Re: [R] Knitr: setting echo = FALSE globally

Hi Rich, I have no idea wha that chunk is not working but I think you can get the same result using the old method Stick the following in an ERT (Insert > Tex Code) <>= opts_chunk$set(echo = FALSE) @ Heck, I've only been using LyX for 4-5 years and already I'm sounding crotchety. John Kane King

Re: [R] R: Re: Differences in output of lme() when introducing interactions

I believe Michael's point is that you need to STOP asking such questions and START either learning some statistics or work with someone who already knows some. You should not be doing such analyses on your own given your present state of statistical ignorance. Cheers, Bert Bert Gunter "Data is

[R] R: Re: Differences in output of lme() when introducing interactions

Dear Michael, thanks for your answer. Despite it answers to my initial question, it does not help me in finding the solution to my problem unfortunately. Could you please tell me which analysis of the two models should I trust then? My goal is to know whether participants’ choices of the depend

Re: [R] modifying a package installed via GitHub

Bob and Charles, Thanks very much for taking the time to write, I greatly appreciate your help. I have been so spoiled by Rstudio for so long that I cannot recall the last time I had to use R CMD install. Although I installed this package from GitHub using devtools, I do not see that an .Rproj exi

Re: [R] modifying a package installed via GitHub

You essentially have it but you can just click the 'build and install' button to rebuild on the changes you made. But technically it would still work pushing to your repo and using devtools. On Monday, July 20, 2015, Stevan Earl wrote: > Bob and Charles, > > Thanks very much for taking the time

[R] plot auto key and text into panels using lattice

Dear all, I am writing some text into several panels which I can do with this script (in capital the variables): xyplot(Y ~ X | Z, data = DATAFRAME, groups = Z, ylab= "Y", xlab="X", main="TITLE", scales = list

Re: [R] R GUI tklistbox get value

Dear j.para.fernandez, Try selecvar <- dat[, as.numeric(tkcurselection(tl))+1] Omitting the comma returns a one-column data frame, not a numeric vector. I hope this helps, John John Fox, Professor McMaster University Hamilton, Ontario, Cana

Re: [R] [FORGED] change text size on a graphics

On 21/07/15 08:24, carol white via R-help wrote: Hi,How is it possible to increase the size of a histogram labels (displayed on the top of the bars)? I thought that if I use cex > 1, it will increase all text size on a plot (axis labels, axis annotation, title of the graphics and histogram labels

Re: [R] change text size on a graphics

On Jul 20, 2015, at 1:24 PM, carol white via R-help wrote: > Hi,How is it possible to increase the size of a histogram labels (displayed > on the top of the bars)? I thought that if I use cex > 1, it will increase > all text size on a plot (axis labels, axis annotation, title of the graphics >

Re: [R] ggplot2 geom_boxplot limits

Here is the answer: http://rpubs.com/INBOstats/zoom_in ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician

[R] change text size on a graphics

Hi,How is it possible to increase the size of a histogram labels (displayed on the top of the bars)? I thought that if I use cex > 1, it will increase all text size on a plot (axis labels, axis annotation, title of the graphics and histogram labels) which I want but it doesn't. Regards, Carol

Re: [R] ggplot2 geom_boxplot limits

On 2015-07-20 Mon 15:19, Thierry Onkelinx wrote: Limits in scales set values outside the limits to NA. Hence the boxplots, smoothers,... change. Use coord_cartesian() to "zoom in". Thanks. What do I do if I also want to use coord_flip(), that is, if I want the boxes to lie horizontally *and*

Re: [R] Value passing in print option

On Jul 19, 2015, at 11:48 PM, Partha Sinha wrote: > i want to pass a value with print option > x<-10 > y<2*x > print("Current value of y is " ) # confused dont know how to pass value > > i want output as Current value of y is 10 With that code we really do not have any assurance that y is 10 (o

Re: [R] Printing row and column names of cells with specific value in a big matrix

Thanks a lot Sarah. I think I've got what I wanted. On Mon, Jul 20, 2015 at 2:55 PM, Sarah Goslee wrote: > Subsetting error. See below. > > On Mon, Jul 20, 2015 at 3:29 PM, gaurav kandoi wrote: >> Hi Sarah, sorry for posting in HTML. >> >> I've two big matrices (5k*4k) with the same structure, i

Re: [R] Knitr: setting echo = FALSE globally

On Mon, 20 Jul 2015, Thierry Onkelinx wrote: We need the source file. Attached to the original message was the TeX output called, 'sample.txt'. I've attached it again, but with the .tex extension. Also, the .lyx file is attached. Rich#LyX 2.1 created this file. For more info see http://www.

Re: [R] Printing row and column names of cells with specific value in a big matrix

Subsetting error. See below. On Mon, Jul 20, 2015 at 3:29 PM, gaurav kandoi wrote: > Hi Sarah, sorry for posting in HTML. > > I've two big matrices (5k*4k) with the same structure, i.e. : > > ,mRNA1,mRNA2,mRNA3 > lncRNA1,0.395646498,0.949950035,0.761770206 > lncRNA2,0.037909944,0.661258022,0.5586

Re: [R] Knitr: setting echo = FALSE globally

On Mon, 20 Jul 2015, Yihui Xie wrote: Section 5.1.3 of the book "Dynamic Documents with R and knitr" is titled "Global Options". I don't know how to make it more clear for readers to find information on global options in the book. Yes, I've read that and have not found where 'opts_chunk$set(

Re: [R] Printing row and column names of cells with specific value in a big matrix

Hi Sarah, sorry for posting in HTML. I've two big matrices (5k*4k) with the same structure, i.e. : ,mRNA1,mRNA2,mRNA3 lncRNA1,0.395646498,0.949950035,0.761770206 lncRNA2,0.037909944,0.661258022,0.558657799 lncRNA3,0.678459646,0.652364052,0.359053653 Now, I would like to extract the names of the

Re: [R] Knitr: setting echo = FALSE globally

We need the source file. Not the output. And please try to make it as small as possible while still reproducing the problem. The smaller the example, the easier it is for us to help you. Op 20-jul.-2015 21:17 schreef "Rich Shepard" : > On Mon, 20 Jul 2015, Thierry Onkelinx wrote: > > Have you tri

Re: [R] ggplot2 geom_boxplot limits

Limits in scales set values outside the limits to NA. Hence the boxplots, smoothers,... change. Use coord_cartesian() to "zoom in". Op 20-jul.-2015 20:29 schreef "Jacob Wegelin" : > > With base graphics, one can use the "ylim" argument to zoom in on a boxplot. > > With ggplot2, using "limits" to t

Re: [R] Printing row and column names of cells with specific value in a big matrix

Without a reproducible example, or at least a non-mangled one (please don't post in HTML), I'm not inclined to try it, but why not use sig_values to index row.names() and col.names() if you're after the names? Sarah On Mon, Jul 20, 2015 at 1:44 PM, gaurav kandoi wrote: > Hi All > > I've two big

Re: [R] jaccards index

On Mon, Jul 20, 2015 at 2:02 PM, Don McKenzie wrote: > Sarah Goslee’s package “ecodist” will compute a Jaccard index, I believe. Indeed it does, and for that matter so does the dist() function in base R. But I couldn't see how that index could be used to normalize data, being a dissimilarity on p

Re: [R] Knitr: setting echo = FALSE globally

On Mon, 20 Jul 2015, Thierry Onkelinx wrote: Have you tried echo = FALSE instead of echo = F. If that doesn't solve your problem, please provide a minimal reproducible example. Yes, I have. Attached is a TeX file renamed to sample.txt (rather than .tex to ensure it is not stripped), a PDF

Re: [R] error reading file DESCRIPTION

On Mon, Jul 20, 2015 at 1:42 PM, William Morgan wrote: > Hello, > > After downloading imview from SourceForge.net > , > I get the following error and warning when trying to install this package: That would be because it isn't an R package

Re: [R] Knitr: setting echo = FALSE globally

Section 5.1.3 of the book "Dynamic Documents with R and knitr" is titled "Global Options". I don't know how to make it more clear for readers to find information on global options in the book. Regards, Yihui -- Yihui Xie Web: http://yihui.name On Mon, Jul 20, 2015 at 12:58 PM, Rich Shepard wro

[R] error reading file DESCRIPTION

Hello, After downloading imview from SourceForge.net , I get the following error and warning when trying to install this package: > install.packages("~/Downloads/imview-src-1.0.1.tar.gz", repos = NULL, type = > "source") Error: error re

[R] Printing row and column names of cells with specific value in a big matrix

Hi All I've two big matrices (5k*4k) with the same structure, i.e. : mRNA1 mRNA2 mRNA3 lncRNA1 0.395646 0.94995 0.76177 lncRNA2 0.03791 0.661258 0.558658 lncRNA3 0.67846 0.652364 0.359054 lncRNA4 0.57769 0.003 0.459127 Now, I would like to extract the names of the row,col pairs whose value

Re: [R] jaccards index

Sarah Goslee’s package “ecodist” will compute a Jaccard index, I believe. You are unlikely to get much help, however, unless you provide more details as to what you are trying to accomplish. See http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example for how to

[R] using dcast with a function of multiple arguments

I am trying to figure out how to use dcast.data.table with a function with multiple arguments. Here is my reproducible example for a simple function of one argument: require(data.table) dt <- as.data.table(mtcars) dcast.data.table(dt, carb ~ cyl, value.var='mpg', fun=mean) If I instead want to

[R] ggplot2 geom_boxplot limits

With base graphics, one can use the "ylim" argument to zoom in on a boxplot. With ggplot2, using "limits" to try to zoom in on a boxplot *changes the box*. Since the box usually indicates the 25th and 75th percentiles of a quantitative variable, this is puzzling. The toy code below demonstrat

Re: [R] To simplify or not simplify?

This forum is for questions about R. There are forums that focus on the theory of statistics (e.g. stats.stackexchage.com), but this particular issue is addressed in many statistics classes as well... and there is not necessarily a simple answer that always applies in all cases so be prepared to

Re: [R] Knitr: setting echo = FALSE globally

Have you tried echo = FALSE instead of echo = F. If that doesn't solve your problem, please provide a minimal reproducible example. Op 20-jul.-2015 20:02 schreef "Rich Shepard" : > Near the beginning of a LyX document I have a knitr chunk with options > that begin with 'global_options', and inc

Re: [R] help with contributed package MTS

Hi, On Mon, Jul 20, 2015 at 2:01 PM, AGUSTIN ALONSO RODRIGUEZ wrote: > I am using R-3.2.1, and when I type install.packages(“MTS”), I get the > message: > > package ‘MTS’ is not available (for R version 3.2.1). It's on CRAN, and passes check for R-release: https://cran.r-project.org/web/checks

Re: [R] To simplify or not simplify?

Off topic . This list is about R programming. Post on a statistics list like stats.stackexchange.com instead. Cheers, Bert Bert Gunter "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." -- Clifford Stoll On Mon, Jul 20, 2015 at 2:02 AM, Georgina

[R] help with contributed package MTS

Dear Sirs: I am using R-3.2.1, and when I type install.packages(�MTS�), I get the message: package �MTS� is not available (for R version 3.2.1). I have tried also to install from local zip files, and I got it, but when I type: library(MTS), I got the message that Rcpp was absent. Woul

[R] Knitr: setting echo = FALSE globally

Near the beginning of a LyX document I have a knitr chunk with options that begin with 'global_options', and includes echo=F. This presents the R code in that chunk from displaying in the compiled PDF file. However, all following knitr chunks are included in the PDF file. Reading the docs (in

[R] jaccards index

hi.. I have a csv file containing 35 coloumns and 193 rows.i want to generate jaccards index to normalise these data.how can i do this also from these data i want to draw boxplot.plz help -- View this message in context: http://r.789695.n4.nabble.com/jaccards-index-tp4710057.html Sent from the

Re: [R] Value passing in print option

Also: cat("Current value of y is",y,"\n") Cheers, K On Mon, Jul 20, 2015 at 8:24 AM Uwe Ligges wrote: > ?paste > > Best, > Uwe Ligges > > > On 20.07.2015 08:48, Partha Sinha wrote: > > i want to pass a value with print option > > x<-10 > > y<2*x > > print("Current value of y is " ) # confused

[R] R GUI tklistbox get value

Hi, i have a dataframe, dat, with 2 variables, one and two. I want to print in R the mean of the selected variable of the dataframe. You can select it with a tklistbox, but when you click OK button, the mean is not displayed, just NA one<-c(5,5,6,9,5,8) two<-c(12,13,14,12,14,12) dat<-

[R] To simplify or not simplify?

Dear R help, This is rather a basic question, but I can't seem to find an answer anywhere else. When I run a model such as lm/aov(height~var1) where var 1 is a categorical variable with 6 levels, I get output that shows some significant parameters and other non significant. Normally I would th

Re: [R] Difference between drop1() vs. anova() for Gaussian glm models

I am somewhat surprised that _anything_ sensible comes out of anova.glm(l, test="Chisq"). I think it is mostly expected that you use F tests for that case. What does seem to come out is the same as for drop1(l, test="Rao"), which gives the scaled score test, which would seem to be equivalent to

Re: [R] best way to globally set parameters for base graphics

Thanks for the reply. It works fine for a single plot-call. But as soon as I call layout() before plotting I again run into the problem that plots are not drawn into one graphic device but another one is opened for the second plot-call. see here; setHook("plot.new", function() par(b

Re: [R] Differences in output of lme() when introducing interactions

In-line On 20/07/2015 15:10, angelo.arc...@virgilio.it wrote: Dear List Members, I am searching for correlations between a dependent variable and a factor or a combination of factors in a repeated measure design. So I use lme() function in R. However, I am getting very different results depen

Re: [R] best way to globally set parameters for base graphics

On 20/07/2015 11:27 AM, Martin Batholdy via R-help wrote: > Hi, > > I am looking for a way to modify the basic setup for any kind of plot. > (everything that is set with the par function – like margins, cex, las etc.) > > I want to do this once – preferably across R sessions and not individually

[R] best way to globally set parameters for base graphics

Hi, I am looking for a way to modify the basic setup for any kind of plot. (everything that is set with the par function – like margins, cex, las etc.) I want to do this once – preferably across R sessions and not individually before every plot. My first attempt was to add a par() with all my

[R] Differences in output of lme() when introducing interactions

Dear List Members, I am searching for correlations between a dependent variable and a factor or a combination of factors in a repeated measure design. So I use lme() function in R. However, I am getting very different results depending on whether I add on the lme formula various factors comp

Re: [R] For Hadley Wickham: Need for a small fix in haven::read_spss

Thank you, Hadley. Yes, you are right - next time I'll email you directly. On Mon, Jul 20, 2015 at 10:01 AM, Hadley Wickham wrote: > (FWIW this would've been better send to me directly or filed on > github, rather than sent to R-help) > > I think this is more of a problem with the way that you're

Re: [R] For Hadley Wickham: Need for a small fix in haven::read_spss

(FWIW this would've been better send to me directly or filed on github, rather than sent to R-help) I think this is more of a problem with the way that you're accessing the info, than the design of the underlying structure. I'd do something like this: attr_default <- function(x, which, default) {

[R] For Hadley Wickham: Need for a small fix in haven::read_spss

Hadley, you've added function labelled to haven, which is great. However, when it so happens that in SPSS a variable has no long label, your code considers it to be NULL rather than an NA. NULL is correct, but NA would probably be better. For example, I've read in an SPSS file: library(haven) sp

[R] Difference between drop1() vs. anova() for Gaussian glm models

Dear list members, I’m having some problems understanding why drop1() and anova() gives different results for *Gaussian* glm models. Here’s a simple example: d = data.frame(x=1:6, group=factor(c(rep("A",2), rep("B", 4 l = glm(x~group, data=d) Running the following code

Re: [R] modifying a package installed via GitHub

Steve, You are able to work with a github package the same as any github repo. If you clone the repo: git clone https://github.com/user/repo.git If using RStudio it is simple enough to create a new project in that new directory (if the .Rproj file does not exist, otherwise open that). Once you

Re: [R] Value passing in print option

?paste Best, Uwe Ligges On 20.07.2015 08:48, Partha Sinha wrote: i want to pass a value with print option x<-10 y<2*x print("Current value of y is " ) # confused dont know how to pass value i want output as Current value of y is 10 [[alternative HTML version deleted]] __