[R] Error Message Cannot use `+.gg()` with a single argument. Did you accidentally put + on a new line?

For some simple reason, I am unable to see the mistake: ggplot(filter(nlsw88, !(is.na(union))), aes(y = wage, x = union, fill = union)) + geom_boxplot() + facet_wrap(~idblack) [[alternative HTML version deleted]] __ R-help@r-project.org

[R] [R-pkgs] New CRAN package: ipfr

/using_ipfr.html Advanced topics: https://cran.r-project.org/web/packages/ipfr/vignettes/common_ipf_problems.html Thank you for your time, Kyle Ward [[alternative HTML version deleted]] ___ R-packages mailing list r-packa...@r-project.org https

[R] Sweave and optional document sections

k(); } cat('\\input{subsection.tex}') } @ Then you can put your subsection logic into subsection.Rnw, just make sure to remove all of the default latex header stuff, just put in the blocks that you want to process: This comes from a subsection. <>= cat(”I’m in a subsection”)

[R] AdehabitatHR Write Spatial Polygon Problem

- SpatialPoints(PID208 [2:3]) mcp(xy, percent=95) mcp(xy, percent=95)$area #to find actual area covered plot(mcp(xy,percent=100)) Anybody know what I might be missing to successfully export the file for use in GIS? Thanks! Kyle [[alternative HTML version deleted]] ___

Re: [R] Lake Analyzer Help

> The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of data. > ~ John Tukey > > 2016-07-13 16:38 GMT+02:00 Kyle Wittmaier <wittmai...@gmail.com>: > >> would providing the scrip

[R] Lake Analyzer Help

I am using LakeAnalyzer in Rstudio to produce heat maps and plots using data from constant monitoring buoys. I have a prewritten script that is functioning on a colleagues computer perfectly. I am using Rstudio 0.99.902 and R 3.3.1. I have added four packages to the project (lattice, manipulate,

[R] [R-pkgs] lavaan.shiny "latent variable analysis with shiny"

ing GitHub, and more information as well as the current development version can be found at https://github.com/kylehamilton/lavaan.shiny William Kyle Hamilton - Graduate Student University of California, Merced - Psychological Sciences psychology.ucmerced.edu - kyleha

[R] R error

Good afternoon, I recently received a ticket from a customer to upgrade from 3.1.1. to 3.2.1. After the upgrade, when he tries to install a package he receives the error below. Could you please advise as to what is wrong? Thank you. Kyle --- Please select a CRAN mirror for use

[R] [R-pkgs] New release of MAVIS (Meta Analysis via Shiny) v1.1 now on CRAN

. The package is developed using GitHub, and more information as well as the current development version can be found at https://github.com/kylehamilton/MAVIS William Kyle Hamilton - Graduate Student University of California, Merced - Psychological Sciences psychology.ucmerced.edu

[R] Star schema

Are there any libraries for R that would enable the import of data stored in star schema? [[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

Re: [R] Discrepant lm() and survreg() standard errors with weighted fits

(lm(y~x, data=test), type=c('HC'))[1,1]^0.5 [1] 0.5885252 vcovHC(lm(y~x, data=test), type=c('HC'))[2,2]^0.5 [1] 0.1676871 (The HC3 method gives SEs which are consistent with those from lm().) I don't understand how survreg() can do better than White? Thanks again for your help, Kyle On Wed

Re: [R] Discrepant lm() and survreg() standard errors with weighted fits

Survreg treats weights as case weights, and lm treats them as sampling weights. Here is a simple example. Data set test2 has two copies of every obs in data set test. test - data.frame(x=1:6, y=c(1,3,2,4,6,5)) test2 - test[c(1:6, 1:6),] summary(lm( y ~ x, data=test))$coef

[R] Discrepant lm() and survreg() standard errors with weighted fits

)) surv_basic_weight = survreg(Surv(time=halog, event=eventcode_det)~uvlog-1, dist='gaussian', init=c(3.33*1.8/9.97), weights=1/(haerrlog^2), robust=T) summary(basic_weight)$coef[2] summary(surv_basic_weight)$table[1,2] # if I leave off robust=T, survreg() SE is still much smaller Thanks, Kyle

Re: [R] survreg with measurement uncertainties

Hrm, thanks. The uncertainties are what they are, though (and the model is what it is, too) -- is there an alternative to modifying them? Maybe another type of analysis that handles upper limits? Kyle On Thu, Jun 13, 2013 at 5:46 AM, Andrews, Chris chri...@med.umich.edu wrote: It seems a line

Re: [R] survreg with measurement uncertainties

] already survreg(Surv(time = data, event = c(1,2,1))~model-1+cluster(id), weights=1/(err^2), dist='gaussian', init=c(2.1)) Thanks, Kyle On Wed, Jun 12, 2013 at 6:51 AM, Terry Therneau thern...@mayo.edu wrote: I will assume that you are talking about uncertainty in the response. Then one simple

[R] survreg with measurement uncertainties

to accomplish this? Thanks, Kyle __ 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

[R] Wrap names.arg text in barplot

Hello! Does anyone know of a handy way to wrap the names.arg text in a barplot? I'm creating a bar plot with rather long labels; I can adjust the margins, but I'd also like to have the text wrap to about 4cm. Thanks! Kyle H. Ambert Doctoral Candidate, Bioinformatics Oregon Health Science

Re: [R] Wrap names.arg text in barplot

Oh! Great idea. I'll give that a try. ---Kyle. On Fri, Apr 27, 2012 at 12:00 PM, William Dunlap wdun...@tibco.com wrote: You can use strwrap and paste to insert newlines into your labels. E.g., wrapped - function(strings, width) vapply(strings, function(s)paste(collapse=\n, strwrap(s

Re: [R] Print the summary of a model to file

You could try the sink function! I use that from time to time: ?sink Kyle H. Ambert Fellow, National Library of Medicine Department of Medical Informatics Clinical Epidemiology Oregon Health Science University ambe...@gmail.com __ R-help@r

[R] devSVG error

this, some setting in devSVG that I can turn on that will capture these things and make them syntactically correct for SVG or is this a bug in devSVG (in that case I'd like to report the bug). Or is this actually valid .svg in which case GIMP and Qt both have bugs. Thanks Kyle [[alternative HTML

[R] insertion of a row between individuals

NOV23 10 group2 Any help would be appreciated. Thanks, Kyle The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying

[R] Issue with installing BRugs

as though I have the correct permissions. (A little Googling also showed that some people have success when simply retrying to do the install - no luck there, either.) Any ideas on how to work around this? I really need that updated version of BRugs! Thanks, Kyle

[R] getDLLVersion

helpful. Technical Notes: OS: win7 32bit Compiler: mingw32 R: 2.11.1 Thanks Kyle [[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

[R] R Extensions getDLLVersion

be a very basic question. If anyone could point me to a good reference on this it would be very helpful. Technical Notes: OS: win7 32bit Compiler: mingw32 R: 2.11.1 Thanks Kyle [[alternative HTML version deleted]] __ R-help@r-project.org

Re: [R] Quartering a plot() ?

If it's specifically drawing the grid that's the trouble, I think the simplest approach is to use the grid() function in the base graphics package. Kyle H. Ambert Fellow, National Library of Medicine Department of Medical Informatics Clinical Epidemiology Oregon Health Science University

[R] mboost: Interpreting coefficients from glmboost if center=TRUE

I'm running R 2.10.1 with mboost 2.0 in order to build predictive models . I am performing prediction on a binomial outcome, using a linear function (glmboost). However, I am running into some confusion regarding centering. (I am not aware of an mboost-specific mailing list, so if the main R list

Re: [R] mboost: Interpreting coefficients from glmboost if center=TRUE

, which do not return scalar coefficients that are readily extractable.) On Sun, Feb 7, 2010 at 6:31 PM, David Winsemius dwinsem...@comcast.net wrote: On Feb 7, 2010, at 5:03 PM, Kyle Werner wrote: I'm running R 2.10.1 with mboost 2.0 in order to build predictive models . I am performing

Re: [R] Graph color

points(c(1:10), col=red) Or, if I wanted to generate a barplot using a shading color other than gray, barplot(c(1:10), col=steelblue) Does that answer your question? Kyle H. Ambert Fellow, National Library of Medicine Department of Medical Informatics Clinical Epidemiology Oregon Health

Re: [R] (no subject)

assigned to the times argument). It might be helpful to know a bit more about the specific problem you're trying to solve though. Kyle H. Ambert Fellow, National Library of Medicine Department of Medical Informatics Clinical Epidemiology Oregon Health Science University On Mon, Jan 25, 2010

[R] GBM package: Extract coefficients

I am using the gbm package for generalized boosted regression models, and would like to be able to extract the coefficients produced for storage in a database. I am already using R to automatically generate formulas that I can export to a database and store. For example, I have been using Dr.

[R] Getting AIC from lrm in Design package

I am trying to obtain the AICc after performing logistic regression using the Design package. For simplicity, I'll talk about the AIC. I tried building a model with lrm, and then calculating the AIC as follows: likelihood.ratio - unname(lrm(succeeded~var1+var2,data=scenario,x=T,y=T)$stats[Model

Re: [R] Getting AIC from lrm in Design package

the same observations) having the lowest AIC. I hope that my understanding of this fundamental formula is correct, but please let me know if not. Thanks. On Sun, Oct 25, 2009 at 10:51 AM, David Winsemius dwinsem...@comcast.net wrote: On Oct 25, 2009, at 9:24 AM, Kyle Werner wrote: I am trying

Re: [R] Getting AIC from lrm in Design package

Dear David, Thank you for the reference to Frank Harrell's excellent text. I will read up to correct my statistical deficiencies offline. Thank you. On Sun, Oct 25, 2009 at 1:24 PM, David Winsemius dwinsem...@comcast.net wrote: On Oct 25, 2009, at 12:55 PM, Kyle Werner wrote: David

Re: [R] Getting the C-index for a dataset that was not used to generate the logistic model

=\fitted.ind\) From there, I could cobble together a dataframe of the actual results in the new dataset with the predicted probabilities based on the model, and regress from there. This allowed me to generate my statistic of interest (the C-index). Again, thank you, Kyle On Thu, Jul 16, 2009 at 9:18

[R] Getting the C-index for a dataset that was not used to generate the logistic model

apply the new data to the model from * logit.lrm* that I generated before. So, can someone point me in the right direction for evaluating the model that I built with trainingData, but getting the C-statistic against my validationData? Thanks so much, Kyle Werner [[alternative HTML version

[R] Getting the C-index for a dataset that was not used to generate the logistic model

data to the model from logit.lrm that I generated before. So, can someone point me in the right direction for evaluating the model that I built with trainingData, but getting the C-statistic against my validationData? Thanks so much, Kyle Werner (Resending because I accidentally HTML formatted my

[R] Sweave \Sexpr{} advice please

$ % end code but, of course, this is poor way of going about it. Any suggestions? Thanks in advance. Regards, Kyle [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

[R] Semi-definite quadratic programming

approach to this problem someone can suggest? Thanks, Kyle [[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

Re: [R] Running R Script on a Sequence of Files

Have you thought about using one of the Python/R interface modules? http://www.omegahat.org/RSPython/ http://rpy.sourceforge.net/ Admittedly, I have not had much success in getting these to work on my machine, but I know others who have. Kyle H. Ambert Graduate Student Department of Medical

Re: [R] Running R Script on a Sequence of Files

Thanks, Barry. I'll use that in the future. ---Kyle. On Fri, Dec 5, 2008 at 11:01 AM, Barry Rowlingson [EMAIL PROTECTED] wrote: 2008/12/5 Chris Poliquin [EMAIL PROTECTED]: Hi, I have about 900 files that I need to run the same R script on. I looked over the R Data Import/Export

[R] question about the tisPlot function in package tis

(2,1)) tisPlot(dat, xTickFreq=monthly, xTickSkip=6) # graph ends in 11/2008, but looks to start some time in late 1999 tisPlot(dat, xTickFreq=monthly, xTickSkip=12) # graph looks to end around 3/2009 ## end TIA, Kyle ___ Research Associate, Macroeconomics

[R] including Sweave tangled code in '.Rnw' document

be 'plot(runif(1000))', perhaps manually enclosed in a verbatim environment \end{document} I am running R-2.6.2 on Ubuntu Hardy Heron. Thanks for all your help with Sweave. I think it is a fantastic tool. Kyle [[alternative HTML version deleted

[R] function for simultaneous confidence interval of regression coefficients

\mathbf{X})^{-1}) \times p \times F_{p, n-p, .95}} Thanks, and sorry for such a dumb question. Either I am not searching for the right thing or this hasn't already been addressed in the lists (perhaps because it is so easy). Kyle [[alternative HTML version deleted

Re: [R] including Sweave tangled code in '.Rnw' document

as it is and the problem has been solved to my satisfaction I have chosen to put off exploration of this package for another day. Best, Kyle On Sun, Nov 30, 2008 at 8:42 AM, Vincent Goulet [EMAIL PROTECTED] wrote: Kyle, In addition to listings already mentioned by Berwin, you may find useful

[R] declaring constants in an Sweave / LaTeX document

sparse. Best, Kyle [[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 provide commented, minimal

[R] Subset based on items in a list.

,]) } } } tmp } but this seems inefficient. As I understand it, the subset function won't really solve my problem, but it seems like there must be something out there that will that I must be forgetting. Does anyone know of a way to solve this problem in an efficient way? Thanks! Kyle H. Ambert

[R] Subset based on items in a list.

,]) } } } tmp } but this seems inefficient. As I understand it, the subset function won't really solve my problem, but it seems like there must be something out there that will that I must be forgetting. Does anyone know of a way to solve this problem in an efficient way? Thanks! Kyle H. Ambert

[R] a question about diparate device quality

, but my new job likes to include them in, say, MS word documents for which I cannot easily use pdf. TIA, Kyle [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

[R] multiple page pdf file using pdf()

previously used devices besides x11 by analogy with printing things to x11. I am running R-2.7.2 on Red Hat Linux. TIA, Kyle [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] multiple page pdf file using pdf()

Peter, Ah, I was under the impression that I had to 'dev.off()' after every plot. Naturally I had wondered about that strange argument that did not seem to do anything... Problem solved, thanks everyone. Many thanks, Kyle On Mon, Sep 29, 2008 at 9:43 AM, Peter Dalgaard [EMAIL PROTECTED]wrote

[R] Extracting dataset from lm output

Dear All, I want to extract the original dataset from a lm output. I know that I can get most of it from model.matrix(lm.out) but I need the dependent variable to be in the first column. Any ideas? Thanks, Kyle Roberts __ R-help@r-project.org

Re: [R] Extracting dataset from lm output

-model.matrix(lm.out) new[,1]-lm.out$model[,1] This seems to do what I need. * Dr. J. Kyle Roberts Department of Literacy, Language, and Learning School of Education and Human Development Southern Methodist University P.O. Box 750381 Dallas, TX  75275

[R] lattice with bwplot

Dear All, How come par(mfrow=c(1,2)) works with boxplot, but not with bwplot? This works par(mfrow=c(1,2)) boxplot(dv~index, depend) boxplot(dv~index, depend2) This does not work par(mfrow=c(1,2)) bwplot(index~dv, depend) bwplot(index~dv, depend2) Thanks, Kyle

[R] rbinom not using probability of success right

suggestion of sample(c(rep (0,545),rep(1,75))) seems to me to be the best way of going about it since conceptually this is what you are doing: taking permutation of a fixed set of numbers. Best, Kyle __ R-help@r-project.org mailing list https://stat.ethz.ch

[R] Using Conditional AIC with lmer

posting this so that 1) This code can be of use to any other souls in the statistical wilderness trying to do model selection with mixed models, and 2) So that wiser minds can point out any errors in our approach. Thanks, Kyle __ R-help@r

[R] Plot a line according to a specified equation

Does anyone know how to graph a line according to a specified equation? I'd like to plot the following hyperbola: Y=139.35/(1+(0.174*X)) I know there's a way to do this, but I'm having a ridiculous time trying to remember how. Thanks! Kyle H. Ambert Department of Behavioral Neuroscience