[R] Regarding R package spatstat

2014-09-30 Thread shivali gangwar
Hi , I am installing a R Package as following - R CMD INSTALL spatstat_1.26-0.tar.gz It seems my installation hangs at byte-compile and prepare package for lazy loading I kept on waiting for 1/2anhr but it hanged at below stage. Please help. ~~~ Target all

Re: [R] Regarding R package spatstat

2014-09-30 Thread Rolf Turner
appear. Hard to say what. R. T. On 01/10/14 00:58, shivali gangwar wrote: Hi , I am installing a R Package as following - R CMD INSTALL spatstat_1.26-0.tar.gz It seems my installation hangs at byte-compile and prepare package for lazy loading I kept on waiting for 1/2anhr but it hanged

[R] Package 'compositions', function acomp() With Missing Data

2014-09-29 Thread Rich Shepard
The acomp() function works well on data sets with no missing data. For example: win.acomp - acomp(win.cast, parts=2:6) win.acomp Filterer Gatherer Grazer Predator Shredder [1,] 0.0667 0.600 0.0667 0.2444000 0.0222 [2,] 0.06120612 0.5714571 0.06120612 0.2653265

[R] package loadable in R 3.1.1 Rterm but not in emacs/ESS

2014-09-26 Thread Christopher W Ryan
I'm running R on Windows 7. Clean install on a brand new computer yesterday. I installed Protext then R then Vincent Goulet's emacs with ESS, in that order. I then installed some R packages, in the R terminal window. Among them was car Today I opened emacs, hit M-x R to start an R session, and

Re: [R] Package 'compositions' and R-3.1.0 [UPDATE]

2014-09-24 Thread Rich Shepard
On Wed, 14 May 2014, Prof Brian Ripley wrote: The compositions package has apparently been archived: Yes, but not giving correct results There is a new version, 1.40 released in June that is in CRAN and loads in R-3.1.1. Cannot attest to its correctness, but I'll read all the docs

[R] package Parallel - accessing remote cores on Windows using plink (PuTTY)

2014-09-19 Thread Tevlin, Dylan
Hello all. My system information: R 2.14.1 x64 Windows 7 I'm attempting to access cores on other machines in my LAN. As setup, I can ping all the machines successfully and it's a private office network where I have access to all computers, so there really shouldn't be any problems arising

Re: [R] package Parallel - accessing remote cores on Windows using plink (PuTTY)

2014-09-19 Thread Jeff Newmiller
While I hope someone with first hand experience or time to try it out pipes up, I noticed something wrong in your description. The ssh command is executed on the local machine, not the remote machine. That command must succeed on the local machine in order to start Rscript on the remote

Re: [R] package Parallel - accessing remote cores on Windows using plink (PuTTY)

2014-09-19 Thread Tevlin, Dylan
, so fingers crossed that works Dylan Tevlin (480) 419-3611 -Original Message- From: Jeff Newmiller [mailto:jdnew...@dcn.davis.ca.us] Sent: Friday, September 19, 2014 8:41 AM To: Tevlin, Dylan; r-help@r-project.org Subject: Re: [R] package Parallel - accessing remote cores on Windows using

Re: [R] package Parallel - accessing remote cores on Windows using plink (PuTTY)

2014-09-19 Thread Tevlin, Dylan
-project.org' Subject: RE: [R] package Parallel - accessing remote cores on Windows using plink (PuTTY) Thanks for your input Jeff, yes that was a misunderstanding on my part about where the system command was actually run, and I think you're right on point, that path to Rscript doesn't make any

[R] package ape read.dna diploid input data

2014-09-17 Thread Sarah Signor
I am fundamentally not understanding something about how this is set up, but after a few hours of googling I am going to ask and I apologize if its quite basic. I have sanger data that I am reading into ape with read.dna. x-read.dna(/Volumes/Storage/file.phy, format = interleaved) It has IUPAC

[R] [R-pkgs] New R package ``bvarsv''

2014-09-13 Thread Krueger, Fabian
Dear R users, please let me draw your attention to my new R package bvarsv (on CRAN since August 28) which implements the Primiceri (Review of Economic Studies, 2005) vector autoregressive model. The model is popular in macroeconomic analysis as it allows to model instabilities (e.g

Re: [R] Built R package with example

2014-09-05 Thread Uwe Ligges
On 04.09.2014 20:02, Karim Mezhoud wrote: Dear All, How can I add folder content examples of needed files to run example? The simple add of folder did not built and reload with the package. If you need additional data, put the data in the package as described in Writing R Extensions. If

[R] Built R package with example

2014-09-04 Thread Karim Mezhoud
Dear All, How can I add folder content examples of needed files to run example? The simple add of folder did not built and reload with the package. Thanks! Karim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

[R] package 'gradientForest' and 'extendedForest'

2014-08-26 Thread Kulupp
Dear experts, I have 5 environmental predictors and abundance data (300 samples, 60 species, transformation: log(x + min(x,x 0) and use the function 'gradientForest' to estimate (R�-weighted) predictor importance (regression trees). The resulting predictor importance in decreasing order is

[R] GSoC 2014 - an R package for working with RRD files

2014-08-11 Thread Plamen Dimitrov
Hello, I'm taking part in Google Summer of Code 2014 wih Ganglia and I spent the past few months implementing an R package that makes it possible to directly import and work with RRD (http://oss.oetiker.ch/rrdtool/) files in R. There are currently three ways to use the package: - importRRD

[R] R Package for Text Manipulation

2014-08-09 Thread Omar André Gonzáles Díaz
Hi all, I want to know, where i can find a package to simulate the functions Search and Replace and Find Words that contain - replace them with..., that we can use in EXCEL. I've look in other places and they say: Reshape2 by Hadley Wickham. How ever, i've investigated it and its not exactly

Re: [R] R Package for Text Manipulation

2014-08-09 Thread Gabor Grothendieck
On Sat, Aug 9, 2014 at 8:15 AM, Omar André Gonzáles Díaz oma.gonza...@gmail.com wrote: Hi all, I want to know, where i can find a package to simulate the functions Search and Replace and Find Words that contain - replace them with..., that we can use in EXCEL. I've look in other places and

Re: [R] R Package for Text Manipulation

2014-08-09 Thread David Winsemius
On Aug 9, 2014, at 5:15 AM, Omar André Gonzáles Díaz wrote: Hi all, I want to know, where i can find a package to simulate the functions Search and Replace and Find Words that contain - replace them with..., that we can use in EXCEL. I've look in other places and they say: Reshape2 by

[R] Package gptk, no default option

2014-08-05 Thread Gyanendra Pokharel
Hi there, Could someone explain the input options in the function gpCreat(q,d,X,y,options) in package gptk? I tried looking at the program gpOptions.R but did not get the way to input the option Many thanks Gyan .. Gyanendra Pokharel University of Guelph Guelph, ON

[R] [R-pkgs] icd9 - a new R package

2014-07-09 Thread Jack Wasey
Dear R people, The new packge 'icd9' provides a range of tools for working with ICD-9-CM codes. http://cran.r-project.org/web/packages/icd9/index.html https://github.com/jackwasey/icd9 ICD-9 (clinical modification) is primarily used for categorizing diseases in the USA for hospital

[R] package: RWinEdt question

2014-07-06 Thread Mari
I just upgraded WinEdt from 5.2 to 8.2. With the older version, invoking library(RWinEdt) started a new instance of WinEdt identified by R-WinEdt as the title. This way, I was able to separate R work from other editing work with two instances of WinEdt running. However, with the newer version

Re: [R] package: RWinEdt question

2014-07-06 Thread Uwe Ligges
The RWinEdt package does not support WinEdt 8.x yet. Versions 5.x and 6.x shoudl be supported. Not sure about 7.x. Unfortunately, the trick to get it working changes with each version of WinEdt these days ... Well, I may be too bad in WinEdt macro programming... I do notn have the new versions

Re: [R] package: RWinEdt question

2014-07-06 Thread Duncan Murdoch
On 06/07/2014, 4:35 PM, Uwe Ligges wrote: The RWinEdt package does not support WinEdt 8.x yet. Versions 5.x and 6.x shoudl be supported. Not sure about 7.x. Unfortunately, the trick to get it working changes with each version of WinEdt these days ... Well, I may be too bad in WinEdt macro

Re: [R] package: RWinEdt question

2014-07-06 Thread Mari
Thank you for your quick reply. Except for the instances issue, RWinEdt seems to be working well with WinEdt 8.2 so I'll continue to use it. (I can't customize keyboard shortcuts in RStudio or some of the other often mentioned editors). I looked at the code for startWinEdt and I can see where

[R] What are the other Options for hiddenActFunc in the RSNNS r package?

2014-07-01 Thread meg
I am trying to figure out the options for hiddenActFunc..any help would be great!! -- View this message in context: http://r.789695.n4.nabble.com/What-are-the-other-Options-for-hiddenActFunc-in-the-RSNNS-r-package-tp4693313.html Sent from the R help mailing list archive at Nabble.com

[R] Assigning document id to each document containing in the Document Term Matrix (R Package tm)

2014-06-24 Thread 张伦
Dear All, When I do DocumentTermMatrix analysis, can I assign a document id to the document (i.e., the row in the attached matrix marked in red)? Here is my code: tdm=DocumentTermMatrix(corpus,control) inspect (tdm2[5:20,9:14]) Terms Docs 002089 002223 002236 002268 002415 002439 5

Re: [R] Help with R package

2014-06-08 Thread Uwe Ligges
On 07.06.2014 23:34, Milan Bimali wrote: Dear R Community, I am in process of developing an R package which in turn depends on a package that is not available in CRAN but has to be downloaded from a web source (as follows). Could someone guide me on how to include the package listed

Re: [R] Package 'effects' plotting allEffects question

2014-06-07 Thread Ista Zahn
See ?Effect On Jun 6, 2014 9:38 PM, Nwinters nicholas.wint...@mail.mcgill.ca wrote: Is there a way to plot just the response function for one variable, instead of every variable on the same plot? my model has 13 variables and the plot produces a graph for each of these on the same plot,

Re: [R] Package 'effects' plotting allEffects question

2014-06-07 Thread Michael Friendly
just use plot(Effect(myvar, mymodel)) On 6/6/2014 11:28 AM, Nwinters wrote: Is there a way to plot just the response function for one variable, instead of every variable on the same plot? my model has 13 variables and the plot produces a graph for each of these on the same plot, which is

[R] Help with R package

2014-06-07 Thread Milan Bimali
Dear R Community, I am in process of developing an R package which in turn depends on a package that is not available in CRAN but has to be downloaded from a web source (as follows). Could someone guide me on how to include the package listed in Depends of the Description file. I have

[R] Package 'effects' plotting allEffects question

2014-06-06 Thread Nwinters
Is there a way to plot just the response function for one variable, instead of every variable on the same plot? my model has 13 variables and the plot produces a graph for each of these on the same plot, which is useless. -- View this message in context:

[R] Package 'effects' plotting allEffects question

2014-06-06 Thread Nwinters
Is there a way to plot just the response function for one variable, instead of every variable on the same plot? my model has 13 variables and the plot produces a graph for each of these on the same plot, which is useless. -- View this message in context:

[R] How to include static PDFs vignettes in an R package

2014-05-20 Thread Luca Scrucca
Hi all, prior to R version 3.0 I used to include a static PDF file as package vignette following the instructions in http://www.icesi.edu.co/CRAN/web/packages/R.rsp/vignettes/NonSweaveVignettes.pdf (I know this is a little bit old), except that the relevant files where in vignette/ directory

Re: [R] How to include static PDFs vignettes in an R package

2014-05-20 Thread Duncan Murdoch
On 20/05/2014, 2:51 AM, Luca Scrucca wrote: Hi all, prior to R version 3.0 I used to include a static PDF file as package vignette following the instructions in http://www.icesi.edu.co/CRAN/web/packages/R.rsp/vignettes/NonSweaveVignettes.pdf (I know this is a little bit old), except that the

Re: [R] package to plot mean and standard deviation directly on data

2014-05-13 Thread Luigi Marongiu
England Armidale NSW 2351 Email: home: mac...@northnet.com.au -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Luigi Marongiu Sent: Tuesday, 13 May 2014 03:50 To: r-help@r-project.org Subject: [R] package to plot mean

Re: [R] package to plot mean and standard deviation directly on data

2014-05-13 Thread Luigi Marongiu
Dear Jim, I have use the brkdn.plot as you suggested and I quite like it since it is easy to use. Would be possible to overlap the confidence bars (SD) with the mean value points? The implemetation leaves a small space as you can see in this figure. I tired with a pch=list(type=o, pch=c(16, 1,

[R] Package 'compositions' and R-3.1.0

2014-05-13 Thread Rich Shepard
I just tried to install 'compositions'. It's apparently not yet available for R-3.1.0. How can I learn when it might be available? TIA, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread Rolf Turner
On 14/05/14 09:21, Rich Shepard wrote: I just tried to install 'compositions'. It's apparently not yet available for R-3.1.0. How can I learn when it might be available? The compositions package has apparently been archived: Package ‘compositions’ was removed from the CRAN repository.

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread David Winsemius
On May 13, 2014, at 2:59 PM, Rolf Turner wrote: On 14/05/14 09:21, Rich Shepard wrote: I just tried to install 'compositions'. It's apparently not yet available for R-3.1.0. How can I learn when it might be available? The compositions package has apparently been archived: Package

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread Rich Shepard
On Wed, 14 May 2014, Rolf Turner wrote: The compositions package has apparently been archived: Package ‘compositions’ was removed from the CRAN repository. Formerly available versions can be obtained from the archive. Archived on 2014-05-01 as undefined-behaviour errors were not corrected

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread Rich Shepard
On Tue, 13 May 2014, David Winsemius wrote: There was just a posting on R-devel today that suggested compiling from source has a good chance to succeed without even fixes. David, I'll try to find that thread and the source. Thanks, Rich -- Richard B. Shepard, Ph.D.| Technically

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread David Winsemius
On May 13, 2014, at 3:40 PM, Rich Shepard wrote: On Tue, 13 May 2014, David Winsemius wrote: There was just a posting on R-devel today that suggested compiling from source has a good chance to succeed without even fixes. David, I'll try to find that thread and the source. The source

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread Rich Shepard
On Tue, 13 May 2014, David Winsemius wrote: The source is in the usual place and there was a solitary posting that reported success with the usual mechanism for building an R packge: R CMD build compositions David, Thank you. I found the package home page and downloaded the source from

Re: [R] Package 'compositions' and R-3.1.0

2014-05-13 Thread Prof Brian Ripley
On 13/05/2014 23:18, David Winsemius wrote: On May 13, 2014, at 2:59 PM, Rolf Turner wrote: On 14/05/14 09:21, Rich Shepard wrote: I just tried to install 'compositions'. It's apparently not yet available for R-3.1.0. How can I learn when it might be available? The compositions package

[R] package to plot mean and standard deviation directly on data

2014-05-12 Thread Luigi Marongiu
Dear all, is there a package, preferably not ggplot, to draw the lines for the standard deviation just by providing the vector with the data? more or less as it happens with the boxplot function. the procedure i implemented herein requires the calculation of the means, standard deviations, limits

Re: [R] package to plot mean and standard deviation directly on data

2014-05-12 Thread Jim Lemon
On Mon, 12 May 2014 06:50:29 PM Luigi Marongiu wrote: Dear all, is there a package, preferably not ggplot, to draw the lines for the standard deviation just by providing the vector with the data? more or less as it happens with the boxplot function. the procedure i implemented herein

Re: [R] package to plot mean and standard deviation directly on data

2014-05-12 Thread Duncan Mackay
-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Luigi Marongiu Sent: Tuesday, 13 May 2014 03:50 To: r-help@r-project.org Subject: [R] package to plot mean and standard deviation directly on data Dear all, is there a package, preferably not ggplot, to draw the lines

[R] R Package making error

2014-05-05 Thread Ashis Deb
Hi all , I have a GUI package function like below , trader-function() { install.packages(Rgtk2) install.packages(cluster) install.packages(gWidgets) install.packages(gWidgetsRGtk2) install.packages(scales) install.packages(RGtk2Extras) install.packages(FuzzyToolkitUoN)

Re: [R] R Package making error

2014-05-05 Thread Sarah Goslee
While I don't particularly like the idea of a package automatically making changes to the system, you can use installed.packages() to see which of your needed packages are already available, and only install the ones that are missing. Better would be to put the whole list in Depends, and let R

[R] How to convert R package and dependencies to debian packages?

2014-04-22 Thread Sathish Kumar
a list of R debian packages here: http://cran.cnr.berkeley.edu/bin/linux/ubuntu/lucid/ But it does not contain all the packages that i need. Is there a way to convert any R package and it's internal dependencies to a Debian package similar to the approach used in creating r-cran-*.deb? Thanks

[R] WANT TO CONVERT R PACKAGE TO A DLL TO USE IN C#

2014-03-24 Thread Ashis Deb
HI ALL, I have a package [[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 http://www.R-project.org/posting-guide.html and

[R] HOW TO MAKE A R PACKAGE TO A DLL FILE TO USE IN C#

2014-03-24 Thread Ashis Deb
HI ALL, I made a package such that when i call the function inside the package like rabbit() , it gives my GUI very well , now I want to convert this package into a Dynamic link library(DLL) ,such that I can use it in C# using RDOT NET

Re: [R] package environment versus namespace environment

2014-03-19 Thread Suraj Gupta
As the author of that post, I must respond... # - first comment --- Ducan: The article that Henrik cited gives a reasonable description up until near the end Suraj: Given the complexity of the topics at hand, the many accolades I've received for the post, and how thoroughly I've

Re: [R] package environment versus namespace environment

2014-03-19 Thread Mark Leeds
Hi Everyone: Suraj will respond to Duncan's comments below promptly. Suraj doesn't have the original thread so I am just helping out by commenting here so that he can respond and the thread can be kept continuous. Mark On Sun, Mar 9, 2014 at 9:09 AM, Duncan Murdoch

Re: [R] package environment versus namespace environment

2014-03-19 Thread Duncan Murdoch
On 14-03-19 1:18 PM, Suraj Gupta wrote: As the author of that post, I must respond... # - first comment --- Ducan: The article that Henrik cited gives a reasonable description up until near the end Suraj: Given the complexity of the topics at hand, the many accolades I've received

Re: [R] package environment versus namespace environment

2014-03-19 Thread Mark Leeds
Hi Duncan: If you think there is anything incorrect in the document, I'd be interested because I refer to that document whenever I'm confused about namespaces, importing etc. Thanks. On Wed, Mar 19, 2014 at 4:31 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 14-03-19 1:18 PM, Suraj

Re: [R] data.table and R package check

2014-03-17 Thread ONKELINX, Thierry
a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Witold E Wolski Verzonden: vrijdag 14 maart 2014 13:16 Aan: r-help@r-project.org Onderwerp: [R] data.table and R package check Hi, using data.table

Re: [R] data.table and R package check

2014-03-17 Thread Prof Brian Ripley
2014 13:16 Aan: r-help@r-project.org Onderwerp: [R] data.table and R package check Hi, using data.table in package code i.e setkey(aligtable,transition_group_id,align_origfilename) aligtable = aligtable[CJ(unique(transition_group_id), unique(align_origfilename))] When I do run R package check I got

[R] data.table and R package check

2014-03-14 Thread Witold E Wolski
Hi, using data.table in package code i.e setkey(aligtable,transition_group_id,align_origfilename) aligtable = aligtable[CJ(unique(transition_group_id), unique(align_origfilename))] When I do run R package check I got warnings such as: convert2msExperiment: no visible binding for global

Re: [R] package environment versus namespace environment

2014-03-10 Thread Duncan Murdoch
On 14-03-09 1:59 PM, Benjamin Tyner wrote: Duncan, Thanks for the explanation and commentary. Starting to make more sense...so, long story short, it seems the first thing one should check is whether base imports utils: packageDescription(base) Package: base Version: 3.0.1

Re: [R] package environment versus namespace environment

2014-03-09 Thread Duncan Murdoch
On 14-03-08 6:42 PM, Benjamin Tyner wrote: Duncan, Thank you for the informative link. So, do the loaded namespaces have an ordering akin to the package search path that determines that functions in the base namespace can see objects in the utils namespace? (I noticed that loadedNamespaces()

Re: [R] package environment versus namespace environment

2014-03-09 Thread Benjamin Tyner
Duncan, Thanks for the explanation and commentary. Starting to make more sense...so, long story short, it seems the first thing one should check is whether base imports utils: packageDescription(base) Package: base Version: 3.0.1 Priority: base Title:

[R] package opVar

2014-03-08 Thread Charles Thuo
Hello, I was attempting to install the package opVAr and got the following message Warning message: package 'opVar' is not available (for R version 3.0.2) Is this package available at all. [[alternative HTML version deleted]] __

Re: [R] package opVar

2014-03-08 Thread Pascal Oettli
Hello, There is no package opVar in the available CRAN packages list. Regards, Pascal On Sat, Mar 8, 2014 at 6:06 PM, Charles Thuo tcmui...@gmail.com wrote: Hello, I was attempting to install the package opVAr and got the following message Warning message: package 'opVar' is not available

Re: [R] package opVar

2014-03-08 Thread Ben Bolker
Pascal Oettli kridox at ymail.com writes: Hello, There is no package opVar in the available CRAN packages list. Regards, Pascal On Sat, Mar 8, 2014 at 6:06 PM, Charles Thuo tcmuigai at gmail.com wrote: [snip] Warning message: package 'opVar' is not available (for R version

Re: [R] package environment versus namespace environment

2014-03-08 Thread Benjamin Tyner
Duncan, Thank you for the informative link. So, do the loaded namespaces have an ordering akin to the package search path that determines that functions in the base namespace can see objects in the utils namespace? (I noticed that loadedNamespaces() just comes back in alphabetical

Re: [R] package environment versus namespace environment

2014-03-08 Thread Henrik Bengtsson
See Suraj Gupta's online article 'How R Searches and Finds Stuff' from March 29, 2012: http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/ It's a very useful write up on this topic. /Henrik On Sat, Mar 8, 2014 at 3:42 PM, Benjamin Tyner bty...@gmail.com wrote: Duncan, Thank

[R] package environment versus namespace environment

2014-03-07 Thread Benjamin Tyner
Hello, I realize that a function in environment: base (for example, function head1 below) is unable to see (without resorting to ::, anyway) objects in utils (for example, head below), since package:base is after package:utils on the search path. However, I'm wondering what is the machinery that

Re: [R] package environment versus namespace environment

2014-03-07 Thread Duncan Murdoch
On 07/03/2014 10:16 AM, Benjamin Tyner wrote: Hello, I realize that a function in environment: base (for example, function head1 below) is unable to see (without resorting to ::, anyway) objects in utils (for example, head below), since package:base is after package:utils on the search path.

[R] multinomial mixed logit model mlogit r-package

2014-02-25 Thread Thomas Schlesinger
I discovered the 'mlogit'-package for multinomial logit models in search of estimating a multinomial mixed logit model. After reading the excellent vignette I discovered that I could not apply my data on any of the described examples. I now write in hope of help with my problem and created a

[R] Package development: overriding a function from one package with a function from another?

2014-02-19 Thread Tal Galili
Dear R users, I am currently working on developing two packages, below is a simplified version of my problem: In package A I have some functions (say sum_twice), and I it calls to another function inside the package (say slow_sum). However, in package B, I wrote another function (say fast_sum),

[R] package parallel help

2014-02-06 Thread Jeffrey Flint
I am looking for ways to reduce my process size for calls to mclapply. I have determined that the size of my process is creating too much overhead for the forking to be faster than a serial run.I am looking for some techniques to experiment with. I have been getting huge efficiency gains

Re: [R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-02-03 Thread Simon Wood
I suppose there may be an error of sorts, but have you considered the fact that solving the error might not gain you admittance into heaven? Look at the RHS of the model: sensor2 + s(site, bs = re) ... and think about the fact that you are smoothing a factor variable. - Actually this is ok.

Re: [R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-02-03 Thread Simon Wood
Hi Katharina, Thanks for sending this. The problem is that the prediction data for site contain levels not available in the (useable non-NA) fit data... levels(m$model$site) [1] KRB NP.FOR WKS.FRE WKS.KRE WKS.RIE WKS.WUE levels(gapData$site) [1] KRB NP.FOR RIE.2 WKS.BBR WKS.FRE

Re: [R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-02-03 Thread Katharina May
Hi Simon, many thanks for looking into this and making me understand the problem! I'll adjust my factor levels right away... Best, Katharina On 3 February 2014 12:42, Simon Wood s.w...@bath.ac.uk wrote: Hi Katharina, Thanks for sending this. The problem is that the prediction data for site

[R] package mgcv - predict with bam: Error in X[ind, ] :, subscript out of bounds

2014-02-03 Thread William Shadish
Dear Simon, your note below says bs=re specifies a Gaussian random effect . I have been using bs = re for data modeled with Poisson and binomial distributions, or variants thereof (e.g., quasi-Poisson). Have I erred in assuming bs =re can be used to obtain random effects for such data? Will

Re: [R] package mgcv - predict with bam: Error in X[ind, ] :, subscript out of bounds

2014-02-03 Thread Gavin Simpson
The two distributions are different. The random effect is assumed to be a Gaussian random variable, just as it is with the GLMMs in the lme4 package. It is fine to use such a random effect within a GAM with a non-Gaussian error distribution, like the ones you describe using. HTH Gavin On 3

Re: [R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-02-02 Thread Katharina May
Hi Simon, thank you for your reply, I really appreciate any help to understand the problem here... Unluckily the package upgrade didn't help with this issue. An example reproducing the error, and a current sessionInfo() Output can be found below. Many thanks once again, Katharina R

Re: [R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-02-02 Thread David Winsemius
On Feb 2, 2014, at 9:52 AM, Katharina May wrote: Hi Simon, thank you for your reply, I really appreciate any help to understand the problem here... Unluckily the package upgrade didn't help with this issue. An example reproducing the error, and a current sessionInfo() Output can be found

Re: [R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-01-31 Thread Simon Wood
Hi Katharina, Could you try upgrading to mgcv_1.7-28, please? There was an occasional problem to do with matching factor levels, which is fixed, but I'm not very confident that is what is going on. If upgrading doesn't work, is there any chance you could send me a small example dataset and

[R] package mgcv - predict with bam: Error in X[ind, ] : subscript out of bounds

2014-01-30 Thread Katharina May
Dear R-Community, I`m trying to apply the mgcv package to fill gaps in sensor data from different sites (9 sites, 2 sensors per site) and do the filling on a site-wise level. Based on http://r.789695.n4.nabble.com/mgcv-gamm-predict-to-reflect-random-s-effects-td3622738.html my model looks like

[R] Creating a R-package in R-Studio

2014-01-29 Thread Kulupp
Dear R-help community, I am creating my first R-package in RStudio and wanted to add datasets to the package. I added an .RData file containing data (a data frame) in the 'data' folder of the package and could load the data as usual by typing in the console: data(xyz). Then I added a .RData

Re: [R] Creating a R-package in R-Studio

2014-01-29 Thread Duncan Murdoch
On 29/01/2014 2:49 PM, Kulupp wrote: Dear R-help community, I am creating my first R-package in RStudio and wanted to add datasets to the package. I added an .RData file containing data (a data frame) in the 'data' folder of the package and could load the data as usual by typing in the console

[R] Strange gcfit output in R package Grofit

2014-01-21 Thread Lucy Rayner
Hi all, I'm trying to use the R growth curve analysis package Grofit. I've used it successfully before but the protocol which previously worked for me is now not giving me the expected output. Entering my data and time info and running Test-grofit(time,data,FALSE) gives me the expected growth

[R] Package TM dataframes

2014-01-10 Thread ramoss
Hi, I am trying to use the package TM on a dataframe get the following error: complaints - tm_map(complaints, tolower) Error in UseMethod(tm_map, x) : no applicable method for 'tm_map' applied to an object of class data.frame Tm doesn't work on dataframes? My data frame consists of 1 text

Re: [R] Package TM dataframes

2014-01-10 Thread David Winsemius
On Jan 10, 2014, at 10:11 AM, ramoss wrote: Hi, I am trying to use the package TM on a dataframe get the following error: complaints - tm_map(complaints, tolower) Error in UseMethod(tm_map, x) : no applicable method for 'tm_map' applied to an object of class data.frame Tm doesn't work

[R] Package LaplacesDemon information

2014-01-03 Thread Vittorio Colagrande
Dear R-group I can not install the package LaplacesDemon in version 3.0.2 of R. I ask whether it is possible or, alternatively, signs for a equivalent package. Thanks you and best regards. Vittorio Colagrande [[alternative HTML version deleted]]

Re: [R] Package LaplacesDemon information

2014-01-03 Thread David Winsemius
On Jan 3, 2014, at 6:45 AM, Vittorio Colagrande wrote: Dear R-group I can not install the package LaplacesDemon in version 3.0.2 of R. I ask whether it is possible or, alternatively, signs for a equivalent package. Thanks you and best regards. Vittorio Colagrande

[R] Any R-package geared towards Endorsement Frequencies?

2014-01-02 Thread Lila Lorne
Happy New Year everyone, I need some help figuring out if there is an R package tailored towards endorsement frequencies. Would y'all here know of any such packages that they would recommend I use? Thanks! Lily If it doesn't challenge you, it doesn't change you - Fred DeVito

Re: [R] Any R-package geared towards Endorsement Frequencies?

2014-01-02 Thread Ista Zahn
if there is an R package tailored towards endorsement frequencies. Would y'all here know of any such packages that they would recommend I use? Thanks! Lily If it doesn't challenge you, it doesn't change you - Fred DeVito [[alternative HTML version deleted

Re: [R] Any R-package geared towards Endorsement Frequencies?

2014-01-02 Thread Lila Lorne
...@gmail.com wrote: Happy New Year everyone, I need some help figuring out if there is an R package tailored towards endorsement frequencies. Would y'all here know of any such packages that they would recommend I use? Thanks! Lily If it doesn't challenge you

Re: [R] Any R-package geared towards Endorsement Frequencies?

2014-01-02 Thread Ista Zahn
at http://cran.r-project.org/web/views/ ? Best, Ista On Thu, Jan 2, 2014 at 9:59 AM, Lila Lorne lilalillia...@gmail.com wrote: Happy New Year everyone, I need some help figuring out if there is an R package tailored towards endorsement frequencies. Would y'all here know of any such packages

Re: [R] Any R-package geared towards Endorsement Frequencies?

2014-01-02 Thread Richard M. Heiberger
help figuring out if there is an R package tailored towards endorsement frequencies. Would y'all here know of any such packages that they would recommend I use? Thanks! Lily If it doesn't challenge you, it doesn't change you - Fred DeVito [[alternative HTML

Re: [R] Package dependencies in building R packages

2013-12-31 Thread Philippe Grosjean
On 30 Dec 2013, at 20:01, Axel Urbiz axel.ur...@gmail.com wrote: Thanks for your kind response Duncan. To be more specific, I'm using the function mvrnorm from MASS. The issue is that MASS depends on survival and I have a function in my package named tt() which conflicts with a function in

Re: [R] Package dependencies in building R packages

2013-12-31 Thread Hadley Wickham
Thanks for your kind response Duncan. To be more specific, I'm using the function mvrnorm from MASS. The issue is that MASS depends on survival and I have a function in my package named tt() which conflicts with a function in survival of the same name. I can think of 2 alternatives solutions

Re: [R] Package dependencies in building R packages

2013-12-31 Thread Paul Gilbert
To: Duncan Murdochmurdoch.dun...@gmail.com Cc:R-help@r-project.org R-help@r-project.org Subject: Re: [R] Package dependencies in building R packages Message-ID: CAAyVsXKCN1Zn4gbG=QkD759kaDadPbgp+9e3W6nPvOLVwAsU=w...@mail.gmail.com Content-Type: text/plain Thanks for your kind response

[R] Package dependencies in building R packages

2013-12-30 Thread Axel Urbiz
Dear users, My package {foo} depends on a function miscFUN which is on package {foo_depend}. This last package also depends on other packages, say {A, B, C}, but miscFUN is not dependent on A, B, C (only on foo_depend). In my package {foo}, is there a way to only have it depend on the function

Re: [R] Package dependencies in building R packages

2013-12-30 Thread Duncan Murdoch
On 13-12-30 1:24 PM, Axel Urbiz wrote: Dear users, My package {foo} depends on a function miscFUN which is on package {foo_depend}. This last package also depends on other packages, say {A, B, C}, but miscFUN is not dependent on A, B, C (only on foo_depend). In my package {foo}, is there a way

Re: [R] Package dependencies in building R packages

2013-12-30 Thread Axel Urbiz
Thanks for your kind response Duncan. To be more specific, I'm using the function mvrnorm from MASS. The issue is that MASS depends on survival and I have a function in my package named tt() which conflicts with a function in survival of the same name. I can think of 2 alternatives solutions to my

Re: [R] Package dependencies in building R packages

2013-12-30 Thread Duncan Murdoch
On 13-12-30 2:01 PM, Axel Urbiz wrote: Thanks for your kind response Duncan. To be more specific, I'm using the function mvrnorm from MASS. The issue is that MASS depends on survival and I have a function in my package named tt() which conflicts with a function in survival of the same name. I

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