Re: [R] Generating uniformly distributed correlated data.

You may also be interested in the "psych" package or possibly "mvtBinaryEP". I found these using "sos": library(sos) tc <- findFn('tetrachoric correlation') # 26 matches tcs <- findFn('tetrachoric correlations')#27 matches tc. <- tc|tcs summary(tc.) # 35 links in 5 pkgs tc. All

Re: [R] Generating uniformly distributed correlated data.

maybe this helps http://comisef.wikidot.com/tutorial:correlateduniformvariates regards enrico > -Ursprüngliche Nachricht- > Von: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] Im Auftrag von Søren Faurby > Gesendet: Sonntag, 20. Februar 2011 03:18 > An: r-help@r-

Re: [R] Scaling Lattice Graphics for tikzDevice

On Sun, Feb 20, 2011 at 5:23 AM, Elliot Joel Bernstein wrote: > > On Feb 18, 2011 11:02 PM, "Deepayan Sarkar" > wrote: >> >> On Fri, Feb 18, 2011 at 11:04 PM, Elliot Joel Bernstein >> wrote: >> > I'm trying to use lattice graphics to produce some small plots for >> > inclusion in a LaTeX file. I

Re: [R] Generating uniformly distributed correlated data.

On Sun, Feb 20, 2011 at 12:18 AM, Peter Langfelder wrote: > On Sat, Feb 19, 2011 at 6:17 PM, Søren Faurby > wrote: >> I wish to generate a vector of uniformly distributed data with a defined >> correlation to another vector >> >> The only function I have been able to find doing something similar

[R] pre-announcement Google Summer of Code 2011 -- R projects

In a little over a month (Mar 28), students will have just over a week (until April 8) to apply to work on Google Summer of Code projects. In the past few years, R has had several such projects funded. Developers and mentors are currently preparing project outlines on the R wiki at http://rwiki.

Re: [R] covar

Relatedness if often defined in terms of the kinship matrix. It may be helpful to search for this. Several packages in R use this matrix including the kinship package. On Wed, Feb 16, 2011 at 3:14 PM, Val wrote: > Hi all, > > I want to construct relatedness among individuals and have a look at th

Re: [R] Seeking help in Package development

May I add that the best documentation for building packages is the "Writing R Extensions" that ships with the current R version. It is always current, precise, and not as outdated as many resources you find "somewhere" in the web - yes, the one cited below is outdated. Uwe Ligges On 19.02.20

[R] inter-specific competition - community matrices and two species models using Lotka-Volterra

Does anyone know of example r-code/packages for carrying out analysis? Preferably this would have examples from real experimental data of two or more competing species... Thanks Chris Buddenhagen [[alternative HTML version deleted]] __ R-help@

Re: [R] inter-specific competition - community matrices and two species models using Lotka-Volterra

On 20 February 2011 16:19, Chris Buddenhagen wrote: > Does anyone know of example r-code/packages for carrying out analysis? > Preferably this would have examples from real experimental data of two or > more competing species... > > In discrete time, you can use a Gompertz model:

Re: [R] Confidence Intervals on Standard Curve

model <- lm(Approximate.Counts~X..Light.Transmission + I(Approximate.Counts^2), data=Standards) Might not be addressing the problem, don't you have Y ~ X + Y^2 here? That's a violation of the assumptions of an lm isn't it? Also for plotting CI on a curve look into ggplot2::geom_ribbon, it's muc

[R] Conditional sum

Hi, I have a DF like this: DF = data.frame(read.table(textConnection("A B C 1 b1 1999 0.25 2 c1 1999 0.25 3 d1 1999 0.25 4 a2 1999 0.25 5 c2 1999 0.25 6 d2 1999 0.25 7 a3 1999 0.25 8 b3 1999 0.25 9 d3 1999 0.25 10 a4 1999 0.25 11 b4 1999 0.25 12 c4 1999 0.25 13 b1

[R] Plot of set

I am in the situation where I have to make a two-dimential plot of a set. If I simplify my data it would be something along the lines of wanting to plot {x,y| x^2+y^2 < = 1}. I am aware of the contour and persp plot, but cannot figure out how to convert one of those to draw the set. I have tri

[R] Help Metafor

Dear Sir, I'm using the "Metafor" package; however, introducing moderators, I'm unable to obtain both I^2 (% of total variability due to heterogeneity) and H^2 (total variability / within-study variance). It is possible to obtain I^2 and H^2 also with moderators? As example _

[R] concatenate vector after strsplit()

ls is a list of character vectors created by strsplit() I want to concatenate the 1st 4 character elements of each list item as a new vector called file. I admit to being confused about list syntax even after numerous readings. Here's what I tried: ls <- list(c("Focused", "10k", "A12", "t04.

Re: [R] concatenate vector after strsplit()

Hi Robert, You might try do.call(rbind, lapply(yourlist, "[", 1:4)) and then write the resulting file using write.table(...). Best, Jorge On Sun, Feb 20, 2011 at 11:13 AM, Robert Baer <> wrote: > ls is a list of character vectors created by strsplit() > > I want to concatenate the 1st 4 char

[R] prevent export of specific functions in NAMESPACE

Hi, I'd like to prevent the export a specific function in the NAMESPACE file. The example in the R documentation uses a regex to prevent export of a set of functions, but as far as I can see there is no easy way to specify that a function of a specific name should not be exported. This thread (http

Re: [R] Conditional sum

mathijsdevaan wrote: > > I have a DF like this: > > DF = data.frame(read.table(textConnection("A B C > 1 b1 1999 0.25 > 2 c1 1999 0.25 > .. > For each factor in A I want to sum the values of C for all years(Bn) prior > to the current year(Bi): > > 1 b1 1999 0.25 0 > 2 c1 1999 0

Re: [R] Plot of set

On Feb 20, 2011, at 4:41 AM, . . wrote: I am in the situation where I have to make a two-dimential plot of a set. If I simplify my data it would be something along the lines of wanting to plot {x,y| x^2+y^2 < = 1}. I am aware of the contour and persp plot, but cannot figure out how to co

Re: [R] concatenate vector after strsplit()

You might try do.call(rbind, lapply(yourlist, "[", 1:4)) Thanks, Jorge, but when I tried this I simply got a matrix of character strings rather than my original list of character strings as in: m = do.call(rbind, lapply(ls, "[", 1:4)) m [,1] [,2] [,3] [,4] [1,] "Focused" "10k" "A12

Re: [R] concatenate vector after strsplit()

On Feb 20, 2011, at 11:13 AM, Robert Baer wrote: ls is a list of character vectors created by strsplit() I want to concatenate the 1st 4 character elements of each list item as a new vector called file. I admit to being confused about list syntax even after numerous readings. Here's wh

Re: [R] concatenate vector after strsplit()

On Feb 20, 2011, at 12:49 PM, David Winsemius wrote: On Feb 20, 2011, at 11:13 AM, Robert Baer wrote: ls is a list of character vectors created by strsplit() I want to concatenate the 1st 4 character elements of each list item as a new vector called file. I admit to being confused about

Re: [R] tikzDevice compiling problem

Thank you! -- View this message in context: http://r.789695.n4.nabble.com/tikzDevice-compiling-problem-tp3309028p3315247.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/li

Re: [R] Conditional sum

Thanks for the quick response, but it doesn't do the trick. There are two problems: 1. The ith value of the newly created variable DF$D also includes the ith value of DF$C (this problem is easily solved by DF$D = DF$D-DF$C.) 2. If group i in DF$group appears more than once in year t, the value of

Re: [R] concatenate vector after strsplit()

On Sun, Feb 20, 2011 at 12:43 PM, Robert Baer wrote: >> You might try >> >> do.call(rbind, lapply(yourlist, "[", 1:4)) > > Thanks, Jorge, but when I tried this I simply got a matrix of character > strings rather than my original list of character strings as in: >> >> m = do.call(rbind, lapply(ls,

Re: [R] concatenate vector after strsplit()

Thanks Jorge and David. Both worked. Looks like I have to read more on "[" as an extractor function for lists. do.call() is also on my list of "low level magic' I don't understand.Appreciate the help! fil1 = do.call(c, lapply(lapply(ls1, "[", 1:4), paste, sep = "", collapse = "-")) fil

Re: [R] Confidence Intervals on Standard Curve

It is, I tried a glm with a poisson distribution, as was suggested to me previously, but the Residual Deviance was too high - the book I'm reading says it suggests overdispersion because it's way above the Residual degrees of freedom: glm(formula = Approximate.Counts ~ X..Light.Transmission, f

Re: [R] concatenate vector after strsplit()

Thanks Gabor. Your suggestions work as well and have been helpful in my understanding, I can't use any excuse of not knowing about "]" in this case! Rob fil3 = sapply(ls1, function(x) paste(x[1:4], collapse = "")) fil4 = sapply(unname(as.data.frame(ls1))[1:4,], paste, collapse = "") fil5 =

Re: [R] Confidence Intervals on Standard Curve

On Feb 20, 2011, at 1:27 PM, Ben Ward wrote: However, the Y ~ X + Y^2 Produces the best fitting line - it is pretty much on the data points - I'm trying to make a standard curve, with which to take readings from a spectrophotometer off of. Rather than what I would normally use models fo

Re: [R] Bootstraps standard error

when I calculate the bootstrap standard errors the results are summarized in a matrix with columns equal to the parameters of the model. In my case I have a matrix like this: [,1] [,2] [,3] [,4] [,5] [,6][,7] [,8][,9] [

Re: [R] Variable length datafile import problem

Hi Ingo, Sorry for being so slow to get back to you. I've had a bit of a problem with my internet connection. Just how large is the data set? You might want to have a look at this thread re size of R data files. http://r.789695.n4.nabble.com/Boundaries-of-R-td3312593.html . In any case, fr

Re: [R] Random Forest & Cross Validation

> I am using randomForest package to do some prediction job on GWAS data. I > firstly split the data into training and testing set (70% vs 30%), then > using training set to grow the trees (ntree=10). It looks that the OOB > error in training set is good (<10%). However, it is not very good for

Re: [R] Bootstraps standard error

On Feb 20, 2011, at 2:20 PM, danielepippo wrote: when I calculate the bootstrap standard errors ... of what? the results are summarized in a matrix with columns equal to the parameters of the model. ... but they are all the same within each row??? In my case I have a matrix like this:

Re: [R] Bootstraps standard error

Can anyone help me please? -- View this message in context: http://r.789695.n4.nabble.com/Bootstraps-standard-error-tp3313322p3315463.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.

[R] Plotting individual trajectories from individual growth model

Hi all, I am trying to plot the fitted trajectories for each individual from an individual growth model (fit with a linear mixed effects model in lme). How can I plot each person's trajectory in the *same* panel, along with the mean-level trajectory? Below is an image of a plot similar to what

Re: [R] joint estimation of two poisson equations

Hi, I have the same problem to find out the standard errors of the parameter in the same package you have used. I couldn't find out how to get standard errors and p-values from the package, so I bootstrapped them. Can you explain your method to find out the standard errors with the bootstrap m

Re: [R] prevent export of specific functions in NAMESPACE

On 11-02-20 11:58 AM, Rajarshi Guha wrote: Hi, I'd like to prevent the export a specific function in the NAMESPACE file. The example in the R documentation uses a regex to prevent export of a set of functions, but as far as I can see there is no easy way to specify that a function of a specific n

Re: [R] inter-specific competition - community matrices and two species models using Lotka-Volterra

Bob O'Hara gmail.com> writes: > > On 20 February 2011 16:19, Chris Buddenhagen wrote: > > > Does anyone know of example r-code/packages for carrying out analysis? > > Preferably this would have examples from real experimental data of two or > > more competing species... > > > > In discrete time

[R] Matrix Help

Listers, I have a simple matrix: -- m <-c(1:7) m <- cbind(m) m [1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6 [7,] 7 --- I want to add a second column using: [[alternative HTML version deleted]] ___

Re: [R] Matrix Help

On Sun, Feb 20, 2011 at 5:55 PM, Dmitry Berman wrote: > Listers, > > I have a simple matrix: > > -- > m <-c(1:7) > m <- cbind(m) > > m > [1,] 1 > [2,] 2 > [3,] 3 > [4,] 4 > [5,] 5 > [6,] 6 > [7,] 7 > --- > > I want to add a second co

Re: [R] Matrix Help

On Feb 20, 2011, at 5:56 PM, Dmitry Berman wrote: On Sun, Feb 20, 2011 at 5:55 PM, Dmitry Berman wrote: Listers, I have a simple matrix: -- m <-c(1:7) m <- cbind(m) m [1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6 [7,] 7 --- I

Re: [R] Matrix Help

On Sun, Feb 20, 2011 at 2:56 PM, Dmitry Berman wrote: > On Sun, Feb 20, 2011 at 5:55 PM, Dmitry Berman wrote: > >> Listers, >> >> I have a simple matrix: >> >> -- >> m <-c(1:7) >> m <- cbind(m) >> >> m >> [1,] 1 >> [2,] 2 >> [3,] 3 >> [4,] 4 >> [5,] 5 >> [6,] 6 >>

Re: [R] barplot, different color for shading lines and bar

The easiest solution may be using par(new=TRUE) and to overlay a coloured barplot with a separate shaded barplot HTH Jannis On 02/19/2011 10:58 PM, Markus Loecher wrote: Dear all, might there be a modified barplot function out there which allows the user to specify a fill color for the bar

[R] QuadTree

Could any one tell me how to implement QuadTree in R? Or are there any packages avaialble to implement it in R. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

[R] Same color key for multiple lattice contour plots

Hi all, I'm trying to make multiple lattice contour plots which have the same color key, to allow good comparisons. However, I run into some problems when fitting the plots to the color key. Basically my strategy to tackle this problem was: 1) define a color key for all plots; 2) calculate the va

[R] list of features from svmpath?

How can I get the list of non-zero features from svmpath at any given lambda? All I get is following information and information about what features were selected. In Iris example, we have 4 features and 60 cases. In my own example which is 200cases by 300 features, I can't figure out how to print

[R] Tips to export R plots (dotplot function) into latex

I'm looking for some tips on how to export R plots into latex. I can't centered the plots in latex (shift to the right). -- -Tony [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

Re: [R] Generating uniformly distributed correlated data.

Thanks to everybody for helpfull answers. In case other people want to generate similar data at one time The one function I have found without any apparant bias ( such as extreme clustering of the datapoints along one or both diagonals in plot(x,y) or a slight bias in the generated correlatio

Re: [R] Confidence Intervals on Standard Curve

On 20/02/2011 18:52, David Winsemius wrote: On Feb 20, 2011, at 1:27 PM, Ben Ward wrote: However, the Y ~ X + Y^2 Produces the best fitting line - it is pretty much on the data points - I'm trying to make a standard curve, with which to take readings from a spectrophotometer off of. Rather

Re: [R] Seeking help in Package development

> Date: Sun, 20 Feb 2011 15:56:41 +0100 > From: lig...@statistik.tu-dortmund.de > To: jwiley.ps...@gmail.com > CC: r-help@r-project.org > Subject: Re: [R] Seeking help in Package development > > May I add that the best documentation for building p

Re: [R] Tips to export R plots (dotplot function) into latex

This sounds more like a LaTeX question than an R question... \begin{center} \includegraphics{...} \end{center} If you had something else in mind please post more details. Best, Ista On Mon, Feb 21, 2011 at 1:03 AM, Antonio Paredes wrote: > I'm looking for some tips on how to export R plots into

Re: [R] barplot, different color for shading lines and bar

Hi: This isn't hard to do with ggplot2. Here's a toy example: d <- data.frame(gp = LETTERS[1:4], frq = c(10, 25, 30, 20)) library(ggplot2) # The fill aesthetic colors the bars, the colour aesthetic does the same for the borders. # (1) Same color for both, use alpha transparency: ggplot(d, aes(

Re: [R] Plotting individual trajectories from individual growth model

Hi: These are sometimes called 'spaghetti plots'; here is a variation on an example in the ggplot2 book by Hadley Wickham using the Oxboys data from package nlme: library(ggplot2) data('Oxboys', package = 'nlme') g <- ggplot(Oxboys, aes(x = age, y = height)) g + geom_line(aes(group = Subject)) +

Re: [R] How to change dataframe to tables

Thanks! It works well. 2011/2/18 Dimitris Rizopoulos > say, 'Dat' is your data frame, then one way to do it is: > > with(Dat, tapply(freq, list(hair, eye, sex), c)) > > > I hope it helps. > > Best, > Dimitris > > > > > On 2/18/2011 8:50 AM, Lao Meng wrote: > >> The data is in the attachment.

Re: [R] How to change dataframe to tables

Thanks! It works well. 2011/2/18 Henrique Dallazuanna > Try this: > > xtabs(Freq ~ Hair + Eye + Sex, Dat) > > Using Dimitri's Dat example. > > On Fri, Feb 18, 2011 at 5:50 AM, Lao Meng wrote: > >> The data is in the attachment. >> >> What I wanna get is: >> , , Sex = Male >> Eye >> Ha

Re: [R] How to change dataframe to tables

Well,it's my daily work on duty,not homework:) 2011/2/18 Dennis Murphy > This is a built-in dataset in R - see ?HairEyeColor and str() it. I smell > homework... > > Dennis > > On Thu, Feb 17, 2011 at 11:50 PM, Lao Meng wrote: > >> The data is in the attachment. >> >> What I wanna get is:

[R] Error in R-SVM help:

Greetings: I am trying to use your R code for R-SVM as follows. Why it dosen't print the LOO.error and the list of features? http://www.stanford.edu/group/wonglab/RSVMpage/R-SVM.html My training data as follows contains 142 cases and 264 features. instead I get en error as below "invalid 'digits