Re: [R] Transform a list of multiple to a data.frame which I want

Hi Yao, Messy, but this is the closest I can get: yhlist<-list(K=matrix(0,ncol=2,nrow=0), GSEGTCSCSSK=matrix(c(6,8),nrow=2,ncol=2), GFSTTCPAHVDDLTPEQVLDGDVNELMDVVLHHVPEAK=matrix(6,ncol=2,nrow=1), LVECIGQELIFLLPNK=matrix(6,ncol=2,nrow=1), NFK=matrix(0,ncol=2,nrow=0), HR=matrix(0,ncol=2,nrow=0)

Re: [R] Boundaries and deldir

On 01/02/2015 10:26 PM, p_connolly wrote: > Just what is meant by dummy points as referred to by the help for the > deldir() function? I understood they indicated the boundary beyond > which triangulation would cease. You should say what package you're asking about. deldir() is not a base R func

[R] Cross compiling R

Hi! I am cross compiling R-3.1.2 for Galileo board with the source code. I am able to configure R-3.1.2 without any errors with the following command : ./configure --host=i586-poky-linux-uclibc CC=i586-poky-linux-uclibc-gcc CXX=i586-poky-linux-uclibc-g++ F77=i586-poky-linux-uclibc-gfortra

Re: [R] the less-than-minus gotcha

"Moral of story, computers do what you tell them, not what you meant." Not only a fortune, but profound wisdom. Jim On Mon, Feb 2, 2015 at 12:38 PM, Kevin E. Thorpe wrote: > Using = has it's problems too. > > For example, > > print(fit <- lm(...)) > > Assigns the result of the lm call to fit a

Re: [R] save program results and graphs to one file

Hi Ragia, There are also the R2HTML and prettyR (see htmlize) packages that will output an R session in HTML format. Jim On Mon, Feb 2, 2015 at 10:51 AM, Henrik Bengtsson wrote: > If you're happy with outputting to a multi-page PDF, then you can just > set the default graphics device to pdf(),

Re: [R] save program results and graphs to one file

With a little effort you could implement Rstudio and try RMD (R Markdown) it is very proficient, look at https://support.rstudio.com/hc/en-us/articles/200552086-Using-R-Markdown Il 01/feb/2015 21:07 "Ragia Ibrahim" ha scritto: > > Dear group, > > I have many plots and numeric results in my R prog

Re: [R] Cross compiling R

Cross-building is not supported (building R is more than just compiling and needs a working R executable). And (see the posting guide) this was not the right list for such a question. On 02/02/2015 07:16, Vivek Rangi wrote: Hi! I am cross compiling R-3.1.2 for Galileo board with the so

Re: [R] Boundaries and deldir

On 02/02/15 16:26, p_connolly wrote: Just what is meant by dummy points as referred to by the help for the deldir() function? I understood they indicated the boundary beyond which triangulation would cease. I thought I would need the x/y elements (as described in the help file at the end of t

Re: [R] the less-than-minus gotcha

On 02/02/15 14:26, Steve Taylor wrote: All the more reason to use = instead of <- Couldn't agree less, Steve. The "<-" should be used for assignment. The "=" sign should be reserved for handling function arguments in the "name=value" form. Doing anything else invites confusion and occasio

Re: [R] aov and Error function

> > aovsubj <- aov(value~group+time+Error(subject),data=dataRMANOVA) > > and > > aovsubjgroup <- aov(value~group+time+Error(subject/group),data=dataRMANOVA) > > > Since no-one else seems to have answered you let me point out that your first > formulation treats subject 1 in the "int" group as bein

Re: [R] the less-than-minus gotcha

I'd rather say that it is good reason to use spaces around operators. Makes the code easier to read too. (_Possible_ to read for some.) We've probably all done it. I did, once upon a time in S-Plus, on the results of a multi-day simulation study: > <>$statistic [1] -1.28 > sim <- sapply(1:1

Re: [R] aov and Error function

On 02 Feb 2015, at 13:09 , S Ellison wrote: > >>> aovsubj <- aov(value~group+time+Error(subject),data=dataRMANOVA) >>> and >>> aovsubjgroup <- aov(value~group+time+Error(subject/group),data=dataRMANOVA) >>> >> Since no-one else seems to have answered you let me point out that your first >> for

Re: [R] the less-than-minus gotcha

On 02-Feb-2015 11:58:10 Rolf Turner wrote: > > On 02/02/15 14:26, Steve Taylor wrote: > >> All the more reason to use = instead of <- > > Couldn't agree less, Steve. The "<-" should be used for assignment. The > "=" sign should be reserved for handling function arguments in the > "name=value"

Re: [R] the less-than-minus gotcha

Rolf Turner is right on the money about not mixing-up '=' and '<-' Though this 'gotcha' will always a threat while '<-' is the assignment operator. The old Algol60 syntax of ':=' was less error-prone, but I guess '<-' is too firmly bedded-in to ever change. Meanwhile, spaces around the assi

[R] Error: OutOfMemoryError (Java): GC overhead limit exceeded

Hello all, When I met this following error message: Error: OutOfMemoryError (Java): GC overhead limit exceeded I usually use the following options to overcome the memory limit: options(java.parameters = "-Xmx1024m") # to reduce the error message "Error: OutOfMemoryError (Java): GC overhead lim

Re: [R] naming rows/columns in 'array of matrices'

In your example, P is a three dimensional array. You can assign names to the three dimensions using the dimnames() function. For example, this command assigns names to the first two dimensions, but leaves the third dimension without names. dimnames(P) <- list(c("live", "dead"), c("live", "dead")

Re: [R] Error: OutOfMemoryError (Java): GC overhead limit exceeded

The memory issue is in Java, not R. You can either be more parsimonious in your use of Java memory (we have no idea what you are doing with it here, so how you do that is up to you), or you can allocate more memory to Java (you may be able to guess how to do that, or read the Java documentation

Re: [R] Error: OutOfMemoryError (Java): GC overhead limit exceeded

On the off-chance, are you using XLConnect or xlsx packages that are using Java to access the spreadsheets? If it is XLConnect, are you access the '.xlsx' style workbooks? If so, can you try using '.xls' workbooks? This is a problem that I have had; the '.xlsx' workbooks take a lot more resource

Re: [R] naming rows/columns in 'array of matrices'

> > I'd also be interested in why the 'direct, brute force' approach > > (above) doesn't work, Your example was a 3-dimensional array, so > rownames(P) <- colnames(P) <- c(live', 'dead') would have worked; rownames() and colnames() work on dimnames[1] and dimnames[2]. But rownames(P[,,1]) cou

Re: [R] the less-than-minus gotcha

> All the more reason to use = instead of <- Definitely not! (As you were told, there are other drawbacks). R does not have to look like C, it *is* different in many ways. If you use a decent IDE for R, you get spaces around ' <- ' for free: Both in ESS and in Rstudio, you can use "[Alt] -"

[R] (Cross-)validating GLM including factors

Dear list, I would like to validate various GLMs, all of them containing (among others) several factors as predictors. I thought about using cv.glm from the boot package, but necessarily got the error "factor xy has new level z". Is there any function to easily cross validate LMs or GLMs contai

Re: [R] (Cross-)validating GLM including factors

This is not an r-help issue. Post on a statistics list like stats.stackexchange.com instead for a variety of opinions.* Cheers, Bert *Which will probably be useless given your paucity of data. But that's just *my* useless opinion. Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "

Re: [R] Transform a list of multiple to a data.frame which I want

Does the following work for you. The only trick is working around the fact that matrix subscripting does not allow out-of-bounds subscripts but vector subscripting does. We do the subscripting in two steps, relying on the drop=TRUE default in the matrix subscripting operator that converts the sin

[R] Multiple Line Widths denextend

Dear All We are using the dendextend package to modify the plot output from a pvclust clustering The model is created with result <- pvclust(chord.1, method.dist="euclidian", method.hclust="average",nboot=10) The plot is then formatted as following dend <- as.dendrogram(result) dend

[R] FFT Normalization Documentation

Hello everyone, the docpage for the fft function states: “Description: Performs the Fast Fourier Transform of an array.” and “Arguments – inverse: if ‘TRUE’, the unnormalized inverse transform is computed (the inverse has a ‘+’ in the exponent of e, but here, we do _not_ divide by ‘1/length(x)’

Re: [R] help plotting my data

Hi, I hope the following works for you. The plot is: Rplot.png > data <- read.table("rHelp_20150202.txt",header=TRUE) > order.data <- order(data$counts,decreasing=TRUE) > order.data [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

Re: [R] Dropping time series observations

Hi, I have a data frame named data and with the statement data[5:length(data[[1]]),] I can get row 5 to the end of the data. > data role counts 1 Agent220 2 Theme169 3 Patient 67 4 Location 41 5 Destination 32 6

[R] using png and identify commands

Hi R users I want to save a plot after using the command identify. I use identify to place labels manually near the points in order to avoid overlapping lines and numbers. x<-c(1,2,3,4,5,6) y<-c(20,30,15,7,25,40) plot(x,y,type="b",ylim=c(0,45)) identify(x,y,labels=y) But when I add png(filenam

Re: [R] Error: OutOfMemoryError (Java): GC overhead limit exceeded

Hello Jim, I already use “.xls” for the loading, but still have the memory issue…. Thanks, Rebecca From: jim holtman [mailto:jholt...@gmail.com] Sent: Monday, February 02, 2015 10:21 AM To: Jeff Newmiller Cc: Yuan, Rebecca; R help (r-help@r-project.org) Subject: Re: [R] Error: OutOfMemoryError

Re: [R] Error: OutOfMemoryError (Java): GC overhead limit exceeded

How big are the worksheets that you are reading in? Do you have multiple ones open at the same time? Have to tried to use 'xlcFreeMemory' to see if this helps? How much RAM to you have on your system? Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what

[R] rJava Scientific Linux 6.5 - Can not install

Hello all, I am having a problem with installing rJava on SL 6.5. I am having compile errors when I try to from CRAN using install.packages("XLConnect", repos=" http://cran.rstudio.com/";). I can provide anything necessary, but I am unsure what to provide. Thank you for your help in advance. outp

Re: [R] How to enable https for R 3.1.2 on windows 8.1

Cc'd back to the list... I am a bad bet for one-on-one help. Showing that your libcurl claims to support HTTPS is progress. I think that at this point you should read the last sentence in the curl FAQ 3.21, which I found by searching for "protocol https not supported or disabled in libcurl". ht

Re: [R] rJava Scientific Linux 6.5 - Can not install

On Mon, Feb 2, 2015 at 1:39 PM, stephen sefick wrote: > Hello all, > > I am having a problem with installing rJava on SL 6.5. I am having compile > errors when I try to from CRAN using install.packages("XLConnect", repos=" > http://cran.rstudio.com/";). I can provide anything necessary, but I am >

Re: [R] rJava Scientific Linux 6.5 - Can not install

Don't know anything about SL but have you installed a Java run time independent of R? --- Jeff NewmillerThe . . Go Live... DCN:Basics: ##.#. ##.#. Live Go...

Re: [R] using png and identify commands

replacing png(...) and dev.off() with dev2bitmap('test.png') seems to work. On Mon, 2015-02-02 at 15:56 -0200, Antonio Silva wrote: > Hi R users > > I want to save a plot after using the command identify. > > I use identify to place labels manually near the points in order to avoid > overlapping

[R] odbcConnectAccess2007 errors with Access databases on new PC

Hello, I've connected R to Microsoft Access databases for years now using odbcConnectAccess2007. I recently got a new computer and R is absolutely refusing to connect to any Access database with the following error message: Warning messages: 1: In odbcDriverConnect(con, ...) : [RODBC] ERROR: st

[R] A good way to debug a c++ library embedded to an R code

Dear all, I am using R CMD SHLIB to compile a c++ code into a library (.so) and dyn.load to load this library into a R code. I am facing some problems in the c++ part that I can not figure out how to solve. Do you recomend any good way to debug this R + C++ program? If I was programming only in C+

Re: [R] odbcConnectAccess2007 errors with Access databases on new PC

On Feb 2, 2015, at 12:00 PM, utz.ryan wrote: > > Hello, > > I've connected R to Microsoft Access databases for years now > using odbcConnectAccess2007. I recently got a new computer and R is > absolutely refusing to connect to any Access database with the following > error message: > > Warning

Re: [R] using png and identify commands

On Mon, Feb 2, 2015 at 9:56 AM, Antonio Silva wrote: > Hi R users > > I want to save a plot after using the command identify. > > I use identify to place labels manually near the points in order to avoid > overlapping lines and numbers. > > x<-c(1,2,3,4,5,6) > y<-c(20,30,15,7,25,40) > plot(x,y,typ

Re: [R] How to enable https for R 3.1.2 on windows 8.1

On Feb 2, 2015, at 10:50 AM, Jeff Newmiller wrote: > Cc'd back to the list... I am a bad bet for one-on-one help. > > Showing that your libcurl claims to support HTTPS is progress. I think that > at this point you should read the last sentence in the curl FAQ 3.21, which I > found by searching

Re: [R] How to enable https for R 3.1.2 on windows 8.1

On Feb 2, 2015, at 10:50 AM, Jeff Newmiller wrote: > Cc'd back to the list... I am a bad bet for one-on-one help. > > Showing that your libcurl claims to support HTTPS is progress. I think that > at this point you should read the last sentence in the curl FAQ 3.21, which I > found by searching

Re: [R] How to enable https for R 3.1.2 on windows 8.1

Changing urls to remove spaces and replace single quotes with double quotes resolved the issue. Apparently windows demands double quotes. Thanks for your help. On Mon, Feb 2, 2015 at 1:50 PM, Jeff Newmiller wrote: > Cc'd back to the list... I am a bad bet for one-on-one help. > > Showing that

Re: [R] rJava Scientific Linux 6.5 - Can not install

Included at the end of this message is the full compiler output. I have installed jre-7 from Oracle; The java-1.7.0-jdk* packages and javacc are installed. It looks like the archiver, header prep., and compiler are missing. I can provide anything else that can help solve my problem. I really apprec

[R] collapse a list of dataframes

Hi all, I'm trying to avoid loops (no real reason, just as an exercise). Given a list: list(data.frame(a=1:3,b=letters[1:3]),data.frame(x=1:5,b=LETTERS[1:5])) Is there an easy way to collapse this to a single dataframe result<-data.frame(a=c(1:3,1:5),b=c(letters[1:3],LETTERS[1:5])) Thanks _

Re: [R] collapse a list of dataframes

How about this, t <- lapply(a,function(x){colnames(x)=c("A","B");return(x)}) do.call(rbind,t) On Mon, Feb 2, 2015 at 4:00 PM, Tom Wright wrote: > Hi all, > > I'm trying to avoid loops (no real reason, just as an exercise). > > Given a list: > > list(data.frame(a=1:3,b=letters[1:3]),data.frame(x

Re: [R] collapse a list of dataframes

Thanks, After posting I came across this page: http://www.r-bloggers.com/concatenating-a-list-of-data-frames/ rbindlist seems to be a pretty good solution. On Mon, 2015-02-02 at 16:09 -0500, dan wang wrote: > How about this, > > > t <- lapply(a,function(x){colnames(x)=c("A","B");return(x)}) > d

Re: [R] using png and identify commands

Thanks Henrik and Tom, job done. Nice solutions. All the best Antonio Olinto 2015-02-02 17:31 GMT-02:00 Henrik Bengtsson : > On Mon, Feb 2, 2015 at 9:56 AM, Antonio Silva > wrote: > > Hi R users > > > > I want to save a plot after using the command identify. > > > > I use identify to place lab

[R] rtools fstream error

Hi, when writing a simple cpp function to be run in R I obtain a compilation error as soon as I include fstream. Any hints of what goes wrong and how to fix it? It's Windows 7 64-bit, R-3.1.2 and Rtools32. An example to recreate the error: #include #include #include using nam

Re: [R] How to enable https for R 3.1.2 on windows 8.1

I am not aware that Windows demands double quotes for anything in R. I think the spaces was the problem. --- Jeff NewmillerThe . . Go Live... DCN:Basics: ##.#. ##.#. Li

Re: [R] rtools fstream error

Try adding the line #define R_NO_REMAP to the top of your file (before any #include's) so the R include files don't define length(x). Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Feb 2, 2015 at 1:11 PM, wrote: > Hi, > > when writing a simple cpp function to be run in R I obtain a comp

Re: [R] A good way to debug a c++ library embedded to an R code

If you are familiar with GDB, you can just start R by "R -d gdb". Dirk gave a good example on SO, please check the link below: http://stackoverflow.com/questions/11345537/debugging-line-by-line-of-rcpp-generated-dll-under-windows Best, KK On Mon, Feb 2, 2015 at 2:00 PM, Charles Novaes de Santa

Re: [R] rtools fstream error

Thank you, it worked. For completeness, had to add Rf_ in front of allocVector (and possibly any other function from Rdefines.h) - Original Message - From: "William Dunlap" To: sun...@telenet.be Cc: r-help@r-project.org Sent: Monday, February 2, 2015 10:29:19 PM Subject: Re: [R]

[R] Plot residuals against standard normal distribution

Hi, I'm having trouble trying to plot the density of the residuals against the standard normal distribution N(0,1). (I'm trying to see if my residuals are well-behaved). I know hwo to calculate the standardized residuals (I guess that there may be a simple way using a R function) and then plot th

[R] Maxent does not work

Yesterday I installed the most recent R and maxent package, but it stopped working. Even a simple command like Model <- maxent(matrix(c(1,2,3,4,5,6,7,8), nrow=2, ncol=4),c(1,-1)) will cause a fatal error in R. I am attaching a screenshot to this email. Any help will be appreciated. Best regards

Re: [R] Plot residuals against standard normal distribution

> On 02 Feb 2015, at 23:42 , Mikael Olai Milhøj wrote: > > Hi, > > I'm having trouble trying to plot the density of the residuals against the > standard normal distribution N(0,1). (I'm trying to see if my residuals are > well-behaved). > > I know hwo to calculate the standardized residuals (I

Re: [R] Boundaries and deldir

On 2015-02-03 00:46, Rolf Turner wrote: [...] The deldir function creates a Delaunay triangulation/Dirichlet tessellation inside a "rectangular window" (denoted by "rw" in the argument list). This is the only boundary invoked or involved. The function plot.tile.list() will *plot* the Dirichl

Re: [R] FFT Normalization Documentation

Dear Eike Petersen, Re: > Hello everyone, > > the docpage for the fft function states: > > “Description: Performs the Fast Fourier Transform of an array.” > > and > > “Arguments – inverse: if ‘TRUE’, the unnormalized inverse transform is > computed > (the inverse has a ‘+’ in the exponent o

Re: [R] Plot residuals against standard normal distribution

Since you are plotting densities, check out the sm package. It has been over a year or so since I've used it, but there was a setting on the univariate densities to check the data against a normal distribution. Best, MEH On Mon, Feb 2, 2015 at 2:42 PM, Mikael Olai Milhøj wrote: > Hi, > > I'm

[R] Asymmetric Cost assignment for SVM | Help

Hi Friends, I want to assign asymmetric cost values at the time training. For example : For false negative cost should be 10 and for For false positive it should be 1. Can some help me with this. Code: svmFit <- train(Y ~ ., data = train, method = "svmRadial",

[R] Updating to R 3.1.1. - impacts on existing packages

Hi list I've signed up for a Coursera course on exploratory data analysis, and the recommendation is to update to R base 3.1.1. I'm currently on 3.0.2. If I do upgrade, what is the best way for me to upgrade all my packages for compatibility? Would this be accomplished through the command:

Re: [R] Updating to R 3.1.1. - impacts on existing packages

On Mon, Feb 2, 2015 at 4:49 PM, Sun Shine wrote: > Hi list > > I've signed up for a Coursera course on exploratory data analysis, and the > recommendation is to update to R base 3.1.1. I'm currently on 3.0.2. > > If I do upgrade, what is the best way for me to upgrade all my packages for > compati

Re: [R] Updating to R 3.1.1. - impacts on existing packages

I think you missed the question, Henrik, which was directed at updating the local 3.1 library with all of the packages that were in the 3.0 library. The usual advice for this is to copy your 3.0 library onto your 3.1 library (duplicate directory structure) so R knows what packages you want to

Re: [R] the less-than-minus gotcha

Responding to several messages in this thread... > > All the more reason to use = instead of <- > Definitely not! Martin and Rolf are right, it's not a reason for that; I wrote that quickly without thinking it through. An "=" user might be more likely to fall for the gotcha, if not spacing the

Re: [R] the less-than-minus gotcha

On Mon, Feb 2, 2015 at 8:57 PM, Steve Taylor wrote: > Responding to several messages in this thread... > >> > All the more reason to use = instead of <- >> Definitely not! > > Martin and Rolf are right, it's not a reason for that; I wrote that quickly > without thinking it through. An "=" user m

Re: [R] the less-than-minus gotcha

I disagree. Assignments in my code are all lines that look like this: variable = expression They are easy to find and easy to read. -Original Message- From: Ista Zahn [mailto:istaz...@gmail.com] Sent: Tuesday, 3 February 2015 3:36p To: Steve Taylor Cc: r-h...@stat.math.ethz.ch Subject:

Re: [R] the less-than-minus gotcha

I did not start out liking <-, but I am quite attached to it now, and even Rcpp feels weird to me now. This may seem like yet another variation on a theme that you don't find compelling, but I find that f(x=x) makes sense when scope is considered, but x=x on its own is silly. That is why I pr

Re: [R] the less-than-minus gotcha

Nobody would write x=x or indeed x<-x; both are silly. If I found myself writing f(x=x) I might smirk at the coincidence, but it wouldn't bother me. I certainly wouldn't confuse it with assigning x to itself. By the way, here's another assignment operator we can use: `:=` = `<-` # this is go

Re: [R] A good way to debug a c++ library embedded to an R code

There's also a section about this in "Writing R extensions": http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Debugging-compiled-code Pierrick On Mon, Feb 2, 2015 at 10:42 PM, Qiang Kou wrote: > If you are familiar with GDB, you can just start R by "R -d gdb". > > Dirk gave a good exa

[R] New to R

Hi, In our data we have 10 people with 10 different attributes , we want to rank the people based on the weightage of these attributes. Suggest the best statistical method to do this. Does Revolution R solves my problem?? Regards, Lalitha Kristipati Associate Software Engineer =

Re: [R] New to R

Please don't cross-post to multiple lists. There is a Posting Guide mentioned in the footer that you probably won't see because you are using Nabble. It would have informed you that the R-devel mailing list was for people interested in modifying R, definitely not this topic. As to your question