Re: [R] ordered and unordered variables

Thanks. As to the data warpbreaks, if I want to analysis the impact of tension(L,M,H) on breaks, should I order the tension or not? Many thanks. At 2013-05-21 20:55:18,David Winsemius dwinsem...@comcast.net wrote: On May 20, 2013, at 10:35 PM, meng wrote: Hi all: If the

Re: [R] problem with transform and get functions

On May 22, 2013, at 01:54 , David Winsemius wrote: { test0 - transform(test, (get(var.names[i])) = 0) There is no `get-` function. You need to use assign. Also note that transform's left hand sides are really names of function arguments and therefore syntactically cannot be expressions.

Re: [R] ordered and unordered variables

On 22.05.2013 07:09, meng wrote: Thanks. As to the data warpbreaks, if I want to analysis the impact of tension(L,M,H) on breaks, should I order the tension or not? No homework questions on this list, please ask your teacher. Best, Uwe Ligges Many thanks. At

[R] Rplot save problem after using identify with R version 3.0.0

Hello R experts, I am having an wired problem to save my RPlot after I use identify option. Points are identified properly, but when I try to save that image I get error as: Error: first argument must be a string (of length 1) or native symbol reference and the image without identified points

Re: [R] keep the centre fixed in K-means clustering

So you just want to compare the distances from each point of your new data to each of the Centres and assign the corresponding number of the centre as in: clust - apply(NewData, 1, function(x) which.min(colSums(x - tCentre)^2 but since the apply loop is rather long here for lots of new

Re: [R] metafor matrix error

Dear Branwen, This means that your design matrix is not of full rank (in a more recent version of the metafor package, the error message is a bit more informative; i.e., please upgrade). Since continent is a factor, this should imply that one of the levels never actually occurs, leading to a

Re: [R] Rplot save problem after using identify with R version 3.0.0

Suparna Mitra suparna.mitra.sm at gmail.com writes: Hello R experts, I am having an wired problem to save my RPlot after I use identify option. Points are identified properly, but when I try to save that image I get error as: Error: first argument must be a string (of length 1) or

Re: [R] Balanced design throws design unbalanced, cannot proceed error

Well spotted. I've changed that now (it was an artifact from previous work), so there's no devicegroup--just device and group, as in the model. So now table(data.AMIDS_d[,2:5]) produces , , width = fat, length = long device group Dingo SNAR NR12 12 NV12 12 RA12

Re: [R] calcul of the mean in a period of time

Hi, I guess you meant this: dat2- read.table(text= patient_id  t scores 1  0    1.6 1  1    2.6 1  2 2.2 1  3 1.8 2  0   

Re: [R] Something Very Easy

Using arun, data set, dat1 Is this type of thing what you want? dat2 - subset(dat1, dat1$Play != B dat1$Offense == Y) with(dat2,table(Play, Offense)) John Kane Kingston ON Canada -Original Message- From: smartpink...@yahoo.com Sent: Tue, 21 May 2013 18:57:56 -0700 (PDT) To:

Re: [R] Balanced design throws design unbalanced, cannot proceed error

Inline ... On Wed, May 22, 2013 at 6:40 AM, Krysta Chauncey kry...@essential-design.com wrote: Well spotted. I've changed that now (it was an artifact from previous work), so there's no devicegroup--just device and group, as in the model. So now table(data.AMIDS_d[,2:5]) produces , , width

[R] Forecasting MA model different to manually computation?

Hi, 3 down vote favorite 1 I am interested in forecasting a MA model.Therefore I have created a very simple data set (three variables). I then adapted a MA(1) model to it. The results are: x-c(2,5,3) m-arima(x,order=c(0,0,1)) Series: x ARIMA(0,0,1) with non-zero mean Coefficients:

[R] Code overloading PC

Hi R user, I was trying to develop a model (logistic regression) for 4001 dependent variables using 15 environmental variables (45000 rows); and then trying to use the models to predict in future. I used following code but it took so much time and consumed 100% of the PC memory. Even though-

Re: [R] Code overloading PC

Hello, In predict.glm, there's no argument 'data', it's 'newdata'. As for your problem, maybe try doing one prediction at a time, write the results to file, then the next. Hope this helps, Rui Barradas Em 22-05-2013 15:20, Kristi Glover escreveu: Hi R user, I was trying to develop a model

Re: [R] Forecasting MA model different to manually computation?

Hello, Since R is open source, you can look at the source code of package forecast to know exactly how it is done. My guess would be x - m$residuals Time Series: Start = 1 End = 3 Frequency = 1 [1] 3.060660 4.387627 3.00 Hope this helps, Rui Barradas Em 22-05-2013 15:13, Neuman Co

Re: [R] Code overloading PC

Hi Rui, Yes you are right, there is no argument 'data. Mistakenly, I wrote only 'data' in the email. but in the r script, I have written newdata. As you suggested, I did trying one prediction at a time, but still- same problem. It is really big data set. May be - should I go 'Matlab' for this

Re: [R] rmean in survfit

One approach is to use the rms package's cph and Mean.cph functions. Mean.cph (cph calls coxph and can compute Kaplan-Meier and other survival estimates) can compute mean restricted life. Frank Dinesh W wrote I am using survfit to generate a survival curve. My population is such that my x axis

Re: [R] Problems with LSD.test

Hi, You didn't provide a reproducible example (http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example)   So, it is difficult to comment. Using the dataset(sweetpotato) library(agricolae) data(sweetpotato) m1-aov(yield~virus, data=sweetpotato) df1-df.residual(m1)

Re: [R] bar plot with non-zero starting level

Hi Jim, Thank you very much. I have started another conversation in the ggplot list. My current code is plot_data - data.frame( xmin = c(1, 1.5, 3, 3.5, 5, 5.5, 7, 7.5, 9, 9.5, 11, 11.5, 13, 13.5) , ymin = c(16.7026, 17.20, 14.9968, 16.32, 16.0630, 15.86, 17.7510, 18.12, -5.01694, -8.86,

Re: [R] problems with saving plots from loop

Thank you very much - now I see my mistake in loop - your hint helped. Thank you again! -- View this message in context: http://r.789695.n4.nabble.com/problems-with-saving-plots-from-loop-tp4667616p4667682.html Sent from the R help mailing list archive at Nabble.com.

[R] DRC package: Weibull W1.3 and W2.3 - where is the difference?

Hi! I am trying to use a 3-parametric Weibull model. I used mselect to find the best-fit model which was W1.3 in one and W2.3 in another case. When searching the internet for formulas, I only find a formula for W1.3, which is: f(x) = 0 + (d-0)\exp(-\exp(b(\log(x)-e))) But what is the formula

Re: [R] keep the centre fixed in K-means clustering

Dear Uwe Just wanted to say thank you so much for this as whilst waiting for a reply from r-help I had been wrting a piece of ugly code as below to do the job and yours looks MUCH smarter and I especially like the use of '-apply()' bit as there is no 'min.col()' function. p.s. my data has 144

Re: [R] Forecasting MA model different to manually computation?

Thanks, but this does not help me, because first of all, I do not know how to look at the source code (just entering fitted() or getAnywhere(fitted()) does not help, second, your solution x-m$residuals does not be a solution, because then the question is, where do the residuals come from?

[R] Multi-state model: msprep Error during data preparation

Hello all, Running the msprep function of the mstate package R showsmethe following error: Error in hlpsrt[, 1] - hlpsrt[, 2] : non-numeric argument to binary operator what hlpsrt is? [[alternative HTML version deleted]] __

[R] How to create a correct matrix in R

Hello Rlisters! In my codes, I need to import a matrix: v - read.table(/home/tiago/matrix.txt, header=FALSE) v-as.matrix(v) v V1 V2 V3 V4 V5 V6 [1,] 1. -0.89847480 -0.73929292 -0.99055335 -0.04514469 0.04056137 [2,]

Re: [R] Forecasting MA model different to manually computation?

So I mean: How can I calculate them manually? 2013/5/22 Neuman Co neumanc...@gmail.com: Thanks, but this does not help me, because first of all, I do not know how to look at the source code (just entering fitted() or getAnywhere(fitted()) does not help, second, your solution x-m$residuals

Re: [R] Forecasting MA model different to manually computation?

mh, this is interesting, I would have expected that the following is valid: If we look at the second value: 4.387627 = 3.5 + (-1)*(5-3.060660) or  4.387627 = 3.5 - (-1)*(5-3.060660) but this does not work. Surprise. Nice question! Von: Neuman Co

[R] reading large csv data sets efficiently

I have a couple of large data sets, on the order of 4GB. they come in .csv files, with about 50 columns and lots of rows. a couple have weird NA values, such as C and B, in numeric columns. I am wondering how good read.csv() is dealing with this stuff on the first pass. d-(read.csv(t.csv,

Re: [R] how to calculate the mean in a period of time?

HI GG, I thought you were referring about the solution that I sent today.  Sorry, I didn't check it. TRy this: dat1- read.table(text= patient_id  number  responsed_at  delais  scores1   scores2   scores3  1  1    2010-05-26 NA   2.6   

Re: [R] bar plot with non-zero starting level

Hi Dennis, Thank you for your constructive advice on plotting CIs in point ranges. I combined the advices from you, Jim, Kaori, and bosie (from IRC) and my own research and produced the following figure: WTP_labels - c(Wild cod, Farmed cod, Farmed salmon, Wild monk, Farmed pangasius, MSC label,

Re: [R] Forecasting MA model different to manually computation?

Rui responded to your first question graciously with a very simple default answer -- subtract the residuals from your observations. That's about as manual as you can be without using pencil and paper. If you can't understand the source code but want to so that you can understand how the

Re: [R] Request for Help on Named Vectors

Hi, May be this helps: month.dayslong-rep(31,7)  names(month.dayslong)- c(January,March,May,July,August,October,December) month.dayslong # January    March  May July   August  October December  #     31   31   31   31   31   31   31  unname(month.dayslong) #[1]

Re: [R] Lattice xyplot multipanels

Dear Rxperts, Using the above example, I have been playing around using viewport under panel-function(...) {...} block in conjunction with panel.groups=function(..) {xyplot.} code block.. I have not bee successful so far.. I was wondering if it is possible to pass user-defined functions (including

Re: [R] as.vector with mode=list and POSIXct

Hi, Jeff. Thanks for your thoughtful suggestions. I do not plan to wait for the hash package to be redesigned to meet my expectations. As a matter of fact, I have: a) Submitted a report of unexpected behavior in hash::values, which the package maintainer quickly replied to and said would

Re: [R] How to create a correct matrix in R

Hi, Couldn't reproduce your error. It is better to dput() the example data: v - read.table(/home/tiago/matrix.txt, header=FALSE) dput(v) v- read.table(matrix1.txt,header=FALSE,sep=) v-as.matrix(v)  v #  V1  V2  V3  V4  V5  V6 #[1,] 

[R] How to test if something doesn't exist

Couldn't exactly explain the subject, so here's the example: idx-which(blah[,1]==xyz) idx integer(0) How do I test that idx has a valid value (namely, 0)? TiA, Joe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] How to test if something doesn't exist

Hi Joe, Not sure about your expected result  blah- paste0(x,1:5)  which(blah==xyz) #integer(0) blah==xyz #[1] FALSE FALSE FALSE FALSE FALSE  any(blah==xyz) #[1] FALSE  sum(blah==xyz) #[1] 0 sum(blah==x1) #[1] 1 A.K. - Original Message - From: Joseph Trubisz jtrub...@me.com To:

Re: [R] using metafor for meta-analysis of before-after studies (escalc, SMCC)

Dear Dr. Viechtbauer: Thank you very much for sparing your precious time to answer my question. I still want to make sure for the third question below: for studies which only reported percentage changes (something like: the metabolite concentration increased by 20%+/-5% after intervention),

Re: [R] How to test if something doesn't exist

#Some cases: ifelse(blah!=xyz,paste0(blah,1),blah) #[1] x11 x21 x31 x41 x51 if(sum(blah==xyz)0) blah else paste0(blah,1) #[1] x11 x21 x31 x41 x51 if(any(blah==xyz)) blah else as.numeric(factor(blah)) #[1] 1 2 3 4 5 A.K. - Original Message - From: Joseph Trubisz jtrub...@me.com

Re: [R] column width in .dbf files using write.dbf ... to be continued

Hello Arnaud, You posted this question a long long time ago, however I found your answer so I decided to post it anyway in case somebody else have the same problem as you and me. You were actually very close in finding your solution. The function DoWritedbf is an internal function from the

Re: [R] as.vector with mode=list and POSIXct

My perception of illogic was in your addition of more data structure complexity when faced with this difficulty. R has best performance when calculations are pushed into simple typed vectors where precompiled code can handle the majority of the work. These are simpler structures, not more

Re: [R] column width in .dbf files using write.dbf ... to be continued

Thanks Bastien, I completely forgot that I asked this question. I learned a lot since then ... actually, now I know how to do it, but it was not the case in 2009 :-) Arnaud 2013/5/22 bastien.ferland-raym...@mrn.gouv.qc.ca Hello Arnaud, You posted this question a long long time ago, however

Re: [R] How to test if something doesn't exist

Joe Testing is something _exists_ is different than testing if something has what you are referring to as a valid value. Here is one way to do what I think you are doing versus testing if something exists validVal - function(x, val){ if (!is.numeric(x)) stop('Not a numeric variable')

Re: [R] problem with transform and get functions

Hi, May be this helps: test1- test[1:5,] test0- test1 for(i in 1:5) test0[,i]=0 test0 #  Y X1 X2 X3 X4 #1 0  0  0  0  0 #2 0  0  0  0  0 #3 0  0  0  0  0 #4 0  0  0  0  0 #5 0  0  0  0  0 A.K. - Original Message - From: Roni Kobrosly roni.kobro...@gmail.com To: r-help@r-project.org Cc:

[R] NADA Package install disappearance

I have been using the NADA package to do some statistical analysis, however I have just found that the package is no longer available for install. I've downloaded an older version ( NADA_1.5-4.tar.gz ) and tried to use install.packages to install it in two versions of R ( 3.0.0 and

Re: [R] as.vector with mode=list and POSIXct

Please let's not turn this into an ad hominem discussion by adding remarks on what the other thinks or knows, as this will get us nowhere fast. Let's focus on the issue, ok? :) Again, the point behind my workaround was to try to change the rest of my program as little as possible while I

Re: [R] list to dataframe

On May 22, 2013, at 5:00 AM, catalin roibu wrote: Hello all! I have a problem to transform this list in a data frame. I try this command as.data.frame, but unsuccessfully. Please help me! thank you very much! structure(list(fns = list(structure(list(r = c(0, 0.048828125, 0.09765625,

Re: [R] as.vector with mode=list and POSIXct

Gents: You've both been polite and thoughtful, but I think you should take your discussion private, no? -- Bert On Wed, May 22, 2013 at 12:57 PM, Alexandre Sieira alexandre.sie...@gmail.com wrote: Please let's not turn this into an ad hominem discussion by adding remarks on what the other

Re: [R] Lattice xyplot multipanels

Dear Rxperts.. Just figured how to add a text at a custom location in panel.groups.. use grid.text(x=unit(value1,npc),y=unit(value2,npc),label=label content) With this, I hope to stop flogging such a valuable black horse! :) On Wed, May 22, 2013 at 10:35 AM, Santosh santosh2...@gmail.com

Re: [R] NADA Package install disappearance

On Wed, 22 May 2013, rwillims wrote: I have been using the NADA package to do some statistical analysis, however I have just found that the package is no longer available for install. I've downloaded an older version ( NADA_1.5-4.tar.gz ) and tried to use install.packages to install it in two

Re: [R] point.in.polygon help

First suggestion is to ask the question on r-sig-geo. There is the over() function in the sp package, though it may require you to put your points in a spatial class object. For a crude brute-force approach that does not easily generalize, but might be the quickest short-term solution for you

Re: [R] reading large csv data sets efficiently

http://cran.r-project.org/web/packages/data.table/index.html On Wed, May 22, 2013 at 12:31 PM, ivo welch ivo.we...@anderson.ucla.eduwrote: I have a couple of large data sets, on the order of 4GB. they come in .csv files, with about 50 columns and lots of rows. a couple have weird NA

Re: [R] as.vector with mode=list and POSIXct

On May 20, 2013, at 2:09 PM, Alexandre Sieira wrote: I was trying to convert a vector of POSIXct into a list of POSIXct, However, I had a problem that I wanted to share with you. Works fine with, say, numeric: v = c(1, 2, 3) v [1] 1 2 3 str(v) num [1:3] 1 2 3 l = as.vector(v,

[R] Linebreaks in cat() functions that call other variables?

Hi everyone, I'm having some difficulty getting the linebreaks I want with the cat() function. I currently have the following function: lab1-function(iv,dv){ a-anova(lm(dv~iv)) cat(df(between) is,a[1,1]) cat(df(within) is, a[2,1]) cat(ss(between) is, a[1,2]) cat(ss(within) is, a[2,2])

Re: [R] Linebreaks in cat() functions that call other variables?

The only permutation you likely didn't try: cat(df(between) is, a[1,1], \ndf(within) is, a[2,1]) \n has to be inside the quotes. HTH. Bryan On May 22, 2013, at 4:34 PM, jordanbrace r24...@mun.ca wrote: Hi everyone, I'm having some difficulty getting the linebreaks I want with the cat()

Re: [R] as.vector with mode=list and POSIXct

You may not have expected it, but that result is what is described: From the help page for `as.vector`: For as.vector, a vector (atomic or of type list). All attributes are removed from the result if it is of an atomic mode, ... And since POSIXct vectors _are_ of atomic mode, all of

Re: [R] Linebreaks in cat() functions that call other variables?

HI, Try: lab2- function(var1,var2,data1){  a- anova(lm(var2~var1,data=data1)) cat(df(between) is,a[1,1],\n)   cat(df(within) is, a[2,1],\n)   cat(ss(between) is, a[1,2],\n)   cat(ss(within) is, a[2,2],\n)  } #or lab3- function(var1,var2,data1){  a- anova(lm(var2~var1,data=data1))

Re: [R] as.vector with mode=list and POSIXct

That's a very interesting point, David. The part I actually didn't know is that the class of an object is an attribute, and that by removing all attributes the function would in effect unclass it. Thank you. --  Alexandre Sieira CISA, CISSP, ISO 27001 Lead Auditor The truth is rarely pure and

[R] group data based on row value

hey, I want to divide my data into three groups based on the value in one column with group name. dat: Var 0 0.2 0.5 1 4 6 I tried: dat - cbind(dat, group=cut(dat$Var, breaks=c(0.1,0.6))) But it doesnt work, I want to group those 0.1 as group A, 0.1-0.6 as group B, 0.6 as group C Thanks for

Re: [R] group data based on row value

Hi, Try: dat- read.table(text= Var 0 0.2 0.5 1 4 6 ,sep=,header=TRUE) res1-within(dat,group-factor(findInterval(Var,c(-Inf,0.1,0.6),rightmost.closed=TRUE),labels=LETTERS[1:3]))  res1  # Var group #1 0.0 A #2 0.2 B #3 0.5 B #4 1.0 C #5 4.0 C #6 6.0 C #or

Re: [R] question

HI, directory- /home/arunksa111/NewData GetFileList - function(directory,number){   setwd(directory)  filelist1-dir()[file.info(dir())$isdir]     direct-dir(directory,pattern = paste(MSMS_,number,PepInfo.txt,sep=), full.names = FALSE, recursive = TRUE)  direct-lapply(direct,function(x)

Re: [R] group data based on row value

dat$group - cut( dat$Var, breaks=c(-Inf,0.1, 0.6,Inf)) levels(dat$group) - LETTERS[1:3] --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.

Re: [R] Forecasting MA model different to manually computation?

Hello, To see the source code, type fitted.Arima (no parenthesis) at an R prompt. It will show that they are computed as I've said. So your second question is in order, where do the residuals come from? To see the source code for arima() type the function name without the parenthesis and it

[R] (no subject)

Dear Bernhard, I am using your R package “var”. I am interested in running impulse response analysis (using ‘irf’) and error variance decomposition (using ‘fevd’). I have two questions: -What decomposition method do you use in your package – Cholesky? -What is the order of entry of the

[R] sample(c(0, 1)...) vs. rbinom

Greetings.  My wife is teaching an introductory stat class at UC Davis.  The class emphasizes the use of simulations, rather than mathematics, to get insight into statistics, and R is the mandated tool.   A student in the class recently inquired about different approaches to sampling from a

[R] Sort data by month

Hello, I have a 'zoo' object containing dates [dd/mm/yr] in the first column and values in the second column. I tried as.Date but did not succeed. Here is an example of date format  01/01/2000 01/02/2000 ... 01/12/2000 01/01/2001 01/02/2001 ... 01/12/2000   etc. I would like to sort all Jans

Re: [R] ordered and unordered variables

It's not homework. I met this question during my practical work via R. The boss is an expert of biology,but he doesn't know statistics.So I must find the right method to this work. At 2013-05-22 17:30:34,Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 22.05.2013 07:09, meng

Re: [R] Sort data by month

Hi, May be this helps. date1-seq.Date(as.Date(01/01/2000,format=%d/%m/%Y),as.Date(31/12/2010,format=%d/%m/%Y),by=day) set.seed(24)  value- rnorm(4018,25)  dat1- data.frame(date1,value)  dat2- do.call(rbind,split(dat1,as.numeric(gsub(.*\\-(.*)\\-.*,\\1,dat1$date1 library(zoo) z1-

Re: [R] ordered and unordered variables

On May 22, 2013, at 7:44 PM, meng wrote: It's not homework. I met this question during my practical work via R. The boss is an expert of biology,but he doesn't know statistics.So I must find the right method to this work. Yes, you must. Unfortunately, the Rhelp mailing list is for

Re: [R] Sort data by month

Hi Ak, I seems to work correctly with your data. Please try it on my data (attached). My data is monthly. The y in column 1 is not provided when I convert my data to zoo.  So, delete the header, y and try to work with the data. Sort all Jans, Febs, etc just as you did. Atem.

[R] adding rows without loops

I'm comparing a variety of datasets with over 4M rows. I've solved this problem 5 different ways using a for/while loop but the processing time is murder (over 8 hours doing this row by row per data set). As such I'm trying to find whether this solution is possible without a loop or one in which

Re: [R] sample(c(0, 1)...) vs. rbinom

You seem to be building an elaborate structure for testing the reproducibility of the random number generator. I suspect that rbinom is calling the random number generator a different number of times when you pass prob=0.5 than otherwise.

Re: [R] sample(c(0, 1)...) vs. rbinom

On May 23, 2013, at 07:01 , Jeff Newmiller wrote: You seem to be building an elaborate structure for testing the reproducibility of the random number generator. I suspect that rbinom is calling the random number generator a different number of times when you pass prob=0.5 than otherwise.

Re: [R] Sort data by month

Hi, dat1- read.csv(me.csv,header=TRUE,stringsAsFactors=FALSE)  dat1$y- as.Date(dat1$y,format=%d/%m/%Y) library(zoo) z1- zoo(dat1[,-1],dat1[,1]) library(xts) library(lubridate) lst1-lapply(split(z1,month(index(z1))),as.xts) head(lst1[[1]]) #    [,1] #1961-01-01  7.45 #1962-01-01 17.63

Re: [R] Sort data by month

HI Atem, No problem. If you want to do some calculations based on monthly data: aggregate(z1,month(index(z1)),mean)  # 1    2    3    4    5    6    7    8 #21.52044 12.64133 20.06044 27.28711 43.41489 70.15022 41.18756 34.28689  # 9   10   11