Re: [R] Subsetting data with svyglm

hi brennan, survey design objects can be subsetted with the same subset() syntax as data.frame objects, so following jeff's advice maybe you want svyglm( formula , design = subset( surveydesign , variable %in% c( 'value a' , 'value b' ) ) ) for some examples of how to construct a survey design wi

Re: [R] Subsetting data with svyglm

This seems like a fundamental misunderstanding on your part of how operators, and in particular logical expressions, work in computer languages. Consider some examples: 1+2 has a numeric answer because 1 and 2 are both numeric. 1+"a" has at the very least not a numeric answer because the values

[R] grofit issues with replicates - probit or logit or glmm

Hello I tried use grofit package in our data set. We provide a subset of our data with X iso, and 4 doses, and insect died was count each day for long 5 days. We started with Y insects per dishes. When one is dead, it was counted and removed. Died insect is cumulative in the next days. i.e. day 1

[R] Subsetting data with svyglm

I am aware that it is possible to specify a subset with a single logical operator when constructing a model, such as: svyglm(formula, design=data, subset=variable=="value"). What I can't figure out is how to specify a subset with two or more logical operators: svyglm(formula, design=data, subset=v

Re: [R] simple question - mean of a row of a data.frame

Hi, rock[2,] is a data frame and you should not use sum() on a data frame, first google hit for the error message gives http://stackoverflow.com/questions/19697498/r-beginner-argument-is-not-numeric-or-logical-returning-na Otherwise I think you should use ?rowSums and ?rowMeans if you have num

[R] simple question - mean of a row of a data.frame

Hi all, Simple question I should know: I'm unclear on the logic of why the sum of a row of a data.frame returns a valid sum but the mean of a row of a data.frame returns NA: sum(rock[2,]) [1] 10901.05 mean(rock[2,],trim=0) [1] NA Warning message: In mean.default(rock[2, ], trim = 0) : argument

Re: [R] piecewise regression and lm() question

On 11/02/2015 4:30 PM, Goldschneider, Jill wrote: > I was playing with some examples of piecewise regression using lm() and have > come across a behavior I'm uncertain about. > Below is simple 3-segment dataset. I compare predicted output of a model > created by one call to lm() to that of 3 mod

Re: [R] AR1 covariance structure for lme object and R/SAS differences in model output

anord biol.lu.se> writes: > [snip snip] > We are working on a data set in which we have measured repeatedly a > physiological response variable (y) > every 20 min for 12 h (time variable; 'x') in subjects ('id') beloning to > one of five groups ('group'; 'A' to 'E'). Data are located at: >

Re: [R] Nonlinear integer programming question

Hi Rebecca, It will be very helpful if you can provide a set of specific functions g(x), h(x) and m(x). -- View this message in context: http://r.789695.n4.nabble.com/Nonlinear-integer-programming-question-tp4703122p4703128.html Sent from the R help mailing list archive at Nabble.com. _

[R] piecewise regression and lm() question

I was playing with some examples of piecewise regression using lm() and have come across a behavior I'm uncertain about. Below is simple 3-segment dataset. I compare predicted output of a model created by one call to lm() to that of 3 models created by 3 calls to lm(). In case A and B, the resul

Re: [R] suggestion for optimal plotting to show significant differences

Petr, My first attempt is to use the simple=TRUE argument to interaction2wt. Then the bwplots in the item|item panel show the behavior of value over day for each item. You get a plot similar to this panel with the growth curve plots from nlme, for example, bwplot(value ~ day | item, data=tes

Re: [R] Download internet videos

Hmmm. Well, a youtube video is a file. Therefore search for "R download file" and you will find the download.file() function. -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 2/11/15, 8:17 AM, "Raoni Rodrigues" wrote: >Hell

Re: [R] AR1 covariance structure for lme object and R/SAS differences in model output

> On 11 Feb 2015, at 16:57 , anord wrote: > > Dear R users, > We are working on a data set in which we have measured repeatedly a > physiological response variable (y) > every 20 min for 12 h (time variable; 'x') in subjects ('id') beloning to > one of five groups ('group'; 'A' to 'E'). Data a

Re: [R] Impute time-series data, perhaps with a Kalman filter - do you know of any R code?

Hi, searching for "kalman filter R" gives this paper that was published in JSS. It may help. @article{Tusell:2010:JSSOBK:v39i02, author = "Fernando Tusell", title = "Kalman Filtering in R", journal = "Journal of Statistical Software", volume = "39", number = "2"

Re: [R] read.table with missing data and consecutive delimiters

Hello, You're missing a dollar sign: 2$$$5, not 2$$5. Hope this helps, Rui Barradas Em 11-02-2015 14:53, Tim Victor escreveu: All, Assume we have data in an ASCII file that looks like Var1$Var2$Var3$Var4 1$2$3$4 2$$5 $$$6 When I execute read.table( 'test.dat', header=TRUE, sep='$' ) I, o

[R] Impute time-series data, perhaps with a Kalman filter - do you know of any R code?

Does anyone have code that uses a Kalman filter to impute time-series data? If not, do you know of any software that can be used to impute time-series data? Thank you, John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Med

[R] Nonlinear integer programming question

I am seeking an optimization routine that can deal with the following problem: Maximize g(x), where x is a vector and g is nonlinear, subject to linear constraints of the form h(x)>0 and m(x)=0 and subject to the constraint that all values of x are 0 or 1. I can't find a nonlinear optimization pr

Re: [R] $ operator is invalid for atomic vectors

Hi, If x is a data frame, then x$getmean will try to get the vector named getmean in x. You put "()" after x$getmean. I think r is confused about it. It appears that you want to call a function named getmean(). -- View this message in context: http://r.789695.n4.nabble.com/operator-is-in

[R] read.table with missing data and consecutive delimiters

All, Assume we have data in an ASCII file that looks like Var1$Var2$Var3$Var4 1$2$3$4 2$$5 $$$6 When I execute read.table( 'test.dat', header=TRUE, sep='$' ) I, of course, receive the following error: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 2 did n

[R] AR1 covariance structure for lme object and R/SAS differences in model output

Dear R users, We are working on a data set in which we have measured repeatedly a physiological response variable (y) every 20 min for 12 h (time variable; 'x') in subjects ('id') beloning to one of five groups ('group'; 'A' to 'E'). Data are located at: https://www.dropbox.com/s/hf455aev3teb5e0/

[R] Problem Solved: optim fails when using arima

I am using arima(x, order=c(p,0,q)) function for my project, which deals with a set of large differenced time series data, data size varies from 8000 to 7. I checked their stationarity before applying arima. Occasionally, arima(x, order=c(p,0,q)) gives me error like following (which stops scrip

Re: [R] prediction intervals for robust regression

On 11/02/2015 19:38, Bert Gunter wrote: Presumably you've checked out: http://cran.r-project.org/web/views/Robust.html If you can estimate the variance of parameter estimates, betahat, then you can estimate the variance of a predicted value, X betahat; add the estimated variance of individuals

Re: [R] prediction intervals for robust regression

Presumably you've checked out: http://cran.r-project.org/web/views/Robust.html If you can estimate the variance of parameter estimates, betahat, then you can estimate the variance of a predicted value, X betahat; add the estimated variance of individuals to this if that's what you're looking for

[R] prediction intervals for robust regression

I have created robust regression models using least trimmed squares and MM-regression (using the R package robustbase). I am now looking to create prediction intervals for the predicted results. While I have seen some discussion in the literature about confidence intervals on the estimates for

Re: [R] Package build help

On Sun, Feb 8, 2015 at 5:15 PM, Duncan Murdoch wrote: > On 08/02/2015 4:06 PM, Glenn Schultz wrote: >> Hello All, >> >> I am in the final stages of building my first package "BondLab" and the >> check throughs the following warning. I think this is namespace thing. I >> have not done anything

Re: [R] Download internet videos

The set of things that R can do is not a subset of the set of things packages may have been written for. Have at it. --- Jeff NewmillerThe . . Go Live... DCN:Basics: ##.#.

Re: [R] How to solve this complex equation

A~ha~!! Thank you, Prof. Peter Dalgaard, so much for your wonderful lesson!!! Learning new things everyday from this R-help mailing list! Chel Hee Lee On 2/11/2015 10:37 AM, peter dalgaard wrote: On 11 Feb 2015, at 17:11 , Chel Hee Lee wrote: The functional form given in the post written

Re: [R] How to solve this complex equation

On 11 Feb 2015, at 17:11 , Chel Hee Lee wrote: > The functional form given in the post written by Ssuhanchen captures my eyes. > It is the cumulative distribution function of Poisson when the number of > counts is less than or equal to 2 with unknown parameter mu=x/2. Since it > is a nonl

[R] A portfolio return function?

For finance applications, I'm surprised that I am unable to find a function to compute the portfolio return (sqrt(t(w) %*% V %*% w)) where w are portfolio weights and V is the cov(returns). The Performance Analytics portfolio return function seems to compute something else. Ernie __

[R] Download internet videos

Hello R-helpers, It is possible donwload youtube videos with R? I made a google search and find no options to do that. Thanks in advanced, Raoni [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and m

Re: [R] How to solve this complex equation

The functional form given in the post written by Ssuhanchen captures my eyes. It is the cumulative distribution function of Poisson when the number of counts is less than or equal to 2 with unknown parameter mu=x/2. Since it is a nonlinear function, there may be multiple solutions but the s

[R] Extract data from Array to Table

Dear All, I am facing the task to extract data from array to table. here an example of array. ##Get A list of Matrices with unequal rows Disease <- NULL Diseases <- NULL ListMatByGene <- NULL for(i in 1:3){ Disease[[i]] <-matrix(sample(-30:30,25+(5* i)),5+i) rownames(Disease[[i]]) <- paste0("Sam

Re: [R] MApply and SubStr

That's exactly what I wanted, thank you very much! My intent was to perform the SubStr operation first, and then apply the types to the columns. I wasn't expecting the two types in the same column. I appreciate your response! On Tue, Feb 10, 2015 at 5:03 PM, David Winsemius wrote: > > On Feb 1

Re: [R] help in anova

I suspect that your "treatment" levels are perfectly nested inside the "soilgroup" levels. If this were the case you can either use one of the factor in your analysis or the other, depending on what you want to analyze. Il giorno Wed, 11 Feb 2015 14:47:18 + Mir Salam ha scritto: > Dear all,

Re: [R] sqldf() difference between R 3.1.2 and 3.0.1

That seems to have worked, both in the new and old version of R. I'll do more unit testing on other files. Thank you, Gabor. -Original Message- From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com] Sent: Wednesday, February 11, 2015 10:22 AM To: Doran, Harold Cc: r-help@r-project.or

Re: [R] sqldf() difference between R 3.1.2 and 3.0.1

On Wed, Feb 11, 2015 at 9:45 AM, Doran, Harold wrote: > I have a function written and tested using R 3.0.1 and sqldf_0.4-7.1 that > works perfectly. However, using this same code with R 3.1.2 and sqldf_0.4-10 > yields the error below that I am having a difficult time deciphering. Hence, > same

Re: [R] How to read this Rpart decision tree?

Hi Kim fancyRpartPlot is a front-end to prp, and you can pass it all of the prp options - it says this in the help for fancyRpartPlot, and that's about all it says. So you need to spend some time reading about prp options, and how to customize your plot to get what you want. There are lots of det

Re: [R] library(Rcmdr) sh: otool: command not found

Dear John, Dear Dan, Many thanks for your response. It works perfectly. Best, - Mail original - De : John Fox À : 'varin sacha' Cc : "'r-help@R-project.org'" Envoyé le : Mercredi 11 février 2015 3h12 Objet : RE: [R] library(Rcmdr) sh: otool: command not found Dear varin sacha, This

Re: [R] factor levels > numeric values

Hi, Suppose your data frame is called data and the name of the factor column is named tobeConverted. I have tried this and it worked. Hope this helps. > as.numeric(as.character(data$tobeConverted)) -- View this message in context: http://r.789695.n4.nabble.com/factor-levels-numeric-values

Re: [R] Mixed-effects model for pre-post randomization design

Marco Barbàra gmail.com> writes: > > DeaR userRs, > > I recently read this Liang-Zeger article: > > http://sankhya.isical.ac.in/search/62b1/fpaper7.html > > in which (among other things) they adopt a random intercept model for > pre-post designed trials, using a conditional likelihood approac

Re: [R] plotting this data

Hi, Here is an implementation. The image is uploaded as Rplot02.png. > gen <- read.table("geno.txt",header=TRUE) > gen Genotype E1 E2E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 E13 E14 E15 E16 E17 E18 1 G1 0.79 2.11 6.21 0.56 4.06 2.13 5.61 0.20 3.32 3.01 5.12 0.77 0

Re: [R] Maxent does not work

Is there any package that can replace maxent for a large number of independent variables? Thanks, Ken Sent from my iPhone > On Feb 2, 2015, at 6:07 PM, Kenneth Z wrote: > > Yesterday I installed the most recent R and maxent package, but it stopped > working. Even a simple command like > M

[R] help in anova

Dear all, I have follwing factors in my data set (G) names(G) relative ht, biomass, treatment, variety, soil group relative height biomass treatment (4 levels)- control+lime, control+ash, contaminated soil+lime, contaminated soil+ash variety (4 levels)- Salix swherinii, Salix mursinifolia, Kl

Re: [R] Rotate array by 90°

Thanks Lee and Huang. That is useful. Best On Fri, Feb 6, 2015 at 1:53 AM, Chel Hee Lee wrote: > > lapply(1:2, function(x) t(A[rev(1:3),,x])) > [[1]] > [,1] [,2] [,3] > [1,] "g" "d" "a" > [2,] "h" "e" "b" > [3,] "i" "f" "c" > > [[2]] > [,1] [,2] [,3] > [1,] "p" "m" "j" > [2,

[R] sqldf() difference between R 3.1.2 and 3.0.1

I have a function written and tested using R 3.0.1 and sqldf_0.4-7.1 that works perfectly. However, using this same code with R 3.1.2 and sqldf_0.4-10 yields the error below that I am having a difficult time deciphering. Hence, same code behaves differently on different versions of R and sqldf()

Re: [R] upgrading issues with Rcpp

arnaud gaboury gmail.com> writes: > Now when trying to update Rcpp: > > gabx hortensia [R] install.packages("Rcpp") > . > Error in unloadNamespace(pkg_name) : > namespace ‘Rcpp’ is imported by ‘reshape2’, ‘plyr’, ‘dplyr’ so > cannot be unloaded > .. > > I can't

[R] upgrading issues with Rcpp

gabx@hortensia [R] sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8LC_PAPER=en_US.UTF-8 LC_NAM

Re: [R] How to read this Rpart decision tree

First: summary(ss.rpart1) or summary(ss.rpart, file="whatever") The printout will be quite long since your tree is so large, so the second form may be best followed by a perusal of the file with your favorite text editor. The file name of "whatever" above should be something you choose, of

[R] Mixed-effects model for pre-post randomization design

DeaR userRs, I recently read this Liang-Zeger article: http://sankhya.isical.ac.in/search/62b1/fpaper7.html in which (among other things) they adopt a random intercept model for pre-post designed trials, using a conditional likelihood approach (I didn't think it possible with only two measuremen

[R] How to read this Rpart decision tree?

Hi all, In the attachment or this link (http://oi58.tinypic.com/35ic9qc.jpg) you'll find the decision tree I made. I used the Rpart package to make the tree and the rattle package using the fancyRpartPlot to plot it. The data in the tree looks different than about every example I have seen bef