[R] cross-nested random structure in glmmPQL

Dear members,   I'm trying to fit a GLMM using glmmPQL with a cross-nested random structure. Basically, I have perfectly crossed observations of whether there is a relation between two people (sender and receiver of relation) and I'd like to do a random structure where the relations to an from

[R] Plotting zoo objects with chron axis

Dear all, I have a problem which I'm not to fix. I have the following two series: a=structure(c(33242.5196150509, 34905.8434338503, 38490.6957848689, 38747.0287172129, 38919.1028597142, 39026.3956586941, 38705.5344288997, 38545.6274379387, 38651.2079354205, 38748.2769580121), index =

[R] decimal separator from comma to dot

This is my reproducible example df-structure(list(IDANT = c(37837L, 37838L, 37839L, 37840L, 37841L, 37842L, 37843L, 40720L, 40721L, 40722L), N_TX = c(6L, 6L, 6L, 4L, 1L, 1L, 1L, 2L, 2L, 1L), TILT = c(0L, 0L, 0L, 0L, 6L, 6L, 6L, 0L, 0L, 0L), DIREZIONE = c(50L, 220L, 110L, 50L, 220L, 110L, 50L,

[R] cat(summary(lm(Y~x, dat = data))) cannot handle lists; dput writes too much...

Is there a way to write the summary of lm objects to a text file on disk? cat won't handle the list, dput writes everything but not in human readable format. Any thoughts? Alex van der Spek __ R-help@r-project.org mailing list

[R] Automatic formula creation

Say I want to compare all 5 term models from a choice of 28 different predictors and one known. All possible combinations of 5 out of 28 is easy to form by combn(). With some string manipulation it is also easy to make a text representation of a formula which is easy to convert by as.formula()

Re: [R] cat(summary(lm(Y~x, dat = data))) cannot handle lists; dput writes too much...

What about sink()? Or capture.outout()? Or running your models as a batch file and saving the results? Sarah On Friday, August 9, 2013, Alex van der Spek wrote: Is there a way to write the summary of lm objects to a text file on disk? cat won't handle the list, dput writes everything but not

Re: [R] Automatic formula creation

Hello, Maybe the following gives you some idea on how to vary the terms. idx - 1:5 # or any other indexes ftext - paste(terms[idx], collapse = ' * ') Hope this helps, Rui Barradas Em 09-08-2013 11:40, Alex van der Spek escreveu: Say I want to compare all 5 term models from a choice of 28

Re: [R] For loop output

To update on the use of this little string, I am trying to use it to automate files to be loaded into a raster stack. I think the issue I have with the string is related to the backslashes. I need to just read the pure text so that the datasets can be sourced, though I am not sure whether the

Re: [R] Problem with dea.boot under R 3.0.1

Dear Daniel, thank you very much for your reply. We checked all inputs and outputs and there were no negative values. We eluded the phenomenon by reinstallung R version 2.14.2 and the old FEAR package. The bootstrapping generated sound bias-corrected efficiency values there, hence we assume it is

Re: [R] decimal separator from comma to dot

Hi, I think this could help you: https://stat.ethz.ch/pipermail/r-help/2008-January/152378.html Best Simon On Aug 9, 2013, at 12:19 PM, maxbre mbres...@arpa.veneto.it wrote: This is my reproducible example df-structure(list(IDANT = c(37837L, 37838L, 37839L, 37840L, 37841L, 37842L,

[R] Calculate McDonald's Omega

Dear all, I'm a newbie to R an would like to calculate McDonald's Omega. I installed the packages psych, GPArotation and used the suggested syntax omega(m,nfactors=3,fm=minres,...). Up to this point, it works. Nevertheless, I read that omega-h is not meaningful for a 1-factor solution. What I'll

[R] errors with hurdle negative binomial mixed effect models

Hello! I am new in the mailing list for R help and I hope to be able to formulate a good question easy to understand. After trying to do many different things to solve an error I do not find the solution. I am modeling my data set with hurdle negative binomial mixed effects, to find the

[R] Data corruption with big numbers.

I am confused about what I believed was artefects from reading .csv files with big numbers. Finally I checked using the console and this is what I get, the same as when importing: longnumber-63502481056038 longnumber [1] 635024810560380032 I have tried setting options(digits=22) and also

Re: [R] Problem loading .r file

Bogaso wrote Hello all, I was trying to load a .r file using source() ... functions ... however getting following error: source(D:/Book Code.r) Error in sys.call(sys.parent()) : node stack overflow I realise the above message is quite old, just a quick reply if anyone is encountering

[R] iterating missing() over function arguments

Hi, Say I have function(aa,bb,cc) { does something } and I want to go through all (or a subset) of function arguments to check if they're missing. Of course, I can check each one in turn, ie. if (missing(aa)) {} if (missing(bb)) {}, etc. But is there a construct like the

Re: [R] Data corruption with big numbers.

FAQ 7.31 is a start. Understand the precision of floating point numbers. You probably only have about 15 digits (54 bits) of significance. If you need unlimited number of digits, there are some other alternatives. On Fri, Aug 9, 2013 at 5:54 AM, Johan Nyberg jo...@infocraft.se wrote: I am

Re: [R] Data corruption with big numbers.

The link to FAQ 7.31 is http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Jean On Fri, Aug 9, 2013 at 8:16 AM, jim holtman jholt...@gmail.com wrote: FAQ 7.31 is a start. Understand the precision of floating point numbers. You probably only

Re: [R] Automatic formula creation

On Aug 9, 2013, at 13:26 , Rui Barradas wrote: Hello, Maybe the following gives you some idea on how to vary the terms. idx - 1:5 # or any other indexes ftext - paste(terms[idx], collapse = ' * ') You're not the first to use this sort of technique - it is happening in various parts

[R] Splitting a categorical variable into multiple variables

Hello R-Help, I have a variable with 32 levels and I'd like to split this into two variables such that both new variables have = 32 variables. This is to handle the limit of 32 level predictor variables in R's Random Forest implementation. Might someone be able to suggest an elegant way to do

Re: [R] decimal separator from comma to dot

Thanks it's the same thread I've been looking at But it's not answering to my questions… -- View this message in context: http://r.789695.n4.nabble.com/decimal-separator-from-comma-to-dot-tp4673414p4673433.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Splitting a categorical variable into multiple variables

If I understand what you mean, just recode them. z - factor(letters[1:3]) z zz - factor(ifelse( z %in% c(a, b),d ,z)) zz Cheers, Bert On Fri, Aug 9, 2013 at 7:10 AM, Claus O'Rourke claus.orou...@gmail.com wrote: Hello R-Help, I have a variable with 32 levels and I'd like to split this into

Re: [R] Method dispatch in S4

Hi Martin, thank you very much for this profound answer! Your added design advice is very helpful, too! For the 'simple example': Sometimes I am still a little overwhelmed from a certain setting in the code and my ideas how I want to handle a process. But I learn from session to session. In

Re: [R] Splitting a categorical variable into multiple variables

... or if you want to keep the unchanged levels the same: zz - factor(ifelse( z %in% c(a, b),d ,levels(z)[z])) -- Bert On Fri, Aug 9, 2013 at 7:35 AM, Bert Gunter bgun...@gene.com wrote: If I understand what you mean, just recode them. z - factor(letters[1:3]) z zz - factor(ifelse( z %in%

Re: [R] laf_open_fwf

Jan, Many thanks for your suggestion! The code runs perfectly fine on the test set. Applying it to the complete data set, however, results in the following error: while (TRUE) { + lines - readLines(con, encoding='LATIN1') + if (length(lines) == 0) break +

Re: [R] Method dispatch in S4

Simon: Have a look at the proto package for which there is a vignette. You may find it suitable for your needs and less intimidating. Cheers, Bert On Fri, Aug 9, 2013 at 7:40 AM, Simon Zehnder szehn...@uni-bonn.de wrote: Hi Martin, thank you very much for this profound answer! Your added

Re: [R] Method dispatch in S4

Hi Bert, thank you very much for your suggestion! I will take a look at it soon! Best Simon On Aug 9, 2013, at 4:45 PM, Bert Gunter gunter.ber...@gene.com wrote: Simon: Have a look at the proto package for which there is a vignette. You may find it suitable for your needs and less

Re: [R] Method dispatch in S4

On 08/09/2013 07:45 AM, Bert Gunter wrote: Simon: Have a look at the proto package for which there is a vignette. You may find it suitable for your needs and less intimidating. Won't help much with S4, though! Some answers here

Re: [R] Method dispatch in S4

Hi Martin, is proto in S3? I will take a look first at the simple package EBImage. Thank you very much for the suggestions! Best Simon On Aug 9, 2013, at 5:01 PM, Martin Morgan mtmor...@fhcrc.org wrote: On 08/09/2013 07:45 AM, Bert Gunter wrote: Simon: Have a look at the proto

[R] help about diallel analysis

cadhyn5ju5gggdbwm1hzs-6emtbjzofqr4fzq905v6gjvnpw...@mail.gmail.complz solve this question and send me commands.. this is a question for diallel analysis(Haymann approach).. file is attached*... * thanks* * cadhyn5ju5gggdbwm1hzs-6emtbjzofqr4fzq905v6gjvnpw...@mail.gmail.com

Re: [R] Splitting a categorical variable into multiple variables

Thanks Bert. I guess I was just wondering if there was a way to create the new factors automatically without me having to hard code the level names manually in my R code. Rgds Claus On Fri, Aug 9, 2013 at 3:42 PM, Bert Gunter gunter.ber...@gene.com wrote: ... or if you want to keep the

Re: [R] For loop output

On Fri, Aug 09, 2013 at 12:33:44PM +0100, Jenny Williams wrote: To update on the use of this little string, I am trying to use it to automate files to be loaded into a raster stack. I think the issue I have with the string is related to the backslashes. I need to just read the pure text so

[R] linking to help pages in other packages

Dear R users, i am trying to get a package compatible with the R CMD check routine but I get errors like this: Missing link(s) in documentation object ‘path/filename.Rd’: ‘ssa’ In the respective file I have put: ##seealso ##\code{\link[Rssa:ssa]{ssa}} Rssa is the package containing the

Re: [R] Automatic formula creation

Thanks much to both Peter and Rui, I am afraid that after 5 years with R I am still not able to understand your method Peter. Will stick with Rui's method for now... Alex On 08/09/2013 04:00 PM, peter dalgaard wrote: On Aug 9, 2013, at 13:26 , Rui Barradas wrote: Hello, Maybe the

Re: [R] For loop output

What happens when you type? test.2 - stack(individual.proj) assuming you want all six or test.2 - stack(individual.proj[c(1,3, 5)]) to combine the 1st, 3rd, and 5th. Eg. Modified from the stack help page fn - system.file(external/test.grd, package=raster) nfn - c(fn, fn, fn) s - stack(nfn)

Re: [R] errors with hurdle negative binomial mixed effect models

Marta Lomas lomasvega at hotmail.com writes: Hello! I am new in the mailing list for R help and I hope to be able to formulate a good question easy to understand. We hope so too :-) [snip] I will take a first crack at this here, but follow-ups should probably be redirected to the

Re: [R] Automatic formula creation

On Aug 9, 2013, at 18:24 , Alex van der Spek wrote: Thanks much to both Peter and Rui, I am afraid that after 5 years with R I am still not able to understand your method Peter. Will stick with Rui's method for now... Oh, come on! How about reading the first case in example(Reduce)?

Re: [R] decimal separator from comma to dot

On Aug 9, 2013, at 7:31 AM, maxbre wrote: Thanks it's the same thread I've been looking at But it's not answering to my questions… Please do read the Posting Guide. You are asked to include context. In this case including the citation to the Archive-stored code would have been courteous as

Re: [R] Method dispatch in S4

Please read the proto vignette before asking further questions about it. It is an alternative to/version of OOP different from S3 and S4. -- Bert On Fri, Aug 9, 2013 at 8:13 AM, Simon Zehnder szehn...@uni-bonn.de wrote: Hi Martin, is proto in S3? I will take a look first at the simple

[R] The time unit of strptime() after performing arithmetic calculation

Hi all, I used strptime() to convert character strings to time and did some subtraction calculation. a-'2012-07-17T07:50' b-'2012-08-27T09:30' strptime(a,format='%Y-%m-%dT%H:%M')-strptime(b,format='%Y-%m-%dT%H:%M') The result shows Time difference of -41.06944 days. However when these

Re: [R] The time unit of strptime() after performing arithmetic calculation

?difftime difftime(strptime(a,format='%Y-%m-%dT%H:%M'), strptime(b,format='%Y-%m-%dT%H:%M')) Time difference of -41.06944 days difftime(strptime(a,format='%Y-%m-%dT%H:%M'), strptime(b,format='%Y-%m-%dT%H:%M'), units = 'hours') Time difference of -985.6667 hours On Fri, Aug 9, 2013 at 1:37

Re: [R] The time unit of strptime() after performing arithmetic calculation

On Aug 9, 2013, at 10:37 AM, Jun Shen wrote: Hi all, I used strptime() to convert character strings to time and did some subtraction calculation. a-'2012-07-17T07:50' b-'2012-08-27T09:30' strptime(a,format='%Y-%m-%dT%H:%M')-strptime(b,format='%Y-%m-%dT%H:%M') The result shows

Re: [R] The time unit of strptime() after performing arithmetic calculation

Thanks Jim and David, The difftime() is exactly what I am looking for. Just out of curiosity why the unit of output is different. here is an example of the dataframe. test-structure(list(SPDTC = c(2012-08-27T09:30, 2012-08-06T10:08, 2012-08-13T07:41, 2012-07-17T07:50, 2012-09-11T10:29),

Re: [R] Splitting a categorical variable into multiple variables

Actually, I think it's pretty trivial if you do it in a smarter way than I previously suggested. I found this by reading ?levels (RTFM, Bert!) z - factor(letters[1:3]) levels(z)[1:2]- d ## no hardcoding names; just use indices z [1] d d c Levels: d c Cheers, Bert On Fri, Aug 9, 2013 at 8:45

[R] Flexmix and variance of error terms

Hi, I am using flexmix to model some data which is modelled with linear regressions. I have results obtained along the lines of that shown below, and can retreive component parameters, but I cannot find a way or retrieving the variance of the sigma (variance of the normal model) can anyone

[R] glmnet inclusion / exclusion of categorical variables

Hello - I have been using GLMNET of the following form to predict multinomial logistic / class dependent variables: mglmnet=glmnet(xxb,yb ,alpha=ty,dfmax=dfm, family=multinomial,standardize=FALSE) I am using both continuous and categorical variables as predictors, and am using

Re: [R] decimal separator from comma to dot

thanks david very humbly I'm asking you and all r-help users to forgive me about violating the rules of this great mailing list, I didn't meant to do that: I simply slipped into that, sorry again! ...and what about the case of many variables to be changed at the same time? seriously, I do not

Re: [R] decimal separator from comma to dot

On Aug 9, 2013, at 11:58 AM, maxbre wrote: thanks david very humbly I'm asking you and all r-help users to forgive me about violating the rules of this great mailing list, I didn't meant to do that: I simply slipped into that, sorry again! ...and what about the case of many variables to

Re: [R] glmnet inclusion / exclusion of categorical variables

Hi, On Fri, Aug 9, 2013 at 6:44 AM, Kevin Shaney kevin.sha...@rosetta.com wrote: Hello - I have been using GLMNET of the following form to predict multinomial logistic / class dependent variables: mglmnet=glmnet(xxb,yb ,alpha=ty,dfmax=dfm, family=multinomial,standardize=FALSE) I am

Re: [R] laf_open_fwf

Christian, In my original example I had an n=1E5 argument in readLines: lines - readLines(con, n=1E5) This ensures that every iteration of the loop only 10 lines are read (which should usually fit into memory). Without this argument readLines tries to read in the complete file. Jan

Re: [R] glmnet inclusion / exclusion of categorical variables

On Aug 9, 2013, at 6:44 AM, Kevin Shaney wrote: Hello - I have been using GLMNET of the following form to predict multinomial logistic / class dependent variables: mglmnet=glmnet(xxb,yb ,alpha=ty,dfmax=dfm, family=multinomial,standardize=FALSE) I am using both continuous and

Re: [R] Plotting zoo objects with chron axis

On Fri, 09 Aug 2013, Manta mantin...@libero.it writes: Dear all, I have a problem which I'm not to fix. I have the following two series: a=structure(c(33242.5196150509, 34905.8434338503, 38490.6957848689, 38747.0287172129, 38919.1028597142, 39026.3956586941, 38705.5344288997,

Re: [R] decimal separator from comma to dot

This is my reproducible example df-structure(list(IDANT = c(37837L, 37838L, 37839L, 37840L, 37841L,  37842L, 37843L, 40720L, 40721L, 40722L), N_TX = c(6L, 6L, 6L,  4L, 1L, 1L, 1L, 2L, 2L, 1L), TILT = c(0L, 0L, 0L, 0L, 6L, 6L,  6L, 0L, 0L, 0L), DIREZIONE = c(50L, 220L, 110L, 50L, 220L, 110L,  50L,

Re: [R] lattice yscale.components: use multiple convenience functions

Not sure if this what you were recommending that I do, but based on what I saw in figures 8.4 and 8.5, I was able to combine the yscale.components.log10ticks function definition with that of yscale.components.logpower into my own custom function: ###default .log10ticks:

Re: [R] decimal separator from comma to dot

Hello, To change several columns you can use lapply. In what follows, idx is the vector of column numbers, corresponding to the columns you want to change: idx - 6 # column numbers df[idx] - lapply(df[idx], function(x) as.numeric(sub(,, ., as.character(x # check the result str(df)

Re: [R] The time unit of strptime() after performing arithmetic calculation

The Details section of the help page for difftime explains why. -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 8/9/13 11:02 AM, Jun Shen jun.shen...@gmail.com wrote: Thanks Jim and David, The difftime() is exactly what I

Re: [R] lattice yscale.components: use multiple convenience functions

On Aug 9, 2013, at 12:50 PM, Taylor, Sean D wrote: Not sure if this what you were recommending that I do, but based on what I saw in figures 8.4 and 8.5, I was able to combine the yscale.components.log10ticks function definition with that of yscale.components.logpower into my own custom

Re: [R] decimal separator from comma to dot

YES, THANK YOU ALL for the good lessons learned both about the netiquette of this mailing list and the R coding max Hi, Try:  df$POT2_TX- df$POT_TX df[,6:7]- lapply(df[,6:7],function(x) as.numeric(as.character(sub(,,.,x  str(df) #'data.frame':    10 obs. of  7 variables: # $ IDANT   

[R] Can ODBC or JDBC calls R?

Hi R helpers, I know there are packages RODBC and RJDBC to enable R to access ODBC and JDBC data. Is there a package/software to do the reverse way: calling R from ODBC or JDBC? Thank you. Regards, Yan [[alternative HTML version deleted]]

Re: [R] The time unit of strptime() after performing arithmetic calculation

The printed view of a difftime object is not necessarily reflective of its internal representation. Also, to avoid unpleasant surprises always use a conversion function with specified units (not auto) if you want to convert between numeric and difftime.

Re: [R] decimal separator from comma to dot

Hi, Try:  df$POT2_TX- df$POT_TX df[,6:7]- lapply(df[,6:7],function(x) as.numeric(as.character(sub(,,.,x  str(df) #'data.frame':    10 obs. of  7 variables: # $ IDANT    : int  37837 37838 37839 37840 37841 37842 37843 40720 40721 40722 # $ N_TX : int  6 6 6 4 1 1 1 2 2 1 # $ TILT : int 

Re: [R] Varying statistical significance in estimates of linear model

For archiving reasons: 1. Practical Regression and Anova using R by Faraway 2. Possible reason: multi-collinearity in predictor variables. Thanks everybody! On Thu, Aug 8, 2013 at 1:43 PM, Stathis Kamperis ekamp...@gmail.com wrote: Hi everyone, I have a response variable 'y' and several

Re: [R] glmnet inclusion / exclusion of categorical variables

Thanks! I tried doing the type.multinomial=grouped argument - but it didn't work for me. Maybe I did something wrong. I thought I understood why it didn't work because of sparse.model.matrix recoding variables (like below to V12 V13} makes GLMNET unable to tell that they actually came from

Re: [R] glmnet inclusion / exclusion of categorical variables

On Aug 9, 2013, at 12:52 PM, kevin.shaney wrote: Thanks! I tried doing the type.multinomial=grouped argument - but it didn't work for me. Maybe I did something wrong. I thought I understood why it didn't work because of sparse.model.matrix recoding variables (like below to V12 V13}

Re: [R] linking to help pages in other packages

Dear Jannis, I think you want \link[package]{function} instead of \link[package:function]{function} \link[Rssa]{ssa} Best regards, Thierry Van: r-help-boun...@r-project.org [r-help-boun...@r-project.org] namens Jannis [bt_jan...@yahoo.de] Verzonden:

[R] easiest way to put italics words in sentences plotted with text()?

Hi, I am plotting some labels that consist of strings in which some words (but only some) should be in italics. E.g. M3: Homo, 5 areas, 2 areas max M4: Pan, 3 areas, 2 areas max I am putting these on the plot with the text() command. The words Homo and Pan should be italicized, since

Re: [R] easiest way to put italics words in sentences plotted with text()?

Hi, May be this gets you started: plot(1,1,xlim=0:1,ylim=0:1) text(0.6,0.8, expression(M3:~italic(Homo)~paste(,, 5 areas, 2 areas max,sep=)))  text(0.6,0.4, expression(M4:~italic(Pan)~paste(,, 3 areas, 2 areas max,sep=))) A.K. - Original Message - From: Nick Matzke

Re: [R] easiest way to put italics words in sentences plotted with text()?

On Aug 9, 2013, at 7:22 PM, arun wrote: Hi, May be this gets you started: plot(1,1,xlim=0:1,ylim=0:1) text(0.6,0.8, expression(M3:~italic(Homo)~paste(,, 5 areas, 2 areas max,sep=))) text(0.6,0.4, expression(M4:~italic(Pan)~paste(,, 3 areas, 2 areas max,sep=))) The plotmath