[R] predict() and heteroskedasticity-robust standard errors

Hello there, I have a linear regression model for which I estimated heteroskedasticity-robust (Huber-White) standard errors using the coeftest function in the lmtest-package. Now I would like to inspect the predicted values of the dependent variable for particular groups and include a confidence

[R] [R-pkgs] roxygen2

Hadley Wickham refactored roxygen, making it more maintainable and robust; the changes are so significant that we decided to nominate it roxygen2: http://cran.r-project.org/web/packages/roxygen2/index.html Some highlights: * it's faster; * usage has been improved (the @usage tag should be

[R] [R-pkgs] rasterVis 0.10-3

Dear useRs, I'd like to announce the release of version 0.10-3 of rasterVis. This package provides a set of methods for enhanced visualization and interaction with the Raster* objects from the raster package. You will find some examples at: http://rastervis.r-forge.r-project.org/. Best, Oscar.

[R] [R-pkgs] pxR 0.20

Dear useRs, I'd like to announce the release of pxR, a package to use the PC-Axis file format in R. PC-Axis is a software family consisting of a number of programs for the Windows and Internet environment used to present statistical information. It is used by national and international institutio

Re: [R] For is.numeric condition in user input

Yes, thats right, readline will give you character and now you need to convert it to numeric to make it work. Thanks SmartG On 25 July 2011 08:51, Ista Zahn wrote: > readline always returns a character. See ?readline for details. > > Best, > Ista > > On Sun, Jul 24, 2011 at 10:59 PM, Bansal, Vi

[R] scripting qqplot and qqnorm

Hi all, I am an R newbie, and I have a question about scripting. I have the following lines which I want to put int\ o a script which I can call from the shell of a Mac/Linux machine : myrns <- read.csv(file="/Users/vihan/test.csv",sep="",header=FALSE) qqnorm(myrns) qqline(myrns) This works fine

Re: [R] Problem with random number simulation

Hi, I was just hoping someone could try running the program to see if they get any output. This is independent research. I just need to run this simulation to see how a computer could be manipulated given certain conditions in the Von Neumann game. Currently, my code is not giving any errors, b

Re: [R] Code is not doing anything

AriGold wrote: > > Hi this is my first post. I am trying to run a simulation for a computer > playing Von Neumann poker and adjusting it's expectation of an opponent's > behavior according to how the opponent plays. > > ... > Debugging length programs is not what this list is supposed to do,

Re: [R] Extracting components from a 'boot' class output in R

Sarath pointed out (privately) that the standard error is not actually stored as part of the bootstrap object. Instead, it is calculated on the fly when you print the bootstrap object; this is done by boot:::print.boot Similarly for bias. (The 'boot:::' is necessary because "'print.boot' is not

Re: [R] For is.numeric condition in user input

readline always returns a character. See ?readline for details. Best, Ista On Sun, Jul 24, 2011 at 10:59 PM, Bansal, Vikas wrote: > Dear all, > > I am using the following function so that user can input a numerical value. > > readnumber<- function() >  { > for(j in 1:10){ >  value=readline("ente

Re: [R] Problem with random number simulation

> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of AriGold > Sent: Sunday, July 24, 2011 5:11 PM > To: r-help@r-project.org > Subject: [R] Problem with random number simulation > > Hi this is my first post. I am trying to run a s

[R] For is.numeric condition in user input

Dear all, I am using the following function so that user can input a numerical value. readnumber<- function() { for(j in 1:10){ value=readline("enter the threshold for number of reads: ") if(is.numeric(value)==T) {return(value) break} else print("wrong number Please enter numerical value ")}

Re: [R] Plotting compound functions--help with defining x-axis as f(x)

Thanks for your assistance, this worked perfectly, and sorry for posting in html! I shall check it's plain text for future postings.. Would it be possible for you to explain why this works? I'm unsure as to why redefining t works, when t is perfectly defined within the script previously. Thank you

[R] Replying on Nabble

Sorry for the non-R question, but how do I reply through the Nabble interface and have my reply emailed to the person I'm replying to (in case they don't use Nabble), with cc to the mailing list? If I choose the option to reply to the person by email, I don't see an option to cc to the mailing lis

Re: [R] a question on plotting nonlinear regression

Mark Seeto wrote: > > > garciap wrote: >> >> Hi to all the people, >> >> I'm having a trouble when trying to plot a quadratic function. I have the >> code: >> >> regression<-nls(Survival~beta1+beta2*PI+beta3*PI^2, data=cubs, >> start=list(beta1 = 1, beta2 = 1, beta3 = 1)) >> plot(Survival~PI,

Re: [R] GLM different results with the same factors

On Jul 24, 2011 Gaiarrido wrote: > Why the order of the factors give different results? I suppose it's > because the order of the > factors, i've just changed "lcc" from the first position to the last in > the model, and the significance > change completely > ...snip < > Ijow can i know what's c

[R] repeated execution of svm(e1071) gives different results, if probability = TRUE is set

Hello, Connoisseurs! Please explain to novices, why svm model gives different results in the loop with the same data? As a result, I can not find the best gamma and cost parameters. Also tune.svm yields results that can not be repeated. How can I avoid this? My sessionInfo: R version 2.11.1 (2010

Re: [R] Histogram of a dataframe subset failing

Thanks! It was late, so this didn't occur to me, but I tried summary() and all values were NA. The subset had resulted in a dataframe with 0 rows somehow, but now that's fixed. -- View this message in context: http://r.789695.n4.nabble.com/Histogram-of-a-dataframe-subset-failing-tp3689884p3690504

[R] Problem with random number simulation

Hi this is my first post. I am trying to run a simulation for a computer playing Von Neumann poker and adjusting it's expectation of an opponent's behavior according to how the opponent plays. This program involves random generation of "hands" and shifting of parameters. However, when I run the

[R] GLM different results with the same factors

I've read something about this problem, but I don't know how can i avoid this problem. Why the order of the factors give different results? I suppose it's because the order of the factors, i've just changed "lcc" from the first position to the last in the model, and the significance change complete

[R] How to merge a matrix and a dataframe with different types of columns

Hi, I hope someone can help here. I have been scratching my head for many hours, trying to find out how to merge two datasets that were created by different means. The initial miniMarket contains dates without discontinuities (weekends). This matrix was created using seq and has a character n

Re: [R] a question on plotting nonlinear regression

garciap wrote: > > Hi to all the people, > > I'm having a trouble when trying to plot a quadratic function. I have the > code: > > regression<-nls(Survival~beta1+beta2*PI+beta3*PI^2, data=cubs, > start=list(beta1 = 1, beta2 = 1, beta3 = 1)) > plot(Survival~PI,data=cubs, ylab="Survival", xlab="P

[R] a question on plotting nonlinear regression

Hi to all the people, I'm having a trouble when trying to plot a quadratic function. I have the code: regression<-nls(Survival~beta1+beta2*PI+beta3*PI^2, data=cubs, start=list(beta1 = 1, beta2 = 1, beta3 = 1)) plot(Survival~PI,data=cubs, ylab="Survival", xlab="PI") lines(cubs$PI, fitted(regressio

[R] How to merge a matrix and a dataframe with different types of columns

Hi, I hope someone can help here. I have been scratching my head for many hours, trying to find out how to merge two datasets that were created by different means. The initial miniMarket contains dates without discontinuities (weekends). This matrix was created using seq and has a character n

Re: [R] Deleting rows and store the deleted rows in new data frame

Or just subset(df, V5 >= 10) See ?subset. HTH, Jorge On Sun, Jul 24, 2011 at 10:01 PM, Bansal, Vikas <> wrote: > Dear Jeff, > > Thanks a lot for your reply. > I was just curious about this thing about grep that it can perform this > kind of thing or not. Otherwise with numerical comparison I

Re: [R] Deleting rows and store the deleted rows in new data frame

Dear Jeff, Thanks a lot for your reply. I was just curious about this thing about grep that it can perform this kind of thing or not. Otherwise with numerical comparison I know it is very easy to do.Like- df <- df[df$V5 >= 10, ] Thanks a lot for your help. Thanking you, Warm Regards Vikas Ban

Re: [R] Binding multiple data frames into single data frame

Hi Madana, No example data, so untested, but I think this will do what you want: do.call("rbind", DF) Cheers, Josh On Sun, Jul 24, 2011 at 5:38 PM, Madana_Babu wrote: > Hi all, > > I have multiple data frames created with equal number of columns in each > data frame by using mclapply() on mul

[R] Binding multiple data frames into single data frame

Hi all, I have multiple data frames created with equal number of columns in each data frame by using mclapply() on multicore processor. The data frames are like DF[[1]], DF[[2]], ... DF[[150]]. Now i want to bind (Similar like rbind()) all these data frames and create one single data frame called

Re: [R] barplot colors

Hi Jim, In most cases, I would highly recommend an alternative to a stacked bar plot (only 4 numbers are communicated, but an entire plot is filled). Depending on the data and your goals, simple points or lines offer easy alternatives. I have also been able to get a lot of mileage out of facetti

Re: [R] Deleting rows and store the deleted rows in new data frame

You can, but you would have to convert them to character first. It would be more sensible to use vector numeric comparisons. I strongly recommend that you go read "An Introduction to R", since you are asking questions that are explained there.

[R] barplot colors

Hi, In barplot(height, col = ...), the col = vector recycles so that the same colors are used for each bar. I would like to use different colors in different bars (corresponding to another piece of information, here, the region of the country being represented). For example, x = matrix(c(5

Re: [R] Deleting rows and store the deleted rows in new data frame

Thanks for your reply. Can I use grep with numbers also? 5961 T 17 0 9 5962 T 17 0 9 5963 A 17 0 9 5964 G 13 0 10 5965 G 13 0 9 5966 G 13 0 13 5967 T 13 0 8 5968 T 13 0 5 5969 A 13 0 13 5970 G 13 0 13 5971 G 13 0 4 5972 G 13 0

Re: [R] Deleting rows and store the deleted rows in new data frame

There's no need to use sapply or loops with grep -- it's already vectorized. So you can find the rows you're interested in with wh = grep('^[.,]+$',df[,9]) store them with sf = df[wh,] and delete them with df = df[-wh,] - Phil Spector

Re: [R] Deleting rows and store the deleted rows in new data frame

Hi Vikas, The following works (I'm not very good with sapply, but the for loop is ok if your data set is not huge). > df <- read.table("test.txt",stringsAsFactors=FALSE) > df V1V2 V3 V4 V5 V6 V7 V8 V9 1 10 135349467 g G 4 0 0 5 ,,,., 2 10 135349468 t T 2 0 0 5 ,,c.,

Re: [R] Rcompression on MAC - where is it?

Hi. On Tue, Jul 12, 2011 at 5:40 PM, Eduardo M. A. M. Mendes wrote: > Hello > > I need to run an r-file that works on Windows on MAC.   The first lines of > the file are: > > library(R.matlab) > library(Rcompression) Are you sure you need Rcompression? If this is about reading (Matlab) MAT fil

[R] Deleting rows and store the deleted rows in new data frame

Dear all, I am using grep but I did not understand the problem as I am doing something wrong.Please help me. I am using this code- sf=data.frame(sapply(df[],function(x) grep('\\.&\\,', df[,9]))) the thing is i have a data frame(df) like this- 10 135349467 g G 4 0

Re: [R] Variable scope in functions - best practices

On Mon, Jul 25, 2011 at 4:14 AM, Noah Silverman wrote: > Hi, > > I'm working on coding some more complex things in R and have need to break > much of the logic into functions. > > I have several "global" variables that I want to change with a given > function.  (The variable has a different valu

Re: [R] inline/Rcpp: Problem with space in path under Windows

On Sun, 24 Jul 2011, Richard M. Heiberger wrote: All Windows files have an equivalent 8.3 name without spaces. It may differ on different machines and countries. You find them by typing dir/x in the cmd window. Or by shortPathName() in R. But that does not help if R itself is generating th

Re: [R] split data frame temporary and work with only part of it?

My recommendation would be to not "subset out" the data, because you are introducing a potential source of error when binding the new data back together with the old data. Preferably, I would work on selecting subsets of the dataset using indices (as suggested in the previous post) and just do the

Re: [R] inline/Rcpp: Problem with space in path under Windows

All Windows files have an equivalent 8.3 name without spaces. It may differ on different machines and countries. You find them by typing dir/x in the cmd window. In the US English, the equivalences usually are c:\>cd c:/ c:\>dir /x Pr* Volume in drive C is Windows7_OS Volume Serial Number is

Re: [R] split data frame temporary and work with only part of it?

On 2011-07-24 10:07, ivo welch wrote: dear R wizards: I have a large data frame, a million rows, 40 columns. In this data frame, there are some (about 100,000) rows which I want to recompute (update), while I want to leave others just as is. this is based on a condition that I need to compute,

Re: [R] R on Multicore for Linux

Hi Lei, Thanks for your solution. It worked. Now I have another query. After creating multiple DF[[i]]'s how do I aggregate them into one data frame say DF (I want to bind all the data frames into one data frame). I have more than 1000 DF[[i]]'s how can I bind them into one DF by recursively? T

Re: [R] inline/Rcpp: Problem with space in path under Windows

Hi Dieter, On 24 July 2011 at 07:12, Dieter Menne wrote: | Hi, Dirk, | | Dirk Eddelbuettel wrote: | > | > | > Thanks for your interest in Rcpp. We generally prefer questions about | > Rcpp / RInside / ... on the rcpp-devel list. | > | I know that list, but I was not sure if Path-questions ar

[R] split data frame temporary and work with only part of it?

dear R wizards: I have a large data frame, a million rows, 40 columns. In this data frame, there are some (about 100,000) rows which I want to recompute (update), while I want to leave others just as is. this is based on a condition that I need to compute, based on what is in a few of the column

Re: [R] Variable scope in functions - best practices

Hi Noah, you could assign your "global variables" into an environment. Then make it the environment of your function, and use the `<<-` operator (or 'assign'). An example: > myData <- new.env() > myData$i <- 0 > iPlusOne <- function() i <<- i+1 > environment(iPlusOne) <- myData > ls() [1] "iPlu

[R] Variable scope in functions - best practices

Hi, I'm working on coding some more complex things in R and have need to break much of the logic into functions. I have several "global" variables that I want to change with a given function. (The variable has a different value after the function is called.) In other languages like C, this is

Re: [R] Plotting compound functions--help with defining x-axis as f(x)

On 23.07.2011 00:50, Aimee Jones wrote: Hi all, I'm having trouble locating a script that will allow to me to create graphs that show compound functions as a function of the simple function, rather than just x (or time as it is in my case). Currently I have the following functions defined in m

Re: [R] wrong name of input file and goto like function

Please do read at least some basic R documentation before posting here! In addition, please read the help pages: help("file.exists") help("stop") vs. help("print") help("break") which is not a function On 24.07.2011 17:35, Bansal, Vikas wrote: Thanks for you reply.I have seen it and I got

Re: [R] An infinite recursion error please explain!

On 23.07.2011 04:29, mousy0815 wrote: Probability<- function(N, f, w, b, y, t, q) { #N is the number of lymph nodes #f is the fraction of Dendritic cells (in the correct node) that have the antigen #w is time in terms of hours #b is the starting position (somewh

Re: [R] wrong name of input file and goto like function

Thanks for you reply.I have seen it and I got that we can use this goto function in the form of double loop. like- for(j in 1:10) { df=read.table(define(),fill=T,sep="\t",colClasses = "character") if() { print("wrong name of the file Please enter again ")} else{ break() } } but i did not find w

Re: [R] Variable scope in functions - best practices

Noah Silverman wrote: > > Hi, > > I'm working on coding some more complex things in R and have need to break > much of the logic into functions. > > I have several "global" variables that I want to change with a given > function. (The variable has a different value after the function is > call

Re: [R] wrong name of input file and goto like function

These are elementary programming constructs. I would suggest you take a look at an online basic (as in elementary, not the Basic language) programming tutorial to see how to do this sort of thing. R does it like many other languages (with ?for, ?while, ?if, etc.). -- Bert On Sun, Jul 24, 2011 at

Re: [R] applying a loop to multiple dataframes

On 22.07.2011 22:42, Sean Bignami wrote: Hello again R-folks, I'm trying to apply a loop to multiple data frames and then organize the data in a manageable form. I have the code for my loop figured out (thanks to help from this list)...it runs up to 2000 iterations of a "while" loop until it

Re: [R] R versions and PostScript files

On 22.07.2011 19:46, pilchat wrote: Thank you David, the useRaster=T does the trick! But, unfortunately, it doesn't work for persp. Is there any way to avoid the sRGB colors at the beginning of the R session? I tried to edit my Rprofile: .First<- function() { a<-system("ls /dati/softwa

Re: [R] inline/Rcpp: Problem with space in path under Windows

Hi, Dirk, Dirk Eddelbuettel wrote: > > > Thanks for your interest in Rcpp. We generally prefer questions about > Rcpp / RInside / ... on the rcpp-devel list. > I know that list, but I was not sure if Path-questions are part of "devel". Dirk Eddelbuettel wrote: > > ... presumably from instal

[R] wrong name of input file and goto like function

Dear all, I have a question and need your help please. I have the following code which is asking user to enter the name of their file. define<- function() { readline("enter the name of your file: ") } df=read.table(define(),fill=T,sep="\t",colClasses = "character") Now I want if user wil

[R] setting distance matrix and clustering methods in heatmap.2

heatmap.2 defaults to dist for calculating the distance matrix and hclust for clustering. Does anyone now how I can set dist to use the euclidean method and hclust to use the centroid method? I provided a compilable sample code bellow. I tried: distfun = dist(method = "euclidean"), but that doesn't

Re: [R] squared "pie chart" - is there such a thing?

I don't usually use stacked bar charts since it is difficult to compare lengths that don't have a common baseline. Naomi On 7/23/2011 11:14 PM, Thomas Levine wrote: > How about just a stacked bar plot? > > barplot(matrix(c(3,5,3),3,1),horiz=T,beside=F) > > Tom > > On Fri, Jul 22, 2011 at 7:14 AM

Re: [R] analizing .txt file with R or an other program

thanks, so I will check out what I can do with R and the ?grep command -- View this message in context: http://r.789695.n4.nabble.com/analizing-txt-file-with-R-or-an-other-program-tp3689025p3690085.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] averaging rows based on string¿?

Hi Dennis, That works brilliantly! Thanks a lot! All the best, A -- View this message in context: http://r.789695.n4.nabble.com/averaging-rows-based-on-string-tp3687689p3690145.html Sent from the R help mailing list archive at Nabble.com. __ R-help

Re: [R] glmnet with binary logistic regression

On 07/23/2011 11:43 AM, fongchun wrote: I was also thinking of a bootstrapping approach where I would actually run cv.glmnet say 100 times and then take the mean/median lambda across all the cv.glmnet runs. This way I generate a confidence interval for my optimal lambda I woud use in the end.

Re: [R] Cox model approximaions (was "comparing SAS and R survival....)

On Fri, Jul 22, 2011 at 2:04 PM, Terry Therneau wrote: >  For time scale that are truly discrete Cox proposed the "exact partial > likelihood". Or "the method of partial likelihood" applied to the discrete logistic model, > I call that the "exact" method and SAS calls it the > "discrete" method.

Re: [R] inline/Rcpp: Problem with space in path under Windows

Hi Dieter, Thanks for your interest in Rcpp. We generally prefer questions about Rcpp / RInside / ... on the rcpp-devel list. On 24 July 2011 at 01:09, Dieter Menne wrote: | I am trying to run inline/Rcpp under Windows 64. The RTools are installed on | a spaceless path D:\rtools. | | Inlining

Re: [R] glmnet with binary logistic regression

10 fold cv has high variation compared to other methods. Use repeated cv or the bootstrap instead (both of which can be used with glmnet by way of the train() function on the caret package). Max On Jul 23, 2011, at 11:43 AM, fongchun wrote: > Hi Patrick, > > Thanks for the reply. I am ref

[R] 2 x 3 table

I am trying to find the likelihood ratio for a 2 x3 table (actually SNP data). I do not want the log likelihood. Is this the correct R code for the following table? Row totals are fixed at 100 each (case control situation). aa Aa AA Total 10 2070 100 20 4050 100 30

[R] Variable scope in functions - best practices

Hi, I'm working on coding some more complex things in R and have need to break much of the logic into functions. I have several "global" variables that I want to change with a given function. (The variable has a different value after the function is called.) In other languages like C, this is

Re: [R] Create a map

On Sat, Jul 23, 2011 at 10:04 AM, Amy Ruiz wrote: >  Hello: > I'm using the library of maps, however, I need to use a map of Puerto Rico, > but > apparently does not exist. I wanted to know if there is any way that I > can create > that map? The 'maps' package (not 'library') is a bit old and g

Re: [R] Fit elipse to xy scatter

DrCJones wrote: > > hat I would like to do is fit an elipse to two lines of identity (at right > angles to each other), as indicated in the following figure: > http://imageshack.us/photo/my-images/30/poincareplotwip.png/ > > http://r-project.markmail.org/thread/kpg3ea665y2ud6cz or, for a robu

Re: [R] Histogram of a dataframe subset failing

DimmestLemming wrote: > > hist(soloData$deaths) > > I get the error, " invalid number of 'breaks' ". > Try str(soloData$deaths) or head(soloData$deaths) or summary(soloData$Death) There may be something wrong with you data. Dieter -- View this message in context: http://r.789695.n4.

[R] Histogram of a dataframe subset failing

Like most help forum users, I'm very new to R. I've been having this problem: I started with a dataframe called fullData. With the subset command, I split it into two separate dataframes, soloData and teamData. The hist() function works when I use... hist( subset(fullData, fullData$playlist_id==

[R] inline/Rcpp: Problem with space in path under Windows

I am trying to run inline/Rcpp under Windows 64. The RTools are installed on a spaceless path D:\rtools. Inlining pure c-code works perfectly. When I try the sample code for cpp in the cxx Documentation, I get: x86_64-w64-mingw32-g++.exe: C:/Program: No such file or directory The path to the com