Re: [R] Open a file to APPEND

2011-09-12 Thread Steve Lianoglou
Hi, On Mon, Sep 12, 2011 at 1:51 AM, Noah Silverman noahsilver...@ucla.edu wrote: Hi, I want to store the output of my program to a file.  However, With subsequent runs of  my code, I'd like to append to the same log file. Currently, I'm using: outfile - file(log.txt, open=w)

Re: [R] Open a file to APPEND

2011-09-12 Thread Noah Silverman
Ahhh, Makes sense. I was too busy scouring the help file command. Didn't think to look at cat(). Thanks! -- Noah Silverman UCLA Department of Statistics 8117 Math Sciences Building #8208 Los Angeles, CA 90095 On Sep 11, 2011, at 11:10 PM, Steve Lianoglou wrote: Hi, On Mon, Sep 12, 2011

[R] findFreqTerms vs minDocFreq in Package 'tm'

2011-09-12 Thread vioravis
I am using 'tm' package for text mining and facing an issue with finding the frequently occuring terms. From the definition it appears that findFreqTerms and minDocFreq are equivalent commands and both tries to identify the documents with terms appearing more than a specified threshold. However, I

Re: [R] envfit vector labels with ordiplot3d

2011-09-12 Thread Briony
Thank you very much for the suggestion. And while I'm here, thank you for vegan and the documentation that goes with it. I tried ordilabel(pl$arrows) but the labels only seem to be in two dimensions. I'm not a skilled enough user of R to edit the ordixyplot function - so I'll pass on that

Re: [R] How download to spreadsheet?

2011-09-12 Thread Yumin
appreciate! The following is my codes. library(quantmod) Loading required package: Defaults Loading required package: xts Loading required package: zoo Attaching package: 'zoo' The following object(s) are masked from 'package:base': as.Date Loading required package: TTR

Re: [R] On-line machine learning packages?

2011-09-12 Thread Jay
If the answer is so obvious, could somebody please spell it out? On Sep 11, 10:59 pm, Jason Edgecombe ja...@rampaginggeek.com wrote: Try this: http://cran.r-project.org/web/views/MachineLearning.html On 09/11/2011 12:43 PM, Jay wrote: Hi, I used the rseek search engine to look for

Re: [R] (no subject)

2011-09-12 Thread Berend Hasselman
li li-13 wrote: Dear all, Can anyone take a look at my program below? There are two functions: f1 (lambda,z,p1) and f2(p1,cl, cu). I fixed p1=0.15 for both functions. For any fixed value of lambda (between 0.01 and 0.99), I solve f1(p1=0.15, lambda=lambda, z)=0 for the corresponding

[R] Solve your R problems

2011-09-12 Thread Patrick Burns
R-help is all about solving R problems. So here ya go: http://www.portfolioprobe.com/2011/09/12/solve-your-r-problems/ -- Patrick Burns pbu...@pburns.seanet.com twitter: @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The

[R] Multiple t.test

2011-09-12 Thread C.H.
Dear R experts, Suppose I have an data frame likes this: example - data.frame(age=c(1,2,3, 4,5,6), height=c(100,110,120,130,140,150), disease=c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE)) example age height disease 1 1100TRUE 2 2110TRUE 3 3120TRUE 4 4130

[R] Latex + R + sweave

2011-09-12 Thread Twaha Mlwilo
Hello all, Good day, I have problem on how to remove the source code from the pdf output.Here I mean this. code in sweave Rnw files = x-c(1,2,3,4,5,6) x mean(x) sd(x) @ then would like it appear as mean = 3.5 sd=1.3 x=1,2,3,4,5,6 thank you in advance

[R] regression on data subsets in datafile

2011-09-12 Thread marcel
I have data of the form tC - textConnection( Subject Dateparameter1 bob 3/2/99 10 bob 4/2/99 10 bob 5/5/99 10 bob 6/27/99 NA bob 8/35/01 10 bob 3/2/02 10 steve 1/2/99 4 steve 2/2/00 7 steve 3/2/01 10 steve 4/2/02 NA steve 5/2/03 16 kevin 6/5/04 24

Re: [R] Solve your R problems

2011-09-12 Thread peter dalgaard
On Sep 12, 2011, at 09:41 , Patrick Burns wrote: R-help is all about solving R problems. So here ya go: http://www.portfolioprobe.com/2011/09/12/solve-your-r-problems/ Grin. Incidentally, I don't think it is quite true that I called you that infernal guy at useR. I might have done so

Re: [R] Hourly data with zoo

2011-09-12 Thread Dennis Murphy
Hi Steven: How about this? d - rep(20110101,24) h - sprintf('%04d', seq(0, 2300, by = 100)) df - data.frame(LST_DATE = d, LST_TIME = h, data = rnorm(24, 0, 1)) df - transform(df, datetime = as.POSIXct(paste(LST_DATE, LST_TIME), format = '%Y%m%d %H%M')) library(zoo) X

Re: [R] Solve your R problems

2011-09-12 Thread Liviu Andronic
On Mon, Sep 12, 2011 at 9:41 AM, Patrick Burns pbu...@pburns.seanet.com wrote: R-help is all about solving R problems. So here ya go: http://www.portfolioprobe.com/2011/09/12/solve-your-r-problems/ Sweet. :) May I suggest a font change: anything but the default CM should do the trick. For one

Re: [R] On-line machine learning packages?

2011-09-12 Thread Dennis Murphy
http://cran.r-project.org/web/views/ Look for 'machine learning'. Dennis On Sun, Sep 11, 2011 at 11:33 PM, Jay josip.2...@gmail.com wrote: If the answer is so obvious, could somebody please spell it out? On Sep 11, 10:59 pm, Jason Edgecombe ja...@rampaginggeek.com wrote: Try this:

Re: [R] Power analysis in hierarchical models

2011-09-12 Thread ONKELINX, Thierry
Dear Tom, I think you failed to generate simulated outcome from the correct model. Hence the zero variance of your random effects. Here is a better working example. library(lme4) fake2 - expand.grid(Bleach = c(Control,Med,High), Temp = c(Cold,Hot), Rep = factor(seq_len(3)), ID = seq_len(8))

Re: [R] Latex + R + sweave

2011-09-12 Thread Liviu Andronic
On Mon, Sep 12, 2011 at 9:21 AM, Twaha Mlwilo uddessy2...@hotmail.com wrote: Hello all, Good day, I have problem on how to remove the source code from the pdf output.Here I mean this.  code in sweave Rnw files  =  x-c(1,2,3,4,5,6) x  mean(x) sd(x) @ then would like it appear as

[R] completing missing samples

2011-09-12 Thread Eran Eidinger
Hello, I have a time-series that has some missing samples. I was thinking on completing them using either zero-order hold or linear interpolation. I am looking for an efiicient way (other than a loop...) of identifiying the missing time slots and filling them. Can you think of any methods that

Re: [R] regression on data subsets in datafile

2011-09-12 Thread Dennis Murphy
Hi: Here's one approach: # date typo fixed in record 5 - changed 35 to 5 tC - textConnection( Subject Dateparameter1 bob 3/2/99 10 bob 4/2/99 10 bob 5/5/99 10 bob 6/27/99 NA bob 8/5/01 10 bob 3/2/02 10 steve 1/2/99 4 steve 2/2/00 7 steve 3/2/01 10 steve

Re: [R] Solve your R problems

2011-09-12 Thread Patrick Burns
Far be it from me to misquote someone. On 12/09/2011 09:17, peter dalgaard wrote: On Sep 12, 2011, at 09:41 , Patrick Burns wrote: R-help is all about solving R problems. So here ya go: http://www.portfolioprobe.com/2011/09/12/solve-your-r-problems/ Grin. Incidentally, I don't think it is

Re: [R] envfit vector labels with ordiplot3d

2011-09-12 Thread Uwe Ligges
Please quote the prior thread, otherwise readers of this mailing list will not get the context. Uwe Ligges On 12.09.2011 01:41, Briony wrote: Thank you very much for the suggestion. And while I'm here, thank you for vegan and the documentation that goes with it. I tried

Re: [R] Hourly data with zoo

2011-09-12 Thread Gabor Grothendieck
On Mon, Sep 12, 2011 at 1:58 AM, steven mosher mosherste...@gmail.com wrote: I have date data as a numeric and hourly data in 0 to 2300 hours in a dataframe. d  -  rep(20110101,24) h  -  seq(from =  0, to  =  2300, by  = 100) df  -  data.frame(LST_DATE  =  d,  LST_TIME  =  h,  data  =  

Re: [R] Multiple t.test

2011-09-12 Thread Raphael Saldanha
Hi! Try something like this: subset(example, disease==TRUE) subset(example, disease==FALSE) On Mon, Sep 12, 2011 at 4:54 AM, C.H. chainsawti...@gmail.com wrote: Dear R experts, Suppose I have an data frame likes this: example - data.frame(age=c(1,2,3, 4,5,6),

Re: [R] Multiple t.test

2011-09-12 Thread Uwe Ligges
On 12.09.2011 13:16, Raphael Saldanha wrote: Hi! Try something like this: subset(example, disease==TRUE) subset(example, disease==FALSE) Hmmm, I think the actual answer to the question is something along this line: sapply(example[names(example)!=disease], function(x) t.test(x ~

Re: [R] regression on data subsets in datafile

2011-09-12 Thread Gabor Grothendieck
On Mon, Sep 12, 2011 at 3:42 AM, marcel marcelcur...@gmail.com wrote: I have data of the form tC - textConnection( Subject Date    parameter1 bob     3/2/99  10 bob     4/2/99  10 bob     5/5/99  10 bob     6/27/99 NA bob     8/35/01 10 bob     3/2/02  10 steve   1/2/99  4 steve  

Re: [R] coxreg vs coxph: time-dependent treatment

2011-09-12 Thread Göran Broström
Dear Ehsan, the cluster option is not implemented in 'eha', although you obviously get no error if trying I'll fix this. Thanks for the report. (So, use 'coxph' with cluster). Göran On Mon, Sep 12, 2011 at 4:43 AM, Ehsan Karim wilds...@hotmail.com wrote: Sorry: there was an error in the

Re: [R] envfit vector labels with ordiplot3d

2011-09-12 Thread Briony
Thank you very much for the suggestion. And while I'm here, thank you for vegan and the documentation that goes with it. Function ordiplot3d uses scatterplot3d, and it returns also all scatterplot3d items, like functions xyz.converter and points3d that can be used for tuning labels. I tried

Re: [R] On-line machine learning packages?

2011-09-12 Thread Jay
In my mind this sequential classification task with feedback is somewhat different from an completely offline, once-off, classification. Am I wrong? However, it looks like the mentality on this topic is to refer me to cran/google in order to look for solutions myself. Oblivious I know about these

Re: [R] R-help Digest, Vol 103, Issue 11

2011-09-12 Thread mihalicza . peter
Szeptember 12-től 26-ig irodán kívül vagyok, és az emailjeimet nem érem el. Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu). Üdvözlettel, Mihalicza Péter I will be out of the office from 12 till 26 September with no access to my emails. In urgent cases please contact

[R] Automated generation of combinations

2011-09-12 Thread Santiago Guallar
Hello,   I'd like to generate automatically all the possible combinations of a set of 8 variables (there are 535, too many to do it by hand). For example:   input: varA, varB, varC output: varA+varB+varC varA+varB varA+varC varB+varC varA    

[R] Display dendrogram in heatmap.2 without reordering col or row

2011-09-12 Thread Markus Lindh
How can I display a heatmap.2 with a column dendrogram without reordering neither column or row? library(vegan) dissimilaritymatrix-data.matrix(vegdist(step3,method=bray)) library(gplots) heatmap-heatmap.2(dissimilaritymatrix,dendrogram=column,Colv=T, Rowv=F,key=TRUE, symkey=FALSE,

Re: [R] NMDS plot and Adonis (PerMANOVA) of community composition with presence absence and relative intensity

2011-09-12 Thread Markus Lindh
How can I display a heatmap.2 with a column dendrogram without reordering neither column or row? library(vegan) dissimilaritymatrix-data.matrix(vegdist(step3,method=bray)) library(gplots) heatmap-heatmap.2(dissimilaritymatrix,dendrogram=column,Colv=T, Rowv=F,key=TRUE, symkey=FALSE,

[R] how to get xlab and ylab in bold?

2011-09-12 Thread Nevil Amos
A very basic query This code plots OK the axis values are in bold but the axis labels are not. how do I get them in bold too? thanks Nevil Amos plot(c(1,1),xlim=c(0,450),ylim=c(0.7,1.4),xlab=Distance (cells) from edge of grid,ylab=Resistance distance,

[R] PerMANOVA of community data

2011-09-12 Thread Markus Lindh
Hi! How can I make a PerMANOVA in R comparing treatments in a matrix that looks something like this: Treatment 1 Treatment 2 Treatment 3 Species 1 0.6 0.2 0 Species 2 0 0.7 0.3 Species

[R] hclust and cutree: identifying branches as classes

2011-09-12 Thread Laurent Fernandez Soldevila
Good afternoon, After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches? This is what we do: srndpchc - hclust(dist(srndpc$x[1:1000,1:3]),method=ward) #creation of hierarchical tree plclust(srndpchc,hmin=2) #visualisation srndpchc2 =

Re: [R] Automated generation of combinations

2011-09-12 Thread Dimitris Rizopoulos
one option is the following: varNames - c(varA, varB, varC, varD) f - function (i) { combn(length(varNames), i, function (x) paste(varNames[x], collapse = + )) } lapply(seq_along(varNames), f) However, in case you're interested in performing a linear regression with these

Re: [R] hclust and cutree: identifying branches as classes

2011-09-12 Thread Peter Langfelder
On Mon, Sep 12, 2011 at 4:59 AM, Laurent Fernandez Soldevila l.fernand...@yahoo.fr wrote: Good afternoon, After cuting a hierarchical tree using cutree(), how to check correspondances between classes and branches? This is what we do: srndpchc -

Re: [R] how to get xlab and ylab in bold?

2011-09-12 Thread Uwe Ligges
On 12.09.2011 12:30, Nevil Amos wrote: A very basic query This code plots OK the axis values are in bold but the axis labels are not. how do I get them in bold too? Add font.lab=2 Uwe Ligges thanks Nevil Amos plot(c(1,1),xlim=c(0,450),ylim=c(0.7,1.4),xlab=Distance (cells) from edge

Re: [R] Multiple t.test

2011-09-12 Thread Mihovil Pletikos
Thank you for your help Yes i wanted to do the t test for all columns except for the grouping column. 2011/9/12 Uwe Ligges lig...@statistik.tu-dortmund.de On 12.09.2011 13:16, Raphael Saldanha wrote: Hi! Try something like this: subset(example, disease==TRUE) subset(example,

[R] number of repetition

2011-09-12 Thread amir
Hi, Is there any function or command in R that show that how many times a number is repeated in an array? Regards, Amir -- ___ Amir Darehshoorzadeh |Comp. Architecture Dept. PhD Student |UPC-Campus Nord, C6-221

Re: [R] number of repetition

2011-09-12 Thread Duncan Murdoch
On 12/09/2011 9:03 AM, amir wrote: Hi, Is there any function or command in R that show that how many times a number is repeated in an array? ?table __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] findFreqTerms vs minDocFreq in Package 'tm'

2011-09-12 Thread Bettina Gruen
On 09/12/2011 04:28 PM, vioravis wrote: I am using 'tm' package for text mining and facing an issue with finding the frequently occuring terms. From the definition it appears that findFreqTerms and minDocFreq are equivalent commands and both tries to identify the documents with terms appearing

Re: [R] Automated generation of combinations

2011-09-12 Thread Andrej Blejec
Try this ltr-LETTERS[1:3] unique(apply(expand.grid(ltr,ltr,ltr),1,function(x) paste(Var,unique(sort(x)),collapse=+,sep=))) [1] VarA VarA+VarB VarA+VarC VarA+VarB+VarC VarB VarB+VarC VarC Andrej -- Andrej Blejec National Institute of Biology Vecna pot 111

Re: [R] On-line machine learning packages?

2011-09-12 Thread Paul Hiemstra
On 09/11/2011 03:42 PM, Jay wrote: What R packages are available for performing classification tasks? That is, when the predictor has done its job on the dataset (based on the training set and a range of variables), feedback about the true label will be available and this information should

[R] barplot in hexagram layout

2011-09-12 Thread Schatzi
dev.new(width=6, height=1.5,mar=c(0,0,0,0)) par(mfrow=c(1,1),mar=c(.5, .5, 1.5, .5), oma=c(.4, 0,.5, 0)) barplot(c(1,1,1,1,1,1),col=c(blue,purple,red,green,orange,yellow), axes = FALSE) I have a barplot that returns six colors in a line. I would like to get the same six color blocks in a hexagram

Re: [R] barplot in hexagram layout

2011-09-12 Thread Schatzi
I'm not sure this is the right location (maybe R-devel would be better). - In theory, practice and theory are the same. In practice, they are not - Albert Einstein -- View this message in context: http://r.789695.n4.nabble.com/barplot-in-hexagram-layout-tp3807600p3807608.html Sent from the

[R] Superimposing titles on dotcharts

2011-09-12 Thread Mikkel Grum
I've created a chart with times that employees have entered data on named tasks as in the following example: Employee - c(rep(Tom, 127),  rep(Dick, 121),  rep(Sally, 130) ) Time - c(seq(as.POSIXct(2011-09-12 07:00:00), as.POSIXct(2011-09-12 14:00:00), 200), seq(as.POSIXct(2011-09-12 07:00:00),

[R] Difference in function arima estimation between 2.11.1 and R 2.12.2

2011-09-12 Thread Luis Felipe Parra
Hello , I have estimated the following model, a sarima: p=9 d=1 q=2 P=0 D=1 Q=1 S=12 In R 2.12.2 Call: arima(x = xdata, order = c(p, d, q), seasonal = list(order = c(P, D, Q), period = S), optim.control = list(reltol = tol)) Coefficients: ar1 ar2 ar3 ar4 ar5

Re: [R] Hourly data with zoo

2011-09-12 Thread steven mosher
Gabor.. thanks. zr - zooreg(rnorm(24), as.chron(2011-01-01), frequency = 24) a couple issues: my date data has missing days and missing hours.. Sorry if I was not clear on that.. I input it to a data frame and dates are of the form 20110101 and hours are in the format 0,100,200 The end goal

[R] Error message for .csv file

2011-09-12 Thread vkent
I would be grateful if anyone could tell me what the error message: Error in NN[i, 1:length(od)] - od : subscript out of bounds means for a large .csv file containing gps coordinates. I am using package SPACECAP and have successfully run it with other .csv files but now keep getting this error

[R] kernel weight

2011-09-12 Thread Soberon Velez, Alexandra Pilar
Hello dear members, I need to calculate by hand a local lineal regression so I need to compute a kernel weight. Does somebody knows how to get a kernel to use as weighted? I can calculate a density kernel function and after pre-multiply it by the sample size. However I know this is not

[R] 1 not equal to 1, and rep command

2011-09-12 Thread Benjamin Høyer
Hi I need to use rep() to get a vector out, but I have spotted something very strange. See the reproducible example below. N - 79 seg - 5 segN - N / seg # = 15.8 d1 - seg - ( segN - floor(segN) ) * seg d1# = 1 rep(2, d1) # = numeric(0), strange - why doesn't it

Re: [R] Error message for .csv file

2011-09-12 Thread Sarah Goslee
Hi, On Mon, Sep 12, 2011 at 11:07 AM, vkent vivien.k...@gmail.com wrote: I would be grateful if anyone could tell me what the error message: Error in NN[i, 1:length(od)] - od : subscript out of bounds It means that either i ends up being larger than the number of rows in NN, or that

[R] Loops on data˜1

2011-09-12 Thread Trying To learn again
Hi all, I have a time series a column vector with the ordered data so that the first column is the first observation and so on. The fact is that I want to run a multiple regression with only intercept. My first task is to run the regression on the first observation (1 from 276) and at the same

Re: [R] Hourly data with zoo

2011-09-12 Thread Gabor Grothendieck
On Mon, Sep 12, 2011 at 11:57 AM, steven mosher mosherste...@gmail.com wrote: Gabor.. thanks. zr - zooreg(rnorm(24), as.chron(2011-01-01), frequency = 24) a couple issues:  my date data  has missing days and missing hours.. Sorry if I was not clear on that.. I input it to a data frame and

Re: [R] Very slow using S4 classes

2011-09-12 Thread André Rossi
Dear Martin Morgan and Martin Maechler... Here is an example of the computational time when a slot of a S4 class is of another S4 class and when it is just one object. I'm sending you the data file. Thank you! Best regards, André Rossi

[R] Writting excel files

2011-09-12 Thread Damian Abalo
Hello. I need to generate, using R code, an excel file with multiple sheets, I wonder if any of you know how to do so. Thanks for the help __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] envfit vector labels with ordiplot3d

2011-09-12 Thread Gavin Simpson
On Mon, 2011-09-12 at 03:24 -0700, Briony wrote: Thank you very much for the suggestion. And while I'm here, thank you for vegan and the documentation that goes with it. Function ordiplot3d uses scatterplot3d, and it returns also all scatterplot3d items, like functions xyz.converter and

Re: [R] Writting excel files

2011-09-12 Thread Marc Schwartz
On Sep 12, 2011, at 10:28 AM, Damian Abalo wrote: Hello. I need to generate, using R code, an excel file with multiple sheets, I wonder if any of you know how to do so. Thanks for the help See the following: R Data Import/Export Manual: http://cran.r-project.org/doc/manuals/R-data.html

Re: [R] Very slow using S4 classes

2011-09-12 Thread Martin Morgan
Hi André... On 09/12/2011 07:20 AM, André Rossi wrote: Dear Martin Morgan and Martin Maechler... Here is an example of the computational time when a slot of a S4 class is of another S4 class and when it is just one object. I'm sending you the data file. Thank you! Best regards, André Rossi

Re: [R] barplot in hexagram layout

2011-09-12 Thread Schatzi
I will try stacking 5 barplots (with 5 bars per plot) and somehow only showing the middle bar for the top and bottom plots and the two end bars for the two middle plots. - In theory, practice and theory are the same. In practice, they are not - Albert Einstein -- View this message in

Re: [R] barplot in hexagram layout

2011-09-12 Thread Schatzi
Here is the new code. It works just like I wanted. dev.new(width=6, height=6.5,mar=c(0,0,0,0)) par(mfrow=c(5,1),mar=c(.5, .5, 1.5, .5), oma=c(.4, 0,.5, 0)) barplot(c(1,1,1,1,1),col=c(white,white,red,white,white), axes = FALSE,border=NA) barplot(c(1,1,1,1,1),col=c(orange,white,white,white,yellow),

Re: [R] 1 not equal to 1, and rep command

2011-09-12 Thread Sarah Goslee
Not so strange, in fact this is FAQ 7.31, and has to do (as you guess) with the way that computers store numbers. You need to do as you did, and use round() or floor() or similar to ensure that you get the results you expect. Sarah 2011/9/12 Benjamin Høyer bdho...@gmail.com: Hi I need to use

Re: [R] Hourly data with zoo

2011-09-12 Thread steven mosher
worked beautifully. Thanks. On Mon, Sep 12, 2011 at 9:45 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Sep 12, 2011 at 11:57 AM, steven mosher mosherste...@gmail.com wrote: Gabor.. thanks. zr - zooreg(rnorm(24), as.chron(2011-01-01), frequency = 24) a couple issues:  my

Re: [R] barplot in hexagram layout

2011-09-12 Thread Schatzi
I updated the code as follows: dev.new(width=2.5, height=3,mar=c(0,0,0,0)) par(mfrow=c(5,1),mar=c(.5, .5, 1.5, .5), oma=c(.4, 0,.5, 0)) barplot(c(1,1,1,1,1),col=c(white,white,red,white,white), axes = FALSE,border=NA) barplot(c(1,1,1,1,1),col=c(orange,white,white,white,yellow), axes =

Re: [R] Error message for .csv file

2011-09-12 Thread Sarah Goslee
Go to your R session. First off, tell the R-help list how you got your csv file into R as NN. read.csv() ? read.table()? Then tell us exactly what code you're using. Where did i come from? Also type in exactly the commands I gave you (four lines), and share the output with the R-help list.

Re: [R] Multiple t.test

2011-09-12 Thread Greg Snow
Here is another approach. A linear regression with a single binomial predictor will give the same results as a pooled t-test (if you insist on non-pooled then use sapply as previously suggested). The lm function will do multiple regressions if given a matrix as the y-variable, so you can do a

Re: [R] 1 not equal to 1, and rep command

2011-09-12 Thread Daniel Nordlund
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Benjamin Høyer Sent: Monday, September 12, 2011 6:19 AM To: r-help@r-project.org Cc: t...@novozymes.com Subject: [R] 1 not equal to 1, and rep command Hi I need to use

Re: [R] suggestion for proportions

2011-09-12 Thread csrabak
Em 9/9/2011 14:32, array chip escreveu: Thanks all again for the suggestions. I agree with Wolfgang that mcnemar.test() is what I am looking for. The accuracy is the proportion of correct diagnosis compared to a gold standard, and I am interested in which diagnosis test is better, not particular

Re: [R] Writting excel files

2011-09-12 Thread Bos, Roger
Marc's links lists many packages. Of those, I would recommend XLConnect. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Marc Schwartz Sent: Monday, September 12, 2011 12:53 PM To: Damian Abalo Cc: r-help Subject: Re: [R] Writting

Re: [R] Difference in function arima estimation between 2.11.1 and R 2.12.2

2011-09-12 Thread Berend Hasselman
Luis Felipe Parra wrote: and as you can see in the results some coefficients (for example ar2 and ar8) are different in the different R versions. does anybody know what might be going on. Was there any change in the arima function between the two versions? You asked the same

Re: [R] Loops on data˜1

2011-09-12 Thread R. Michael Weylandt
I may be totally off base with this, but I'm wondering what exactly this would suggest or why you want to do it. Specifically multiple regression with only intercept -- how is it multiple if you don't have any regressors? Furthermore, you want to run a regression on a single data point -- really?

[R] plot 3 lines with ggplot2

2011-09-12 Thread J Toll
Hi, I am trying to learn to use ggplot2 for what I had hoped would be a fairly simple task. I have a relatively small data.frame (100 by 4). The first column contains symbols. The 2nd, 3rd and 4th columns represent percentage weightings for each symbol using 3 different methodologies. For

[R] function to include factors in summary data frame

2011-09-12 Thread Wade Wall
Hi all, I have a dataframe that includes data on individuals that are distributed across multiple rows. I have aggregated the data using ddply, but I have columns in the original data frame that are factors ( such as sites A, B, and C) that I would like to include in the new data frame. I have

[R] Centering lines on barplot centers.

2011-09-12 Thread gerald.jean
Hello, I am trying to port one of my plotting S+ functions to R and I am having difficulties!!! I am including here only the troublesome code! I first produce a barplot, saving the positions of the bar's centers. par(mar = c(6.1, 5.1, 4.1, 4.1), mgp = c(3, 3.0, 0)) ticks.loc -

Re: [R] Centering lines on barplot centers.

2011-09-12 Thread Greg Snow
Setting par(usr=something) does not survive the creating of a new high level plot. Using par(new=TRUE) is to be avoided if at all possible (it just leads to problems like yours), it would be better for you to use matlines instead of matplot which adds lines to the current plot. If you want to

Re: [R] Error message for .csv file

2011-09-12 Thread vkent
I am using the package SPACECAP which provides an interface for R. I used this interface to import the csv file into R as well as the other two csv files that are required. This is the output I get when querying the error message Error in NN[i, 1:length(od)] - od : subscript out of bounds

[R] Multiple regression intercept

2011-09-12 Thread burdy
Hi I am having difficulty interpretive the multiple regression output. I would like to know what it means when one of the factors is assigned as the intercept? In my data I am looking at the relationship between environmental parameters and biological production. One of my variables in the

[R] Multilevel model in lme4 and nlme

2011-09-12 Thread jonas garcia
Dear list, I am trying to fit some mixed models using packages lme4 and nlme. I did the model selection using lmer but I suspect that I may have some autocorrelation going on in my data so I would like to have a look using the handy correlation structures available in nlme. The problem is

Re: [R] findFreqTerms vs minDocFreq in Package 'tm'

2011-09-12 Thread vioravis
Thanks, Bettina. -- View this message in context: http://r.789695.n4.nabble.com/findFreqTerms-vs-minDocFreq-in-Package-tm-tp3806644p3808134.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list

[R] nested anova-R chrashing

2011-09-12 Thread joerg stephan
Hi, I tried to do a nested Anova with the attached Data. My response variable is survivors and I would like to know the effect of (insect-egg clutch) size, position (of clutch on twig) and clone (/plant genotype) on the survival of eggs (due to predation). Each plant was provided with three

[R] creating a new column with values from another

2011-09-12 Thread holly shakya
I have 2 columns for weight. There are NAs in each column but not for the same observation. Some observations have values for both. I would want to prioritize the WT2 values so I would like to do the following: From this: ID WT1WT2 1 134 NA 2 145 155 1

Re: [R] function to include factors in summary data frame

2011-09-12 Thread Daniel Malter
I have read it three times and still no concrete idea what you are actually trying to do, mainly because there is no information as to which level/variable you are aggregating on. It'd help if you provided the aggregated data (or sample rows thereof) so that we know what you want the result to be.

Re: [R] Error message for .csv file

2011-09-12 Thread David Winsemius
You are asking a question about a package that seldom appears on rhelp, leading me to infer that there is not a large user community that reads this mailing list. You are also not providing the data needed to reproduced the problem. You would be better off taking the time to contact the

[R] Problem in put.var.ncdf

2011-09-12 Thread Claudia Stocker
Dear all, I have a problem in writing a variable to a NetCDF-File. My code works pretty well until the step put.var.ncdf(): # Get variables #- data1 - open.ncdf(PREC_me_03-1500.nc) prec1 - get.var.ncdf(data1,PRECT) dim.time - get.var.ncdf(data1,time2) close.ncdf(data1)

Re: [R] creating a new column with values from another

2011-09-12 Thread Daniel Malter
You can do this using ifelse(). See example below. x-rpois(100,100) NA.x-sample(1:100,40) x[NA.x]=NA y-rpois(100,100) NA.y-sample(1:100,40) y[NA.y]=NA z-ifelse(!is.na(y),y,ifelse(!is.na(x),x,NA)) HTH, Daniel holly shakya wrote: I have 2 columns for weight. There are NAs in each column

Re: [R] Multilevel model in lme4 and nlme

2011-09-12 Thread Ben Bolker
jonas garcia garcia.jonas80 at googlemail.com writes: I am trying to fit some mixed models using packages lme4 and nlme. I did the model selection using lmer but I suspect that I may have some autocorrelation going on in my data so I would like to have a look using the handy correlation

Re: [R] Multiple regression intercept

2011-09-12 Thread Daniel Malter
This suggests that this is a dangerous office to be in because this is a basic question. I am sure somebody in your office knows this. Anyway, the baseline gives you the average value of the group that constitutes the baseline when all other covariates are zero. Let's say you measure whether men

Re: [R] Problem in put.var.ncdf

2011-09-12 Thread David William Pierce
On Mon, Sep 12, 2011 at 1:32 PM, Claudia Stocker cstoc...@climate.unibe.ch wrote: Dear all, I have a problem in writing a variable to a NetCDF-File. My code works pretty well until the step put.var.ncdf(): [...code omitted...] R prints the following error: #- Error in

Re: [R] plot 3 lines with ggplot2

2011-09-12 Thread J Toll
Justin, Thanks for your help. On Mon, Sep 12, 2011 at 2:19 PM, Justin Haynes jto...@gmail.com wrote: the data you've given is all character vectors! Yes, I'm sorry about that. I should not have used cbind when forming my data.frame. It changed my numeric data to character. This command

[R] calc.relimp pmvd for US R-user

2011-09-12 Thread YAddo
Dear All: I am calculating the relative importance of a regressor in a linear model. Does anyone know how I can obtain/install the 'pmvd' computation type? I am a US user. Regards, Y -- View this message in context:

Re: [R] On-line machine learning packages?

2011-09-12 Thread Jason Edgecombe
I already provided the link to the task view, which provides a list of the more popular machine learning algorithms for R. Do you have a particular algorithm or technique in mind? Does it have a name? How does sequential classification differ form running a one-off classifier for each run?

Re: [R] Solve your R problems

2011-09-12 Thread Carl Witthoft
Love the page. Just out of interest, is this an updated version or the same ol' Inferno document? And why do I keep thinking you (Patrick Burns) are the Hab's coach? :-) -- - Sent from my Cray XK6 __ R-help@r-project.org mailing list

Re: [R] Very slow using S4 classes

2011-09-12 Thread André Rossi
Thank you a lot Morgan. Your suggestion helped me to speed up my code. But I still believe that the inefficience is an S4 issue. Best regards, André Rossi 2011/9/12 Martin Morgan mtmor...@fhcrc.org Hi André... On 09/12/2011 07:20 AM, André Rossi wrote: Dear Martin Morgan and Martin

Re: [R] calc.relimp pmvd for US R-user

2011-09-12 Thread Ben Bolker
YAddo linkyox at gmail.com writes: Dear All: I am calculating the relative importance of a regressor in a linear model. Does anyone know how I can obtain/install the 'pmvd' computation type? I am a US user. I didn't know what the heck you were talking about, but having looked at

Re: [R] Solve your R problems

2011-09-12 Thread Rolf Turner
On 13/09/11 11:27, Carl Witthoft wrote: Love the page. Just out of interest, is this an updated version or the same ol' Inferno document? And why do I keep thinking you (Patrick Burns) are the Hab's coach? :-) Now *that's* a blast from the past! Burns coached the Canadiens way back

Re: [R] nested anova-R chrashing

2011-09-12 Thread Ben Bolker
joerg stephan stephanj at rhrk.uni-kl.de writes: Hi, I tried to do a nested Anova with the attached Data. My response variable is survivors and I would like to know the effect of (insect-egg clutch) size, position (of clutch on twig) and clone (/plant genotype) on the survival of eggs

[R] Question on reading nodes info from all random forests generated trees

2011-09-12 Thread k
Hi All, I have a quick question on random forests. Simply, I am not sure how to read the values of independent variables related to the highest value of a response variable from all trees generated from random forests. It is easy to do this in a single regression tree. But I am not clear how

[R] as.POSIXct on vector weird output

2011-09-12 Thread bradford
I don't know R, so maybe I've done something wrong, but I'm working off an example I saw on the web and wondering why as.POXIXct isn't returning the same result on f$V1 as it is on z. Did I do something wrong? Or is it a problem with my build? f$V1 [1] 09/11/2011 13:46:39 09/11/2011 13:45:18

[R] nls, the four parameter logisitc equation, and prediction band

2011-09-12 Thread sg
I have uploaded a datafile that contains the following two variables: time (X value) and response (Y value). This is a fairly extensive file (with 16000 entries). I have two questions: 1. I want to use the following equation to regress Y on X: Y-hat = min + (max-min)/(1 + (X/EC50)^Hillslope).

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