Re: [R] R- package for Parametric Survival Analysis with Left-censored data

2013-11-27 Thread Göran Broström
On 11/20/2013 08:17 AM, peter dalgaard wrote: On 20 Nov 2013, at 04:15 , David Winsemius dwinsem...@comcast.net wrote: On Nov 19, 2013, at 5:30 PM, Vinod Mishra wrote: Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival

[R] R- package for Parametric Survival Analysis with Left-censored data

2013-11-19 Thread Vinod Mishra
Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival Analysis model with Left-censored (delayed entry) data in it. I recently received reviewers comment on my submitted article, where the reviewer suggested that only R has

Re: [R] R- package for Parametric Survival Analysis with Left-censored data

2013-11-19 Thread David Winsemius
On Nov 19, 2013, at 5:30 PM, Vinod Mishra wrote: Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival Analysis model with Left-censored (delayed entry) data in it. I recently received reviewers comment on my submitted

Re: [R] R- package for Parametric Survival Analysis with Left-censored data

2013-11-19 Thread peter dalgaard
On 20 Nov 2013, at 04:15 , David Winsemius dwinsem...@comcast.net wrote: On Nov 19, 2013, at 5:30 PM, Vinod Mishra wrote: Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival Analysis model with Left-censored (delayed

Re: [R] r package to solve for Nash equilibrium

2013-11-13 Thread Rolf Turner
On 11/12/13 02:49, Dereje Fentie wrote: Is there an r package out there that solves for pure strategy* Nash equilibrium of a two-person game*? A search for Nash equilibrium in r provides a link to the *GNE* package which solves for the Generalized Nash equilibrium. But what I would like to solve

[R] package ‘build-essential’ is not available (for R version 3.0.2)

2013-11-11 Thread Charles Evans
Hello, I have searched on the R-Project site, R-Help archives, and the Internet at large, and I cannot find a solution to my problem. I am running R version 3.0.2 (2013-09-25) -- Frisbee Sailing on Ubuntu 13.04. When I try to install several packages, including quantmod, with dependencies=T

Re: [R] package ‘build-essential’ is not available (for R version 3.0.2)

2013-11-11 Thread Joshua Ulrich
Have you read these instructions? http://cran.r-project.org/bin/linux/ubuntu/README.html They say to run sudo apt-get install r-base-dev which should install 'build-essential' (which is an Ubuntu package, not an R package). -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading

[R] r package to solve for Nash equilibrium

2013-11-11 Thread Dereje Fentie
Is there an r package out there that solves for pure strategy* Nash equilibrium of a two-person game*? A search for Nash equilibrium in r provides a link to the *GNE* package which solves for the Generalized Nash equilibrium. But what I would like to solve is a pure strategy Nash equilibrium

[R] Set system font in R package Cairo in Mac OS X

2013-11-10 Thread Sverre Stausland
Because of the issue raised in https://stat.ethz.ch/pipermail/r-help/2013-November/362896.html, I am switching to R on Mac OS X (10.6.8) to create some plots. Using CairoPDF(), however, the commands I use in Windows (7) to select my fonts don't have any effect on Mac OS X, where the output .pdf

Re: [R] Package(s) for making waffle plot-like figures?

2013-11-03 Thread Zhao Jin
Thank you very much for your codes and your descriptions. I ran them with my data, and they worked well! I am so happy to learn that your R codes and package could help me make these plots: I was baffled by this task and have been searching for solutions. I thought I was missing some arguments

Re: [R] Package(s) for making waffle plot-like figures?

2013-11-02 Thread Jim Lemon
On 11/02/2013 10:35 AM, Zhao Jin wrote: Dear all, I am trying to make a series of waffle plot-like figures for my data to visualize the ratios of amino acid residues at each position. For each one of 37 positions, there may be one to four different amino acid residues. So the data consist of

[R] Package(s) for making waffle plot-like figures?

2013-11-01 Thread Zhao Jin
Dear all, I am trying to make a series of waffle plot-like figures for my data to visualize the ratios of amino acid residues at each position. For each one of 37 positions, there may be one to four different amino acid residues. So the data consist of the positions, what residues are there, and

[R] Package for PAV and MPAV algorithms

2013-10-28 Thread Babak Bastan
Hi experts, Is there any packag for PAV and MPAV algorithms (Pattern Anomaly Value) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] Package to manipulate timestamp data in format HH:MM:SS:sss

2013-09-12 Thread Alecia M Moser
Hello - I have imported timestamp data (collected in OpenSHAPA) into R as .csv file. Some columns in the data frame have timestamps in the format HH:MM:SS:sss. I have not found a package that will allow simple addition and subtraction of columns with this format, although 'strptime' in

Re: [R] Package to manipulate timestamp data in format HH:MM:SS:sss

2013-09-12 Thread jim holtman
Use POSIXct for the date/time stamp. For your data you will have to substitute a period ('.') for the last colon (:), but that is easy to do with 'sub'. You will get millisecond precision, but just barely; don't try for microseconds since for that is the limit of precision with floating point

Re: [R] Package installation and path.package

2013-09-09 Thread Prof Brian Ripley
On 09/09/2013 02:09, David Winsemius wrote: On Sep 8, 2013, at 8:00 AM, Simon Zehnder wrote: Dear R-Users and R-Devels, I am writing right now my own package that makes use of 'tempfile' and there within with 'path.package'. When I install it, I get the error: Error in

Re: [R] Package installation and path.package

2013-09-09 Thread Simon Zehnder
I am following your suggestion and move this discussion to the R-devel list. Best Simon On Sep 9, 2013, at 7:58 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 09/09/2013 02:09, David Winsemius wrote: On Sep 8, 2013, at 8:00 AM, Simon Zehnder wrote: Dear R-Users and R-Devels,

[R] Package installation and path.package

2013-09-08 Thread Simon Zehnder
Dear R-Users and R-Devels, I am writing right now my own package that makes use of 'tempfile' and there within with 'path.package'. When I install it, I get the error: Error in path.package(mypackage) : none of the packages are loaded. I understand the error, but I would like to have a

Re: [R] Package installation and path.package

2013-09-08 Thread David Winsemius
On Sep 8, 2013, at 8:00 AM, Simon Zehnder wrote: Dear R-Users and R-Devels, I am writing right now my own package that makes use of 'tempfile' and there within with 'path.package'. When I install it, I get the error: Error in path.package(mypackage) : none of the packages are loaded.

[R] The new rockchalk R package (Free Webinar)

2013-09-03 Thread Ray DiGiacomo, Jr.
Hello R Users, Are you interested in making your regression analysis in R easier to explain to your colleagues and customers? This free one-hour webinar will provide a general introduction to rockchalk, an R package that provides a collection of functions that ease the presentation

[R] package seriation- how to manage font size and label margin

2013-09-02 Thread Suparna Mitra
Hello R experts, I am trying to use hmap from package seriation or bertinplot. I have two questions: How can I specify smaller font? I tried with pushViewport(viewport(layout=grid.layout(nrow = 1, ncol = 2), + gp = gpar(fontsize = 8))) but didn't work for the font with bertinplot. Also for hmap

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-23 Thread R. Michael Weylandt
On Mon, Aug 19, 2013 at 6:07 PM, Shang Zuofeng zuofengsh...@gmail.com wrote: So this is an alternative method. The package can be installed from source() rather than rebuilt. Although the warnings exist, the package itself may still be useful. Can you let me know how to installed from source?

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-20 Thread Shang Zuofeng
-project.org Subject: Re: [R] How to rebuild an R package that has been removed from CRAN? Thanks, Dan! The package is assist which can be downloaded from the following link: http://cran.r-project.org/src/contrib/Archive/assist/ The one I chose was assist_3.1.2.tar.gz I have

[R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread Shang Zuofeng
Dear All, My project requires the use of a specific R package. However, this R package has been removed from CRAN. But its older version can be found. Unfortunately, the older version cannot be used. The thing is, after I downloaded the older version and unzip it into the library folder of R

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread Daniel Nordlund
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Shang Zuofeng Sent: Monday, August 19, 2013 1:26 PM To: r-help@r-project.org Subject: [R] How to rebuild an R package that has been removed from CRAN? Dear All, My project

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread Shang Zuofeng
PM To: r-help@r-project.org Subject: [R] How to rebuild an R package that has been removed from CRAN? Dear All, My project requires the use of a specific R package. However, this R package has been removed from CRAN. But its older version can be found. Unfortunately, the older version

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread Daniel Nordlund
Nordlund Bothell, WA USA _ From: Shang Zuofeng [mailto:zuofengsh...@gmail.com] Sent: Monday, August 19, 2013 2:16 PM To: Daniel Nordlund Cc: r-help@r-project.org Subject: Re: [R] How to rebuild an R package that has been removed from CRAN? Thanks, Dan! The package is assist which can

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread Uwe Ligges
...@gmail.com] Sent: Monday, August 19, 2013 2:16 PM To: Daniel Nordlund Cc: r-help@r-project.org Subject: Re: [R] How to rebuild an R package that has been removed from CRAN? Thanks, Dan! The package is assist which can be downloaded from the following link: http://cran.r-project.org/src/contrib

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread Daniel Nordlund
] On Behalf Of David Winsemius Sent: Monday, August 19, 2013 4:43 PM To: Uwe Ligges Cc: r-help@r-project.org help Subject: Re: [R] How to rebuild an R package that has been removed from CRAN? On Aug 19, 2013, at 4:12 PM, Uwe Ligges wrote: On 20.08.2013 01:06, Daniel Nordlund wrote: The file

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread William Dunlap
to rebuild an R package that has been removed from CRAN? Yeah, I tried building the package and got essentially the same warnings and decided that further assistance required someone above my pay grade. :-) Daniel Nordlund Bothell, WA USA -Original Message- From: r-help-boun...@r

Re: [R] How to rebuild an R package that has been removed from CRAN?

2013-08-19 Thread David Winsemius
Subject: Re: [R] How to rebuild an R package that has been removed from CRAN? Thanks, Dan! The package is assist which can be downloaded from the following link: http://cran.r-project.org/src/contrib/Archive/assist/ The one I chose was assist_3.1.2.tar.gz I have changed

[R] package ridge-how to obtain R squared

2013-08-16 Thread ZhouYuepeng
Dear all, I'm using package ridge to deal with multicollinearity. It's been convenient to automatically choose lambda. However, how do I tell whether the OLS results have been improved after applying ridge regression? I only notice that more variables become statistically significant and some

[R] package ridge-how to obtain R squared

2013-07-29 Thread ZhouYuepeng
Dear all, I'm using package ridge to deal with multicollinearity. It's been convenient to automatically choose lambda. However, how do I tell whether the OLS results have been improved after applying ridge regression? I only notice that more variables become statistically significant and some

[R] [R-pkgs] Version 1.0 of the R package frontier released

2013-07-22 Thread Arne Henningsen
Dear all I am happy to announce that version 1.0 of the frontier package is available on CRAN. The R package frontier provides tools for analysing efficiency and productivity using the stochastic frontier approach. This R package is based on Tim Coelli's DOS software FRONTIER 4.1 and has been

[R] R Package License

2013-07-17 Thread Li, Yan
HI Helpers, How could we use R and R packages licensed under GPL into commercial products? Is it allowed to load a library and get the results from it and using the results for commercial use? Thank you so much! Regards, Yan [[alternative HTML version deleted]]

Re: [R] R Package License

2013-07-17 Thread Marc Schwartz
On Jul 17, 2013, at 10:56 AM, Li, Yan yan...@ibi.com wrote: HI Helpers, How could we use R and R packages licensed under GPL into commercial products? Is it allowed to load a library and get the results from it and using the results for commercial use? Thank you so much! Regards, Yan

[R] Appropriate forum for announcing R package updates

2013-07-10 Thread Frank Harrell
I have been confused about the appropriate e-mail address to use to make announcements to r-help for major package update. In the past I've submitted to r-packa...@lists.r-project.org without seeing the announcement appear on r-help. Thanks for any guidance. Frank -- Frank E Harrell Jr

Re: [R] Appropriate forum for announcing R package updates

2013-07-10 Thread Frank Harrell
/Appropriate-forum-for-announcing-R-package-updates-tp4671238p4671242.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] Appropriate forum for announcing R package updates

2013-07-10 Thread Marc Schwartz
On Jul 10, 2013, at 1:29 PM, Frank Harrell f.harr...@vanderbilt.edu wrote: I have been confused about the appropriate e-mail address to use to make announcements to r-help for major package update. In the past I've submitted to r-packa...@lists.r-project.org without seeing the announcement

[R] Package PLM

2013-07-03 Thread Eliano Marques
Hi Giovanni and Yves, My is Eliano Marques, i'm a master degree econometrician from ISEG in Portugal. I was trying to use your R package with a specific output i cannot get the same results that i'm getting in Stata. Could you please let me know if the below is correct or if i'm missing

[R] renaming of miktex package broke R package building

2013-06-24 Thread Sancar Adali
the inconsolata miktex package (inconsolata-zi4 in CTAN) which contains the font of the same name was recently updated. It now contains the file zi4.sty instead of inconsolata.sty. When I was building an R package, the help(or vignette) file pdf couldn't built , because R couldn't find

Re: [R] renaming of miktex package broke R package building

2013-06-24 Thread Berend Hasselman
On 24-06-2013, at 18:21, Sancar Adali sad...@gmail.com wrote: the inconsolata miktex package (inconsolata-zi4 in CTAN) which contains the font of the same name was recently updated. It now contains the file zi4.sty instead of inconsolata.sty. When I was building an R package, the help

[R] Package random forest: can corr.bias be harmful?

2013-06-21 Thread Christian Kampichler
There exists an option corr.bias for making regression analyses with the R package randomForest. The manual warns “Experimental. Use at your own risk.” What does corr.bias precisely do and why can it be dangerous to use it? As far as I know the bias correction is based on a linear regression

Re: [R] Package random forest: can corr.bias be harmful?

2013-06-21 Thread Benjamin
...@sovon.nl wrote: There exists an option corr.bias for making regression analyses with the R package randomForest. The manual warns “Experimental. Use at your own risk.” What does corr.bias precisely do and why can it be dangerous to use it? As far as I know the bias correction is based on a linear

Re: [R] Problems with R package building

2013-06-20 Thread jpm miao
Hi, Following your advice, I install R tools from http://cran.r-project.org/bin/windows/Rtools/ Rtools215.exe http://cran.r-project.org/bin/windows/Rtools/Rtools215.exe Files are automatically installed here: C:\Rtools I run the code again and get the message Creating directories ...

Re: [R] Problems with R package building

2013-06-20 Thread Pascal Oettli
Hi, Did you run R CMD build test1pkg in a command prompt window? Regards, Pascal On 20/06/13 17:01, jpm miao wrote: Hi, Following your advice, I install R tools from http://cran.r-project.org/bin/windows/Rtools/ Rtools215.exe http://cran.r-project.org/bin/windows/Rtools/Rtools215.exe

Re: [R] Problems with R package building

2013-06-20 Thread jpm miao
I ran it in a common window of R. It's said that I need to run it under DOS. I also open the command window of DOS C:\Documents and Settings\miao ,where miao is my username, and ran it, but it doesn't work either. An error message emerges. Miao 2013/6/20 Pascal Oettli kri...@ymail.com Hi,

Re: [R] Problems with R package building

2013-06-20 Thread Berend Hasselman
On 20-06-2013, at 10:01, jpm miao miao...@gmail.com wrote: Hi, Following your advice, I install R tools from http://cran.r-project.org/bin/windows/Rtools/ Rtools215.exe http://cran.r-project.org/bin/windows/Rtools/Rtools215.exe Files are automatically installed here: C:\Rtools I

Re: [R] Problems with R package building

2013-06-20 Thread jpm miao
Hi, What do you mean by Windows in a Windows console window? Is it the black screen of DOS? I change the directory of the DOS window to D:\R\pkgtest D:\R\pkgtest\test1pkg and run the command R CMD build test1pkg under each of the two paths, and the error message remains. Miao

Re: [R] Package zoo - na.rm ignored?

2013-06-18 Thread Gabor Grothendieck
On Mon, Jun 17, 2013 at 7:03 PM, Katharina May may.kathar...@googlemail.com wrote: many thanks for the enlightenment - I guess I completely misunderstood the na.rm option here... Looking at the help file the na argument seems not suffiiciently well explained. Will improve. -- GKX Group, GKX

Re: [R] package expm: matrix powers within a product of matrices: operation precedence

2013-06-18 Thread Ben Bolker
Rainer K. SACHS rainersachs at berkeley.edu writes: Thanks, that clears everything up completely. It might be worth adding your comment to the available documentation. This request should probably go the maintainer of the expm package (library(expm); maintainer(expm)), who may or may not

[R] package expm: matrix powers within a product of matrices: operation precedence

2013-06-17 Thread Rainer Sachs
package expm: matrix powers within a product of matrices: operation precedence I want to double check that for M and N kxk mtrices and v a k-vector M%^%2%*%N%*%v is not automatically read as (M%^%2)%*%N%*%v or M%*%N%^%2%*%v is not automatically read as M%*%(N%^%2)%*%v or both

Re: [R] package expm: matrix powers within a product of matrices: operation precedence

2013-06-17 Thread William Dunlap
] On Behalf Of Rainer Sachs Sent: Monday, June 17, 2013 1:20 PM To: r-help@r-project.org Subject: [R] package expm: matrix powers within a product of matrices: operation precedence package expm: matrix powers within a product of matrices: operation precedence I want to double check

[R] Package zoo - na.rm ignored?

2013-06-17 Thread Katharina May
Dear R Users, I've got a strange problem, which I do not really understand: when I use na.spline from the zoo package, the option na.rm is just being ignored, see this adjusted example from the na.spline help page: d0 - as.Date(2000-01-01) z - zoo(c(NA, 11, 13, NA, 15,

Re: [R] Package zoo - na.rm ignored?

2013-06-17 Thread Gabor Grothendieck
On Mon, Jun 17, 2013 at 6:23 PM, Katharina May may.kathar...@googlemail.com wrote: Dear R Users, I've got a strange problem, which I do not really understand: when I use na.spline from the zoo package, the option na.rm is just being ignored, see this adjusted example from the na.spline help

Re: [R] Package zoo - na.rm ignored?

2013-06-17 Thread Katharina May
many thanks for the enlightenment - I guess I completely misunderstood the na.rm option here... On 18 June 2013 00:50, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Jun 17, 2013 at 6:23 PM, Katharina May may.kathar...@googlemail.com wrote: Dear R Users, I've got a strange

Re: [R] package expm: matrix powers within a product of matrices: operation precedence

2013-06-17 Thread Rainer K. SACHS
problem.) Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Rainer Sachs Sent: Monday, June 17, 2013 1:20 PM To: r-help@r-project.org Subject: [R] package expm: matrix

[R] Problems with R package building

2013-06-14 Thread jpm miao
Hi, I try to build a toy package by running the following codes in an R program require(stats) f - function(x,y) x+y g - function(x,y) x-y d - data.frame(a=1, b=2) e - rnorm(1000) package.skeleton(list=c(f,g,d,e), name=test1pkg, path=D:/R/pkgtest) Then the program runs smoothly Creating

Re: [R] Problems with R package building

2013-06-14 Thread Michael Weylandt
On Jun 14, 2013, at 7:18, jpm miao miao...@gmail.com wrote: Hi, I try to build a toy package by running the following codes in an R program require(stats) f - function(x,y) x+y g - function(x,y) x-y d - data.frame(a=1, b=2) e - rnorm(1000) package.skeleton(list=c(f,g,d,e),

[R] Problem in linking a library in R package

2013-06-14 Thread Gaurav Sehrawat
Hello everyone , I am facing a simple problem , I trying to add functionality in one of R package . I want a profiling library to link to R package so that when R package is used the profiling out put comes automatically with that. Problem is that I am not able to link it with the package , I

Re: [R] Problem in linking a library in R package

2013-06-14 Thread Duncan Murdoch
On 13-06-14 3:47 AM, Gaurav Sehrawat wrote: Hello everyone , I am facing a simple problem , I trying to add functionality in one of R package . I want a profiling library to link to R package so that when R package is used the profiling out put comes automatically with that. Problem is that I

Re: [R] Problem in linking a library in R package

2013-06-14 Thread Gaurav Sehrawat
I have posted the question on stackoverflow but no satisfied there. Here is the Link : http://stackoverflow.com/questions/17049966/how-to-include-a-shared-library-so-or-library-in-a-r-package Thanks On Fri, Jun 14, 2013 at 7:15 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 13-06-14 3

[R] Package for maximizing likelihood function with EM algorithm

2013-06-11 Thread Anhai Jin
Hi R users, I am trying to figure out if there is a package in R that can maximize likelihood function with EM algorithm. Right now, I have derived the log-likelihood function, which is a function of 9 indicator variables with 14 parameters. Is there a package that I can specify the

Re: [R] Package for maximizing likelihood function with EM algorithm

2013-06-11 Thread Berend Hasselman
On 11-06-2013, at 21:14, Anhai Jin a...@iknowtion.com wrote: Hi R users, I am trying to figure out if there is a package in R that can maximize likelihood function with EM algorithm. Right now, I have derived the log-likelihood function, which is a function of 9 indicator variables with

Re: [R] Package 'ChoiceModelR' - Xbetas.csv? Rbetas.csv? betadraws?

2013-06-09 Thread Uwe Ligges
On 07.06.2013 21:25, Dimitri Liakhovitski wrote: Hope to get some clarity from the creators of a (wonderful) package ChoiceModelR. I am using the main function 'choicemodelr'. Since we do not know if these creators are reading the list, why not ask them directly? Best, Uwe Ligges

[R] Package 'ChoiceModelR' - Xbetas.csv? Rbetas.csv? betadraws?

2013-06-07 Thread Dimitri Liakhovitski
Hope to get some clarity from the creators of a (wonderful) package ChoiceModelR. I am using the main function 'choicemodelr'. Everything works. ?choicemodelr says average of MCMC draws of unit-level model coefficients are written to Xbetas.csv Question 1: Is this a typo? The real file created

[R] Package unpacks (successfully and MD5 sums checked but will not load not a valid package

2013-05-28 Thread dbertin
utils:::menuInstallLocal() package ‘surv2sample’ successfully unpacked and MD5 sums checked library(surv2sample) Error in library(surv2sample) : ‘surv2sample’ is not a valid installed package Furthermore, if I go through Packages-Load package from the top bar surv2sample isn't in the list.

Re: [R] Package unpacks (successfully and MD5 sums checked but will not load not a valid package

2013-05-28 Thread Berend Hasselman
On 28-05-2013, at 22:41, dbertin dber...@uoguelph.ca wrote: utils:::menuInstallLocal() package ‘surv2sample’ successfully unpacked and MD5 sums checked library(surv2sample) Error in library(surv2sample) : ‘surv2sample’ is not a valid installed package Furthermore, if I go through

Re: [R] How could I see the source code of functions in an R package?

2013-05-17 Thread Duncan Murdoch
On 13-05-17 12:01 AM, David Winsemius wrote: Do this search with your favorite search tool Accessing the sources ligges (Uwe Ligges is the author of a comprehensive article on the topic in R News.) That article is also linked from the R help system. After help.start(), look for technical

[R] How could I see the source code of functions in an R package?

2013-05-16 Thread jpm miao
Hi, How could I see the source code of functions in an R package? If we type ?function_name , we will see documentations of the function_name. If we type function_name, is what returns just the source code? Could we just save it in an .R file and modify as we want? However, it seems

Re: [R] How could I see the source code of functions in an R package?

2013-05-16 Thread arun
I see the source code of functions in an R package?    If we type ?function_name , we will see documentations of the function_name.    If we type function_name, is what returns just the source code? Could we just save it in an .R file and modify as we want? However, it seems that sometimes

Re: [R] How could I see the source code of functions in an R package?

2013-05-16 Thread David Winsemius
Do this search with your favorite search tool Accessing the sources ligges (Uwe Ligges is the author of a comprehensive article on the topic in R News.) -- David. On May 16, 2013, at 6:58 PM, jpm miao wrote: Hi, How could I see the source code of functions in an R package? If we type

[R] Build R package with libjpeg - Symbol not found: _jpeg_CreateCompress

2013-05-15 Thread DcInfSys1
can not find the jpeg_createCompress function. Can anybody help? :-) -- View this message in context: http://r.789695.n4.nabble.com/Build-R-package-with-libjpeg-Symbol-not-found-jpeg-CreateCompress-tp4667129.html Sent from the R help mailing list archive at Nabble.com

Re: [R] Need help to building R package with devtools

2013-05-14 Thread Hadley Wickham
Can someone help what I need to do to make 'devtools' work? A quick asking around indicates that Rtools 3.0 should work fine for 2.15.3 maintenance. Thus, the issue is probably a purely formal bug in devtools's version comparison logic, and you need to pester its maintainer. Unless it has

[R] Need help to building R package with devtools

2013-05-12 Thread Christofer Bogaso
Hello again, I am using library(devtools) to build my custom package. Therefore I installed (normal/default installation) the RTools from 'http://cran.r-project.org/bin/windows/Rtools/' with Rtools30.exe. However I am getting following error: library(devtools) WARNING: Rtools is required to

Re: [R] Need help to building R package with devtools

2013-05-12 Thread peter dalgaard
On May 12, 2013, at 10:55 , Christofer Bogaso wrote: Hello again, I am using library(devtools) to build my custom package. Therefore I installed (normal/default installation) the RTools from 'http://cran.r-project.org/bin/windows/Rtools/' with Rtools30.exe. However I am getting

Re: [R] Need help to building R package with devtools

2013-05-12 Thread John Kane
Just a guess but it looks like you need to upgrade to the latest release (2013-04-03, Masked Marvel) John Kane Kingston ON Canada -Original Message- From: bogaso.christo...@gmail.com Sent: Sun, 12 May 2013 14:40:10 +0545 To: r-help@r-project.org Subject: [R] Need help to building R

[R] Package Seqminer: Fundamental usage question

2013-05-10 Thread Darren Obbard
Hi, I am trying to use the package 'SeqMiner zhanxw.com/seqminer/, and I would like to use any of the functions readVCFToMatrixByRange() readVCFToMatrixByGene() readVCFToListByGene() or readVCFToListByRange() I have run the example code on the test datasets, and have got the expected output.

Re: [R] R package for bootstrapping (comparing two quadratic regression models)

2013-05-06 Thread Adams, Jean
with someone about what you have, where it came from, and what questions you are trying to answer. Jean On Fri, May 3, 2013 at 6:08 PM, Elaine Kuo elaine.kuo...@gmail.com wrote: Hello , I want to compare two quadratic regression models with non-parametric bootstrap. However, I do not know which R

Re: [R] R package for bootstrapping (comparing two quadratic regression models)

2013-05-06 Thread Elaine Kuo
...@gmail.comwrote: Hello , I want to compare two quadratic regression models with non-parametric bootstrap. However, I do not know which R package can serve the purpose, such as boot, rms, or bootstrap, DeltaR. Please kindly advise and thank you. Elaine The two quadratic regression models

Re: [R] Package survey: singularities in linear regression models

2013-05-05 Thread Thomas Lumley
Ok, that's more helpful. The problem is with replicate-weight designs, and it's because svyglm() uses the fitted coefficients from the point estimate as starting values for fitting the replicates. And even if that is changed, the computation of the replicate variance doesn't like all the

Re: [R] Package survey: singularities in linear regression models

2013-05-03 Thread Sebastian Weirich
Well, I have uploaded the data in the public folder of my dropbox. Due to data confidentiality, I haved to change the labels. To load the data: con - url( http://dl.dropboxusercontent.com/u/101865137/datEx.rda; ) print(load(con)) # The replicate weights were created according to the jackknife

[R] R package for bootstrapping (comparing two quadratic regression models)

2013-05-03 Thread Elaine Kuo
Hello , I want to compare two quadratic regression models with non-parametric bootstrap. However, I do not know which R package can serve the purpose, such as boot, rms, or bootstrap, DeltaR. Please kindly advise and thank you. Elaine The two quadratic regression models are y1=a1x^2+b1x+c1 y1

[R] Package survey: singularities in linear regression models

2013-05-02 Thread Sebastian Weirich
Hello, I want to specify a linear regression model in which the metric outcome is predicted by two factors and their interaction. glm() computes effects for each factor level and the levels of the interaction. In the case of singularities glm() displays NA for the corresponding coefficients.

Re: [R] Package survey: singularities in linear regression models

2013-05-02 Thread Thomas Lumley
On Fri, May 3, 2013 at 2:27 AM, Sebastian Weirich sebastian.weir...@iqb.hu-berlin.de wrote: Hello, I want to specify a linear regression model in which the metric outcome is predicted by two factors and their interaction. glm() computes effects for each factor level and the levels of the

[R] Package VIF

2013-04-17 Thread Jaap van Wyk
Hi Could you perhaps possibly help me. I would like to use the package VIF but cannot get results I attach the .csv file and my R code. What do I have to do ? Any help is greatly appreciated. library(VIF) coal - read.csv(e:/freekvif/cqa1.csv,header=TRUE) y - as.numeric(coal$AI) x -

[R] prediction.strength in r package fpc

2013-04-08 Thread Eugenie Yin
Hi i am using prediction.strength with k-medoids algorithms. There are simple examples like prediction.strength(iriss,2,3,M=3,method=pam) I wrote my code like prediction.strength(data,2,6,M=10,clustermethod=pamkCBI,DIST,krange=2:6,diss=TRUE,usepam=TRUE) because i am using the dissimilarity

Re: [R] Package ‘FAdist’ - Log-Pearson Type III Distribution

2013-04-07 Thread David Winsemius
On Apr 6, 2013, at 10:08 PM, Katherine Gobin wrote: Dear Sir, I am referring to your package FAdist. I wish to know how to estimate the parameters of the distribution - Log-Pearson Type III Distribution? I suppose I could look up the maintainer of that package and try to see if they

[R] Package ‘FAdist’ - Log-Pearson Type III Distribution

2013-04-06 Thread Katherine Gobin
Dear Sir, I am referring to your package FAdist. I wish to know how to estimate the parameters of the distribution - Log-Pearson Type III Distribution? Will it be possible for you to guide me or inform the package in R, I can use to estimate the parameters. Regards Katherine

[R] Controlling print messages/warnings and error output in R package

2013-03-26 Thread Saptarshi Guha
Hello, If i were to embed R (in C), i could over ride ptr_R_ShowMessage = Re_ShowMessage; ptr_R_WriteConsoleEx =Re_WriteConsoleEx; where Re_ShowMessage,Re_WriteConsoleEx are my own functions. How would i do this in a package? I would like the flexibility of having my function be called

Re: [R] Error message installing package R package

2013-03-21 Thread Pramod Anugu
I am getting error messages while installing R package lme4. Please advice thanks Pramod trying URL 'http://cran.mtu.edu/src/contrib/lme4_0.99-0.tar.gz' Content type 'application/x-gzip' length 1074142 bytes (1.0 Mb) opened URL

Re: [R] Error message installing package R package

2013-03-21 Thread Ben Bolker
Pramod Anugu pramod.r.anugu at jsums.edu writes: I am getting error messages while installing R package lme4. Please advice This would be better on the r-sig-mixed-mod...@r-project.org list. You haven't told us, but I'm guess from what you've pasted below that you're on a Unix system

[R] on R package vignette

2013-03-20 Thread Han Lin Shang
Dear R core team and R users, I am building a vignette for an existing R package on CRAN. In the example section of the vignette document, I require a non-cran R package (currently available at my co-author's personal website) for loading data. My question is: I am not sure if I am allowed

Re: [R] on R package vignette

2013-03-20 Thread Prof Brian Ripley
On 20/03/2013 10:28, Han Lin Shang wrote: Dear R core team and R users, I am building a vignette for an existing R package on CRAN. In the example section of the vignette document, I require a non-cran R package (currently available at my co-author's personal website) for loading data. My

Re: [R] package ‘contingency.tables’ is not available (for R version 2.15.2)

2013-03-08 Thread Milan Bouchet-Valat
Le lundi 04 mars 2013 à 14:43 -0600, Joanna Papakonstantinou a écrit : Thank you. I actually ended up using: CrossTable(mdt) Cell Contents |-| | N | | Chi-square contribution | | N / Row Total | | N / Col Total

[R] package ‘contingency.tables’ is not available (for R version 2.15.2)

2013-03-04 Thread Joanna Papakonstantinou
I am trying to create contingency tables (to evaluate prior to performing Pearson's Chi-Squared test for independence). I would like to see column and row totals as well as expected and observed values and cell counts. I tried to use the package contingency. tables but get the following warning:

Re: [R] package ‘contingency.tables’ is not available (for R version 2.15.2)

2013-03-04 Thread Milan Bouchet-Valat
Le lundi 04 mars 2013 à 12:37 -0600, Joanna Papakonstantinou a écrit : I am trying to create contingency tables (to evaluate prior to performing Pearson's Chi-Squared test for independence). I would like to see column and row totals as well as expected and observed values and cell counts. I

Re: [R] package ‘contingency.tables’ is not available (for R version 2.15.2)

2013-03-04 Thread Joanna Papakonstantinou
Thank you. I actually ended up using: CrossTable(mdt) Cell Contents |-| | N | | Chi-square contribution | | N / Row Total | | N / Col Total | | N / Table Total | |-| Total Observations in

Re: [R] package ReadImages

2013-02-25 Thread Uwe Ligges
, 2013 5:54 PM To: PIKAL Petr Cc: r-help Subject: Re: [R] package ReadImages For some of the fancier transforms it may be easier to use an outside tool such as Imagemagick which will do a lot of these things. There is even a C++ interface to imagemagick that may work nicely with packages like

Re: [R] package ReadImages

2013-02-24 Thread PIKAL Petr
suggested options. Regards Petr From: Greg Snow [mailto:538...@gmail.com] Sent: Friday, February 22, 2013 5:54 PM To: PIKAL Petr Cc: r-help Subject: Re: [R] package ReadImages For some of the fancier transforms it may be easier to use an outside tool such as Imagemagick which will do a lot

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