Re: [R-es] Contrastes de Rangos Alineados

2015-07-06 Thread Carlos Ortega
Hola, No sé si en tus búsquedas llegaste a ver esto, ofrecen una alternativa de cálculo. http://r.789695.n4.nabble.com/Scheirer-Ray-Hare-td3818476.html Otra alternativa a la duda que planteas, es escribir al propio autor del paquete... Saludos, Carlos Ortega www.qualityexcellence.es El 4 de

[R] Hypergeometric Function seems to give wrong results

2015-07-06 Thread Carlos Nasher via R-help
Hello R helpers, I need to evaluate the Hypergeometric Function of the 2nd kind (Tricomi confluent hypergeometric function). Therefore I'm using the kummerU function from the fAsianOptions package. It seems to me that kummerU is giving wrong results. Here's an example: library(fAsianOptions)

Re: [R] igraph plot slowness

2015-07-06 Thread Loris Bennett
Hi Jim, jim holtman jholt...@gmail.com writes: Here is what it does locally on my PC: library(igraph) topo_data - read.table(text = ibcore01ibswitch01 + ibcore01ibswitch02 + ibcore01ibswitch03 + ibcore02ibswitch01 + ibcore02ibswitch02 +

Re: [R] Variance estimates for survreg vs. lm

2015-07-06 Thread Therneau, Terry M., Ph.D.
The difference is that survreg is using a maximum likelihood estimate (MLE) of the variance and that lm is using the unbiased (MVUE) estimate of variance. For simple linear regression, the former divides by n and the latter by n-p. The difference in your variances is exactly n/(n-p) = 10/8.

Re: [R] Rgui not working in Windows Version 8.1

2015-07-06 Thread John C Frain
I am running R version 3.2.1 Patched (2015-07-02 r68625) -- World-Famous Astronaut Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) and do not have any problems with Rgui. The output from Sys.info() is Sys.info() sysname

[R-es] Fwd: Contrastes de Rangos Alineados

2015-07-06 Thread Ing . Agr . Gustavo Giménez
-- Mensaje reenviado -- De: Carlos Ortega c...@qualityexcellence.es Fecha: 6 de julio de 2015, 7:03 Asunto: Re: [R-es] Contrastes de Rangos Alineados Para: Ing. Agr. Gustavo Giménez gune...@gmail.com Cc: Lista R r-help-es@r-project.org Hola, No sé si en tus búsquedas llegaste a

[R-es] Pasar un listado de variables como argumento de una función

2015-07-06 Thread Griera
Hola: Quiero que una función realice una serie de cálculos pero eliminando las variables que no interesan (diferentes según e fichero a analizar). Intento pasar esta lista como argumento con un c(VAR1, VAR2, etc), pero no lo consigo. Un ejemplo seria: DATOS - data.frame(SE=c(M, H, M, M, H),

Re: [R] what constitutes a 'complete sentence'?

2015-07-06 Thread Rolf Turner
On 07/07/15 07:10, William Dunlap wrote: [Rolf Turner wrote.] The CRAN guidelines should be rewritten so that they say what they *mean*. If a complete sentence is not actually required --- and it seems abundantly clear that it is not --- then guidelines should not say so. Rather they should

Re: [R] Invalid URL for R documentation

2015-07-06 Thread Marc Schwartz
On Jul 6, 2015, at 10:10 AM, Paul paul.domas...@gmail.com wrote: I tried accessing http://cran.r-project.org/doc/manuals/r-release/R- intro.html, which is linked to from http://cran.r- project.org/manuals.html. I get the message that the URL could not be found by the server. Just

[R] NaN produced from log() with positive input

2015-07-06 Thread Maram Salem
Dear All I'm trying to find the maximum likelihood estimator of a certain distribution based on the newton raphson method using maxLik package. I wrote the log-likelihood , gradient, and hessian functionsusing the following code. #Step 1: Creating the theta vector theta -vector(mode =

[R] Sphericity for a repeated measure ANOVA with whithin and between subjects design, using R

2015-07-06 Thread angelo.arc...@virgilio.it
Dear List Members, I need to perform a four-way ANOVA with repeated measures and to calculate the sphericity for eventual correction of the degree of freedom of the F ratio. I have three within subjects factors (Emotion, having 5 levels, Material, having 4 levels, Shoes, having 2 levels)

Re: [R] opendap accessibility on Windows

2015-07-06 Thread Roy Mendelssohn - NOAA Federal
Hi Christina: My memory is that Pierce had problems getting the netcdf4 library to work with OpeNDAP included on Windows. OPeNDAP does work with ncdf4 on a Mac or a Linux box. So one option is to run on a Linux VM on Windows. There may be more direct options, depending on what datasets you

[R] Leave one out procedure - R

2015-07-06 Thread Vyshnnavi Parthasarathy
Hello, I am still in the process of familiarizing myself with R, pardon me if this is basic. I want to run a leave one out procedure for a 40 member dataset. At the moment I am doing it via a simple for loop. I wanted to know if there is a superior way to do it. I read about the loocv command here

Re: [R] what constitutes a 'complete sentence'?

2015-07-06 Thread Duncan Murdoch
On 06/07/2015 5:09 PM, Rolf Turner wrote: On 07/07/15 07:10, William Dunlap wrote: [Rolf Turner wrote.] The CRAN guidelines should be rewritten so that they say what they *mean*. If a complete sentence is not actually required --- and it seems abundantly clear that it is not --- then

Re: [R] Sphericity for a repeated measure ANOVA with whithin and between subjects design, using R

2015-07-06 Thread John Fox
Dear Angelo, One way to do this is with the Anova() function in the car package; see the following article in the R Journal: @Article{RJournal:2013-1:fox-friendly-weisberg, author = {John Fox and Michael Friendly and Sanford Weisberg}, title= {Hypothesis Tests for Multivariate

Re: [R] Web/Server Interface for R files

2015-07-06 Thread Ista Zahn
souce() works for URLs, so this should just work for http. Did you try it? Best, Ista On Mon, Jul 6, 2015 at 12:28 AM, Kunal Shah kunalshah...@gmail.com wrote: Hello, I have the following code From excel.link package xl.workbook.activate(ADSnippetXLS.xlsx)

Re: [R] Rgui not working in Windows Version 8.1

2015-07-06 Thread Erin Hodgess
I have tried that already...no luck. Thank you though! Sincerely, Erin On Mon, Jul 6, 2015 at 8:22 AM, John C Frain fra...@gmail.com wrote: I am running R version 3.2.1 Patched (2015-07-02 r68625) -- World-Famous Astronaut Copyright (C) 2015 The R Foundation for Statistical Computing

Re: [R] Invalid URL for R documentation

2015-07-06 Thread ProfJCNash
I'm also getting a 404. Tried https just in case. But http://cran.utstat.utoronto.ca/manuals.html works and I can copy the link for R-intro and it works there. http://cran.utstat.utoronto.ca/doc/manuals/r-release/R-intro.html Very odd. JN On 15-07-06 11:24 AM, Paul wrote:

[R] PCAgrid scores cannot be predicted correctly

2015-07-06 Thread Manuel Weinkauf
I have been running into a problem with the PCAgrid() function of the R-package pcaPP. When trying to predict the scores of new data using the resulting PCA, the predicted score values are wrong. This is true for both, using the predict() function and for calculating the scores manually after

Re: [R] Rgui not working in Windows Version 8.1

2015-07-06 Thread peter dalgaard
Hm, could you perhaps see whether R or RGui is the culprit by trying to start R in a Terminal (DOS box). If such a thing still exists in Windows 8.1, that is (I don't _do_ windows...). -Peter On 06 Jul 2015, at 18:37 , Erin Hodgess erinm.hodg...@gmail.com wrote: I have tried that

Re: [R] Rgui not working in Windows Version 8.1

2015-07-06 Thread Erin Hodgess
I'll try that next. Love the I don't do Windows. Do they give you a pane? On Mon, Jul 6, 2015 at 1:30 PM, peter dalgaard pda...@gmail.com wrote: Hm, could you perhaps see whether R or RGui is the culprit by trying to start R in a Terminal (DOS box). If such a thing still exists in Windows

Re: [R] what constitutes a 'complete sentence'?

2015-07-06 Thread William Dunlap
The CRAN guidelines should be rewritten so that they say what they *mean*. If a complete sentence is not actually required --- and it seems abundantly clear that it is not --- then guidelines should not say so. Rather they should say, clearly and comprehensibly, what actually *is* required.

Re: [R] Rgui not working in Windows Version 8.1

2015-07-06 Thread John C Frain
You might try starting Rterm or Rgui with the option --vanilla. If this starts the you have a corrupted .Rdata file or there is a problem with something in your environment. Have a look at appendix B of an introduction to R and you may be able to work out what is wrong. Check that some part of

Re: [R] Rmarkdown / knitr naming the output file

2015-07-06 Thread Yihui Xie
There is no direct way to get it, but you can get 1) the input filename via knitr::current_input(), and 2) the output format via knitr::opts_knit$get('rmarkdown.pandoc.to'). You may be able to figure out the output filename based on these two pieces of information. Regards, Yihui -- Yihui Xie

Re: [R] Leave one out procedure - R

2015-07-06 Thread John Kane
Hi Vyshnnavi, I'd suggest having a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and http://adv-r.had.co.nz/Reproducibility.html for some hints on how to ask questions on the R-help List. At the moment I don't think you have supplied enough

[R] R: RE: Bonferroni post hoc test in R for repeated measure ANOVA with mixed within and between subjects design

2015-07-06 Thread angelo.arc...@virgilio.it
Dear Michael, thank you for your answer, however, I am not asking for the tukey with the bonferroni adjustment, but doing the post hoc with the bonferroni method. Apparently this is done easily in SPSS, I am wondering whether it is possible with R. Can anyone help me? Thanks in advance

Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)

2015-07-06 Thread Duncan Mackay
Hi Luigi Not exactly sure what you want Have a look at https://stat.ethz.ch/pipermail/r-help/2007-May/132785.html and https://stat.ethz.ch/pipermail/r-help/2007-July/135551.html otherwise have a look at ?trellis.focus and https://stat.ethz.ch/pipermail/r-help/2006-July/109585.html failing

[R] problem understanding grid coordinate systems

2015-07-06 Thread Johannes Huesing
According to R Graphics by Paul Murrell, the coordinates that were used for the most recent lattics plot can be retrieved with native units. I have difficulties to access these coordinates. The following code renders the following results: library(grid) library(lattice) pl - xyplot(1:10 ~

Re: [R] opendap accessibility on Windows

2015-07-06 Thread Michael Sumner
On Tue, 7 Jul 2015 at 01:38 Christina Hernandez chernan...@gmri.org wrote: Hello, I am working on a project where we are accessing large data files via opendap. Myself and two of the higher-ups on the project are working on Windows machines, and we have been unable to access remote files

Re: [R] what constitutes a 'complete sentence'?

2015-07-06 Thread peter dalgaard
On 06 Jul 2015, at 23:19 , Duncan Murdoch murdoch.dun...@gmail.com wrote: On 06/07/2015 5:09 PM, Rolf Turner wrote: On 07/07/15 07:10, William Dunlap wrote: [Rolf Turner wrote.] The CRAN guidelines should be rewritten so that they say what they *mean*. If a complete sentence is not

Re: [R] what constitutes a 'complete sentence'?

2015-07-06 Thread John Fox
Dear Peter, I think that the grammatical term you're looking for is verb phrase. Best, John On Tue, 7 Jul 2015 00:12:25 +0200 peter dalgaard pda...@gmail.com wrote: On 06 Jul 2015, at 23:19 , Duncan Murdoch murdoch.dun...@gmail.com wrote: On 06/07/2015 5:09 PM, Rolf Turner wrote:

Re: [R] R: RE: Bonferroni post hoc test in R for repeated measure ANOVA with mixed within and between subjects design

2015-07-06 Thread John Fox
Dear Angelo, The Bonferroni p-value is just the ordinary p-value times the number of tests, so, since R supports multiplication, you can apply the Bonferroni adjustment in R. Because Bonferroni tests for multiple comparisons can be very conservative, asking why you want to use them is a fair

[R] Bonferroni post hoc test in R for repeated measure ANOVA with mixed within and between subjects design

2015-07-06 Thread angelo.arc...@virgilio.it
Dear List Members, I need to perform a Bonferroni post hoc test in R on a table with three within subjects factors (Emotion, having 5 levels, Material, having 4 levels, Shoes, having 2 levels) and one between subject factor (Musician, having 2 levels). I normally use the Tukey method

Re: [R] Invalid URL for R documentation

2015-07-06 Thread Paul
Marc Schwartz marc_schwartz at me.com writes: | It would appear that the HTML and EPUB files for the Release | versions of the manuals are not present, unless they are in the | process of being generated right now. The PDFs, dated July 6, 2015, | are present: | |

Re: [R] question

2015-07-06 Thread Mark Sharp
Lida, Please send the code that you ran. It is almost certain that you have a vector being formed that is the wrong length. There should be only one vector that you use to increment through the loop and that is the character vector formed when you read in your_met_file to form the met

Re: [R] Greek letters in column titles.

2015-07-06 Thread David L Carlson
Expanding slightly on Ista's answer, this may help if you are using Windows and want the symbol to appear in the console or in plots beta - intToUtf8(0x03B2) # or intToUtf8(946) a - 0:9 names(a) - paste0(beta, a) a β0 β1 β2 β3 β4 β5 β6 β7 β8 β9 0 1 2 3 4 5 6 7 8 9 plot(0:9, 0:9,

Re: [R] Invalid URL for R documentation

2015-07-06 Thread Paul
On Mon, Jul 6, 2015 at 10:10 AM, Paul Paul.Domaskis at gmail.com wrote: ...http://cran.r-project.org/doc/manuals/r-release/R-intro.html John McKown john.archie.mckown at gmail.com writes: I get a 404 on that page as well. Curiously, the R-patched and R-devel links work. Looks like the

[R] opendap accessibility on Windows

2015-07-06 Thread Christina Hernandez
Hello, I am working on a project where we are accessing large data files via opendap. Myself and two of the higher-ups on the project are working on Windows machines, and we have been unable to access remote files using the ncdf4 package. We have followed the package author's notes for

Re: [R] Rmarkdown / knitr naming the output file

2015-07-06 Thread Thierry Onkelinx
Dear Aurora, You acn try specifying a YAML block in the Rmd file and then render() it with the rmarkdown package. --- title: Your title output: pdf_document: pandoc_args: [ --output=doc1.pdf ] --- Note that I haven't tested it. Best regards, ir. Thierry Onkelinx Instituut voor

[R] Web/Server Interface for R files

2015-07-06 Thread Kunal Shah
Hello, I have the following code From excel.link package xl.workbook.activate(ADSnippetXLS.xlsx) source('ActiveDeltaSnippet2.R') ActiveDeltaSnippet2.R takes data from ADSnippetXLS, performs some computations on the data and outputs the data back into ADSnippetXLS.xlsx I dont want

[R] Task estimation - Monte Carlo

2015-07-06 Thread Mohan.Radhakrishnan
Hi I am trying to simulate task estimation person days using this type of R code. But I am not sure about reasoning here. Should the distribution be beta or triangular or something else ? How do we get the values of mu,z and s here ? Are there any explanations available ? Sections of some

Re: [R] Invalid URL for R documentation

2015-07-06 Thread Duncan Murdoch
On 06/07/2015 11:10 AM, Paul wrote: I tried accessing http://cran.r-project.org/doc/manuals/r-release/R- intro.html, which is linked to from http://cran.r- project.org/manuals.html. I get the message that the URL could not be found by the server. Just wondering if I'm doing something stunningly

Re: [R] question

2015-07-06 Thread Lida Zeighami
Hi Mark, Thank you so much for your help. I run your code and it works great for 5*1 character vector but if I run it for 682*1 character vector it has some error like this: Error in model.frame.default(formula = formula, ...) : variable lengths differ (found for 'egfr_v1_ckdepi') Would you

[R] Invalid URL for R documentation

2015-07-06 Thread Paul
I tried accessing http://cran.r-project.org/doc/manuals/r-release/R- intro.html, which is linked to from http://cran.r- project.org/manuals.html. I get the message that the URL could not be found by the server. Just wondering if I'm doing something stunningly un- smart (it would not be the first

Re: [R] Invalid URL for R documentation

2015-07-06 Thread John McKown
I get a 404 on that page as well. Curiously, the R-patched and R-devel links work. Looks like the webmaster has some work to do! The pages are still available on the Revolution Analytics mirror site: http://cran.revolutionanalytics.com/ On Mon, Jul 6, 2015 at 10:10 AM, Paul

[R] Rmarkdown / knitr naming the output file

2015-07-06 Thread AURORA GONZALEZ VIDAL
Hello. I have a question for Rmarkdown users. Is there any way to give a name to the output document inside the Rmd? For example, my rmd's name is bb.Rmd but when I knitr to pdf I want it to name the pdf differently than bb.pdf, for example, doc1.pdf. Is there any way to do this? Thank you very

Re: [R] Bonferroni post hoc test in R for repeated measure ANOVA with mixed within and between subjects design

2015-07-06 Thread Meyners, Michael
Untested, but if anything, your best bet is likely something like summary(glht(lme_H2H, linfct=mcp(Emotion = Tukey)), test=adjusted(bonferroni)) should work (despite the question why you'd want to use Bonferroni rather than Tukey For a reference, see the book on the topic by the package