Re: [R] How can output tables be converted to data files?

Yes. "p" is not "P" . Re-read the "value" section of the ?rcorr if this is not clear. -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Apr 5,

[R] plotting gam plots from mgcv package

Dear List I am fitting some GAM models using the package mgcv. When plotting the response curves of the individual predictors using gam.plot I get a dotted line of the confidence interval around the fitted line. Does anybody know a way to make these as grey area around the fitted lined instead of

Re: [R] How can output tables be converted to data files?

David: If I may, I was successful in writing csv files for rcorr, n, but not pvalue, which is empty. I set digits=5, thinking the small numbers might not show with default setting. Here's the code I used. Do you see a bug? Thanks. Bruce Y <- rcorr(as.matrix(X)) digits=5 write.csv(Y$p, file =

Re: [R] Package Query

Hi Ruchika, Maybe the hdeco package will help. Jim On Wed, Apr 5, 2017 at 2:28 PM, Ruchika Salwan wrote: > Hey, > > Is there any package in R that handles graph decomposition? A package > created specifically for flat/hierarchical decomposition of graphs. > > Thanks,

Re: [R] Replying to replies in the forum

Thanks a lot. On Wed, Apr 5, 2017 at 10:23 PM, Jeff Newmiller wrote: > There is no conclusively client-free solution, which is why it is not in the > Posting Guide. > > However, as a general rule, start with a fresh email to start a thread, and > reply-to-all to the

Re: [R] How can output tables be converted to data files?

Thanks, David. __ Bruce Ratner PhD > On Apr 5, 2017, at 5:49 PM, David L Carlson wrote: > > Data files is pretty vague. If you save the output of a function such as > rcorr(), you can extract any of the parts you need. Step 1 is to read the > documentation:

Re: [R] help with package ranks

Hi Davide, The error message is probably due to a zero length dimension in: W[,ind.positives] I would look at W (data frame?) to see where this might occur. That is, does W have a set of proteins with _no_ annotations? Perhaps manually removing that set will get the function running. Jim On

Re: [R] How can output tables be converted to data files?

Data files is pretty vague. If you save the output of a function such as rcorr(), you can extract any of the parts you need. Step 1 is to read the documentation: ?rcorr Under the section labeled "Value" you will see that rcorr() returns a list with 3 matrices named r, n, and P: > Y <-

Re: [R] system call removes special characters from text output

Don, Thank you for your reply. I found no problems in the perl script, but I found that I had inadvertently swapped file names in my call to system(" script.pl file1 file2") works as expected system(script.pl file2 file1) produces the output that formed my original query. Thanks so much, and I

[R] How can output tables be converted to data files?

Hi R'ers: This code produces: 3x3 rcorr matrix, one-element vector, and 3x3 p-value matrix. I would like to use these outputs as data files. How can these output tables be converted to data files? Any assistance is appreciated. Thanks. Bruce library(Hmisc) mtcars5 <-

Re: [R] system call removes special characters from text output

I can't reproduce this. On my system, the contents of an executable file named tmp.pl: #! /opt/local/bin/perl print "[A/B]\n"; At a shell prompt: [72]% ./tmp.pl [A/B] Inside R: > system(' ./tmp.pl') [A/B] -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627

Re: [R] ggplot2 question plot mean/error bars

Dear Rxperts.. Here is the updated code.. to the above example.. how do I make the white circles as "white filled" so that lines in the circles are not shown.? Thanks and much appreciated Santosh q <- data.frame(G=rep(paste("G",1:3,sep=""),each=50),D=rep(

Re: [R] as.POSIXct character string is not in a standard unambiguous format

Hi, I can't answer the question about R 3.3.3, but I don't see anything in the update notes. http://mirror.its.dal.ca/cran/doc/manuals/r-release/NEWS.html In the meantime, would it skirt your issue if you explicitly stated the format? x <- as.POSIXct("2002-02-02 02:02", format = "%Y-%m-%d

Re: [R] Replying to replies in the forum

> On Apr 5, 2017, at 1:26 PM, Tunga Kantarcı wrote: > > My question is specifically about what I should use in the subject > line when replying, because I do not trust mail clients, or to myself > as I use different clients sometimes. Hence, I wanted to learn a > client

Re: [R] Replying to replies in the forum

There is no conclusively client-free solution, which is why it is not in the Posting Guide. However, as a general rule, start with a fresh email to start a thread, and reply-to-all to the message you want to reply to. The threading is managed by hidden message ids, not subjects. -- Sent

[R] ggplot2 question plot mean/error bars

Hello Rxperts.. I am trying to generate a mean+/- error plot.. using ggplot2.. with filled black and white circles and black lines, but no overlap of lines and circles (symbols). Also, with no top and right lines of the plot box. I remember having done this before.. unable to reproduce how I did!

Re: [R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

OK this confused me. I thought object oriented coding should be preferred because it allows cleaner, more efficient coding. But your reply suggests it should be preferred because "R" is more efficient in that way. Anyhow, this thread should indeed not become a discussion point for this and I

Re: [R] Replying to replies in the forum

My question is specifically about what I should use in the subject line when replying, because I do not trust mail clients, or to myself as I use different clients sometimes. Hence, I wanted to learn a client free solution to correctly send replies. Now, the posting guide is not explicit about

Re: [R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

Bert, Good distinction... For clarification, I was referring to the "whole object approach" versus an "object oriented" approach. Regards, Marc > On Apr 5, 2017, at 12:43 PM, Bert Gunter wrote: > > ... Probably need to distinguish "whole object approach" from

Re: [R] Replying to replies in the forum

> On Apr 5, 2017, at 11:41 AM, Tunga Kantarcı wrote: > > OK I cannot figure this out clearly in the guidelines of posting. When > I reply to a message I should out "Re:" in front of the subject line > of the original post. So if the subject line of the original post it

Re: [R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

... Probably need to distinguish "whole object approach" from "object oriented" approach. They are different and almost orthogonal in R. R tutorials discuss such matters, and there are many good ones on the Web, including the "Intro to R" tutorial that ships with R. The OP should spend some time

Re: [R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

> On Apr 5, 2017, at 11:34 AM, Tunga Kantarcı wrote: > > Thanks a lot Marc, for informing that R is object oriented, implying > that one should always try to vectorise the code (although I am not so > clear why this should be the case) but also for all the references

[R] Replying to replies in the forum

OK I cannot figure this out clearly in the guidelines of posting. When I reply to a message I should out "Re:" in front of the subject line of the original post. So if the subject line of the original post it is "this is a post", then I should use "Re: this is a post" in the subject line, for my

Re: [R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

Thanks a lot Marc, for informing that R is object oriented, implying that one should always try to vectorise the code (although I am not so clear why this should be the case) but also for all the references you provide. __ R-help@r-project.org mailing

Re: [R] taking a small piece of large tiff

On Wed, 5 Apr 2017 at 20:13 jim holtman wrote: > if you have 8GB of memory it should be easy to handle. > > > TIFF is a container format and may be compressed internally, and so could expand out as a matrix it might be very many times larger than the file size implies.

Re: [R] differential use of R version

Maybe you can use .libPaths to choose a different library .libPaths("/myhome/Documents/R/R-3.0.2/library") Or /usr/bin/R command in linux is a shell script, you can edit some paths and make it work. ( I haven't tried it though) -Original Message- From: "Bogdan Tanasa"

[R] as.POSIXct character string is not in a standard unambiguous format

Hi I have lots of issues when I try to install R 3.3.3 during the "make check" step. Every time a call to as.POSIXct is done in test scripts, I got the same error message: e.g. x <- as.POSIXct("2002-02-02 02:02") Error in as.POSIXlt.character(x, tz, ...) : character string is not in a

Re: [R] taking a small piece of large tiff

Hi, You'll get a lot of help if you take this question to the R-sig-geo list https://stat.ethz.ch/mailman/listinfo/r-sig-geo In the meantime, you might want to try reading this using raster::raster() and then cropping to your desired region. Here's a discussion that may help you...

Re: [R] Package Query

There is a package called sos that helps you answer such questions yourself. There are also Task View pages on CRAN that help you identify useful packages. -- Sent from my phone. Please excuse my brevity. On April 4, 2017 9:28:32 PM PDT, Ruchika Salwan wrote: >Hey,

Re: [R] Package Query

On the rseek.org search site, "graph decomposition" brought up what looked like some relevant hits. So search there if you haven't done so already. -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka

Re: [R] differential use of R version

Hello, Unless you have strong reasons why not, use the most recent one, R 3.3. Hope this helps, Rui barradas Em 05-04-2017 03:47, Bogdan Tanasa escreveu: Dear all, please could you advise me on the following : on a server, in a folder "x86_64-redhat-linux-gnu-library", i have 2 versions of

Re: [R] taking a small piece of large tiff

Ok. I have a tiff of size over 2GB. It covers a sixth of the Earth's surface and I'm trying to cut a UK piece out of it. The tiff I start with seems to be too large for R to handle. Sent from my iPhone > On 4 Apr 2017, at 18:37, jim holtman wrote: > > How big is

[R] Package Query

Hey, Is there any package in R that handles graph decomposition? A package created specifically for flat/hierarchical decomposition of graphs. Thanks, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE

[R] help with package ranks

Hello, I'm Davide. I'm using the package RANKS, in particular the functions do.GBA, do.RW, do.RANKS. To the funcs are given 2 different Matrix. One is a a simmetryc adjacency Matrix(called "M"), where rows and columns are protein, and the other is an annotation Matrix(called "ann"), where protein

Re: [R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

> On Apr 5, 2017, at 8:00 AM, Tunga Kantarcı wrote: > > I have the MATLAB code pasted below that calculates yields to maturity. > > IRR = zeros(length(c),length(M)) > > The ith row and jth column is the price of the bond with coupon c(i) > and maturity M(j). > > for

[R] Yield to maturity calculation - bndyield equivalent of MATLAB in R

I have the MATLAB code pasted below that calculates yields to maturity. IRR = zeros(length(c),length(M)) The ith row and jth column is the price of the bond with coupon c(i) and maturity M(j). for i = 1:3 for j = 1:3 if j == 1 IRR(i,j) =

Re: [R] taking a small piece of large tiff

if you have 8GB of memory it should be easy to handle. Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. On Wed, Apr 5, 2017 at 3:23 AM, Louisa Reynolds wrote: > Ok. I have a

Re: [R] differential use of R version

Thank you Rui. I have been using a package (TitanCNA) in BioC on an older version of R (3.3.1); now after switching to R3.3.3, I am getting an error (below), and I do not know how to fix it. Any suggestions are welcome. Error in `[<-.data.frame`(`*tmp*`, indRef, "refCount", value = NULL) :