Re: [R] I'd like to request that my R CRAN package is not tested on Solaris OS

Lampros, You can use Rhub for testing packages on various platforms. I had a similar issue to you...I had a tiny bug that was only failing on M1mac. I was able to resolve it by repeatedly testing my package on Rhub. Here's how I did that: https://github.com/kwstat/nipals/issues/5 Kevin W

Re: [R] Stratifying data with xyplot

> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducibl

[R] [R-pkgs] New package: nipals

s://cran.r-project.org/web/packages/nipals/vignettes/nipals_optimization.html Please report any issues through the Github page: https://github.com/kwstat/nipals Kevin Wright -- Kevin Wright [[alternative HTML version deleted]] ___ R-packages mail

[R] rgl crash on windows 7

rary/3.4/httpuv/libs/x64/httpuv.dll TRUE mime c:/kw/R/win-library/3.4/mime/libs/x64/mime.dll TRUE rgl c:/kw/R/win-library/3.4/rgl/libs/x64/rgl.dll FALSE Can I manually load the DLLs and then load rgl? Any tips on how to proceed would be appreciated. -- Kevi

Re: [R] About MC simulation of AR1 model in R

Try this example to simulate AR1xAR1 variance structure. Kevin Wright library(mvtnorm) library(asreml) set.seed(300) nr <- 10; nc <- 8 # number of rows and columns colcor <- .9 # correlation for columns, rows rowcor <- .1 sigAR <- diag(nr) sigAR <- rowcor^ abs(row(sigAR) -

Re: [R] ASReml-R lack of documentation

Patrick, The asreml (VSNi) forum seems to still be working with a few posts every month: https://www.vsni.co.uk/forum/viewforum.php?f=7 Kevin Wright On Mon, Feb 27, 2017 at 2:29 AM, Patrick Connolly < p_conno...@slingshot.co.nz> wrote: > Has anyone had any success contac

Re: [R] Add annotation text outside of an xyplot (lattice package)

. The R code showing how this works is here: https://github.com/kwstat/pagenum/blob/master/R/pagenum.r Kevin Wright On Thu, Sep 22, 2016 at 9:04 AM, Jun Shen wrote: > Dear list, > > Just wonder if there is a way to add annotation text outside an xyplot, > (e.g. the bottom of th

[R] Problems trying to generate a prime factor vector

Hi, I am very new to 'R' and am trying to write an R function which returns the prime factors of a given number(n) Unfortunately, the function only works for very small numbers, if for example I pass 18 to the function a mysteriously long vector is returned. I have not been able to find where or

Re: [R] (no subject)

https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]]

Re: [R] Lattice: raw data and prediction of a non linear fitted function

to add a groups argument to a layer and then use latticeExtra to combine layers. Kevin Wright On Wed, Aug 5, 2015 at 7:24 AM, François Collin wrote: > Dear all, > > I have a question about lattice use. I would like to use it to represent: > - my raw data as points, > - and the r

Re: [R] How to add error bars to a line xyplot (lattice package)

> > Bert Gunter > Genentech Nonclinical Biostatistics > (650) 467-7374 > > "Data is not information. Information is not knowledge. And knowledge > is certainly not wisdom." > Clifford Stoll > > > > > On Tue, Jan 27, 2015 at 2:56 PM, Kevin Wrigh

Re: [R] How to add error bars to a line xyplot (lattice package)

__ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Kevin Wright ___

Re: [R] How do I really, I mean really, unload a package?

/30791.html In that sense, it appears that it is not possible to completely undo the loading of a package. Thanks to Bill Dunlap and Professor Ripley. Kevin Wright On Wed, Sep 24, 2014 at 2:16 PM, William Dunlap wrote: > Running pkg::func or pkg:::func has the side effect of loading pk

Re: [R] How do I really, I mean really, unload a package?

Ah, here is the answer from the man page for ::: "...pkg:::name returns the value of the internal variable name. The namespace will be loaded if it was not loaded before the call, but the package will not be attached to the search path." Kevin On Wed, Sep 24, 2014 at 1:56 PM, Ke

[R] How do I really, I mean really, unload a package?

Sorry if this is well-known, but I can't find an answer or maybe just don't know how to ask Google the right question. If I run the following code in R (3.1.1), I find that lattice:::xyplot.formula is still available (or maybe just a promise to it ... ???) even though I've used detach and unloadNa

[R] cairo_pdf crashing R on Windows

I'm having trouble with cairo_pdf crashing R on Windows. How can I debug this? This is a "exited abnormally" type crash, so I can't drop into the browser and look at the call stack. Kevin -- Kevin Wright [[alternative

Re: [R] How to test for open pdf file on Windows before calling cairo_pdf ?

ke sure to > close any opened graphics devices, not to leave incomplete image files > behind if there is an errors and so on. There are plenty of option > for it, e.g. the default output directory is "./figures/", which can > be changed. (The need for argument ext="pdf&

[R] How to test for open pdf file on Windows before calling cairo_pdf ?

g command is called that an error is generated. Is there a way to test if a pdf file can be written to by cairo_pdf ? I'd rather not wrap all plotting commands with try()I have many such commands in my script and the choice of which one is f

Re: [R] Import data from Excel to R

was to use the XLConnect package and read the xlsx file directly. Kevin Wright On Wed, Sep 10, 2014 at 3:51 AM, Omar André Gonzáles Díaz < oma.gonza...@gmail.com> wrote: > The best way is to save the file as CSV... after you can simply import it > with this comand in R: > > re

[R] New details about Cochran and Cox's chocolate cake data

.html In that posting, Bill mentioned that the experiment details were not quite clear on a detail, so I went to the source document and transcribed a few of the details. (See below). I'm posting them here for posterity and the curiosity of anyone interested. Kevin Wright Source: Frances E

Re: [R] Skipping .Rd files and using Org-mode instead?

anks for > the answer anyway. > > -- > cheers, > Thorsten > > __________ > 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.h

Re: [R] Correlelogram with partial correlation coefficients

t; # option 2: bolding: > #text(0.5, 0.5, r, cex = cex.cor, font=fonts) > } > corrgram(climvar4, type="data", order=F, lower.panel=panel.shadeNtextP, > upper.panel=NULL, cex=1.3) > > Thanks so much in advance! > > Bill > > _

Re: [R] lattice change font of one specific axis label in each panel

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://www.R-project.org/posting-guide.

Re: [R] Urgent Inquiry

; > > > > > ______ > 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 provide commented, minimal, self-contained, re

Re: [R] Multiple corrgrams or joining jpg/png

__ > 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 provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternati

[R] The difference between SAS and R

SAS uses words. R uses symbols. See this: http://xkcd.com/1306/ (Yes, I know IML uses plenty of symbols. It's just supposed to be funny. And somewhat true.) -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-projec

Re: [R] Exporting R graphics into Word without losing graph quality

Another nice thing about your solution is that circles look like circles, and not like diamonds (when viewed on screen). Thanks. Kevin Wright On Mon, Dec 16, 2013 at 8:02 PM, Steve Taylor wrote: > Unfortunately the win.metafile() device does not support semi-transparent > colours, w

Re: [R] Heatmap, and heatmap.2 gave different figures for the same dataset

Read the help page for both and pay particular attention to the "scale" argument. Kevin Wright On Thu, Dec 12, 2013 at 9:45 AM, capricy gao wrote: > I have a huge dataset(15k X 18) and tried to use the heatmap in R to > examine the patterns. However, I found that heatmap an

Re: [R] data distribution for lme

On Tue, Dec 10, 2013 at 7:33 PM, Rolf Turner wrote: > > See inline below. > > > On 12/11/13 11:28, Bert Gunter wrote: > >> This is not really an R question -- it is statistics. >> In any case, you should do better posting this on the >> R-Sig-Mixed-Models list, which concerns itself with matters l

Re: [R] (no subject)

___ > 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 provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alt

[R] What graphics device settings are used by Rcmd check ?

rit and am trying to find the settings used by Rcmd check. Where do I look for these? -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the pos

Re: [R] Data Security when using R

SE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-project.org mailin

Re: [R] plot correlation matrix

gt; https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- Kevin Wright [[alternative HTML version deleted]] __

Re: [R] package:nlme unexpected varIdent behaviour

gt; > > --- > Sonya Odsen > M.Sc. Candidate > University of Alberta > Dept. of Renewable Resources > od...@ualberta.ca > > [[alternative HTML version deleted]] > > ______ > R-help@r-project.org mailing list >

Re: [R] Daily average temperature from monthly average temperature

thly-average-temperature-tp4675752.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://ww

[R] Should I wrap more package examples in \dontrun{} ?

ta" packages. In roughly that order. In the interest of long-term package stability I'm thinking about wrapping more of the examples in my package in \dontrun{}. Especially the parts that depend on other packages. I'm interested to know how other package developers approach this

Re: [R] RSM

n 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 provide commented, minimal, self-contained, reproducib

Re: [R] corrgram (package corrgram): how to plot multiple correlograms in the same page?

_ > 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 provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML

Re: [R] Fwd: about plantbreeding library

ject.org/posting-guide.html> > > Give a reproducible example to show what you try to do and why it does > not > > work. > > Sincerely > > > > Marc Girondot > > > > -- > > __** > > Marc

Re: [R] Lattice: bwplot - changing box colors in legend and plot when using panel.groups = function... and panel = panel.superpose

par.ylab.text = font.settings, axis.text = font.settings, #strip.shingle=list(col=c("red","blue")), superpose.symbol=list(fill=c("red","blue")), # boxplots #superpose.fill=list(col=c("red","blue")), superpose.polygon=list(col=c("red&q

Re: [R] question for diallel analysis

ng list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]] ___

Re: [R] diallel analysis

TML 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 provide commented, minimal, self-cont

Re: [R] Strange behaviour of R graphics copied to PowerPoint

on 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 provide commented, minimal, self-contained, r

Re: [R] measuring distances between colours?

> > + rbind(all.names[which.min(sq.dist)], min(sq.dist)) > > > + } > > > + function(cols.hex, near=.25){ > > > + cols.hsv <- rgb2hsv(col2rgb(cols.hex)) > > > + cols.near <- apply(cols.hsv, 2, find.near) > > > +

Re: [R] measuring distances between colours?

#x27;group' colors in lattice. Kevin Wright rgb2col <- function(cols.hex, near=.25){ # Given a vector of hex colors, find the nearest 'named' R colors # If no color closer than 'near' is found, return the hex color # Authors: John Fox, Martin Maechler, Kevin Wri

Re: [R] negative correlation with corSymm in nlme or another way?

1 autocorrelation is negative--evidence of competition plot(ACF(m1), alpha=.05, grid=TRUE) Kevin Wright On Sun, May 5, 2013 at 1:12 PM, Seth wrote: > Hi, > > I have a nonlinear model with residuals that are negatively autocorrelated > at short distances. > > I can find no spatial

Re: [R] Why can't R understand if(num!=NA)?

oject.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 provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version d

Re: [R] the joy of spreadsheets (off-topic)

.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PL

Re: [R] Colour branches/labels of dendrogram according to a grouping variable

al, mesodermal). > > /johannes > > __ > 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 provide commented, minimal, self-contained, reproducible code.

Re: [R] Shapiro-Wilk normality test

> 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 provide commented, minimal, self-contained, reproducible code. > -- Kevin W

Re: [R] Cannot rescale a constant/zero column error.

Sounds like one of your data columns is constant. The variance of a constant is 0, and scaling would then divide by 0, which is impossible. Kevin Wright On Wed, Oct 31, 2012 at 7:47 AM, fillay89 wrote: > I am trying to run the R Script below, I have actually simplified it to > just

Re: [R] corrgram

Um, Bert, did you try my example? It uses grid graphics to annotate a base-graphics plot. Kevin On Tue, Sep 25, 2012 at 10:50 AM, Bert Gunter wrote: > Inline: > > On Tue, Sep 25, 2012 at 8:42 AM, Kevin Wright wrote: >> Claudia, When you are asking a question about a parti

Re: [R] corrgram

> 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 provide commented, minimal, self-contained, reproducible code. -- Kevin Wri

Re: [R] Plotting US States: Issue with filled colors cycling

uot;West Virginia","Wisconsin","Wyoming") > > dState = data.frame( col=rbinom(51,size=2,prob=.6)+1, state=state ) > > for( i in 1:51 ){ > dTemp = dState[1:i,] > map("state", regions = dTemp$state, > # boundary = TRUE, > # lty =

[R] CairoWin on Windows 7 doesn't refresh

f the graphics window. Anybody else experience this? -- Kevin Wright __ 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 provide commented, mi

Re: [R] Obtain residuals from a Principal Component Analysis

(X - m1$scores %*% t(m1$loadings),8) We can create a lower-rank approximation of X by using the first 2 (or however many) principal components: m1$scores[,1:2] %*% t(m1$loadings[,1:2]) I think of "residuals" as being the difference between the original matrix X and this lower-rank approxi

Re: [R] Obtain residuals from a Principal Component Analysis

Just use 'predict' on the fitted model and subtract the predicted values from the data. Kevin Wright On Wed, Jul 25, 2012 at 5:02 AM, petohtalrayn wrote: > Hi everyone, > > I am relatively new to R, and I need to perform the principal components > analysis of a data mat

Re: [R] Mixed Models providing a correlation structure.

gt; 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://www.R-project.org/posting-guide.html > a

Re: [R] visualize correlation matrix

nfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Kevin Wright __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/

Re: [R] Reading a bunch of csv files into R

elp > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Kevin Wright __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-

Re: [R] Correlograms: using boxes and different variables on rows and columns

-- > View this message in context: > http://r.789695.n4.nabble.com/Correlograms-using-boxes-and-different-variables-on-rows-and-columns-tp4631309.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-proj

Re: [R] R2 in multilevel modelling

> Chiara > > __ > 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 provide commented, minimal, self-c

Re: [R] pca biplot.princomp has a bug?

most-varying direction of the data. The arrows are pointing in the direction of the variables, as projected into the 2-d plane of the biplot. There is no bug. Kevin Wright On Wed, Apr 25, 2012 at 11:29 AM, Michael wrote: >x=rmvnorm(2000, rep(0, 6), diag(c(5, rep(1,5 >x=s

Re: [R] How do i read the source code of "biplot"?

f "biplot"? > > Thank you! > >[[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.o

Re: [R] Quick question about princomp/biplot

n/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]] __ R-help

Re: [R] PCA sensitive to outliers?

o/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]] __ R-help@r-projec

Re: [R] sdev, variance in prcomp

understood some thing? > > Best, > > Carol > > > __ > 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 provide commented, minimal, self-contained, reprod

Re: [R] Best way to search r- functions and mailing list?

t > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Kevin Wright [[alternative HTML version deleted]] _

Re: [R] What are the color's name in heat.color(5)

ernative 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 provide commented, minimal

Re: [R] How to start R in maximized size???

...) > > > > Duncan Murdoch > > __ > 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 provide commented, minima

Re: [R] Correlograms

If I understand your question correctly, install the corrgram package from CRAN. Then, library(corrgram) cm <- cor(iris[ , 1:4]) corrgram(cm, type="corr") Also, see help for the "vote" data: ?vote Kevin Wright On Tue, Jan 10, 2012 at 2:06 PM, Natbyah wrote: &

Re: [R] optim seems to be finding a local minimum

help@r-project.org mailing list > https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide http://www.R-project.org/** > posting-guide.html <http://www.R-project.org/p

Re: [R] 2^k*r experimental design and anova

s using ggplot2. > > TIA, > Best regards, > Giovanni > __ > 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 pr

Re: [R] Difficulty with lme

Generally, the only way to estimate f1:f2 is if you have all combinations of data present for these two factors. Sometimes it makes sense to include f1:f2 as a random effect in the model (which does NOT need balanced data) but that is something you have to decide. Kevin On Wed, Oct 5, 2011 at 2

Re: [R] Needed help with 3 factor anova !!!

For example, library(agridat) ?gomez.stripsplitplot Kevin Wright On Wed, Oct 5, 2011 at 3:13 PM, Dennis Murphy wrote: > Try Googling 'Three factor ANOVA R'; it didn't take long to find a few > relevant hits. > > Dennis > > On Wed, Oct 5, 2011 at 10:56 AM,

Re: [R] Newer Matrix Factorization Techniques

Bioconductor has the pcaMethods package, with multiple options for PCA, including a robust L1-norm SVD. Kevin Wright On Thu, Sep 1, 2011 at 5:16 AM, Igor Carron wrote: > Hi, > > I am not sure if this should go to r-help or r-dev list. I have looked > at some archives of R librarie

Re: [R] Easier ways to create .Rd files?

I like the roxygen2 package for combining code and documentation. If you use Emacs + ESS, it will even create much of the roxygen code for you (and auto-revise it if you change the function arguments). Kevin Wright On Tue, Aug 23, 2011 at 6:55 PM, Jonathan Greenberg wrote: > R-helpers: >

Re: [R] problem in asreml function in wgaim package

You are correct. asreml is a commercial package which requires a license. See the download site for more information. Kevin Wright On Fri, Aug 12, 2011 at 12:52 PM, ram basnet wrote: > Dear Uwe Ligges, > > Thanks for response. > I mean this R package is not free package. > &

Re: [R] question about linear mixed model

Note: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Also, your question may be more appropriate for the R mixed-models mailing list. Kevin On Sun, Jul

Re: [R] problem with corrgram function

This bug has been fixed. Kevin On Tue, Jun 28, 2011 at 6:11 AM, Niels Janssen wrote: > Dear list, > > I have a problem with the "corrgram" function. It does not seem to "color" > large negative correlations, while the same correlation, if positive, > provides no problems. Is this a bug? > >

Re: [R] In a formula, what is the interaction of the intercept and a factor?

Kevin On Wed, Jun 1, 2011 at 9:44 AM, Kevin Wright wrote: > > On Wed, Jun 1, 2011 at 1:19 AM, Prof Brian Ripley > wrote: > > [text deleted] > > >> Note that you usually want to do '*' when you say 'interact with': >> >>> mode

Re: [R] In a formula, what is the interaction of the intercept and a factor?

(Intercept) 11 21 ... Why is "group" simply vanishing in the second model? I tried to dig into this until I hit .Internal(model.matrix Kevin > > > On Tue, 31 May 2011, Kevin Wright wrote: > > For a pedagogical purpose, I was trying to show

[R] In a formula, what is the interaction of the intercept and a factor?

For a pedagogical purpose, I was trying to show how the formula for a simple regression line (~1+x) could be crossed with a factor (~1:group + x:group) to fit separate regressions by group. For example: set.seed(201108) dat <- data.frame(x=1:15, y=1:15+rnorm(15), group = sample(c('A',

Re: [R] R Style Guide -- Was Post-hoc tests in MASS using glm.nb

John Chambers is also very widely quoted describing the aim of S as "to turn ideas into software, quickly and faithfully." Perhaps S3 is for people wanting to do things "quickly" and S4 is for those wanting to do things "faithfully". Kevin On Wed, May 18, 2011 at 7:39 PM, wrote: > I used to th

Re: [R] Email out of R (code)

How does this compare to create.post() ? Kevin On Tue, May 17, 2011 at 3:44 PM, Daniel Malter wrote: > Hi all, > > I thought I would post code to send an email out of R. The code uses > Grothendieck and Bellosta's interface package rJython for executing Python > from R. The code itself provide

Re: [R] biplots for PCA

Did you try tweaking the value of the "expand" parameter? See the help page of biplot for more info. Kevin On Fri, May 13, 2011 at 4:38 AM, Anna Renwick wrote: > Hi all > > I have produced a biplot for a PCA (see attached pdf) that I ran however > the > names of the variables which are placed

[R] Discovery version of ASREML now free

/ (Inquiries may be delayed due to Easter weekend.) Kevin Wright [[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

[R] Which should I use? system.file() path.package() find.package()

functions, so I am wondering, is there is a preferred approach? Kevin Wright [[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-p

Re: [R] Conveting SAS Proc mixed to R code

> I am trying to teach myself R and replicate some previous SAS analysis. > Could someone please help me translate the following SAS code into R. > > Proc mixed method=ml > Class Group Treatment Stream Time Year; > Model Logrpk=Treatment Time Treatment*Time; > Random Group Stream (Group Treatment)

Re: [R] How to see a R code from a package?

See help for getAnywhere() Kevin On Thu, Apr 14, 2011 at 11:24 AM, Soyeon Kim wrote: > Dear R users, > > Hi. I want know R code of a function: predict.cv.glmnet (which is > included in glmnet package). > Could you let me know how I can see the R code of the function? > > Thank you, > Soyeon Ki

Re: [R] How to save heatmap as image or pdf

?pdf On Mon, Mar 28, 2011 at 12:57 PM, chakri_amateur wrote: > Hello Everyone, > > > I am using R for creating heatmap from a square matrix. Below is my script > to do so > > > my_map <- read.csv("Desktop/input.csv", sep=",") > > my_matrix <- data.matrix(my_map) > > my_heatmap <- heatmap(my_matri

Re: [R] strange PREDICTIONS from a PIECEWISE LINEAR (mixed) MODEL

1. Try using set.seed for better reproducibility. 2. Does this really work for you? I get mydf <- data.frame(x, y,id) mod2<-lme(y ~ x + x*(x>-1), random=~x|id, + data=mydf) Error in lme.formula(y ~ x + x * (x > -1), random = ~x | id, data = mydf) : nlminb problem, convergence error c

Re: [R] colour palette for positive/negative range

ot;,"blue")) RedGrayBlue2 <- colorRampPalette(c("red", "lightgray", "blue")) pie(rep(1,21), col=RedWhiteBlue(21)) Kevin Wright On Fri, Mar 18, 2011 at 10:37 AM, Frank Schwach wrote: > Hi, > > I'm plotting a heatmap with values rangi

Re: [R] Write File to Shared Drive

The original poster did not say what operating system was being used. From my own experience on Windows, I always used "/" for reading from the local hard drive, but when I started working with Windows network shares/folders, I had to switch back to "\\" due to an unknown "feature" (bug?). Kevin

Re: [R] computing var-covar matrix with much missing data

One option is the nearPD function in the Matrix package. Other options include robust estimation of the covariance matrix. You should Google this. It's been discussed before. Kevin Wright On Mon, Jan 31, 2011 at 11:30 AM, Mike Miller > wrote: > Is there an R function for

Re: [R] boxplot - code for labeling outliers - any suggestions for improvements?

(OrchardSprays, "treatment", "decrease", >> > "colpos") >> > >> > >> > >> > >> > ----Contact >> > Details:--- >> > Contact me: tal.gal...@gm

Re: [R] Manual two-stage least squares in R

0-day free trial). Not sure if this would help you at all. Good luck, Kevin Wright On Tue, Jan 25, 2011 at 2:47 PM, Katharina Ley wrote: > Hi, > > I am trying to manipulate a gls regression model output to adjust for use of > two-stage least squares. Basically, I want to estimate a m

Re: [R] Setting bioconductor repository in .Rprofile. Is there a permanent way?

Now that is _simple_. Thanks. Kevin On Mon, Jan 24, 2011 at 1:49 PM, Kevin Wright wrote: > Of course, before posting my question, I did RTFM and RTFcode and > RTFmailinglists.  The key word in my question was "simpler".  I > rejected copying a modified version of the "

Re: [R] Setting bioconductor repository in .Rprofile. Is there a permanent way?

";, CRANextra="http://www.stats.ox.ac.uk/pub/RWin";, BioCsoft=rr["BioCsoft","URL"], Rforge="http://r-forge.r-project.org";)) options(repos=repos) rm(pp, rr, repos) Martin, I appreciated your clever tr

[R] Setting bioconductor repository in .Rprofile. Is there a permanent way?

conductor mirror can be selected by setting options("BioC_mirror"): the default value is "http://www.bioconductor.org";. The word "default" is a bit confusing here, because when I start R, I see: R> options()$BioC_mirror NULL -- Kevin Wright ___

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