Re: [R] Help on best way to calculate and plot overall mean from dataset with two treatment groups

2014-02-13 Thread PIKAL Petr
Hi Posting in HTML results in scrambled mail. Maybe you want ?aggregate Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Rewarp Sent: Thursday, February 13, 2014 12:55 AM To: r-help@r-project.org Subject: [R]

Re: [R] simple linear regression

2014-02-13 Thread PIKAL Petr
Hi ?lm ?summary ?- Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of frankreynolds Sent: Wednesday, February 12, 2014 8:22 PM To: r-help@r-project.org Subject: [R] simple linear regression okay so how do you

Re: [R] Help on best way to calculate and plot overall mean from dataset with two treatment groups

2014-02-13 Thread Rewarp
Sorry if the email became messed up. I have written the full thing on pastebin. pastebin.com/AXvGstaR Thanks for the suggestion. I will play test with aggregate! *--Bitmessage http://bitmessage.org/ me* *BM-2D97QV3Y4VRfjayrWahqE61XKuQw6dJvj6* On 13 February 2014 06:51, PIKAL Petr

Re: [R] simple linear regression

2014-02-13 Thread Marc Girondot
Le 12/02/2014 20:22, frankreynolds a écrit : okay so how do you run a simple linear regression, obtain the summary of that, and then put it in an object? Generally, it is just being polite to add: Please, thanks... these little words could help a lot. You should learn to use google. There

[R] grep for multiple pattern?

2014-02-13 Thread Rainer M Krug
Hi I want to search for multiple pattern as grep is doing for a single pattern, but this obviously not work: grep(an, month.name) [1] 1 grep(em, month.name) [1] 9 11 12 grep(eb, month.name) [1] 2 grep(c(an, em, eb), month.name) [1] 1 Warning message: In grep(c(an, em, eb), month.name) :

Re: [R] Actual code for LDA

2014-02-13 Thread Uwe Ligges
On 12.02.2014 15:55, ben1983 wrote: Hi All, I've been trying to write my own code for LDA (linear discrim) so I can modify it to be weighted LDA since some of my groups are outliers. However, the code I write for standard LDA gives me slightly different results to those from R

Re: [R] grep for multiple pattern?

2014-02-13 Thread PIKAL Petr
Hi Maybe I am missing something but isn't this which(letters %in% c(a, x)) what you want? Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Rainer M Krug Sent: Thursday, February 13, 2014 3:43 PM To:

Re: [R] grep for multiple pattern?

2014-02-13 Thread Marc Schwartz
On Feb 13, 2014, at 8:43 AM, Rainer M Krug rai...@krugs.de wrote: Hi I want to search for multiple pattern as grep is doing for a single pattern, but this obviously not work: grep(an, month.name) [1] 1 grep(em, month.name) [1] 9 11 12 grep(eb, month.name) [1] 2 grep(c(an, em, eb),

[R] plyr: colvar value corresponding to max Date

2014-02-13 Thread Dan Murphy
I can do this in multiple steps with summarise, joins, etc., but can't help thinking it can be accomplished in one plyr call. Here's a small example: require(plyr) require(lubridate) data - data.frame( + date = rep(as.Date(ymd(20140101 + (0:3) * 100)), 2), + state = rep(c(A, B), each =

[R] Grouping on a Distance Matrix

2014-02-13 Thread Dario Strbenac
Hello, I'm looking for a function that groups elements below a certain distance threshold, based on a distance matrix. In other words, I'd like to group samples without using a standard clustering algorithm on the distance matrix. For example, let the distance matrix be : A B C

[R] RHadoop

2014-02-13 Thread mansi sethi
sir/mam may i know how to install RHadoop on windows? Mansi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] How to plot a shifted Gamma distribution

2014-02-13 Thread Rodrigo Cesar Silva
I have the parameters of a gamma distribution that I am trying to plot. The parameters are shape = 2, scale = 5.390275 and the minimum value x0 is 65.44945. Since the gamma is shifted by x0, we have Mean = shape*scale + x0 = 76.23 My question is, how can I do it in r?

Re: [R] grep for multiple pattern?

2014-02-13 Thread jim holtman
use the | in regular expressions: grep(c(an|em|eb, month.name) Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. On Thu, Feb 13, 2014 at 9:43 AM, Rainer M Krug rai...@krugs.de wrote: Hi I want to search

Re: [R] Grouping on a Distance Matrix

2014-02-13 Thread Bert Gunter
You need to re-think. What you said is nonsense. Use an appropriate clustering algorithm. (a can be near b; b can be near c; but a is not near c, using near = closer than threshhold) Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information

Re: [R] grep for multiple pattern?

2014-02-13 Thread Rainer M Krug
On 02/13/14, 17:23 , jim holtman wrote: use the | in regular expressions: grep(c(an|em|eb, month.name http://month.name/) Thanks - again a reason to learn regexp. Cheers, Rainer Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you

Re: [R] plyr: colvar value corresponding to max Date

2014-02-13 Thread Ista Zahn
ddply(data, state, function(x) x[x$date == max(x$date), ])$value On Thu, Feb 13, 2014 at 11:13 AM, Dan Murphy chiefmur...@gmail.com wrote: I can do this in multiple steps with summarise, joins, etc., but can't help thinking it can be accomplished in one plyr call. Here's a small example:

Re: [R] plyr: colvar value corresponding to max Date

2014-02-13 Thread arun
Hi, Try ?which.max() # unique values for the combination.  ddply(data,.(state),summarize,max_date=value[which.max(date)])[,2] #or  ddply(data,.(state),summarize,max_date=value[date == max(date)])[,2] A.K. On Thursday, February 13, 2014 11:15 AM, Dan Murphy chiefmur...@gmail.com wrote: I can

Re: [R] grep for multiple pattern?

2014-02-13 Thread Prof Brian Ripley
On 13/02/2014 16:25, Rainer M Krug wrote: On 02/13/14, 17:23 , jim holtman wrote: use the | in regular expressions: grep(c(an|em|eb, month.name http://month.name/) Thanks - again a reason to learn regexp. Note though that is an *extended* regex. They are the default in R, but not for

Re: [R] How to plot a shifted Gamma distribution

2014-02-13 Thread Ted Harding
On 13-Feb-2014 15:30:43 Rodrigo Cesar Silva wrote: I have the parameters of a gamma distribution that I am trying to plot. The parameters are shape = 2, scale = 5.390275 and the minimum value x0 is 65.44945. Since the gamma is shifted by x0, we have Mean = shape*scale + x0

Re: [R] How to plot a shifted Gamma distribution

2014-02-13 Thread Greg Snow
It is not hard to write your own function: dsgamma - function(x, x0=0, ...) { dgamma(x-x0,...) } and similar for the other functions. You might also want to look at ?curve for plotting (your plotting is fine, curve is just another option). On Thu, Feb 13, 2014 at 8:30 AM, Rodrigo Cesar Silva

Re: [R] Inquiry

2014-02-13 Thread Patrick Burns
One place to look is: http://www.burns-stat.com/documents/tutorials/impatient-r/ This gives basic information on using R, and if that doesn't suffice, gives some hints about asking questions. Welcome to the R world. Pat On 13/02/2014 02:01, Kei_Takeuchi wrote: Dear R users, Hello, this is

Re: [R] metafor package

2014-02-13 Thread Nathan Pace
I appreciate the several replies. efac = 2 had already been set in the forest call. Adding lwd = 2 in the forest call has improved the visibility of the credibility interval. Nathan -Original Message- From: Viechtbauer Wolfgang (STAT) wolfgang.viechtba...@maastrichtuniversity.nl

[R] the unwanted persistence of refClass methods

2014-02-13 Thread Ross Boylan
Redefining methods of a refClass does not change the methods for existing instances. I found this somewhat surprising, and also pretty inconvenient for debugging. The documentation for reference classes does say that their methods should be minimalist, which I suppose is partly because of

[R] minor version upgrade requires library refresh?

2014-02-13 Thread Ross Boylan
If R changes from 3.0.1 to 3.0.2, or more generally from m.n.p to m.n.q, is it necessary to refresh libraries to match the version, e.g., with update.packages(checkBuilt=TRUE, ask=FALSE)? The R Windows FAQ 2.8 says For those with a personal library (folder R\win-library\x.y of your home

[R] Standardisation of variables with Lasso (glmnet)

2014-02-13 Thread Martin Spindler
Dear all, I am working with glmnet but the problem arises also in all other Lasso implementations: It is ususally recommended to standardize the variables / use intercept and this works well with the implemented options: x - matrix(rnorm(1), ncol=50) y - rnorm(200)

[R] I am new to R

2014-02-13 Thread Shikami Kennedy
Hello there, I am new to R and have no previous experience using any other statistics software. Can someone send me basic R notes to help me start off for the very first time? *With Kind regards,* * God bless you* * Shikami K. Akweyu Manager; Fisheries ComponentKenya Coastal Development

Re: [R] grep for multiple pattern?

2014-02-13 Thread Keith Jewell
On 13/02/2014 15:51, Marc Schwartz wrote: On Feb 13, 2014, at 8:43 AM, Rainer M Krug rai...@krugs.de wrote: Hi I want to search for multiple pattern as grep is doing for a single pattern, but this obviously not work: grep(an, month.name) [1] 1 grep(em, month.name) [1] 9 11 12 grep(eb,

Re: [R] Java 7.51 broke rJava?

2014-02-13 Thread Yury V Bukhman
Thanks for the suggestion, Jeff! As it turned out, the automatic Java update installed the 32-bit version of Java for me. Installing the 64-bit version fixed this. Regards, Yury On 2/12/2014 7:10 PM, Jeff Newmiller wrote: Have you investigated the suggestion in the error message yet?

Re: [R] I am new to R

2014-02-13 Thread Kehl Dániel
Dear Shikami, R comes with excellent material, look for it in your /doc/manual folder, start with R-intro.pdf. Have fun on your hopfully long journey with R! daniel Feladó: r-help-boun...@r-project.org [r-help-boun...@r-project.org] ; meghatalmaz#243;:

Re: [R] Aggregation

2014-02-13 Thread arun
HI Farnoosh, You can use ?dcast() library(plyr)  dcast(DataA,ID~Var1,value.var=Var2) #  ID   A   B #1  1 100  50 #2  2 200 100 A.K. On Thursday, February 13, 2014 2:59 PM, farnoosh sheikhi farnoosh...@yahoo.com wrote: Hi Arun, I hope all is well. I need to aggregate a data like below:

Re: [R] Aggregation

2014-02-13 Thread arun
Sorry, the library should be library(reshape2) On Thursday, February 13, 2014 4:27 PM, arun smartpink...@yahoo.com wrote: HI Farnoosh, You can use ?dcast() library(plyr)  dcast(DataA,ID~Var1,value.var=Var2) #  ID   A   B #1  1 100  50 #2  2 200 100 A.K. On Thursday, February 13, 2014

[R] abbreviate function using 'with'

2014-02-13 Thread e-letter
Readers, A csv file was created: column1,column2,column3,column4 1,10,3,2 2,20,6,4 3,30,12,16 4,40,24,256 The csv was imported: testcsv-read.csv('/path/to/test.csv') testsum-testcsv[2,2]+testcsv[2,3]+testcsv[2,4] What is the correct syntax to abbreviate the following command using the

Re: [R] I am new to R

2014-02-13 Thread David Carlson
The official documentation is at http://cran.r-project.org/manuals.html There are also many introductory guides that have been written by R users at http://cran.r-project.org/other-docs.html Including for example: Using R for Data Analysis and Graphics by John Maindonald R for Beginners by

Re: [R] abbreviate function using 'with'

2014-02-13 Thread Rolf Turner
On 14/02/14 10:46, e-letter wrote: Readers, A csv file was created: column1,column2,column3,column4 1,10,3,2 2,20,6,4 3,30,12,16 4,40,24,256 The csv was imported: testcsv-read.csv('/path/to/test.csv') testsum-testcsv[2,2]+testcsv[2,3]+testcsv[2,4] What is the correct syntax to abbreviate

Re: [R] Changing Character Value

2014-02-13 Thread arun
Hi Farnoosh, If I understand it correctly, dat -read.table(text=Var1 Great5 great 'less great2' 'approx great11',sep=,header=TRUE,stringsAsFactors=FALSE)  dat$Var1 - gsub(.*(great).*,\\L\\1,dat$Var1,ignore.case=TRUE,perl=TRUE)  dat$Var1 #[1] great great great great A.K. On Thursday, February

[R] NextMethod in boxcox

2014-02-13 Thread Gene Leynes
I was trying to understand the boxcox function in MASS to get a better understanding of where and how the log-Likelihood values are calculated. By using debug(boxcox) I found this code while running the examples: m - length(lambda) object - lm(object, y = TRUE, qr = TRUE, ...)

Re: [R] Aggregation

2014-02-13 Thread farnoosh sheikhi
Thanks:)   Regards, Farnoosh Sheikhi On Thursday, February 13, 2014 1:29 PM, arun smartpink...@yahoo.com wrote: Sorry, the library should be library(reshape2) On Thursday, February 13, 2014 4:27 PM, arun smartpink...@yahoo.com wrote: HI Farnoosh, You can use ?dcast() library(plyr)  

[R] Printing a matrix in latexVerbatim without rownames.

2014-02-13 Thread Gil Gamesh
Hi, I'm printing a bunch of summary tables to a latex file using latexVerbatim from the Hmisc package. An example looks like this... x Visit N Min. 1st Qu. Median Mean 3rd Qu. Max. NAs [1,] 1 92 25 27.28 29.05 29.47 31.75 34.8 0 And I'm using commands like this...

Re: [R] Changing Character Value

2014-02-13 Thread farnoosh sheikhi
Perfect. Thank you so much.   Regards, Farnoosh Sheikhi On Thursday, February 13, 2014 2:16 PM, arun smartpink...@yahoo.com wrote: Hi Farnoosh, If I understand it correctly, dat -read.table(text=Var1 Great5 great 'less great2' 'approx great11',sep=,header=TRUE,stringsAsFactors=FALSE)  

Re: [R] abbreviate function using 'with'

2014-02-13 Thread e-letter
On 13/02/2014, Rolf Turner r.tur...@auckland.ac.nz wrote: What you've written is simply not (anything like!) R syntax. You should learn to speak R if you are going to use R. Agree; was reviewing the help text examples invoked by '?with'. In this particular instance testsum -

Re: [R] NextMethod in boxcox

2014-02-13 Thread Bert Gunter
Have you tried: ?NextMethod ? -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. H. Gilbert Welch On Thu, Feb 13, 2014 at 2:17 PM, Gene Leynes gleyne...@gmail.com wrote: I

Re: [R] Biomod model access

2014-02-13 Thread Matthew Bayly
Hi great that was easy I feel like a bit of a fool for not figuring this out. TO LOAD ALL SAVED MODELS AT ONCE: library(biomod2) # change directory to where you stored you’re original models (my documents is default if you did not specify). Go into the file models *# TO LOAD ALL SAVED MODELS

[R] Unicode symbols not working with ggplot in R

2014-02-13 Thread francesca casalino
Hi, I am trying to produce a ggplot graph using specific characters in the labels, but ggplots doesn't seem to support certain symbols. For example, when I type: print(\u25E9) it shows a square which is half black, but when I try to use it in ggplot it doesn't print. I am using facet_wrap, but

Re: [R] What is the effect of how.many in the contrast function

2014-02-13 Thread Prof Brian Ripley
There is no contrast() function in R itself, but this seems to be about contrasts(). On 14/02/2014 04:35, jimj wrote: I have been asked to see if there is a linear trend in 3 groups of data (5 points each) by using ANOVA and linear contrasts. The 3 groups represent data collected in 2010,2011