linked to lat&long coordinates (x&y). These coordinates are not however on a regular grid. I also have some shapefiles on which I would like to overlay the data. I can plot the shapefiles (country/city outlines) and overplot the data, but only using quil

Re: [R] Problem with x labels of barplot

2011-07-14 Thread Don
Thanks a lot! Great help! -- View this message in context: http://r.789695.n4.nabble.com/Problem-with-x-labels-of-barplot-tp3667337p3667498.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.

Re: [R] Sum weights of independent variables across models (AIC)

2011-07-14 Thread Michael Just
This is what I was looking for. When I initially read about model.avg I didn't recognize it also provided variable scores. Thank you kindly, Mike __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the postin

[R] SQldf with sqlite and H2

2011-07-14 Thread Mandans
SQldf with sqlite and H2 I have a large csv file (about 2GB) and wanted to import the file into R and do some filtering and analysis. Came across sqldf ( a great idea and product) and was trying to play around to see what would be the best method of doing this. csv file is comma delimited with

Re: [R] Add a density line to a cumulative histogram - second try

2011-07-14 Thread Thomas Stewart
This is a hack which uses the output of the density function. rrr <- cumsum(diff(cumsum(denspoints$y))*diff(denspoints$x)) lines(denspoints$x[-512],rrr) I don't believe this is the best solution, because it is not a direct estimate of the cumulative density function. I think there are methods fo

Re: [R] How to read 20 columns from the file

2011-07-14 Thread Jim Lemon
On 07/14/2011 10:35 PM, Jim Lemon wrote: On 07/13/2011 10:08 PM, Kishorenalluri wrote: Hi Jim, Saving is not a problem. I wanted to load/read the columns from the file followed by plotting the area plot using ggplot2. I am a basic user. I am trying to reproduce the plot similar to the example g

Re: [R] How to read 20 columns from the file

2011-07-14 Thread Jim Lemon
On 07/13/2011 10:08 PM, Kishorenalluri wrote: Hi Jim, Saving is not a problem. I wanted to load/read the columns from the file followed by plotting the area plot using ggplot2. I am a basic user. I am trying to reproduce the plot similar to the example given here. http://processtrends.c

Re: [R] t-test on a data-frame.

2011-07-14 Thread Sarah Goslee
Hi Student (since you have no other name), On Thu, Jul 14, 2011 at 6:42 AM, Economics Student wrote: > Dear R-helpers, > > In a data frame I have 100 securities,monthly closing value,from 1995 to > present,which I have to > > 1. Sampling with replacement,make 50 samples of 10 securities each,each

Re: [R] Problem with x labels of barplot

2011-07-14 Thread Duncan Murdoch
On 11-07-14 7:51 AM, Don wrote: Hello everyone, i am currently creating a barplot. This barplot takes a vector of ~200 datapoints. Each datapoint represents one bar. http://img96.imageshack.us/i/human1w.png/ (Ok as you see, it is not only one barplot, but a series of barplots). Now, these barpl

[R] Add a density line to a cumulative histogram - second try

2011-07-14 Thread Jochen1980
Hi list, this is my second try for first post on this list (I tried to post via email and nothing appeared in my email-inbox, so now I try to use the nabble-web-interface) - I hope that you will only have to read one post in your inbox! Okay, my question ... I was able to plot a histogram and add

[R] Problem with x labels of barplot

2011-07-14 Thread Don
Hello everyone, i am currently creating a barplot. This barplot takes a vector of ~200 datapoints. Each datapoint represents one bar. http://img96.imageshack.us/i/human1w.png/ (Ok as you see, it is not only one barplot, but a series of barplots). Now, these barplots represent a human chromosome.

[R] Var.calc in Matching

2011-07-14 Thread lglew
Hi, I already have matched samples, which were matched using different software. I need to calculate Abadie-Imbens standard errors, together with the average treatment effect. I know that the Matching package enables me to calculate these after a Matching procedure, but is there any way to do it o

[R] t-test on a data-frame.

2011-07-14 Thread Economics Student
Dear R-helpers, In a data frame I have 100 securities,monthly closing value,from 1995 to present,which I have to 1. Sampling with replacement,make 50 samples of 10 securities each,each sample hence will be a data frame with 10 columns. 2. With uniform probabilty,mark a month from 2000 onwards as

Re: [R] Scaling in SVM

2011-07-14 Thread Meffy
Thanks! For testing purposes this rescaling works! But unfortunately due to timing constraints I'm not able to do the rescaling of the data, so as I mentioned I have to work on with unscaled data. So I have to calculate $f(\vec x) = sum_{i \in sv} coefs_i \langle \vec x_i \cdot \vec x \rangle - \rh

Re: [R] R-help Digest, Vol 101, Issue 14

2011-07-14 Thread mihalicza . peter
Július 7-től 14-ig irodán kívül vagyok, és az emailjeimet nem érem el. Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu). Üdvözlettel, Mihalicza Péter I will be out of the office from 7 July till 14 July with no access to my emails. In urgent cases please contact Ms. Ed

Re: [R] Adding vertical space before and after Sweave chunk

2011-07-14 Thread Duncan Murdoch
On 11-07-14 3:23 AM, Mark Heckmann wrote: Thanks Duncan, the problem now is that, the space between R code and R output is also increased. I would like to avoid this, i.e. vertical space R code NO SPACE R results vertical space Don't modify \topsep then, just put the spacing directly into the

[R] Gui editor / viewer for large data

2011-07-14 Thread Andreas Borg
Dear all, I am searching for a possibility to view large data sets (e.g. stored in ffdf objects) in a GUI window in a memory-efficient way. So far I looked at gtkDfEdit (package RGtk2Extras) and gdf (package gWidgets). Both operate (as far as I can see) on data frames stored in memory. gtkDfEd

Re: [R] R in Batch mode

2011-07-14 Thread Bos, Roger
Duncan's suggestion is probably the way to go, but I will just point out that R does have a facility to perform a task when an error occurs. I have my code set up to send me an email when my batch code fails. (email() is a function I wrote that executes sql command to send email via dbmail.) .Err

[R] Re: Sum weights of independent variables across models (AIC)

2011-07-14 Thread Kamil Bartoń
?model.avg Look at "relative importance". > Message: 102 > Date: Wed, 13 Jul 2011 18:01:14 -0500 > From: Michael Just > To: r-help > Subject: [R] Sum weights of independent variables across models (AIC) > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hello, > I'd lik

Re: [R] How to translate string to variable inside a command in an easy way in R

2011-07-14 Thread Ivan Calandra
Hi! What about as.forumla()? Like this: form <- as.formula(paste("num", y, "~MemberID", sep="")) agg<-aggregate(form, right.a, sum) Would it work as you expect to? HTH, Ivan Le 7/13/2011 19:30, Daniel Nordlund a écrit : -Original Message- From: r-help-boun...@r-project.org [mailto:r-

Re: [R] Adding vertical space before and after Sweave chunk

2011-07-14 Thread Mark Heckmann
Thanks Duncan, the problem now is that, the space between R code and R output is also increased. I would like to avoid this, i.e. vertical space R code NO SPACE R results vertical space TIA, Mark Am 14.07.2011 um 02:13 schrieb Duncan Murdoch: > On 13/07/2011 7:14 PM, Mark Heckmann wrote: >> I

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