Re: [R] Optimisation and NaN Errors using clm() and clmm()
On 18 April 2013 18:38, Thomas Foxley thomasfox...@aol.com wrote: Rune, Thank you very much for your response. I don't actually have the models that failed to converge from the first (glmulti) part as they were not saved with the confidence set. glmulti generates thousands of models so it seems reasonable that a few of these may not converge. The clmm() model I provided was just an example - not all models have 17 parameters. There were only one or two that produced errors (the example I gave being one of them), perhaps overparameterisation is the root of the problem. Regarding incomplete data - there are only 103 (of 314) records where I have data for every predictor. The number of observations included will obviously vary for different models, models with fewer predictors will include more observations. glmulti acts as a wrapper for another function, meaning (in this case) na's are treated as they would be in clm(). Is there a way around this (apart from filling in the missing data)? I believe its possible to limit model complexity in the glmulti call - which may or may not increase the number of observations - how would this affect interpretation of the results? Since the likelihood (and hence also AIC-like criteria) depends on the number of observations, I would make sure that only models with the same number of observations are compared using model selection criteria. This means that I would make a data.frame with complete observations either by just deleting all rows with one or more missing predictors or by imputing some data points. If one or a couple of variables are responsible for most of the missing observations, you could disregard these variables before deleting rows with NAs. As I said, I am no expert in model averaging or glmulti usage, so there might be better approaches or other opinions on this. Cheers, Rune __ 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] Spider Plot
On 04/20/2013 06:29 AM, XINLI LI wrote: Does any one have a sample code for a Spider Plot as attached? Hi Xing, Have a look at the third example in the radial.plot function (plotrix). 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.
[R] how to set the row name of a specific row
Hello, I am adding rows to a matrix using rbind() and I would like to also add a row name to the added row in order to do some sorting after the adding rows part is finished. is this possible? Best, Simone -- Simone Gabbriellini, PhD PostDoc@DISI, University of Bologna mobile: +39 340 39 75 626 email: simone.gabbriell...@unibo.it academia.edu: http://goo.gl/7pq62 DigitalBrains srl Amministratore mobile: +39 340 39 75 626 email: simone.gabbriell...@digitalbrains.it home: www.digitalbrains.it [[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] MOS-test using package vegan
Dear all, I am using MOStest in vegan to examine the hump-shaped of a quadratic regression model. In the manual of vegan, it mentions that the value of MOStest include isHump. My result showed the quadratic regression is hump-shaped according to the p-value (nearly 0). However, the value isHump did not show up. Please kindly help where to find isHump. Further, I do not understand the result of the function plot for the MOStested regression model, after reading the manual of vegan. (There are three graphs in the result, y-x plot, residuals and fitted regression model, and cook's distance) Please kindly share any references to interpret the graphs. Thank you. Elaine code library(vegan) mos_test - MOStest(BMN, DIS, family=gaussian) plot(mos_test) [[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 set the row name of a specific row
Hello, It is possible, but do the other rows have names? x - matrix(1:12, 4) x - rbind(x, c(13:15)) rownames(x)[5] - abcd x Hope this helps, Rui Barradas Em 20-04-2013 10:58, Simone Gabbriellini escreveu: Hello, I am adding rows to a matrix using rbind() and I would like to also add a row name to the added row in order to do some sorting after the adding rows part is finished. is this possible? Best, Simone __ 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 set the row name of a specific row
Hi Rui, yes, all the other rows have names! Thanks, works perfecty 2013/4/20 Rui Barradas ruipbarra...@sapo.pt Hello, It is possible, but do the other rows have names? x - matrix(1:12, 4) x - rbind(x, c(13:15)) rownames(x)[5] - abcd x Hope this helps, Rui Barradas Em 20-04-2013 10:58, Simone Gabbriellini escreveu: Hello, I am adding rows to a matrix using rbind() and I would like to also add a row name to the added row in order to do some sorting after the adding rows part is finished. is this possible? Best, Simone -- Simone Gabbriellini, PhD PostDoc@DISI, University of Bologna mobile: +39 340 39 75 626 email: simone.gabbriell...@unibo.it academia.edu: http://goo.gl/7pq62 DigitalBrains srl Amministratore mobile: +39 340 39 75 626 email: simone.gabbriell...@digitalbrains.it home: www.digitalbrains.it [[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] R CMD build
I have no idea where I must R CMD build... I am using Windows 7 wiht pearl installed http://stat.ethz.ch/R-manual/R-patched/library/utils/html/PkgUtils.html its completely unclear for me ... sorry Knut __ 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] Assigning factor to character vector
Hi! Yesterday I accidentally discovered this: a - LETTERS[1:5] a [1] A B C D E a[1] - factor(a[1]) a [1] 1 B C D E BUT: b - factor(LETTERS[1:5]) b [1] A B C D E Levels: A B C D E b[1] - factor(b[1]) b [1] A B C D E Levels: A B C D E b[1] - as.character(b[1]) b [1] A B C D E Levels: A B C D E I think this would definitely deserve a mention in the R Inferno... I guess this is documented somewhere (though I could not find anything in help([-). Would someone be kind enough to give me the explanation of this behavior? I suspect this has something to do with the coercion order, but I do not really get why a[1] does not get assigned the result of as.character(factor(a[1]))... Probably, there is no special-casing of factors, which are handled as integer vectors? Wouldn't it be useful to print a warning when this happens, since nobody reasonable would rely on such a special behavior? I wish R had a safe mode where all these tricky implicit coercion cases would warn... :-/ Regards __ 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] R CMD build
On Sat, Apr 20, 2013 at 8:09 AM, Knut Krueger r...@knut-krueger.de wrote: I was looking for the problem at least two days.. and just after writing to the list I found rcmd.exe in the C:\Program Files\R\R-2.15.2\bin\i386 directory. install http://sourceforge.net/projects/mingw/?source=dlp chage the path variable of windows and set the path in front of the others C:\MinGW\msys\1.0\bin\ problems with windows 7 : Rund the cmd console as administrator and it is working Maybe anybody can add this to http://stat.ethz.ch/R-manual/R-patched/library/utils/html/PkgUtils.html Note that there is a separate directory for the 64-bit R executables. Also, downloading MinGW should not be needed. Rtools already contains the needed UNIX utilities. You might want to look into the Windows batch files at http://batchfiles.googlecode.com . -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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] Assigning factor to character vector
Sorry, I failed to cc: the list. I also added a slight edit below to clarify my final statement. -- Bert On Sat, Apr 20, 2013 at 7:17 AM, Bert Gunter bgun...@gene.com wrote: Milan: 1. The R Inferno was written by Pat Burns and is not in any way an official R document. So it is a Pat Burns not an R issue. You can contact him directly, if you wish -- though he monitors this list and almost surely has seen this. 2. EVerything works exactly as documented and expected. See the R Language definition ... and perhaps the Intro to R tutorial.. Inline comments below. Cheers, Bert On Sat, Apr 20, 2013 at 5:49 AM, Milan Bouchet-Valat nalimi...@club.fr wrote: Hi! Yesterday I accidentally discovered this: a - LETTERS[1:5] a [1] A B C D E a is a character vector. a[1] - factor(a[1]) The RHS is an vector of integers with additional attributes that define a factor The replacement of the first element of a, a character vector, by an integer causes the integer to be silently coerced to a character. The default S3 replacement method is used -- see ?UseMethod. or the R Intro for info on S3 methods a [1] 1 B C D E BUT: b - factor(LETTERS[1:5]) b is a factor b [1] A B C D E Levels: A B C D E b[1] - factor(b[1]) b [1] A B C D E Levels: A B C D E b[1] - as.character(b[1]) The replacement method for a factor is used in b[1] - factor(b[1]) See ?[-.factor . Cheers, Bert The replacement b [1] A B C D E Levels: A B C D E I think this would definitely deserve a mention in the R Inferno... I guess this is documented somewhere (though I could not find anything in help([-). Would someone be kind enough to give me the explanation of this behavior? I suspect this has something to do with the coercion order, but I do not really get why a[1] does not get assigned the result of as.character(factor(a[1]))... Probably, there is no special-casing of factors, which are handled as integer vectors? Wouldn't it be useful to print a warning when this happens, since nobody reasonable would rely on such a special behavior? I wish R had a safe mode where all these tricky implicit coercion cases would warn... :-/ Regards __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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] Editing data sheet issue with write.table append
a) Your terminology data sheet is foreign to R (and this mailing list). It implies a computing model that R does not use. b) You appear to be complaining about the behavior of software other than R on the R-help mailing list, which is pointless. c) I think the chances of adding code to base R to fix the broken behavior of another software package is highly unlikely, particularly when from your description you might or might not end up with the missing newline depending on whether you choose to modify any particular file outside R. Putting in a newline every time would make R just as broken as Excel. 4) You can put in newlines before or after your write.table call using the ?cat function. Read the data input and output manual for details... but beware that write.table is a high-level function that intentionally tries to generate a coherent representation of the data table as a single block of text. If you need to tweak within that text then you may need to make your own special output function. --- 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. Vinny Moriarty vwmoria...@gmail.com wrote: I'm running R 2.15.2 on Max OS X 10.6.8 If I write a simple file Data1-1 DF-data.frame(Data1) colnames(DF)-Col1 and write to a csv file write.table(DF,file=Data.csv,sep=,,row.names=FALSE,col.names=TRUE) I can then append to it no problem Data2-2 Data3-4 DF2-data.frame(Data2) DF3-data.frame(Data3) write.table(DF2,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=TRUE) write.table(DF3,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=TRUE) All good so far. But the problem arises if I then need to edit the data sheet and continue to append using the above code. If I open up the data sheet in excel and delete a line, the next time I try and append the data as above the first new line of data starts at the end of the last row of data (though all subsequent new lines are appended properly). I'm sure when I manually delete the line in excel I am removing the invisible carriage return character, causing the first line of new data to be added onto where the carriage return used to be. Is there a way to specify in append=TRUE to always start with a new line of data in the spreadsheet? Failing that, is there a work around to avoid this problem? [[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] Assigning factor to character vector
Le samedi 20 avril 2013 à 07:22 -0700, Bert Gunter a écrit : Sorry, I failed to cc: the list. I also added a slight edit below to clarify my final statement. -- Bert On Sat, Apr 20, 2013 at 7:17 AM, Bert Gunter bgun...@gene.com wrote: Milan: 1. The R Inferno was written by Pat Burns and is not in any way an official R document. So it is a Pat Burns not an R issue. You can contact him directly, if you wish -- though he monitors this list and almost surely has seen this. Sure, I did not imply that the R Inferno was an official document. 2. EVerything works exactly as documented and expected. See the R Language definition ... and perhaps the Intro to R tutorial.. But is there a mention of what happens precisely to assignments from factors? I could not find it. For example, the R Language Definition does not mention coercion in the Subset Assignment section [1]. Inline comments below. Cheers, Bert On Sat, Apr 20, 2013 at 5:49 AM, Milan Bouchet-Valat nalimi...@club.fr wrote: Hi! Yesterday I accidentally discovered this: a - LETTERS[1:5] a [1] A B C D E a is a character vector. a[1] - factor(a[1]) The RHS is an vector of integers with additional attributes that define a factor The replacement of the first element of a, a character vector, by an integer causes the integer to be silently coerced to a character. The default S3 replacement method is used -- see ?UseMethod. or the R Intro for info on S3 methods Thanks, but I already understand this part. My surprise comes from the fact that the default replacement method coerces a factor to a character in a way which is different from calling as.character() on it. It acts as if attributes were dropped _before_ coercion (and thus everything happens as if the factor was a mere integer). a [1] 1 B C D E BUT: b - factor(LETTERS[1:5]) b is a factor b [1] A B C D E Levels: A B C D E b[1] - factor(b[1]) b [1] A B C D E Levels: A B C D E b[1] - as.character(b[1]) The replacement method for a factor is used in b[1] - factor(b[1]) See ?[-.factor . Yeah, this part was here to show the asymmetric character of the factor - character assignments. Regards 1: http://cran.r-project.org/doc/manuals/R-lang.html#Subset-assignment Cheers, Bert The replacement b [1] A B C D E Levels: A B C D E I think this would definitely deserve a mention in the R Inferno... I guess this is documented somewhere (though I could not find anything in help([-). Would someone be kind enough to give me the explanation of this behavior? I suspect this has something to do with the coercion order, but I do not really get why a[1] does not get assigned the result of as.character(factor(a[1]))... Probably, there is no special-casing of factors, which are handled as integer vectors? Wouldn't it be useful to print a warning when this happens, since nobody reasonable would rely on such a special behavior? I wish R had a safe mode where all these tricky implicit coercion cases would warn... :-/ Regards __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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] Editing data sheet issue with write.table append
On Apr 20, 2013, at 1:29 AM, Vinny Moriarty wrote: I'm running R 2.15.2 on Max OS X 10.6.8 If I write a simple file Data1-1 DF-data.frame(Data1) colnames(DF)-Col1 and write to a csv file write.table(DF,file=Data.csv,sep=,,row.names=FALSE,col.names=TRUE) I can then append to it no problem Data2-2 Data3-4 DF2-data.frame(Data2) DF3-data.frame(Data3) write.table(DF2,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=TRUE) write.table(DF3,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=TRUE) All good so far. But the problem arises if I then need to edit the data sheet and continue to append using the above code. If I open up the data sheet in excel and delete a line, the next time I try and append the data as above the first new line of data starts at the end of the last row of data (though all subsequent new lines are appended properly). I'm sure when I manually delete the line in excel I am removing the invisible carriage return character, causing the first line of new data to be added onto where the carriage return used to be. Is there a way to specify in append=TRUE to always start with a new line of data in the spreadsheet? No. Failing that, is there a work around to avoid this problem? You could always execute this before each append effort to restore the Excel-induced missing end of line character: cat\n, file=Data.csv, append=TRUE) -- 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] Editing data sheet issue with write.table append
R is nice because it can deal with other less flexible software and many people
must use Excel at their jobs.
You can write a function that detects if your file ends with a newline and use
it
to add a newline exactly when needed. E.g., the following compares the last
few bytes in the file to the newline pattern that you specify and returns TRUE
if
the file ends with a newline. It reads in chunks so it doesn't waste space
with very
large files. In your situation you can do
if (!fileEndsWithNewline(outputFile)) cat(\n, append=TRUE, file=outputFile)
before each call to write.table(append=TRUE).
I suppose the check should be modified to check that the file is not empty, as
you don't
want a newline before any of your data in that case.
fileEndsWithNewline - function(file, chunksize=4096, newline=if
(.Platform$OS.type==windows) \r\n else \n)
{
rawNewline - charToRaw(newline)
stopifnot(chunksize = length(rawNewline))
conn - file(file, rb)
on.exit(close(conn))
prevChunk - raw()
repeat {
thisChunk - readBin(conn, what=raw, n=chunksize)
if (length(thisChunk) chunksize) {
# concatenate in case newline is spread over two chunks
lastChunk - c(prevChunk, thisChunk)
break
}
prevChunk - thisChunk
}
length(lastChunk) = length(rawNewline) all(rawNewline ==
tail(lastChunk, 2))
}
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Jeff Newmiller
Sent: Saturday, April 20, 2013 8:14 AM
To: Vinny Moriarty; r-help@r-project.org
Subject: Re: [R] Editing data sheet issue with write.table append
a) Your terminology data sheet is foreign to R (and this mailing list). It
implies a
computing model that R does not use.
b) You appear to be complaining about the behavior of software other than R
on the R-
help mailing list, which is pointless.
c) I think the chances of adding code to base R to fix the broken behavior of
another
software package is highly unlikely, particularly when from your description
you might or
might not end up with the missing newline depending on whether you choose to
modify
any particular file outside R. Putting in a newline every time would make R
just as broken
as Excel.
4) You can put in newlines before or after your write.table call using the
?cat function.
Read the data input and output manual for details... but beware that
write.table is a
high-level function that intentionally tries to generate a coherent
representation of the
data table as a single block of text. If you need to tweak within that text
then you may
need to make your own special output function.
---
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.
Vinny Moriarty vwmoria...@gmail.com wrote:
I'm running R 2.15.2 on Max OS X 10.6.8
If I write a simple file
Data1-1
DF-data.frame(Data1)
colnames(DF)-Col1
and write to a csv file
write.table(DF,file=Data.csv,sep=,,row.names=FALSE,col.names=TRUE)
I can then append to it no problem
Data2-2
Data3-4
DF2-data.frame(Data2)
DF3-data.frame(Data3)
write.table(DF2,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=T
RUE)
write.table(DF3,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=T
RUE)
All good so far.
But the problem arises if I then need to edit the data sheet and
continue
to append using the above code. If I open up the data sheet in excel
and
delete a line, the next time I try and append the data as above the
first
new line of data starts at the end of the last row of data (though all
subsequent new lines are appended properly).
I'm sure when I manually delete the line in excel I am removing the
invisible carriage return character, causing the first line of new data
to
be added onto where the carriage return used to be.
Is there a way to specify in append=TRUE to always start with a new
line of
data in the spreadsheet? Failing that, is there a work around to avoid
this
problem?
[[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] Spider Plot
Check the archives. About 4 years ago, I asked on help with doing spider-plots used in geologic literature and got a bunch of helpful results. Best, Mark Hall Winnemucca BLM On Fri, Apr 19, 2013 at 1:41 PM, Janesh Devkota janesh.devk...@gmail.comwrote: Xing, I cannot open the attachment. Can you attach the png file or pdf or any other format ? -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of XINLI LI Sent: Friday, April 19, 2013 3:30 PM To: r-help Subject: [R] Spider Plot Does any one have a sample code for a Spider Plot as attached? Thanks, Xing __ 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. [[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] Reshape or Plyr?
H all, I have relative abundance data from 100 sites. This is from acoustic monitoring and usually the data is for 2-3 nights but in some cases my be longer like months or years for each location.. The data output from my management data base is proved by species by night for each location so data frame would look like this below. What I need to do is sum the Survey_time by Spec_Code for each location name and divide summed AI values for each Spec_code by the summed Survey time to adjust for unit effort then standardize it all by *10 to represent the relative abundance by survey hour to 10 hours. How best to do this? Using Plyr or reshape? Location name SPEC_CODE Start_Day Survey_Time AI Std AI 079-f2p1-AcetunaBuzz2/14/2012 12.11 0.8264463 079-f2p1-AcetunaBuzz2/14/2012 12.11 0.8264463 079-f2p1-AcetunaEumspp 2/14/2012 12.11 0.8264463 079-f2p1-AcetunaFrag2/14/2012 12.118 14.87603 079-f2p1-AcetunaMolspp 2/14/2012 12.15 4.132231 079-f2p1-AcetunaMolspp 2/14/2012 12.15 4.132231 079-f2p1-AcetunaPhyllo 2/14/2012 12.12 1.652893 079-f2p1-AcetunaPtedav 2/14/2012 12.11 0.8264463 079-f2p1-AcetunaPtegym 2/14/2012 12.11 0.8264463 079-f2p1-AcetunaPtepar 2/14/2012 12.12 1.652893 079-f2p1-AcetunaRhotum 2/14/2012 12.16 4.958678 079-f2p1-AcetunaSacbil 2/14/2012 12.16 4.958678 079-f2p1-AcetunaSaclep 2/14/2012 12.111 9.090909 079-f2p1-AcetunaBuzz2/15/2012 12.12 1.652893 079-f2p1-AcetunaBuzz2/15/2012 12.12 1.652893 079-f2p1-AcetunaMolmol 2/15/2012 12.11 0.8264463 079-f2p1-AcetunaMolspp 2/15/2012 12.17 5.785124 079-f2p1-AcetunaMolspp 2/15/2012 12.17 5.785124 079-f2p1-AcetunaNocalb 2/15/2012 12.16 4.958678 079-f2p1-AcetunaPhyllo 2/15/2012 12.11 0.8264463 079-f2p1-AcetunaPtedav 2/15/2012 12.11 0.8264463 079-f2p1-AcetunaPtegym 2/15/2012 12.14 3.305785 079-f2p1-AcetunaPtepar 2/15/2012 12.14 3.305785 079-f2p1-AcetunaPteper 2/15/2012 12.13 2.479339 079-f2p1-AcetunaRhotum 2/15/2012 12.17 5.785124 079-f2p1-AcetunaSacbil 2/15/2012 12.12 1.652893 079-f2p1-AcetunaSaclep 2/15/2012 12.16 4.958678 079-f2p1-AcetunaBuzz2/16/2012 12.21 0.8196721 079-f2p1-AcetunaBuzz2/16/2012 12.21 0.8196721 079-f2p1-AcetunaEumspp 2/16/2012 12.24 3.278688 079-f2p1-AcetunaMolspp 2/16/2012 12.22 1.639344 079-f2p1-AcetunaMolspp 2/16/2012 12.22 1.639344 079-f2p1-AcetunaMyokea 2/16/2012 12.21 0.8196721 079-f2p1-AcetunaNocalb 2/16/2012 12.24 3.278688 079-f2p1-AcetunaPhyllo 2/16/2012 12.21 0.8196721 079-f2p1-AcetunaPtedav 2/16/2012 12.21 0.8196721 079-f2p1-AcetunaPtegym 2/16/2012 12.21 0.8196721 079-f2p1-AcetunaPtepar 2/16/2012 12.23 2.459016 079-f2p1-AcetunaPteper 2/16/2012 12.21 0.8196721 079-f2p1-AcetunaRhotum 2/16/2012 12.217 13.93443 079-f2p1-AcetunaSacbil 2/16/2012 12.23 2.459016 079-f2p1-AcetunaSaclep 2/16/2012 12.215 12.29508 Thanks for any suggestions. Excel will be a mess to try to do that. Bruce [[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] Editing data sheet issue with write.table append
Thanks Bill , that works great.
It occurred to me upon reading the other responses that rather than try and
work around this issue with excel, another option would be to just always
append to the top line of the data sheet (1 line below the header). That
way I would be assured a proper carriage return, and a reverse
chronological order is fine with me
Thanks again to all
On Sat, Apr 20, 2013 at 7:21 AM, William Dunlap wdun...@tibco.com wrote:
R is nice because it can deal with other less flexible software and many
people
must use Excel at their jobs.
You can write a function that detects if your file ends with a newline and
use it
to add a newline exactly when needed. E.g., the following compares the
last
few bytes in the file to the newline pattern that you specify and returns
TRUE if
the file ends with a newline. It reads in chunks so it doesn't waste
space with very
large files. In your situation you can do
if (!fileEndsWithNewline(outputFile)) cat(\n, append=TRUE,
file=outputFile)
before each call to write.table(append=TRUE).
I suppose the check should be modified to check that the file is not
empty, as you don't
want a newline before any of your data in that case.
fileEndsWithNewline - function(file, chunksize=4096, newline=if
(.Platform$OS.type==windows) \r\n else \n)
{
rawNewline - charToRaw(newline)
stopifnot(chunksize = length(rawNewline))
conn - file(file, rb)
on.exit(close(conn))
prevChunk - raw()
repeat {
thisChunk - readBin(conn, what=raw, n=chunksize)
if (length(thisChunk) chunksize) {
# concatenate in case newline is spread over two chunks
lastChunk - c(prevChunk, thisChunk)
break
}
prevChunk - thisChunk
}
length(lastChunk) = length(rawNewline) all(rawNewline ==
tail(lastChunk, 2))
}
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf
Of Jeff Newmiller
Sent: Saturday, April 20, 2013 8:14 AM
To: Vinny Moriarty; r-help@r-project.org
Subject: Re: [R] Editing data sheet issue with write.table append
a) Your terminology data sheet is foreign to R (and this mailing
list). It implies a
computing model that R does not use.
b) You appear to be complaining about the behavior of software other
than R on the R-
help mailing list, which is pointless.
c) I think the chances of adding code to base R to fix the broken
behavior of another
software package is highly unlikely, particularly when from your
description you might or
might not end up with the missing newline depending on whether you
choose to modify
any particular file outside R. Putting in a newline every time would
make R just as broken
as Excel.
4) You can put in newlines before or after your write.table call using
the ?cat function.
Read the data input and output manual for details... but beware that
write.table is a
high-level function that intentionally tries to generate a coherent
representation of the
data table as a single block of text. If you need to tweak within that
text then you may
need to make your own special output function.
---
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.
Vinny Moriarty vwmoria...@gmail.com wrote:
I'm running R 2.15.2 on Max OS X 10.6.8
If I write a simple file
Data1-1
DF-data.frame(Data1)
colnames(DF)-Col1
and write to a csv file
write.table(DF,file=Data.csv,sep=,,row.names=FALSE,col.names=TRUE)
I can then append to it no problem
Data2-2
Data3-4
DF2-data.frame(Data2)
DF3-data.frame(Data3)
write.table(DF2,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=T
RUE)
write.table(DF3,file=Data.csv,sep=,,row.names=FALSE,col.names=FALSE,append=T
RUE)
All good so far.
But the problem arises if I then need to edit the data sheet and
continue
to append using the above code. If I open up the data sheet in excel
and
delete a line, the next time I try and append the data as above the
first
new line of data starts at the end of the last row of data (though all
subsequent new lines are appended properly).
I'm sure when I manually delete the line in excel I am removing the
invisible carriage return character, causing the first line of new data
to
be added onto
[R] Calculate confidence intervals in mgcv for unconditional on the, smoothing parameters
Dear R-Help members, I am using Simon Wood`s mgcv package version1.7-22and R version 3.0.0 (2013-04-03) for fitting a GAM-Model to the LIDAR Data contained in the SemiPar package. Here is the code for fitting the model and for plotting the result: data(lidar) attach(lidar) ### # mgcv fitting ### gam_fit - gam(logratio ~ s(range, k = 40, bs = cr), gamma = 1.4, method = REML) plot(gam_fit, res = TRUE, shade = TRUE, pch = °) Since the confidence interval in the above plot is pointwise, I would like to calculate the critical value needed in order to construct a simultaneous confidence band. Here isthe code(it`s a bit lengthy and has to be tidied up but I wanted to to some manual calculations on the objects afterwards) ### # Simulate 10 coefficient vectors from the posterior for ß and calculate the critical value ### cov_beta_diff - vcov(gam_fit) basis_matrix - model.matrix(gam_fit) reml_sigma_squared - gam.vcomp(gam_fit) sigma_2_epsilon - reml_sigma_squared[2,1]^2 smooth_matrix - basis_matrix%*%vcov(gam_fit,dispersion=1)%*%t(basis_matrix) stdv_f_x - sqrt(diag(sigma_2_epsilon * smooth_matrix)) set.seed(123) R_sim - 10 mean_val - rep(0, nrow(cov_beta_diff)) coef_diff - mvrnorm(n = R_sim, mu = mean_val , Sigma = cov_beta_diff) Xp - predict(gam_fit, type = lpmatrix) sim_bet - Xp %*% t(coef_diff) abs_ratio - abs(sim_bet / stdv_f_x) ratio_max - apply(abs_ratio, 2, max) cv - quantile(ratio_max, probs = 0.95) So everything is fine until this point. My problem is:everything has been presented conditional on the smoothing parameter estimated in gam_fit. How can I calculate a critical value for thesimultaneous confidence band that is not conditioned on the estimated smoothing parameter? Simon Wood seems to offer a solution in his book Generalized Additive Models: An introduction with R. But I couldn`t figure where to look for it and out how to implement it using R. Any help is appreciated Best Alex [[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] creating dummy variables
Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal [[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] R copying script code to clipboard
Hi everyone I am trying to figure out why, and how to stop R, from copying my entire script text to the clipboard when I either select the run all option or select the entire script and ctrl+r. Since my script imports data from the clipboard it is non-functional when R overwrites the data I saved in the clipboard. Thanks in advance Thomas __ 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 subtotal by rows
Dear All, Thanks for helping me to redress the problem. Cheers, Shyam Basnet Nepal - Original Message - From: arun smartpink...@yahoo.com To: Janesh Devkota janesh.devk...@gmail.com Cc: R help r-help@r-project.org; shyam basnet shyamabc2...@yahoo.com Sent: Saturday, April 20, 2013 12:52 AM Subject: Re: [R] how to subtotal by rows HI, If you wanted to use colSums, may be this works: ddply(jd1,.(fid,year),function(x) colSums(x[,-c(1,2)],na.rm=TRUE)) # fid year rice wheat maize #1 1 1995 5 3 2 #2 1 1996 4 2 6 #3 2 1995 3 8 4 #4 2 1996 7 6 7 A.K. - Original Message - From: arun smartpink...@yahoo.com To: Janesh Devkota janesh.devk...@gmail.com Cc: R help r-help@r-project.org; shyam basnet shyamabc2...@yahoo.com; Rui Barradas ruipbarra...@sapo.pt Sent: Friday, April 19, 2013 6:25 PM Subject: Re: [R] how to subtotal by rows Hi Janesh, There is a difference in output between these : ddply(jd1,.(fid,year),colSums,na.rm=T) #especially the first two columns # fid year rice wheat maize #1 3 5985 5 3 2 #2 3 5988 4 2 6 #3 6 5985 3 8 4 #4 6 5988 7 6 7 ddply(jd1,.(fid,year),colwise(sum,na.rm=T)) # fid year rice wheat maize #1 1 1995 5 3 2 #2 1 1996 4 2 6 #3 2 1995 3 8 4 #4 2 1996 7 6 7 aggregate(jd1[,3:5],by=list(jd1$year,jd1$fid),FUN=sum,na.rm=TRUE) # Group.1 Group.2 rice wheat maize #1 1995 1 5 3 2 #2 1996 1 4 2 6 #3 1995 2 3 8 4 #4 1996 2 7 6 7 A.K. From: Janesh Devkota janesh.devk...@gmail.com To: shyam basnet shyamabc2...@yahoo.com Cc: r-help@R-project.org r-help@r-project.org Sent: Friday, April 19, 2013 3:32 PM Subject: Re: [R] how to subtotal by rows You can also use this short command. library(plyr) ddply(jd1,.(fid,year),colSums,na.rm=T) Janesh On Fri, Apr 19, 2013 at 2:30 PM, Janesh Devkota janesh.devk...@gmail.comwrote: Hello Shyam, This is one way to do it jd1 - read.table(text= fid year rice wheat maize 1 1995 5 NA NA 1 1995 NA 3 NA 1 1995 NA NA 2 1 1996 4 NA NA 1 1996 NA 2 NA 1 1996 NA NA 6 2 1995 3 NA NA 2 1995 NA 8 NA 2 1995 NA NA 4 2 1996 7 NA NA 2 1996 NA 6 NA 2 1996 NA NA 7 , sep=, header=T) jd1 library(plyr) ddply(jd1,.(fid,year),summarise, rice=sum(rice,na.rm=T),wheat=sum(wheat,na.rm=T),maize=sum(maize,na.rm=T)) Good luck Janesh On Fri, Apr 19, 2013 at 10:59 AM, shyam basnet shyamabc2...@yahoo.comwrote: Dear R-users, I have a dataset as like below, and I want to subtotal the values of rice,wheat and maize by year for each fid. fid year rice wheat maize 1 1995 5 NA NA 1 1995 NA 3 NA 1 1995 NA NA 2 1 1996 4 NA NA 1 1996 NA 2 NA 1 1996 NA NA 6 2 1995 3 NA NA 2 1995 NA 8 NA 2 1995 NA NA 4 2 1996 7 NA NA 2 1996 NA 6 NA 2 1996 NA NA 7--- And, my output should look like below: fid year rice wheat maize 1 1995 5 3 2 1 1996 4 2 6 2 1995 3 8 4 2 1996 7 6 7I am looking for some ideas or r-codes on resolving my problem. I appreciate your kind help, Thanks a lot, Sincerely yours, Shyam Nepal [[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. [[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] creating dummy variables
Dummy variables are not needed in R. Bert Sent from my iPhone -- please excuse typos. On Apr 20, 2013, at 11:23 AM, shyam basnet shyamabc2...@yahoo.com wrote: Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal [[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] matrix of size 30^5
Dear R helpers Reproducible example: #warning - this causes a hard freeze on the machines I've tried it on matrix.holder- matrix(rnorm(150), nrow=30, ncol=5) Out= expand.grid(matrix.holder[,1],matrix.holder[,2],matrix.holder[,3],matrix.holder[,4], matrix.holder[,5]) Problem: I'm running an analysis that I would like to do using a matrix containing all the possible combinations of the elements in a [30,5] matrix. Briefly, each possible combination is used to index and subset another matrix. I then run some models on the data in the subsetted matrix and then sometimes export the model results based on a couple criteria. 24,300,000 combinations seems to be too big for R on my computer (Intel i5, about 2.5 GB RAM free, 4 GB total, Rx64 2.15 ) to handle. Requests: 1. Can you tell me how I can estimate the amount of memory a matrix will require before I create it? 2. Do you have recommendations for packages that allow the user to send an object directly to the hard drive? I guess it would have to be partially created in RAM and then dumped to the HD, but the point is that there isn't room for whole thing to be created and then written in pieces to the HD (which even I think I could do). And then of course if it was written as one big piece to the HD, I would need to be able to read it in piece by piece. 3. I also see packages out there to connect R to C. Anyone have ideas for one designed or containing functions designed for this type of problem? Background: When I tried to throw expand.grid() at a matrix of size [30,5] (24,300,000 combinations), my computer choked (I assume due to RAM memory limits, but it might be that doing that just takes a long time and I wasn't ready to stare at a frozen computer for very long). I'm currently working around the problem with five nested loops, with all the drawbacks of and limits imposed by that approach (the biggest for me is that I'd like to attempt to multithread with some of the packages that exist for that). I don't have any formal training in computer science, and the only programming language I use enough to do something of this complexity is R, so programming the whole thing in C (which all the remote sensing folks across the hall said would make creation of this matrix trivial) isn't an easy alternative for me. Thanks! Ben Caldwell Graduate Fellow University of California, Berkeley [[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] creating dummy variables
Hello Shyam, if your data is stored in variable dataset, for example, the following code will create the desired dummy-coded variables and attach them to the dataset: ## #init vars SWHE=BARL - vector(length=nrow(dataset)) SWHE[]=BARL[] - 0 #initialize dummy-coded vars with all 0s #fill in variables SWHE[grep(SWHE, dataset$crop)] - 1 #grep returns the indices where a match is found, see ?grep BARL[grep(BARL, dataset$crop)] - 1 #attach new dummy codes to dataset dataset$SWHE - SWHE dataset$BARL - BARL ## Hope this helps, Patrick 2013/4/20 shyam basnet shyamabc2...@yahoo.com Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal [[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. [[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] R CMD build
Am 20.04.2013 15:50, schrieb Gabor Grothendieck: Note that there is a separate directory for the 64-bit R executables. Does it make any difference to check and pack the source files iwth 32 or 64 bit? Also, downloading MinGW should not be needed. Rtools already contains the needed UNIX utilities. Yes indeed it works better than MinGW You might want to look into the Windows batch files at http://batchfiles.googlecode.com . At least it would be very helpful for windows user to give the hint to the executable rcmd.exe build ... instead of R cmd build ... I already set up an linux system today to solve the problem Thank you Knut __ 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] Source Code
Dear all, How can I get the source code of text function? Regards Eva [[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] matrix of size 30^5
On Apr 20, 2013, at 2:19 PM, Benjamin Caldwell wrote: Dear R helpers Reproducible example: #warning - this causes a hard freeze on the machines I've tried it on matrix.holder- matrix(rnorm(150), nrow=30, ncol=5) Out= expand.grid(matrix.holder[,1],matrix.holder[,2],matrix.holder[,3],matrix.holder[,4], matrix.holder[,5]) On my machine: object.size(Out) 972014344 bytes So with proper setup you might be able to work with this on a 4GB machine, but not likely to be able to do so on the machine you are describing below. Problem: I'm running an analysis that I would like to do using a matrix containing all the possible combinations of the elements in a [30,5] matrix. Briefly, each possible combination is used to index and subset another matrix. I then run some models on the data in the subsetted matrix and then sometimes export the model results based on a couple criteria. 24,300,000 combinations seems to be too big for R on my computer (Intel i5, about 2.5 GB RAM free, 4 GB total, Rx64 2.15 ) to handle. Requests: 1. Can you tell me how I can estimate the amount of memory a matrix will require before I create it? Roughly: 5* 8* prod(dim(mat)) # 8 bytes per double 5*8*(30^5)/972014344 [1] 0.852# so my estimate was accurate on a ratio basis to 5 decimal places. 2. Do you have recommendations for packages that allow the user to send an object directly to the hard drive? I guess it would have to be partially created in RAM and then dumped to the HD, but the point is that there isn't room for whole thing to be created and then written in pieces to the HD (which even I think I could do). And then of course if it was written as one big piece to the HD, I would need to be able to read it in piece by piece. 3. I also see packages out there to connect R to C. Anyone have ideas for one designed or containing functions designed for this type of problem? Are you saying you have facility with C programming? (And you really have not described the problem. Perhaps a redesign of the solution could accommodate your limited computing resources. Background: When I tried to throw expand.grid() at a matrix of size [30,5] (24,300,000 combinations), my computer choked (I assume due to RAM memory limits, but it might be that doing that just takes a long time and I wasn't ready to stare at a frozen computer for very long). It took 7 seconds on my 6 year-old MacPro. I'm currently working around the problem with five nested loops, with all the drawbacks of and limits imposed by that approach (the biggest for me is that I'd like to attempt to multithread with some of the packages that exist for that). I don't have any formal training in computer science, and the only programming language I use enough to do something of this complexity is R, so programming the whole thing in C (which all the remote sensing folks across the hall said would make creation of this matrix trivial) isn't an easy alternative for me. There are many threads on Rhelp and advice in various manuals about how to avoid memory limitations. Thanks! Ben Caldwell Graduate Fellow University of California, Berkeley -- 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] Source Code
On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote: Dear all, How can I get the source code of text function? What is the 'text function'? Try typing the name of the function at the prompt without any parentheses after it. If its written in R, then it should be visible. Michael Regards Eva [[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] Source Code
This is what I get when typing text: text function (x, ...) UseMethod(text) bytecode: 0x12cb4964 environment: namespace:graphics The text function let you add text in a plot. How can I obtain the source code?. Thanks. Eva --- El dom, 21/4/13, R. Michael Weylandt michael.weyla...@gmail.com michael.weyla...@gmail.com escribió: De: R. Michael Weylandt michael.weyla...@gmail.com michael.weyla...@gmail.com Asunto: Re: [R] Source Code Para: Eva Prieto Castro evapcas...@yahoo.es CC: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Fecha: domingo, 21 de abril, 2013 00:34 On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote: Dear all, How can I get the source code of text function? What is the 'text function'? Try typing the name of the function at the prompt without any parentheses after it. If its written in R, then it should be visible. Michael Regards Eva [[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. [[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] creating dummy variables
On Apr 20, 2013, at 2:03 PM, Bert Gunter wrote: Dummy variables are not needed in R. Bert Bert is correct on this point, but if you what to know how the regression functions in R do this behind the scenes then you could always look at: ?model.matrix # where _some_ of the the automagical stuff happens model.matrix( ~ crop, data=dat[,crop, drop=FALSE]) (Intercept) cropSWHE 1 11 2 11 3 10 4 10 5 11 6 11 7 10 8 10 attr(,assign) [1] 0 1 attr(,contrasts) attr(,contrasts)$crop [1] contr.treatment Sent from my iPhone -- please excuse typos. On Apr 20, 2013, at 11:23 AM, shyam basnet shyamabc2...@yahoo.com wrote: Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source Code
Hello,
The output you got means that text is generic, so you need something
like text.default
text.default
function (x, y = NULL, labels = seq_along(x), adj = NULL, pos = NULL,
offset = 0.5, vfont = NULL, cex = 1, col = NULL, font = NULL,
...)
{
if (!missing(y) (is.character(y) || is.expression(y))) {
labels - y
y - NULL
}
labels - as.graphicsAnnot(labels)
if (!is.null(vfont))
vfont - c(typeface = pmatch(vfont[1L], Hershey$typeface),
fontindex = pmatch(vfont[2L], Hershey$fontindex))
.External.graphics(C_text, xy.coords(x, y, recycle = TRUE),
labels, adj, pos, offset, vfont, cex, col, font, ...)
invisible()
}
bytecode: 0x05efecc0
environment: namespace:graphics
Hope this helps,
Rui Barradas
Em 20-04-2013 23:38, Eva Prieto Castro escreveu:
This is what I get when typing text:
text
function (x, ...)
UseMethod(text)
bytecode: 0x12cb4964
environment: namespace:graphics
The text function let you add text in a plot.
How can I obtain the source code?.
Thanks.
Eva
--- El dom, 21/4/13, R. Michael Weylandt michael.weyla...@gmail.com
michael.weyla...@gmail.com escribió:
De: R. Michael Weylandt michael.weyla...@gmail.com
michael.weyla...@gmail.com
Asunto: Re: [R] Source Code
Para: Eva Prieto Castro evapcas...@yahoo.es
CC: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch
Fecha: domingo, 21 de abril, 2013 00:34
On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote:
Dear all,
How can I get the source code of text function?
What is the 'text function'?
Try typing the name of the function at the prompt without any parentheses after
it. If its written in R, then it should be visible.
Michael
Regards
Eva
[[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.
[[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] Source Code
On Apr 20, 2013, at 3:34 PM, R. Michael Weylandt michael.weyla...@gmail.com wrote: On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote: Dear all, How can I get the source code of text function? What is the 'text function'? Try typing the name of the function at the prompt without any parentheses after it. If its written in R, then it should be visible. (It's not, .. or at least it might not seem so to a newbR.) text function (x, ...) UseMethod(text) bytecode: 0x10191f780 environment: namespace:graphics methods(text) text.default graphics:::trext.formula And then to go further ... I think she may need the added information in Uwe Ligges classic R-News article: http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf -- 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] creating dummy variables
Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. Thanks, Eva --- El dom, 21/4/13, David Winsemius dwinsem...@comcast.net escribió: De: David Winsemius dwinsem...@comcast.net Asunto: Re: [R] creating dummy variables Para: Bert Gunter gunter.ber...@gene.com CC: r-help@R-project.org r-help@r-project.org, shyam basnet shyamabc2...@yahoo.com Fecha: domingo, 21 de abril, 2013 00:38 On Apr 20, 2013, at 2:03 PM, Bert Gunter wrote: Dummy variables are not needed in R. Bert Bert is correct on this point, but if you what to know how the regression functions in R do this behind the scenes then you could always look at: ?model.matrix # where _some_ of the the automagical stuff happens model.matrix( ~ crop, data=dat[,crop, drop=FALSE]) (Intercept) cropSWHE 1 1 1 2 1 1 3 1 0 4 1 0 5 1 1 6 1 1 7 1 0 8 1 0 attr(,assign) [1] 0 1 attr(,contrasts) attr(,contrasts)$crop [1] contr.treatment Sent from my iPhone -- please excuse typos. On Apr 20, 2013, at 11:23 AM, shyam basnet shyamabc2...@yahoo.com wrote: Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal 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. [[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] Source Code
Thanks!. The problem is that I can't see the source code in .Internal(txt...
text.default
function (x, y = NULL, labels = seq_along(x), adj = NULL, pos = NULL,
offset = 0.5, vfont = NULL, cex = 1, col = NULL, font = NULL,
...)
{
if (!missing(y) (is.character(y) || is.expression(y))) {
labels - y
y - NULL
}
labels - as.graphicsAnnot(labels)
if (!is.null(vfont))
vfont - c(typeface = pmatch(vfont[1L], Hershey$typeface),
fontindex = pmatch(vfont[2L], Hershey$fontindex))
.Internal(text(xy.coords(x, y, recycle = TRUE), labels, adj,
pos, offset, vfont, cex, col, font, ...))
}
bytecode: 0x12b4cdb4
environment: namespace:graphics
Regards,
Eva
--- El dom, 21/4/13, David Winsemius dwinsem...@comcast.net escribió:
De: David Winsemius dwinsem...@comcast.net
Asunto: Re: [R] Source Code
Para: R. Michael Weylandt michael.weyla...@gmail.com
michael.weyla...@gmail.com
CC: Eva Prieto Castro evapcas...@yahoo.es, r-h...@stat.math.ethz.ch
r-h...@stat.math.ethz.ch
Fecha: domingo, 21 de abril, 2013 00:45
On Apr 20, 2013, at 3:34 PM, R. Michael Weylandt michael.weyla...@gmail.com
wrote:
On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote:
Dear all,
How can I get the source code of text function?
What is the 'text function'?
Try typing the name of the function at the prompt without any parentheses
after it. If its written in R, then it should be visible.
(It's not, .. or at least it might not seem so to a newbR.)
text
function (x, ...)
UseMethod(text)
bytecode: 0x10191f780
environment: namespace:graphics
methods(text)
text.default
graphics:::trext.formula
And then to go further ... I think she may need the added information in
Uwe Ligges classic R-News article:
http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf
--
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] Source Code
On Apr 20, 2013, at 4:05 PM, Eva Prieto Castro wrote:
Thanks!. The problem is that I can't see the source code in .Internal(txt...
Exactly which was why I provided the link to Ligges' article. (So now you
_are_ expected to do some self-study.)
--
David.
text.default
function (x, y = NULL, labels = seq_along(x), adj = NULL, pos = NULL,
offset = 0.5, vfont = NULL, cex = 1, col = NULL, font = NULL,
...)
{
if (!missing(y) (is.character(y) || is.expression(y))) {
labels - y
y - NULL
}
labels - as.graphicsAnnot(labels)
if (!is.null(vfont))
vfont - c(typeface = pmatch(vfont[1L], Hershey$typeface),
fontindex = pmatch(vfont[2L], Hershey$fontindex))
.Internal(text(xy.coords(x, y, recycle = TRUE), labels, adj,
pos, offset, vfont, cex, col, font, ...))
}
bytecode: 0x12b4cdb4
environment: namespace:graphics
Regards,
Eva
--- El dom, 21/4/13, David Winsemius dwinsem...@comcast.net escribió:
De: David Winsemius dwinsem...@comcast.net
Asunto: Re: [R] Source Code
Para: R. Michael Weylandt michael.weyla...@gmail.com
michael.weyla...@gmail.com
CC: Eva Prieto Castro evapcas...@yahoo.es, r-h...@stat.math.ethz.ch
r-h...@stat.math.ethz.ch
Fecha: domingo, 21 de abril, 2013 00:45
On Apr 20, 2013, at 3:34 PM, R. Michael Weylandt michael.weyla...@gmail.com
wrote:
On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote:
Dear all,
How can I get the source code of text function?
What is the 'text function'?
Try typing the name of the function at the prompt without any parentheses
after it. If its written in R, then it should be visible.
(It's not, .. or at least it might not seem so to a newbR.)
text
function (x, ...)
UseMethod(text)
bytecode: 0x10191f780
environment: namespace:graphics
methods(text)
text.default
graphics:::trext.formula
And then to go further ... I think she may need the added information in
Uwe Ligges classic R-News article:
http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf
--
David Winsemius
Alameda, CA, USA
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] creating dummy variables
On Apr 20, 2013, at 3:56 PM, Eva Prieto Castro wrote: Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. I suppose you might want individual instruction, but Rhelp was established with certain principles (expressed in the Posting Guide), one of which is that persons posting to Rhelp should have made demonstrated effort on their own to study the offered documentation. You are not demonstrating that you have yet understood this principle. -- David. Thanks, Eva --- El dom, 21/4/13, David Winsemius dwinsem...@comcast.net escribió: De: David Winsemius dwinsem...@comcast.net Asunto: Re: [R] creating dummy variables Para: Bert Gunter gunter.ber...@gene.com CC: r-help@R-project.org r-help@r-project.org, shyam basnet shyamabc2...@yahoo.com Fecha: domingo, 21 de abril, 2013 00:38 On Apr 20, 2013, at 2:03 PM, Bert Gunter wrote: Dummy variables are not needed in R. Bert Bert is correct on this point, but if you what to know how the regression functions in R do this behind the scenes then you could always look at: ?model.matrix # where _some_ of the the automagical stuff happens model.matrix( ~ crop, data=dat[,crop, drop=FALSE]) (Intercept) cropSWHE 1 11 2 11 3 10 4 10 5 11 6 11 7 10 8 10 attr(,assign) [1] 0 1 attr(,contrasts) attr(,contrasts)$crop [1] contr.treatment Sent from my iPhone -- please excuse typos. On Apr 20, 2013, at 11:23 AM, shyam basnet shyamabc2...@yahoo.com wrote: Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal 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. 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] creating dummy variables
To all who ask about dummy variables in R: Please please read the Introduction to R section on Statistical Models in R or other tutorial (there are many on the web) on regression modeling in R. (For that matter -- please read all of this or other basic R tutorial before posting here!). An excellent but somewhat terse and technical discussion can be found in the latest edition of VR's MASS -- the chapter on linear models. I do not intend to (poorly) try to recapitulate what others have already (well) explained. Do Your Homework! Documentation within R can be found in ?lm ?formula ?contrasts ?model.matrix These may not make much sense unless you have done your homework first -- or already understand the statistical issues. -- Bert On Sat, Apr 20, 2013 at 3:56 PM, Eva Prieto Castro evapcas...@yahoo.eswrote: Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. Thanks, Eva --- El *dom, 21/4/13, David Winsemius dwinsem...@comcast.net* escribió: De: David Winsemius dwinsem...@comcast.net Asunto: Re: [R] creating dummy variables Para: Bert Gunter gunter.ber...@gene.com CC: r-help@R-project.org r-help@r-project.org, shyam basnet shyamabc2...@yahoo.com Fecha: domingo, 21 de abril, 2013 00:38 On Apr 20, 2013, at 2:03 PM, Bert Gunter wrote: Dummy variables are not needed in R. Bert Bert is correct on this point, but if you what to know how the regression functions in R do this behind the scenes then you could always look at: ?model.matrix # where _some_ of the the automagical stuff happens model.matrix( ~ crop, data=dat[,crop, drop=FALSE]) (Intercept) cropSWHE 1 11 2 11 3 10 4 10 5 11 6 11 7 10 8 10 attr(,assign) [1] 0 1 attr(,contrasts) attr(,contrasts)$crop [1] contr.treatment Sent from my iPhone -- please excuse typos. On Apr 20, 2013, at 11:23 AM, shyam basnet shyamabc2...@yahoo.comhttp://mc/compose?to=shyamabc2...@yahoo.com wrote: Hello R-users, The below is a snippet of my data: fid crop year value 5_1_1 SWHE 1995 171 5_1_1 SWHE 1997 696 5_1_1 BARL 1996 114 5_1_1 BARL 1997 344 5_2_2 SWHE 1995 120 5_2_2 SWHE 1996 511 5_2_2 BARL 1996 239 5_2_2 BARL 1997 349 Here, I want to create dummy variables with the names of the content of a column 'crop' in a way that the new variable 'SWHE' would receive a value of 1 if the column 'crop' contains 'SWHE' and 0 otherwise. So, I would have two new variables SWHE and BARL as below: fid crop year value SWHE BARL 5_1_1 SWHE 1995 171 1 0 5_1_1 SWHE 1997 696 1 0 5_1_1 BARL 1996 114 0 1 5_1_1 BARL 1997 344 0 1 5_2_2 SWHE 1995 120 1 0 5_2_2 SWHE 1996 511 1 0 5_2_2 BARL 1996 239 0 1 5_2_2 BARL 1997 349 0 1 Cheers, Shyam Nepal David Winsemius Alameda, CA, USA __ R-help@r-project.org http://mc/compose?to=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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] Source Code
On Apr 20, 2013, at 7:13 PM, David Winsemius dwinsem...@comcast.net wrote:
On Apr 20, 2013, at 4:05 PM, Eva Prieto Castro wrote:
Thanks!. The problem is that I can't see the source code in .Internal(txt...
Exactly which was why I provided the link to Ligges' article. (So now you
_are_ expected to do some self-study.)
Note also that the graphics code isn't exactly the easiest either (to my mind)
-- perhaps you could say a bit about what you are after and we'll try to give
pointers as best we're able.
MW
(Sorry for brain borking in the text() function earlier -- I blame it on the
travel!)
--
David.
text.default
function (x, y = NULL, labels = seq_along(x), adj = NULL, pos = NULL,
offset = 0.5, vfont = NULL, cex = 1, col = NULL, font = NULL,
...)
{
if (!missing(y) (is.character(y) || is.expression(y))) {
labels - y
y - NULL
}
labels - as.graphicsAnnot(labels)
if (!is.null(vfont))
vfont - c(typeface = pmatch(vfont[1L], Hershey$typeface),
fontindex = pmatch(vfont[2L], Hershey$fontindex))
.Internal(text(xy.coords(x, y, recycle = TRUE), labels, adj,
pos, offset, vfont, cex, col, font, ...))
}
bytecode: 0x12b4cdb4
environment: namespace:graphics
Regards,
Eva
--- El dom, 21/4/13, David Winsemius dwinsem...@comcast.net escribió:
De: David Winsemius dwinsem...@comcast.net
Asunto: Re: [R] Source Code
Para: R. Michael Weylandt michael.weyla...@gmail.com
michael.weyla...@gmail.com
CC: Eva Prieto Castro evapcas...@yahoo.es, r-h...@stat.math.ethz.ch
r-h...@stat.math.ethz.ch
Fecha: domingo, 21 de abril, 2013 00:45
On Apr 20, 2013, at 3:34 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
On Apr 20, 2013, at 6:23 PM, Eva Prieto Castro evapcas...@yahoo.es wrote:
Dear all,
How can I get the source code of text function?
What is the 'text function'?
Try typing the name of the function at the prompt without any parentheses
after it. If its written in R, then it should be visible.
(It's not, .. or at least it might not seem so to a newbR.)
text
function (x, ...)
UseMethod(text)
bytecode: 0x10191f780
environment: namespace:graphics
methods(text)
text.default
graphics:::trext.formula
And then to go further ... I think she may need the added information
in Uwe Ligges classic R-News article:
http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf
--
David Winsemius
Alameda, CA, USA
David Winsemius
Alameda, CA, USA
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and provide commented, minimal, self-contained, reproducible code.
[R] Foundation for Open Access Statistics
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Re: [R] creating dummy variables
On 21/04/13 10:56, Eva Prieto Castro wrote: Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. As others have said --- do some self-study. But a brief answer is that in any reasonable modelling problem in which dummy variables might arise, R creates the dummy variables that it uses automagically , behind the scenes, from the *factors* whose levels correspond to the dummy variables. Summary: Learn about and understand *factors*; forget about dummy variables. cheers, Rolf Turner __ 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] R CMD build
On Sat, Apr 20, 2013 at 3:10 PM, Knut Krueger r...@knut-krueger.de wrote: Am 20.04.2013 15:50, schrieb Gabor Grothendieck: Note that there is a separate directory for the 64-bit R executables. Does it make any difference to check and pack the source files iwth 32 or 64 bit? Also, downloading MinGW should not be needed. Rtools already contains the needed UNIX utilities. Yes indeed it works better than MinGW You might want to look into the Windows batch files at http://batchfiles.googlecode.com . At least it would be very helpful for windows user to give the hint to the executable rcmd.exe build ... instead of R cmd build ... FYI, R CMD build ... works just fine on Windows (and I'm sure R cmd build ... won't). /Henrik I already set up an linux system today to solve the problem Thank you Knut __ 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] R CMD build
On Sat, Apr 20, 2013 at 10:14 PM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: On Sat, Apr 20, 2013 at 3:10 PM, Knut Krueger r...@knut-krueger.de wrote: Am 20.04.2013 15:50, schrieb Gabor Grothendieck: Note that there is a separate directory for the 64-bit R executables. Does it make any difference to check and pack the source files iwth 32 or 64 bit? Also, downloading MinGW should not be needed. Rtools already contains the needed UNIX utilities. Yes indeed it works better than MinGW You might want to look into the Windows batch files at http://batchfiles.googlecode.com . At least it would be very helpful for windows user to give the hint to the executable rcmd.exe build ... instead of R cmd build ... FYI, R CMD build ... works just fine on Windows (and I'm sure R cmd build ... won't). That is correct but if one were using the batchfiles I mentioned then both work. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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] The secret of wisdom, power and knowledge is humility.
Dear all, Thank for your friendliness. I have read several documents and I'm sure that if I have time to read ALL documents in the world I would not need to be part of this list, because of my capabilities... I have used this idea (factors) in several cases in which dummy variables arise, but I asked about the question because (in relation with my humility) I thought I had used the idea incorrectly. Nevertheless, I have noticed all I know is all I have to know about this question. Regards. Eva --- El dom, 21/4/13, Rolf Turner rolf.tur...@xtra.co.nz escribió: De: Rolf Turner rolf.tur...@xtra.co.nz Asunto: Re: [R] creating dummy variables Para: Eva Prieto Castro evapcas...@yahoo.es CC: r-help@R-project.org r-help@r-project.org Fecha: domingo, 21 de abril, 2013 03:16 On 21/04/13 10:56, Eva Prieto Castro wrote: Hi, Why do you write that dummy variables are not needed in R?. I would like you explain it. As others have said --- do some self-study. But a brief answer is that in any reasonable modelling problem in which dummy variables might arise, R creates the dummy variables that it uses automagically , behind the scenes, from the *factors* whose levels correspond to the dummy variables. Summary: Learn about and understand *factors*; forget about dummy variables. cheers, Rolf Turner [[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.
