Re: [R] problem with labeling plots, possibly in font defaults
See http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-see-no-text-in-a-Quartz-plot_0021 And the default font is not serif ... that FAQ says it is Arial, but I do not know if that is current. Mac-specific questions to R-sig-mac please. (This must be Mac-specific as the default device, quartz(), is.) On 07/08/2014 23:24, David Winsemius wrote: On Aug 7, 2014, at 12:59 PM, Tim Blass wrote: Hello, I am using R 3.1.1 on a (four year old) MacBook, running OSX 10.9.4. I just tried making and labeling a plot as follows: x-rnorm(10) y-rnorm(10) plot(x,y) title(main=random points) which produces a scatter plot of the random points, but without the title and without any numbers along the axes. If I then run par(family=sans) plot(x,y,main=plot title) the plot has the title and the numbers on the axes (also and 'x' and 'y' appear as default labels for the axes). I do not know what is going on, but maybe there is some problem in the default font settings (I don't know if that could be an R issue or an issue specific to my Mac)? It hasn't happened to me recently (since updating from Leopard and SnowLeapard to Lion) but it used to happen pretty frequently that I would get a duplicate font that printed empty square boxes. (I wasn't the only one. It got reported several times on R-SIG-Mac.) One could fix that sort of problem by deleting the offending duplicate entry using Font Book.app Since this is happening with the default serif font, you would probably find the duplicate in Times. (It used to be happening to me with Symbol.) quartzFonts()$serif [1] Times-Roman Times-Bold Times-Italic Times-BoldItalic This is clearly not a big problem (at least for now) since I can put labels on plots by running par(), but if it is indicative of a larger underlying problem (or if there is a simple fix) I would like to know. Thank you! David Winsemius Alameda, CA, USA -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Some hpc problems with doMPI and runmpi (I know there is R-SIG-HPC)
Hello,
In your email, you speak about foreach()%dopar%, but in your script,
it is foreach()%do%.
Best,
Pascal
On Thu, Aug 7, 2014 at 7:19 PM, André Ziervogel
andre.ziervo...@psychol.uni-giessen.de wrote:
Dear R people,
I’ve been doing some hpc using R and openmpi. Unfortunately I’ve encoutred a
major problem and it’s nature is hard to pin down:
Essentially I call mpirun Rscipt … as soon as the script reaches a
foreach()%dopar% it halts indefinitely. I’ve attached the qsub script:
#!/bin/bash
#$ -S /bin/bash
#$ -N test_14
#$ -cwd
#$ -V
#$ -o /fhgfs/g61570/Spectral Databases/log/test_14_$JOB_ID
#$ -j y
#$ -q regular
#$ -pe openmpi 8
#$ -l h_rt=00:15:00
#$ -l h_vmem=1.9G
#$ -m eas
#$ -M andre.ziervo...@psychol.uni-giessen.de
module add gcc
module add openmpi/gcc/64/1.6.5
module add R/gcc/3.0.1
date #log start time
echo Number of slots . $NSLOTS
mpirun Rscript /fhgfs/g61570/Spectral\ Databases/test_10.r
/fhgfs/g61570/Spectral\ Databases/log/test_14.Rout
date
exit
and the R file:
suppressMessages(library('doMPI'))
skylla.cluster - startMPIcluster()
registerDoMPI(skylla.cluster)
cat(paste(COMM SIZE: , mpi.comm.size(0), cluster size: ,
clusterSize(skylla.cluster), \n,sep = ))
tmp.time - proc.time()
sample - foreach(i=seq(from=0, to=1000, by =1),.combine='c',.inorder=TRUE)
%do%
{
r - sqrt(i^2 + i^2) + .Machine$double.eps * factorial(i)
sin(r) / r
}
cat(paste(Processing seriell time: , \n, sep = ))
print(proc.time() - tmp.time)
#print(sample)
tmp.time - proc.time()
sample - foreach(i=seq(from=0, to=1000, by =1),.combine='c',.inorder=TRUE)
%dopar%
{
r - sqrt(i^2 + i^2) + .Machine$double.eps * factorial(i)
sin(r) / r
}
cat(paste(Processing parallel time: , \n, sep = ))
print(proc.time() - tmp.time)
#print(sample)
closeCluster(skylla.cluster)
# mpi.close.Rslaves()
# mpi.exit()
mpi.quit(save='no‘)
Any suggestions would be highly appreciated! Thanks!
Best
André
--
Dipl. Psych André Ziervogel
andre.ziervo...@psychol.uni-giessen.de
--
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--
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan
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Re: [R] Output from file.info()$mtime
On 07/08/2014 23:37, Fisher Dennis wrote: R 3.1.1 OS X (and Windows) Colleagues I have some code that manages files. Previously (as late as 3.1.0), the command: file.info(FILENAME)$mtime == “” yielded T/F Now, it triggers an error: Error in as.POSIXlt.character(x, tz, ...) : character string is not in a standard unambiguous format I looked through Peter Dalgaard’s list of changes in 3.1.1 and I cannot find anything that would explain the change between versions. I have fixed the problem. However, I am concerned that other problems may be lurking (i.e., the changes might affect other commands). Of note, I ran: str(file.info(FILENAME)$mtime) in both versions of R and the results did not differ Can anyone explain what changed so that I can search my code efficiently? Can you explain how that managed to give TRUE (sic)? It was always a POSIXct timestamp, and as such is never equal (assuming that your mail client mangled ASCII double quotes). I believe the relevant report is https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15829 Thanks in advance. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com __ 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, self-contained, reproducible code.
[R] map column name in matrix to multiple elements
Hi: I am requesting help on matrix mapping. I have a matrix that is 5000 rows x 3000 columns in R env. Matrix: A BC D E S1 0.01 0.2 -0.3 0.8-1 S2 -21.4 2.3 3.1-2 S3 -4 -3-20.42.1 I have another excel sheet, which when I import will have two columns.. ColMapelement A Apple A Arcade A Almira B Boy B Balloon B Bat C Cat . I want to create another matrix with elements as column names and map ColMap values onto elements. new matrix: Apple Arcade AlmiraBoy Ballon S1 0.01 0.010.01 0.2 0.2 S2 -2 -2-2 1.4 1.4 S3 -4 -4-4 -3 -3 .. I have no idea how I could do this in R. would any one help please. Thanks [[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, self-contained, reproducible code.
Re: [R] map column name in matrix to multiple elements
Using dput() to provide your data is enormously easier. Assuming the original column names of your data frame correspond to the ColMap column of the second data frame, it's very straightforward: mat - structure(list(A = c(0.01, -2, -4), B = c(0.2, 1.4, -3), C = c(-0.3, 2.3, -2), D = c(0.8, 3.1, 0.4), E = c(-1, -2, 2.1)), .Names = c(A, B, C, D, E), class = data.frame, row.names = c(S1, S2, S3)) matnames - structure(list(ColMap = c(A, A, A, B, B, B, C), element = c(Apple, Arcade, Almira, Boy, Balloon, Bat, Cat)), .Names = c(ColMap, element), class = data.frame, row.names = c(NA, -7L)) mat - mat[, matnames$ColMap] colnames(mat) - matnames$element R mat Apple Arcade Almira Boy Balloon Bat Cat S1 0.01 0.01 0.01 0.2 0.2 0.2 -0.3 S2 -2.00 -2.00 -2.00 1.4 1.4 1.4 2.3 S3 -4.00 -4.00 -4.00 -3.0-3.0 -3.0 -2.0 Sarah On Fri, Aug 8, 2014 at 9:04 AM, Adrian Johnson oriolebaltim...@gmail.com wrote: Hi: I am requesting help on matrix mapping. I have a matrix that is 5000 rows x 3000 columns in R env. Matrix: A BC D E S1 0.01 0.2 -0.3 0.8-1 S2 -21.4 2.3 3.1-2 S3 -4 -3-20.42.1 I have another excel sheet, which when I import will have two columns.. ColMapelement A Apple A Arcade A Almira B Boy B Balloon B Bat C Cat . I want to create another matrix with elements as column names and map ColMap values onto elements. new matrix: Apple Arcade AlmiraBoy Ballon S1 0.01 0.010.01 0.2 0.2 S2 -2 -2-2 1.4 1.4 S3 -4 -4-4 -3 -3 .. I have no idea how I could do this in R. would any one help please. Thanks -- Sarah Goslee http://www.functionaldiversity.org __ 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, self-contained, reproducible code.
[R] color palettes
Hi, Is there any way to take one color of each color family from a color palettes like rainbow? For ex, if there are different blues differentiated by intensity, hue etc, taking one of them. In this case, when using rainbow(n), then how to select 1 color of each family, for ex 1 blue, 1 red etc? It doesn't matter which intensity, hue etc is taken as long as 1 color from each family is taken. Thanks Carol [[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, self-contained, reproducible code.
Re: [R] Output from file.info()$mtime
Professor Ripley You asked “how that managed to give TRUE? (I apologize for the mangled quotes — the error occurred with plain quotes). All that I can say is that R versions = 3.1.0 allowed my code to execute without error. The bug report appears to address the issue. I typically review Dalgaard’s list of changes in each new version — it does not contain anything about this bug fix. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com On Aug 8, 2014, at 1:54 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 07/08/2014 23:37, Fisher Dennis wrote: R 3.1.1 OS X (and Windows) Colleagues I have some code that manages files. Previously (as late as 3.1.0), the command: file.info(FILENAME)$mtime == “” yielded T/F Now, it triggers an error: Error in as.POSIXlt.character(x, tz, ...) : character string is not in a standard unambiguous format I looked through Peter Dalgaard’s list of changes in 3.1.1 and I cannot find anything that would explain the change between versions. I have fixed the problem. However, I am concerned that other problems may be lurking (i.e., the changes might affect other commands). Of note, I ran: str(file.info(FILENAME)$mtime) in both versions of R and the results did not differ Can anyone explain what changed so that I can search my code efficiently? Can you explain how that managed to give TRUE (sic)? It was always a POSIXct timestamp, and as such is never equal (assuming that your mail client mangled ASCII double quotes). I believe the relevant report is https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15829 Thanks in advance. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com __ 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, self-contained, reproducible code.
Re: [R] color palettes
I would suggest not using pie charts and not trying to make 1000 color distinctions. Also read all of my original post and do some research. cols - hsv(.6, seq(0, 1, length.out=1000), .9) pie(1:1000, labels=, col=cols, border=NA) David From: carol white [mailto:wht_...@yahoo.com] Sent: Friday, August 8, 2014 9:03 AM To: David L Carlson Subject: Re: [R] color palettes Well I'm using 1000 colors in a pie chart and get the same color but different intensity. I can't fix myself as the number of colors are high. So what would you suggest? Thanks carol On Friday, August 8, 2014 3:58 PM, David L Carlson dcarl...@tamu.edumailto:dcarl...@tamu.edu wrote: I think your question is too vague to answer since we don't know what you are trying to do or how many colors you need. The easy answer is that you don't need to use rainbow() at all, just use color names: mycolors - c(red, green, blue, violet) and you will have one of each. For example, col=mycolors(2) will plot using green (and so will col=green). There are lots of color names in R: length(colors(distinct=TRUE)) [1] 502 The longer answer is that there are many color palettes and ways of selecting, manipulating, and choosing colors. The built in functions include palettes such as rainbow, heat.colors, terrain.colors, topo.colors, cm.colors, and gray and ways of specifying colors (in addition to using names) including rgb, hsv, and hcl. In addition, there are several packages for creating color palettes including RColorBrewer, colortools, colorspace, and munsell. - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org] On Behalf Of carol white Sent: Friday, August 8, 2014 8:27 AM To: r-help@r-project.orgmailto:r-help@r-project.org Subject: [R] color palettes Hi, Is there any way to take one color of each color family from a color palettes like rainbow? For ex, if there are different blues differentiated by intensity, hue etc, taking one of them. In this case, when using rainbow(n), then how to select 1 color of each family, for ex 1 blue, 1 red etc? It doesn't matter which intensity, hue etc is taken as long as 1 color from each family is taken. Thanks Carol [[alternative HTML version deleted]] __ R-help@r-project.orgmailto: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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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, self-contained, reproducible code.
Re: [R] color palettes
You might take a look at the RColorBrewer package. Sarah On Fri, Aug 8, 2014 at 9:26 AM, carol white wht_...@yahoo.com wrote: Hi, Is there any way to take one color of each color family from a color palettes like rainbow? For ex, if there are different blues differentiated by intensity, hue etc, taking one of them. In this case, when using rainbow(n), then how to select 1 color of each family, for ex 1 blue, 1 red etc? It doesn't matter which intensity, hue etc is taken as long as 1 color from each family is taken. Thanks Carol -- Sarah Goslee http://www.functionaldiversity.org __ 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, self-contained, reproducible code.
[R] FW: color palettes
I think your question is too vague to answer since we don't know what you are trying to do or how many colors you need. The easy answer is that you don't need to use rainbow() at all, just use color names: mycolors - c(red, green, blue, violet) and you will have one of each. For example, col=mycolors(2) will plot using green (and so will col=green). There are lots of color names in R: length(colors(distinct=TRUE)) [1] 502 The longer answer is that there are many color palettes and ways of selecting, manipulating, and choosing colors. The built in functions include palettes such as rainbow, heat.colors, terrain.colors, topo.colors, cm.colors, and gray and ways of specifying colors (in addition to using names) including rgb, hsv, and hcl. In addition, there are several packages for creating color palettes including RColorBrewer, colortools, colorspace, and munsell. - David L Carlson Department of Anthropology Texas AM University College Station, TX 77840-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of carol white Sent: Friday, August 8, 2014 8:27 AM To: r-help@r-project.org Subject: [R] color palettes Hi, Is there any way to take one color of each color family from a color palettes like rainbow? For ex, if there are different blues differentiated by intensity, hue etc, taking one of them. In this case, when using rainbow(n), then how to select 1 color of each family, for ex 1 blue, 1 red etc? It doesn't matter which intensity, hue etc is taken as long as 1 color from each family is taken. Thanks Carol [[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, self-contained, reproducible code. __ 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, self-contained, reproducible code.
Re: [R] color palettes
?rainbow ?col2rgb rainbow(8) col2rgb(rainbow(8)[5]) col2rgb(rainbow(8)[5])[1] col2rgb(rainbow(8)[5])[2] col2rgb(rainbow(8)[5])[3] On Fri, Aug 8, 2014 at 6:26 AM, carol white wht_...@yahoo.com wrote: Hi, Is there any way to take one color of each color family from a color palettes like rainbow? For ex, if there are different blues differentiated by intensity, hue etc, taking one of them. In this case, when using rainbow(n), then how to select 1 color of each family, for ex 1 blue, 1 red etc? It doesn't matter which intensity, hue etc is taken as long as 1 color from each family is taken. Thanks Carol [[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, self-contained, reproducible code. __ 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, self-contained, reproducible code.
[R] Need help on boot strapping
Dear Team,
I am getting this error while running the boot-strapping functions.
==
mod.db.hub-glm(TOTAL~1+IPD,family=poisson,data=db)
fit-fitted(mod.db.hub)
e-residuals(mod.db.hub)
X-model.matrix(mod.db.hub)
boot.huber.fixed-function(data,indices,maxit=20) {
Y-fit+e[indices]
mod-glm(Y~X-1,family=poisson,maxit=maxit)
coefficients(mod)
}
library(boot)
db.fix.boot-boot(db,boot.huber.fixed,2000,maxit=20)
db.fix.boot
boot.ci(db.fix.boot,index=1,type=c(bca,perc,poisson))
boot.ci(db.fix.boot,index=2,type=c(bca,perc,poisson))
==
Error in eval(expr, envir, enclos) :
negative values not allowed for the 'Poisson' family
In addition: Warning messages:
1: In dpois(y, mu, log = TRUE) : non-integer x = 25.006412
2: In dpois(y, mu, log = TRUE) : non-integer x = 26.969411
3: In dpois(y, mu, log = TRUE) : non-integer x = 66.352323
4: In dpois(y, mu, log = TRUE) : non-integer x = 61.083519
5: In dpois(y, mu, log = TRUE) : non-integer x = 20.596770
6: In dpois(y, mu, log = TRUE) : non-integer x = 43.428258
7: In dpois(y, mu, log = TRUE) : non-integer x = 1108.263554
8: In dpois(y, mu, log = TRUE) : non-integer x = 61.937982
9: In dpois(y, mu, log = TRUE) : non-integer x = 419.991213
10: In dpois(y, mu, log = TRUE) : non-integer x = 47.369133
Can you explain to me how to get rid of these ?
Thanks
Aravindhan
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[R] inverse Gaussian data transformation in R?
Anyone know of an R package that will allow me to do an inverse Gaussian/Wald distribution transform of my data (reaction times)? Thanks! __ 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, self-contained, reproducible code.
[R] boot strapping poisson getting warnings and negative values
Dear Team,
I am getting this error while running the boot-strapping functions.
==
mod.db.hub-glm(TOTAL~1+IPD,family=poisson,data=db)
fit-fitted(mod.db.hub)
e-residuals(mod.db.hub)
X-model.matrix(mod.db.hub)
boot.huber.fixed-function(data,indices,maxit=20) { Y-fit+e[indices]
mod-glm(Y~X-1,family=poisson,maxit=maxit)
coefficients(mod)
}
library(boot)
db.fix.boot-boot(db,boot.huber.fixed,2000,maxit=20)
db.fix.boot
boot.ci(db.fix.boot,index=1,type=c(bca,perc,poisson))
boot.ci(db.fix.boot,index=2,type=c(bca,perc,poisson))
==
Error in eval(expr, envir, enclos) :
negative values not allowed for the 'Poisson' family In addition: Warning
messages:
1: In dpois(y, mu, log = TRUE) : non-integer x = 25.006412
2: In dpois(y, mu, log = TRUE) : non-integer x = 26.969411
3: In dpois(y, mu, log = TRUE) : non-integer x = 66.352323
4: In dpois(y, mu, log = TRUE) : non-integer x = 61.083519
5: In dpois(y, mu, log = TRUE) : non-integer x = 20.596770
6: In dpois(y, mu, log = TRUE) : non-integer x = 43.428258
7: In dpois(y, mu, log = TRUE) : non-integer x = 1108.263554
8: In dpois(y, mu, log = TRUE) : non-integer x = 61.937982
9: In dpois(y, mu, log = TRUE) : non-integer x = 419.991213
10: In dpois(y, mu, log = TRUE) : non-integer x = 47.369133
Can you explain to me how to get rid of these ?
Thanks
Aravindhan
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] glmnet, Error in apply(nz, 1, median) : dim(X) must have a positive length
Hello all, In glmnet package, cv.glmnet is giving error data(iris) df-data.frame(iris$Sepal.Length, iris$Sepal.Width, iris$Petal.Length, iris$Petal.Width) x- as.matrix(df) y- as.numeric(iris$Species) fit = glmnet(x, y, family = multinomial, type.multinomial = grouped) plot(fit, xvar = lambda, label = TRUE, type.coef = 2norm) cvfit=cv.glmnet(x, y, family=multinomial, type.multinomial = grouped, parallel = TRUE) Error in apply(nz, 1, median) : dim(X) must have a positive length In addition: Warning message: from glmnet Fortran code (error code -62); Convergence for 62th lambda value not reached after maxit=10 iterations; solutions for larger lambdas returned Why am I getting this error? Thanks [[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, self-contained, reproducible code.
Re: [R] Problems installing Packages
Dear Sven, I am running into this exact some problem in Ubuntu 14.04. I have R 3.1.1 freshly installed and OpenJDK 7 (I do not need BLAS, as far as I know). Trying to install rj and rj.dg I get the exact same error messages as you were getting Error: cannot determine complete Java config. Were you able to solve this and install these packages? Thank you, Luís __ 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, self-contained, reproducible code.
Re: [R] boot strapping poisson getting warnings and negative values
On 08-08-2014, at 16:12, K Aravindhan vind1...@yahoo.co.in wrote:
Dear Team,
I am getting this error while running the boot-strapping functions.
do you really have to post identical messages within 4 to 5 minutes?
One message is enough and be patient and wait!
Berend
==
mod.db.hub-glm(TOTAL~1+IPD,family=poisson,data=db)
fit-fitted(mod.db.hub)
e-residuals(mod.db.hub)
X-model.matrix(mod.db.hub)
boot.huber.fixed-function(data,indices,maxit=20) { Y-fit+e[indices]
mod-glm(Y~X-1,family=poisson,maxit=maxit)
coefficients(mod)
}
library(boot)
db.fix.boot-boot(db,boot.huber.fixed,2000,maxit=20)
db.fix.boot
boot.ci(db.fix.boot,index=1,type=c(bca,perc,poisson))
boot.ci(db.fix.boot,index=2,type=c(bca,perc,poisson))
==
Error in eval(expr, envir, enclos) :
negative values not allowed for the 'Poisson' family In addition: Warning
messages:
1: In dpois(y, mu, log = TRUE) : non-integer x = 25.006412
2: In dpois(y, mu, log = TRUE) : non-integer x = 26.969411
3: In dpois(y, mu, log = TRUE) : non-integer x = 66.352323
4: In dpois(y, mu, log = TRUE) : non-integer x = 61.083519
5: In dpois(y, mu, log = TRUE) : non-integer x = 20.596770
6: In dpois(y, mu, log = TRUE) : non-integer x = 43.428258
7: In dpois(y, mu, log = TRUE) : non-integer x = 1108.263554
8: In dpois(y, mu, log = TRUE) : non-integer x = 61.937982
9: In dpois(y, mu, log = TRUE) : non-integer x = 419.991213
10: In dpois(y, mu, log = TRUE) : non-integer x = 47.369133
Can you explain to me how to get rid of these ?
Thanks
Aravindhan
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Re: [R] dynamic runSum
On Thu, Aug 7, 2014 at 9:32 AM, amarjit chandhial a.chandh...@btinternet.com wrote: Hello, runSum calculates a running sum looking back a fixed distance n, e.g. 20. How do I calculate a dynamic runSum function for an xts object? In otherwords, I want to calculate a running sum at each point in time looking back a variable distance. In this example, values governed by the vector VL. The width argument in rollapplyr in the zoo package can be a vector. It can't be NA though so we have used 1 in those cases here and at the end used na.omit to get rid of the junk at the beginning: na.omit(rollapplyr(acf1, ifelse(is.na(acf1$VL), 1, acf1$VL), sum)) __ 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, self-contained, reproducible code.
[R] circlize package: some error message
I recently tried to run some sample code from R package: circlize, and got an error message (please see below) = library(circlize) circos.genomicInitialize(df) df = data.frame(name = c(TP53, TP63, TP73), + start = c(7565097, 189349205, 3569084), + end = c(7590856, 189615068, 3652765), + stringsAsFactors = FALSE) df name start end 1 TP53 7565097 7590856 2 TP63 189349205 189615068 3 TP73 3569084 3652765 circos.genomicInitialize(df) circos.clear() circos.genomicInitialize(df, major.by = 1) Error in seq.default(xlim[1], 10^nchar(round(max(x2 - x1 + 1))), by = major.by) : wrong sign in 'by' argument === And my session information: sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8LC_COLLATE=C [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] circlize_0.1.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0Biobase_2.24.0 BiocGenerics_0.10.0 [4] DBI_0.2-7 DESeq2_1.4.5GenomeInfoDb_1.0.2 [7] GenomicRanges_1.16.3IRanges_1.22.9 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 Rcpp_0.11.2 RcppArmadillo_0.4.320.0 [13] XML_3.98-1.1XVector_0.4.0 annotate_1.42.1 [16] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.1 [19] lattice_0.20-29 locfit_1.5-9.1 parallel_3.1.1 [22] splines_3.1.1 stats4_3.1.1survival_2.37-7 [25] xtable_1.7-3 === Wonder anyone could please help me out with this? Thank you very much for your time.:) [[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, self-contained, reproducible code.
[R] how to process multiple data files using R loop
I have 16 files and would like to check the information of their first two
lines, what I did:
ls(pattern=P_)
[1] P_3_utr_source_data P_5_utr_source_data
[3] P_exon_per_gene_cds_source_data P_exon_per_gene_source_data
[5] P_exon_source_data P_first_exon_oncds_source_data
[7] P_first_intron_oncds_source_data P_first_intron_ongene_source_data
[9] P_firt_exon_ongene_source_data P_gene_cds_source_data
[11] P_gene_source_data P_intron_source_data
[13] P_last_exon_oncds_source_data P_last_exon_ongene_source_data
[15] P_last_intron_oncds_source_data P_last_intron_ongene_source_data
for(i in ls(pattern=P_)){head(i, 2)}
It obviously does not work since nothing came out
What I would like to see for the output is :
head(P_3_utr_source_data,2)
V1
1 1
2 1
head(P_5_utr_source_data,2)
V1
1 1
2 1
.
.
.
Could anybody help me with this?
Thank you very much for your time:)
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] Installing manual package problem
Running R 3.03 on Windows 7 I am trying to install a package from a github repository. https://github.com/google/glassbox I downloaded the repository as a zip file, extracted it to get the glassbox folder and re-zipped it with 7-zip. I then ran #-Start code---# install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL, type=source) #-# The output message said Installing package into âC:/Users/jholland/Documents/R/win-library/3.0â (as âlibâ is unspecified) library(glassbox) Error in library(glassbox) : âglassboxâ is not a valid installed package I'm not sure what I'm doing wrong. When I look in the R library folder (...R/win-library/3.0) I see the glassbox folder there. I'm new to using packages not from the CRAN list so I'm trying to learn fast. I tried some searching and this seems to be what I'm suppossed to do, but perhaps I need to use dev mode ? Thank you for the help. ~James [[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, self-contained, reproducible code.
Re: [R] how to process multiple data files using R loop
On Aug 8, 2014, at 11:25 AM, Fix Ace wrote:
I have 16 files and would like to check the information of their first two
lines, what I did:
ls(pattern=P_)
[1] P_3_utr_source_data P_5_utr_source_data
[3] P_exon_per_gene_cds_source_data P_exon_per_gene_source_data
[5] P_exon_source_dataP_first_exon_oncds_source_data
[7] P_first_intron_oncds_source_data P_first_intron_ongene_source_data
[9] P_firt_exon_ongene_source_dataP_gene_cds_source_data
[11] P_gene_source_dataP_intron_source_data
[13] P_last_exon_oncds_source_data P_last_exon_ongene_source_data
[15] P_last_intron_oncds_source_data P_last_intron_ongene_source_data
The results from `ls()` are not actual R names but rather are character
vectors. To promote a character value to an R language-name you need the
`get` function:
for(i in ls(pattern=P_)){head(i, 2)}
for(i in ls(pattern=P_)){ head(get(i), 2)} # Should work.
David.
It obviously does not work since nothing came out
What I would like to see for the output is :
head(P_3_utr_source_data,2)
V1
1 1
2 1
head(P_5_utr_source_data,2)
V1
1 1
2 1
.
.
.
Could anybody help me with this?
Thank you very much for your time:)
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
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Re: [R] how to process multiple data files using R loop
for(i in ls(pattern=P_)){ head(get(i), 2)} # Should work.
You also need to use print(head(...)) if you want to see the printed
output from each iteration.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Aug 8, 2014 at 4:36 PM, David Winsemius dwinsem...@comcast.net wrote:
On Aug 8, 2014, at 11:25 AM, Fix Ace wrote:
I have 16 files and would like to check the information of their first two
lines, what I did:
ls(pattern=P_)
[1] P_3_utr_source_data P_5_utr_source_data
[3] P_exon_per_gene_cds_source_data P_exon_per_gene_source_data
[5] P_exon_source_dataP_first_exon_oncds_source_data
[7] P_first_intron_oncds_source_data P_first_intron_ongene_source_data
[9] P_firt_exon_ongene_source_dataP_gene_cds_source_data
[11] P_gene_source_dataP_intron_source_data
[13] P_last_exon_oncds_source_data P_last_exon_ongene_source_data
[15] P_last_intron_oncds_source_data P_last_intron_ongene_source_data
The results from `ls()` are not actual R names but rather are character
vectors. To promote a character value to an R language-name you need the
`get` function:
for(i in ls(pattern=P_)){head(i, 2)}
for(i in ls(pattern=P_)){ head(get(i), 2)} # Should work.
David.
It obviously does not work since nothing came out
What I would like to see for the output is :
head(P_3_utr_source_data,2)
V1
1 1
2 1
head(P_5_utr_source_data,2)
V1
1 1
2 1
.
.
.
Could anybody help me with this?
Thank you very much for your time:)
[[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, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Installing manual package problem
I re-zipped it because when I downloaded from GitHub, it had the actual glassbox folder within the glassbox-master folder, so I zipped that glassbox folder because my understanding was the install.package On Aug 8, 2014, at 1:29 PM, James Holland wrote: Running R 3.03 on Windows 7 I am trying to install a package from a github repository. https://github.com/google/glassbox I downloaded the repository as a zip file, extracted it to get the glassbox folder and re-zipped it with 7-zip. Why? I then ran #-Start code---# install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL, type=source) I'm a Mac user but when I look at the directory created by expanding that zip file, it appears ready to just move/drag to the library without further installation. It is, however, not named 'glassbox' but rather 'glassbox-master' so perhaps you forgot to rename it? The output message said Installing package into âC:/Users/jholland/Documents/R/win-library/3.0â (as âlibâ is unspecified) library(glassbox) Error in library(glassbox) : âglassboxâ is not a valid installed package I'm not sure what I'm doing wrong. When I look in the R library folder (...R/win-library/3.0) I see the glassbox folder there. I'm new to using packages not from the CRAN list so I'm trying to learn fast. I tried some searching and this seems to be what I'm suppossed to do, but perhaps I need to use dev mode ? Thank you for the help. ~James [[alternative HTML version deleted]] This is a plain text mailing list. -- David Winsemius Alameda, CA, USA [[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, self-contained, reproducible code.
Re: [R] Logical operators and named arguments
On Sat, Aug 9, 2014 at 9:56 AM, Patrick Burns pbu...@pburns.seanet.com
wrote:
On 07/08/2014 07:21, Joshua Wiley wrote:
Hi Ryan,
It does work, but the *apply family of functions always pass to the first
argument, so you can specify e2 = , but not e1 =. For example:
sapply(1:3, ``, e2 = 2)
[1] FALSE FALSE TRUE
That is not true:
But it is passed as the first argument, not by name, but positionally. The
reason it works with your gt() is because R with regular functions is
flexible:
f - function(x, y) x y
f(1:3, x = 2)
[1] TRUE FALSE FALSE
but primitives ARE positionally matched
``(1:3, 2)
[1] FALSE FALSE TRUE
``(1:3, e1 = 2)
[1] FALSE FALSE TRUE
gt - function(x, y) x y
sapply(1:3, gt, y=2)
[1] FALSE FALSE TRUE
sapply(1:3, gt, x=2)
[1] TRUE FALSE FALSE
Specifying the first argument(s) in an apply
call is a standard way of getting flexibility.
I'd hazard to guess that the reason the original
version doesn't work is because `` is Primitive.
There's speed at the expense of not behaving quite
the same as typical functions.
Pat
From ?sapply
'lapply' returns a list of the same length as 'X', each element of
which is the result of applying 'FUN' to the corresponding element
of 'X'.
so `` is applied to each element of 1:3
``(1, ...)
``(2, ...)
``(3, ...)
and if e2 is specified than that is passed
``(1, 2)
``(2, 2)
``(3, 2)
Further, see ?Ops
If the members of this group are called as functions, any
argument names are removed to ensure that positional matching
is always used.
and you can see this at work:
``(e1 = 1, e2 = 2)
[1] FALSE
``(e2 = 1, e1 = 2)
[1] FALSE
If you want to the flexibility to specify which argument the elements of X
should be *applied to, use a wrapper:
sapply(1:3, function(x) ``(x, 2))
[1] FALSE FALSE TRUE
sapply(1:3, function(x) ``(2, x))
[1] TRUE FALSE FALSE
HTH,
Josh
On Thu, Aug 7, 2014 at 2:20 PM, Ryan rec...@bwh.harvard.edu wrote:
Hi,
I'm wondering why calling with named arguments doesn't work as
expected:
args()
function (e1, e2)
NULL
sapply(c(1,2,3), ``, e2=0)
[1] TRUE TRUE TRUE
sapply(c(1,2,3), ``, e1=0)
[1] TRUE TRUE TRUE
Shouldn't the latter be FALSE?
Thanks for any help,
Ryan
The information in this e-mail is intended only for th...{{dropped:23}}
__
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PLEASE do read the posting guide http://www.R-project.org/
posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @burnsstat @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of:
'Impatient R'
'The R Inferno'
'Tao Te Programming')
--
Joshua F. Wiley
Ph.D. Student, UCLA Department of Psychology
http://joshuawiley.com/
Senior Analyst, Elkhart Group Ltd.
http://elkhartgroup.com
Office: 260.673.5518
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Re: [R] color palettes
On Fri, 8 Aug 2014 06:26:35 AM carol white wrote: Hi, Is there any way to take one color of each color family from a color palettes like rainbow? For ex, if there are different blues differentiated by intensity, hue etc, taking one of them. In this case, when using rainbow(n), then how to select 1 color of each family, for ex 1 blue, 1 red etc? It doesn't matter which intensity, hue etc is taken as long as 1 color from each family is taken. Hi Carol, Since you have asked a question about a fundamental aspect of graphic representation, I'll try to answer it. Be warned, it will be a rather discursive answer. Whenever we try to communicate information about a number of things, where the information is different for each thing, it is essential to securely link the correct information to each thing. In compact graphic representations such as R plots, this usually resolves to labels of some sort. So we could construct a pie chart of the number of emails sent by each person in the present discourse using the names of the people involved. If we simply label each sector of the resulting plot with the names of the people, it will be reasonably informative in displaying each person's contribution. If we venture beyond the comfortable pale of the R help list and try to do this with something like Twitter, where I understand there may be thousands or even millions of contributors on a subject, the pie chart blurs into a chromatic dazzle with an unintelligible fringe of names. We might try to rescue the situation by aggregating the tweets into a few categories such as helpful, sarcastic and noise, but this does not solve the problem of how to display the comparative contributions of the twits involved. So one answer to your question of How can I intelligibly label hundreds of things with colors? may be You can't unless your audience is made up of spectrographs. Plots that attempt to display information about too many things using line types, symbol types and colors often simply confuse the audience. My feeling is that it is the responsibility of the person choosing the method of communication to make sure that it communicates well. So if we want to display something meaningful about the hypothetical pandemonium of tweets above, we might choose to display the categories (helpful, sarcastic and noise) broken down by the sex of the twits. Perhaps in your case you might want to break down the functional category of the genes you are examining by the up- or down-regulation of those genes in different cell types. Your question touches things like How many letters should there be in the alphabet? and How many acronyms for psychological tests can be meaningfully used in a paragraph? At any rate, I thank you for giving me an idea about graphic illustration. Jim __ 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, self-contained, reproducible code.
Re: [R] circlize package: some error message
On Aug 8, 2014, at 11:28 AM, Fix Ace wrote: I recently tried to run some sample code from R package: circlize, and got an error message (please see below) = library(circlize) circos.genomicInitialize(df) df = data.frame(name = c(TP53, TP63, TP73), + start = c(7565097, 189349205, 3569084), + end = c(7590856, 189615068, 3652765), + stringsAsFactors = FALSE) df name start end 1 TP53 7565097 7590856 2 TP63 189349205 189615068 3 TP73 3569084 3652765 circos.genomicInitialize(df) circos.clear() circos.genomicInitialize(df, major.by = 1) Error in seq.default(xlim[1], 10^nchar(round(max(x2 - x1 + 1))), by = major.by) : wrong sign in 'by' argument === And my session information: sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8LC_COLLATE=C [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] circlize_0.1.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.26.0Biobase_2.24.0 BiocGenerics_0.10.0 [4] DBI_0.2-7 DESeq2_1.4.5GenomeInfoDb_1.0.2 [7] GenomicRanges_1.16.3IRanges_1.22.9 RColorBrewer_1.0-5 [10] RSQLite_0.11.4 Rcpp_0.11.2 RcppArmadillo_0.4.320.0 [13] XML_3.98-1.1XVector_0.4.0 annotate_1.42.1 [16] genefilter_1.46.1 geneplotter_1.42.0 grid_3.1.1 [19] lattice_0.20-29 locfit_1.5-9.1 parallel_3.1.1 [22] splines_3.1.1 stats4_3.1.1survival_2.37-7 [25] xtable_1.7-3 === Wonder anyone could please help me out with this? Thank you very much for your time.:) [[alternative HTML version deleted]] Your failure to post in plain text makes this message very difficult to read. Unless there is someone with more patience than I have who responds in the next 12 hours, you might consider reposting after reading the Posing Guide. -- David Winsemius Alameda, CA, USA __ 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, self-contained, reproducible code.
Re: [R] Installing manual package problem
On Aug 8, 2014, at 1:29 PM, James Holland wrote: Running R 3.03 on Windows 7 I am trying to install a package from a github repository. https://github.com/google/glassbox I downloaded the repository as a zip file, extracted it to get the glassbox folder and re-zipped it with 7-zip. Why? I then ran #-Start code---# install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL, type=source) I'm a Mac user but when I look at the directory created by expanding that zip file, it appears ready to just move/drag to the library without further installation. It is, however, not named 'glassbox' but rather 'glassbox-master' so perhaps you forgot to rename it? The output message said Installing package into ‘C:/Users/jholland/Documents/R/win-library/3.0’ (as ‘lib’ is unspecified) library(glassbox) Error in library(glassbox) : ‘glassbox’ is not a valid installed package I'm not sure what I'm doing wrong. When I look in the R library folder (...R/win-library/3.0) I see the glassbox folder there. I'm new to using packages not from the CRAN list so I'm trying to learn fast. I tried some searching and this seems to be what I'm suppossed to do, but perhaps I need to use dev mode ? Thank you for the help. ~James [[alternative HTML version deleted]] This is a plain text mailing list. -- David Winsemius Alameda, CA, USA __ 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, self-contained, reproducible code.
Re: [R] Logical operators and named arguments
On 07/08/2014 07:21, Joshua Wiley wrote:
Hi Ryan,
It does work, but the *apply family of functions always pass to the first
argument, so you can specify e2 = , but not e1 =. For example:
sapply(1:3, ``, e2 = 2)
[1] FALSE FALSE TRUE
That is not true:
gt - function(x, y) x y
sapply(1:3, gt, y=2)
[1] FALSE FALSE TRUE
sapply(1:3, gt, x=2)
[1] TRUE FALSE FALSE
Specifying the first argument(s) in an apply
call is a standard way of getting flexibility.
I'd hazard to guess that the reason the original
version doesn't work is because `` is Primitive.
There's speed at the expense of not behaving quite
the same as typical functions.
Pat
From ?sapply
'lapply' returns a list of the same length as 'X', each element of
which is the result of applying 'FUN' to the corresponding element
of 'X'.
so `` is applied to each element of 1:3
``(1, ...)
``(2, ...)
``(3, ...)
and if e2 is specified than that is passed
``(1, 2)
``(2, 2)
``(3, 2)
Further, see ?Ops
If the members of this group are called as functions, any
argument names are removed to ensure that positional matching
is always used.
and you can see this at work:
``(e1 = 1, e2 = 2)
[1] FALSE
``(e2 = 1, e1 = 2)
[1] FALSE
If you want to the flexibility to specify which argument the elements of X
should be *applied to, use a wrapper:
sapply(1:3, function(x) ``(x, 2))
[1] FALSE FALSE TRUE
sapply(1:3, function(x) ``(2, x))
[1] TRUE FALSE FALSE
HTH,
Josh
On Thu, Aug 7, 2014 at 2:20 PM, Ryan rec...@bwh.harvard.edu wrote:
Hi,
I'm wondering why calling with named arguments doesn't work as
expected:
args()
function (e1, e2)
NULL
sapply(c(1,2,3), ``, e2=0)
[1] TRUE TRUE TRUE
sapply(c(1,2,3), ``, e1=0)
[1] TRUE TRUE TRUE
Shouldn't the latter be FALSE?
Thanks for any help,
Ryan
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Re: [R] Installing manual package problem
I re-zipped it because when I downloaded from GitHub, it had the actual glassbox folder within the glassbox-master folder, so I zipped that glassbox folder because my understanding was the install.package function only works on zipped files. And it does seem like it installed within my R library (I see the glassbox folder in there) but the library function doesn't attach the package. ~James On Fri, Aug 8, 2014 at 6:50 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 8, 2014, at 1:29 PM, James Holland wrote: Running R 3.03 on Windows 7 I am trying to install a package from a github repository. https://github.com/google/glassbox I downloaded the repository as a zip file, extracted it to get the glassbox folder and re-zipped it with 7-zip. Why? I then ran #-Start code---# install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL, type=source) I'm a Mac user but when I look at the directory created by expanding that zip file, it appears ready to just move/drag to the library without further installation. It is, however, not named 'glassbox' but rather 'glassbox-master' so perhaps you forgot to rename it? The output message said Installing package into âC:/Users/jholland/Documents/R/win-library/3.0â (as âlibâ is unspecified) library(glassbox) Error in library(glassbox) : âglassboxâ is not a valid installed package I'm not sure what I'm doing wrong. When I look in the R library folder (...R/win-library/3.0) I see the glassbox folder there. I'm new to using packages not from the CRAN list so I'm trying to learn fast. I tried some searching and this seems to be what I'm suppossed to do, but perhaps I need to use dev mode ? Thank you for the help. ~James [[alternative HTML version deleted]] This is a plain text mailing list. -- David Winsemius Alameda, CA, USA [[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, self-contained, reproducible code.
Re: [R] Installing manual package problem
The obvious suggestion is to not repack the package file. You should also be sure to read the Posting Guide, which points out that this is a plain text mailing list (HTML is not a what-you-see-is-what-we-see format). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On August 8, 2014 1:29:14 PM PDT, James Holland holland.ag...@gmail.com wrote: Running R 3.03 on Windows 7 I am trying to install a package from a github repository. https://github.com/google/glassbox I downloaded the repository as a zip file, extracted it to get the glassbox folder and re-zipped it with 7-zip. I then ran #-Start code---# install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL, type=source) #-# The output message said Installing package into ���C:/Users/jholland/Documents/R/win-library/3.0��� (as ���lib��� is unspecified) library(glassbox) Error in library(glassbox) : ���glassbox��� is not a valid installed package I'm not sure what I'm doing wrong. When I look in the R library folder (...R/win-library/3.0) I see the glassbox folder there. I'm new to using packages not from the CRAN list so I'm trying to learn fast. I tried some searching and this seems to be what I'm suppossed to do, but perhaps I need to use dev mode ? Thank you for the help. ~James [[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, self-contained, reproducible code. __ 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, self-contained, reproducible code.
Re: [R] how to process multiple data files using R loop
On 09/08/14 06:25, Fix Ace wrote: I have 16 files and would like to check the information of their first two lines, what I did: ls(pattern=P_) [1] P_3_utr_source_data P_5_utr_source_data [3] P_exon_per_gene_cds_source_data P_exon_per_gene_source_data [5] P_exon_source_dataP_first_exon_oncds_source_data [7] P_first_intron_oncds_source_data P_first_intron_ongene_source_data [9] P_firt_exon_ongene_source_dataP_gene_cds_source_data [11] P_gene_source_dataP_intron_source_data [13] P_last_exon_oncds_source_data P_last_exon_ongene_source_data [15] P_last_intron_oncds_source_data P_last_intron_ongene_source_data SNIP Point of order: You do ***NOT*** have 16 files as it stands. The output from ls() indicates that you have 16 ***objects*** (presumably data frames) in your work space or global environment. (If the data were originally in 16 separate files, these files have apparently already been read into R.) If you are going to use R, learn to distinguish the relevant concepts and to use the appropriate terminology. Otherwise you will confuse everyone, including yourself, and get things totally wrong. It is really no more difficult to use correct terminology than it is to use incorrect terminology --- and the former has the advantage of not misleading all concerned. Dave Winsemius has already told you how to solve your immediate problem, using get(). cheers, Rolf Turner -- Rolf Turner Technical Editor ANZJS __ 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, self-contained, reproducible code.
[R] grofit package problem inputting dataset
I've recently wanted to analyze some data sets of growth curves; so, I decided to try out the grofit package the dataset inputting gave me some issues. I've been trying to replicate the example from the grofit package with R foo - ran.data(100, 25) time - foo$time data - foo$data write.csv(file=data.csv, foo) sink(file=sink.txt) foo sink() also to see if there is another problem I'm missing i've used sink() to see the actual output of this data. The sink call provides a dataframe object, however I'm trying to use my own data in this. Is there a way to create the dataframe object in excel (I've tried following the example from the write.csv() output). I know there is a problem with the input method by following the .csv output and i could use follow the sink() output to create my data frame object; however, I'm not sure about how i would do this with a large dataset with lets say 1000 data points. Has anyone ran into this issue and is there a quick work around? the sink() output $data X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 X16 X17 1 Test I A 0.06195419 0.314959772 0.398263408 0.091132317 1.012083039 0.35122189 1.78719671 2.47453614 3.25305005 3.9829927 5.2863775 5.8576975 7.2154323 8.501599 8.405278 2 Test I B 0.09543701 0.441797809 -0.345308045 0.462532336 1.324153423 1.20722268 1.71422886 2.40135394 2.79558398 3.8981917 5.3614344 5.8423570 6.8511538 7.192188 8.344946 3 Test I C 0.16386938 -0.178975999 0.464790443 0.325264753 0.033088580 0.79395919 0.63525411 1.71685521 2.62738577 2.5209004 4.4535178 4.9102966 6.8867905 6.996433 7.553863 4 Test I D 0.14198175 0.100778235 -0.164231759 -0.322266709 0.571067561 1.24234632 1.54056165 1.96933568 2.97097469 3.7711348 3.8414402 5.2768758 5.6688960 7.041779 7.651093 5 Test I E 0.25390711 0.039312093 -0.463351713 0.628339527 0.418403984 0.56460811 1.26348242 1.56823878 1.93588943 3.3141874 3.0360158 3.7567956 5.6896075 5.873556 6.524754 6 Test I F 0.22319304 -0.076464713 0.074501305 -0.160924707 0.384392150 0.76412340 1.36118116 1.50356468 2.53322106 3.4924520 4.5054475 4.6222326 5.5347148 6.349000 7.482548 7 Test I G 0.28095487 -0.728248588 0.479450323 0.542078371 0.757460716 0.10292177 1.01113655 1.14448036 2.19976257 3.3030023 3.0848547 4.1877661 5.2832997 5.485825 6.375234 8 Test I A 0.32135093 -0.036980401 -0.068313544 -0.059620107 0.440995143 0.48424749 0.65644521 1.38482000 2.05964880 2.2548116 2.6813025 3.5085200 4.7988415 5.017753 5.405950 9 Test I B 0.31930456 0.169104577 0.100637447 0.070003632 0.304209263 1.72301034 ... $time [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9][,10][,11][,12][,13][,14][,15][,16][,17] [,18][,19][,20] [1,] 1.105562 2.429351 3.303547 4.941900 5.370762 6.939251 7.546835 8.400435 9.602104 10.85058 11.27732 12.12658 13.80886 14.03953 15.88684 16.63256 17.85349 18.29452 19.94482 20.74473 [2,] 1.842357 2.183849 3.528340 4.761010 5.610834 6.473241 7.771216 8.575116 9.544966 10.79126 11.61007 12.91479 13.21070 14.27869 15.30520 16.32062 17.71822 18.94936 19.58821 20.46276 [3,] 1.787510 2.734994 3.063325 4.788528 5.676988 6.096337 7.373838 8.047332 9.042756 10.35715 11.47604 12.84095 13.14183 14.77351 15.81132 16.63433 17.37387 18.51372 19.83332 20.74899 [4,] 1.074662 2.386418 3.734951 4.889867 5.994899 6.483399 7.603956 8.826142 9.536391 10.01653 11.03079 12.60530 13.00965 14.70169 15.17157 16.75678 17.85311 18.22975 19.28407 20.73184 [5,] 1.748113 2.185892 3.236870 4.294671 5.093055 6.910312 7.881226 8.067719 9.632505 10.26807 11.03523 12.75277 13.66110 14.30814 15.61313 16.62628 17.98222 18.95378 19.46946 20.17275 the write.csv() output data.X1 data.X2 data.X3 data.X4 data.X5 data.X6 data.X7 data.X8 data.X9 1 Test I A 0.061954188 0.314959772 0.398263408 0.091132317 1.012083039 0.351221894 1.787196715 2 Test I B 0.095437013 0.441797809 -0.345308045 0.462532336 1.324153423 1.207222678 1.714228858 3 Test I C 0.16386938 -0.1789759990.464790443 0.325264753 0.03308858 0.793959194 0.63525411 4 Test I D 0.141981749 0.100778235 -0.164231759 -0.3222667090.571067561 1.242346317 1.540561647 5 Test I E 0.253907113 0.039312093 -0.463351713 0.628339527 0.418403984 0.564608113 1.263482418 6 Test I F 0.223193041 -0.0764647130.074501305 -0.1609247070.38439215 0.764123401 1.361181159 7 Test I G 0.280954867 -0.7282485880.479450323 0.542078371 0.757460716 0.102921772 1.011136548 8
