Re: [R] changing Swaeve output settings for .pdf and .eps - is there a way?
markheckmann wrote:
The pdf() settings do not affect Sweave settings when producing a .pdf
graphic. How can I change the Sweave default settings to e.g. 3 inch?
Try setting the width and height options in the figure chunk:
fig1,echo=F,plot=T,pdf=T,width=5,height=3
plot(1:10
@
To make a certain set of dimensions the defaults, use \SweaveOpts:
\SweaveOpts{width=5,height=3}
-Charlie
-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
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[R] question about the Text Mining package tm
Hello. I am trying to work with the text mining package tm. I have a directory called textsTweet1 which contains three files short.txt myTextFile.txt myTextFile.csv short.txt contains one line: THE CAT IN THE HAT\n myTextFile contains some tweets from Twitter. The first few lines of myTextFile.txt are: @oliviamunn I miss a good Yakaniku...I miss Japan...I NEED COCO EVERYBODY. I NEED TO GET ON JAPAN TIME NOW. NO SLEEP!!!SAKURA at Niigata, Japan http://ff.im/-29ufG19:30 [BS Japan] 絶対可憐チルドレン #50 「一意奮闘！オーバー・ザ・フューチャー」RT@ kvsrinath Japan's New Flat Screens: The Eco-Friendly TV . http://is.gd/sIS7 #greenMold99 says: Introduction to Chiropractic and manual therapeutics when unfit.Choice of schools in Japan, and mo... http://i.sitesays.com/lc7Japan Said to Sell 17 Trillion Yen of Extra Bonds - Bloomberg Actually there were no new lines in the original file but I inserted a new line before every occurrence of http. I ran the following code: library(tm) my.path - 'C:\\dataForR\\textsTweet1\\' my.path.csv-'C:\\dataForR\\textsTweet1\\myTextFile.csv' (ovid - Corpus(DirSource(my.path), readerControl = list(reader = readPlain, language = la))) Response from R: A text document collection with 3 text documents Warning message: In readLines(filename, encoding = encoding) : incomplete final line found on 'C:\dataForR\textsTweet1\/short.txt' Then I ran the TermDocMatrix function. It is supposed to take a file and more or less count the occurrences of each word in the file. Or as the documentation says Constructs a term-document matrix tdm-TermDocMatrix(ovid) Data(tdm)[1:2, 105:107] 2 x 3 sparse Matrix of class dgCMatrix revealed said sakura 1.. . 2 15 15 15 Data(tdm)[1:21, 100:105] Error in intI(i, n = di[1], dn = dn[[1]]) : index larger than maximal 3 I don't understand why I am getting only two lines. I can see that the first line is for the short.txt file and the second line seems to be for the whole myTextFile.txt file. How can I get TermDocMatrix to output each row of myTextFile.txt as a separate row? Thanks very much. -- View this message in context: http://www.nabble.com/question-about-the-Text-Mining-package-tm-tp23091573p23091573.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] vertex ordering by date on a network diagram
Dear R helpers I am working with a csv file containing data about a citation graph. This csv file contains a column with an id of the paper containing the citation the next with the id of the paper being cited and the third the date of publication (dd/mm/). I can create a directed network with vertices distributed randomly but cant seem to order them so that the oldest publications lie at the top and get younger moving down the graph. Any help would be very much appreciated Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] changing Swaeve output settings for .pdf and .eps - is there a way?
markheckmann wrote:
The pdf() settings do not affect Sweave settings when producing a .pdf
graphic. How can I change the Sweave default settings to e.g. 3 inch?
Also, even if you set the width of your plot to 3 inches, the plot will be
expanded to 80% of the textwidth by default. To disable this (i.e you set
width=3 and your plot is actually 3 inches) use
\usepackage[nogin]{Sweave}.
You will have to copy Sweave.sty to your local directory or to your texmf
directory for this to work.
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[R] [R-pkgs] Major bigmemory revision released.
The re-engineered bigmemory package is now available (Version 3.5 and above) on CRAN. We strongly recommend you cease using the older versions at this point. bigmemory now offers completely platform-independent support for the big.matrix class in shared memory and, optionally, as filebacked matrices for larger-than-RAM applications. We're working on updating the package vignette, and a draft is available upon request (just send me an email if you're interested). The user interface is largely unchanged. Feedback, bug reports, etc... are welcome. Jay Emerson Michael Kane -- John W. Emerson (Jay) Assistant Professor of Statistics Department of Statistics Yale University http://www.stat.yale.edu/~jay [[alternative HTML version deleted]] ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] Odp: splitting vector into equal sets
utkarshsinghal utkarsh.sing...@global-analytics.com napsal dne
16.04.2009 17:20:10:
Hi Pikal,
Thanks for your comments and apologies for not providing a clear
example. But
you have completely ignored the small example I mentioned:
Well, this is not exactly an example. So let us clarify things a bit. You
do not explain how to handle your vector at all.
One option
split(1:20, factor(1:3))
splits your vector to 3 groups. It recycles 1:3 so every third observation
is put into one vector.
This function randomly samples a vector and gives you list with 3 almost
equal groups and can be easily expanded to arbitrary number of groups.
function(x) {
x1-sample(x, ceiling(length(x)/3))
x.-x[-x1]
x2-sample(x., ceiling(length(x.)/2))
x3-x[-c(x2,x1)]
list(x1,x2,x3)
}
Here are two functions which compute how many members are in each group
and how many are left.
20%%3
[1] 2
20%/%3
[1] 6
split(x, rep(letters[1:3], each=length(x)%/%3))
and this splits your vector to 3 portions and put last 2 values to the
first vector.
I think I gave you some insights how to handle such problem.
I want to split rnorm(20) into three equal groups.
Note that here number of observations is not a multiple of number of
groups.
For that I want an option where I can specify how to treat these extra
which extra observations, first 2, last 2, arbitrary 2?
observations, i.e., to put these observations into the 1st group or the
last
group or one in each group starting from 1st or starting from last
Only **you** know how exactly **you** want to handle it so **you** need to
elaborate a function **yourself**. If the function shall split arbitrary
length vector to arbitrary number of groups and put extra values to
arbitrary groups it would not be a simple case and it would need a little
bit of programming work.
Also I dont want to calculate the number of observations going in each
group beforehand.
You do not need to calculate it yourself. R will do it for you if you tell
it.
Regards
Petr
Regards
Utkarsh
Petr PIKAL wrote:
Hi
r-help-boun...@r-project.org napsal dne 16.04.2009 15:23:15:
Hi R,
I have explored R archives a lot but couldn't find an efficient way of
doing the following:
I want to split a vector into sets of equal sizes. Is there any inbuilt
function of doing so with the option of specifying how to treat the
remaining observations. For example: suppose I want to split 20
observations in 3 groups, then I also want the option to put the extra
two observations into the 1st group or the last group or one in each
group starting from 1st or starting from last.
I have already tried the cut the quantcut function but of no use.
Any help will be appreciated. Note that I am looking for an R function
rather than lines of code.
Did you try split?
e.g.
split(rnorm(12), rep(1:3,4))
gives list with 3 vectors. Then you can use lapply, sapply or other list
functions to make some computation.
Or I could be completely wrong what you really want as you did not
provide
any example.
Regards
Petr
Regards
Utkarsh
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[R] Sourcecode documentation
Hi all, I am searching for a tool or a package that can generate a documentation file e.g. html, txt from defined commands like params, function etc - a tool like javadoc but featuring R. NaturalDocs support R but is a little bit to heavy for my needs. 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.
[R] rnorm() converted to daily
yearly 8% drift, 25% sd why are x and y so different (x and z look ok)? Does this have something to do with biases due to the relationship between population and sample-estimates as a function of n samples and sd? Or am I doing something wrong? --- set.seed( 1 ); x - mean( rnorm( 10, mean=0.08, sd=0.25 )); set.seed( 1 ); y - mean( rnorm( 10, mean=(0.08/252), sd=(0.25/sqrt(252)) )) * 252; set.seed( 1 ); z - mean( rnorm( 10, mean=(0.08/252), sd=0.001 )) * 252; # --- x# 0.07943898 y# 0.07109407 z# 0.07943449 -- View this message in context: http://www.nabble.com/rnorm%28%29-converted-to-daily-tp23092444p23092444.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] Turning off warnings from cor.test
I would like to turn off the warnings from cor.test while retaining exact=NULL. Is that possible ? cor.test(c(1,2,3,3,4,5), c(1,2,3,3,4,5), method = spearman) Spearman's rank correlation rho data: c(1, 2, 3, 3, 4, 5) and c(1, 2, 3, 3, 4, 5) S = 0, p-value 2.2e-16 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 1 Warning message: In cor.test.default(c(1, 2, 3, 3, 4, 5), c(1, 2, 3, 3, 4, 5), method = spearman) : Cannot compute exact p-values with ties __ 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] Turning off warnings from cor.test
check option 'warn' in the on-line help file of ?options(), e.g., you can use something like this: op - options(warn = (-1)) # suppress warnings cor.test(c(1,2,3,3,4,5), c(1,2,3,3,4,5), method = spearman) options(op) # reset the default value, if you want I hope it helps. Best, Dimitris Daren Tan wrote: I would like to turn off the warnings from cor.test while retaining exact=NULL. Is that possible ? cor.test(c(1,2,3,3,4,5), c(1,2,3,3,4,5), method = spearman) Spearman's rank correlation rho data: c(1, 2, 3, 3, 4, 5) and c(1, 2, 3, 3, 4, 5) S = 0, p-value 2.2e-16 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 1 Warning message: In cor.test.default(c(1, 2, 3, 3, 4, 5), c(1, 2, 3, 3, 4, 5), method = spearman) : Cannot compute exact p-values with ties __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] Linear model with interaction
Hi all,
I have a question about linear model with interaction:
I created a data frame df like this:
df
V1 V2 V3 V4 V5
1 6.414094 c t a g
2 6.117286 t a g t
3 5.756922 a g t g
4 6.090402 g t g t
...
which holds the response in the first column and letters (a,c,g,t) in the
other columns. I am interested to see if there are interactions between the
neigbouring letters so I have defined the following linear model:
lm-lm(df[,1] ~ (df[,2]:df[,3]) + (df[,3]:df[,4]) + (df[,4]:df[,5]) )
the result then looks like this:
Coefficients: (1 not defined because of singularities)
Estimate Std. Error t value Pr(|t|)
(Intercept)8.8987163 0.0211457 420.828 2e-16 ***
df[, 2]a:df[, 3]a -0.1021543 0.0253486 -4.030 5.59e-05 ***
df[, 2]c:df[, 3]a0.0535562 0.0255685 2.095 0.036213 *
df[, 2]g:df[, 3]a0.0224073 0.0318965 0.703 0.482372
df[, 2]t:df[, 3]a0.0024165 0.0259862 0.093 0.925911
df[, 2]a:df[, 3]c0.0355502 0.0260197 1.366 0.171861
df[, 2]c:df[, 3]c0.0433014 0.0252535 1.715 0.086415 .
df[, 2]g:df[, 3]c0.147 0.0309441 4.758 1.97e-06 ***
df[, 2]t:df[, 3]c0.0613779 0.0270601 2.268 0.023323 *
df[, 2]a:df[, 3]g0.0646498 0.0299286 2.160 0.030770 *
df[, 2]c:df[, 3]g0.1302731 0.0359439 3.624 0.000290 ***
df[, 2]g:df[, 3]g0.1512754 0.0360951 4.191 2.78e-05 ***
df[, 2]t:df[, 3]g0.1084278 0.0339142 3.197 0.001389 **
df[, 2]a:df[, 3]t -0.0249016 0.0262402 -0.949 0.342633
df[, 2]c:df[, 3]t0.0860302 0.0253518 3.393 0.000691 ***
df[, 2]g:df[, 3]t0.0241031 0.0358496 0.672 0.501372
df[, 2]t:df[, 3]t NA NA NA NA
df[, 3]a:df[, 4]1 -0.0970149 0.0143730 -6.750 1.50e-11 ***
df[, 3]c:df[, 4]1 -0.0153732 0.0152519 -1.008 0.313486
df[, 3]g:df[, 4]1 -0.0706682 0.0225665 -3.132 0.001740 **
df[, 3]t:df[, 4]1 -0.0581889 0.0158485 -3.672 0.000241 ***
df[, 3]a:df[, 4]20.0485333 0.0150167 3.232 0.001231 **
df[, 3]c:df[, 4]2 -0.0790008 0.0150513 -5.249 1.54e-07 ***
df[, 3]g:df[, 4]20.0604465 0.0217557 2.778 0.005465 **
df[, 3]t:df[, 4]20.0232283 0.0167224 1.389 0.164826
df[, 3]a:df[, 4]30.0740046 0.0182221 4.061 4.89e-05 ***
df[, 3]c:df[, 4]30.0797502 0.0234485 3.401 0.000672 ***
df[, 3]g:df[, 4]30.0720160 0.0253456 2.841 0.004495 **
df[, 3]t:df[, 4]30.0778484 0.0221196 3.519 0.000433 ***
df[, 4]a:df[, 5]1 -0.0916618 0.0143707 -6.378 1.81e-10 ***
df[, 4]c:df[, 5]1 -0.0138048 0.0152609 -0.905 0.365691
df[, 4]g:df[, 5]1 -0.0700765 0.0225639 -3.106 0.001900 **
df[, 4]t:df[, 5]1 -0.0734513 0.0158534 -4.633 3.62e-06 ***
df[, 4]a:df[, 5]20.0438002 0.0150128 2.918 0.003531 **
df[, 4]c:df[, 5]2 -0.1107056 0.0150634 -7.349 2.04e-13 ***
df[, 4]g:df[, 5]20.0652739 0.0217520 3.001 0.002694 **
df[, 4]t:df[, 5]20.0219305 0.0167259 1.311 0.189811
df[, 4]a:df[, 5]30.0804106 0.0182290 4.411 1.03e-05 ***
df[, 4]c:df[, 5]30.0970780 0.0234745 4.135 3.55e-05 ***
df[, 4]g:df[, 5]30.0704516 0.0253372 2.781 0.005430 **
df[, 4]t:df[, 5]30.0911914 0.0221237 4.122 3.77e-05 ***
questions:
1.) What could be the reason that the lm function changes the names of the
interactions terms (after the first undefined coefficient)
from a:a, c:a, g:a, ... to a:1, c:1, g:1, ... and obviously omits direct
calculation of interaction terms of the form a:4, c:4, g:4, t:4 which
(if I correctly assume) correspond to a:t, c:t, g:t, t:t.
2.) How I have to correctly define a data frame new_df for a new sequence of
letters to get the predicted response by using the predict function, I tried
something like this:
new_df[2:5]=as.data.frame(t('g'))
new_df[1]=0
predict(lm, new_df)
and also the original data frame which was used to fit the model:
predict(lm, df[1,])
outputs all predicted values with respect to the previously fitted linear
model and gives Warning messages:
1: 'newdata' had 1 rows but variable(s) found have 7020 rows
2: In predict.lm(lm_pm, new_df) :
prediction from a rank-deficient fit may be misleading
Thanks for any help,
Marian
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Re: [R] there are fontencoding problem in Sweave
2009/4/17 Peter Dalgaard p.dalga...@biostat.ku.dk
Doesn't \usepackage[noae]{Sweave} do the trick? Sweave.sty has this
conditionalized.
Yes, it is working. Thanks
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Re: [R] Sourcecode documentation
_ wrote: Hi all, I am searching for a tool or a package that can generate a documentation file e.g. html, txt from defined commands like params, function etc - a tool like javadoc but featuring R. NaturalDocs support R but is a little bit to heavy for my needs. Thank you. Google for roxygen -- Romain Francois Independent R Consultant +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr __ 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] Kruskal's MDS results
A few people suggested taking a look at Ripley's book MASS. I know the formula listed there. The point is that the manual for the isoMDS function says it's stress output is in percent. Does this mean, the stress reported by isoMDS is just the stress value in MASS (which ranges from 0 to 1) value multiplied by 100? I've haven't been able to find any resource that expresses stress in values from 0 to 100. So, this would be a convention introduced by the authors of the package? In general, I think the R manuals could do with a bit more explaining on the output of the functions. I understand that some knowledge of statistics is assumed when working with R but sometimes the documentation on the returned values is really sparse. Even when familiar with the domain, there are several different conventions followed by different authors. This should be clear when reading the manual. I know a lot of hard work gets into writing software, but it seems sometimes people are less keen on documenting their hard work properly. stephen sefick wrote: You can look in MASS 4 for this formula on page 308 . Go to the source and ask the horse he'll give you an answer that you endorse. On Thu, Apr 16, 2009 at 8:13 AM, Bob Green bgr...@dyson.brisnet.org.au wrote: Dieter, You could always try the Classification, clustering, and phylogeny estimation list which often includes posts regarding MDS: http://lists.sunysb.edu/index.cgi?A0=CLASS-L regards Bob __ 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] rnorm() converted to daily
Ken-JP: Does this have something to do with biases due to the relationship between population and sample-estimates as a function of n samples and sd? Or am I doing something wrong? --- set.seed( 1 ); x - mean( rnorm( 10, mean=0.08, sd=0.25 )); set.seed( 1 ); y - mean( rnorm( 10, mean=(0.08/252), sd=(0.25/sqrt(252)) )) * 252; set.seed( 1 ); z - mean( rnorm( 10, mean=(0.08/252), sd=0.001 )) * 252; Yes, you’re doing something wrong. While it is true¹ that rnorm(n, a, b) will give the same results as rnorm(n, 0, 1) * b + a, it is *not* true that the above calculations would return the same numbers. That’s the reason the the means differ. ¹ True in practice, but not documented as far as I can see, so you should not depend on it. -- Karl Ove Hufthammer __ 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] Turning off warnings from cor.test
DR == Dimitris Rizopoulos d.rizopou...@erasmusmc.nl on Fri, 17 Apr 2009 09:44:49 +0200 writes: DR check option 'warn' in the on-line help file of ?options(), e.g., you DR can use something like this: DR op - options(warn = (-1)) # suppress warnings DR cor.test(c(1,2,3,3,4,5), c(1,2,3,3,4,5), method = spearman) DR options(op) # reset the default value, if you want [yes, do that!] To make this more self-contained and error-proof, there has been the function suppressWarnings(.) for several years now. Hence, I'd strongly recommend suppressWarnings( cor.test(c(1,2,3,3,4,5), c(1,2,3,3,4,5), method = spearman) ) instead of the above. Regards, Martin Maechler, ETH Zurich DR I hope it helps. DR Best, DR Dimitris DR Daren Tan wrote: I would like to turn off the warnings from cor.test while retaining exact=NULL. Is that possible ? cor.test(c(1,2,3,3,4,5), c(1,2,3,3,4,5), method = spearman) Spearman's rank correlation rho data: c(1, 2, 3, 3, 4, 5) and c(1, 2, 3, 3, 4, 5) S = 0, p-value 2.2e-16 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 1 Warning message: In cor.test.default(c(1, 2, 3, 3, 4, 5), c(1, 2, 3, 3, 4, 5), method = spearman) : Cannot compute exact p-values with ties __ 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. DR -- DR Dimitris Rizopoulos DR Assistant Professor DR Department of Biostatistics DR Erasmus University Medical Center DR Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands DR Tel: +31/(0)10/7043478 DR Fax: +31/(0)10/7043014 DR __ DR R-help@r-project.org mailing list DR https://stat.ethz.ch/mailman/listinfo/r-help DR PLEASE do read the posting guide http://www.R-project.org/posting-guide.html DR 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] [R-pkgs] FD: R package to measure functional diversity indices
Dear useRs, The FD package is intended for ecologists interested in functional diversity (FD). It measures different functional diversity indices from multiple traits (any type of traits). The first version of FD (1.0-0) is now available on CRAN: http://cran.r-project.org/web/packages/FD/ The main functions of FD are: dbFD: Compute different multidimensional FD indices gowdis: Gower dissimilarity, including options for variable weights, asymetric binary variables, and implementing Podani's (1999) extension to ordinal variables fdisp: Functional dispersion functcomp: Functional composition (community-weighted means ot trait values, or CWM) I hope that FD will be useful to you. Feedback would be appreciated. Sincerely, Etienne Laliberté Rural Ecology Research Group School of Forestry University of Canterbury Private Bag 4800 Christchurch 8140, New Zealand Phone: +64 3 366 7001 ext. 8365 Fax: +64 3 364 2124 www.elaliberte.info ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] rnorm() converted to daily
Hi Karl, Your comment is very interesting. Do you mean I should favor: rnorm(n, 0, 1) * b + a over rnorm(n, a, b) ? What is the proper/safe way to use rnorm()? FWIW, set.seed( 1 ); yy - mean( rnorm( 10 ) * (0.25/sqrt(252)) + (0.08/252)) * 252; yy # 0.07109407 still gives me what I had before (but I shouldn't depend on it being the same, right)? -- View this message in context: http://www.nabble.com/rnorm%28%29-converted-to-daily-tp23092444p23093334.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] rnorm() converted to daily
SD in y is more than 15 times (!!!) larger than in x and z, respectively, and hence SD of the mean y is also larger. 100,000 values are not enough to stabilize this. You could have obtained 0.09 or even larger as well. Try y with different seeds, y varies much more than x and z do. Or check the variances: var.x - var(replicate(100, mean( rnorm( 10, mean=0.08, sd=0.25 var.y - var(replicate(100, mean( rnorm( 10, mean=(0.08/252), sd=(0.25/sqrt(252)) )) * 252)) var.z - var(replicate(100, mean( rnorm( 10, mean=(0.08/252), sd=0.001 )) * 252)) I guess what you are doing wrong is assuming that 0.25/sqrt(252) is similar to 0.25/252, the latter being close so 0.001, while the former is obviously not. Try to replace 0.25 in y by 0.0158, than you should be close enough. HTH, Michael -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ken-JP Sent: Freitag, 17. April 2009 09:26 To: r-help@r-project.org Subject: [R] rnorm() converted to daily yearly 8% drift, 25% sd why are x and y so different (x and z look ok)? Does this have something to do with biases due to the relationship between population and sample-estimates as a function of n samples and sd? Or am I doing something wrong? --- set.seed( 1 ); x - mean( rnorm( 10, mean=0.08, sd=0.25 )); set.seed( 1 ); y - mean( rnorm( 10, mean=(0.08/252), sd=(0.25/sqrt(252)) )) * 252; set.seed( 1 ); z - mean( rnorm( 10, mean=(0.08/252), sd=0.001 )) * 252; # --- x# 0.07943898 y# 0.07109407 z# 0.07943449 -- View this message in context: http://www.nabble.com/rnorm%28%29-converted-to-daily-tp23092444p23092444 .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] Manipulate single line in textfile
Hello all, Is it possible to modify a single line in a textfile? I know it is possible to load the whole text file, do the change, and save this as a new file. However, this is not practical in my case, because the document is huge and cannot be fully loaded in R. Any idea? Best, Guillaume __ 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] rnorm() converted to daily
Ken-JP: Do you mean I should favor: rnorm(n, 0, 1) * b + a over rnorm(n, a, b) No, as I said, they give exactly the same results. -- Karl Ove Hufthammer __ 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] Manipulate single line in textfile
On Fri, Apr 17, 2009 at 9:20 AM, Guillaume Filteau filt...@unc.edu wrote: Hello all, Is it possible to modify a single line in a textfile? I know it is possible to load the whole text file, do the change, and save this as a new file. However, this is not practical in my case, because the document is huge and cannot be fully loaded in R. Any idea? You seek seek! Rough outline: Open the file as a read-write connection using con = file(fileName, open=r+) Seek to where you want to change the line using seek(con, where = linelength*linenumber) Write the new text using cat(my new text,file=con) Close the connection using close(con). Note this works if the lines are all the same length, since the position used in seek() is in bytes. You might be able to scan() or readLines() up to the point you want to change and then read off the byte position with seek(con,where=NA). Note that seek keeps a read and a write position. Further complications include making sure you don't write over end-of-line characters - your replacement text has to be the same size as the existing text. read help(connection) and help(seek) for more help :) And test it on something else first, lest ye stomp on the original. And keep backups. 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.
[R] matching subvectors in vector sets
Hi, I've got a list of ~2 elements that look like this: [1] A00096:A00096:A00096:A00096:A02178:A02178:A07776 [2] A00046:A00076:A01101:A04146:A05671:A07169 [3] A00038:A00932:A02185:A02370:A02818:A02818:A02818:A02818:A04732:A07142:A07142 [4] A00096:A01352:A01352:A02023:A05001:A05001:A07776 [5] A00036:A00047:A00059:A00503:A00904:A00904:A00904:A01023:A01023:A01399:A02029:A03941:A07679 [6] A00041:A00533:A00855:A02178:A02178:A02178:A05671:A05671:A05671:A05671:A05671:A05671:A05671 ... And I would like to have a table with the frequency of occurrences for matching subvectors in all elements, i.e., not only the number of times a vector is found but also how many times a subvector (of at least 2 ids) is found. How can I do that? Thanks in advance, Albert. [[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] get() versus getAnywhere()
Benjamin Tyner wrote:
Many thanks Duncan. Perhaps this merits a more explicit note in the
documentation?
The quote I gave is from the documentation. How could it be more explicit?
Duncan Murdoch
Duncan Murdoch wrote:
On 4/16/2009 9:52 AM, Benjamin Tyner wrote:
Hi
Using R 2.8.1. I have list object called AuxData. Inside a browser(),
get(AuxData)
succeeds, while
getAnywhere(AuxData)
fails with the error no object named âAuxDataâ was found. I'm
curious to know if this could be a bug. If yes, I'll try to come up
with a reproducible example.
It's not a bug. getAnywhere doesn't really mean anywhere, it means
visible on the search path, registered as an S3 method or in a name
space but not exported. On the other hand, the browser will show you
the local evaluation frame. So I'd expect the browser to be able to
see x below, but getAnywhere wouldn't find it, because it's not in one
of the places listed above.
f - function(x) {
browser()
getAnywhere(x)
}
f(1)
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Re: [R] changing Swaeve output settings for .pdf and .eps - is there a way?
cameron.bracken wrote:
markheckmann wrote:
The pdf() settings do not affect Sweave settings when producing a .pdf
graphic. How can I change the Sweave default settings to e.g. 3 inch?
Also, even if you set the width of your plot to 3 inches, the plot will be
expanded to 80% of the textwidth by default. To disable this (i.e you set
width=3 and your plot is actually 3 inches) use
\usepackage[nogin]{Sweave}.
You will have to copy Sweave.sty to your local directory or to your texmf
directory for this to work.
You shouldn't need Sweave.sty in your local directory for this to work.
You aren't changing it,
just using one of its options.
There are other ways to control the size: it isn't always 80%. I
normally use something like
\setkeys{Gin}{width=0.75\textwidth} to control it. You can reset this a
number of times in
the same document. (Read the LaTeX docs for graphicx to see the other
keys that can be set.)
Duncan Murdoch
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Re: [R] map of china without regions
Ray Brownrigg Ray.Brownrigg at ecs.vuw.ac.nz writes: Sorry, can't be done at the moment with the maps package. ... You *might* be able to achieve what you want by selecting only those line segments that provide portions of the external border, but I would suggest that other packages (perhaps someone will suggest the best) are more likely to be able to provide what you want without so much effort. You could subset from the mapdata worldHires dataset: map(worldHires,china,fill=TRUE, col=transparent) or alternatively for a similar geographical footprint: library(maptools) data(wrld_simpl) plot(wrld_simpl[wrld_simpl$ISO2 %in% c(CN, TW),]) depending on your needs. Roger Bivand HTH Ray Brownrigg On Fri, 17 Apr 2009, Cuvelier Etienne wrote: Hello, I use the map package in conjunction with the mapdata package, and I want to draw the map of China without interior regions. __ 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] Kruskal's MDS results
Dieter Vanderelst Dieter.Vanderelst at ua.ac.be writes:
A few people suggested taking a look at Ripley's book MASS. I know the formula
listed there.
The point is that the manual for the isoMDS function says it's stress output
is in percent. Does this mean,
the stress reported by isoMDS is just the stress value in MASS (which ranges
from 0 to 1) value multiplied by
100? I've haven't been able to find any resource that expresses stress in
values from 0 to 100. So, this
would be a convention introduced by the authors of the package?
Yes, it is stress multplied with 100 which makes it per cent instead of per
unit. You can see this also in the software. The extract is from VR_mds_fn
function in MASS.c:
sstar = 0.0;
tstar = 0.0;
for (i = 0; i n; i++) {
tmp = y[i] - yf[i];
sstar += tmp * tmp;
tstar += y[i] * y[i];
}
ssq = 100 * sqrt(sstar / tstar);
The last line has the multiplication, the previous collect the terms for the
stress.
Best wishes, Jari Oksanen
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[R] multiplot numbering
Hi, I have a multiplot in which i need to label each plot as (a) (b) etc. preferably on the right side of each plot. My layout is one plot below the other.How can i do this? -- Rajesh.J [[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] Numeric data calculated in bwplot
Hi, i was wondering if there is a way to extract statistic calculated by the function bwplot in numeric format, i.e. a list with values of borders mean etc. Going through the help i couldn't find it, and text of the function itself(bwplot) is very long. Thanks -- View this message in context: http://www.nabble.com/Numeric-data-calculated-in-bwplot-tp23096219p23096219.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] How to control distance between rows of figures in multiple plots
?par look at the 'mar' parameter. On Thu, Apr 16, 2009 at 11:54 PM, Gundala Viswanath gunda...@gmail.com wrote: Dear all, I have a plot with 2 x 2 figures matrix in it. pdf(~/Desktop/myplot.pdf,width=13,height=7) par(mfrow=c(2,2)) # follow by some code Now the distance between figures of row 1 and row 2 is too wide. How can I modify? - Gundala Viswanath Jakarta - Indonesia __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] multiplot plot spacing and text strip
?par(mar=...) ?mtext On Thu, Apr 16, 2009 at 11:31 PM, rajesh j akshay.raj...@gmail.com wrote: Hi everyone, I have a certain requirement and I'm not sure what to do.I need to reduce the spacing between plots in a multiplot. Make them really close together such that they almost touch. Also, I need to add a rectangular strip under my plot(very close to it) such that the strip contains some text describing it. Any help is appreciated -- Rajesh.J [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] Kruskal's MDS results
Dieter Vanderelst Dieter.Vanderelst at ua.ac.be writes: The point is that the manual for the isoMDS function says it's stress output is in percent. Does this mean, the stress reported by isoMDS is just the stress value in MASS (which ranges from 0 to 1) value multiplied by 100? I've haven't been able to find any resource that expresses stress in values from 0 to 100. So, this would be a convention introduced by the authors of the package? A comment about novelty of using percentages. I also had a look at some NMDS resources, and the first I found were two Kruskal's papers that happened to be on my desk (Psychometrika 29, 1-27 and Psychometrika 29, 115-129, both from 1964). Both of these expressed stress in percents. Certainly this is not a convention introduced by the authors of the package, since they are much too young to have done that prior to 1964. Cheers, Jari Oksanen __ 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] Manipulate single line in textfile
You can also read/write portions of the text till you get to the line you want to change, change it and then continue copying the lines. This is what would be done with any other software approach in trying to replace 'text' that may not be the same length. On Fri, Apr 17, 2009 at 4:20 AM, Guillaume Filteau filt...@unc.edu wrote: Hello all, Is it possible to modify a single line in a textfile? I know it is possible to load the whole text file, do the change, and save this as a new file. However, this is not practical in my case, because the document is huge and cannot be fully loaded in R. Any idea? Best, Guillaume __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] Presenting R Results in Webpages
Jason Rupert wrote: I apologize in advance that this question is not specific to R, but I thought some R users may be using this in their work process flow. I would like to be able to have a tool (prefer scriptable) that will take two images and some pre-written text and put it on an simple webpage. That is, it would look something like the following: |-| |Title| | | | || || Some basic txt | | | Image1 | | Image2 | ... | | || || ... | |_| R comes in because I have R scripts creating the images I would like to import. There will be 14-18 pages of these type of slides, but the key is we will be producing these over and over. I tried doing something like this in PowerPoint, but not impressed with the linking capability or Macros. Thanks for any feedback and again appologize that this is not exactly a specific R question. Hi Jason, You could do something similar with htmlize in the prettyR package, and get exactly what you want with a bit of HTML editing. Get an R script that will generate the two images, then the text. Then insert a few tags like this: (All of the HTML before the first image) table tr td img src=Image1.png td img src=Image2.png td Text that you want in the right hand cell /table (the rest of the HTML) 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] error bars in matplot
Tim Smith wrote:
Hi,
I was trying to get error bars in my matplot. I looked at an earlier thread,
and the sample code that I made is:
#--
library(plotrix)
mat1 - matrix(sample(1:30,10),nrow=5,ncol=2)
ses - matrix(sample(1:3,10,replace=T),nrow=5,ncol=2)
vect - seq(20,100,20)
rownames(mat1) - rownames(ses) - vect
colnames(mat1) - colnames(ses) - letters[1:2]
matplot(mat1,pch=c('x','o'),type = b,lwd = 2,lty = c(1,2),
col = c(green,black),cex.main = 1.8,cex=2,cex.lab=1.5,
main = Graph 1,xlab = Numbers 1,ylab = Numbers 2,cex.axis =
1.6,axes=F)
plotCI(rep(vect,2),mat1,ses2,pch=NA,add=T,
col=rep(c(green,black),each=nrow(mat1)))
axis(1,1:5,labels = vect,cex.axis=1.5)
axis(2,cex.axis=1.5)
#--
I don't get the error bars though. If I set 'add = F' in plotCI function, then
I can see the error bars, but they just can't be added to the matplot. What am
I doing wrong? Is there any other way to get the error bars?
Hi Tim,
Try the dispersion function in plotrix to add error bars. You will
probably have to add ylim=c(0,29) to your matplot command.
dispersion(rep(1:5,2),mat1,ses)
Jim
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and provide commented, minimal, self-contained, reproducible code.
[R] R 2.9.0 is released
I've rolled up R-2.9.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. You can get it (later today) from http://cran.r-project.org/src/base/R-2/R-2.9.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. In case of impatience, try http://www.biostat.ku.dk/~pd/R-release Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 70447ae7f2c35233d3065b004aa4f331 INSTALL 433182754c05c2cf7a04ad0da474a1d0 README 4f004de59e24a52d0f500063b4603bcb OONEWS ff4bd9073ef440b1eb43b1428ce96872 ONEWS 7861f511a3f8e8598c9b84d65e93c389 NEWS 7abcbbc7480df75a11a00bb09783db90 THANKS 070cca21d9f8a6af15f992edb47a24d5 AUTHORS a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB eb723b61539feef013de476e68b5c50a COPYING 020479f381d5f9038dcb18708997f5da RESOURCES b96e9596f947794c5628712f8016aa90 FAQ a5b79a2bc1372136cda4674b5f46d146 R-2.9.0.tar.gz a5b79a2bc1372136cda4674b5f46d146 R-latest.tar.gz This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.9.0 SIGNIFICANT USER-VISIBLE CHANGES o expand.grid() by default no longer coerces strings into factors. NEW FEATURES o Package 'Matrix' is now a recommended package contained in the basic R distribution. It provides S4 classes and methods for dense and sparse matrices, often by using the numerical libraries Lapack and from the SuiteSparse collection CHOLMOD, CSparse, and SPQR among others. o pdf() and postscript() gain a 'useKerning' argument to place strings using kerning (which had previously been ignored in display but not in strwidth), based in part on an idea and code from Ei-ji Nakama. The default is TRUE. Kerning involving spaces is now ignored (it was previously only used in the computation of string widths). o seq.default() and seq.int() ensure that the result is within the interval [from, to] even when the last value would previously have been slightly out of range because of the allowance for rounding error in computing the number of elements. o boxplot() gains a simple 'matrix' method, enabling boxplot(mat) instead of boxplot(data.frame(mat)). o zip.file.extract() gains an optional 'dir' argument (but use unzip() instead). o source() with 'encoding' specified (and not as unknown) marks the encoding of character strings in Latin-1 and UTF-8 locales. o parse(text=z) now marks the encoding of character strings in Latin-1 and UTF-8 locales if 'z' is of known encoding (that is all elements are either ASCII or marked as Latin-1 or UTF-8). o sprintf() does stricter error checking on input formats to avoid passing invalid formats to the OS (which have a tendency to crash under such inputs). o expand.grid() gains a 'stringsAsFactor' argument to ask for automatic conversion of character vectors to factors (which happened for many years but was not previously documented, and is no longer the default). o bxp() now coputes the 'ylim' including the outliers only if 'outline = TRUE'. (Wish of PR#13196) o barplot() gains a 'args.legend' argument. (Wish of PR#13265). o RweaveLatexSetup() now accepts all (and not just some) options passed through from Sweave() o cumsum(x) and cumprod(x) for double precision x now use a long double accumulator where available and so more closely match sum() and prod() in potentially being more accurate. o plot() methods for stepfun (and hence ecdf) gain an 'col' argument, allowing to set all three colors simultaneously. o Iterating over a factor in a for loop now coerces to a character vector (rather than using the integer codes). o data.frame() now recycles columns of list arguments, not just vectors and factors. o plot.ts(plot.type=multiple) now makes use of *.lab and *.axis graphical parameters (wish of PR#13134 and 13135). o Classes can be exported from a name space using the NAMESPACE file directive 'exportClassPattern' which has the same syntax as 'exportPattern'. o strftime() now converts its first argument with as.POSIXlt() and so is no longer an alias for format.POSIXLt. o body-() now treats list values consistently with other types: they no longer need to be wrapped in a list() call. o option(pdfbrowser) is now set on Windows as well as on Unix-alikes. o object.size() now returns an object of class object_size and has a print() method. o
[R] Using spdep example data and R code : bbox should never contain infinite values
Hi, I am facing with a problem when running a code against the sample data from spdep. I am getting SpatialPoints object : bbox should never contain infinite values In additionl Warning Messages: 1. In min(x): no non-missing arguments to min; returning Inf 2. In max(x): no non-missing arg... The code I am trying to execute: sidgams-opgamdata=as(nc, data.frame), radius=30, step=10, alpha=.002) gampoints-SpatialPoints(sidsgam[,c(x,y)]*1000, CRS(+proj=utm +zone=18 +datum=WGS84)) The input dataset is a modified polygon (in WGS datum) of North Carolina that comes with spdep, but using some other additional fields for calculation. I would be very happy to receive a suggestion on corecting this. Thanks! Dejan [[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] Numeric data calculated in bwplot
library(lattice) x - bwplot(voice.part ~ height, data=singer, xlab=Height (inches)) str(x) I have not done this before, but the output of str should give you a starting point for extracting numeric values contained in one of the numerous lists. hope this helps Stephen Sefick On Fri, Apr 17, 2009 at 8:03 AM, Yuri Volchik yuri.volc...@gmail.com wrote: Hi, i was wondering if there is a way to extract statistic calculated by the function bwplot in numeric format, i.e. a list with values of borders mean etc. Going through the help i couldn't find it, and text of the function itself(bwplot) is very long. Thanks -- View this message in context: http://www.nabble.com/Numeric-data-calculated-in-bwplot-tp23096219p23096219.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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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 create the null distribution
Hi,
I want to bootstrap the likelihood ratio test for testing linear
restrictions on the parameters of a regression model. The aim is to perform
a size and power analysis. My question is, as indicated by the subject, how
do I approximate the null distribution? The code that I ran looks like
boot.test - function(data, indeces, maxit=20) {
+ y1 - fit1+e1[indeces]
+ mod1 - glm(y1 ~ X1-1, maxit=maxit)
+ y2 - fit2+e2[indeces]
+ mod2 - glm(y2~1, maxit=maxit)
+ t - 2*(logLik(mod1)-logLik(mod2))
+ t
+ }
boot.lrtest - boot(data=M1, statistic=boot.test, R=1999, maxit=100)
However, I suspect that I am not bootstrapping under the null hypothesis.
How do I perform the bootstrap under the null? I would really appriciate any
help, I feel rather lost.
/Anders
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Re: [R] Kruskal's MDS results
Thank you for clearing this out. Jari Oksanen wrote: Dieter Vanderelst Dieter.Vanderelst at ua.ac.be writes: The point is that the manual for the isoMDS function says it's stress output is in percent. Does this mean, the stress reported by isoMDS is just the stress value in MASS (which ranges from 0 to 1) value multiplied by 100? I've haven't been able to find any resource that expresses stress in values from 0 to 100. So, this would be a convention introduced by the authors of the package? A comment about novelty of using percentages. I also had a look at some NMDS resources, and the first I found were two Kruskal's papers that happened to be on my desk (Psychometrika 29, 1-27 and Psychometrika 29, 115-129, both from 1964). Both of these expressed stress in percents. Certainly this is not a convention introduced by the authors of the package, since they are much too young to have done that prior to 1964. Cheers, Jari Oksanen __ 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] matching subvectors in vector sets
Starting by the first entry: A00096:A00096:A00096:A00096:A02178:A02178:A07776 and supposing there aren't any other subvectors identical in the set, the algorithm will slide through the vector, first in pairs, then in trios, then in sets of four, etc, and count the occurrences: A00096:A00096 3 A00096:A02178 1 A02178:A02178 1 A02178:A07776 1 A00096:A00096:A00096 2 A00096:A00096:A02178 1 A00096:A02178:A02178 1 A02178:A02178:A07776 1 A00096:A00096:A00096:A00096 1 A00096:A00096:A00096:A02178 1 A00096:A00096:A02178:A02178 1 A00096:A02178:A02178:A07776 1 A00096:A00096:A00096:A00096:A02178 1 A00096:A00096:A00096:A02178:A02178 1 A00096:A00096:A02178:A02178:A07776 1 A00096:A00096:A00096:A00096:A02178:A02178 1 A00096:A00096:A00096:A02178:A02178:A07776 1 A00096:A00096:A00096:A00096:A02178:A02178:A07776 1 On Fri, Apr 17, 2009 at 1:04 PM, jim holtman jholt...@gmail.com wrote: Can you provide the output that you would expect from the data you gave. I am not sure what you mean by a 'subvector'. On Fri, Apr 17, 2009 at 5:25 AM, Albert Vilella avile...@gmail.com wrote: Hi, I've got a list of ~2 elements that look like this: [1] A00096:A00096:A00096:A00096:A02178:A02178:A07776 [2] A00046:A00076:A01101:A04146:A05671:A07169 [3] A00038:A00932:A02185:A02370:A02818:A02818:A02818:A02818:A04732:A07142:A07142 [4] A00096:A01352:A01352:A02023:A05001:A05001:A07776 [5] A00036:A00047:A00059:A00503:A00904:A00904:A00904:A01023:A01023:A01399:A02029:A03941:A07679 [6] A00041:A00533:A00855:A02178:A02178:A02178:A05671:A05671:A05671:A05671:A05671:A05671:A05671 ... And I would like to have a table with the frequency of occurrences for matching subvectors in all elements, i.e., not only the number of times a vector is found but also how many times a subvector (of at least 2 ids) is found. How can I do that? Thanks in advance, Albert. [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] cast function in package reshape
Hello R useRs,
I have a function which returns a list of functions :
freq1 - function(x) {
lev - unique(x[!is.na(x)])
nlev - length(lev)
args - alist(x=)
if (nlev == 1) {
body - c({, sum(!is.na(x)), })
f - function() {}
formals(f) - as.pairlist(args)
body(f) - parse(text = body)
namef - paste(freq, as.character(nlev), sep = _)
assign(namef, f)
res - list(get(namef))
names(res) - namef
}
if (nlev 1) {
res - NULL
namesf - NULL
for (i in 1:nlev) {
body - c({, paste(sum(x[!is.na(x)] ==, as.character(lev[i]), ),
sep = ), })
f - function() {}
formals(f) - as.pairlist(args)
body(f) - parse(text = body)
namef - paste(freq, as.character(lev[i]), sep = _)
assign(namef, f)
namesf - c(namesf, namef)
res - c(res, get(namef))
}
names(res) - namesf
}
return(res)
}
df - data.frame(id = 1:50, x = sample(c(NA, 1), 50, T), y = sample(1:2, 50,
T), z = sample(letters[1:2], 50, T))
freq1(df$x)
$freq_1
function (x)
{
sum(!is.na(x))
}
environment: 0x03d99684
freq1(df$y)
$freq_2
function (x)
{
sum(x[!is.na(x)] == 2)
}
environment: 0x03d6c930
$freq_1
function (x)
{
sum(x[!is.na(x)] == 1)
}
environment: 0x03d6c930
I would like to use this list of functions with cast function (in package
reshape by Hadley Wickham) :
cast(melt(df, id = c(id, z), measure = c(x, y)), variable +
result_variable ~ z, fun = function(x) freq1(x), margins = grand_col)
Erreur dans freq1(x) : objet res non trouvé
Here the result I would like to have :
variable a b (all)
1x freq_1 10 1424
2y freq_1 18 3250
3y freq_2 9 1423
I admit it is a bit far-fetched, but is this actually possible ?
Thank you very much.
David
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Presenting R Results in Webpages
You could perhaps use asciidoc http://www.methods.co.nz/asciidoc/and ascii http://eusebe.github.com/ascii/package (but I'm not sure you could obtain exactly the layout you describe...). 2009/4/17 Jim Lemon j...@bitwrit.com.au Jason Rupert wrote: I apologize in advance that this question is not specific to R, but I thought some R users may be using this in their work process flow. I would like to be able to have a tool (prefer scriptable) that will take two images and some pre-written text and put it on an simple webpage. That is, it would look something like the following: |-| |Title| | | | || || Some basic txt | | | Image1 | | Image2 | ... | | || || ... | |_| R comes in because I have R scripts creating the images I would like to import. There will be 14-18 pages of these type of slides, but the key is we will be producing these over and over. I tried doing something like this in PowerPoint, but not impressed with the linking capability or Macros. Thanks for any feedback and again appologize that this is not exactly a specific R question. Hi Jason, You could do something similar with htmlize in the prettyR package, and get exactly what you want with a bit of HTML editing. Get an R script that will generate the two images, then the text. Then insert a few tags like this: (All of the HTML before the first image) table tr td img src=Image1.png td img src=Image2.png td Text that you want in the right hand cell /table (the rest of the HTML) 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. [[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] S+FinMetrics
please !, what is the R equivalents for the S-plus package : S+FinMetrics thanks hassan [[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] Presenting R Results in Webpages
and also R2HTML. 2009/4/17 David Hajage dhajag...@gmail.com You could perhaps use asciidoc http://www.methods.co.nz/asciidoc/and ascii http://eusebe.github.com/ascii/package (but I'm not sure you could obtain exactly the layout you describe...). 2009/4/17 Jim Lemon j...@bitwrit.com.au Jason Rupert wrote: I apologize in advance that this question is not specific to R, but I thought some R users may be using this in their work process flow. I would like to be able to have a tool (prefer scriptable) that will take two images and some pre-written text and put it on an simple webpage. That is, it would look something like the following: |-| |Title| | | | || || Some basic txt | | | Image1 | | Image2 | ... | | || || ... | |_| R comes in because I have R scripts creating the images I would like to import. There will be 14-18 pages of these type of slides, but the key is we will be producing these over and over. I tried doing something like this in PowerPoint, but not impressed with the linking capability or Macros. Thanks for any feedback and again appologize that this is not exactly a specific R question. Hi Jason, You could do something similar with htmlize in the prettyR package, and get exactly what you want with a bit of HTML editing. Get an R script that will generate the two images, then the text. Then insert a few tags like this: (All of the HTML before the first image) table tr td img src=Image1.png td img src=Image2.png td Text that you want in the right hand cell /table (the rest of the HTML) 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. [[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] S+FinMetrics
Resources include: * Rmetrics * The finance task view on CRAN * The R-sig-finance mailing list Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) Hassan Mohamed wrote: please !, what is the R equivalents for the S-plus package : S+FinMetrics thanks hassan [[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] cast function in package reshape
On Fri, Apr 17, 2009 at 8:38 AM, David Hajage dhajag...@gmail.com wrote:
Hello R useRs,
I have a function which returns a list of functions :
freq1 - function(x) {
lev - unique(x[!is.na(x)])
nlev - length(lev)
args - alist(x=)
if (nlev == 1) {
body - c({, sum(!is.na(x)), })
f - function() {}
formals(f) - as.pairlist(args)
body(f) - parse(text = body)
namef - paste(freq, as.character(nlev), sep = _)
assign(namef, f)
res - list(get(namef))
names(res) - namef
}
if (nlev 1) {
res - NULL
namesf - NULL
for (i in 1:nlev) {
body - c({, paste(sum(x[!is.na(x)] ==, as.character(lev[i]), ),
sep = ), })
f - function() {}
formals(f) - as.pairlist(args)
body(f) - parse(text = body)
namef - paste(freq, as.character(lev[i]), sep = _)
assign(namef, f)
namesf - c(namesf, namef)
res - c(res, get(namef))
}
names(res) - namesf
}
return(res)
}
df - data.frame(id = 1:50, x = sample(c(NA, 1), 50, T), y = sample(1:2, 50,
T), z = sample(letters[1:2], 50, T))
freq1(df$x)
$freq_1
function (x)
{
sum(!is.na(x))
}
environment: 0x03d99684
freq1(df$y)
$freq_2
function (x)
{
sum(x[!is.na(x)] == 2)
}
environment: 0x03d6c930
$freq_1
function (x)
{
sum(x[!is.na(x)] == 1)
}
environment: 0x03d6c930
I would like to use this list of functions with cast function (in package
reshape by Hadley Wickham) :
cast(melt(df, id = c(id, z), measure = c(x, y)), variable +
result_variable ~ z, fun = function(x) freq1(x), margins = grand_col)
Erreur dans freq1(x) : objet res non trouvé
Here the result I would like to have :
variable a b (all)
1 x freq_1 10 14 24
2 y freq_1 18 32 50
3 y freq_2 9 14 23
I admit it is a bit far-fetched, but is this actually possible ?
Something like this?
df - data.frame(
id = 1:50,
x = sample(c(NA, 1), 50, T),
y = sample(1:2, 50, T),
z = sample(letters[1:2], 50, T)
)
dfm - melt(df, id = c(id, z))
f1 - function(base)
function(x) table(factor(x, levels = unique(base)))
cast(dfm, variable + result_variable ~ z, f1(dfm$value),
margins = grand_col)
I think f1 effectively does what your freq1 function does, but always
returns the same number of results, a requirement of the aggregation
function in cast.
Hadley
--
http://had.co.nz/
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Re: [R] Lattice xyplot with text under x-axis
A million thanks Deepayan! That works great. Deepayan Sarkar wrote: On Wed, Apr 15, 2009 at 8:59 AM, kate.m katherine...@gmail.com wrote: Hi All, I have a data set which I need to plot and show the values of one of the variables as a second x-axis. library(lattice) year-c(2001,2002,2003,2004,2005,2006) fac-c(arts,arts,arts,sci,sci,sci) staff-c(95,98,99,32,31,36) part-c(32,31,33,15,16,14) df1-data.frame(year,fac,staff,part) xyplot(part~year, type=o, xlab=, ylab=) n.val.text-paste(n = , df1$staff, sep = ) mtext(n.val.text, side = 1, line = 3, at = axTicks(1), cex = 0.9) This works OK. Not really... The problem comes in when I plot the data in panels. xyplot(part~year | fac, as.table=TRUE, type=o, between=list(x=1,y=1), xlab=, ylab=, scales=list(x=list(alternating=3),y=list(alternating=3), relation=free)) The mtext code doesn't work anymore. I think it needs some sort of panel function (panel.groups?) which would tell it to show the appropriate values of staff under their respective year for each fac and each panel. Something like xyplot(part~year | fac, as.table=TRUE, type=o, between=list(x=1,y=1), scales = list(relation = free, x = list(at = year, labels = paste(year, n.val.text, sep = \n -Deepayan __ 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. -- View this message in context: http://www.nabble.com/Lattice-xyplot-with-text-under-x-axis-tp23061842p23098408.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] Coloring X, Y and Main Label
Dear all, I have no problem coloring the axis and plot, following these procedures: http://www.nabble.com/Coloring-X-and-Y-axis-tt22989739r0.html#a22989739 However the X,Y and Main Label stays in black. How can we change their colors? - Gundala Viswanath Jakarta - Indonesia __ 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] Modular Arithmetic Error?
Hi, I'm using the '%%' operator in some code, and am running into the following erroneous outcome: 1.2 %% 0.2 [1] 0.2 Unless I'm very mistaken, the result should be 0 (indeed, 12 %% 2 does result in 0). Furthermore: 1.20001 %% 0.2 [1] 0.2 (1.2+1e17) %% .2 [1] 0 Warning message: probable complete loss of accuracy in modulus (Warning comes up only when it is giving a closer-to-correct answer) What makes it even stranger is this result: (1.2 %% 0.2) == 0.2 [1] FALSE Does anybody know what's going on here? This seems like very bad behavior. Thanks, Peter __ 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] Modular Arithmetic Error?
A few further oddities (no longer having to do with modular arithmetic): (0.3 * 3) == 0.9 [1] FALSE (0.2 * 6) == 1.2 [1] FALSE This is bad behavior, right? I feel like I'm going crazy. I'm using R version 2.8.1 (2008-12-22). Thanks, Peter __ 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] Modular Arithmetic Error?
That is more or less FAQ 7.31: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-the se-numbers-are-equal_003f ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 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 iuhz7j...@sneakemail.com Verzonden: vrijdag 17 april 2009 16:15 Aan: r-help@r-project.org Onderwerp: [R] Modular Arithmetic Error? Hi, I'm using the '%%' operator in some code, and am running into the following erroneous outcome: 1.2 %% 0.2 [1] 0.2 Unless I'm very mistaken, the result should be 0 (indeed, 12 %% 2 does result in 0). Furthermore: 1.20001 %% 0.2 [1] 0.2 (1.2+1e17) %% .2 [1] 0 Warning message: probable complete loss of accuracy in modulus (Warning comes up only when it is giving a closer-to-correct answer) What makes it even stranger is this result: (1.2 %% 0.2) == 0.2 [1] FALSE Does anybody know what's going on here? This seems like very bad behavior. Thanks, Peter __ 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. 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] Modular Arithmetic Error?
You should read the FAQ 7.31 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of iuhz7j...@sneakemail.com Sent: Friday, April 17, 2009 10:30 AM To: r-help@r-project.org Subject: Re: [R] Modular Arithmetic Error? A few further oddities (no longer having to do with modular arithmetic): (0.3 * 3) == 0.9 [1] FALSE (0.2 * 6) == 1.2 [1] FALSE This is bad behavior, right? I feel like I'm going crazy. I'm using R version 2.8.1 (2008-12-22). Thanks, Peter __ 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] Coloring X, Y and Main Label
Dear Gundala, See col.lab and col.main arguments in ?par. plot(1,col.lab='red',col.main='blue',main='Title here') HTH, Jorge On Fri, Apr 17, 2009 at 10:14 AM, Gundala Viswanath gunda...@gmail.comwrote: Dear all, I have no problem coloring the axis and plot, following these procedures: http://www.nabble.com/Coloring-X-and-Y-axis-tt22989739r0.html#a22989739 However the X,Y and Main Label stays in black. How can we change their colors? - Gundala Viswanath Jakarta - Indonesia __ 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] Modular Arithmetic Error?
check the R FAQ, and in particular entry 7.31: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Best, Dimitris iuhz7j...@sneakemail.com wrote: A few further oddities (no longer having to do with modular arithmetic): (0.3 * 3) == 0.9 [1] FALSE (0.2 * 6) == 1.2 [1] FALSE This is bad behavior, right? I feel like I'm going crazy. I'm using R version 2.8.1 (2008-12-22). Thanks, Peter __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] Modular Arithmetic Error?
That explains it, thanks. all.equal() gets it right. I always knew I had to be careful with rounding errors, just not with something like (0.2*6)... I guess I'll just have to avoid using '%%' or '%/%' with non-integers, at least if I need it to sometimes come out even. Thanks again, Peter That is more or less FAQ 7.31: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f __ 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 of points in a 3d plot of a PCA
Dear all, I'm trying to perform a principal components analysis of a sample of individuals, and to plot it in 3D, assigning different colors according to the population each individual belongs to. Given that the matrix I have to use for the PCA cannot contain cualitative variables (here, the population of origin), I have no idea how can I do this in R. ANy help? Thanks in advance Alejandro González Departamento de Biodiversidad y Conservación Real Jardín Botánico Consejo Superior de Investigaciones Científicas Claudio Moyano, 1 28014 Madrid, Spain Tel +0034 914203017 __ 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] Modular Arithmetic Error?
On Apr 17, 2009, at 9:29 AM, iuhz7j...@sneakemail.com wrote: A few further oddities (no longer having to do with modular arithmetic): (0.3 * 3) == 0.9 [1] FALSE (0.2 * 6) == 1.2 [1] FALSE This is bad behavior, right? No... (0.3 * 3) - 0.9 [1] -1.110223e-16 (0.2 * 6) - 1.2 [1] 2.220446e-16 However: all.equal(0.3 * 3, 0.9) [1] TRUE all.equal(0.2 * 6, 1.2) [1] TRUE See ?all.equal I feel like I'm going crazy. Only because you don't understand the etiology of the behavior. Read: R FAQ 7.31 Why doesn't R think these numbers are equal? http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f and call us in the morning :-) HTH, Marc Schwartz __ 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 of points in a 3d plot of a PCA
On 4/17/2009 10:43 AM, Alejandro González wrote: Dear all, I'm trying to perform a principal components analysis of a sample of individuals, and to plot it in 3D, assigning different colors according to the population each individual belongs to. Given that the matrix I have to use for the PCA cannot contain cualitative variables (here, the population of origin), I have no idea how can I do this in R. ANy help? Thanks in advance As long as the order of rows in the matrix is unchanged when you calculate the pc scores, you should be able to use a separate dataframe or vector to give information about each row, and to work out a colour for plotting it. For example: X - matrix(rnorm(1000), 100, 10) # Make up a fake population based on the first column popn - round(X[,1]) colour - popn - min(popn) + 1 pc - princomp(X) library(rgl) plot3d(pc$scores[,1:3], col=colour) Duncan Murdoch Alejandro González Departamento de Biodiversidad y Conservación Real Jardín Botánico Consejo Superior de Investigaciones Científicas Claudio Moyano, 1 28014 Madrid, Spain Tel +0034 914203017 __ 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] Create histogram from data matrix
Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? Thanks a lot for any assistance or advice! Sincerely, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ 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] Using trace
Well, yes, of course I could add the code to the function by hand. I
could also calculate square roots by hand. But -- as in every other
basic programming environment -- there exists an R function 'trace'
which appears to automate the process, and I can't figure out how to
use it to handle this most elementary and standard case. Clearly I'm
missing something.
-s
On Thu, Apr 16, 2009 at 9:26 PM, ronggui ronggui.hu...@gmail.com wrote:
Can you just print what you need to know? For example:
fact - function(x) {
+ if(x1) ans - 1 else ans - x*fact(x-1)
+ print(sys.call())
+ cat(sprintf(X is %i\n,x))
+ print(ans)
+ }
fact(4)
fact(x - 1)
X is 0
[1] 1
fact(x - 1)
X is 1
[1] 1
fact(x - 1)
X is 2
[1] 2
fact(x - 1)
X is 3
[1] 6
fact(4)
X is 4
[1] 24
2009/4/13 Stavros Macrakis macra...@alum.mit.edu:
I would like to trace functions, displaying their arguments and return
value, but I haven't been able to figure out how to do this with the
'trace' function.
After some thrashing, I got as far as this:
fact - function(x) if(x1) 1 else x*fact(x-1)
tracefnc - function() dput(as.list(parent.frame()), #
parent.frame() holds arg list
control=NULL)
trace(fact,tracer=tracefnc,print=FALSE)
but I couldn't figure out how to access the return value of the
function in the 'exit' parameter. The above also doesn't work for
... arguments. (More subtly, it forces the evaluation of promises
even if they are otherwise unused -- but that is, I suppose, a weird
and obscure case.)
Surely someone has solved this already?
What I'm looking for is something very simple, along the lines of
old-fashioned Lisp trace:
defun fact (i) (if ( i 1) 1 (* i (fact (+ i -1)
FACT
(trace fact)
(FACT)
(fact 3)
1 (FACT 3)
2 (FACT 2)
3 (FACT 1)
4 (FACT 0)
4 (FACT 1)
3 (FACT 1)
2 (FACT 2)
1 (FACT 6)
6
Can someone help? Thanks,
-s
__
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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.
--
HUANG Ronggui, Wincent
PhD Candidate
Dept of Public and Social Administration
City University of Hong Kong
Home page: http://asrr.r-forge.r-project.org/rghuang.html
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Generate bivariate binomial data
Dear all, Could someone point me to a function or algorithm to generate random bivariate binomial data? Some details about what I'm trying to do. I have a dataset of trees who were categorised as not damaged or damaged. Each tree is measured twice (once in two consecutive years). The trees can recover from the damage but the data is clearly correlated. As a (un)damaged tree is more likely to stay (un)damaged. A GEE-model indicates a correlation of about 0.6 between the measures on the same tree. I need to simulate similar dataset to do some power calculations. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 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 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] error bars in matplot
Thanks Mathieu and Jim,
That worked!
From: Jim Lemon j...@bitwrit.com.au
Cc: r r-h...@stat.math.ethz.ch
Sent: Friday, April 17, 2009 7:45:39 AM
Subject: Re: [R] error bars in matplot
Tim Smith wrote:
Hi,
I was trying to get error bars in my matplot. I looked at an earlier thread,
and the sample code that I made is:
#--
library(plotrix)
mat1 - matrix(sample(1:30,10),nrow=5,ncol=2)
ses - matrix(sample(1:3,10,replace=T),nrow=5,ncol=2)
vect - seq(20,100,20)
rownames(mat1) - rownames(ses) - vect
colnames(mat1) - colnames(ses) - letters[1:2]
matplot(mat1,pch=c('x','o'),type = b,lwd = 2,lty = c(1,2),
col = c(green,black),cex.main = 1.8,cex=2,cex.lab=1.5,
main = Graph 1,xlab = Numbers 1,ylab = Numbers 2,cex.axis =
1.6,axes=F)
plotCI(rep(vect,2),mat1,ses2,pch=NA,add=T,
col=rep(c(green,black),each=nrow(mat1)))
axis(1,1:5,labels = vect,cex.axis=1.5)
axis(2,cex.axis=1.5)
#--
I don't get the error bars though. If I set 'add = F' in plotCI function,
then I can see the error bars, but they just can't be added to the matplot.
What am I doing wrong? Is there any other way to get the error bars?
Hi Tim,
Try the dispersion function in plotrix to add error bars. You will
probably have to add ylim=c(0,29) to your matplot command.
dispersion(rep(1:5,2),mat1,ses)
Jim
[[alternative HTML version deleted]]
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Re: [R] Using trace
Here is a partial solution:
trace(fact,quote({cat(sprintf(x= %i\n,x));return}),print=T)
[1] fact
fact(4)
Tracing fact(4) on entry
x= 4
Tracing fact(x - 1) on entry
x= 3
Tracing fact(x - 1) on entry
x= 2
Tracing fact(x - 1) on entry
x= 1
Tracing fact(x - 1) on entry
x= 0
[1] 24
2009/4/17 Stavros Macrakis macra...@alum.mit.edu:
Well, yes, of course I could add the code to the function by hand. I
could also calculate square roots by hand. But -- as in every other
basic programming environment -- there exists an R function 'trace'
which appears to automate the process, and I can't figure out how to
use it to handle this most elementary and standard case. Clearly I'm
missing something.
-s
On Thu, Apr 16, 2009 at 9:26 PM, ronggui ronggui.hu...@gmail.com wrote:
Can you just print what you need to know? For example:
fact - function(x) {
+ if(x1) ans - 1 else ans - x*fact(x-1)
+ print(sys.call())
+ cat(sprintf(X is %i\n,x))
+ print(ans)
+ }
fact(4)
fact(x - 1)
X is 0
[1] 1
fact(x - 1)
X is 1
[1] 1
fact(x - 1)
X is 2
[1] 2
fact(x - 1)
X is 3
[1] 6
fact(4)
X is 4
[1] 24
2009/4/13 Stavros Macrakis macra...@alum.mit.edu:
I would like to trace functions, displaying their arguments and return
value, but I haven't been able to figure out how to do this with the
'trace' function.
After some thrashing, I got as far as this:
fact - function(x) if(x1) 1 else x*fact(x-1)
tracefnc - function() dput(as.list(parent.frame()), #
parent.frame() holds arg list
control=NULL)
trace(fact,tracer=tracefnc,print=FALSE)
but I couldn't figure out how to access the return value of the
function in the 'exit' parameter. The above also doesn't work for
... arguments. (More subtly, it forces the evaluation of promises
even if they are otherwise unused -- but that is, I suppose, a weird
and obscure case.)
Surely someone has solved this already?
What I'm looking for is something very simple, along the lines of
old-fashioned Lisp trace:
defun fact (i) (if ( i 1) 1 (* i (fact (+ i -1)
FACT
(trace fact)
(FACT)
(fact 3)
1 (FACT 3)
2 (FACT 2)
3 (FACT 1)
4 (FACT 0)
4 (FACT 1)
3 (FACT 1)
2 (FACT 2)
1 (FACT 6)
6
Can someone help? Thanks,
-s
__
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.
--
HUANG Ronggui, Wincent
PhD Candidate
Dept of Public and Social Administration
City University of Hong Kong
Home page: http://asrr.r-forge.r-project.org/rghuang.html
--
HUANG Ronggui, Wincent
PhD Candidate
Dept of Public and Social Administration
City University of Hong Kong
Home page: http://asrr.r-forge.r-project.org/rghuang.html
__
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] args and test of passed paramters
Hi,
I would like to call a R script sometimes with:
R --slave --vanilla --args Debug=1 N=25 test.R
and sometimes with
R --slave --vanilla Debug=1 test.R
or similar.
Inside the R script I get the arguments with:
args=(commandArgs(TRUE))
if(length(args)==0){
print(===No arguments supplied. =)
}else{
for(i in 1:length(args)){
eval(parse(text=args[[i]]))
}
}
But I don't know, how can I test inside the script if the parameter N
was passed to script or not. I am looking for something like
is.defined(N), but I could not find it until now.
Any hint?
Juergen
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Re: [R] Generate bivariate binomial data
Hi Thierry, I think it should be possible to generate such correlated data using a mixed model approach: 1) Generate pairs of correlated linear predictor values using an ordinary linear mixed model setup (for example using rnorm() repeatedly) 2) Back-transform these values using the inverse logit (or similar link function) to obtain probabilities 3) Draw binomial responses using the probabilities from 2) (using rbinom()) You may need to use trial-and-error to get the right amount of correlation. Christian __ 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] issue with L-BFGS-B in optim (optim just hangs)
Dear R-help list, Just a wrap up for this issue. Thanks to Ravi Varadan and Paul Smith for useful feedback (both on and off list). It seems like the culprit was another function being called within optim, namely adapt (used to solve numerically a double integral in the likelihood I am maximizing). From what I was able to track down, it is adapt that just hangs. I do not know exactly why, but decreasing the precision in adapt, using parameter eps, solves it somewhat. I have not yet investigated thoroughly if decreasing eps does have an impact on my results, but that is another story! Best, Tiago Ravi Varadhan wrote: Hi Tiago, It is hard for me to speculate without knowing more about your problem. Here is what I would suggest, assuming your problem specification and its computer implementation are correct: (1) You may try to terminate the algorithm by specifying a different stopping criterion than the default values, and see whether the solution is of acceptable accuracy. You can increase factr and/or pgtol to see if this problem goes away. (2) Another option is to increase lmm parameter, which is the number of BFGS updates saved for approximating the hessian. Results in Zhu et al. (ACM 1997) show that increasing lmm tends to improve the reliability of the algorithm. Try, for example, lmm=17 (default is lmm = 5). Also, try using trace to get more information on what goes on. I can also suggest some alternative solutions: (3). An easy solution is to try a different optimization algorithm: YOU can try either nlminb() or spg() in package BB. (4). If it is easy to do so, specify analytic score function, i.e. the gradient of log-likelohood, and re-run optim() or nlminb() or spg(). Hope this helps, Ravi. Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tiago Marques Sent: Wednesday, April 15, 2009 10:57 AM To: r-help@r-project.org Subject: [R] issue with L-BFGS-B in optim (optim just hangs) Dear R-Help List, I am using optim, with method=L-BFGS-B, to maximize a likelihood inside a large simulation exercise. This runs fine for most simulated data sets, but for some reason, about 1 out of 100 times, optim will just hang. Using a dumb approach to the problem (i.e. printing the parameter values each time the function being maximized is evaluated), I tracked down when this happens, and although I do not understand optim's behavior or what triggers it, it seems to happen specifically when one of the parameter boundaries is reached - and then the function just stops being evaluated. But there is nothing special with the parameter boundary, i.e., if I decrease or increase the boundary using say lower and upper arguments in optim, the function seems to hang at the new values. So it does not seem to be a specific value that triggers the behavior, but the fact that the value is the boundary defined in the function call. As anyone seen this behavior before? Is it me missing something or is this some bug in method=L-BFGS-B? Any suggestions on how to deal with it? Many thanks for any useful feedback, Tiago -- Tiago André Marques Research Unit for Wildlife Population Assessment Centre for Research into Ecological and Environmental Modelling University of St Andrews The Observatory Buchanan Gardens St Andrews Fife KY16 9LZ Scotland Tel: 00441334461842 Fax: 00441334461800 (Scotland office) Tel: 00351210198736 (Portugal home) http://www-maths.mcs.st-andrews.ac.uk/homepages/tam2.html http://www.creem.st-and.ac.uk/tiago/ The University of St Andrews is a charity registered in Scotland : No SC013532 __ 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] R on Windows and RMySQL
I have successfully installed R (version 2.8.1) and RMySQL (version 0.7-4) on my PC (Windows). Now I have a problem running RMySQL on R. I constantly receive the following error-message: Error in utils::readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) : Registry-Schlüssel 'S' nicht gefunden Error : .onLoad in 'loadNamespace' für 'RMySQL' fehlgeschlagen Fehler: Laden von Paket/Namensraum für 'RMySQL' fehlgeschlagen Does anyone have a clue what I should do? I don`t have any experience in such issues. I have not installed MySQL on my PC. Could this be the solution to my problem? Is it true that RMySQL does work properly on R only if you first install MySQL? Thanks for your answer... __ 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] numbers loop in R
I would like to create a matrix in R that looks similar to this:
[,1] [,2] [,3] [,4]
[1,] NaN 1 2 3
[2,] NaN 1 2 4
[3,] NaN 1 2 5
[4,] NaN 2 3 4
[5,] NaN 2 3 5
[6,] NaN345
I have the loop below:
where A for example is 5
matrixx-function(A){
B=matrix(NaN,nrow=(A+1),ncol=4)
for(k in 1:(A+1)){
for(i in 1:(A-2)){
for(j in (i+2):A){
}
}
}
B[k,]=c(NaN,i,(i+1),j)
print(B)
}
But it only prints the final line in:
matrixx(5)
[,1] [,2] [,3] [,4]
[1,] NaN NaN NaN NaN
[2,] NaN NaN NaN NaN
[3,] NaN NaN NaN NaN
[4,] NaN NaN NaN NaN
[5,] NaN NaN NaN NaN
[6,] NaN345
Could anyone give me a hand? Would be much appreciated.
Thanks Emma
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Re: [R] Numeric data calculated in bwplot
On 4/17/09, Yuri Volchik yuri.volc...@gmail.com wrote: Hi, i was wondering if there is a way to extract statistic calculated by the function bwplot in numeric format, i.e. a list with values of borders mean etc. See ?boxplot.stats -Deepayan __ 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 on Windows and RMySQL
On 4/17/2009 6:48 AM, s...@access.unizh.ch wrote: I have successfully installed R (version 2.8.1) and RMySQL (version 0.7-4) on my PC (Windows). Now I have a problem running RMySQL on R. I constantly receive the following error-message: Error in utils::readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) : Registry-Schlüssel 'S' nicht gefunden Error : .onLoad in 'loadNamespace' für 'RMySQL' fehlgeschlagen Fehler: Laden von Paket/Namensraum für 'RMySQL' fehlgeschlagen Does anyone have a clue what I should do? I don`t have any experience in such issues. I have not installed MySQL on my PC. Could this be the solution to my problem? Is it true that RMySQL does work properly on R only if you first install MySQL? That's what it looks like. I'm not sure why it is reporting 'S' as a problem, but when I execute that line I see readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) $`MySQL Server 5.0` $`MySQL Server 5.0`$Location [1] F:\\Program Files\\MySQL\\MySQL Server 5.0\\ $`MySQL Server 5.0`$Version [1] 5.0.22 and when I change the key to a nonexistent one I see readRegistry(SOFTWARE\\foobar, hive = HLM, maxdepth = 2) Error in readRegistry(SOFTWARE\\foobar, hive = HLM, maxdepth = 2) : Registry key 'S' not found I'll take a look at readRegistry and try to improve the error message. Duncan Murdoch __ 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] issue with L-BFGS-B in optim (optim just hangs)
Tiago, If you have an improper integral, i.e. with at least one of the limits being infinite, it is generally not a good idea to use large positive or negative values to compute such integrals. You should use integrate (calling it twice) to compute your double integral. This might solve your problem, assuming that is your problem. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: Tiago Marques [mailto:ti...@mcs.st-and.ac.uk] Sent: Friday, April 17, 2009 11:56 AM To: Ravi Varadhan Cc: r-help@r-project.org Subject: Re: [R] issue with L-BFGS-B in optim (optim just hangs) Dear R-help list, Just a wrap up for this issue. Thanks to Ravi Varadan and Paul Smith for useful feedback (both on and off list). It seems like the culprit was another function being called within optim, namely adapt (used to solve numerically a double integral in the likelihood I am maximizing). From what I was able to track down, it is adapt that just hangs. I do not know exactly why, but decreasing the precision in adapt, using parameter eps, solves it somewhat. I have not yet investigated thoroughly if decreasing eps does have an impact on my results, but that is another story! Best, Tiago Ravi Varadhan wrote: Hi Tiago, It is hard for me to speculate without knowing more about your problem. Here is what I would suggest, assuming your problem specification and its computer implementation are correct: (1) You may try to terminate the algorithm by specifying a different stopping criterion than the default values, and see whether the solution is of acceptable accuracy. You can increase factr and/or pgtol to see if this problem goes away. (2) Another option is to increase lmm parameter, which is the number of BFGS updates saved for approximating the hessian. Results in Zhu et al. (ACM 1997) show that increasing lmm tends to improve the reliability of the algorithm. Try, for example, lmm=17 (default is lmm = 5). Also, try using trace to get more information on what goes on. I can also suggest some alternative solutions: (3). An easy solution is to try a different optimization algorithm: YOU can try either nlminb() or spg() in package BB. (4). If it is easy to do so, specify analytic score function, i.e. the gradient of log-likelohood, and re-run optim() or nlminb() or spg(). Hope this helps, Ravi. -- -- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -- -- -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tiago Marques Sent: Wednesday, April 15, 2009 10:57 AM To: r-help@r-project.org Subject: [R] issue with L-BFGS-B in optim (optim just hangs) Dear R-Help List, I am using optim, with method=L-BFGS-B, to maximize a likelihood inside a large simulation exercise. This runs fine for most simulated data sets, but for some reason, about 1 out of 100 times, optim will just hang. Using a dumb approach to the problem (i.e. printing the parameter values each time the function being maximized is evaluated), I tracked down when this happens, and although I do not understand optim's behavior or what triggers it, it seems to happen specifically when one of the parameter boundaries is reached - and then the function just stops being evaluated. But there is nothing special with the parameter boundary, i.e., if I decrease or increase the boundary using say lower and upper arguments in optim, the function seems to hang at the new values. So it does not seem to be a specific value that triggers the behavior, but the fact that the value is the boundary defined in the function call. As anyone seen this behavior before? Is it me missing something or is this some bug in method=L-BFGS-B? Any suggestions on how to deal with it? Many thanks for any useful feedback, Tiago -- Tiago André Marques Research Unit for Wildlife Population Assessment Centre for Research into Ecological and Environmental Modelling University of St Andrews The Observatory Buchanan Gardens St Andrews Fife KY16 9LZ Scotland Tel: 00441334461842 Fax:
Re: [R] matching subvectors in vector sets
How about this:
x - A00096:A00096:A00096:A00096:A02178:A02178:A07776
x.s - unlist(strsplit(x, :))
for (i in 2:length(x.s)){
+ x.seq - embed(length(x.s):1, i)
+ print(table(apply(x.seq, 1, function(z){
+ paste(x.s[z], collapse=:)
+ })))
+ }
A00096:A00096 A00096:A02178 A02178:A02178 A02178:A07776
3 1 1 1
A00096:A00096:A00096 A00096:A00096:A02178 A00096:A02178:A02178
A02178:A02178:A07776
211
1
A00096:A00096:A00096:A00096 A00096:A00096:A00096:A02178
A00096:A00096:A02178:A02178 A00096:A02178:A02178:A07776
1 1
1 1
A00096:A00096:A00096:A00096:A02178 A00096:A00096:A00096:A02178:A02178
A00096:A00096:A02178:A02178:A07776
1 1
1
A00096:A00096:A00096:A00096:A02178:A02178
A00096:A00096:A00096:A02178:A02178:A07776
1
1
A00096:A00096:A00096:A00096:A02178:A02178:A07776
1
On Fri, Apr 17, 2009 at 9:33 AM, Albert Vilella avile...@gmail.com wrote:
Starting by the first entry:
A00096:A00096:A00096:A00096:A02178:A02178:A07776
and supposing there aren't any other subvectors identical in the set, the
algorithm will slide through the vector, first in pairs, then in trios, then
in sets of four, etc, and count the occurrences:
A00096:A00096
3
A00096:A02178
1
A02178:A02178
1
A02178:A07776
1
A00096:A00096:A00096
2
A00096:A00096:A02178
1
A00096:A02178:A02178
1
A02178:A02178:A07776
1
A00096:A00096:A00096:A00096
1
A00096:A00096:A00096:A02178
1
A00096:A00096:A02178:A02178
1
A00096:A02178:A02178:A07776
1
A00096:A00096:A00096:A00096:A02178
1
A00096:A00096:A00096:A02178:A02178
1
A00096:A00096:A02178:A02178:A07776
1
A00096:A00096:A00096:A00096:A02178:A02178
1
A00096:A00096:A00096:A02178:A02178:A07776
1
A00096:A00096:A00096:A00096:A02178:A02178:A07776
1
On Fri, Apr 17, 2009 at 1:04 PM, jim holtman jholt...@gmail.com wrote:
Can you provide the output that you would expect from the data you
gave. I am not sure what you mean by a 'subvector'.
On Fri, Apr 17, 2009 at 5:25 AM, Albert Vilella avile...@gmail.com
wrote:
Hi,
I've got a list of ~2 elements that look like this:
[1]
A00096:A00096:A00096:A00096:A02178:A02178:A07776
[2]
A00046:A00076:A01101:A04146:A05671:A07169
[3]
A00038:A00932:A02185:A02370:A02818:A02818:A02818:A02818:A04732:A07142:A07142
[4]
A00096:A01352:A01352:A02023:A05001:A05001:A07776
[5]
A00036:A00047:A00059:A00503:A00904:A00904:A00904:A01023:A01023:A01399:A02029:A03941:A07679
[6]
A00041:A00533:A00855:A02178:A02178:A02178:A05671:A05671:A05671:A05671:A05671:A05671:A05671
...
And I would like to have a table with the frequency of occurrences for
matching subvectors in all elements, i.e., not
only the number of times a vector is found but also how many times a
subvector (of at least 2 ids) is found.
How can I do that?
Thanks in advance,
Albert.
[[alternative HTML version deleted]]
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--
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Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Using trace
Yes, that is similar to the solution in my original posting, but
doesn't solve the problem I was having with that solution, namely
reporting on the return value.
-s
On Fri, Apr 17, 2009 at 11:28 AM, ronggui ronggui.hu...@gmail.com wrote:
Here is a partial solution:
trace(fact,quote({cat(sprintf(x= %i\n,x));return}),print=T)
[1] fact
fact(4)
Tracing fact(4) on entry
x= 4
Tracing fact(x - 1) on entry
x= 3
Tracing fact(x - 1) on entry
x= 2
Tracing fact(x - 1) on entry
x= 1
Tracing fact(x - 1) on entry
x= 0
[1] 24
2009/4/17 Stavros Macrakis macra...@alum.mit.edu:
Well, yes, of course I could add the code to the function by hand. I
could also calculate square roots by hand. But -- as in every other
basic programming environment -- there exists an R function 'trace'
which appears to automate the process, and I can't figure out how to
use it to handle this most elementary and standard case. Clearly I'm
missing something.
-s
On Thu, Apr 16, 2009 at 9:26 PM, ronggui ronggui.hu...@gmail.com wrote:
Can you just print what you need to know? For example:
fact - function(x) {
+ if(x1) ans - 1 else ans - x*fact(x-1)
+ print(sys.call())
+ cat(sprintf(X is %i\n,x))
+ print(ans)
+ }
fact(4)
fact(x - 1)
X is 0
[1] 1
fact(x - 1)
X is 1
[1] 1
fact(x - 1)
X is 2
[1] 2
fact(x - 1)
X is 3
[1] 6
fact(4)
X is 4
[1] 24
2009/4/13 Stavros Macrakis macra...@alum.mit.edu:
I would like to trace functions, displaying their arguments and return
value, but I haven't been able to figure out how to do this with the
'trace' function.
After some thrashing, I got as far as this:
fact - function(x) if(x1) 1 else x*fact(x-1)
tracefnc - function() dput(as.list(parent.frame()), #
parent.frame() holds arg list
control=NULL)
trace(fact,tracer=tracefnc,print=FALSE)
but I couldn't figure out how to access the return value of the
function in the 'exit' parameter. The above also doesn't work for
... arguments. (More subtly, it forces the evaluation of promises
even if they are otherwise unused -- but that is, I suppose, a weird
and obscure case.)
Surely someone has solved this already?
What I'm looking for is something very simple, along the lines of
old-fashioned Lisp trace:
defun fact (i) (if ( i 1) 1 (* i (fact (+ i -1)
FACT
(trace fact)
(FACT)
(fact 3)
1 (FACT 3)
2 (FACT 2)
3 (FACT 1)
4 (FACT 0)
4 (FACT 1)
3 (FACT 1)
2 (FACT 2)
1 (FACT 6)
6
Can someone help? Thanks,
-s
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--
HUANG Ronggui, Wincent
PhD Candidate
Dept of Public and Social Administration
City University of Hong Kong
Home page: http://asrr.r-forge.r-project.org/rghuang.html
--
HUANG Ronggui, Wincent
PhD Candidate
Dept of Public and Social Administration
City University of Hong Kong
Home page: http://asrr.r-forge.r-project.org/rghuang.html
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Re: [R] Create histogram from data matrix
It would be easier if you were to make a data frame of fake values to illustrate your point, so that we could just copy it into an R session and see if we can't get it to work. So, a stab in the dark would to look at ggplot2 specifically the hist argument in qplot and the facets, the lattice package, or reshape to change the format of your data. If you want me to fool around with it use dput and take a small subset of your data or make up data to be able to be copied into an R session. hope that helps, Stephen On Fri, Apr 17, 2009 at 10:59 AM, Paul Warren Simonin paul.simo...@uvm.edu wrote: Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? Thanks a lot for any assistance or advice! Sincerely, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ 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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] numbers loop in R
I would have expected to see the assignment to B[k,] inside the loops.
And to see some connection with the k index in the inner loops if you
did not want all of the rows to be similar. Because the assignment is
outside the loops, it happens only once.
-- David Winsemius
On Apr 17, 2009, at 11:11 AM, emj83 wrote:
I would like to create a matrix in R that looks similar to this:
[,1] [,2] [,3] [,4]
[1,] NaN 1 2 3
[2,] NaN 1 2 4
[3,] NaN 1 2 5
[4,] NaN 2 3 4
[5,] NaN 2 3 5
[6,] NaN345
I have the loop below:
where A for example is 5
matrixx-function(A){
B=matrix(NaN,nrow=(A+1),ncol=4)
for(k in 1:(A+1)){
for(i in 1:(A-2)){
for(j in (i+2):A){
}
}
}
B[k,]=c(NaN,i,(i+1),j)
print(B)
}
But it only prints the final line in:
matrixx(5)
[,1] [,2] [,3] [,4]
[1,] NaN NaN NaN NaN
[2,] NaN NaN NaN NaN
[3,] NaN NaN NaN NaN
[4,] NaN NaN NaN NaN
[5,] NaN NaN NaN NaN
[6,] NaN345
Could anyone give me a hand? Would be much appreciated.
Thanks Emma
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Heritage Laboratories
West Hartford, CT
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Re: [R] numbers loop in R
try this:
matrixx-function(A){
+ B=matrix(NaN,nrow=(A+1),ncol=4)
+ k - 1
+ for (i in 3:A){
+ for (j in i:A) {
+ B[k,] - c(NaN, i-2, i-1, j)
+ k - k + 1
+ }
+ }
+ B
+ }
matrixx(5)
[,1] [,2] [,3] [,4]
[1,] NaN123
[2,] NaN124
[3,] NaN125
[4,] NaN234
[5,] NaN235
[6,] NaN345
On Fri, Apr 17, 2009 at 11:11 AM, emj83 stp08...@shef.ac.uk wrote:
I would like to create a matrix in R that looks similar to this:
[,1] [,2] [,3] [,4]
[1,] NaN 1 2 3
[2,] NaN 1 2 4
[3,] NaN 1 2 5
[4,] NaN 2 3 4
[5,] NaN 2 3 5
[6,] NaN 3 4 5
I have the loop below:
where A for example is 5
matrixx-function(A){
B=matrix(NaN,nrow=(A+1),ncol=4)
for(k in 1:(A+1)){
for(i in 1:(A-2)){
for(j in (i+2):A){
}
}
}
B[k,]=c(NaN,i,(i+1),j)
print(B)
}
But it only prints the final line in:
matrixx(5)
[,1] [,2] [,3] [,4]
[1,] NaN NaN NaN NaN
[2,] NaN NaN NaN NaN
[3,] NaN NaN NaN NaN
[4,] NaN NaN NaN NaN
[5,] NaN NaN NaN NaN
[6,] NaN 3 4 5
Could anyone give me a hand? Would be much appreciated.
Thanks Emma
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+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] Create histogram from data matrix
On Fri, Apr 17, 2009 at 9:59 AM, Paul Warren Simonin paul.simo...@uvm.edu wrote: Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? In fact, this is very easy to do with ggplot2: install.packages(ggplot2) library(ggplot2) qplot(value, weight = numofobservations, data = mydf, geom=histogram) Hadley -- http://had.co.nz/ __ 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 on Windows and RMySQL
On 4/17/2009 12:26 PM, Duncan Murdoch wrote: On 4/17/2009 12:26 PM, Duncan Murdoch wrote: On 4/17/2009 6:48 AM, s...@access.unizh.ch wrote: I have successfully installed R (version 2.8.1) and RMySQL (version 0.7-4) on my PC (Windows). Now I have a problem running RMySQL on R. I constantly receive the following error-message: Error in utils::readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) : Registry-Schlüssel 'S' nicht gefunden Error : .onLoad in 'loadNamespace' für 'RMySQL' fehlgeschlagen Fehler: Laden von Paket/Namensraum für 'RMySQL' fehlgeschlagen Does anyone have a clue what I should do? I don`t have any experience in such issues. I have not installed MySQL on my PC. Could this be the solution to my problem? Is it true that RMySQL does work properly on R only if you first install MySQL? That's what it looks like. I'm not sure why it is reporting 'S' as a problem, but when I execute that line I see readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) $`MySQL Server 5.0` $`MySQL Server 5.0`$Location [1] F:\\Program Files\\MySQL\\MySQL Server 5.0\\ $`MySQL Server 5.0`$Version [1] 5.0.22 and when I change the key to a nonexistent one I see readRegistry(SOFTWARE\\foobar, hive = HLM, maxdepth = 2) Error in readRegistry(SOFTWARE\\foobar, hive = HLM, maxdepth = 2) : Registry key 'S' not found I'll take a look at readRegistry and try to improve the error message. Duncan Murdoch On 4/17/2009 6:48 AM, s...@access.unizh.ch wrote: I have successfully installed R (version 2.8.1) and RMySQL (version 0.7-4) on my PC (Windows). Now I have a problem running RMySQL on R. I constantly receive the following error-message: Error in utils::readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) : Registry-Schlüssel 'S' nicht gefunden Error : .onLoad in 'loadNamespace' für 'RMySQL' fehlgeschlagen Fehler: Laden von Paket/Namensraum für 'RMySQL' fehlgeschlagen Does anyone have a clue what I should do? I don`t have any experience in such issues. I have not installed MySQL on my PC. Could this be the solution to my problem? Is it true that RMySQL does work properly on R only if you first install MySQL? That's what it looks like. I'm not sure why it is reporting 'S' as a problem, but when I execute that line I see readRegistry(SOFTWARE\\MySQL AB, hive = HLM, maxdepth = 2) $`MySQL Server 5.0` $`MySQL Server 5.0`$Location [1] F:\\Program Files\\MySQL\\MySQL Server 5.0\\ $`MySQL Server 5.0`$Version [1] 5.0.22 and when I change the key to a nonexistent one I see readRegistry(SOFTWARE\\foobar, hive = HLM, maxdepth = 2) Error in readRegistry(SOFTWARE\\foobar, hive = HLM, maxdepth = 2) : Registry key 'S' not found I'll take a look at readRegistry and try to improve the error message. The problem with the error message was simply a typo in the format string. Easy to fix. Your problem is the lack of MySQL on your system. Also easy to fix? Duncan Murdoch __ 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] numbers loop in R
On Fri, Apr 17, 2009 at 12:19 PM, jim holtman jholt...@gmail.com wrote:
try this:
matrixx-function(A){
+ B=matrix(NaN,nrow=(A+1),ncol=4)
+ k - 1
+ for (i in 3:A){
+ for (j in i:A) {
+ B[k,] - c(NaN, i-2, i-1, j)
+ k - k + 1
+ }
+ }
+ B
+ }
matrixx(5)
[,1] [,2] [,3] [,4]
[1,] NaN 1 2 3
[2,] NaN 1 2 4
[3,] NaN 1 2 5
[4,] NaN 2 3 4
[5,] NaN 2 3 5
[6,] NaN 3 4 5
Here's a solution without the loop. I think it illustrates the intent
of the algorithm more clearly.
candidates - t(combn(5,3))
firstdiff - candidates[,2] - candidates[, 1]
cbind(NaN, candidates[firstdiff == 1, ])
Hadley
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[R] Margins in lattice and device resolution
Hi all, I believe I've run into this before, but I seem to have totally forgotten. No headway in the last couple of hours either. How do I make sure that points and margins remain the same absolute size as I change the resolution of a device? (I'm running 2.9.1 patched, on a Win XP-machine) Many thanks in advance, Gustaf Ps: As an afterthought, might it be that this behaviour is related to the receng grid-bug for text size in lattice when changing resolution? Example: . ###This give a totally squished graph, where the actual plotting area is minimal CairoPNG(example.png,width = 480, height = 480, dpi=600, pointsize = 12, bg = white) bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, panel = panel.superpose, panel.groups = panel.linejoin, xlab = treatment, key = list(lines = Rows(trellis.par.get(superpose.line), c(1:7, 1)), text = list(lab = as.character(unique(OrchardSprays$rowpos))), columns = 4, title = Row position)) dev.off() ### This gives a more norma looking graph CairoPNG(example2.png,width = 480, height = 480, dpi=20, pointsize = 12, bg = white) bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, panel = panel.superpose, panel.groups = panel.linejoin, xlab = treatment, key = list(lines = Rows(trellis.par.get(superpose.line), c(1:7, 1)), text = list(lab = as.character(unique(OrchardSprays$rowpos))), columns = 4, title = Row position)) dev.off() -- Gustaf Rydevik, M.Sci. tel: +46(0)703 051 451 address:Essingetorget 40,112 66 Stockholm, SE skype:gustaf_rydevik __ 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] Create histogram from data matrix
here is one way: mydata - data.frame(observ=sample(1:10,20,TRUE), value=sample(1:6,20,TRUE)) mydata observ value 1 3 6 2 4 2 3 6 4 4 10 1 5 3 2 6 9 3 7 10 1 8 7 3 9 7 6 10 1 3 11 3 3 12 2 4 13 7 3 14 4 2 15 8 5 16 5 5 17 8 5 18 10 1 19 4 5 20 8 3 hist(rep(mydata$value, mydata$observ)) On Fri, Apr 17, 2009 at 10:59 AM, Paul Warren Simonin paul.simo...@uvm.edu wrote: Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? Thanks a lot for any assistance or advice! Sincerely, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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] Lattice xyplot with text under x-axis
Still on this question, I'm having problems with displaying the text when repeated values are present. For example: library(lattice) year-c(2001,2002,2003,2001,2002,2003,2001,2002,2003,2001,2002,2003) fac-c(arts,arts,arts,arts,arts,arts,sci,sci,sci,sci,sci,sci) type-c(est,est,est,early,early,early,est,est,est,early,early,early) staff-c(95,98,99,32,31,36,57,52,55,24,23,26) part-c(32,31,33,15,16,14,40,41,43,15,17,19) df1-data.frame(year,fac,type, staff,part) n.val.text-paste(n = , df1$staff, sep = ) xyplot(part~year | type+fac, as.table=TRUE, type=o, between=list(x=1,y=1),xlab=,ylab=, scales = list(relation = free, x = list(at = year, labels =paste(year, n.val.text, sep = \n This attempts to place all the values of staff under each year. Is there a any way to correct this? http://www.nabble.com/file/p23103168/lattice_xyplot_with_axis_text.png Deepayan Sarkar wrote: On Wed, Apr 15, 2009 at 8:59 AM, kate.m katherine...@gmail.com wrote: Hi All, I have a data set which I need to plot and show the values of one of the variables as a second x-axis. library(lattice) year-c(2001,2002,2003,2004,2005,2006) fac-c(arts,arts,arts,sci,sci,sci) staff-c(95,98,99,32,31,36) part-c(32,31,33,15,16,14) df1-data.frame(year,fac,staff,part) xyplot(part~year, type=o, xlab=, ylab=) n.val.text-paste(n = , df1$staff, sep = ) mtext(n.val.text, side = 1, line = 3, at = axTicks(1), cex = 0.9) This works OK. Not really... The problem comes in when I plot the data in panels. xyplot(part~year | fac, as.table=TRUE, type=o, between=list(x=1,y=1), xlab=, ylab=, scales=list(x=list(alternating=3),y=list(alternating=3), relation=free)) The mtext code doesn't work anymore. I think it needs some sort of panel function (panel.groups?) which would tell it to show the appropriate values of staff under their respective year for each fac and each panel. Something like xyplot(part~year | fac, as.table=TRUE, type=o, between=list(x=1,y=1), scales = list(relation = free, x = list(at = year, labels = paste(year, n.val.text, sep = \n -Deepayan __ 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. -- View this message in context: http://www.nabble.com/Lattice-xyplot-with-text-under-x-axis-tp23061842p23103168.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] From daily series to monthly and viceversa
any update anybody? I'm really stucked! -- View this message in context: http://www.nabble.com/From-daily-series-to-monthly-and-viceversa-tp23064454p23103052.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] Monotone Transformation
Hi, I am trying to use R to mimic what I did in SAS. proc transreg data=x ; model identity(GSI)=monotone(group1); output out=d2 pprefix=M; run; Accroding to SAS documentation, the MONOTONE transfomation algorithm comes from (Kruskal 1964, secondary approach to ties). I have tried ace. it does provide some kind of monotone transformation, but it is not what I expected. Here is how sas output look like: Obs GSITGSI group1Tgroup1 1 0.813010.81301 1 1.55594 2 0.793590.79359 2 1.55594 3 1.269001.26900 3 2.59702 4 2.026802.02680 4 4.29111 group1 is the inital value. Tgroup1 is the monotone transformed value. Here is how Transformed value output from ace: $tx [,1] [1,] -0.5698602 [2,] -0.1899534 [3,] 0.1899534 [4,] 0.5698602 Does anybody have any idea whether I could do the similar thing in R? If I can do it, which function I should use? Thanks, Jingyu -- View this message in context: http://www.nabble.com/Monotone-Transformation-tp23103202p23103202.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] Create histogram from data matrix
Thank you all for your advice. I have received some good tips, but it was suggested I write back with a small simulated data set to better illustrate my needs. So, currently my data frame looks something like: ID (date) Temperature Number of fish 200706183 5 456 200706183 5 765 200706183 4 567 200706183 3 876 200706183 3 888 200706183 2 111 200706184 8 2345 200706184 8 654 200706184 8 7786 200706184 7 345 200706184 6 234 200706184 6 123 I need to create a plots for each ID (date) of the number of fish observed at each temperature. Obviously my data frame is much larger. These plots do not have to be in a specific histogram format, but it seems this may be appropriate. Thanks for any additional advice as to how this may be done, either using plot commands or reformatting my data. It seemed the ggplot2 options may be good but so far I have tried qplot with no success: my most recent code looks like: qplot(temp,number of fish, geom=histogram,binwidth=1) I have tried various tweaks of this, but no success. Thanks for any advice! -Paul Simonin Quoting stephen sefick ssef...@gmail.com: It would be easier if you were to make a data frame of fake values to illustrate your point, so that we could just copy it into an R session and see if we can't get it to work. So, a stab in the dark would to look at ggplot2 specifically the hist argument in qplot and the facets, the lattice package, or reshape to change the format of your data. If you want me to fool around with it use dput and take a small subset of your data or make up data to be able to be copied into an R session. hope that helps, Stephen On Fri, Apr 17, 2009 at 10:59 AM, Paul Warren Simonin paul.simo...@uvm.edu wrote: Hello! Thanks for reading this request for assistance. I have a question regarding creating a histogram-like figure from data that are not currently in the correct format for the hist command. Specifically, my data have been processed and are in a matrix with columns containing the variables of interest and separate columns containing the number of times this variable was observed (counts). This data frame/matrix is rather large (1600 rows), and there are multiple rows corresponding to the same variable level (e.g., temperature=8, 5 observations in one row, then the next: temperature=8, 9 observations, and so on). In other words, the data are not one long vector R can read and plot as a histogram, nor are they condensed. My goal is to create a figure in which one axis is bins (e.g., temperature values) and the other is number of observations in this bin (e.g., number of organisms seen). My question is: Is there a way R can be told to read my data to create a plot like that I desire? So far I have tried several options, including bar plots with no success. If there is no way to do this with my data as the are currently arrange, is there an efficient way to re-arrange them? Thanks a lot for any assistance or advice! Sincerely, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ 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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ 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] changing Swaeve output settings for .pdf and .eps - is there a way?
Duncan Murdoch-2 wrote:
There are other ways to control the size: it isn't always 80%. I
normally use something like \setkeys{Gin}{width=0.75\textwidth} to control
it. You can reset this a
number of times in the same document. (Read the LaTeX docs for graphicx
to see the other
keys that can be set.)
The reason I suggested using the nogin option is because the default
behavior has always seemed very unintuitive to me. It seems that setting a
width and/or height parameter should be the only thing that needs to be done
to determine the size of the graphic. I know this is documented but I think
it is overly confusing to a new user. I know the first time I set width=3
and the plot still spanned 80% of the page threw me off.
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[R] Separating variables in read.table
If I have a table (we'll call it, test) containing two columns (as below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
15 0.835 0.271 8.108 0.0852 5.348 0.7482
22 1.000 0.237 6.370 0.0838 8.056 0.7160
29 1.150 0.192 6.441 0.0821 6.960 0.3130
37 0.990 0.202 5.154 0.0792 5.690 0.3617
44 0.840 0.184 5.896 0.0812 6.932 0.1139
58 0.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables without
having to code:
i - test$i
x1 - test$x1
x2 - test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
This email message, including any attachments, is for th...{{dropped:6}}
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[R] Matrix package,solve() errors and crashes
Hello All,
I am working on graph object using IGRAPH package wanted to do Bonacich
Power. This is my graph object.
The file 'Graph.RData' (4.2 MB) is available for download at
http://dropbox.unl.edu/uploads/20090424/cfe4fcb854bb17f2/Graph.RData
Graph size
Vertices: 20984
Edges: 326033
Directed: FALSE
No graph attributes.
Vertex attributes: name.
No edge attributes.
When I use bonacich power it goes out of memory
Error in get.adjacency.dense(graph, type = type, attr = attr, names =
names, :
At vector.pmt:409 : cannot reserve space for vector, Out of memory
I got help from IGRAPH community to use sparse Matrix
http://igraph.wikidot.com/r-recipes#toc6
bonpow.sparse - function(graph, nodes=V(graph), loops=FALSE,
exponent=1, rescale=FALSE, tol=1e-07) {
## remove loops if requested
if (!loops) {
graph - simplify(graph, remove.multiple=FALSE, remove.loops=TRUE)
}
## sparse adjacency matrix
d - get.adjacency(graph, sparse=TRUE)
## sparse identity matrix
id - spMatrix(vcount(graph), vcount(graph),
i=1:vcount(graph), j=1:vcount(graph),
x=rep(1, vcount(graph)))
id - as(id, dgCMatrix)
## solve it
ev - solve(id - exponent * d, tol=tol) %*% degree(graph, mode=out)
if (rescale) {
ev - ev/sum(ev)
} else {
ev - ev * sqrt(vcount(graph)/sum((ev)^2))
}
ev[as.numeric(nodes) + 1]
}
## test graph
test.g - simplify(ba.game(1000,m=2))
## test run
system.time(bp1 - bonpow(test.g))
system.time(bp2 - bonpow.sparse(test.g))
## check that they are the same
max(abs(bp1-bp2))
I get following error and sometime it crashes.
In solve(id - exponent * d, tol = tol) :
Reached total allocation of 1535Mb: see help(memory.size).I increased the
memory size and still it is not helpful
Help on this would be great.
These are steps I followed
1. Created graph object using Igraph version 0.6 on R 2.8.1 windows XP
2. Bonpow(g)
3. Bonpow.sparse function
sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_0.999375-23 lattice_0.17-20igraph_0.6
loaded via a namespace (and not attached):
[1] grid_2.8.1
Thanks in advance
Nathan
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generate bivariate binomial data
On Fri, 17 Apr 2009, ONKELINX, Thierry wrote: Dear all, Could someone point me to a function or algorithm to generate random bivariate binomial data? Some details about what I'm trying to do. I have a dataset of trees who were categorised as not damaged or damaged. Each tree is measured twice (once in two consecutive years). The trees can recover from the damage but the data is clearly correlated. As a (un)damaged tree is more likely to stay (un)damaged. A GEE-model indicates a correlation of about 0.6 between the measures on the same tree. The commonly used sampling models for such count data (see Bishop, Fienberg, and Holland, Discrete Multivariate Analysis, 1975.) involve four parameters. There are various parameterizations. In your case, the total sample size (N), the proportion of undamaged trees at the first (pr.undam.1), and the proportions at the second time conditional on the first (p.undam.2.undam.1, p.undam.2.dam.1) seems like reasonable way to parameterize the problem to do your simulation. If you have the marginal counts and the correlation, you can transform them to the above parameterization by hacking through the algebra to find the expected 2 by 2 table of counts as a function of the latter parameters. Then y - rbinom( N, 1, pr.undam.1 ) x - rbinom( N, 1, ifelse(y==1, pr.undam.2.undam.1, pr.undam.2.dam.1 ) table(x,y) should get you started HTH, Chuck I need to simulate similar dataset to do some power calculations. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 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 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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ 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] Separating variables in read.table
If I have a table (we'll call it, test) containing seven columns (as below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
15 0.835 0.271 8.108 0.0852 5.348 0.7482
22 1.000 0.237 6.370 0.0838 8.056 0.7160
29 1.150 0.192 6.441 0.0821 6.960 0.3130
37 0.990 0.202 5.154 0.0792 5.690 0.3617
44 0.840 0.184 5.896 0.0812 6.932 0.1139
58 0.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables without
having to code:
i - test$i
x1 - test$x1
x2 - test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
This email message, including any attachments, is for th...{{dropped:6}}
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Separating variables in read.table
Dear Patrick,
Perhaps attach might be what you are looking for.
attach(test)
i
x1
x2
.
.
.
y
HTH,
Jorge
On Fri, Apr 17, 2009 at 3:23 PM, Richardson, Patrick
patrick.richard...@vai.org wrote:
If I have a table (we'll call it, test) containing two columns (as
below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
15 0.835 0.271 8.108 0.0852 5.348 0.7482
22 1.000 0.237 6.370 0.0838 8.056 0.7160
29 1.150 0.192 6.441 0.0821 6.960 0.3130
37 0.990 0.202 5.154 0.0792 5.690 0.3617
44 0.840 0.184 5.896 0.0812 6.932 0.1139
58 0.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables
without having to code:
i - test$i
x1 - test$x1
x2 - test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
This email message, including any attachments, is for ...{{dropped:13}}
__
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] ColorRamp different from ColorRampPalette
I try to use ColorRamp as ColorRampPalette (i.e. with the same gradient), but it seems there is a nuance that I've missed. pal.crp-colorRampPalette( c(blue, white, red), space = rgb) plot(rep(0,40),pch=16,col=pal.crp(40)) # is great But, using the same gradient with colorRamp is giving erratic colors. pal.cr-colorRamp( c(blue, white, red), space = rgb) plot(rep(0,40),pch=16,col=pal.cr((0:40)/40)) # is not great From the help : colorRamp returns a function that maps values between 0 and 1 to colors ...colors I guess taken from the gradient, but I don't get the gradient. Etienne -- View this message in context: http://www.nabble.com/ColorRamp-different-from-ColorRampPalette-tp23104641p23104641.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] Separating variables in read.table
see ?attach
Etienne
Richardson, Patrick a écrit :
If I have a table (we'll call it, test) containing two columns (as below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
150.835 0.271 8.108 0.0852 5.348 0.7482
221.000 0.237 6.370 0.0838 8.056 0.7160
291.150 0.192 6.441 0.0821 6.960 0.3130
370.990 0.202 5.154 0.0792 5.690 0.3617
440.840 0.184 5.896 0.0812 6.932 0.1139
580.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables
without having to code:
i - test$i
x1 - test$x1
x2 - test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
This email message, including any attachments, is for ...{{dropped:12}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] real numeric variable transforms into factor:
Hi Test made in: R in windows Vista OS, R version 2.8.1 From FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-convert-factors-to-numeric_003f It may happen that when reading numeric data into R (usually, when reading in a file), they come in as factors. If |f| is such a factor object, you can use as.numeric(as.character(f)) to get the numbers back. 1: Why it may happen? Why R transforms x1 from real numeric with decimal values into factor??? 2: Doesn't it look strange to get internal numbers when one applies as.numeric(x$x1)? 3. What are the internal numbers mentioned in the FAQ? Why is needed to write: as.numeric(as.character(x$x1)) to get finally the right numbers I read with read.table? Are the missing values shown as dot to force R (or the programmer who wrote the function read.table) to consider x1 as factor? Is it possible who is maintaining the read.table function to improve it to recognize numbers with decimal places as numeric and not as factors and dots as missing values which transform into NA? The data file saved as text: test.txt ob,x1,y1 1,1.1,1/1 2,2.1,1/2 3,3.2,2/2 4,.,0/0 5,4.5,1/1 6,5.1,0/0 7,6.3,1/1 8,.,1/2 reading it from d directory: x-read.table(file=d:\\test\\test.txt,header=T,sep=',') x ob x1 y1 1 1 1.1 1/1 2 2 2.1 1/2 3 3 3.2 2/2 4 4 . 0/0 5 5 4.5 1/1 6 6 5.1 0/0 7 7 6.3 1/1 8 8 . 1/2 as.numeric(x$x1) [1] 2 3 4 1 5 6 7 1 as.numeric(as.character(x$x1)) [1] 1.1 2.1 3.2 NA 4.5 5.1 6.3 NA Warning message: NAs introduced by coercion Thanks, Aldi [[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] ColorRamp different from ColorRampPalette
Look at the output of pal.cr((0:40)/40) Hadley On Fri, Apr 17, 2009 at 2:42 PM, Etienne B. Racine etienn...@gmail.com wrote: I try to use ColorRamp as ColorRampPalette (i.e. with the same gradient), but it seems there is a nuance that I've missed. pal.crp-colorRampPalette( c(blue, white, red), space = rgb) plot(rep(0,40),pch=16,col=pal.crp(40)) # is great But, using the same gradient with colorRamp is giving erratic colors. pal.cr-colorRamp( c(blue, white, red), space = rgb) plot(rep(0,40),pch=16,col=pal.cr((0:40)/40)) # is not great From the help : colorRamp returns a function that maps values between 0 and 1 to colors ...colors I guess taken from the gradient, but I don't get the gradient. Etienne -- View this message in context: http://www.nabble.com/ColorRamp-different-from-ColorRampPalette-tp23104641p23104641.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. -- http://had.co.nz/ __ 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] ColorRamp different from ColorRampPalette
Thanks Hadley, Is it the solution you would recommend ? rgb(pal.cr((0:40)/40), maxColorValue=255) Etienne hadley wrote: Look at the output of pal.cr((0:40)/40) Hadley On Fri, Apr 17, 2009 at 2:42 PM, Etienne B. Racine etienn...@gmail.com wrote: I try to use ColorRamp as ColorRampPalette (i.e. with the same gradient), but it seems there is a nuance that I've missed. pal.crp-colorRampPalette( c(blue, white, red), space = rgb) plot(rep(0,40),pch=16,col=pal.crp(40)) # is great But, using the same gradient with colorRamp is giving erratic colors. pal.cr-colorRamp( c(blue, white, red), space = rgb) plot(rep(0,40),pch=16,col=pal.cr((0:40)/40)) # is not great From the help : colorRamp returns a function that maps values between 0 and 1 to colors ...colors I guess taken from the gradient, but I don't get the gradient. Etienne -- View this message in context: http://www.nabble.com/ColorRamp-different-from-ColorRampPalette-tp23104641p23104641.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. -- http://had.co.nz/ __ 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. -- View this message in context: http://www.nabble.com/ColorRamp-different-from-ColorRampPalette-tp23104641p23105080.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] Separating variables in read.table
Patrick -
There's no simple way to do what you want, because
R discourages you from having lots of separate
related objects. Instead, you are encouraged to store
your objects in an organized form, such as a list,
data frame or matrix. For your example, I'm assuming
you are using the word table to describe a data.frame.
If this is the case , you can refer to the individual
columns of test as
test[,1]
test[,2]
etc.
or
test$x1
test$x2
etc.
or
test[,'x1']
test[,'x2']
Also remember that R has functions that can operate on
each row or column of a matrix or data frame. So if you
wanted the means of each column of test, you could write
apply(test,2,mean)
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Fri, 17 Apr 2009, Richardson, Patrick wrote:
If I have a table (we'll call it, test) containing two columns (as below):
i x1 x2 x3 x4 x5 y
0 1.125 0.232 7.160 0.0859 8.905 1.5563
7 0.920 0.268 8.804 0.0865 7.388 0.8976
15 0.835 0.271 8.108 0.0852 5.348 0.7482
22 1.000 0.237 6.370 0.0838 8.056 0.7160
29 1.150 0.192 6.441 0.0821 6.960 0.3130
37 0.990 0.202 5.154 0.0792 5.690 0.3617
44 0.840 0.184 5.896 0.0812 6.932 0.1139
58 0.650 0.200 5.336 0.0806 5.400 0.1139
Is there a simple command to break this table into individual variables without
having to code:
i - test$i
x1 - test$x1
x2 - test$x2
.
.
.
And so on. .
Many Thank for any assistance.
Patrick
This email message, including any attachments, is for th...{{dropped:6}}
__
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] real numeric variable transforms into factor:
On Apr 17, 2009, at 2:52 PM, Aldi Kraja wrote: Hi Test made in: R in windows Vista OS, R version 2.8.1 From FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-do-I-convert-factors-to-numeric_003f It may happen that when reading numeric data into R (usually, when reading in a file), they come in as factors. If |f| is such a factor object, you can use as.numeric(as.character(f)) to get the numbers back. 1: Why it may happen? Why R transforms x1 from real numeric with decimal values into factor??? 2: Doesn't it look strange to get internal numbers when one applies as.numeric(x$x1)? 3. What are the internal numbers mentioned in the FAQ? Why is needed to write: as.numeric(as.character(x$x1)) to get finally the right numbers I read with read.table? Are the missing values shown as dot to force R (or the programmer who wrote the function read.table) to consider x1 as factor? Is it possible who is maintaining the read.table function to improve it to recognize numbers with decimal places as numeric and not as factors and dots as missing values which transform into NA? The data file saved as text: test.txt ob,x1,y1 1,1.1,1/1 2,2.1,1/2 3,3.2,2/2 4,.,0/0 5,4.5,1/1 6,5.1,0/0 7,6.3,1/1 8,.,1/2 reading it from d directory: x-read.table(file=d:\\test\\test.txt,header=T,sep=',') x ob x1 y1 1 1 1.1 1/1 2 2 2.1 1/2 3 3 3.2 2/2 4 4 . 0/0 5 5 4.5 1/1 6 6 5.1 0/0 7 7 6.3 1/1 8 8 . 1/2 as.numeric(x$x1) [1] 2 3 4 1 5 6 7 1 as.numeric(as.character(x$x1)) [1] 1.1 2.1 3.2 NA 4.5 5.1 6.3 NA Warning message: NAs introduced by coercion Thanks, Aldi Looks like you are taking data from SAS perhaps, where the missing value indicator is '.'. In R, where type.convert() is used to determine the data types for incoming text data, you get: type.convert(.) [1] . Levels: . That is, a factor. What you want to do is to set the 'na.strings' argument to read.table() to '.' rather than the default 'NA', so that the periods are interpreted as missing values and set to NA during import. Thus: # Create from your data in the clipboard (on OSX) DF - read.table(pipe(pbpaste), header = TRUE, sep = ,, na.strings = .) DF ob x1 y1 1 1 1.1 1/1 2 2 2.1 1/2 3 3 3.2 2/2 4 4 NA 0/0 5 5 4.5 1/1 6 6 5.1 0/0 7 7 6.3 1/1 8 8 NA 1/2 str(DF) 'data.frame': 8 obs. of 3 variables: $ ob: int 1 2 3 4 5 6 7 8 $ x1: num 1.1 2.1 3.2 NA 4.5 5.1 6.3 NA $ y1: Factor w/ 4 levels 0/0,1/1,1/2,..: 2 3 4 1 2 1 2 3 This is now because: type.convert(., na.strings = .) [1] NA See ?read.table and ?type.convert for more information. HTH, Marc Schwartz __ 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] Separating variables in read.table
Richardson, Patrick patrick.richard...@vai.org [Fri, Apr 17, 2009 at 09:31:35PM CEST]: If I have a table (we'll call it, test) containing seven columns (as below): i x1 x2 x3 x4 x5 y 0 1.125 0.232 7.160 0.0859 8.905 1.5563 7 0.920 0.268 8.804 0.0865 7.388 0.8976 150.835 0.271 8.108 0.0852 5.348 0.7482 221.000 0.237 6.370 0.0838 8.056 0.7160 291.150 0.192 6.441 0.0821 6.960 0.3130 370.990 0.202 5.154 0.0792 5.690 0.3617 440.840 0.184 5.896 0.0812 6.932 0.1139 580.650 0.200 5.336 0.0806 5.400 0.1139 Is there a simple command to break this table into individual variables without having to code: i - test$i x1 - test$x1 x2 - test$x2 ?attach Does this do what you want? -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:johan...@huesing.name from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ 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.
