Re: [R] Excel User interface for R
On Mon, Mar 4, 2013 at 1:39 PM, Tammy Ma metal_lical...@live.com wrote:
HI,
Assume I have the data frame generated from R as the following:
Product Price market_share
A 10010%
B 1109%
C 12020%
D 90 61%
What I want to do is to have this kind of excel user interface by changing
price of certain products, to get the impact of market share generated from R:
if I change A price from 100 to 90, and change B price from 110 to 100, based
on the calculation in R, I want to get the result from excel, for example,
Product Price market_share
A 9020%
B 100 12%
C 120 10%
D 90 58%
I want to have the excel interface which make me be able to change the value
in excel cell, then based on the calculation in R, then exported market share
impact in excel.
DO you have recommendation for such user interface or sth which make me
achieve this task?
This is just not how you *think* in R. Formulas in Excel are all
hidden, and stuff happens automatically, and if columns are all
dependent on one another then you are redundantly storing information.
If I was doing a table like this I would only store the original
information, and then write some functions to produce the spreadsheet
with all the derived columns. I would only change the original
information, and then re-run the function that generates the report.
Now, I really don't understand in your example how changing the price
of A from 100 to 90 results in a change of market_share from 10% to
20%, so I guess there must be some complex formula going on. I'll
simplify
Suppose your data is Product, Price, and Unit Sales:
d =
data.frame(Product=c(A,B,C,D),Price=c(100,110,120,90),Sales=c(3,5,3,7))
d
Product Price Sales
1 A 100 3
2 B 110 5
3 C 120 3
4 D90 7
And in Excel you would normally compute market share by value as
100*Price * Sales / SUM(Price*Sales). Then in R:
d$ShareByValue = 100 * d$Price * d$Sales / sum(d$Price*d$Sales)
d
Product Price Sales ShareByValue
1 A 100 3 16.30435
2 B 110 5 29.89130
3 C 120 3 19.56522
4 D90 7 34.23913
But if the price of Product A was wrong, and you have to change it to
90, then yes, you have to re-run the function:
d$Price=90
d$ShareByValue = 100 * d$Price * d$Sales / sum(d$Price*d$Sales)
d
Product Price Sales ShareByValue
1 A90 3 16.7
2 B90 5 27.8
3 C90 3 16.7
4 D90 7 38.9
But now we can get a bit smarter. Let's write a function that computes
the share by value:
computeShare = function(d){100*d$Price*d$Sales/sum(d$Price*d$Sales)}
computeShare(d)
[1] 16.7 27.8 16.7 38.9
So we just have to do:
d$Share = computeShare(d)
and we can re-use that function on other data (with the same named
columns). If there are any bugs in that function they only need fixing
in one place. Yes, if your data changes then all your columns may need
adjusting, but you just write a script or a function that does it. I
think something like this:
updateSales = function(d){
d$Share = computeShare(d)
d$TotalItemCost = totalItemCost(d)
d$Tax = taxTate*d$TotalItemCost
totalTax = sum(d$Tax)
list(data=d,totalTax=totalTax)
}
is a lot easier to understand than hunting round spreadsheet cells to
find that one formula you typed in wrong...
Barry
__
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] Mysterious issues with reading text files from R in ArcGIS and Excel
I appreciate the help and suggestions. I was afraid that this question would be considered off topic, but thought I would give it a try to see if anyone else gets these results from R output files. As I do not know what a hex editor or hexbin are I guess I will not be able to continue this discussion here. I will take Duncan's suggestion and try R-Geo? ~K From: Jeff Newmiller jdnew...@dcn.davis.ca.us Murdoch murdoch.dun...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Monday, March 4, 2013 6:29 PM Subject: Re: [R] Mysterious issues with reading text files from R in ArcGIS and Excel Your description of diagnosis uses non-R software (off topic here). Please either describe the difference in the files (you may need a hex editor or the hexbin package to detect the differences) or supply the files that behave differently (this may require some alternate route than this mailing list if there are odd characters at fault). For what it is worth, TXT is not a clearly-defined format, so this could be more effectively addressed by using a more specific format for data exchange. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. [[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] Mysterious issues with reading text files from R in ArcGIS and Excel
I would try write.csv or write.table with row.names = FALSE - just a guess, and do follow up on R-Sig-Geo if need be. Cheers, Mike On Tuesday, March 5, 2013, Kerry wrote: I appreciate the help and suggestions. I was afraid that this question would be considered off topic, but thought I would give it a try to see if anyone else gets these results from R output files. As I do not know what a hex editor or hexbin are I guess I will not be able to continue this discussion here. I will take Duncan's suggestion and try R-Geo? ~K From: Jeff Newmiller jdnew...@dcn.davis.ca.us javascript:; Murdoch murdoch.dun...@gmail.com javascript:; Cc: r-help@r-project.org javascript:; r-help@r-project.orgjavascript:; Sent: Monday, March 4, 2013 6:29 PM Subject: Re: [R] Mysterious issues with reading text files from R in ArcGIS and Excel Your description of diagnosis uses non-R software (off topic here). Please either describe the difference in the files (you may need a hex editor or the hexbin package to detect the differences) or supply the files that behave differently (this may require some alternate route than this mailing list if there are odd characters at fault). For what it is worth, TXT is not a clearly-defined format, so this could be more effectively addressed by using a more specific format for data exchange. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.us javascript:;Basics: ##.#. ##.#. 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. [[alternative HTML version deleted]] -- Michael Sumner Hobart, Australia e-mail: mdsum...@gmail.com [[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] Agreement and Consistency of 2D data
Hi,
I have two different imaging modalities (for the identification of areas of
infarcted myocardium) that I need to compare regarding agreement and
consistency.
However, I don't think that methods like Cohen's Kappa, PCC, Bland-Altmann
or ICC are sufficient here as there is not just a pairwise but also a
spatial relationship between measured data points. For example if the
results of the two imaging modalities are slightly misaligned their
agreement might be still much better than the mentioned tests might
indicate (at least from a practical point of view). On the other hand the
number of non-infarcted myocardial segments often heavily outweighs the
number of infarcted segments which seems to introduce a bias towards better
agreement in most examinations.
Here is an example data set, where I've calculated the ICC.
What would be the correct way to assess agreement and consistency here?
# modality 1
lgemtx - as.matrix(read.table('
http://cluster010.ovh.net/~myvideoc/R20130305/lge_mtx.csv'))
# modality 2
petmtx - as.matrix(read.table('
http://cluster010.ovh.net/~myvideoc/R20130305/pet_mtx.csv'))
# ICC
# note: modalities are inverse
# thus in modality1 0 denotes a normal segment and 100 a complete
infarction of the segment
# and vice versa in modality2
library(irr)
print(icc(cbind(100 - c(pet_mtx), c(lge_mtx)), model=twoway, type=c))
print(icc(cbind(100 - c(pet_mtx), c(lge_mtx)), model=twoway, type=a))
If the matrices are mapped to polar plots (also called bullseye plots) one
can visually assess their agreement.
Each matrix row defines one circle starting at 0° with columns equally
mapped to segments of 3,6° width.
The first row defines the outmost circle, the last row defines the inner
circle.
Here are the corresponding plots for the matrices given above (red is
infarction).
http://cluster010.ovh.net/~myvideoc/R20130305/LGE.png
http://cluster010.ovh.net/~myvideoc/R20130305/PET.png
I know, this is not a pure R question but more a general statistical one.
Hopefully it is still ok to post it here :-)
Best, Felix
[[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 function for estimating historical-VaR
You might have a look at:
http://www.portfolioprobe.com/2012/12/17/a-look-at-historical-value-at-risk/
which points to a function for historical VaR.
As Nello said, we really need to know what it is
that you think doesn't work, before we can help
you with what you have.
It probably doesn't really matter, but doing a
full sort is wasteful compared with what 'quantile'
does.
If you have further questions and they are finance
oriented as opposed to being about R programming, then
you should post to R-sig-finance (you have to subscribe
before posting).
Pat
On 04/03/2013 16:25, Blaser Nello wrote:
Does it just not work or does it not do the right thing? The reason it doesn't
work is that you are writing 'T = length(returns) x_foc = vector(length=n) N =
T-(n+1)' on one line instead of using three lines. However, your description of
what you want to do also doesn't seem to correspond to the function. Please
clarify what exactly you want the function to do. You could also write the
current function as follows.
VaR_foc - function(returns, value=1000, p=.01, n=300) {
N - length(returns)-n-1
op - N*p
unlist(lapply(1:n, function(i) {-sort(returns[i:(N+i)])[op]*value}))
}
Nello Blaser
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of ? ???
Sent: Montag, 4. März 2013 14:07
To: R-help@r-project.org
Subject: [R] R function for estimating historical-VaR
Hi everyone!! I am new in R and I want to create a simple R function for
estimating historical-VaR. In y_IBM returns, there are 2300 observations. For
evaluation I take the next 2000 observations, then I abandon the latest 300
observations. Firstly, I use the window which has the fix length and contains
the observations from 1 to 2000 to estimate the VaR. At first I take 2000 obs.
and reorder these series in ascending order, from smallest return to largest
return. Each ordered return is assigned an index value (1, 2, ...). At the 99%
confidence level, the daily VaR under historical simulation method equals the
return corresponding to the index number calculated as follows:
(1-0.99)*2000 (the number of our window) =20. The return corresponding to index
20 is the daily historical simulation VaR.
I repeat the first step except the window changes the observations from 2 to
2001. Such a process provides 300 one-step ahead VaR.
My function is:
VaR_foc - function (returns, value = 1000, p = 0.01, n=251) { T =
length(returns) x_foc = vector(length=n) N = T-(n+1)
m=sort(returns[1:N])
op = as.integer(N*p) # p % smallest
for (i in 2:n) {
g= returns[i:(N+i)]
ys = sort(g) # sort returns
x_foc[[1]] = -m[op]*value # VaR number
x_foc[i] = -ys[op]*value
}
return(x_foc)
}
VaR_foc (returns=y_IBM)
But the fucntion doesn't work, can smbd help me wh
[[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.
--
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')
__
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] What package can I use to help me categorize comment responses?
Le lundi 04 mars 2013 à 20:28 +, Lopez, Dan a écrit : Hi, We have comment questions from a survey that we need to categorize. What package and functions can I use in R to help do this? If you are asking for some kind of clustering based on vocabulary, then have a look at the tm package and the articles that present it. If you want an integrated solution with a graphical user interface, then my package RcmdrPlugin.temis performs hierarchical clustering using Ward's method and a Chi-squared distance. My two cents __ 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 spalettes for black/white printing
Hi everybody! Does anyone know a good way to color my images so that when I print them out on a non-color-printer the colors used can be distinguished well? As I have many categories I would not want to assign the colors c(black, grey, white) by hand. Thank you! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Color spalettes for black/white printing
Have a look at bpy.colors() Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens David Studer Verzonden: dinsdag 5 maart 2013 11:56 Aan: r-help@r-project.org Onderwerp: [R] Color spalettes for black/white printing Hi everybody! Does anyone know a good way to color my images so that when I print them out on a non-color-printer the colors used can be distinguished well? As I have many categories I would not want to assign the colors c(black, grey, white) by hand. Thank you! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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_create_a_package?
On 03/05/2013 02:42 PM, Jyoti Sharma wrote: hello sir myself Jyoti Sharma, and i am working as preoject fellow in IGIB Delhi. I need your help to know how to create a package as well as how to post that package to the CRAN mirror, for public use. i have used package.skeleton() command but its not working properly. So, please suggest me the right way asap. i'll be very thankful to you. Hi Jyoti, Creating packages is not a trivial task. The only ASAP solution that I could suggest is to read the first and third sections in Creating packages (Package structure and Checking and building packages) in the Writing R Extensions document that comes with R. To see this, invoke: help.start() in an R session and it should be the second link down on the left of the page that appears. 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] Color spalettes for black/white printing
That is bpy.colors() in the contributed sp package on CRAN, not in R itself. On Tuesday, March 5, 2013, ONKELINX, Thierry wrote: Have a look at bpy.colors() Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium + 32 2 525 02 51 + 32 54 43 61 85 thierry.onkel...@inbo.be javascript:; www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org javascript:; [mailto: r-help-boun...@r-project.org javascript:;] Namens David Studer Verzonden: dinsdag 5 maart 2013 11:56 Aan: r-help@r-project.org javascript:; Onderwerp: [R] Color spalettes for black/white printing Hi everybody! Does anyone know a good way to color my images so that when I print them out on a non-color-printer the colors used can be distinguished well? As I have many categories I would not want to assign the colors c(black, grey, white) by hand. Thank you! [[alternative HTML version deleted]] __ R-help@r-project.org javascript:; 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. * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * * Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org javascript:; 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. -- Michael Sumner Hobart, Australia e-mail: mdsum...@gmail.com [[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 spalettes for black/white printing
On Tue, 5 Mar 2013, David Studer wrote: Hi everybody! Does anyone know a good way to color my images so that when I print them out on a non-color-printer the colors used can be distinguished well? As I have many categories I would not want to assign the colors c(black, grey, white) by hand. The colorspace package provides a wide range of colors that - when printed on a grayscale printer - still preserve an increasing/decreasing gray palette. To explore these, see choose_palette() in colorspace which opens a GUI, let's you play around with the palettes, see them in example displays, and also let's you collapse them to gray colorse (option: desaturate). Furtheremore, you can explore the effects of different types of color blindness (provided that the dichromat package is installed). Best, Z Thank you! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, 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_create_a_package?
Hello, Another document that could help is Friedrich Leisch, Creating R Packages: A Tutorial, that can be found at http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf Hope this helps, Rui Barradas Em 05-03-2013 11:15, Jim Lemon escreveu: On 03/05/2013 02:42 PM, Jyoti Sharma wrote: hello sir myself Jyoti Sharma, and i am working as preoject fellow in IGIB Delhi. I need your help to know how to create a package as well as how to post that package to the CRAN mirror, for public use. i have used package.skeleton() command but its not working properly. So, please suggest me the right way asap. i'll be very thankful to you. Hi Jyoti, Creating packages is not a trivial task. The only ASAP solution that I could suggest is to read the first and third sections in Creating packages (Package structure and Checking and building packages) in the Writing R Extensions document that comes with R. To see this, invoke: help.start() in an R session and it should be the second link down on the left of the page that appears. 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-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] plotmath: angle brackets
Dear all, is it possible to print angle brackets (LaTeX notation: \langle, \rangle)? I found that lceil and lfloor are available, see demo(plotmath). But langle and rangle are not. I tried to print utf8 characters directly as well without success. I have also read something about a tikzDevice package. But obviously this is not available anymore. Any suggestions? Greetings Donatella __ 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] survfit plot question
1. A censored observation 2. It does not relate to either 3. See ?print.survfit . Recall also that the mean of a positive random variable is the integral from 0 to infinity of the survival function. The truncated mean is the integral from 0 to tau (819 in your case) of the survival function. Chris -Original Message- From: Steve Einbender [mailto:steve.einben...@gmail.com] Sent: Monday, March 04, 2013 7:44 AM To: r-help Subject: [R] survfit plot question Hello, I create a plot from a coxph object called fit.ads4: plot(survfit(fit.ads4)) plot is located at: https://www.dropbox.com/s/9jswrzid7mp1u62/survfit%20plot.png I also create the following survfit statistics: print(survfit(fit.ads4),print.rmean=T) Call: survfit(formula = fit.ads4) records n.maxn.start events *rmean *se(rmean) median0.95LCL0.95UCL 203.0 100.0 100.0 103.0 486.7 24.4 387.0 340.0 467.0 * restricted mean with upper limit = 819 Questions: 1. What is the cross mark in the plot ? 2. How does the cross mark in the plot relate to either the rmean or the median from survfit ? 3. What is the meaning of the restricted mean ? The upper limit noted in the output is the end of the observation period (i.e., it is always the Stop value in the Censored observation) Thanks for taking the time to review Steve [[alternative HTML version deleted]] ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues __ 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] Generating 1-bit and 8-bit BMP files using R
On 3/5/2013 12:51 AM, Ingo Reinhold wrote: Hi, I'm trying to use the data which I generate within R to make images in .bmp format to be lateron printed by a printer. My first thought was the RImageJ package, but this seems to be discontinued. What I am currently doing is generating a matrix of grey values, which needs to be parsed into the right image format. Is anyone aware of a package or rather easy way to generate these images using R? Sorry to hear this about RImageJ. I did find that old versions are still available in the repository archive: http://cran.r-project.org/src/contrib/Archive/RImageJ/ Some of the capabilities you might be looking for are available in EBImage on Bioconductor, but I don't remember specifically whether the .bmp format was supported. Rob Many thanks, Ingo [[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. -- Robert W. Baer, Ph.D. Professor of Physiology Kirksille College of Osteopathic Medicine A. T. Still University of Health Sciences Kirksville, MO 63501 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] R function for estimating historical-VaR
Cross-posted, verbatim, on stackoverflow:
http://stackoverflow.com/q/15203347/271616
--
Joshua Ulrich | about.me/joshuaulrich
FOSS Trading | www.fosstrading.com
R/Finance 2013: Applied Finance with R | www.RinFinance.com
On Mon, Mar 4, 2013 at 7:07 AM, Аскар Нысанов nysanas...@mail.ru wrote:
Hi everyone!! I am new in R and I want to create a simple R function for
estimating historical-VaR. In y_IBM returns, there are 2300 observations.
For evaluation I take the next 2000 observations,
then I abandon the latest 300 observations. Firstly, I use the window which
has the fix
length and contains the observations from 1 to 2000 to estimate the VaR. At
first I take 2000 obs. and reorder these series in ascending order, from
smallest return to largest return. Each ordered return is assigned an index
value (1, 2, ...). At the 99% confidence level, the daily VaR under
historical simulation method equals the return corresponding to the index
number calculated as follows:
(1-0.99)*2000 (the number of our window) =20. The return corresponding to
index 20 is the daily historical simulation VaR.
I repeat the first step except the window changes the observations from 2 to
2001. Such a process provides 300 one-step ahead VaR.
My function is:
VaR_foc - function (returns, value = 1000, p = 0.01, n=251) {
T = length(returns)
x_foc = vector(length=n)
N = T-(n+1)
m=sort(returns[1:N])
op = as.integer(N*p) # p % smallest
for (i in 2:n) {
g= returns[i:(N+i)]
ys = sort(g) # sort returns
x_foc[[1]] = -m[op]*value # VaR number
x_foc[i] = -ys[op]*value
}
return(x_foc)
}
VaR_foc (returns=y_IBM)
But the fucntion doesn't work, can smbd help me wh
[[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] How to reference to the `stats` package in academical paper
The question is in the title. Then, I would like to know how I should refer to the documentation regarding the use of each functions. Thanks, Julien Mehl Vettori [[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] Problem with R CMD check and the inconsolata font business
On 11/3/2011 3:30 PM, Brian Diggs wrote: Well, I figured it out. Or at least got it working. I had to run initexmf --mkmaps because apparently there was something wrong with my font mappings. I don't know why; I don't know how. But it works now. I think installing the font into the Windows Font directory was not necessary. I'm including the solution in case anyone else has this problem. Many thanks Brian Diggs! I just had the same problem and that fixed it. Matthew __ 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] boxplot with frequencies(counts)
Dear All, I have a table as following position type count 1 2 100 1 3 51 1 5 64 1 8 81 1 6 32 2 2 41 2 3 85 and so on Normally if would have a vector of 2,3,4,5... by position position and plot them by position. But now i have counts of these types. Is there a way to compute boxplot of such kind of data ? Regards, KM [[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 reference to the `stats` package in academical paper
Dear Julien,
Check
citation('stats')
HTH,
Jorge.-
On Wed, Mar 6, 2013 at 12:05 AM, Julien Mvdb julien.m...@gmail.com wrote:
The question is in the title.
Then, I would like to know how I should refer to the documentation
regarding the use of each functions.
Thanks,
Julien Mehl Vettori
[[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] Fwd: Re: How to reference to the `stats` package in academical paper
Julien, I would just try your best given the journal's style guide and wait for them to change it. For what it is worth, my last paper was corrected as follows. (In text)...one-way analysis of variance (ANOVA) in R [version 2.14.2 (R Core Team, 2012)]. (reference section) R Core Team. 2012. R: A language and environment for statistical computing. 11 Oct. 2012. http://www.R-project.org/. Andrew On 03/05/2013 07:05 AM, Julien Mvdb wrote: The question is in the title. Then, I would like to know how I should refer to the documentation regarding the use of each functions. Thanks, Julien Mehl Vettori [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] caret pls model statistics
Does anyone know of any literature on the kappa statistic with plsda? I have been trying to find papers that used plsda for classification and have yet to come across this kappa value. All the papers I come across typically have R2 as an indicator of model fit. I want to make sure I conduct such analysis appropriately, any guidance is appreciated. Regards, Charles On Sun, Mar 3, 2013 at 4:38 PM, Max Kuhn mxk...@gmail.com wrote: That the most common formula, but not the only one. See Kvålseth, T. (1985). Cautionary note about $R^2$. *American Statistician *, *39*(4), 279285. Traditionally, the symbol 'R' is used for the Pearson correlation coefficient and one way to calculate R^2 is... R^2. Max On Sun, Mar 3, 2013 at 3:16 PM, Charles Determan Jr deter...@umn.eduwrote: I was under the impression that in PLS analysis, R2 was calculated by 1- (Residual sum of squares) / (Sum of squares). Is this still what you are referring to? I am aware of the linear R2 which is how well two variables are correlated but the prior equation seems different to me. Could you explain if this is the same concept? Charles On Sun, Mar 3, 2013 at 12:46 PM, Max Kuhn mxk...@gmail.com wrote: Is there some literature that you make that statement? No, but there isn't literature on changing a lightbulb with a duck either. Are these papers incorrect in using these statistics? Definitely, if they convert 3+ categories to integers (but there are specialized R^2 metrics for binary classification models). Otherwise, they are just using an ill-suited score. How would you explain such an R^2 value to someone? R^2 is a function of correlation between the two random variables. For two classes, one of them is binary. What does it mean? Historically, models rooted in computer science (eg neural networks) used RMSE or SSE to fit models with binary outcomes and that *can* work work well. However, I don't think that communicating R^2 is effective. Other metrics (e.g. accuracy, Kappa, area under the ROC curve, etc) are designed to measure the ability of a model to classify and work well. With 3+ categories, I tend to use Kappa. Max On Sun, Mar 3, 2013 at 10:53 AM, Charles Determan Jr deter...@umn.eduwrote: Thank you for your response Max. Is there some literature that you make that statement? I am confused as I have seen many publications that contain R^2 and Q^2 following PLSDA analysis. The analysis usually is to discriminate groups (ie. classification). Are these papers incorrect in using these statistics? Regards, Charles On Sat, Mar 2, 2013 at 10:39 PM, Max Kuhn mxk...@gmail.com wrote: Charles, You should not be treating the classes as numeric (is virginica really three times setosa?). Q^2 and/or R^2 are not appropriate for classification. Max On Sat, Mar 2, 2013 at 5:21 PM, Charles Determan Jr deter...@umn.eduwrote: I have discovered on of my errors. The timematrix was unnecessary and an unfortunate habit I brought from another package. The following provides the same R2 values as it should, however, I still don't know how to retrieve Q2 values. Any insight would again be appreciated: library(caret) library(pls) data(iris) #needed to convert to numeric in order to do regression #I don't fully understand this but if I left as a factor I would get an error following the summary function iris$Species=as.numeric(iris$Species) inTrain1=createDataPartition(y=iris$Species, p=.75, list=FALSE) training1=iris[inTrain1,] testing1=iris[-inTrain1,] ctrl1=trainControl(method=cv, number=10) plsFit2=train(Species~., data=training1, method=pls, trControl=ctrl1, metric=Rsquared, preProc=c(scale)) data(iris) training1=iris[inTrain1,] datvars=training1[,1:4] dat.sc=scale(datvars) pls.dat=plsr(as.numeric(training1$Species)~dat.sc, ncomp=3, method=oscorespls, data=training1) x=crossval(pls.dat, segments=10) summary(x) summary(plsFit2) Regards, Charles On Sat, Mar 2, 2013 at 3:55 PM, Charles Determan Jr deter...@umn.edu wrote: Greetings, I have been exploring the use of the caret package to conduct some plsda modeling. Previously, I have come across methods that result in a R2 and Q2 for the model. Using the 'iris' data set, I wanted to see if I could accomplish this with the caret package. I use the following code: library(caret) data(iris) #needed to convert to numeric in order to do regression #I don't fully understand this but if I left as a factor I would get an error following the summary function iris$Species=as.numeric(iris$Species) inTrain1=createDataPartition(y=iris$Species, p=.75, list=FALSE) training1=iris[inTrain1,] testing1=iris[-inTrain1,] ctrl1=trainControl(method=cv, number=10) plsFit2=train(Species~., data=training1, method=pls, trControl=ctrl1, metric=Rsquared,
Re: [R] chisq.test
If you wanted to do a t.test
res1-do.call(cbind,lapply(seq_len(nrow(m)),function(i)
do.call(rbind,lapply(split(rbind(m[i,-1],n),1:nrow(rbind(m[i,-1],n))),
function(x) {x1- rbind(x,m[i,-1]); t.test(x1[1,],x1[2,])$p.value}
res2-do.call(cbind,lapply(seq_len(ncol(res1)),function(i)
c(c(tail(res1[seq(1,i,1),i],-1),1),res1[-c(1:i),i])))
attr(res2,dimnames)-NULL
res2
# [,1] [,2] [,3] [,4]
#[1,] 1.000 1.000 1.000 0.6027881
#[2,] 1.000 1.000 1.000 0.5790103
#[3,] 1.000 1.000 1.000 1.000
#[4,] 0.6027881 0.6027881 0.5637881 1.000
#here, the first column is testing a2, against a2, a,c,t, second c2, against t,
c2, a,c, third c3 against c,t,c3,a, and fourth t2 against a,c,t, and t2.
A.K.
From: Vera Costa veracosta...@gmail.com
To: arun smartpink...@yahoo.com
Sent: Tuesday, March 5, 2013 9:38 AM
Subject: Re: chisq.test
ok, thank you.
I will test. Thank you very much
From: Vera Costa veracosta...@gmail.com
To: arun smartpink...@yahoo.com
Sent: Tuesday, March 5, 2013 8:23 AM
Subject: Re: chisq.test
Sorry if my explanation isn't good...
I have this tables:
m-structure(list(id = structure(1:4, .Label = c(a2, c2, c3,
t2), class = factor), `1` = c(0L, 0L, 0L, 1L), `2` = c(8L,
8L, 6L, 10L), `3` = c(2L, 2L, 4L, 5L)), .Names = c(id, 1,
2, 3), row.names = c(a2, c2, c3, t2), class = data.frame)
n-structure(c(0, 0, 1, 8, 7, 10, 2, 3, 5), .Dim = c(3L, 3L), .Dimnames =
list(
c(a, c, t), c(1, 2, 3)))
and I need to apply a chisq.test between all. I need to compare a2 to a,c an
t. After compare c2 with a,c,and t.After c3 with a,c,and t
And the output will be some like this:
a b c
a2 xxx xxx
c2 xxx xxx
c3 xxx xxx
t2 xxx xxx
where is the p-values.
It isn't possible?
Vera
__
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] survfit plot question
On 03/05/2013 05:00 AM, r-help-requ...@r-project.org wrote: Hello, I create a plot from a coxph object called fit.ads4: plot(survfit(fit.ads4)) Questions: 1. What is the cross mark in the plot ? 2. How does the cross mark in the plot relate to either the rmean or the median from survfit ? Try help(plot.survfit). Read the description of mark.time. 3. What is the meaning of the restricted mean ? The upper limit noted in the output is the end of the observation period (i.e., it is always the Stop value in the Censored observation) help(print.survfit) __ 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] Excel User interface for R
This request is very completely satisfied by RExcel. Please look at rcom.univie.ac.at for full information including download information. Follow up should be on the rcom email list. You can sign up at the website. On Mon, Mar 4, 2013 at 8:39 AM, Tammy Ma metal_lical...@live.com wrote: HI, Assume I have the data frame generated from R as the following: Product Price market_share A 10010% B 1109% C 12020% D 90 61% What I want to do is to have this kind of excel user interface by changing price of certain products, to get the impact of market share generated from R: if I change A price from 100 to 90, and change B price from 110 to 100, based on the calculation in R, I want to get the result from excel, for example, Product Price market_share A 9020% B 100 12% C 120 10% D 90 58% I want to have the excel interface which make me be able to change the value in excel cell, then based on the calculation in R, then exported market share impact in excel. DO you have recommendation for such user interface or sth which make me achieve this task? Thanks. Kind regards, Lingyi [[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] Error message from flexsurvreg
I'm working on a survival analysis project and, based on previous work of my colleagues on similar projects, am trying to estimate an AFT model with a generalized gamma distribution. When I execute the following code: flexsurvreg(timesurv ~ cycles + rcycle + cyctime, dist=gengamma) I get the following error message: Error in optim(optpars, minusloglik.flexsurv, t = Y[, time], dead = Y[, : non-finite finite-difference value [4] I get an almost identical error (a 3 in the brackets instead of a 4) if I use the dist = weibull. But have no problems when I run survreg with Weibull distribution on the same data. I've seen some messages about similar errors for other functions, but don't think the responses apply (at least not in a what I understand). I tried setting initial values based on the survreg output values and that didn't help. Also, I checked and none of the variables are particularly well-correlated. Any idea how to deal with this? Thanks, -- Brett Close [[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
This is my first time to use R. For clarification: I made an oa design for 4 factors with the following levels: one with 4 levels, 2 with 3 levels, 1 with 6 levels. Using DoE package, I have generated 72 runs (setting the columns=min3). However, the numbers of generalized words of lengths 3 and 4 is still equal to 2.00e+00 and 4.559372e-33, respectively. I am concerned that these will affect my estimates since my study is only interested in obtaining the orthogonal main effects of the factors. How can I improve my design so that I can be ensured of the main effects? Thank you very much. Jonson M. Javier [[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] different colors for two wireframe spheres
Dear List, I have the code below adapted from the lattice-package examples to draw two spheres. I would now like to give both different surface colors, e.g. one red and one blue. ## 3-D surface parametrized on a 2-D grid n - 10 tx - matrix(seq(-pi, pi, length.out = 2*n), 2*n, n) ty - matrix(seq(-pi, pi, length.out = n) / 2, 2*n, n, byrow = T) xx - cos(tx) * cos(ty) yy - sin(tx) * cos(ty) zz - sin(ty) zzz - zz bxx - xx+5 byy - yy+5 bzzz - zzz+5 xx=rbind(xx,rep(NA,n),bxx) yy=rbind(yy,rep(NA,n),byy) zzz=rbind(zzz,rep(NA,n),bzzz) gr-rbind(matrix(1,n,2*n),rep(NA,n),matrix(2,n,2*n)) wireframe(zzz ~ xx + yy, groups=gr,col.groups=c(red,blue)) I tried various parameters as col.groups, col.regions but I have the impression that the groups argument in the wireframe command can only be used when supplying a data argument, which does not allow to plot the spheres as far as I tried. Is there a solution for this? Cheers David Schellenberger __ 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] Zelig package: Coxph model problems
Hi, I'm having problems with the Zelig package - when using the below R displays the follwing message (I'm running R i386 2.15.3 for Windows and have updated all the Zelig packages): z.out-zelig(Surv(psurv2, pcens2) ~ ren_sup3 + age, data=data_urgent, model=coxph) ** The model coxph is not available with the currently loaded packages, ** and is not an official Zelig package. ** The model's name may be a typo. Any suggestions? Regards, Steve Knight __ 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] generalized gamma distribution
To who(m) it may concern: I'm so beginner with R , I have a data set and want to compare the Generalized gamma distribution with different K (gamma shape parameter) for my data, in other hand wanna to fit the gengamma distribution when K has different value for example k=1, 2, 5, 10 ,… would you please to help me how could I do it? Best Marzieh __ 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] positioning of R windows
I've updated to the latest version of R, but still the problem persists. Another thing I noticed (but failed to mention before) is that when I initially open the change working directory dialog box, the little line labeled Folder: (under the window showing the folder tree) does show the current folder for a split second before reverting back to the folder Computer. But the tree always just selects Computer and below that lists the C drive and the D drive. Anyway, I am convinced now that it is not an R issue, but rather something about my computer, specifically. Glenn Stauffer -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: Friday, March 01, 2013 8:25 AM To: Glenn Stauffer Cc: 'Prof Brian Ripley'; r-help@r-project.org Subject: Re: [R] positioning of R windows On 13-02-28 11:10 AM, Duncan Murdoch wrote: On 28/02/2013 11:00 AM, Glenn Stauffer wrote: Ahh, I should have known about the MDI and SDI options - choosing SDI lets me do what I want. Thanks. On #2, I realized that when the change directory dialog window pops up, if I resize it, R remembers the resizing so that now the entire window is visible. I should have tried that before I posted. No luck though on getting the change directory dialog box to begin at the current working directory the same manner as 'save' or 'open' dialog boxes. I'll update to the new R version In the 2.15.3 release candidate, I see this: The first time I open that control, it starts in the current working directory. After that, it starts in the last directory chosen in that control. If I've used setwd() in the console to change, it doesn't see the change. This might be fixable, but not for tomorrow. It is now changed so that it starts in the current working directory, whether that was chosen by dialog or setwd(). This will appear in 3.0.0. Duncan Murdoch Duncan Murdoch Thanks, Glenn Stauffer -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Prof Brian Ripley Sent: Thursday, February 28, 2013 1:52 AM To: r-help@r-project.org Subject: Re: [R] positioning of R windows On 27/02/2013 22:33, Glenn Stauffer wrote: I have 2 (related, I think) questions about positioning of windows within R. 1. I often work with a second monitor and sometimes like to arrange 1 or more plot windows on the second monitor, while keeping the console on the primary monitor (so I can see things better). I used to be able to do this (when using Windows XP), but it seems that now (using Windows 7) I can't even move the plot window outside of the parent R window. Is this a Windows 7 issue, or something I can fix with R preferences? Run RGui with --sdi I don't believe it was ever intentionally possible to move MDI windows outside the frame. 2. When I use the file menu to change directories I noticed 2 differences from Win XP to Win 7. In Win 7, 1) the bottom of the pop-up window is off the bottom of my computer, and 2) the directory tree defaults to something close to the root, regardless of the current working directory. In Win XP, the directory tree defaulted to the current working directory, which made it easy to jump up one folder, etc. Is there any way to make this the default behavior? Ask Microsoft not to change the behaviour of their common controls API. I am using R 2.15.1 Which is not current: R 2.15.3 will be released tomorrow. And you are comparing an old OS (Win7) with a very old one (XP): R for Windows was adapted for Win7 and before that, Vista, several years ago. Thanks, Glenn Stauffer [[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] positioning of R windows
On 05/03/2013 10:22 AM, Glenn Stauffer wrote: I've updated to the latest version of R, That's a little ambiguous. Do you mean 2.15.3? I didn't put the new change into that, because it was too late. You can try a build of the development version, which will be released as 3.0.0 in April, and you should see different behaviour. Duncan Murdoch but still the problem persists. Another thing I noticed (but failed to mention before) is that when I initially open the change working directory dialog box, the little line labeled Folder: (under the window showing the folder tree) does show the current folder for a split second before reverting back to the folder Computer. But the tree always just selects Computer and below that lists the C drive and the D drive. Anyway, I am convinced now that it is not an R issue, but rather something about my computer, specifically. Glenn Stauffer -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: Friday, March 01, 2013 8:25 AM To: Glenn Stauffer Cc: 'Prof Brian Ripley'; r-help@r-project.org Subject: Re: [R] positioning of R windows On 13-02-28 11:10 AM, Duncan Murdoch wrote: On 28/02/2013 11:00 AM, Glenn Stauffer wrote: Ahh, I should have known about the MDI and SDI options - choosing SDI lets me do what I want. Thanks. On #2, I realized that when the change directory dialog window pops up, if I resize it, R remembers the resizing so that now the entire window is visible. I should have tried that before I posted. No luck though on getting the change directory dialog box to begin at the current working directory the same manner as 'save' or 'open' dialog boxes. I'll update to the new R version In the 2.15.3 release candidate, I see this: The first time I open that control, it starts in the current working directory. After that, it starts in the last directory chosen in that control. If I've used setwd() in the console to change, it doesn't see the change. This might be fixable, but not for tomorrow. It is now changed so that it starts in the current working directory, whether that was chosen by dialog or setwd(). This will appear in 3.0.0. Duncan Murdoch Duncan Murdoch Thanks, Glenn Stauffer -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Prof Brian Ripley Sent: Thursday, February 28, 2013 1:52 AM To: r-help@r-project.org Subject: Re: [R] positioning of R windows On 27/02/2013 22:33, Glenn Stauffer wrote: I have 2 (related, I think) questions about positioning of windows within R. 1. I often work with a second monitor and sometimes like to arrange 1 or more plot windows on the second monitor, while keeping the console on the primary monitor (so I can see things better). I used to be able to do this (when using Windows XP), but it seems that now (using Windows 7) I can't even move the plot window outside of the parent R window. Is this a Windows 7 issue, or something I can fix with R preferences? Run RGui with --sdi I don't believe it was ever intentionally possible to move MDI windows outside the frame. 2. When I use the file menu to change directories I noticed 2 differences from Win XP to Win 7. In Win 7, 1) the bottom of the pop-up window is off the bottom of my computer, and 2) the directory tree defaults to something close to the root, regardless of the current working directory. In Win XP, the directory tree defaulted to the current working directory, which made it easy to jump up one folder, etc. Is there any way to make this the default behavior? Ask Microsoft not to change the behaviour of their common controls API. I am using R 2.15.1 Which is not current: R 2.15.3 will be released tomorrow. And you are comparing an old OS (Win7) with a very old one (XP): R for Windows was adapted for Win7 and before that, Vista, several years ago. Thanks, Glenn Stauffer [[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] positioning of R windows
I'm sorry - yes I meant 2.15.3. But I think it probably does not matter. Others are not seeing the behavior that I am (with any version), so I don't think R is the problem. But I will post if I ever get it figured out. Thanks, Glenn Stauffer -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: Tuesday, March 05, 2013 10:58 AM To: Glenn Stauffer Cc: 'Prof Brian Ripley'; r-help@r-project.org Subject: Re: [R] positioning of R windows On 05/03/2013 10:22 AM, Glenn Stauffer wrote: I've updated to the latest version of R, That's a little ambiguous. Do you mean 2.15.3? I didn't put the new change into that, because it was too late. You can try a build of the development version, which will be released as 3.0.0 in April, and you should see different behaviour. Duncan Murdoch but still the problem persists. Another thing I noticed (but failed to mention before) is that when I initially open the change working directory dialog box, the little line labeled Folder: (under the window showing the folder tree) does show the current folder for a split second before reverting back to the folder Computer. But the tree always just selects Computer and below that lists the C drive and the D drive. Anyway, I am convinced now that it is not an R issue, but rather something about my computer, specifically. Glenn Stauffer -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: Friday, March 01, 2013 8:25 AM To: Glenn Stauffer Cc: 'Prof Brian Ripley'; r-help@r-project.org Subject: Re: [R] positioning of R windows On 13-02-28 11:10 AM, Duncan Murdoch wrote: On 28/02/2013 11:00 AM, Glenn Stauffer wrote: Ahh, I should have known about the MDI and SDI options - choosing SDI lets me do what I want. Thanks. On #2, I realized that when the change directory dialog window pops up, if I resize it, R remembers the resizing so that now the entire window is visible. I should have tried that before I posted. No luck though on getting the change directory dialog box to begin at the current working directory the same manner as 'save' or 'open' dialog boxes. I'll update to the new R version In the 2.15.3 release candidate, I see this: The first time I open that control, it starts in the current working directory. After that, it starts in the last directory chosen in that control. If I've used setwd() in the console to change, it doesn't see the change. This might be fixable, but not for tomorrow. It is now changed so that it starts in the current working directory, whether that was chosen by dialog or setwd(). This will appear in 3.0.0. Duncan Murdoch Duncan Murdoch Thanks, Glenn Stauffer -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Prof Brian Ripley Sent: Thursday, February 28, 2013 1:52 AM To: r-help@r-project.org Subject: Re: [R] positioning of R windows On 27/02/2013 22:33, Glenn Stauffer wrote: I have 2 (related, I think) questions about positioning of windows within R. 1. I often work with a second monitor and sometimes like to arrange 1 or more plot windows on the second monitor, while keeping the console on the primary monitor (so I can see things better). I used to be able to do this (when using Windows XP), but it seems that now (using Windows 7) I can't even move the plot window outside of the parent R window. Is this a Windows 7 issue, or something I can fix with R preferences? Run RGui with --sdi I don't believe it was ever intentionally possible to move MDI windows outside the frame. 2. When I use the file menu to change directories I noticed 2 differences from Win XP to Win 7. In Win 7, 1) the bottom of the pop-up window is off the bottom of my computer, and 2) the directory tree defaults to something close to the root, regardless of the current working directory. In Win XP, the directory tree defaulted to the current working directory, which made it easy to jump up one folder, etc. Is there any way to make this the default behavior? Ask Microsoft not to change the behaviour of their common controls API. I am using R 2.15.1 Which is not current: R 2.15.3 will be released tomorrow. And you are comparing an old OS (Win7) with a very old one (XP): R for Windows was adapted for Win7 and before that, Vista, several years ago. Thanks, Glenn Stauffer [[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
Re: [R] plotmath: angle brackets
On 05/03/2013 12:05, Donatella Quagli wrote: Dear all, is it possible to print angle brackets (LaTeX notation: \langle, \rangle)? I found that lceil and lfloor are available, see demo(plotmath). But langle and rangle are not. I tried to print utf8 characters directly as well without success. I have also read something about a tikzDevice package. But obviously this is not available anymore. Any suggestions? You can use anything from the Adobe Symbol font, see ?plotmath. symbol(0xe1) and symbol(0xf1) look the nearest match. Greetings Donatella -- 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.
[R] Reading outdated .Rprofile file
Hi there:
I'm having a weird problem with my startup procedure. R.app is reading an
unknown .Rprofile file.
First, I'm on a Mac Os 10.6.8 running R.app 2.15.0
On startup
getwd()
[1] /Users/simon
But: the contents of my .Rprofile file in my home directory when viewed with a
text editor are:
.First-function() {
source(/Users/simon/Documents/R/functions/trim.leading.R)
source(/Users/simon/Documents/R/functions/trim.trailing.R)
source(/Users/simon/Documents/R/functions/trim.R)
source(/Users/simon/Documents/R/functions/pseudor2.R)
source(/Users/simon/Documents/R/functions/dates.R)
source(/Users/simon/Documents/R/functions/andersen.R)
source(/Users/simon/Documents/R/functions/tabfun.R)
source(/Users/simon/Documents/R/functions/cox_snell.R)
source(/Users/simon/Documents/R/functions/cor.prob.R)
source(/Users/simon/Documents/R/functions/kmo.R)
source(/Users/simon/Documents/R/functions/residual.stats.R)
source(/Users/simon/Documents/R/functions/missings.plot.R)
}
but then, when I type .First from the command line I get
function ()
{
source(/Users/simon/Documents/R/functions/sample_size.R)
source(/Users/simon/Documents/R/functions/pseudor2.R)
source(/Users/simon/Documents/R/functions/dates.R)
source(/Users/simon/Documents/R/functions/andersen.R)
source(/Users/simon/Documents/R/functions/tabfun.R)
source(/Users/simon/Documents/R/functions/cox_snell.R)
source(/Users/simon/Documents/R/functions/cor.prob.R)
source(/Users/simon/Documents/R/functions/kmo.R)
}
Needless to say, I get an error because the file sample.size.R was deleted a
long time ago.
So how do I get R.app to read the updated .Rprofile file?
__
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] Reading outdated .Rprofile file
Preamble: There is a dedicated R-Mac-SIG list where this would have been more
appropriately directed. and followups should be directed there (and the R-help
address removed so we do not have two simulatnaous threads.)
On Mar 5, 2013, at 8:38 AM, Simon Kiss wrote:
Hi there:
I'm having a weird problem with my startup procedure. R.app is reading an
unknown .Rprofile file.
First, I'm on a Mac Os 10.6.8 running R.app 2.15.0
There have been several updates to the R.app that went with R 2.15.0 that
should not be at all disruptive to acquire. R.app version numbers are not in
sync with R versions so that doesn't tell us what R.app you have. This is the
current R.app (based on what is at the r.research.att.com website) : Mac OS X
GUI rev. 6451
On startup
getwd()
[1] /Users/simon
But: the contents of my .Rprofile file in my home directory when viewed with
a text editor are:
What is your home directory and does your understanding agree with what you
see when you use the Preferences panel from within a running version of R.app?
inline: Snapz Pro XScreenSnapz028.png
I'm also running OSX 10.6.8, but R version 2.15.2 (2012-10-26) Platform:
x86_64-apple-darwin9.8.0/x86_64 (64-bit). Looking at the Get Info panel for the
GUI I see I am also somewhat out-of-date: R.app GUI 1.53 (6335 Leopard build
64-bit).
I noticed that R 2.15.3 is now available. (I had been checking over the last
several days and this is the first time I noticed that it had appeared.)
.First-function() {
source(/Users/simon/Documents/R/functions/trim.leading.R)
source(/Users/simon/Documents/R/functions/trim.trailing.R)
source(/Users/simon/Documents/R/functions/trim.R)
source(/Users/simon/Documents/R/functions/pseudor2.R)
source(/Users/simon/Documents/R/functions/dates.R)
source(/Users/simon/Documents/R/functions/andersen.R)
source(/Users/simon/Documents/R/functions/tabfun.R)
source(/Users/simon/Documents/R/functions/cox_snell.R)
source(/Users/simon/Documents/R/functions/cor.prob.R)
source(/Users/simon/Documents/R/functions/kmo.R)
source(/Users/simon/Documents/R/functions/residual.stats.R)
source(/Users/simon/Documents/R/functions/missings.plot.R)
}
but then, when I type .First from the command line I get
function ()
{
source(/Users/simon/Documents/R/functions/sample_size.R)
source(/Users/simon/Documents/R/functions/pseudor2.R)
source(/Users/simon/Documents/R/functions/dates.R)
source(/Users/simon/Documents/R/functions/andersen.R)
source(/Users/simon/Documents/R/functions/tabfun.R)
source(/Users/simon/Documents/R/functions/cox_snell.R)
source(/Users/simon/Documents/R/functions/cor.prob.R)
source(/Users/simon/Documents/R/functions/kmo.R)
}
Needless to say, I get an error because the file sample.size.R was deleted a
long time ago.
So how do I get R.app to read the updated .Rprofile file?
Could there be another .Profile file? (They are invisible by default in the
MacOS using Finder.app.)
--
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.
[R] permutest
I'm working with capscale and permutest for the first time, and having trouble getting statistical analyses for more than one constraining variable. I've read the documentation, but setting first=FALSE or using by=axis doesn't seem to be helping. capscale seems to be fine, I receive output for more than one constrained axis. What am I doing wrong? capscale.Nrem.results-capscale(as.dist(qiime.data$distmat)~ N+rem+N*rem+Condition(dateFac), factor.frame) capscale.Nrem.results Inertia Proportion Rank Total 1.454538 Real Total 1.459802 1.00 Conditional0.117117 0.0802281 Constrained0.386228 0.2645763 Unconstrained 0.956457 0.655197 22 Imaginary -0.005264 2 Inertia is squared Unknown distance Eigenvalues for constrained axes: CAP1CAP2CAP3 0.29869 0.05395 0.03359 Eigenvalues for unconstrained axes: MDS1MDS2MDS3MDS4MDS5MDS6MDS7MDS8 0.27719 0.13725 0.11048 0.06691 0.05551 0.04940 0.03892 0.03468 (Showed only 8 of all 22 unconstrained eigenvalues) sig.Nrem - permutest(capscale.Nrem.results,permutations=999, by=margin, model=direct,first=FALSE) sig.Nrem Permutation test for capscale Call: capscale(formula = as.dist(qiime.data$distmat) ~ N + rem + Condition(dateFac) + N:rem, data = factor.frame) Permutation test for all constrained eigenvalues Pseudo-F: 2.961281 (with 3, 22 Degrees of Freedom) Significance: 0.001 Based on 999 permutations under direct model. [[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-help Digest, Vol 121, Issue 5
On R 2.15.2 and ArcGIS 9.3.1, it works for me in ArcCatalog but you have to follow the particulars here: http://webhelp.esri.com/arcgisdesktop/9.3/index.cfm?TopicName=Accessing_delimited_text_file_data For example: write.table(test, '***.tab', sep = '\t', row.names = F) The extension .tab and sep = '\t' are required for text files. Didn't test row.names=T but I wouldn't count on that working either. Jason Law Statistician City of Portland, Bureau of Environmental Services Water Pollution Control Laboratory 6543 N Burlington Avenue Portland, OR 97203-5452 503-823-1038 jason@portlandoregon.gov -Original Message- Date: Mon, 04 Mar 2013 10:48:39 -0500 From: Duncan Murdoch murdoch.dun...@gmail.com To: Kerry kernichol...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Subject: Re: [R] Mysterious issues with reading text files from R in ArcGIS and Excel Message-ID: 5134c257.6020...@gmail.com Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/03/2013 10:09 AM, Kerry wrote: It seems within the last ~3 months Ive been having issues with writing text or csv files from a R data frame. The problem is multifold and it is hard to filter out what is going on and where the problem is. So, Im hoping someone else has come across this and may provide insight. I think you need to provide a simple example for us to try, either by putting a small example of one of your files online for us to download, or (better) by giving us self-contained code to duplicate the problem. You might also get better help (especially about ArcGIS) on the R-sig-Geo mailing list: https://stat.ethz.ch/mailman/listinfo/r-sig-geo. Duncan Murdoch My current settings for R: R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C [5] LC_TIME=Swedish_Sweden.1252 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] adehabitat_1.8.11 shapefiles_0.6foreign_0.8-51tkrplot_0.0-23 ade4_1.5-1 loaded via a namespace (and not attached): [1] tools_2.15.2 I am using Microsoft Excel 2010 and ArcGIS 10.1sp1 for Desktop Basically, no matter what data frame I am working on, when I export it to a text file to be use in Excel or ArcGIS problems arise. Im not sure if it is R or these other programs, maybe forums for ArcGIS might be more appropriate, but this problem only occurs when I use tables that have been produced from an R session. When I try to open a text file in Excel, either I get an error message stating The file you are trying to open is in a different format than specified by the file extension. Verify that the file is not corrupted and is from a trusted source. Followed by Excel has detected that 'file.txt' is a SYLK file, but cannot load it. Either the file has errors or is not a SYLK file format. Click OK to open the file in a different format Then the file opens Otherwise, the file opens fine the first time through - and looks ok. I can't figure out what Im doing different between the two commands of write.table as they are always written the same: write.csv(file, file = D:/mylocations/fileofinterest.csv) or write.table(file, file = D:/mylocations/fileofinterest.txt) Sometimes I will try to add sep = , or sep = ; but these don't make a difference (which I didn't figure they would). The other program I use is ArcGIS and bringing in a txt file from R is really messing things up as 2 new columns of information are typically added and date/time data is usually lost with txt files, but not with csv files. For instance - a text file that looks like this in Excel: id x ydateR1dmedR1dmean R1error R2error 1 F07001 1482445 6621768 2007-03-05 10:00:53 2498.2973 2498.2973 FALSE FALSE 2 F07001 1481274 6619628 2007-03-05 12:00:41 657.1029 657.1029FALSE FALSE 3 F07001 1481279 6619630 2007-03-05 14:01:12 660.3569 660.3569FALSE FALSE 4 F07001 1481271 6619700 2007-03-05 16:00:39 620.1397 620.1397FALSE FALSE in ArcGIS now looks like this: Field1idid_Xid_YxydateR1dmedR1dmean R1errorR2errorOBJECTID * 1F07001118.0818119.485541e+01514824456621768NA2498.297272498.29727FALSEFALSE1 2F07001118.0818119.485541e+01514812746619628NA657.102922657.102922FALSEFALSE2 3F07001118.0818119.485541e+01514812796619630NA660.356911660.356911FALSEFALSE3 4F07001118.0818119.485541e+01514812716619700NA620.139702620.139702FALSEFALSE4 5F07001118.0818119.485541e+01514808496620321NA378.186792378.186792FALSEFALSE5 Where did id_X and id_Y come from?? What are they?? What happened to the Date column??? Why does the date column show up when I use write.csv but not write.table? Thank you for your help. ~K [[alternative HTML version deleted]]
[R] Simulate binary correlated data
Dear R experts, I am trying to simulate correlated binary data and have stumbled upon the following problem: With the help of binarySimCLF or mvpBinaryEp I have been able to simulate correlating binary vectors given certain mean values and a desired correlation. My problem is that these procedures do not allow you to specify the exact vector for which you want to generate a correlated vector. Is there anyway to do this? Maybe I can clarify my question by explaining what my goal is: I want to generate one Binary Vector (A), generate a correlated binary Vector (B), then generate a third binary Vector (C) that is correlated to B so that I can then see the occuring correlations between A and C. Thank you in advance, Marbles -- View this message in context: http://r.789695.n4.nabble.com/Simulate-binary-correlated-data-tp4660366.html Sent from the R help mailing list archive at Nabble.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] Is there a serial autocorrelation test for FGLS-FE fitted with PGGLS?
Dears, a simple question here: is there any AR1 and AR2 test for FGLS-FE fitted with the pggls function of plm package? (one example would be the Baltagi-Wu LBI test) Thanks for your attention! [[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] useR! 2013 registration open
We are happy to inform you that registration for useR! 2013 is now open, see http://www.R-project.org/useR-2013 This meeting of the R user community will take place at the University of Castilla-La Mancha, Albacete, Spain, July 10-12, 2013. Pre-conference tutorials will be offered on July 9. A list of tutorials is available at http://www.r-project.org/useR-2013/Tutorials/ Submission of contributed talks and posters is still open. More information can be found here: http://www.r-project.org/useR-2013#Call In addition to regular talks and posters, all participants are invited to present a Lightning Talk, for which no abstract is required. The format for Lightning Talks is a 15-slide version of Pecha Kucha. Registered participants will be contacted to provide an informative title in due course. Thanks to Revolution Analytics, Google, R-Studio and Oracle, we have a number of bursaries available for Ph.D. students. These will cover registration fees and, if possible, travel expenses. If you would like to apply you need to: - Register for the conference and include Apply for Bursary in the Comments section of the Registration form - Submit an abstract using the standard procedure (remember that deadline is 31 March 2013). Only those applicants who submit an abstract will be considered. - Send a summary of your CV, motivation letter (including title of your abstract) and support letter from your advisor to user-2...@r-project.org . In the subject of the e-mail state clearly that it is a bursary application. Deadline for bursary applications is 15th April 2013. We look forward to seeing you at useR! 2013 in Albacete! -- Virgilio Gómez Rubio Departamento de Matemáticas Escuela de Ingenieros Industriales - Albacete Avda. España s/n - 02071 Albacete - SPAIN Tlf: (+34) 967 59 92 00 ext. 8250/8242 __ 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] Zelig package: Coxph model problems
I think Zelig uses model=cox.ph ( https://github.com/zeligdev/ZeligMisc/blob/master/tests/coxph.R) -thomas On Wed, Mar 6, 2013 at 2:54 AM, Stephen Knight stephenkni...@doctors.org.uk wrote: Hi, I'm having problems with the Zelig package - when using the below R displays the follwing message (I'm running R i386 2.15.3 for Windows and have updated all the Zelig packages): z.out-zelig(Surv(psurv2, pcens2) ~ ren_sup3 + age, data=data_urgent, model=coxph) ** The model coxph is not available with the currently loaded packages, ** and is not an official Zelig package. ** The model's name may be a typo. Any suggestions? Regards, Steve Knight __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Thomas Lumley Professor of Biostatistics University of Auckland [[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 short course, BYU Summer Institute of Applied Statistics
For anyone looking for an intermediate to advanced level short course on R this summer, I will be presenting at the BYU Summer Institute of Applied Statistics June 19-21, 2013. The official page is here: http://statistics.byu.edu/r-beyond-basics-38th-annual-summer-institute-applied-statistics This course is intended for those who have worked through and have a fairly good understanding of An Introduction to R and will go into the more advanced uses and programming of R beyond the introduction. This is put on by the Statistics department at Brigham Young University in Provo, Utah (if you come, plan an extra day or so to enjoy the mountains). -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[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] ggplot2: two time series with different dates in a single plot
Hi Using the ggplot2 package, I would like to obtain a plot that contains two time series that have data points on different dates. For instance, one data frame looks like: date1, value1 2010-01-05, 2921.74 2010-01-08, 2703.89 2010-01-14, 3594.21 2010-01-20, 3659.22 The other data frame looks like date2, value2 2010-01-01, 285.85 2010-01-02, 229.20 2010-01-05, 333.91 2010-01-06, 338.27 2010-01-07, 272.85 2010-01-08, 249.04 2010-01-09, 240.07 2010-01-10, 255.06 2010-01-11, 275.42 2010-01-12, 252.39 I would like to plot these two time series in one and the same plot, with date on the X axis and value on the Y axis. And while you're at it: how would you proceed to get a secondary Y axis for the second dataframe? Thanks a lot! Matthijs Daelman [[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] Error message
Dear all,
I got an error message when running the following code.
Can anyone give any suggestions on fixing this type of error?
Thank you very much in advance.
Hanna
integrand - function(x, rho, a, b, z){
+ x1 - x[1]
+ x2 - x[2]
+ Sigma - matrix(c(1, rho, rho, 1), 2,2)
+ mu - rep(0,2)
+ f - pmnorm(c((z-a*x1)/b, (z-a*x2)/b), mu,
Sigma)*dmnorm(c(0,0), mu, diag(2))
+ f
+}
adaptIntegrate(integrand, lower=rep(-Inf, 2), upper=c(2,2),
+ rho=0.1, a=0.6, b=0.3, z=3, maxEval=1)
Error in if (any(lower upper)) stop(lowerupper integration limits) :
missing value where TRUE/FALSE needed
[[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] ggplot2: two time series with different dates in a single plot
On Tue, Mar 5, 2013 at 3:30 PM, Matthijs Daelman matthijs.dael...@gmail.com wrote: Hi Using the ggplot2 package, I would like to obtain a plot that contains two time series that have data points on different dates. For instance, one data frame looks like: date1, value1 2010-01-05, 2921.74 2010-01-08, 2703.89 2010-01-14, 3594.21 2010-01-20, 3659.22 The other data frame looks like date2, value2 2010-01-01, 285.85 2010-01-02, 229.20 2010-01-05, 333.91 2010-01-06, 338.27 2010-01-07, 272.85 2010-01-08, 249.04 2010-01-09, 240.07 2010-01-10, 255.06 2010-01-11, 275.42 2010-01-12, 252.39 I would like to plot these two time series in one and the same plot, with date on the X axis and value on the Y axis. And while you're at it: how would you proceed to get a secondary Y axis for the second dataframe? Lines1 - date1, value1 2010-01-05, 2921.74 2010-01-08, 2703.89 2010-01-14, 3594.21 2010-01-20, 3659.22 Lines2 - date2, value2 2010-01-01, 285.85 2010-01-02, 229.20 2010-01-05, 333.91 2010-01-06, 338.27 2010-01-07, 272.85 2010-01-08, 249.04 2010-01-09, 240.07 2010-01-10, 255.06 2010-01-11, 275.42 2010-01-12, 252.39 library(zoo) library(ggplot2) # create two zoo time series objects z1 - read.zoo(text = Lines1, header = TRUE, sep = ,) z2 - read.zoo(text = Lines2, header = TRUE, sep = ,) # combine them into a single multivariate time series z - na.approx(merge(z1, z2)) # single panel autoplot(z, facet = NULL) # or, multiple panels with different Y axes autoplot(z) + facet_free() Different left and right are generally frowned upon but if you want that anyways look at the examples in ?plot.zoo -- 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] different colors for two wireframe spheres
On Mar 5, 2013, at 3:28 AM, David Schellenberger Costa wrote: Dear List, I have the code below adapted from the lattice-package examples to draw two spheres. I would now like to give both different surface colors, e.g. one red and one blue. ## 3-D surface parametrized on a 2-D grid n - 10 tx - matrix(seq(-pi, pi, length.out = 2*n), 2*n, n) ty - matrix(seq(-pi, pi, length.out = n) / 2, 2*n, n, byrow = T) xx - cos(tx) * cos(ty) yy - sin(tx) * cos(ty) zz - sin(ty) zzz - zz bxx - xx+5 byy - yy+5 bzzz - zzz+5 xx=rbind(xx,rep(NA,n),bxx) yy=rbind(yy,rep(NA,n),byy) zzz=rbind(zzz,rep(NA,n),bzzz) gr-rbind(matrix(1,n,2*n),rep(NA,n),matrix(2,n,2*n)) wireframe(zzz ~ xx + yy, groups=gr,col.groups=c(red,blue)) You might try: wireframe(zzz ~ xx + yy, groups=gr, drape=TRUE ) Notice that in help(wireframe): Details you find a sentence: Note that this feature does not work with groups, subscripts, subset, etc. Conditioning variables are also not supported in this case. This sentence refers back to the paragraph beginning For single panel plots, wireframe can also plot parametrized 3-D surfaces... that describes the method you are using to draw those spheres. I tried various parameters as col.groups, col.regions but I have the impression that the groups argument in the wireframe command can only be used when supplying a data argument, which does not allow to plot the spheres as far as I tried. Is there a solution for this? Cheers David Schellenberger __ 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] Simulate binary correlated data
On Tue, Mar 5, 2013 at 7:07 PM, Marbles max-ihm...@gmx.de wrote: Dear R experts, I am trying to simulate correlated binary data and have stumbled upon the following problem: With the help of binarySimCLF or mvpBinaryEp I have been able to simulate correlating binary vectors given certain mean values and a desired correlation. My problem is that these procedures do not allow you to specify the exact vector for which you want to generate a correlated vector. Is there anyway to do this? Maybe I can clarify my question by explaining what my goal is: I want to generate one Binary Vector (A), generate a correlated binary Vector (B), then generate a third binary Vector (C) that is correlated to B so that I can then see the occuring correlations between A and C. IIRC, knowing the correlation between A B and the correlation between B C is not enough to uniquely specify the correlation between A C (or perhaps even to bound it). Therefore i think your question is ill-defined. Though I might be wrong in the specific case of binary variates... Cheers, MW Thank you in advance, Marbles -- View this message in context: http://r.789695.n4.nabble.com/Simulate-binary-correlated-data-tp4660366.html Sent from the R help mailing list archive at Nabble.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-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] Function completely locks up my computer if the input is too big
Dear r-help,
Somewhere in my innocuous function to rotate an object in Cartesian space
I've created a monster that completely locks up my computer (requires a
hard reset every time). I don't know if this is useful description to
anyone - the mouse still responds, but not the keyboard and not windows
explorer.
The script only does this when the input matrix is large, and so my initial
runs didn't catch it as I used a smaller matrix to speed up the test runs.
When I tried an input matrix with a number of dimensions in the same order
of magnitude as the data I want to read in, R and my computer choked. This
was a surprise for me, as I've always been able to break execution in the
past or do other tasks. So i tried it again, and still no dice.
Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely
cause the issue.
Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
loop to do this function piece-wise for larger data and see if that helps.
Script is attached and appended below.
Thanks
Ben Caldwell
#compass to polar coordinates
compass2polar - function(x) {-x+90}
#degrees (polar) to radians
Deg2Rad - function(x) {(x*pi)/180}
# radians to degrees
Rad2Deg - function (rad) (rad/pi)*180
# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x y of equal length
Pol2Car - function(distance,deg) {
rad - Deg2Rad(compass2polar(deg))
rad - rep(rad, length(distance))
x - ifelse(is.na(distance), NA, distance * cos(rad))
y - ifelse(is.na(distance), NA, distance * sin(rad))
x-round(x,2)
y-round(y,2)
cartes- list(x,y)
name-c('x','y')
names(cartes)-name
cartes
}
#rotate an object, with assumed origin at 0,0, in any number of degrees
rotate - function(x,y,tilt){ 8
d2 - x^2+y^2
rotate.dis-sqrt(d2)
or.rad - atan(x/y)
or.deg - Rad2Deg(or.rad)
n - length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] - 0}
}
# browser()
tilt.in - tilt + or.deg
xy-Pol2Car (distance=rotate.dis, deg=tilt.in)
# if(abs(tilt) = 0) {
# shift.frame - cbind(xy$x, xy$y)
# shift.frame.val - shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
# shift.x- shift.frame.val[1] * -1
# shift.y- shift.frame.val[2] * -1
# x-xy$x + shift.x
# y-xy$y + shift.y
# }
# name - c('x', 'y')
# xy-list(x,y)
# names(xy)-name
xy
}
x - seq(0,5, .5)
y - seq(0,5, .5)
z - seq(0,5, .5)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
#this works fine
rotated-rotate(dquad$x, dquad$y, 45)
points(rotated$x, rotated$y, col='green')
# profiling of both time and memory
Rprof(“myFunction.out”, memory.profiling=T)
y - myFunction(x)
Rprof(NULL)
summaryRprof(“myFunction.out”, memory=”both”)
#
x - seq(0,5, .1)
y - seq(0,5, .1)
z - seq(0,5, .1)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
# running the below locks up my machine (commented out to avoid accidental
run)
# rotated-rotate(dquad$x, dquad$y, 45)
__
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] Reading Wyoming radiosonde data files with RadioSonde package
Hi, I need to do some analysis on historic daily radiosonde data I download from the Wyoming Univ. web page ( http://weather.uwyo.edu/upperair/sounding.html). I am trying to use the RadioSonde package (V 1.3), but the format of the files from Wyoming don't match what RadioSonde is expecting. Has anyone used the Radiosonde package on the Wyoming data? Here is a sample of the Wyoming file format: 40179 Bet Dagan Observations at 00Z 22 Feb 2013 - PRES HGHT TEMP DWPT RELH MIXR DRCT SKNT THTA THTE THTV hPa m C C %g/kgdeg knot K K K - 70.0 18430 -64.5 265 91 446.1 446.1 59.6 19417 -60.9 265 83 475.1 475.1 50.0 20500 -62.5 265 75 495.8 495.8 46.7 20920 -64.3 501.2 501.2 38.3 22137 -63.5 532.5 532.5 33.3 23012 -56.3 573.2 573.2 30.0 23670 -59.9 580.8 580.8 28.1 24078 -60.5 590.0 590.0 20.5 26056 -57.1 656.0 656.0 Station information and sounding indices Station number: 40179 Observation time: 130222/ Station latitude: 32.00 Station longitude: 34.81 Station elevation: 35.0 Mean mixed layer potential temperature: 0.00 Mean mixed layer mixing ratio: 0.00 Here is the code I tried: filename - 'D:\\Data\\sounding_test3.txt' datakey - -- varkey -PRES unitkey - hPa sample.sonde - getsonde(filename, datakey, varkey, unitkey) Error in getsonde(filename, datakey, varkey, unitkey) : (getsonde): could not find a unique match for the data string Thanks, Ilik Win7 OS 64-bit, R version 2.13.0. [[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] Meaning of error message when exporting to MS Excel
Hi,
I’m attempting to export data (split into multiple files from one large
dataset) from R to excel using the excel.link package. The code for export
is as follows:
for(i in practicesNN){
#Create relevant data for input
#Separate out all parts of data – PracticeName is removed from example
data for privacy reasons
detailedH-dataExport2[dataExport1$PracticeName == i
dataExport1$RISK_LEVEL == 'High',]
detailedM-dataExport2[dataExport1$PracticeName == i
dataExport1$RISK_LEVEL == 'Medium',]
detailedL-dataExport2[dataExport1$PracticeName == i
dataExport1$RISK_LEVEL == 'Low',]
print(paste(i,2))
x-paste(i,.xls,sep=)
#Open excel template
xl.workbook.open(Template.xls)
#Create practice specific file
xl.workbook.save(x)
#Activate detailed High risk sheet
xl.sheet.activate(High Risk detailed)
#Update detailed High risk spreadsheet
xlrc[a1]-detailedH
#Activate detailed Medium risk sheet
xl.sheet.activate(Medium Risk detailed)
#Update detailed Medium risk spreadsheet
xlrc[a1]-detailedM
#Activate detailed Low risk sheet
xl.sheet.activate(Low Risk detailed)
#Update detailed Low risk spreadsheet
xlrc[a1]-detailedL
#Save spreadsheet
xl.workbook.save(x)
#Close spreadsheet
xl.workbook.close(x)
}
I attached an example file of data of the first 8 rows of the first xls. The
columns of the spreadsheet are filled until it gets to column ‘HbA1c_mmol’
which produces the following error:
Error in apply(r.obj[, iter], 1, paste, collapse = \t) :
dim(X) must have a positive length
I removed the offending column and the same occurs when column ‘BMI’ is
encountered. Having searched for similar error message I have been unable to
deduce the meaning of the error, particularly the ‘apply(r.obj[, iter], 1,
paste, collapse = \t)’ part. Can anyone explain what the error message
means and how to resolve it?
Many thanks,
Dove ExampleData.csv
http://r.789695.n4.nabble.com/file/n4660378/ExampleData.csv
--
View this message in context:
http://r.789695.n4.nabble.com/Meaning-of-error-message-when-exporting-to-MS-Excel-tp4660378.html
Sent from the R help mailing list archive at Nabble.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] Simulate binary correlated data
Thank you for your response! I know that it is not enough to uniquely specify the correlation. That is why i would like to simulate it so that i can see how the resulting correlations between A and C are distributed in dependence of the correlations between AB and BC. -- View this message in context: http://r.789695.n4.nabble.com/Simulate-binary-correlated-data-tp4660366p4660380.html Sent from the R help mailing list archive at Nabble.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] Simulate binary correlated data
Btw: I have done this for non-binary variables already. If anyone is
interested, it looks like this.
I am pretty new to R, so excuse the potentially unelegant code.
# Implement library
library(ecodist)
# Prepare ACOutcome vector
ACOutcomes = c()
# Set desired variablelength Number of simulations
VarLength = 1000
NSim = 1
# Set desired range for correlations
rangeAB = c(0.0, 1.0)
rangeBC = c(0.0, 1.0)
# Start n simulation runs
n = 0
while(n NSim) {n=n+1;
# Set desired correlations between Variables
DesCorAB = runif(1, rangeAB[1], rangeAB[2])
DesCorBC = runif(1, rangeBC[1], rangeBC[2])
# Simulate A and B with desired correlation between them
DatasetAB = corgen(len=VarLength, r=DesCorAB, epsilon=0.00)
A = DatasetAB$x
B = DatasetAB$y
# Option of saving correlation between A B
cor(A, B, method = pearson)
# Simulate C with desired correlation to B
C = corgen(x=B, r=DesCorBC, epsilon = 0.00)$y
# Calculate correlation between A C
corAC = cor(A, C, method = pearson)
# Save correlation AC into vector
ACOutcomes = append(ACOutcomes, corAC)
;}
# Show results: Mean, Minimum, Maximum
hist(ACOutcomes, breaks = 100)
mean(ACOutcomes)
min(ACOutcomes)
max(ACOutcomes)
--
View this message in context:
http://r.789695.n4.nabble.com/Simulate-binary-correlated-data-tp4660366p4660382.html
Sent from the R help mailing list archive at Nabble.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] Questions on implementing logistic regression
Hi there, I am trying to write a tool which involves implementing logistic regression. With the batch gradient descent method, the convergence is guaranteed as it is a convex problem. However, I find that with the stochastic gradient decent method, it typically converges to some random points (i.e., not very close to the minimum point resulted from the batch method). I have tried different ways of decreasing the learning rate, and different starting points of weights. However, the performance (e.g., accuracy, precision/recall, ...) are comparable (to the batch method). I understand that this is possible, since SGD(stochastic gradient descent) uses an approximation to the real cost each step. Does it matter? I guess it does since otherwise the interpretation of the weights would not make much sense even the accuracy is comparable. If it matters, I wonder if you have some suggestions on how to make it converge or getting close to the global optimal point. 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] Function completely locks up my computer if the input is too big
Tena koe Benjamin
I haven't looked at you code in detail, but in general ifelse is slow and can
generally be avoided. For example,
ben - 1:10^7
system.time(BEN - ifelse(ben10, NA, -ben))
user system elapsed
1.310.241.56
system.time({BEN1 - -ben; BEN1[BEN1 -10] - NA})
user system elapsed
0.170.030.20
all.equal(BEN, BEN1)
[1] TRUE
HTH ...
Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Benjamin Caldwell
Sent: Wednesday, 6 March 2013 10:18 a.m.
To: r-help
Subject: [R] Function completely locks up my computer if the input is too big
Dear r-help,
Somewhere in my innocuous function to rotate an object in Cartesian space I've
created a monster that completely locks up my computer (requires a hard reset
every time). I don't know if this is useful description to anyone - the mouse
still responds, but not the keyboard and not windows explorer.
The script only does this when the input matrix is large, and so my initial
runs didn't catch it as I used a smaller matrix to speed up the test runs.
When I tried an input matrix with a number of dimensions in the same order of
magnitude as the data I want to read in, R and my computer choked. This was a
surprise for me, as I've always been able to break execution in the past or do
other tasks. So i tried it again, and still no dice.
Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely cause
the issue.
Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a loop to
do this function piece-wise for larger data and see if that helps.
Script is attached and appended below.
Thanks
Ben Caldwell
#compass to polar coordinates
compass2polar - function(x) {-x+90}
#degrees (polar) to radians
Deg2Rad - function(x) {(x*pi)/180}
# radians to degrees
Rad2Deg - function (rad) (rad/pi)*180
# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x y of equal length
Pol2Car - function(distance,deg) {
rad - Deg2Rad(compass2polar(deg))
rad - rep(rad, length(distance))
x - ifelse(is.na(distance), NA, distance * cos(rad))
y - ifelse(is.na(distance), NA, distance * sin(rad))
x-round(x,2)
y-round(y,2)
cartes- list(x,y)
name-c('x','y')
names(cartes)-name
cartes
}
#rotate an object, with assumed origin at 0,0, in any number of degrees
rotate - function(x,y,tilt){ 8
d2 - x^2+y^2
rotate.dis-sqrt(d2)
or.rad - atan(x/y)
or.deg - Rad2Deg(or.rad)
n - length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] - 0}
}
# browser()
tilt.in - tilt + or.deg
xy-Pol2Car (distance=rotate.dis, deg=tilt.in)
# if(abs(tilt) = 0) {
# shift.frame - cbind(xy$x, xy$y)
# shift.frame.val - shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
# shift.x- shift.frame.val[1] * -1
# shift.y- shift.frame.val[2] * -1
# x-xy$x + shift.x
# y-xy$y + shift.y
# }
# name - c('x', 'y')
# xy-list(x,y)
# names(xy)-name
xy
}
x - seq(0,5, .5)
y - seq(0,5, .5)
z - seq(0,5, .5)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
#this works fine
rotated-rotate(dquad$x, dquad$y, 45)
points(rotated$x, rotated$y, col='green')
# profiling of both time and memory
Rprof(myFunction.out, memory.profiling=T)
y - myFunction(x)
Rprof(NULL)
summaryRprof(myFunction.out, memory=both)
#
x - seq(0,5, .1)
y - seq(0,5, .1)
z - seq(0,5, .1)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
# running the below locks up my machine (commented out to avoid accidental
run)
# rotated-rotate(dquad$x, dquad$y, 45)
The contents of this e-mail are confidential and may be ...{{dropped:14}}
__
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] Reading Wyoming radiosonde data files with RadioSonde package
Sure looks as if that second --... line is causing another attempt at parsing for varkey and unitkey which for 70.0 and 59.6 just won't make sense to getsonde. It's a pain but I'd experiment by removing that second ... line. Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Tue, 5 Mar 2013, Ilan Levy wrote: Hi, I need to do some analysis on historic daily radiosonde data I download from the Wyoming Univ. web page ( http://weather.uwyo.edu/upperair/sounding.html). I am trying to use the RadioSonde package (V 1.3), but the format of the files from Wyoming don't match what RadioSonde is expecting. Has anyone used the Radiosonde package on the Wyoming data? Here is a sample of the Wyoming file format: 40179 Bet Dagan Observations at 00Z 22 Feb 2013 - PRES HGHT TEMP DWPT RELH MIXR DRCT SKNT THTA THTE THTV hPa m C C %g/kgdeg knot K K K - 70.0 18430 -64.5 265 91 446.1 446.1 59.6 19417 -60.9 265 83 475.1 475.1 50.0 20500 -62.5 265 75 495.8 495.8 46.7 20920 -64.3 501.2 501.2 38.3 22137 -63.5 532.5 532.5 33.3 23012 -56.3 573.2 573.2 30.0 23670 -59.9 580.8 580.8 28.1 24078 -60.5 590.0 590.0 20.5 26056 -57.1 656.0 656.0 Station information and sounding indices Station number: 40179 Observation time: 130222/ Station latitude: 32.00 Station longitude: 34.81 Station elevation: 35.0 Mean mixed layer potential temperature: 0.00 Mean mixed layer mixing ratio: 0.00 Here is the code I tried: filename - 'D:\\Data\\sounding_test3.txt' datakey - -- varkey -PRES unitkey - hPa sample.sonde - getsonde(filename, datakey, varkey, unitkey) Error in getsonde(filename, datakey, varkey, unitkey) : (getsonde): could not find a unique match for the data string Thanks, Ilik Win7 OS 64-bit, R version 2.13.0. [[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] Function completely locks up my computer if the input is too big
I see you have profiling calls in there. Have you used them?
It is often fruitful to see how the time for a function grows as size of the
input or output grows. Have you tried that?
A concrete suggestion is to change
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] - 0}
}
to
or.deg[is.na(or.deg)] - 0
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 Benjamin Caldwell
Sent: Tuesday, March 05, 2013 1:18 PM
To: r-help
Subject: [R] Function completely locks up my computer if the input is too big
Dear r-help,
Somewhere in my innocuous function to rotate an object in Cartesian space
I've created a monster that completely locks up my computer (requires a
hard reset every time). I don't know if this is useful description to
anyone - the mouse still responds, but not the keyboard and not windows
explorer.
The script only does this when the input matrix is large, and so my initial
runs didn't catch it as I used a smaller matrix to speed up the test runs.
When I tried an input matrix with a number of dimensions in the same order
of magnitude as the data I want to read in, R and my computer choked. This
was a surprise for me, as I've always been able to break execution in the
past or do other tasks. So i tried it again, and still no dice.
Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely
cause the issue.
Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
loop to do this function piece-wise for larger data and see if that helps.
Script is attached and appended below.
Thanks
Ben Caldwell
#compass to polar coordinates
compass2polar - function(x) {-x+90}
#degrees (polar) to radians
Deg2Rad - function(x) {(x*pi)/180}
# radians to degrees
Rad2Deg - function (rad) (rad/pi)*180
# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x y of equal length
Pol2Car - function(distance,deg) {
rad - Deg2Rad(compass2polar(deg))
rad - rep(rad, length(distance))
x - ifelse(is.na(distance), NA, distance * cos(rad))
y - ifelse(is.na(distance), NA, distance * sin(rad))
x-round(x,2)
y-round(y,2)
cartes- list(x,y)
name-c('x','y')
names(cartes)-name
cartes
}
#rotate an object, with assumed origin at 0,0, in any number of degrees
rotate - function(x,y,tilt){ 8
d2 - x^2+y^2
rotate.dis-sqrt(d2)
or.rad - atan(x/y)
or.deg - Rad2Deg(or.rad)
n - length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] - 0}
}
# browser()
tilt.in - tilt + or.deg
xy-Pol2Car (distance=rotate.dis, deg=tilt.in)
# if(abs(tilt) = 0) {
# shift.frame - cbind(xy$x, xy$y)
# shift.frame.val - shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
# shift.x- shift.frame.val[1] * -1
# shift.y- shift.frame.val[2] * -1
# x-xy$x + shift.x
# y-xy$y + shift.y
# }
# name - c('x', 'y')
# xy-list(x,y)
# names(xy)-name
xy
}
x - seq(0,5, .5)
y - seq(0,5, .5)
z - seq(0,5, .5)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
#this works fine
rotated-rotate(dquad$x, dquad$y, 45)
points(rotated$x, rotated$y, col='green')
# profiling of both time and memory
Rprof(myFunction.out, memory.profiling=T)
y - myFunction(x)
Rprof(NULL)
summaryRprof(myFunction.out, memory=both)
#
x - seq(0,5, .1)
y - seq(0,5, .1)
z - seq(0,5, .1)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
# running the below locks up my machine (commented out to avoid accidental
run)
# rotated-rotate(dquad$x, dquad$y, 45)
__
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] Issues when using interaction term with a lagged variable
Hi there! Today I tried to estimate models using both plm and pgmm functions, with an interaction between X1 and lag(X2, 1). And I notice two issues. Let Y=b_1 * X_1 + b_2 * X_2 + b_3 * X_1 * x_2 + e be our model. 1) When using plm, I got different results when I coded the interaction term with I(X1 * lag(X2, 1)) and when I just saved this multiplication X1 * lag(X2, 1) in a different variable of the dataset and then used it. in the regression. 2) With pgmm it is not even possible to run a formula which contains I(X1 * lag(X2, 1)). How can I pass such interaction? Thanks in advance 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.
Re: [R] histogram
HI Elisa, Just noticed the order of elements in vec1: You have to replace `vec1` dat2- as.dist(dat1[,-1],upper=F,diag=F) vec1- as.vector(dat2) head(vec1) #[1] 5.796656 43.523023 38.193750 44.730182 6.511703 2.904954 #the order is based on columns #with dat1- read.csv(rightest.csv,sep=,,header=TRUE,check.names=FALSE) label1=c(0-25,25-50,50-75) dat1New- dat1[,-1] vec1- unlist(lapply(seq_len(nrow(dat1New)),function(i) dat1New[i,][1:which(dat1New[i,]==0)-1])) head(vec1) # 1 1 2 1 2 3 # 5.796656 43.523023 36.305633 38.193750 31.623020 5.391179 #correct order dat1[1:4,1:4] # St. 1 2 3 #1 1 0.00 5.796656 43.523023 #2 2 5.796656 0.00 36.305633 #3 3 43.523023 36.305633 0.00 #4 4 38.193750 31.623020 5.391179 Name2-unlist(lapply(0:123,function(i) if(length(rep(i+1,i)=1)) paste((,paste(rep(i+1,i)[1],seq_along(rep(i+1,i)),sep=,),),sep=) else NULL)) dat3New- data.frame(Name2,vec1) resNew-t(aggregate(.~Name2,data=dat3New,function(x) table(cut(x,breaks=seq(0,75,25),labels=label1 colnames(resNew)- resNew[1,] resNew1- resNew[-1,] row.names(resNew1)-gsub(vec1.,,row.names(resNew1)) Names3-apply(resNew1,1,function(x) paste(names(which(x!=0)),collapse=,)) res2- data.frame(Frequency=apply(resNew1,1,function(x) sum(1*(x!=0))), stations=Names3,stringsAsFactors=FALSE) A.K. - Original Message - From: arun smartpink...@yahoo.com To: eliza botto eliza_bo...@hotmail.com Cc: Sent: Tuesday, March 5, 2013 8:12 AM Subject: Re: histogram Dear Elisa, I already sent you the solution. Name2-unlist(lapply(0:123,function(i) if(length(rep(i+1,i)=1)) paste((,paste(rep(i+1,i)[1],seq_along(rep(i+1,i)),sep=,),),sep=) else NULL)) dat3New- data.frame(Name2,vec1) resNew-t(aggregate(.~Name2,data=dat3New,function(x) table(cut(x,breaks=seq(0,75,25),labels=label1 colnames(resNew)- resNew[1,] resNew1- resNew[-1,] row.names(resNew1)-gsub(vec1.,,row.names(resNew1)) Names3-apply(resNew1,1,function(x) paste(names(which(x!=0)),collapse=,)) res2- data.frame(Frequency=apply(resNew1,1,function(x) sum(1*(x!=0))), stations=Names3,stringsAsFactors=FALSE) A.K. From: eliza botto eliza_bo...@hotmail.com To: smartpink...@yahoo.com smartpink...@yahoo.com Sent: Tuesday, March 5, 2013 7:04 AM Subject: RE: histogram Dear Arun, Extremely sorry for replying you late. i really wanted to calculate the index of dat3. It alright for me, even if the size of output is really large. thanks in advance Elisa __ 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] histogram
Hi,
I guess this is what you wanted.
Attaching a plot from a subset (lstSub)
dat1- read.csv(rightest.csv,sep=,,header=TRUE,check.names=FALSE)
label1=c(0-25,25-50,50-75)
Name1-unlist(lapply(0:123,function(i) rep(i+1,i)))
dat1New- dat1[,-1]
vec1- unlist(lapply(seq_len(nrow(dat1New)),function(i)
dat1New[i,][1:which(dat1New[i,]==0)-1]))
dat3-data.frame(Name1,vec1)
dat3$Categ-as.character(cut(dat3$vec1,breaks=seq(0,75,25),labels=label1))
source(k.txt)
lst1- split(dat3,dat3$Name1)
#lstSub-split(dat3,dat3$Name1)[1:4]
pdf(ElisaNew0_25.pdf)
lapply(lst1,function(x) {indx025-which(x$Categ==0-25);
indx2550-which(x$Categ==25-50);indx5075-which(x$Categ==50-75);
if(length(indx025)=1)
{matplot(k[,indx025],ylim=c(0,5),type=l,col=grey,main=paste(range
0-25,line=,unique(x$Name1),sep= ),xlab=T,ylab=Q);
lines(k[,unique(x$Name1)],type=l,col=black)} else NULL})
dev.off()
pdf(ElisaNew25_50New.pdf)
lapply(lst1,function(x) {indx025-which(x$Categ==0-25);
indx2550-which(x$Categ==25-50);indx5075-which(x$Categ==50-75);
if(length(indx2550)=1)
{matplot(k[,indx2550],ylim=c(0,5),type=l,col=grey,main=paste(range
25-50,line=,unique(x$Name1),sep= ),xlab=T,ylab=Q);
lines(k[,unique(x$Name1)],type=l,col=black)} else NULL})
dev.off()
pdf(ElisaNew50_75.pdf)
lapply(lst1,function(x) {indx025-which(x$Categ==0-25);
indx2550-which(x$Categ==25-50);indx5075-which(x$Categ==50-75);
if(length(indx5075)=1)
{matplot(k[,indx5075],ylim=c(0,5),type=l,col=grey,main=paste(range
50-75,line=,unique(x$Name1),sep= ),xlab=T,ylab=Q);
lines(k[,unique(x$Name1)],type=l,col=black)} else NULL})
dev.off()
A.K.
From: eliza botto eliza_bo...@hotmail.com
To: smartpink...@yahoo.com smartpink...@yahoo.com
Sent: Tuesday, March 5, 2013 5:04 PM
Subject: RE: histogram
Dear Arun,
Thanks for the update.
Any success with the recently asked question?
thanks
elisa
Date: Tue, 5 Mar 2013 14:00:29 -0800
From: smartpink...@yahoo.com
Subject: Re: histogram
To: eliza_bo...@hotmail.com
CC: r-help@r-project.org
HI Elisa,
Just noticed the order of elements in vec1:
You have to replace `vec1`
dat2- as.dist(dat1[,-1],upper=F,diag=F)
vec1- as.vector(dat2)
head(vec1)
#[1] 5.796656 43.523023 38.193750 44.730182 6.511703 2.904954 #the order
is based on columns
#with
dat1- read.csv(rightest.csv,sep=,,header=TRUE,check.names=FALSE)
label1=c(0-25,25-50,50-75)
dat1New- dat1[,-1]
vec1- unlist(lapply(seq_len(nrow(dat1New)),function(i)
dat1New[i,][1:which(dat1New[i,]==0)-1]))
head(vec1)
# 1 1 2 1 2 3
# 5.796656 43.523023 36.305633 38.193750 31.623020 5.391179 #correct order
dat1[1:4,1:4]
# St. 1 2 3
#1 1 0.00 5.796656 43.523023
#2 2 5.796656 0.00 36.305633
#3 3 43.523023 36.305633 0.00
#4 4 38.193750 31.623020 5.391179
Name2-unlist(lapply(0:123,function(i) if(length(rep(i+1,i)=1))
paste((,paste(rep(i+1,i)[1],seq_along(rep(i+1,i)),sep=,),),sep=) else
NULL))
dat3New- data.frame(Name2,vec1)
resNew-t(aggregate(.~Name2,data=dat3New,function(x)
table(cut(x,breaks=seq(0,75,25),labels=label1
colnames(resNew)- resNew[1,]
resNew1- resNew[-1,]
row.names(resNew1)-gsub(vec1.,,row.names(resNew1))
Names3-apply(resNew1,1,function(x) paste(names(which(x!=0)),collapse=,))
res2- data.frame(Frequency=apply(resNew1,1,function(x) sum(1*(x!=0))),
stations=Names3,stringsAsFactors=FALSE)
A.K.
- Original Message -
From: arun smartpink...@yahoo.com
To: eliza botto eliza_bo...@hotmail.com
Cc:
Sent: Tuesday, March 5, 2013 8:12 AM
Subject: Re: histogram
Dear Elisa,
I already sent you the solution.
Name2-unlist(lapply(0:123,function(i)
if(length(rep(i+1,i)=1))
paste((,paste(rep(i+1,i)[1],seq_along(rep(i+1,i)),sep=,),),sep=)
else NULL))
dat3New- data.frame(Name2,vec1)
resNew-t(aggregate(.~Name2,data=dat3New,function(x)
table(cut(x,breaks=seq(0,75,25),labels=label1
colnames(resNew)- resNew[1,]
resNew1- resNew[-1,]
row.names(resNew1)-gsub(vec1.,,row.names(resNew1))
Names3-apply(resNew1,1,function(x) paste(names(which(x!=0)),collapse=,))
res2- data.frame(Frequency=apply(resNew1,1,function(x) sum(1*(x!=0))),
stations=Names3,stringsAsFactors=FALSE)
A.K.
From: eliza botto eliza_bo...@hotmail.com
To: smartpink...@yahoo.com smartpink...@yahoo.com
Sent: Tuesday, March 5, 2013 7:04 AM
Subject: RE: histogram
Dear Arun,
Extremely sorry for replying you late. i really wanted to calculate the index
of dat3. It alright for me, even if the size of output is really large.
thanks in advance
Elisa
ElisaNew25_50.pdf
Description: Adobe PDF document
__
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,
[R] Wilcox-Off?
A potentially ridiculous question, but why does R use wilcox (e.g., pwilcox or wilcox.test) instead of the full name Wilcoxon? I've browsed (but not scoured) the help files and Peter Dalgaard's book, but I'm coming up empty. Purely for brevity or have I missed something massive? ## Reproducible example ;-) ? wilcox.test ## End Reproducible Example Cheers, Michael __ 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] Questions on implementing logistic regression
I may be missing something, but what does this have to do specifically with R? I believe this is OT here and you need to post elsewhere, e.g. perhaps on stats.stackexchange.com. -- Bert On Tue, Mar 5, 2013 at 1:36 PM, Ivan Li machinelearning2...@gmail.com wrote: Hi there, I am trying to write a tool which involves implementing logistic regression. With the batch gradient descent method, the convergence is guaranteed as it is a convex problem. However, I find that with the stochastic gradient decent method, it typically converges to some random points (i.e., not very close to the minimum point resulted from the batch method). I have tried different ways of decreasing the learning rate, and different starting points of weights. However, the performance (e.g., accuracy, precision/recall, ...) are comparable (to the batch method). I understand that this is possible, since SGD(stochastic gradient descent) uses an approximation to the real cost each step. Does it matter? I guess it does since otherwise the interpretation of the weights would not make much sense even the accuracy is comparable. If it matters, I wonder if you have some suggestions on how to make it converge or getting close to the global optimal point. 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. -- 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] Questions on implementing logistic regression
Perhaps I should have added and FWIW, R, like essentially all statistical software, has logistic regression already built in, if I understand what you mean by the term (which I may not), via glm's. -- Bert On Tue, Mar 5, 2013 at 1:36 PM, Ivan Li machinelearning2...@gmail.com wrote: Hi there, I am trying to write a tool which involves implementing logistic regression. With the batch gradient descent method, the convergence is guaranteed as it is a convex problem. However, I find that with the stochastic gradient decent method, it typically converges to some random points (i.e., not very close to the minimum point resulted from the batch method). I have tried different ways of decreasing the learning rate, and different starting points of weights. However, the performance (e.g., accuracy, precision/recall, ...) are comparable (to the batch method). I understand that this is possible, since SGD(stochastic gradient descent) uses an approximation to the real cost each step. Does it matter? I guess it does since otherwise the interpretation of the weights would not make much sense even the accuracy is comparable. If it matters, I wonder if you have some suggestions on how to make it converge or getting close to the global optimal point. 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. -- 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] Function completely locks up my computer if the input is too big
Hi all,
Thanks for the suggestions. Updating the function as below to break the
problem into chunks seemed to do the trick - perhaps there is a relatively
small limit to the size of a vector that R can work with?
Best
rotate - function(x,y,tilt,threshold){
df.main-data.frame(x,y)
if(length(x) threshold){
l - round(length(x)/ threshold, 0)
dfchunk - split(df.main, factor(sort(rank(row.names(df.main))%%l)))
n-length(summary(dfchunk)[,1])
xy-vector(list, n)
for (i in 1:n){
wk.df - dfchunk[[i]]
x - wk.df$x
y - wk.df$y
d2 - x^2+y^2
rotate.dis-sqrt(d2)
or.rad - atan(x/y)
or.deg - Rad2Deg(or.rad)
or.deg[is.na(or.deg)] - 0
tilt.in - tilt + or.deg
xy[[i]]-data.frame(Pol2Car(distance=rotate.dis, deg=tilt.in))
}
xy-do.call(rbind, xy[1:n])
} else {
d2 - x^2+y^2
rotate.dis-sqrt(d2)
or.rad - atan(x/y)
or.deg - Rad2Deg(or.rad)
n - length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] - 0}
}
tilt.in - tilt + or.deg
xy-data.frame(Pol2Car (distance=rotate.dis, deg=tilt.in))
}
xy
}
*Ben Caldwell*
Graduate Fellow
University of California, Berkeley
130 Mulford Hall #3114
Berkeley, CA 94720
Office 223 Mulford Hall
(510)859-3358
On Tue, Mar 5, 2013 at 1:44 PM, Peter Alspach
peter.alsp...@plantandfood.co.nz wrote:
Tena koe Benjamin
I haven't looked at you code in detail, but in general ifelse is slow and
can generally be avoided. For example,
ben - 1:10^7
system.time(BEN - ifelse(ben10, NA, -ben))
user system elapsed
1.310.241.56
system.time({BEN1 - -ben; BEN1[BEN1 -10] - NA})
user system elapsed
0.170.030.20
all.equal(BEN, BEN1)
[1] TRUE
HTH ...
Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Benjamin Caldwell
Sent: Wednesday, 6 March 2013 10:18 a.m.
To: r-help
Subject: [R] Function completely locks up my computer if the input is too
big
Dear r-help,
Somewhere in my innocuous function to rotate an object in Cartesian space
I've created a monster that completely locks up my computer (requires a
hard reset every time). I don't know if this is useful description to
anyone - the mouse still responds, but not the keyboard and not windows
explorer.
The script only does this when the input matrix is large, and so my
initial runs didn't catch it as I used a smaller matrix to speed up the
test runs.
When I tried an input matrix with a number of dimensions in the same order
of magnitude as the data I want to read in, R and my computer choked. This
was a surprise for me, as I've always been able to break execution in the
past or do other tasks. So i tried it again, and still no dice.
Now I need the function to work as subsequent functions/functionality are
dependent, and I can't see anything on the face of it that would likely
cause the issue.
Any insight on why this happens in general or specifically in my case are
appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
loop to do this function piece-wise for larger data and see if that helps.
Script is attached and appended below.
Thanks
Ben Caldwell
#compass to polar coordinates
compass2polar - function(x) {-x+90}
#degrees (polar) to radians
Deg2Rad - function(x) {(x*pi)/180}
# radians to degrees
Rad2Deg - function (rad) (rad/pi)*180
# polar to cartesian coordinates - assumes degrees those from a compass.
output is a list, x y of equal length
Pol2Car - function(distance,deg) {
rad - Deg2Rad(compass2polar(deg))
rad - rep(rad, length(distance))
x - ifelse(is.na(distance), NA, distance * cos(rad))
y - ifelse(is.na(distance), NA, distance * sin(rad))
x-round(x,2)
y-round(y,2)
cartes- list(x,y)
name-c('x','y')
names(cartes)-name
cartes
}
#rotate an object, with assumed origin at 0,0, in any number of degrees
rotate - function(x,y,tilt){ 8
d2 - x^2+y^2
rotate.dis-sqrt(d2)
or.rad - atan(x/y)
or.deg - Rad2Deg(or.rad)
n - length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] - 0}
}
# browser()
tilt.in - tilt + or.deg
xy-Pol2Car (distance=rotate.dis, deg=tilt.in)
# if(abs(tilt) = 0) {
# shift.frame - cbind(xy$x, xy$y)
# shift.frame.val - shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
# shift.x- shift.frame.val[1] * -1
# shift.y- shift.frame.val[2] * -1
# x-xy$x + shift.x
# y-xy$y + shift.y
# }
# name - c('x', 'y')
# xy-list(x,y)
# names(xy)-name
xy
}
x - seq(0,5, .5)
y - seq(0,5, .5)
z - seq(0,5, .5)
dquad-expand.grid(x,y,z)
name-c(y,x,z)
names(dquad)-name
plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
#this works fine
rotated-rotate(dquad$x, dquad$y, 45)
points(rotated$x, rotated$y, col='green')
# profiling of both time and memory
Rprof(myFunction.out, memory.profiling=T)
y - myFunction(x)
Rprof(NULL)
Re: [R] Issues when using interaction term with a lagged variable
Actually, the problem number 2 is easy to solve: instead of using I(X1 * lag(X2,1)), one should use X1:lag(X2,1). It works. The issue number 1 remains, though. And also affects this solution for number 2. It means: results are different with one uses X1:lag(X2,1) whithin the formula or uses a new variable previouysly created with X1*lag(X2,1). Any insights here would be very hepful. 2013/3/5 Richard Asturia richard.astu...@gmail.com Hi there! Today I tried to estimate models using both plm and pgmm functions, with an interaction between X1 and lag(X2, 1). And I notice two issues. Let Y=b_1 * X_1 + b_2 * X_2 + b_3 * X_1 * x_2 + e be our model. 1) When using plm, I got different results when I coded the interaction term with I(X1 * lag(X2, 1)) and when I just saved this multiplication X1 * lag(X2, 1) in a different variable of the dataset and then used it. in the regression. 2) With pgmm it is not even possible to run a formula which contains I(X1 * lag(X2, 1)). How can I pass such interaction? Thanks in advance 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.
Re: [R] plotmath: angle brackets
Indeed! Thank you! __ 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] Wilcox-Off?
On 2013-03-05 14:51, R. Michael Weylandt wrote: A potentially ridiculous question, but why does R use wilcox (e.g., pwilcox or wilcox.test) instead of the full name Wilcoxon? I've browsed (but not scoured) the help files and Peter Dalgaard's book, but I'm coming up empty. Purely for brevity or have I missed something massive? ## Reproducible example ;-) ? wilcox.test ## End Reproducible Example Cheers, Michael I would guess that it's the brevity argument; witness pnorm, pchisq, punif, ppois, pbinom, phyper, ... But maybe Kurt knows better since he's down as the author of pwilcox. Peter Ehlers __ 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] Zelig package: Coxph model problems
On Mar 5, 2013, at 5:54 AM, Stephen Knight wrote: Hi, I'm having problems with the Zelig package - when using the below R displays the follwing message (I'm running R i386 2.15.3 for Windows and have updated all the Zelig packages): z.out-zelig(Surv(psurv2, pcens2) ~ ren_sup3 + age, data=data_urgent, model=coxph) ** The model coxph is not available with the currently loaded packages, ** and is not an official Zelig package. ** The model's name may be a typo. When this question (or at least something like it ) was asked last November on the Zelig mailing lis, rolling back to earlier versions was the suggestion: http://comments.gmane.org/gmane.comp.lang.r.zelig/848 I do not see any mention of coxph or cox.ph as a model specification in the current docs for that package. -- 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.
[R] Constrained cubic smoothing spline
Hello everone, Anyone who knows how to force a cubic smoothing spline to pass through a particular point? I found on website someone said that we can use cobs package to force the spline pass through certain points or impose shape constraints (increasing, decreasing). However, this package is using B-spline and can only do linear and quadratic B-spline. In my research, I need to force a cubic smoothing spline to pass a point. Thanks! Victor [[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] About basic logical operators
Hello everyone, I have a basic question regarding logical operators. x-seq(-1,1,by=0.02) x [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 [61] 0.20 0.22 0.24 0.26 0.28 0.30 0.32 0.34 0.36 0.38 0.40 0.42 [73] 0.44 0.46 0.48 0.50 0.52 0.54 0.56 0.58 0.60 0.62 0.64 0.66 [85] 0.68 0.70 0.72 0.74 0.76 0.78 0.80 0.82 0.84 0.86 0.88 0.90 [97] 0.92 0.94 0.96 0.98 1.00 x[x=0.02] [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02 0.00 x[x0.2] [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 [61] 0.20 Why does x[x=0.02] return no 0.02 but x[x0.2] return a subsample with 0.02? Anyone who can tell me why? Thanks! Victor [[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] About basic logical operators
not sure if you meant to use both 0.2 and 0.02, but i believe your unexpected results are a floating point issue.. start here http://r.789695.n4.nabble.com/That-dreaded-floating-point-trap-td3418142.html and here http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and google floating point r for more detail :) On Tue, Mar 5, 2013 at 7:53 PM, Victor hyk victor_...@yahoo.ca wrote: Hello everyone, I have a basic question regarding logical operators. x-seq(-1,1,by=0.02) x [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 [61] 0.20 0.22 0.24 0.26 0.28 0.30 0.32 0.34 0.36 0.38 0.40 0.42 [73] 0.44 0.46 0.48 0.50 0.52 0.54 0.56 0.58 0.60 0.62 0.64 0.66 [85] 0.68 0.70 0.72 0.74 0.76 0.78 0.80 0.82 0.84 0.86 0.88 0.90 [97] 0.92 0.94 0.96 0.98 1.00 x[x=0.02] [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02 0.00 x[x0.2] [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 0.16 0.18 [61] 0.20 Why does x[x=0.02] return no 0.02 but x[x0.2] return a subsample with 0.02? Anyone who can tell me why? Thanks! Victor [[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] About basic logical operators
faq 7.31 --- 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. Victor hyk victor_...@yahoo.ca wrote: Hello everyone, � I have a basic question regarding logical operators. x-seq(-1,1,by=0.02) x � [1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 �[13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 �[25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 �[37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 �[49] -0.04 -0.02� 0.00� 0.02� 0.04� 0.06� 0.08� 0.10� 0.12� 0.14� 0.16� 0.18 �[61]� 0.20� 0.22� 0.24� 0.26� 0.28� 0.30� 0.32� 0.34� 0.36� 0.38� 0.40� 0.42 �[73]� 0.44� 0.46� 0.48� 0.50� 0.52� 0.54� 0.56� 0.58� 0.60� 0.62� 0.64� 0.66 �[85]� 0.68� 0.70� 0.72� 0.74� 0.76� 0.78� 0.80� 0.82� 0.84� 0.86� 0.88� 0.90 �[97]� 0.92� 0.94� 0.96� 0.98� 1.00 x[x=0.02] �[1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02� 0.00 x[x0.2] �[1] -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80 -0.78 [13] -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56 -0.54 [25] -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32 -0.30 [37] -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08 -0.06 [49] -0.04 -0.02� 0.00� 0.02� 0.04� 0.06� 0.08� 0.10� 0.12� 0.14� 0.16� 0.18 [61]� 0.20 Why does x[x=0.02] return� no 0.02 but x[x0.2] return a subsample with 0.02? Anyone who can tell me why? Thanks! Victor [[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] aov() and anova() making faulty F-tests
Dear useRs, I've just encountered a serious problem involving the F-test being carried out in aov() and anova(). In the provided example, aov() is not making the correct F-test for an hypothesis involving the expected mean square (EMS) of a factor divided by the EMS of another factor (i.e., instead of the error EMS). Here is the example: Expected Mean Squaredf Mi σ2+18σ2M 1 Ij σ2+6σ2MI+12Ф(I) 2 MIij σ2+6σ2MI 2 ε(ijk)lσ2 30 The clear test for Ij is EMS(I) / EMS(MI) - F(2,2) However, observe the following example carried out in R, M - rep(c(M1, M2), each = 18) I - as.ordered(rep(rep(c(5,10,15), each = 6), 2)) y - c(44,39,48,40,43,41,27,20,25,21,28,22,35,30,29,34,31,38,12,7,6,11,7,12,15,10,12,17,11,13,22,15,27,22,21,19) dat - data.frame(M, I, y) summary(aov(y~M*I, data = dat)) DfSum Sq Mean Sq F value Pr(F) m 1 3136.0 3136.0295.85 2e-16 *** i2 513.7 256.9 24.23 5.45e-07 *** m:i 2 969.5 484.7 45.73 7.77e-10 *** Residuals 30 318.010.6 --- In this example aov has taken the F-ratio of MS(I) / MS(ε) - F(2,30) = 24.23 with F-crit = qf(0.95,2,3) = 9.55 -- significant However, as stated above, the correct F-ratio is MS(I) / MS(MI) - F(2,2) = 0.53 with F-crit = qf(0.95,2,2) = 19 -- non-significant Why is aov() miscalculating the F-ratio, and is there a way to fix this without prior knowledge of the appropriate test (e.g., EMS(I)/EMS(MI)? Thanks for your help, Patrick -- View this message in context: http://r.789695.n4.nabble.com/aov-and-anova-making-faulty-F-tests-tp4660407.html Sent from the R help mailing list archive at Nabble.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] CARET and NNET fail to train a model when the input is high dimensional
The following code fails to train a nnet model in a random dataset using caret: nR - 700 nCol - 2000 myCtrl - trainControl(method=cv, number=3, preProcOptions=NULL, classProbs = TRUE, summaryFunction = twoClassSummary) trX - data.frame(replicate(nR, rnorm(nCol))) trY - runif(1)*trX[,1]*trX[,2]^2+runif(1)*trX[,3]/trX[,4] trY - as.factor(ifelse(sign(trY)0,'X1','X0')) my.grid - createGrid(method.name, grid.len, data=trX) my.model - train(trX,trY,method=method.name,trace=FALSE,trControl=myCtrl,tuneGrid=my.grid, metric=ROC) print(Done) The error I get is: task 2 failed - arguments imply differing number of rows: 1334, 666 However, everything works if I reduce nR to, say 20. Any thoughts on what may be causing this? Is there a place where I could report this bug other than this mailing list? Here is my session info: sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] nnet_7.3-5 pROC_1.5.4 caret_5.15-052 foreach_1.4.0 [5] cluster_1.14.3 plyr_1.8reshape2_1.2.2 lattice_0.20-13 loaded via a namespace (and not attached): [1] codetools_0.2-8 compiler_2.15.2 grid_2.15.2 iterators_1.0.6 [5] stringr_0.6.2 tools_2.15.2 Thanks, 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] aov() and anova() making faulty F-tests
Your subject line is patent nonsense. The aov() and anova() functions have been around for decades. If they were doing something wrong it would have been noticed long since. You should realize that the fault is in your understanding, not in these functions. I cannot really follow your convoluted and messy code, but it would appear that you want to consider M and I to be random effects. Where have you informed aov() as to the presence of these random effects? cheers, Rolf Turner On 03/06/2013 03:36 PM, PatGauthier wrote: Dear useRs, I've just encountered a serious problem involving the F-test being carried out in aov() and anova(). In the provided example, aov() is not making the correct F-test for an hypothesis involving the expected mean square (EMS) of a factor divided by the EMS of another factor (i.e., instead of the error EMS). Here is the example: Expected Mean Squaredf Mi σ2+18σ2M 1 Ij σ2+6σ2MI+12Ф(I) 2 MIij σ2+6σ2MI 2 ε(ijk)lσ2 30 The clear test for Ij is EMS(I) / EMS(MI) - F(2,2) However, observe the following example carried out in R, M - rep(c(M1, M2), each = 18) I - as.ordered(rep(rep(c(5,10,15), each = 6), 2)) y - c(44,39,48,40,43,41,27,20,25,21,28,22,35,30,29,34,31,38,12,7,6,11,7,12,15,10,12,17,11,13,22,15,27,22,21,19) dat - data.frame(M, I, y) summary(aov(y~M*I, data = dat)) DfSum Sq Mean Sq F value Pr(F) m 1 3136.0 3136.0295.85 2e-16 *** i2 513.7 256.9 24.23 5.45e-07 *** m:i 2 969.5 484.7 45.73 7.77e-10 *** Residuals 30 318.010.6 --- In this example aov has taken the F-ratio of MS(I) / MS(ε) - F(2,30) = 24.23 with F-crit = qf(0.95,2,3) = 9.55 -- significant However, as stated above, the correct F-ratio is MS(I) / MS(MI) - F(2,2) = 0.53 with F-crit = qf(0.95,2,2) = 19 -- non-significant Why is aov() miscalculating the F-ratio, and is there a way to fix this without prior knowledge of the appropriate test (e.g., EMS(I)/EMS(MI)? Thanks for your help, __ 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] Wilcox-Off?
I would guess that it's the brevity argument; witness pnorm, pchisq, punif, ppois, pbinom, phyper, ... But maybe Kurt knows better since he's down as the author of pwilcox. I can only guess it was the brevity argument also. The [...]wilcox functions were added to S+ in June 1990, with no comment on the name choice in the checkin log, and the R authors probably copied the name from S+. 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 Peter Ehlers Sent: Tuesday, March 05, 2013 4:59 PM To: R. Michael Weylandt Cc: r-help Subject: Re: [R] Wilcox-Off? On 2013-03-05 14:51, R. Michael Weylandt wrote: A potentially ridiculous question, but why does R use wilcox (e.g., pwilcox or wilcox.test) instead of the full name Wilcoxon? I've browsed (but not scoured) the help files and Peter Dalgaard's book, but I'm coming up empty. Purely for brevity or have I missed something massive? ## Reproducible example ;-) ? wilcox.test ## End Reproducible Example Cheers, Michael I would guess that it's the brevity argument; witness pnorm, pchisq, punif, ppois, pbinom, phyper, ... But maybe Kurt knows better since he's down as the author of pwilcox. Peter Ehlers __ 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] How to combine conditional argument and logical argument in R to create subset of data...
Dear R user I have data created using code below b-matrix(2:21,nrow=4) b[,1:3]=NA b[4,2]=5 b[3,1]=6 Now the data is b [,1] [,2] [,3] [,4] [,5] [1,] NA NA NA 14 18 [2,] NA NA NA 15 19 [3,] 6 NA NA 16 20 [4,] NA5 NA17 21 I want to keep data in column 4 greater than 15 and the value in column 1 2 either greater than 4 or is 'NA'. So I would like to have my outcome as below... [3,] 6 NA NA 16 20 [4,] NA 5 NA 17 21 I thought something like the code below gonna to work but it only returns the last row,e.g NA 5 NA 17 21. ... bb-b[which( (b[,2]4 | b[,2]==NA) (b[,1]4 | b[,1]==NA) b[,4]15) ,]) Please could anyone help? Many thanks in advance HJ [[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 combine conditional argument and logical argument in R to create subset of data...
Hi, b[b[,4]15 (b[,1]4|is.na(b[,1])) (b[,2]4|is.na(b[,2])),] # [,1] [,2] [,3] [,4] [,5] #[1,] 6 NA NA 16 20 #[2,] NA 5 NA 17 21 A.K. - Original Message - From: HJ YAN yhj...@googlemail.com To: r-help@r-project.org Cc: Sent: Tuesday, March 5, 2013 9:33 PM Subject: [R] How to combine conditional argument and logical argument in R to create subset of data... Dear R user I have data created using code below b-matrix(2:21,nrow=4) b[,1:3]=NA b[4,2]=5 b[3,1]=6 Now the data is b [,1] [,2] [,3] [,4] [,5] [1,] NA NA NA 14 18 [2,] NA NA NA 15 19 [3,] 6 NA NA 16 20 [4,] NA 5 NA 17 21 I want to keep data in column 4 greater than 15 and the value in column 1 2 either greater than 4 or is 'NA'. So I would like to have my outcome as below... [3,] 6 NA NA 16 20 [4,] NA 5 NA 17 21 I thought something like the code below gonna to work but it only returns the last row,e.g NA 5 NA 17 21. ... bb-b[which( (b[,2]4 | b[,2]==NA) (b[,1]4 | b[,1]==NA) b[,4]15) ,]) Please could anyone help? Many thanks in advance HJ [[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] installing biOps on MacOSX fails
thanks for your answer. The problem in my case was that Mac was loading R (32-bit) version rather than R64 (64-bit). Since many libraries in this Mac are compiled for 64 architecture. So naturally the installation did not work at all. Please make use of my case for future reference. soichi 2013/3/4 Prof Brian Ripley rip...@stats.ox.ac.uk See the recent discussion on R-sig-mac (the place to ask questions about OS X). On 04/03/2013 11:00, ishi soichi wrote: version.string R version 2.15.2 (2012-10-26) I am trying to install biOps on MacOS X 10.8.2 First, I have tiff, fftw-3, jpeg and set paths like cd /usr/include sudo ln -s /usr/local/include/fftw3.h for x in /usr/local/include/j*.h; do sudo ln -s $x; done for x in /usr/local/include/tiff*.h; do sudo ln -s $x; done cd /usr/lib for x in /usr/local/lib/libfftw3.*; do sudo ln -s $x; done for x in /usr/local/lib/libjpeg.*; do sudo ln -s $x; done for x in /usr/local/lib/libtiff.*; do sudo ln -s $x; done then run, install.packages(biOps, repos=http://cran.md.tsukuba.**ac.jp/http://cran.md.tsukuba.ac.jp/, type=source) but it gives errors like the following. Can you tell me why ? it looks like R cannot find the libraries.. R does nothing: it is the linker which cannot find the libraries. See the discussion on R-sig-mac ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.**framework/Versions/2.15/** Resources/library/biOps/libs/**i386/biOps.so': dlopen(/Library/Frameworks/R.**framework/Versions/2.15/** Resources/library/biOps/libs/**i386/biOps.so, 6): Symbol not found: _TIFFClose Referenced from: /Library/Frameworks/R.**framework/Versions/2.15/** Resources/library/biOps/libs/**i386/biOps.so Expected in: flat namespace in /Library/Frameworks/R.**framework/Versions/2.15/** Resources/library/biOps/libs/**i386/biOps.so Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.**framework/Versions/2.15/** Resources/library/biOps' The downloaded source packages are in '/private/var/folders/hk/**1clspzcd49d173p3pvpk1f3wgn** /T/RtmpFpgBgP/downloaded_**packages' Warning message: In install.packages(biOps, repos = http://cran.md.tsukuba.ac.jp/**;, : installation of package 'biOps' had non-zero exit status library(biOps) Error in library(biOps) : there is no package called 'biOps' [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~**ripley/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-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html 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] corAR(1) with GLS: does it fit a random or a pooling model?
Dears, I am specifying a panel model with GLS function and corCAR1 and cor AR1 parameters to correct for serial autocorrelation. But I have one seemingly trivial question: those models fitted that way are random effects models or pooling models? Thanks again, Tomas Notes [[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] Learning the R way – A Wish
Dear Mark-- I've just spent an hour and a half reading chapters from Hadley's book. It is phenomenal. Thanks for pointing it out to me --andrewH On Mon, Mar 4, 2013 at 9:04 PM, Mark Leeds marklee...@gmail.com wrote: Hi Andrew: Not that I've gone through it all yet but the draft of hadley's book at https://github.com/hadley/devtools/wiki/Introduction has a lot if not all of the commands you refer to and all of their gory details along with many examples. No matter what you're budget, given that the book will be finished in dec, 2013, I would print out the current draft ( it changes frequently so your draft will become not current pretty quickly ) and make a binding ( actually I had to make two bindings out of it ) and go through it slowly. I was doing that for a while and it was quite enlightening until I got sidetracked with other things. On Mon, Mar 4, 2013 at 6:42 PM, andrewH ahoer...@rprogress.org wrote: There is something that I wish I had that I think would help me a lot to be a better R programmer, that I think would probably help many others as well. I put the wish out there in the hopes that someone might think it was worth doing at some point. I wish I had the code of some substantial, widely used package lm, say heavily annotated and explained at roughly the level of R knowledge of someone who has completed an intro statistics course using R and picked up some R along the way. The idea is that you would say what the various blocks of code are doing, why the authors chose to do it this way rather than some other way, point out coding techniques that save time or memory or prevent errors relative to alternatives, and generally, to explain what it does and point out and explain as many of the smarter features as possible. Ideally, this would include a description at least at the conceptual level if not at the code level of the major C functions that the package calls, so that you understand at least what is happening at that level, if not the nitty-gritty details of coding. I imagine this as a piece of annotated code, but maybe it could be a video of someone, or some couple of people, scrolling through the code and talking about it. Or maybe something more like a wiki page, with various people contributing explanations for different lines, sections, and practices. I am learning R on my own from books and the internet, and I think I would learn a lot from a chatty line-by-line description of some substantial block of code by someone who really knows what he or she is doing perhaps with a little feedback from some people who are new about where they get lost in the description. There are a couple of particular things that I personally would hope to get out of this. First, there are lots of instances of good coding practice that I think most people pick up from other programmers or by having individual bits of code explained to them that are pretty hard to get from books and help files. I think this might be a good way to get at them. Second, there are a whole bunch of functions in R that I call meta-programming functions dont know if they have a more proper name. These are things that are intended primarily to act on R language objects or to control how R objects are evaluated. They include functions like call, match.call, parse and deparse, deparen, get, envir, substitute, eval, etc. Although I have read the individual documentation for many of these command, and even used most of them, I dont think I have any fluency with them, or understand well how and when to code with them. I think reading a good-sized hunk of code that uses these functions to do a lot of things that packages often need to do in the best-practice or standard R way, together with comments that describe and explain them would help a lot with that. (There is a good smaller-scale example of this in Friedrich Leischs tutorial on creating R packages). These are things I think I probably share with many others. I actually have an ulterior motive for suggesting lm in particular that is more peculiar to me, though not unique I am sure. I would like to understand how formulas work well enough to use them in my own functions. I do not think there is any way to get that from the help documentation. I have been working on a piece of code that I suspect is reinventing, but in an awkward and kludgey way, a piece of the functionality of formulas. So far as I have been able to gather, the only place they are really explained in detail is in chapters 2 3 of the White Book, Statistical Models in S. Unfortunately, I do not have ready access to a major research library and I have way, way outspent my book budget. Someday Ill probably buy a copy, but for the time being, I am stuck without it. So it would be great to have a piece of code that uses them explained in detail. Warmest regards to all, andrewH -- View this message
Re: [R] Learning the R way – A Wish
Thanks, David! That bookfinder.com search is awesome! I checked four sites and the best price i found for the white Bokk used was $99 + $4 shipping. This was a quarter of that. So i just bought it. The Venables and Ripley book was actually part of my previous budget-busting splurge. I agree with everything good you have to say. their writing is elegant, concise, and surprisingly complete on many topics. Their discussion of the dot dot dot fnction alone was worth the price of the book. But it still didn't help me much with formulas. The real meat of the formula function is buried in a C function called by lm and the other packages that use it. It is pretty hard to get at how it really works. Especially since I do not know any C. Appreciatively, andrewH On Mon, Mar 4, 2013 at 4:58 PM, David Winsemius dwinsem...@comcast.netwrote: On Mar 4, 2013, at 3:42 PM, andrewH wrote: There is something that I wish I had that I think would help me a lot to be a better R programmer, that I think would probably help many others as well. I put the wish out there in the hopes that someone might think it was worth doing at some point. I wish I had the code of some substantial, widely used package lm, say heavily annotated and explained at roughly the level of R knowledge of someone who has completed an intro statistics course using R and picked up some R along the way. The idea is that you would say what the various blocks of code are doing, why the authors chose to do it this way rather than some other way, point out coding techniques that save time or memory or prevent errors relative to alternatives, and generally, to explain what it does and point out and explain as many of the smarter features as possible. Ideally, this would include a description at least at the conceptual level if not at the code level of the major C functions that the package calls, so that you understand at least what is happening at that level, if not the nitty-gritty details of coding. I imagine this as a piece of annotated code, but maybe it could be a video of someone, or some couple of people, scrolling through the code and talking about it. Or maybe something more like a wiki page, with various people contributing explanations for different lines, sections, and practices. I am learning R on my own from books and the internet, and I think I would learn a lot from a chatty line-by-line description of some substantial block of code by someone who really knows what he or she is doing perhaps with a little feedback from some people who are new about where they get lost in the description. There are a couple of particular things that I personally would hope to get out of this. First, there are lots of instances of good coding practice that I think most people pick up from other programmers or by having individual bits of code explained to them that are pretty hard to get from books and help files. I think this might be a good way to get at them. Second, there are a whole bunch of functions in R that I call meta-programming functions dont know if they have a more proper name. These are things that are intended primarily to act on R language objects or to control how R objects are evaluated. They include functions like call, match.call, parse and deparse, deparen, get, envir, substitute, eval, etc. Although I have read the individual documentation for many of these command, and even used most of them, I dont think I have any fluency with them, or understand well how and when to code with them. I think reading a good-sized hunk of code that uses these functions to do a lot of things that packages often need to do in the best-practice or standard R way, together with comments that describe and explain them would help a lot with that. (There is a good smaller-scale example of this in Friedrich Leischs tutorial on creating R packages). These are things I think I probably share with many others. I actually have an ulterior motive for suggesting lm in particular that is more peculiar to me, though not unique I am sure. I would like to understand how formulas work well enough to use them in my own functions. I do not think there is any way to get that from the help documentation. I have been working on a piece of code that I suspect is reinventing, but in an awkward and kludgey way, a piece of the functionality of formulas. So far as I have been able to gather, the only place they are really explained in detail is in chapters 2 3 of the White Book, Statistical Models in S. Unfortunately, I do not have ready access to a major research library and I have way, way outspent my book budget. Someday Ill probably buy a copy, but for the time being, I am stuck without it. So it would be great to have a piece of code that uses them explained in detail. Not sure that you have a valid
[R] lm and Formula tutorial
Dear all, I was reading last night the lm and the Formula manual page, and 'I have to admit that I had tough time to understand their syntax. Is there a simpler guide for the dummies like me to start with? I would like to thank you in advance for your help Regards 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.
Re: [R] Learning the R way – A Wish
Thanks, Andrew! I'll put it on my list. I have not been through much of it yet, but the exercises on count data are excelent and at least one of them is immediately helpful to a current project. With appreciation, andrewH On Mon, Mar 4, 2013 at 7:28 PM, Andrew Koeser arborkoe...@yahoo.com wrote: The book that helped me break into R and more advanced texts was Crawley's Statistics: An Introduction with R. Very light read that assumes no prior knowledge with stats or R. I am using it to teach my fellow grad students R and all agree it was worth scrimping pennies to get. He also has a series of exercises (for free) that may be close to what you need. http://www3.imperial.ac.uk/**naturalsciences/research/**statisticsusingrhttp://www3.imperial.ac.uk/naturalsciences/research/statisticsusingr Andrew On 03/04/2013 05:42 PM, andrewH wrote: There is something that I wish I had that I think would help me a lot to be a better R programmer, that I think would probably help many others as well. I put the wish out there in the hopes that someone might think it was worth doing at some point. I wish I had the code of some substantial, widely used package lm, say heavily annotated and explained at roughly the level of R knowledge of someone who has completed an intro statistics course using R and picked up some R along the way. The idea is that you would say what the various blocks of code are doing, why the authors chose to do it this way rather than some other way, point out coding techniques that save time or memory or prevent errors relative to alternatives, and generally, to explain what it does and point out and explain as many of the smarter features as possible. Ideally, this would include a description at least at the conceptual level if not at the code level of the major C functions that the package calls, so that you understand at least what is happening at that level, if not the nitty-gritty details of coding. I imagine this as a piece of annotated code, but maybe it could be a video of someone, or some couple of people, scrolling through the code and talking about it. Or maybe something more like a wiki page, with various people contributing explanations for different lines, sections, and practices. I am learning R on my own from books and the internet, and I think I would learn a lot from a chatty line-by-line description of some substantial block of code by someone who really knows what he or she is doing perhaps with a little feedback from some people who are new about where they get lost in the description. There are a couple of particular things that I personally would hope to get out of this. First, there are lots of instances of good coding practice that I think most people pick up from other programmers or by having individual bits of code explained to them that are pretty hard to get from books and help files. I think this might be a good way to get at them. Second, there are a whole bunch of functions in R that I call meta-programming functions dont know if they have a more proper name. These are things that are intended primarily to act on R language objects or to control how R objects are evaluated. They include functions like call, match.call, parse and deparse, deparen, get, envir, substitute, eval, etc. Although I have read the individual documentation for many of these command, and even used most of them, I dont think I have any fluency with them, or understand well how and when to code with them. I think reading a good-sized hunk of code that uses these functions to do a lot of things that packages often need to do in the best-practice or standard R way, together with comments that describe and explain them would help a lot with that. (There is a good smaller-scale example of this in Friedrich Leischs tutorial on creating R packages). These are things I think I probably share with many others. I actually have an ulterior motive for suggesting lm in particular that is more peculiar to me, though not unique I am sure. I would like to understand how formulas work well enough to use them in my own functions. I do not think there is any way to get that from the help documentation. I have been working on a piece of code that I suspect is reinventing, but in an awkward and kludgey way, a piece of the functionality of formulas. So far as I have been able to gather, the only place they are really explained in detail is in chapters 2 3 of the White Book, Statistical Models in S. Unfortunately, I do not have ready access to a major research library and I have way, way outspent my book budget. Someday Ill probably buy a copy, but for the time being, I am stuck without it. So it would be great to have a piece of code that uses them explained in detail. Warmest regards to all, andrewH -- View this message in context: http://r.789695.n4.nabble.com/**
Re: [R] Learning the R way – A Wish
Dear Patrick-- After the official Core Team's R manuals and the individual function help pages, I have found The R Inferno to be the single most useful piece of documentation when I have gotten stuck with a R problems. It is the only introduction that seems to be aware of the ambiguities present in the official documentation and of some of the ways one can get stuck in traps of misunderstanding. Plus, it is enjoyably witty. When I first started using it, I found it ranged from very useful to pretty frustrating. I did not always understand what the examples you presented were trying to say. It is still true that I occasionally wish for a little more discursive explanatory style, but as time goes by I find that I am increasingly likely to get the point just from the example. Many thanks, Andrew On Tue, Mar 5, 2013 at 1:46 AM, Patrick Burns pbu...@pburns.seanet.comwrote: Andrew, That sounds like a sensible document you propose. Perhaps I'll do a few blog posts along that vein -- thanks. I presume you know of 'The R Inferno', which does a little of what you want. Pat On 04/03/2013 23:42, andrewH wrote: There is something that I wish I had that I think would help me a lot to be a better R programmer, that I think would probably help many others as well. I put the wish out there in the hopes that someone might think it was worth doing at some point. I wish I had the code of some substantial, widely used package lm, say heavily annotated and explained at roughly the level of R knowledge of someone who has completed an intro statistics course using R and picked up some R along the way. The idea is that you would say what the various blocks of code are doing, why the authors chose to do it this way rather than some other way, point out coding techniques that save time or memory or prevent errors relative to alternatives, and generally, to explain what it does and point out and explain as many of the smarter features as possible. Ideally, this would include a description at least at the conceptual level if not at the code level of the major C functions that the package calls, so that you understand at least what is happening at that level, if not the nitty-gritty details of coding. I imagine this as a piece of annotated code, but maybe it could be a video of someone, or some couple of people, scrolling through the code and talking about it. Or maybe something more like a wiki page, with various people contributing explanations for different lines, sections, and practices. I am learning R on my own from books and the internet, and I think I would learn a lot from a chatty line-by-line description of some substantial block of code by someone who really knows what he or she is doing perhaps with a little feedback from some people who are new about where they get lost in the description. There are a couple of particular things that I personally would hope to get out of this. First, there are lots of instances of good coding practice that I think most people pick up from other programmers or by having individual bits of code explained to them that are pretty hard to get from books and help files. I think this might be a good way to get at them. Second, there are a whole bunch of functions in R that I call meta-programming functions dont know if they have a more proper name. These are things that are intended primarily to act on R language objects or to control how R objects are evaluated. They include functions like call, match.call, parse and deparse, deparen, get, envir, substitute, eval, etc. Although I have read the individual documentation for many of these command, and even used most of them, I dont think I have any fluency with them, or understand well how and when to code with them. I think reading a good-sized hunk of code that uses these functions to do a lot of things that packages often need to do in the best-practice or standard R way, together with comments that describe and explain them would help a lot with that. (There is a good smaller-scale example of this in Friedrich Leischs tutorial on creating R packages). These are things I think I probably share with many others. I actually have an ulterior motive for suggesting lm in particular that is more peculiar to me, though not unique I am sure. I would like to understand how formulas work well enough to use them in my own functions. I do not think there is any way to get that from the help documentation. I have been working on a piece of code that I suspect is reinventing, but in an awkward and kludgey way, a piece of the functionality of formulas. So far as I have been able to gather, the only place they are really explained in detail is in chapters 2 3 of the White Book, Statistical Models in S. Unfortunately, I do not have ready access to a major research library and I have way, way outspent my book budget. Someday Ill probably buy a copy,
Re: [R] Constrained cubic smoothing spline
Victor, It's a bit clunky, but you can use the 'pcls' function in package 'mgcv' for this, by adapting the examples in the help file. The examples themselves deal with inequality constraints imposing monotonicity, but 'pcls' also allows you to impose equality constraints. The examples are based on penalized cubic regression splines (i.e. cubic splines with fewer knots than you have data). You could use essentially the same code for full smoothing splines, but it is somewhat inefficient for that purpose, and will be prohibitively expensive for large datasets: operations count is O(np^2) where p is number of spline coefficients, so setting p=n can get costly. Simon On 06/03/13 01:07, Victor hyk wrote: Hello everone, Anyone who knows how to force a cubic smoothing spline to pass through a particular point? I found on website someone said that we can use cobs package to force the spline pass through certain points or impose shape constraints (increasing, decreasing). However, this package is using B-spline and can only do linear and quadratic B-spline. In my research, I need to force a cubic smoothing spline to pass a point. Thanks! Victor [[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. -- Simon Wood, Mathematical Science, University of Bath BA2 7AY UK +44 (0)1225 386603 http://people.bath.ac.uk/sw283 __ 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.
