Re: [R] Randomness tests

2015-09-23 Thread Johannes Huesing
Giorgio Garziano [Tue, Sep 22, 2015 at 10:24:25PM CEST]: Hi, to test randomness of time series whose values can only be +1 and -1, are all following randomness tests applicable or only a part of ? I don't know the details of all those tests but the general problem is that the alternative

Re: [R] Error: pandoc version 1.12.3 or higher is required and was not found

2015-09-23 Thread Yihui Xie
I guess the confusion here is the relationship between knitr::pandoc() and rmarkdown::render(). The error message you saw was from rmarkdown::render(), which requires Pandoc 1.12.3. The easiest way to go to use rmarkdown (I mean the R package rmarkdown) is to use RStudio, and you don't even need to

Re: [R] reproducing Graphpad IC50 in R with drc package

2015-09-23 Thread David Winsemius
On Sep 23, 2015, at 9:21 AM, Jon Arsenault wrote: > I've been banging my head against the wall a bit with this and would be > ecstatic if someone could help. > > Initial data: > > Response Dose > 1 285.17 0.125 > 2 377.65 0.250 > 3 438.99 0.500 > 4 338.46 1.000 > 5

Re: [R] Error: pandoc version 1.12.3 or higher is required and was not found

2015-09-23 Thread David Winsemius
On Sep 23, 2015, at 4:13 AM, Ryszard Czermiński wrote: > I am trying to use R Markdown, but call to render() gives me an error: > Error: pandoc version 1.12.3 or higher is required and was not found. > > As I understand [http://yihui.name/knitr/demo/pandoc/] pandoc is a function > defined in kni

Re: [R] get lm by file .cvs

2015-09-23 Thread David Winsemius
On Sep 23, 2015, at 10:09 AM, raoman ramirez wrote: > well i have info<-read.csv(file, header=T) > and i want try thatmodel<-lm(info[1]~info[2]) > is for metod backward selection but i don't know how Can you explain why you want to apply backward selection to a model with a single predictor ve

Re: [R] [FORGED] Error from lme4: "Error: (p <- ncol(X)) == ncol(Y) is not TRUE"

2015-09-23 Thread Rolf Turner
On 24/09/15 01:57, Rory Wilson wrote: In reply to Rolf Turner and Jean Adams who have been helping me: This does appear to be an issue with NA values in the non-factor variables. In the (non-reproducible) example below, we can see that removing the NAs solves the problem. However, from what I ca

Re: [R] Sampling the Distance Matrix

2015-09-23 Thread David L Carlson
I think the OP wanted rows where all values were greater than .9. If so, this works: > set.seed(42) > dst <- dist(cbind(rnorm(20), rnorm(20))) > dst2 <- as.matrix(dst) > diag(dst2) <- NA > idx <- which(apply(dst2, 1, function(x) all(na.omit(x)>.9))) > idx 13 18 19 13 18 19 > dst2[idx, idx]

Re: [R] Compare two normal to one normal

2015-09-23 Thread Charles C. Berry
On Tue, 22 Sep 2015, John Sorkin wrote: Charles, I am not sure the answer to me question, given a dataset, how can one compare the fit of a model of the fits the data to a mixture of two normal distributions to the fit of a model that uses a single normal distribution, can be based on the g

Re: [R] Sampling the Distance Matrix

2015-09-23 Thread William Dunlap
> mm <- cbind(1/(1:5), sqrt(1:5)) > d <- dist(mm) > d 1 2 3 4 2 0.6492864 3 0.9901226 0.3588848 4 1.250 0.6369033 0.2806086 5 1.4723668 0.8748970 0.5213550 0.2413050 > which(as.matrix(d)>0.9, arr.ind=TRUE) row col 3 3 1 4 4 1 5 5 1 1 1 3 1 1

[R] Error of matrix and dimnames when using SVM in R

2015-09-23 Thread uc la via R-help
Hi all! I am having problems with using SVM in R I have a data frame `trainData` which contains 198 rows and  looks like Matchup Win HomeID AwayID A_TWPCT A_WST6 A_SEED B_TWPCT B_WST6 B_SEED2010_1115_1457   1   1115   1457   0.531  5 16   0.567  4 16 2010_1124_1358   1   1124  

[R] Sampling the Distance Matrix

2015-09-23 Thread Lorenzo Isella
Dear All, Suppose you have a distance matrix stored like a dist object, for instance x<-rnorm(20) y<-rnorm(20) mm<-as.matrix(cbind(x,y)) dst<-(dist(mm)) Now, my problem is the following: I would like to get the rows of mm corresponding to points whose distance is always larger of, let's say, 0

Re: [R] retaining characters in a csv file

2015-09-23 Thread Daniel Nordlund
On 9/23/2015 5:57 AM, Therneau, Terry M., Ph.D. wrote: Thanks for all for the comments, I hadn't intended to start a war. My summary: 1. Most important: I wasn't missing something obvious. This is always my first suspicion when I submit something to R-help, and it's true more often than not

[R] Progress bar in random forest model

2015-09-23 Thread Mohammad Tanvir Ahamed via R-help
Hi , I am using randomForest model in R . For large number of tree my program takes long time to complete . In "randomForest" function i can use "do.trace=TRUE" to see the real time progress . Sample out put in real time on R console is as follows ntree OOB 1 2 3 4

[R] get lm by file .cvs

2015-09-23 Thread raoman ramirez
well i have info<-read.csv(file, header=T) and i want try thatmodel<-lm(info[1]~info[2]) is for metod backward selection but i don't know how thanks for help [[alternative HTML version deleted]] __ R-he

[R] reproducing Graphpad IC50 in R with drc package

2015-09-23 Thread Jon Arsenault
I've been banging my head against the wall a bit with this and would be ecstatic if someone could help. Initial data: Response Dose 1 285.17 0.125 2 377.65 0.250 3 438.99 0.500 4 338.46 1.000 5 227.87 2.000 6 165.96 0.010 7 302.92 0.125 8 418.50

Re: [R] [FORGED] Error from lme4: "Error: (p <- ncol(X)) == ncol(Y) is not TRUE"

2015-09-23 Thread Rory Wilson
In reply to Rolf Turner and Jean Adams who have been helping me: This does appear to be an issue with NA values in the non-factor variables. In the (non-reproducible) example below, we can see that removing the NAs solves the problem. However, from what I can see to this point, there does not see

[R] Running R on a hosting o server

2015-09-23 Thread Marco
> Hi all, > > Hope I can Explain: > > I want to "run" online some function (code written by me) so that this code > "saves" an output file on my server and my html webpage read the file R > plots and save (really manually I would run R function, open Filezilla, and > pass the output png o jpg fil

Re: [R] doubt with Odds ratio - URGENT HELP NEEDED

2015-09-23 Thread Rosa Oliveira
Dear Michael, I found some of the errors, but others I wasn’t able to. And my huge huge problem concerns OR and OR confidence interval :( New Corrected code: casedata <-read.spss("tas_05112008.sav") tas.data<-data.frame(casedata) #Delete patients that were not discha

Re: [R] retaining characters in a csv file

2015-09-23 Thread John Kane
> -Original Message- > From: r.tur...@auckland.ac.nz > Sent: Wed, 23 Sep 2015 13:26:58 +1200 > To: pda...@gmail.com .. > I would say that this phenomenon ("Excel does it") is *overwhelming* > evidence that it is bad practice!!! :-) Fortune? _

Re: [R] [FORGED] Re: Compare two normal to one normal

2015-09-23 Thread Mark Leeds
Hi Rolf: I have read a decent amount about the AIC but that was a long, long time ago. I too am no expert on it and John should read some of the AIC literature John: There's one whole supposedly great text just on AIC but I don't have it. Link is here. Of course, it's absurdly expensive but do

[R] How to config the RStudio

2015-09-23 Thread Cleber Borges
Dear useRs, 1) how to configure the plot command into windows device by default in RStudio? 2) in layout panels, how to config for one panel to start in "minimized mode" ? (i would like to see only the "Environment panel" opened and only the headers of the other panel) when start RStudio. TI

Re: [R] doubt with Odds ratio - URGENT HELP NEEDED

2015-09-23 Thread Michael Dewey
Dear Rosa Can you remove all the code which is not relevant to calculating the odds ratio so we can see what is going on? On 23/09/2015 16:06, Rosa Oliveira wrote: Dear Michael, I found some of the errors, but others I wasn’t able to. And my huge huge problem concerns OR and OR confidence

Re: [R] Error: pandoc version 1.12.3 or higher is required and was not found

2015-09-23 Thread Duncan Murdoch
On 23/09/2015 7:13 AM, Ryszard Czermiński wrote: > I am trying to use R Markdown, but call to render() gives me an error: > Error: pandoc version 1.12.3 or higher is required and was not found. > > As I understand [http://yihui.name/knitr/demo/pandoc/] pandoc is a function > defined in knitr, whic

Re: [R] retaining characters in a csv file

2015-09-23 Thread Therneau, Terry M., Ph.D.
Thanks for all for the comments, I hadn't intended to start a war. My summary: 1. Most important: I wasn't missing something obvious. This is always my first suspicion when I submit something to R-help, and it's true more often than not. 2. Obviously (at least it is now), the CSV standard

Re: [R] Running R on a hosting o server

2015-09-23 Thread John McKown
On Tue, Sep 22, 2015 at 2:55 PM, bgnumis bgnum wrote: > Hi all, > > Hope I can Explain: > > I want to "run" online some function (code written by me) so that this code > "saves" an output file on my server and my html webpage read the file R > plots and save (really manually I would run R functio

Re: [R] Error: pandoc version 1.12.3 or higher is required and was not found

2015-09-23 Thread Marc Schwartz
> On Sep 23, 2015, at 6:13 AM, Ryszard Czermiński > wrote: > > I am trying to use R Markdown, but call to render() gives me an error: > Error: pandoc version 1.12.3 or higher is required and was not found. > > As I understand [http://yihui.name/knitr/demo/pandoc/] pandoc is a function > define

[R] Error: pandoc version 1.12.3 or higher is required and was not found

2015-09-23 Thread Ryszard Czermiński
I am trying to use R Markdown, but call to render() gives me an error: Error: pandoc version 1.12.3 or higher is required and was not found. As I understand [http://yihui.name/knitr/demo/pandoc/] pandoc is a function defined in knitr, which I have installed and it has pandoc() function defined. L

Re: [R] doubt with Odds ratio - URGENT HELP NEEDED

2015-09-23 Thread Michael Dewey
Dear Rosa It would help if you posted the error messages where they occur so that we can see which of your commands caused which error. However see comment inline below. On 22/09/2015 22:17, Rosa Oliveira wrote: Dear all, I’m trying to compute Odds ratio and OR confidence interval. I’m re

[R] Appropriate specification of random effects structure for EEG/ERP data: including Channels or not?

2015-09-23 Thread Paolo Canal
Dear r-help list, I work with EEG/ERP data and this is the first time I am using LMM to analyze my data (using lme4). The experimental design is a 2X2: one manipulated factor is agreement, the other is noun (agreement being within subjects and items, and noun being within subjects and between i

[R] Issues fitting Gompertz-Makeham model to mortality data

2015-09-23 Thread Marion Keast
Good evening, I have a very basic knowledge of how to use R and am struggling with my code to fit a Gompertz-Makeham model to data. The code and error message is as follows: > data <- hmd.mx("AUS","mkeas...@hotmail.com","1Mrkqazwsx", "country") Warning message: In hmd.mx("AUS", "mkeas...@hotmail.

[R] help:parLapply error

2015-09-23 Thread chunjing....@chetuobang.com
Dear all: I use R(version 3.2.2)'s parallel processing code as follows: cat("parall cal rtic:",nListLink, ",params:",length(arimaPreParams),"start...","\n") cl <- makeCluster(getOption("cl.cores", 12)); system.time({ res <- parLapply(cl,1:

Re: [R] Unexpected/undocumented behavior of 'within': dropping variable names that start with '.'

2015-09-23 Thread Martin Maechler
> Hadley Wickham > on Sun, 20 Sep 2015 14:23:43 -0400 writes: > The problem is that within.data.frame calls as.list.environment with > the default value of all.names = FALSE. I doubt this is a deliberate > feature, and is more likely to be a minor oversight. Indeed; Thank

Re: [R] Loading data chartseries

2015-09-23 Thread Joshua Ulrich
On Tue, Sep 22, 2015 at 3:10 PM, bgnumis bgnum wrote: > Hi all, > > I want to plot this data on file.txt that has this format > > 01/01/2000;970,1877 > 02/01/2000;970,2224 > 03/01/2000;969,0336 > 04/01/2000;958,3023 > 05/01/2000;952,8527 > > I´m trying to plot with quantmode with this code but it