[R] Three-dimensional contingency table

Hi, I am trying to assemble a three-way contingency table examining the presence/absence of mussels, water depth (Depth1 and Depth 2) and water velocity (Flow vs. No Flow). I have written the following code listed below; however, when run the glm I get the following message, Error in

[R] Please sigh me out from the R-help. Thank you!

[[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 http://www.R-project.org/posting-guide.html and provide commented, minimal,

Re: [R] Please sigh me out from the R-help. Thank you!

https://stat.ethz.ch/mailman/listinfo/r-help At the bottom of the webpage. -c On 08/29/2010 03:58 AM, Kaigang Li wrote: [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] approxfun-problems (yleft and yright ignored)

pbrbrbr/p [[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 http://www.R-project.org/posting-guide.html and provide commented,

[R] calculations with dates

Hi, I have a data.frame with factors in columns like startdate enddate 27SEP2005 01JAN2006 How can I calculate the duration between those two dates and move this in a extra column in the data.frame. Thanks, André [[alternative HTML version deleted]]

Re: [R] calculations with dates

Try this: x startdate enddate 1 27SEP2005 01JAN2006 x$start - as.Date(x$startdate, format=%d%b%Y) x$end - as.Date(x$enddate, format=%d%b%Y) x startdate enddate startend 1 27SEP2005 01JAN2006 2005-09-27 2006-01-01 x$duration - x$end - x$start x startdate enddate

Re: [R] About plot graphs

Hi Greg, Thanks for your advice. data(women) women height weight 1 58115 2 59117 3 60120 4 61123 5 62126 6 63129 7 64132 8 65135 9 66139 10 67142 11 68146 12 69150 13 70154 14

Re: [R] About plot graphs

Hi David, Thanks for your advice. B.R. Stephen L - Original Message From: David Winsemius dwinsem...@comcast.net To: Stephen Liu sati...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sun, August 29, 2010 1:52:50 AM Subject: Re: [R] About plot graphs On Aug 28, 2010,

Re: [R] Three-dimensional contingency table

Hi, Your example works fine for me. My guess is that you have one of wd, wv, MP, or Count defined as a global variable. This is the main reason the use of attach() is discouraged by many people on this list. The safer thing to do is model1 - glm(Count~MP+wd+wv,poisson. data = frame) -Ista On

[R] extracting year from date

Hi, Sorry for this simple question but I searched the internet and can't find the answer. From a date I want the year extracted: data$start[1 [1] 2006-11-01 Thanks for the answer, Andre [[alternative HTML version deleted]] __

Re: [R] extracting year from date

Try this: format(data$start, %Y) On Sun, Aug 29, 2010 at 11:32 AM, André de Boer rnie...@gmail.com wrote: Hi, Sorry for this simple question but I searched the internet and can't find the answer. From a date I want the year extracted: data$start[1 [1] 2006-11-01 Thanks for the

Re: [R] Question regarding significance of a covariate in a coxme survival model

The likelihood ratio test is more reliable when one model is nested in the other. This true for your case. AIC/SBC are usually used when two models are in a hiearchical structure. Please also note that any decision made made based on AIC/SBC scores are very subjective since no sampling

Re: [R] Question regarding significance of a covariate in a coxme survival model

The likelihood ratio test is more reliable when one model is nested in the other. This true for your case. AIC/SBC are usually used when two models are in a hiearchical structure. Please also note that any decision made made based on AIC/SBC scores are very subjective since no sampling

Re: [R] Three-dimensional contingency table

I didn't see any error when I ran your code in my computer: numbers - c(1134,956,328,529,435,599,27,99) dim(numbers) - c(2,2,2) numbers , , 1 [,1] [,2] [1,] 1134 328 [2,] 956 529 , , 2 [,1] [,2] [1,] 435 27 [2,] 599 99 dimnames(numbers)[[3]] -list(Mussels, No

Re: [R] Question regarding significance of a covariate in a coxme survival model

My suggestion: If compare model 1 and model 2 with model 0 respectively, the (penalized) likelihood ratio test is valid. IF you compare model 2 with model 3, the (penalized) likelihood ratio test is invalid. You may want to use AIC/SBC to make a subjective decision. -- View this message in

Re: [R] Question regarding significance of a covariate in a coxme survival model

My suggestion for Teresa: If compare model 1 and model 2 with model 0 respectively, the (penalized) likelihood ratio test is valid. IF you compare model 2 with model 3, the (penalized) likelihood ratio test is invalid. You may want to use AIC/SBC to make a subjective decision. -- View this

[R] how to take a os.path.basename

Hi, all I made a simple R script to take the basename of a file without directory names. path.splitted - strsplit('/path/to/a_basename', '/') path.length - length(path.splitted[[1]]) basename - path.splitted[[1]][path.length] # basename - 'a_basename' Is there a simple function for this?

Re: [R] how to take a os.path.basename

Take a look on ?basename help page. On Sun, Aug 29, 2010 at 12:07 PM, Hyunchul Kim hyunchul.kim@gmail.comwrote: Hi, all I made a simple R script to take the basename of a file without directory names. path.splitted - strsplit('/path/to/a_basename', '/') path.length -

[R] take component names of a list

Hi, all I want to take a vector of component names of a list. list.a - list('x'=1, 'y'=2) how to get a c('x','y') from list.a? Thanks in advance, Hyunchul [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] take component names of a list

Try this: names(list.a) On Sun, Aug 29, 2010 at 12:51 PM, Hyunchul Kim hyunchul.kim@gmail.comwrote: Hi, all I want to take a vector of component names of a list. list.a - list('x'=1, 'y'=2) how to get a c('x','y') from list.a? Thanks in advance, Hyunchul [[alternative

[R] need help for a repackaging problem!

Hy, I had a mistake on a function of a package i have created! I have solved it and then i repackaged and installed the modified package. I use to launch R from Excel! And so when i launch R, and next call my function from the workspace, i still find the problem on my function. And when i read on

Re: [R] take component names of a list

check at the online help file of function ?names(), and then try this: names(list.a) I hope it helps. Best, Dimitris On 8/29/2010 5:51 PM, Hyunchul Kim wrote: Hi, all I want to take a vector of component names of a list. list.a- list('x'=1, 'y'=2) how to get a c('x','y') from list.a?

Re: [R] Three-dimensional contingency table

On Aug 28, 2010, at 10:58 PM, Randklev, Charles wrote: Hi, I am trying to assemble a three-way contingency table examining the presence/absence of mussels, water depth (Depth1 and Depth 2) and water velocity (Flow vs. No Flow). I have written the following code listed below; however,

[R] Saving plot to tiff, with high resolution for publication ?

Hello all. A Journal we are sending an article to is asking for the following: To ensure the best reproduction quality of your figures we would appreciate high resolution files. All figures should preferably be in TIFF or EPS format... and should have the following resolution: Graph: 800 - 1200

[R] Interpreting cv.glm

Hey! Just a quick question: How do you interpret cross-validation error? For my model the function cv.glm returns a cross validation error of 0.31 does this mean to say that model has an accuracy of 0.69 (69 Percent of points are correctly classified)? Thanks, Mark -- View this message

[R] Finding source files automatically within a script

Hi there, Ive tried trawling the lists for a solution but I could not find any matches. I am typing up all my code on a Linux machine and I call this other script file from my script file using source(foo.r). Now sometimes i access my folder from my Windows machine at work (the files are on

Re: [R] Saving plot to tiff, with high resolution for publication ?

On Sun, Aug 29, 2010 at 5:46 PM, Tal Galili tal.gal...@gmail.com wrote: Hello all. A Journal we are sending an article to is asking for the following:  To ensure the best reproduction quality of your figures we would appreciate high resolution files. All figures should preferably be in TIFF

[R] Finding functions of large dataset for numerical integration

Hello everyone, I have been trying to figure out away to integrate under a spline produced by the package tps(fields). As the package does not output functions I am trying to do something similar to the trapezium rule. My data are 3D (x, y z). I have extracted from the surface output by Tps the

Re: [R] Saving plot to tiff, with high resolution for publication ?

Hi Tal, You have set the resolution, but you have not set the width/height. The res argument generally controls how many pixels per inch (PPI which is often used similarly to DPI). So if you want 800 DPI and you want it to be a 4 x 4 inch graph something like: tiff(file = temp.tiff, width =

[R] glm prb (Error in `contrasts-`(`*tmp*`, value = contr.treatment) : )

glm(A~B+C+D+E+F,family = binomial(link = logit),data=tre,na.action=na.omit) Error in `contrasts-`(`*tmp*`, value = contr.treatment) : contrasts can be applied only to factors with 2 or more levels however, glm(A~B+C+D+E,family = binomial(link = logit),data=tre,na.action=na.omit) runs fine

Re: [R] Saving plot to tiff, with high resolution for publication ?

On Aug 29, 2010, at 12:46 PM, Tal Galili wrote: Hello all. A Journal we are sending an article to is asking for the following: To ensure the best reproduction quality of your figures we would appreciate high resolution files. All figures should preferably be in TIFF or EPS format... and

Re: [R] glm prb (Error in `contrasts-`(`*tmp*`, value = contr.treatment) : )

On Aug 29, 2010, at 3:13 PM, moleps wrote: glm(A~B+C+D+E+F,family = binomial(link = logit),data=tre,na.action=na.omit) Error in `contrasts-`(`*tmp*`, value = contr.treatment) : contrasts can be applied only to factors with 2 or more levels however, glm(A~B+C+D+E,family = binomial(link =

Re: [R] Finding source files automatically within a script

On Sun, Aug 29, 2010 at 1:13 PM, Abhisek shi...@gmail.com wrote: Hi there, Ive tried trawling the lists for a solution but I could not find any matches.  I am typing up all my code on a Linux machine and I call this other script file from my script file using source(foo.r).  Now sometimes i

Re: [R] Finding functions of large dataset for numerical integration

On Aug 29, 2010, at 3:42 PM, sam.e wrote: Hello everyone, I have been trying to figure out away to integrate under a spline produced by the package tps(fields). As the package does not output functions I am trying to do something similar to the trapezium rule. My data are 3D (x, y

Re: [R] Question regarding significance of a covariate in a coxme survival

Using a p-value to make any kind of decision is questionable to begin with, and especially unreliable in choosing covariates in regression. Old studies, e.g. by Walls and Weeks and by Bendel and Afifi, have shown that if predictive ability is the criterion of interest and one wishes to use

Re: [R] Using termplot() with transformations of x

Hi the two models are identical because of having the same independent variable and dependent variable.they produce different termplot()s because of they base on different variables,one is x,the other is logx.see the lateral axis. Sure; this is all obvious from the code and the plots.

[R] CRAN (and crantastic) updates this week

CRAN (and crantastic) updates this week New packages * ProjectTemplate (0.1-2) Maintainer: John Myles White Author(s): John Myles White http://crantastic.org/packages/ProjectTemplate The ProjectTemplate package provides a function, create.project(), that automatically

[R] Putting legend *outside* plotting area

Is there a simple way to put a legend outside the plot area for a simple plot? I found... (at http://www.harding.edu/fmccown/R/) # Expand right side of clipping rect to make room for the legend *par(xpd=T, mar=par()$mar+c(0,0,0,4))* # Graph autos (transposing the matrix) using heat colors, #

[R] SVM comparison

I'm trying to run an epsilon regression model, and am comparing the results between e1071 and kernlab. I believe that I'm calling the ksvm and svm functions the same way but I'm getting different results: library(e1071); library(kernlab) ksvm(x=1:100, y=(1:100)/5, type=eps-svr,

Re: [R] Putting legend *outside* plotting area

Hi, On Aug 29, 2010, at 8:00 PM, Worik R wrote: Is there a simple way to put a legend outside the plot area for a simple plot? I found... (at http://www.harding.edu/fmccown/R/) # Expand right side of clipping rect to make room for the legend *par(xpd=T, mar=par()$mar+c(0,0,0,4))* #

Re: [R] Using termplot() with transformations of x

On Aug 26, 2010, at 7:10 PM, Peter Dunn wrote: Hi all I was playing with termplot(), and came across what appears to be an inconsistency. It would appreciate if someone could enlighten me: # First, generate some data: y - rnorm(100) x - runif(length(y),1,2) # Now find the log of x:

[R] log y 'axis' of histogram

All, I have been trying to get calls to hist(...) to be plotted with the y-axis having a log scale. I have tried: par(ylog=TRUE) I have also looked at the histogram package. Suggestions welcome. -- Derek M. Jones tel: +44 (0) 1252 520 667 Knowledge Software Ltd

Re: [R] log y 'axis' of histogram

How about computing the log of you variable and calling hist() on the log data. logy - log(y) Hhist(logy) John John Sorkin Chief Biostatistics and Informatics Univ. of Maryland School of Medicine Division of Gerontology and Geriatric Medicine jsor...@grecc.umaryland.edu -Original

[R] complete list of Sweave tags (control sequences)

Hello all, Is there a complete list of Sweave tags (control sequences) and their usage? For instance, I know a few blow. But I don’t really know how to use them. It seems to me that there is nowhere to find further information. I would really appreciate any input. Thanks! Heyi   The

Re: [R] log y 'axis' of histogram

Hi Derek, Here is an option using the package ggplot2: library(ggplot2) x - sample(x = 10:50, size = 50, replace = TRUE) qplot(x = x, geom = histogram) + scale_y_log() However, the log scale is often inappropriate for histograms, because the y-axis represents counts, which could potentially be

[R] Making cuts on multivariate data

I'm a newbie to R and I was hoping someone could answer a simple question. I want to read in an ASCII file with 3 columns - x,y,z. Let's say there is a lot of data - 100,000 entries. I then want to histogram x values that pass arbitrary (and complicated) cuts on y and/or z. Likewise, I

[R] while loop until end of file

Hi Guys, stumped by a simple problem. I would like to take a file of the form Pair group param1 1 D 10 1 D 10 1 R 10 1 D 10 2 D 10 2 D 10 2 D 10 2

Re: [R] while loop until end of file

Eh? ## First calculate the means: mns - with(alldata, tapply(param1, list(Pair, group), mean)) ## now put the results into a data frame res - data.frame(mns, dif = mns[, D] - mns[, R]) ## Then write it out if that's your thing. -Original Message- From: r-help-boun...@r-project.org

Re: [R] while loop until end of file

Hi Marcel, Not quite sure what you want the while loop for. Does this do what you want? mydat - read.table(textConnection( Pair group param1 1 D 10 1 D 10 1 R 10 1 D 10 2 D 10 2

Re: [R] Making cuts on multivariate data

On Aug 29, 2010, at 10:50 PM, Erik Ramberg wrote: I'm a newbie to R and I was hoping someone could answer a simple question. I want to read in an ASCII file with 3 columns - x,y,z. Let's say there is a lot of data - 100,000 entries. I then want to histogram x values that pass

[R] Johansen test

Hi all, I am working on exporting Johansen test statistics (Johansen test: ca.jo in package urca)to Excel. The problem is that the function output is not a number, but like this: # # Johansen-Procedure Unit Root / Cointegration Test #

[R] sum of some matrix columns

Hi, I have the following matrix cc - matrix (1:21, 3) cc[,3:4]- 0 cc [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,]1400 13 16 19 [2,]2500 14 17 20 [3,]3600 15 18 21 and I would like to sum just the values in columns

Re: [R] Making cuts on multivariate data

On Aug 30, 2010, at 12:57 AM, David Winsemius wrote: On Aug 29, 2010, at 10:50 PM, Erik Ramberg wrote: I'm a newbie to R and I was hoping someone could answer a simple question. I want to read in an ASCII file with 3 columns - x,y,z. Let's say there is a lot of data - 100,000 entries.

Re: [R] Question regarding significance of a covariate in a coxme survival

What statistical measure(s) tend to be answering ALL(?) question of practical interest? -- View this message in context: http://r.789695.n4.nabble.com/Re-Question-regarding-significance-of-a-covariate-in-a-coxme-survival-tp2399386p2399524.html Sent from the R help mailing list archive at

[R] Read in a all-character file and specify field separator and records separator

Dear list I used to use python or awk do preliminary process and then feed into R. In some circumstances, the data transmission becomes quite a pain. I am wondering if there is a convenient way to read in R text file (not data, text file in common sense) and specify field separator and records

Re: [R] Johansen test

Hi, I believe what you are looking for is in the teststat slot sjd.v...@teststat sjd.v...@teststat[1] # first one etc. HTH, Josh On Sun, Aug 29, 2010 at 9:12 PM, aurumor aurum_g...@yahoo.com.hk wrote: Hi all, I am working on exporting Johansen test statistics (Johansen test: ca.jo in

[R] LOOping problem with R

Dear Guys, I do converting codes from Fortran into R and got stuck in solving LOOPING procedure with R. In FORTRAN, it is (DO and END DO) for looping in the net. In R, it is (FOR with { }). I believe there is something wrong with my coding in R, do hope that you can help me solving following

Re: [R] Read in a all-character file and specify field separator and records separator

On Sun, Aug 29, 2010 at 9:18 PM, Yong Wang wangyo...@gmail.com wrote: Dear list I used to use python or awk do preliminary process and then feed into R. In some circumstances, the data transmission becomes quite a pain. I am wondering if there is a convenient way to read in R text file (not

Re: [R] Read in a all-character file and specify field separator and records separator

On Aug 30, 2010, at 12:18 AM, Yong Wang wrote: Dear list I used to use python or awk do preliminary process and then feed into R. In some circumstances, the data transmission becomes quite a pain. I am wondering if there is a convenient way to read in R text file (not data, text file in

Re: [R] sum of some matrix columns

On Aug 29, 2010, at 8:47 PM, Lorenzo Cattarino wrote: Hi, I have the following matrix cc - matrix (1:21, 3) cc[,3:4]- 0 cc [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,]1400 13 16 19 [2,]2500 14 17 20 [3,]3600 15 18 21