Re: [R] data manipulation

On 15-05-2013, at 08:15, catalin roibu wrote: > Hello all! > I have a problem with my data. > My initial data is a list years and months (see below). I want to transpose > my data (12 rows (months) and year values as column). I try t(spi3), but > the year values do not appear as column names, bu

[R] NMDS using Vegan

Hello R experts, I am new to Vegan and use trying to follow the tutorial to perform NMDS for my data. But after performing the metaMDS, when I plotted my results the default plot shows MDS1 vs MDS2. Thought according to the tutorial Default ordination plot should display NMDS1vs NMDS2. Why is thi

[R] data manipulation

Hello all! I have a problem with my data. My initial data is a list years and months (see below). I want to transpose my data (12 rows (months) and year values as column). I try t(spi3), but the year values do not appear as column names, but as values. Please help me to solve this problem! Thank yo

[R] fast time series similarity (iSAX, UCR DTW, UCR ED) implementations for R?

Hello. I'm looking for a fast way to group by similarity many (5-10k) long (2-10k points) time series. Using PAM on distance matrix obtained via as.dist(1-abs(cor(data))) produces usable results but it's rather slow and doesn't catch slightly shifted time series. DTW implementation from package 'd

Re: [R] Broken line questions

Hi, You may also replace the NAs using ?na.approx() from library(zoo). library(zoo)  mydata2<- mydata  mydata2$MW01<-na.approx(mydata2$MW01)  plot(MW01~Year,data=mydata2,col=ifelse(D_MW01,"black","red"),ylab="END (mg/L)",pch=ifelse(D_MW01,19,24),cex=1) with(mydata2,lines(Year,MW01,lty=c(1),col="

Re: [R] Post hoc test for GLM with poisson distribution

On May 14, 2013, at 21:04 , Bel Braz wrote: > Hi R-people, > > I performed controlled experiments to evaluated the seeds germination of > two palms under four levels of water treatments. I conducted a generalized > linear model (GLM) with a Poisson distribution to verify whether there were > sig

Re: [R] Sampling Weights and lmer() update?

Arguably you are looking in the wrong place (there's a special mixed-models mailing list for R), but I can answer the question. No. At least, there's nothing in lme4, and I haven't done anything (since I want a more general solution than Stata and MLWiN implement) and I'd be surprised if someone

Re: [R] Broken line questions

Hi, It is because of the unequal lengths of x and y. I was able to plot without the errors.  But, not sure if this is what you wanted. mydata <- read.table("TestData.csv", header=TRUE, sep="\t") reg1<-lm(MW01~Year,data=mydata)   plot(MW01~Year,data=mydata[!is.na(mydata$MW01),],col=ifelse(D_MW01,"

[R] R-Help: nparLD Package Non-parametric Repeated Measures

Hi, I'm trying to analyze repeated measurements of body temperature data collected from 7 randomly chosen subjects (e.g. turtles). I am using R, along with the nparLD package to test for an effect of diel period (fixed factor: day or night) and season (sub-plot fixed factor: spring, summer, fall)

Re: [R] How to capture the expression corresponding to the i param in the [ function

On May 14, 2013, at 8:02 PM, David Winsemius wrote: I think you need to read ?setClass and ?setMethod. There is an example of defining a "[" method for a class that inherits from 'data.frame'. I suspect you need to capture the various possibilities for the arguments being present or missin

Re: [R] Changing Order of Factor Levels in Mixed Model (nlme)

Edward Patzelt umn.edu> writes: > > R Help - > > Why is that in the results below, changing the order of the factor > (trialType2: levels - DD, SD, DS, SS) changes the estimates in the fixed > effects tests? I think you're not doing what you expected. By sorting the factor, you are _not_ ch

Re: [R] How to capture the expression corresponding to the i param in the [ function

I think you need to read ?setClass and ?setMethod. There is an example of defining a "[" method for a class that inherits from 'data.frame'. I suspect you need to capture the various possibilities for the arguments being present or missing. -- David Sent from my iPhone On May 14, 2013, at 5:

[R] empirical and GPD for time series simulation

Hi, Does anyone know how to simulate a long time series (say 1000 daily series) or generally a series, with inverse empirical distribution and generalized pareto distribution (meaning to say the time series has a marginal distribution of empirical and GPD distribution.) using the R package? Does

Re: [R] Help me please: gplot, facets_wrap and ordering of x axis dates

Your value column will be input as character because of the "<" signs and you need to convert the dates in %m/%d/%y format to real R dates. -- David Sent from my iPhone On May 14, 2013, at 3:59 PM, David Lyon wrote: > I have a text file of data as below and doing a ggplot line plot of all the

Re: [R] need means on all boxplots, but only half of them got that

>boxplot( Daten$weight~interaction(Daten$Dosis,Daten$sex, drop=TRUE)) >means<-tapply( Daten$weight, Daten$Dosis, mean) >points(means, pch=5, col="red", lwd=5) > > ...only the boxplots for male got that point on them, > its really weird because I don't thin

[R] Post hoc test for GLM with poisson distribution

Hi R-people, I performed controlled experiments to evaluated the seeds germination of two palms under four levels of water treatments. I conducted a generalized linear model (GLM) with a Poisson distribution to verify whether there were significant differences in the number of seed germination (N

Re: [R] Help me please: gplot, facets_wrap and ordering of x axis dates

Thank you for supplying the code. It would be easier to help you if we also had some data to work with. ?dput https://github.com/hadley/devtools/wiki/Reproducibility I think reorder() is likely to do the trick but I don't have enough time to mock up some data and check at the moment. Have a

[R] Help me please: gplot, facets_wrap and ordering of x axis dates

I have a text file of data as below and doing a ggplot line plot of all the ids as separate mini line plots which works with the following code. Problem how do I order the dates for each id plot on the x axis so that the dates are going from oldest to most recent Thanks in advance Dave

Re: [R] Unexpected behavior of "apply" when FUN=sample

This is Circle 8.1.47 of 'The R Inferno'. http://www.burns-stat.com/documents/books/the-r-inferno/ Pat On 14/05/2013 09:52, Luca Nanetti wrote: Dear experts, I wanted to signal a peculiar, unexpected behaviour of 'apply'. It is not a bug, it is per spec, but it is so counterintuitive that I

[R] Specifying Correlation Structures in Linear Multivariate State Space Models

I am investigating various R packages that facilitate estimation of linear Gaussian multivariate state space models. I stumbled across the MARSS package (http://cran.r-project.org/web/packages/MARSS/index.html), which I believe is very well done, but am finding one missing feature that I cannot liv

Re: [R] ?on-consequitve # of lags in VAR (package 'vars")?

My question has been answered elsewhere, but here is the answer: ?restrict On Mon, May 13, 2013 at 8:49 PM, Dimitri Liakhovitski < dimitri.liakhovit...@gmail.com> wrote: > Hello! > > I was wondering if it is at all possible (in "vars" or maybe outside of > it?) to include non-consequite lags int

Re: [R] query in plot(intervals....

On Tue, May 14, 2013 at 10:05 AM, Michelle Morters wrote: > Hi - > > I would like the plot ordered by intercept. > One way will be to tweak the ?intervals.lmList object require(nlme) fm1 <- intervals(lmList(distance ~ age | Subject, Orthodont)) fm2 <- fm1[order(fm1[,2,1]),,] class(fm2) <- class(

Re: [R] query re plot(confint(lmList...

Or better yet see ?dput, sorry. John Kane Kingston ON Canada > -Original Message- > From: jrkrid...@inbox.com > Sent: Tue, 14 May 2013 09:20:59 -0800 > To: mm...@hermes.cam.ac.uk, r-help@r-project.org > Subject: Re: [R] query re plot(confint(lmList... > > Please don't post in html. The

Re: [R] query re plot(confint(lmList...

On 14/05/2013 11:54 AM, Michelle Morters wrote: Hi - My sample size is about 190, consequently the plot output (below) is quite squashed up and the id numbers down the L axis overlay each other and are not legible plot(confint(lmList(x ~ slope | id, data), pooled = TRUE), order = 1) Is it poss

Re: [R] 3D plot

On 14/05/2013 1:10 PM, Amir wrote: Dear all, I need to plot more than one surface in 3D using R. I tried with "persp" function, it produce only one surface. Could you please help me how can I do it? The X and Y axis are the same but I have Z1 and Z2. I want to have both results in one grap

Re: [R] query re plot(confint(lmList...

Please don't post in html. The list strips it out and we, now, have no idea of what you are doing. Have a look at https://github.com/hadley/devtools/wiki/Reproducibility for suggestions on how to ask a qustion here. Sample code and sample data (see ?dupt) are usually desirable. John Kane Kin

[R] Changing Order of Factor Levels in Mixed Model (nlme)

R Help - Why is that in the results below, changing the order of the factor (trialType2: levels - DD, SD, DS, SS) changes the estimates in the fixed effects tests? > tmp.dat4$trialType2 <- sort(tmp.dat4$trialType, decreasing = TRUE) > mod2c <- lme(proportion.down ~ trialType2, data = tmp.dat4, ra

[R] 3D plot

Dear all, I need to plot more than one surface in 3D using R. I tried with "persp" function, it produce only one surface. Could you please help me how can I do it? The X and Y axis are the same but I have Z1 and Z2. I want to have both results in one graph. Thanks Amir -- ___

[R] query in plot(intervals....

Hi - I would like the plot ordered by intercept. Ordering is doable if the intervals function is substituted with the confint function and order=1 included. Is ordering doable with intervals function, please? Thanks! M results<-lmList(x~slope|id,data) plot(intervals(results)) [[al

[R] query re plot(confint(lmList...

Hi - My sample size is about 190, consequently the plot output (below) is quite squashed up and the id numbers down the L axis overlay each other and are not legible plot(confint(lmList(x ~ slope | id, data), pooled = TRUE), order = 1) Is it possible to either reduce the size of the id numbers

Re: [R] where clauses - help

On 14/05/2013 11:06 AM, martinizza wrote: hello, I wrote a foreach loop containing "where clauses". R indicates an error in the compilation of the "where clause". Could you please tell me why not right? foreach (series. combine = c)%:% when (mydata [3] = u [1]) % Dopar% (mydata [5] / sum (mydata

Re: [R] where clauses - help

On May 14, 2013, at 17:06 , martinizza wrote: > hello, I wrote a foreach loop containing "where clauses". R indicates an > error in the compilation of the "where clause". > Could you please tell me why not right? > > foreach (series. combine = c)%:% when (mydata [3] = u [1]) % Dopar% (mydata > [

Re: [R] Dataframe and conditions

#this should also work  within(X,a<- ifelse(b,c,a)) #  a b c #1 2  TRUE 2 #2 2  TRUE 2 #3 1 FALSE 2 #4 1 FALSE 2 #5 1 FALSE 2 #6 2  TRUE 2 A.K. - Original Message - From: Pascal Oettli To: fgrelier Cc: r-help@r-project.org Sent: Tuesday, May 14, 2013 4:47 AM Subject: Re: [R] Dataf

[R] where clauses - help

hello, I wrote a foreach loop containing "where clauses". R indicates an error in the compilation of the "where clause". Could you please tell me why not right? foreach (series. combine = c)%:% when (mydata [3] = u [1]) % Dopar% (mydata [5] / sum (mydata [5])) L 'error reported by R is: Error: un

[R] Problem with constrained nlsList model

I have some longitudinal data I'm fitting with an asymptotic growth function constrained to the origin. Visual inspection of the dataset suggests this is reasonable! > library(nlme) > results <- groupedData(y~Days | ID, data=results) > m1 <- nlsList(SSasympOrig, na.omit(results)) > m1 Call: Mo

Re: [R] Dataframe and conditions

Thanks a lot Guys That works I appreciate your helps Best regards Frederic FREDERIC GRELIER – DIRECTEUR DATA T +33 (0) 1 83 94 04 08 - P +33 (0) 6 70 50 01 05 - F +33 (0) 1 53 19 41 84 WWW.WEBORAMA.COM - 15, RUE CLAVEL - 75019 PARIS -Message d'origine- De 

Re: [R] Need help to building R package with devtools

>> Can someone help what I need to do to make 'devtools' work? > > A quick asking around indicates that Rtools 3.0 should work fine for 2.15.3 > maintenance. Thus, the issue is probably a purely formal bug in devtools's > version comparison logic, and you need to pester its maintainer. Unless it

Re: [R] Possible bug in 'data.table'

Manta libero.it> writes: > > Dear R users, > > I may have found a bug in the function 'data.table'. I have a similar > question as the one in this post: > > http://stackoverflow.com/questions/3367190/ aggregate-and-weighted-mean-in-r > [snip] > While I run the command > > temp[,list(we

Re: [R] points overlay axis

Let's try again after restraining Outlook's desire to use html. set.seed(42) dat <- matrix(c(runif(48), 0, 0), 25, 2, byrow=TRUE) # Complete plot symbol on axes, but axis on top plot(dat, xaxs="i", yaxs="i", pch=16, col="red", xpd=TRUE) # Complete plot symbol on axes with symbol on top plot(dat,

Re: [R] points overlay axis

Try this set.seed(42) dat <- matrix(c(runif(48), 0, 0), 25, 2, byrow=TRUE) # Complete plot symbol on axes, but axis on top plot(dat, xaxs="i", yaxs="i", pch=16, col="red", xpd=TRUE) # Complete plot symbol on axes with symbol on top plot(dat, xaxs="i", yaxs="i", type="n") points(dat, xaxs="i", yaxs

[R] need help for Imbalanced classification problems!!!

Hi all, I am facing the imbalanced classification problems. That means I have a dataset, in which the ratio of majority data to minority data is 100:1 (or more). In addition, the independent variables are many and this is a binary classification questions. The model I built give poor predictive

[R] apcluster webinar: Thursday, June 13, 2013, 7:00pm CEST

Dear colleagues, This is to inform you that I will be giving a webinar on the apcluster package on Thursday, June 13, 2013, 7:00pm CEST (10:00am PDT). The outline of the one-hour webinar is as follows: - Introduction to affinity propagation (AP) clustering - The apcluster package, its algorit

Re: [R] Select the column from the data.frame?

Hi, Try: set.seed(24) dat1<- as.data.frame(matrix(sample(1:60,15*5,replace=TRUE),ncol=15)) colnames(dat1)<- paste0("a",c(3,1,5,7,2,8,11,14:15,10,9,6,12:13,4))   subDat1<-dat1[colnames(dat1)[as.numeric(gsub("[A-Za-z]","",colnames(dat1)))<=10]]  subDat1 #  a3 a1 a5 a7 a2 a8 a10 a9 a6 a4 #1 18 56 37 5

[R] Problem with R websocket package

Hello to everybody, I'm repeating my post as the previous one was posted in HTML - sorry guys! I seem to be in struggle with the websockets in R. I wanted to download the streaming data from the BitCoin exchange MtGox directly to R, but R cannot establish the connection. The websocket specs a

Re: [R] points overlay axis

Probably but since we don't know what you are doing, it is very hard to give any advice. Please read this for a start https://github.com/hadley/devtools/wiki/Reproducibility and give us a clear statement of the problem Thanks John Kane Kingston ON Canada > -Original Message- > Fr

[R] points overlay axis

Hi, I'm trying to do quite a simple task, but I'm stuck. I've set xaxs = 'i' as I want the origin to be (0,0), but unfortunately I have points that are sat on the axis. R draws the axis over the points, which hides the points somewhat and looks unsightly. Is there any way of getting a point to be

Re: [R] Unexpected behavior of "apply" when FUN=sample

t(apply(test,1,sample)) will also do. As the OP noted, the results are simply transposed. So if an operation is to be applied to rows, yielding modified rows, simply transpose the results. Cheers, Tsjerk On Tue, May 14, 2013 at 12:07 PM, Ted Harding wrote: > On 14-May-2013 09:46:32 Duncan Murd

[R] Possible bug in 'data.table'

Dear R users, I may have found a bug in the function 'data.table'. I have a similar question as the one in this post: http://stackoverflow.com/questions/3367190/aggregate-and-weighted-mean-in-r I have a dataset with assets, quantity traded, date and time. I would like to calculate the value weig

Re: [R] Unexpected behavior of "apply" when FUN=sample

On Tue, May 14, 2013 at 4:52 AM, Luca Nanetti wrote: > Dear experts, > > I wanted to signal a peculiar, unexpected behaviour of 'apply'. It is not a > bug, it is per spec, but it is so counterintuitive that I thought it could > be interesting. > > I have an array, let's say "test", dim=c(7,5). > >

Re: [R] Unexpected behavior of "apply" when FUN=sample

On 14-May-2013 09:46:32 Duncan Murdoch wrote: > On 13-05-14 4:52 AM, Luca Nanetti wrote: >> Dear experts, >> >> I wanted to signal a peculiar, unexpected behaviour of 'apply'. >> It is not a bug, it is per spec, but it is so counterintuitive >> that I thought it could be interesting. >> >> I have a

Re: [R] Unexpected behavior of "apply" when FUN=sample

Hello, The problem is that apply returns the results vector by vector and in R vectors are column vectors. This is not exclusive of apply with sample as the function to be called, but of apply in general. Try, for instance apply(test, 1, identity) # transposes the array The rows are returne

Re: [R] Unexpected behavior of "apply" when FUN=sample

On Tue, 14 May 2013, Luca Nanetti writes: > Dear experts, > > I wanted to signal a peculiar, unexpected behaviour of 'apply'. It is not a > bug, it is per spec, but it is so counterintuitive that I thought it could > be interesting. > > I have an array, let's say "test", dim=c(7,5). > >> test <-

Re: [R] Unexpected behavior of "apply" when FUN=sample

On 13-05-14 4:52 AM, Luca Nanetti wrote: Dear experts, I wanted to signal a peculiar, unexpected behaviour of 'apply'. It is not a bug, it is per spec, but it is so counterintuitive that I thought it could be interesting. I have an array, let's say "test", dim=c(7,5). test <- array(1:35, dim=

Re: [R] How to capture the expression corresponding to the i param in the [ function

Dear David, First, I would like to say thank you for your very soon reply. Second, I want to clarify the question because it seems to not carrying exactly what I want to ask. Let take an example on R data.frame: V1 <- 1 df2 <- df[V1== 1,] # df is a data.frame, this command is correct, right? The

[R] Unexpected behavior of "apply" when FUN=sample

Dear experts, I wanted to signal a peculiar, unexpected behaviour of 'apply'. It is not a bug, it is per spec, but it is so counterintuitive that I thought it could be interesting. I have an array, let's say "test", dim=c(7,5). > test <- array(1:35, dim=c(7, 5)) > test [,1] [,2] [,3] [,4]

Re: [R] Dataframe and conditions

Hello, One approach is using "ifelse": > X <- data.frame(a=c(1,1,1,1,1,1), b=c(TRUE,TRUE,FALSE,FALSE,FALSE,TRUE), c=c(2,2,2,2,2,2)) > X a b c 1 1 TRUE 2 2 1 TRUE 2 3 1 FALSE 2 4 1 FALSE 2 5 1 FALSE 2 6 1 TRUE 2 > > X <- within(X, a <- ifelse(b==TRUE, c, a)) > X a b c 1 2 TRUE 2

Re: [R] Dataframe and conditions

Hello, Try the following. X$a[X$b] <- X$c[X$b] Hope this helps, Rui Barradas Em 14-05-2013 09:06, fgrelier escreveu: I have in a dataframe X : 3 Variables X$a , X$b, X$c I would like to replace in X the values of X$a by the values of X$c but only when X$b=="TRUE" I have tried to put in

[R] Dataframe and conditions

I have in a dataframe X : 3 Variables X$a , X$b, X$c I would like to replace in X the values of X$a by the values of X$c but only when X$b=="TRUE" I have tried to put in place a loop but as I have a lot of rows it is very very long to run. Thanks for your help -- View this message in cont

[R] Problem with R websocket package

Hello to everybody,   I seem to be in struggle with the websockets in R. I wanted to download the streaming data from the BitCoin exchange MtGox directly to R, but R cannot establish the connection. The websocket specs are defined as: * Host: websocket.mtgox.com or socketio.mtgox.com

Re: [R] question about poisson regression

Many thanks. Another question: model<- glm(count ~ drug*result, family = poisson) > anova(model,test="Chisq") Df Deviance Resid. Df Resid. Dev Pr(>Chi) NULL3 47.522 drug 10.032 2 47.491 0.85858 result

[R] empirical and GPD time series simulation

Hi, Does anyone know how to simulate a long time series (say 1000 daily series) or generally a series, with inverse empirical distribution and generalized pareto distribution (meaning to say the time series has a marginal distribution of empirical and GPD distribution.)? Does anybody know if ther

Re: [R] question about poisson regression

On Tue, 14 May 2013, meng wrote: Many thanks. Another question: model<- glm(count ~ drug*result, family = poisson) > anova(model,test="Chisq")          Df Deviance Resid. Df Resid. Dev  Pr(>Chi)     NULL                            3     47.522               drug         1    0.032         2