[R] Installing df2genind version clash?

Dear list members, I want to install the df2genind package to create a genind-class object for adegenet. Despite recent updates of R (now version R 4.3.0) and RStudio (now version 2023-03-1 Build 446), I get the following warning/error message: ---

[R] Plotting prediction curves and CIs from GAM models

oS and ToD? If not, how can I find/create one? 2. How can I produce a "topography"-plot of the predicted count numbers over ToD vs DoS, similar to the one for the tensor estimates produced by plot.gam? Thanks in advance for any references, comments and suggestions. Have a nice day, Adriaan

Re: [R] CARET and NNET fail to train a model when the input is high dimensional

let's you fit > the model. Off the top of my head, you could use something like: > >MaxNWts = length(levels(trY))*(max(my.grid$.size) * (nCol + 1) + > max(my.grid$.size) + 1) > > Also, this one of the methods for getting help (the other is to just email > me). I also try

[R] CARET and NNET fail to train a model when the input is high dimensional

The following code fails to train a nnet model in a random dataset using caret: nR <- 700 nCol <- 2000 myCtrl <- trainControl(method="cv", number=3, preProcOptions=NULL, classProbs = TRUE, summaryFunction = twoClassSummary) trX <- data.frame(replicate(nR, rnorm(nCol))) trY <- runif(1)*trX[,1

[R] CARET. Relationship between data splitting trainControl

I have carefully read the CARET documentation at: http://caret.r-forge.r-project.org/training.html, the vignettes, and everything is quite clear (the examples on the website help a lot!), but I am still a confused about the relationship between two arguments to trainControl: "method" "index" and

[R] party::cforest - predict?

What is the function call interface for predict in the package party for cforest? I am looking at the documentation (the vignette) and ?cforest and from the examples I see that one can call the function predict on a cforest classifier. The method predict seems to be a method of the class RandomFor

Re: [R] CARET: Any way to access other tuning parameters?

really need to read the documentation. Almost every question that >>> you have has been addressed in the existing material. For this one, there >>> is a section on custom models here: >>> >>>http://caret.r-forge.r-project.org/training.html >>> >

Re: [R] CARET: Any way to access other tuning parameters?

rge.r-project.org/training.html > > Max > > > On Wed, Feb 13, 2013 at 9:58 AM, James Jong wrote: > >> The documentation for caret::train shows a list of parameters that one can >> tune for each method classification/regression method. For example, for >> the

[R] CARET: Any way to access other tuning parameters?

The documentation for caret::train shows a list of parameters that one can tune for each method classification/regression method. For example, for the method randomForest one can tune mtry in the call to train. But the function call to train random forests in the original package has many other p

[R] Putting priors on which factors to sample more from, in random forests

I was wondering if anyone knows of a random forest implementation (or way of tweaking the standard randomForest library) that allows one to specify some sort of variable importance a* *priori. For example, say that I know that some variables/factors could be more informative than others for class

Re: [R] caret: Errors with createGrid for rf (randomForest)

That was the problem. Thanks David! James On Tue, Feb 12, 2013 at 2:08 PM, David Winsemius wrote: > > On Feb 12, 2013, at 10:53 AM, James Jong wrote: > > > When I try to crate a grid of parameters for training with caret I get >

[R] caret: Errors with createGrid for rf (randomForest)

When I try to crate a grid of parameters for training with caret I get various errors: > my_grid <- createGrid("rf") Error in if (p <= len) { : argument is of length zero > my_grid <- createGrid("rf", 4) Error in if (p <= len) { : argume

[R] Training with very few positives

I have a binary classification problem where the fraction of positives is very low, e.g. 20 positives in 10,000 examples (0.2%) What is an appropriate cross validation scheme for training a classifier with very few positives? I currently have the following setup: =

[R] Statistics of prediction for multiple models with caret

I am trying to get statistics of prediction for binary classification problems and for various training models with caret. Below is an example that illustrates my need: -- library(caret) # ... Get X and Y for training a binary classification problem. X is i

[R] rpy2 (Python <--> R)

Hi - I am having trouble installing rpy2. I have already compiled R as a shared library, but I do not have admin privileges on so I am trying to install rpy2 with: pip install -user rpy2 but I am getting the following error: ./rpy/rinterface/_rinterface.c

[R] Correct value of R_HOME

What is the purpose of the variable R_HOME? What value should I set it to? Thanks, James [[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 ht

[R] Questions about caret - Best place to ask?

Hi there. I am relatively new to R and to the community. I have previously asked my R questions at R-help (through Nabble, not sure if there is a better way other than Nabble or regular email), and StackOverflow with the [R] tag. I have some questions that are somewhat specific about the packag

Re: [R] Sourcing my file does not print command outputs

** ** > > The summary information and dotplot printed just fine. > > ** ** > > Dan > > ** ** > > Daniel J. Nordlund > > Washington State Department of Social and Health Services > > Planning, Performance, and Accountability > > Research a

Re: [R] Saving model and other objects from caret

What are the *RDS counterparts? What is the difference? James On Thu, Feb 7, 2013 at 5:00 PM, Michael Weylandt wrote: > > > On Feb 7, 2013, at 9:51 PM, James Jong wrote: > > > Thanks Stephan. I can't believe I didn't try that first. I greatly > > appreciat

Re: [R] Saving model and other objects from caret

**loading-a-model-in-r<http://stackoverflow.com/questions/14761496/saving-and-loading-a-model-in-r> > > Best, > Stephan > > > > > On 07.02.2013 22:33, James Jong wrote: > >> Say I train a model in caret, e.g.: >> >> RFmodel <- train(X,Y,method=

[R] Fwd: Sourcing my file does not print command outputs

; Daniel J. Nordlund > Washington State Department of Social and Health Services > Planning, Performance, and Accountability > Research and Data Analysis Division > Olympia, WA 98504-5204 > > From: James Jong [mailto:ribonucle...@gmail.com] > Sent: Thursday, February 07, 2013 1:30

[R] Saving model and other objects from caret

Say I train a model in caret, e.g.: RFmodel <- train(X,Y,method='rf',trControl=myCtrl,tuneLength=1) How can I save this to disk and load it later in R? How about an object of the class "resamples"? resamps <- resamples( list( RF = RFmodel, SVM = SVMmodel,

Re: [R] Sourcing my file does not print command outputs

(DSHS/RDA) < nord...@dshs.wa.gov> wrote: > > -Original Message- > > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > > project.org] On Behalf Of John Kane > > Sent: Thursday, February 07, 2013 10:57 AM > > To: James Jong; r-help@r-project.org

[R] Saving history across sessions

I have an environment variable `$R_HISTFILE` pointing to `/home/my.username/.RHistory` and the following code in my `.Rprofile` in my home directory: .Last <- function() { if (!any(commandArgs()=='--no-readline') && interactive()){ require(utils)

[R] Sourcing my file does not print command outputs

I looked at the documentation of source() and summary(), and I could not find the reason why calling something like: > summary(resamps) from the command line, works (it prints the summary) whereas calling summary(resampls) from a file that I source with source("my_file.r") does not print anyth

[R] obtain linear regression parameters from qplot

Hi, My question is how to get linear regression parameters (e.g. slope, y-intercept, etc.) from the fittings in qplot. My code looks like this, Fig1 = qplot(data=subset(totalD, (Name=="increase1"), x=Time, y=Intensity, main="Total Data") Fig1 + stat_smooth(method="lm") I can get the linear regre

[R] Dealing with unix signal

help in advance. Thanks, Jong __ 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.

[R] How to verify R is running with multi-threads

f77blas -lpthread -latlas" --with-blas="-lgotocblas -lgotoblas -lpthread" Not sure if my options are correct or not. Thank you for your and comment or advice in advance. Thanks, Jong __ R-help@r-project.org mailing list https://stat.et

[R] generic questions about probability and simulation -- not directly related to R

Dear helpers, As the title says, my question is not directly related to R. I find, however, that there are many people who are both knowledgeable and kind in this email list, and so decided to give it a try. I do stochastic simulations. Parameter values used in simulation often come from the obs

[R] drawing direction fields

Dear useRs, I am trying to draw direction fields for some differential equations. So for I couldn't find much information on that. Could anybody give me a hint how to draw a direction field using R? -- 734 274 2394 Jong-Hoon Kim [[alternative HTML version de

[R] drawing direction fields

Dear useRs, I am trying to draw direction fields for some differential equations. So for I couldn't find much information on that. Could anybody give me a hint how to draw a direction field using R? Jong-Hoon __ R-help@r-project.org mailing