Re: [R] How to apply a function to subsets of a data frame *and* obtain a data frame again?

You might want to look at package plyr and use ddply. HTH, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove > -Original Message- > From: r-help-boun...@r-project.org [ma

Re: [R] glmnet

y the variables selected in the previous step. Good luck! Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove > -Original Message- > From: r-help-boun...@r-project.org [ma

Re: [R] counting columns that fulfill specific criteria

to name any variable t, as this is also the function for transposing a matrix, and could end up being confusing at the least. Second: for most practical purposes, it's better to leave out the *100. Good luck, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure

Re: [R] problem (and solution) to rle on vector with NA values

making the new behavior optional (through a new parameter na.action or similar, with the default the original behavior) is an option? Feel free to run your own version of rle in any case. I suggest you rename it, though, as it may cause problems for some packages. Nick Sabbe -- ping: nick.sa

Re: [R] Rcpp and Object Factories

You might want to send this message to the Rcpp mailing list at: Rcpp-devel mailing list rcpp-de...@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel It will improve your chances of getting a swift (if not helpful) reply. Nick Sabbe -- ping

Re: [R] Simple order() data frame question.

Try (df1[order(-df1[,2]),]) Adding the minus within the [ leaves out the column (in this case column 2). See ?"[". HTH. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove ---

Re: [R] Looping over graphs in igraph

you're interested about, based on graph object g #for now I'm just returning edge and vertex counts return(c(v=vcount(g), e=ecount(g))) }) colnames(result)<-unique(dfr$Graph.ID) print(result) HTH, Nick Sabbe -- ping: nick.sa...@ugent.be

Re: [R] Lasso with Categorical Variables

(invisible(factorsToDummyVariables.old (ds[20:30,]))) ## user system elapsed ## 2.110.002.15 If you have to do this quite often, the difference surely adds up... More improvements may be possible. This function only works if you don't include interactions, though. Nick Sabbe --

[R] abline outside of plot region

orks. I set col.ticks to match the color of my abline (in the nonsimplified code), and this works too, but unfortunately, the label below the tick is not in this color, and a parameter for this is not present in axis. Suggestions for either? Note: I'm on windows 7 with R 2.13. Nick Sabbe -

Re: [R] Reference variables by string in for loop

Hi Michael. This is a classic :-) ObjectsOfInterest<- list(one_df, two_df, three_df) for(namedf in ObjectsOfInterest){...} or probably even better sapply(ObjectsOfInterest, function(namedf){...}) hth. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coup

Re: [R] Assignments inside lapply

No, that does not work. You cannot do assignment within (l)apply. Nor in any other function for that matter. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message

Re: [R] programming: telling a function where to look for the entered variables

#columnsOfInterest or similar, and pass that instead of c(xvarname, yvarname) ) return(indextable) } myfunct.better("yes", lvarname="lvar", xvarname="xvar", yvarname="yvar", dataframe=Fulldf) HTH, Nick Sabbe -- ping: nick.sa...@ugent.be li

Re: [R] programming: telling a function where to look for the entered variables

subset(Fulldf, lvar==subgroup, select=c("xvar","yvar")) Which should become something like (untested but should be close): Data.tmp <- Fulldf[Fulldf[,"lvar"]==subgroup, c("xvar","yvar")] This should be a lot easier to translate based on column n

Re: [R] choosing best 'match' for given factor

. And similarly depending, I may be better still if you remove the rows that you're not interested in as well (some more but similar index trickery required then. HTH, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring

Re: [R] Graph many points without hiding some

ing box is in cube-form (scaling variables) #note: if you want to flip an axis, use -1 in the statement above axes3d() #Show axes title3d(main = main, sub=paste("Green is low", ulab, ", red is high") xlab = xlab, ylab = ylab, zlab = zlab)

Re: [R] a for loop to lapply

d, like: given a matrix with two columns, create a vector holding the differences and the sums of the columns - I know this can be done without *apply as well, but apart from that it is a more attainable exercise). Good luck to you on that! HTH, Nick Sabbe -- ping: nick.sa...@ugent.be link: http:

Re: [R] A question on glmnet analysis

he L1 penalty is not differentiable). Some 'solutions' exist (bootstrap, for one), but they have all been shown to have (statistical) properties that make them - at the least - doubtful. I know, because I'm working on this. Short answer: there is no way to do this (at this time). HTH (and ha

Re: [R] One to One Matching multiple vectors

Hello Vincy. You probably want y[match(z,x)] Or, more instructional: whereAreZInX<-match(z, x) y[whereAreZInX] HTH, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Mess

[R] Generic mixup?

terrible misunderstanding of what comprises a generic function? Thx, Nick Sabbe -- ping: nick.sa...@ugent.be link: <http://biomath.ugent.be/> http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapp

Re: [R] speed up process

b=names(mydata1)[k]) lapply(seq_along(mydata_list), function(j){ foo_reg(dat=mydata_list[[j]], xvar=ind.xvar, yvar=k, mycol=j, pos=mypos[j], name.dat=names(mydata_list)[j]) return(NULL) }) invisible(NULL) }) HTH, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomat

Re: [R] glmnet with binary predictors

t the 'best' value for the penalization parameter from the plot (see ?plot.cv.glmnet), or you can use some numerical argument to find the reasonable extreme value for the criterion. Really boilerplate, I guess. Good luck. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ug

[R] Preparing dataset for glmnet: factors to dummies

taframe, I don't have the option to do this conversion before the imputation, so I really need the conversion itself to work quickly. Thanks, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disappro

[R] Injecting code in a package?

n-package bound copy of the function, I want to make sure that when I call pkg::plot.something, this works as before, but when, from within this function, pkg:: plot.something.internal is called, I want it to call _my_ version of it. Any takes? Nick Sabbe -- ping: nick.sa...@ugent.b

[R] get type functions (was: RE: plot not generic)

Vito Muggeo (UniPa) [mailto:vito.mug...@unipa.it] Sent: vrijdag 28 januari 2011 14:42 To: Nick Sabbe Cc: r-help@r-project.org Subject: Re: [R] plot not generic dear Nick, getAnywhere("plot.glmnet") Note the message you get when you type methods(plot) ... >>> Non-visible

[R] plot not generic

noticed that R does not recognize 'plot' as a generic function, and as such, showMethods does not work. This seems to conflict with the documentation for plot. So 2 questions: . How can I find the code of plot.glmnet . Why is plot not seen as generic? Thx.

Re: [R] Using a list as multidimensional indexer

t;a",]. I tried some variants of Ind3<-list(Mm,"b",NULL) do.call("[", Ind3) But all of these return integer(0). So the actual new question is: how do I pass a 'missing' argument through a do.call? Thanks for any pointers, Nick Sabbe -- ping: nick.sa...@ugent

[R] Using a list as multidimensional indexer

("b","g") This holds, for each dimension, an indexer for that dimension. Now I would like to get the element pointed at by the list. The obvious solutions don't seem to work, and I can't seem to get do.call to call the indexer ('[') on my mul

Re: [R] expand.grid

-c(rv,NA) } #cat("levels with na: ", rv, "\n") return(rv) } expand.combs<-function(dfr, includeNA=FALSE, onlyOccurring=FALSE) { expand.grid(lapply(dfr, getLevels, includeNA, onlyOccurring)) } Thx. Nick Sabbe -- ping: nick.sa...@ugent.be link

[R] expand.grid

t;). It would also be nice to be able to choose whether or not NA's are included. I'm convinced that some package holds a readymade solution, and I'm trying to switch from always writing my own stuff (get the number of levels per column, then use some apply magic) to using what is t

Re: [R] Repeating value occurence

ern<- c(-1,0,1,0) rep(pattern, ceiling(n/length(pattern)))[1:n] If you want a sequence of random real numbers between -1 and 1, use runif(10, min=-1, max=1) Here's hoping I haven't just solved your homework... Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink:

Re: [R] Numbers in a string

Hi Felipe, gsub("[^0123456789]", "", "AB15E9SDF654VKBN?dvb.65") results in "15965465". Would that be what you are looking for? Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent

Re: [R] problem accessing complex list data frames

Hello Germán. You probably want something like: sapply(vmat, function(curMat){ curMat[,999] != 0 }) Or if you want the indices, just surround this with a which. HTH. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653

[R] Dataframe from list of similar lists: not _a_ way, but _the best_ way

f R? Or is there any way in which this depends on the specifics of my function (for nontrivial functions and list sizes)? Thanks! Nick Sabbe -- ping: nick.sa...@ugent.be link: <http://biomath.ugent.be/> http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/

Re: [R] small problem in coding

ent, you can access g by: lamda["g"] as in: > Q<-exp(lamda["g"]) It looks like you've got a misunderstanding of how R variables work, but maybe I just misunderstood your question... HTH, Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be

Re: [R] Simple Function

and search for <<-, for more information). * apart from that: you may want to avoid the for loop here altogether: y[i:10]<-(i:10)+1 f[i:10]<-y[(i-1):9]/2 gives you the same result, but more in the R fashion (in general, you want to avoid explicit for loops in R) HTH, Nick Sabbe --

Re: [R] How to eliminate this for loop ?

ld also like to see an example where they prove to be the better way to go (by any criteria, but preferably speed or perhaps other resource usage) Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapp

Re: [R] Help with Iterator

hecked whether the rest of your code is OK) Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org

Re: [R] How to eliminate this for loop ?

Whenever you use a recursion (that cannot be expressed otherwise), you always need a (for) loop. Apply and the like do not allow to use the intermediary results (i.e. a[i-1] to calculate a[i]). So: no, it cannot be avoided in your case, I guess. Nick Sabbe -- ping: nick.sa...@ugent.be link

Re: [R] Find index of a string inside a string?

For simple searches, use grep with fixed=TRUE. Check ?grep. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-help-boun...@r-project.org [mailto:r-help

Re: [R] if statement and truncated distribution

return(val) } Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sa

Re: [R] Random Integer Number in Uniform Distribution

Check ?sample. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Gundala

Re: [R] printing a variable during a loop

diately. A likely consequence will be that your code will run somewhat slower. For using some output as 'progress control' you definitely want to turn the option off. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/