Re: [R] Interface to open source Reporting tools
Dieter Menne wrote: srinivasa raghavan srinivasraghav at gmail.com writes: I am interested to generate dashboard and reports based on data from MS Access. These reports need to be posted on a weekly basis to the web. The reporting interface should provide facilities for what if scenarios. Is it possible to interface R analysis results to good open source reporting tools like Jasper Reports. what is the appropriate system requirements for carrying out real time reporting using R. You could use package XML to produce jrxml output; or, probably easier for not too complex reports, HTML could be generated by RHTML directly, including images. You probably mean R2HTML? Best, Philippe Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] How to Solve the Error( error:cannot allocate vector of size 1.1 Gb)
Hi, Gurus Thanks to your good helps, I have managed starting the use of a text mining package so called tm in R under the OS of Win XP. However, during running the tm package, I got another mine like memory problem. What is a the best way to solve this memory problem among increasing a physical RAM, or doing other recipes, etc? ### ## my R Script's Outputs ## ### memory.limit(size = 2000) NULL corpus.ko - Corpus(DirSource(test_konews/), + readerControl = list(reader = readPlain, + language = UTF-8, load = FALSE)) corpus.ko.nowhite - tmMap(corpus.ko, stripWhitespace) corpus - tmMap(corpus.ko.nowhite, tmTolower) tdm - TermDocMatrix(corpus) findAssocs(tdm, city, 0.97) error:cannot allocate vector of size 1.1 Gb - Thanks for your precious time, -- Kum-Hoe Hwang, Ph.D. Phone : 82-31-250-3516 Email : phdhw...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package tests
There is a mechanism for testing code in R packages (R CMD check), see the Writing R extensions manual. If you need more flexibility for your tests, you could look at RUnit on CRAN, or svUnit on R-Forge (http://r-forge.r-project.org, on CRAN soon). For the later one, you install it by: install.packages(svUnit, repos=http://R-Forge.R-project.org;) These is a vignette associated with svUnit: vignette(svUnit) Note that RUnit and svUnit are test suite code compatible, but they use very different mechanisms internally. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Nathan S. Watson-Haigh wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I was wondering if anyone could point me in the right direction for reading up on writing tests in R. I'm writing some functions for inclusion into a package and would like to test them to ensure they're doing what I expect them to do. Are these approaches used for testing packages in CRAN? Cheers, Nathan - -- - Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkluio8ACgkQ9gTv6QYzVL5X9QCgwvg5xjwZW2A2Z5G41iADu1Kz hIkAoI5ISuAtHyQ+JwJSRBAc9q/oyeEt =cqm4 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Odp: Moving a Data Frame Column
Hi r-help-boun...@r-project.org napsal dne 15.01.2009 04:47:39: Dear R-Users if I have a data frame (or zoo data) as follows: Run Bike Walk Drive 1 2 7 5 5 2 4 2 8 3 2 1 How can I re-order it so that it reads: Drive Run Bike Walk 5 1 2 7 2 5 2 4 1 8 3 2 i.e. Drive has been copied and pasted to the left most column. test Run Bike Walk Drive 1 127 5 2 524 2 3 832 1 test2 - test[, c(4,1,2,3)] Drive Run Bike Walk 1 5 127 2 2 524 3 1 832 if you want it in new data frame or test - test[, c(4,1,2,3)] if you want to overwrite it. Regards Petr Thanks for your help. James -- View this message in context: http://www.nabble.com/Moving-a-Data-Frame- Column-tp21470798p21470798.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.
Re: [R] R package tests
I think the OP was asking about test suites that test the software. The R package structure includes a test/ directory which you can use to put tests. For example, in the onion package I check that I have got my signs and multiplication table correctly implemented: stopifnot(Hi*Hj == Hk) stopifnot(Hj*Hi == -Hk) stopifnot(Hj*Hk == Hi) stopifnot(Hk*Hj == -Hi) stopifnot(Hk*Hi == Hj) stopifnot(Hi*Hk == -Hj) [and a whole lot of others] and the elliptic package includes a whole bunch of code that verifies identities that appear in AMS-55. It also includes numerical verification that the functions, using randomish arguments, match the output of mathematica or maple. Philippe Grosjean wrote: There is a mechanism for testing code in R packages (R CMD check), see the Writing R extensions manual. If you need more flexibility for your tests, you could look at RUnit on CRAN, or svUnit on R-Forge (http://r-forge.r-project.org, on CRAN soon). For the later one, you install it by: install.packages(svUnit, repos=http://R-Forge.R-project.org;) These is a vignette associated with svUnit: vignette(svUnit) Note that RUnit and svUnit are test suite code compatible, but they use very different mechanisms internally. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Nathan S. Watson-Haigh wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I was wondering if anyone could point me in the right direction for reading up on writing tests in R. I'm writing some functions for inclusion into a package and would like to test them to ensure they're doing what I expect them to do. Are these approaches used for testing packages in CRAN? Cheers, Nathan - -- - Dr. Nathan S. Watson-Haigh OCE Post Doctoral Fellow CSIRO Livestock Industries Queensland Bioscience Precinct St Lucia, QLD 4067 Australia Tel: +61 (0)7 3214 2922 Fax: +61 (0)7 3214 2900 Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html - -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAkluio8ACgkQ9gTv6QYzVL5X9QCgwvg5xjwZW2A2Z5G41iADu1Kz hIkAoI5ISuAtHyQ+JwJSRBAc9q/oyeEt =cqm4 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Logical function to turn missing values to 0's
Use the is.na function to test for NA values. And do read about
vectorizing your code. You don't need loops for this problem. Without
loops your code will run more than 400 times faster!
n - 1000
x - matrix(data=rep(c(1,2,3,NA), n), ncol=n, nrow=n)
system.time({
+ y - matrix(data=0, ncol=ncol(x), nrow=nrow(x))
+ for(i in 1:nrow(x)) {
+ for(j in 1:ncol(x)) {
+ y[i,j] - ifelse(is.na(x[i,j]), 0, x[i,j])
+ }
+ }
+ })
user system elapsed
45.170.30 45.61
system.time(y - ifelse(is.na(x), 0, x))
user system elapsed
0.600.150.75
system.time({
+ y - x
+ y[is.na(x)] - 0
+ })
user system elapsed
0.110.000.11
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 rafamoral
Verzonden: woensdag 14 januari 2009 23:32
Aan: r-help@r-project.org
Onderwerp: [R] Logical function to turn missing values to 0's
I have a dataset which contains some missing values, and I need to
replace
them with zeros. I tried using the following:
x - matrix(data=rep(c(1,2,3,NA),6), ncol=6, nrow=6)
y - matrix(data=0, ncol=ncol(x), nrow=nrow(x))
for(i in 1:nrow(x)) {
for(j in 1:ncol(x)) {
y[i,j] - ifelse(x[i,j]==NA, 0, x[i,j])
}}
But y returns an NA matrix.
I'd appreciate any help.
--
View this message in context:
http://www.nabble.com/Logical-function-to-turn-missing-values-to-0%27s-t
p21466785p21466785.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] publication statistics from Web of Science
For the record, I thought I'd share two findings:
First, the web of science website does seem to have some sort of API,
as discussed here:
http://scientific.thomson.com/support/faq/webservices/
It does not seem like a trivial thing to set up though.
Second, because I could not pass the search term easily in the
address, I looked into Google scholar instead, where a typical search
looks like:
http://scholar.google.co.uk/scholar?as_q=plasmonicsnum=10btnG=Search+Scholaras_epq=as_oq=as_eq=as_occt=anyas_sauthors=as_publication=as_ylo=as_yhi=1960as_allsubj=allhl=enlr=
here it is trivial to create such a string with the desired keyword
and dates, and retrieve the number of results using readLines(url) and
grep.
Thanks to Phil Spector for some pointers.
Best wishes,
baptiste
On 14 Jan 2009, at 13:44, baptiste auguie wrote:
Dear list,
This is a bit of an off-topic question, but I'm hoping to get some
advice from more experienced people. I've used the website Web of
Science to manually collect publication counts responding to several
keywords as a function of date, since the 1960s.
http://apps.isiknowledge.com/RAMore.do?product=UAsearch_mode=sid=p1g9lf...@eja6pjhkdqid=1ra_mode=morera_name=PublicationYeardb_id=UGBviewType=raMore
This is a really long and error-prone process. Once the data was
collected I rearranged it in a form R could read (see example in the
end), this step wasn't too bad. Finally, I plotted histograms to show
the temporal trends.
I have two questions:
- Is there a package or external tool to facilitate the collection of
data from this kind of online search tool? I could not find any public
API for this website, although some tools like Endnote clearly access
the database somehow. I'd be very grateful for any pointer.
- I feel like the display and choice of search terms is very arbitrary
and subjective. Any general advice on how to present this data better
is most welcome. (I should mention that i'd rather not involve any
complicated statistical analysis, I only want to make sure that the
presentation is not horribly biased).
Best regards,
baptiste
statistics - list(list(values=read.table(textConnection(
date count
2007 600
2006 588
2008 555
2005 430
2004 418
2003 334
2002 277
2001 239
2000 226
1997 184
1999 184
1998 182
1996 129
1995 108
1994 92
1993 67
1992 53
1991 47
1990 37
1989 14
1988 11
1983 10
1987 7
1985 6
1986 6
1981 5
1984 5
1979 4
1982 4
2009 3
1971 2
1933 1
1973 1
1974 1
1977 1
1978 1
1980 1), head=T),type=1, cumSum=4833, search=photonics),
list(values=read.table(textConnection(
date count
2008 129
2007 92
2006 50
2005 26
2004 15
2003 4
1972 1
2001 1
2002 1), head=T),type=1, cumSum=319, search=plasmonics),
list(values=read.table(textConnection(
date count
2008 3207
2007 3105
2006 2666
2005 2323
2004 1910
2003 1552
2002 1372
2001 1292
2000 1095
1999 992
1998 863
1997 771
1996 643
1995 484
1993 418
1994 407
1992 345
1991 321
1990 120
1989 91
1988 82
1987 78
1981 77
1986 73
1983 72
1978 69
1979 68
1985 66
1976 63
1975 62
1980 59
1984 54
1982 52
1973 50
1977 50
1972 46
1974 43
1971 38
1969 28
1970 28
2009 26
1968 18
1967 11
1966 8
1962 5
1963 4
1900 3
1960 3
1961 3
1948 2
1912 1
1949 1
1950 1
1953 1
1954 1
1959 1
1964 1
1965 1), head=T),type=1, cumSum=25226, search=plasmonics+ plasmon),
list(values=read.table(textConnection(
date count
2008 2716
2007 2640
2006 2257
2005 1991
2004 1625
2003 1302
2002 1129
2001 1056
2000 862
1999 814
1998 650
1997 574
1996 427
1995 338
1994 272
1993 260
1991 187
1992 176
1990 62
1989 51
1981 41
1988 41
1987 36
1986 32
1983 30
1980 29
1982 28
1984 28
1985 27
1975 25
1976 23
2009 23
1973 22
1979 22
1972 15
1974 15
1977 13
1971 10
1978 10
1970 9
1968 7
1969 7
1966 1 ), head=T),type=2, cumSum=19883, search=surface plasmon),
list(values=read.table(textConnection(
date count
2008 324
2007 295
2006 248
2005 220
2004 156
2003 126
2002 113
2000 86
2001 84
1996 66
1999 59
1997 53
1998 53
1993 39
1992 34
1994 29
1995 29
1991 25
1973 2
1987 2
1970 1
1972 1
1978 1
1983 1
1984 1
1989 1
2009 1 ), head=T),type=2, cumSum=2050, search=localised or particle
plasmon),
list(values=read.table(textConnection(
date count
2007 196
2008 165
2005 141
2006 141
2003 112
2004 109
2002 83
2001 75
1999 62
2000 51
1998 38
1997 29
1995 13
1996 11
1993 6
1992 4
1994 4
1991 2
2009 2
1990 1), head=T),type=2, cumSum=1245, search=SPR sensor),
list(values=read.table(textConnection(
date count
2008 290
2007 225
2006 167
2005 138
2004 101
2003 79
2001 54
2002 51
2000 42
1998 31
1999 30
1997 27
1996 25
1992 20
1995 20
1991 15
1994 14
1993 10
1973 2
1984 2
1990 2
2009 2
1963 1
1972 1
1974 1
1977 1
1978 1
1982 1
1983 1
1988 1
1989 1), head=T), cumSum=1356,type=1, search=light scattering
gold))
str(statistics)
treatOne - function(ml){
data.frame(ml$values, search= as.character(ml$search))
}
# treatOne(statistics[[1]])
library(plyr)
stats.list - llply(statistics[-3], treatOne)
stats.df - do.call(rbind, stats.list)
stats.melt - melt(stats.df,
Re: [R] R package tests
Hi Nathan, in addition to what others have already mentioned there is some documentation in the Writing R Extensions Manual: - on the supported structure of packages, indicating where test code might be added http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Package-subdirectories - and the recommended standard approach to check a package http://stat.ethz.ch/R-manual/R-patched/doc/manual/R-exts.html#Checking-and-building-packages and a wiki article on how to combine the standard check (viz R CMD check) with any of the unit testing approaches http://wiki.r-project.org/rwiki/doku.php?id=developers:runits=unit%20test Examples for the standard approach employed by R can be found in the R source repository https://svn.r-project.org/R/trunk/src/library/stats/tests/ and for unit test based checking e.g. Rmetrics http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/?root=rmetrics or BioConductor examples https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase/inst/UnitTests/ where you need the access info provided here http://wiki.fhcrc.org/bioc/DeveloperPage Regards, Matthias Nathan S. Watson-Haigh wrote: I was wondering if anyone could point me in the right direction for reading up on writing tests in R. I'm writing some functions for inclusion into a package and would like to test them to ensure they're doing what I expect them to do. Are these approaches used for testing packages in CRAN? Cheers, Nathan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthias Burger Project Manager/ Biostatistician Epigenomics AGKleine Praesidentenstr. 110178 Berlin, Germany phone:+49-30-24345-371 fax:+49-30-24345-555 http://www.epigenomics.com matthias.bur...@epigenomics.com -- Epigenomics AG Berlin Amtsgericht Charlottenburg HRB 75861 Vorstand: Geert Nygaard (CEO/Vorsitzender) Oliver Schacht PhD (CFO) Aufsichtsrat: Prof. Dr. Dr. hc. Rolf Krebs (Chairman/Vorsitzender) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 a chromosome location map by locus ID
Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here: http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv I've tried some things, but nothing worked like I would like it to see. Maybe there is some kind of package that does this for you, but I did not find it yet. Thanx Sake -- View this message in context: http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21474206.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] Kaplan-Meier Plot
thank you, it worked properly. On Thu, Jan 15, 2009 at 4:53 AM, Marc Schwartz marc_schwa...@comcast.netwrote: on 01/14/2009 03:32 PM John Lande wrote: dear all, I want to plot a kaplan Meier plot with the following functions, but I fail to produce the plot I want: library(survival) tim - (1:50)/6 ind - runif(50) ind[ind 0.5] - 1; ind[ind 0.5] - 0; MS - runif(50) pred - vector() pred[MS 0.3] - 0; pred[MS = 0.3] - 1 df - as.data.frame(cbind(MS, tim, pred, ind)) names(df) - c(MS, time, pred, class) df$time[df$time 6] - 6 surv - Surv(as.numeric(as.vector(df$time)), as.numeric(as.vector(df$class))) dfPval - summary(coxph(Surv(as.numeric(as.vector(df$time)), as.numeric(as.vector(df$class))) ~ pred, df))$sctest par(mfrow = c(2,2)) plot(survfit(surv ~ df$pred), col=c(red,green), ylab = percentage of survival, xlab = survival years) plot(survfit(surv ~ df$pred), col=c(red,green), lwd = 8, ylab = percentage of survival, xlab = survival years) plot(survfit(surv ~ df$pred), col=c(red,green), lwd = 8, ylab = percentage of survival, xlab = survival years, cex = 2) I would like to increase the tickness of the censorship's pitch. as you can see with cex = 2, I can elongate the arms of the censorship, but I cant find how to increase the tickness of the pitch. how to do this? John, Is this what you want? par(mfrow = c(2, 1)) # Normal plot plot(survfit(Surv(time, status) ~ x, data = aml)) # Set par(lwd = 3) to increase the thickness of the censoring marks # Don't frame the plot region, as it uses par(lwd) par(lwd = 3) plot(survfit(Surv(time, status) ~ x, data = aml), frame = FALSE) # Reset par(lwd) to normal to frame the plot region par(lwd = 1) box() Note that given the way in which the plot code has been set up, using 'lwd' in the function call affects the survivorship function line and not the censoring marks. By setting par(lwd = 3) prior to the plot call, this will be used internally when the marks are plotted using points(), without affecting the other lines, save the plot region frame. Just so that you don't think that you missed something obvious, this was a little trial and error after reviewing the R code for survival:::plot.survfit to see how the arguments from the function call are passed to the internal plotting functions. Combined also with some knowledge of how the graphic pars are handled... HTH, Marc Schwartz [[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] regexp problem (was: Re: publication statistics from Web of Science)
Whoops, it seems I could use some help with regular expressions...
Consider the following two functions, creating a search string, and
retrieving the content from the url,
makeURLsearch - function(key, dates=c(NULL, NULL)){
base.search - http://scholar.google.co.uk/scholar?;
key.search - paste(as_q=, key,, sep=)
other.search - num=10btnG=Search
+
Scholar
as_epq=as_oq=as_eq=as_occt=anyas_sauthors=as_publication=
dates.search - paste(as_ylo=, dates[1], as_yhi=, dates[2],
as_allsubj=allhl=enlr=, sep=)
full.search - paste(base.search, key.search, other.search,
dates.search, sep=)
return(full.search)
}
makeURLsearch(plasmonics)
makeURLsearch(photonics, c(1980, NULL))
retrieveNumberPublications - function(url){
x - readLines(url)
y - grep('of about',x, value=TRUE)
z - gsub('of about\\s+/b','\\1',y[1],perl=TRUE) # this does not
do what I wanted
# the bit to retrieve is the number below
# b10/b of about b21,900/b for bbphotonics/b
z
}
retrieveNumberPublications( makeURLsearch(photonics, c(2008,
NULL)) )
I can isolate the long string containing the result I want, but not
single out the value which lies between b10/b of about
b21,900/b for bbphotonics/b .
Any regexp guru to help me out? I've never got my head around these,
other than trivial cases.
Many thanks,
baptiste
On 15 Jan 2009, at 09:45, baptiste auguie wrote:
For the record, I thought I'd share two findings:
First, the web of science website does seem to have some sort of API,
as discussed here:
http://scientific.thomson.com/support/faq/webservices/
It does not seem like a trivial thing to set up though.
Second, because I could not pass the search term easily in the
address, I looked into Google scholar instead, where a typical search
looks like:
http://scholar.google.co.uk/scholar?as_q=plasmonicsnum=10btnG=Search+Scholaras_epq=as_oq=as_eq=as_occt=anyas_sauthors=as_publication=as_ylo=as_yhi=1960as_allsubj=allhl=enlr=
here it is trivial to create such a string with the desired keyword
and dates, and retrieve the number of results using readLines(url) and
grep.
Thanks to Phil Spector for some pointers.
Best wishes,
baptiste
_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
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[R] Job as doctorial candidate
Ladies and gentlemen, this email is directed to all German-speaking members of the r-help list. We from the chair of statistics and quantitative methods on the Catholic University of Eichstätt-Ingolstadt, Germany, are searching for a new colleague. You will find the corresponding job offer in the attachment. If you are interested, please don´t shy and send us your application on the address, called in the attachment. You can also find the job offer on http://www.ku-eichstaett.de/stellenausschreibungen/stellen/wissenschaftlich/ HF_sections/content/ZZiQGkU3pLDLYB Yours sincerely, Holger Kömm _ Holger Kömm holger.ko...@ku-eichstaett.de LSQM - Lehrstuhl für Statistik und Quantitative Methoden Prof. Dr. Ulrich Küsters Auf der Schanz 49 85049 Ingolstadt Fon: +49 841 937-1847 Fax: +49 841 937-1965 Ausschreibung-WiMa-Statistik-www ku-eichstaett.pdf Description: Adobe PDF document __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] remove columns containing all zeros (or other value)
How about:
remove.constant.values-function(x,MARGIN,value2remove) {
is.constant.line-function(x,value2remove) { return(any(x!=value2remove)) }
return(unlist(apply(x,MARGIN,is.constant.line,value2remove)))
}
x[,remove.constant.values(x,2,0)]
Jim
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[R] Seemingly Unrelated Negative Binomial (SUNB) estimation
Dear all, I am trying to estimate a system of equations with a Seemingly Unrelated Regression. However because of the characteristics of the data I'd like to do it with a negative binomial estimation. Would anybody know how to implement a Seemingly Unrelated Negative Binomial (SUNB) estimation in R? Thank you in advance for your help. Best regards, Elisa Lanzi -- Elisa Lanzi PhD student in Economics and Organisation School of Advanced Studies in Venice (SSAV) email: elisa.la...@unive.it website: http://venus.unive.it/elisa.lanzi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Summary of Total Object.Size in R Script
Sorry for my late reply.
Thank you so much Jim. This script of yours
is very2 useful. I have used it.
- Gundala Viswanath
Jakarta - Indonesia
On Wed, Jan 14, 2009 at 12:17 AM, jim holtman jholt...@gmail.com wrote:
Here is a function I use to see how big the objects in my workspace are:
my.ls -
+ function (pos = 1, sorted = F)
+ {
+ .result - sapply(ls(pos = pos, all.names = TRUE), function(..x)
object.size(eval(as.symbol(..x
+ if (sorted) {
+ .result - rev(sort(.result))
+ }
+ .ls - as.data.frame(rbind(as.matrix(.result), `**Total` =
sum(.result)))
+ names(.ls) - Size
+ .ls$Size - formatC(.ls$Size, big.mark = ,, digits = 0,
+ format = f)
+ .ls$Mode - c(unlist(lapply(rownames(.ls)[-nrow(.ls)],
function(x) mode(eval(as.symbol(x),
+ ---)
+ .ls
+ }
my.ls()
SizeMode
.my.env 28 environment
.Random.seed 2,528 numeric
.required 72 character
my.ls6,712function
**Total 9,340 ---
On Tue, Jan 13, 2009 at 9:53 AM, Gundala Viswanath gunda...@gmail.com wrote:
Dear all,
Is there a way we can find the total object.size of
all the objects in our R script?
The reason we want to do this because we want to know
how much memory does our R script require overall.
Rprofmem(), doesn't seem to do it.
and Unix 'top' command is dynamic and
it doesn't give the exact byte size.
- Gundala Viswanath
Jakarta - Indonesia
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] noise in time series
Hi, here's a possibility! Your problem can be restated as given 2 observers giving 2 measures what is their level of agreement - the classical measure here is the Kappa (see sec 10.5 of Categorical Data Analysis by Alan Agresti (in Ed 1 - Ed 2 should also have it!) and you can also model the situation (same section of book). I had a similar problem comparing time series modelled by two (or more) different methods in my PhD some years back. I had several series so it was a bit easier. Obviously, it's a bit of a problem with 2 time series but if they are sufficiently long (say 200+ obs) you could proceed as follows: Take k sub-sample series of length say 35+ obs. Then fit say about 5 different arima models to each (if you know seasonal adjustment X11ARIMA the 5 basic models used there are good options - I can't remember them!) You can now create a 2X2 table (method 1 X method 2) each with 5 outcome model types and then count the number of models falling into each cell. Then apply the agreement measure! Obviously, there will be dependence across the selected series that will not be accounted for in the outcome frequencies, but if the time series are reasonably long this shouldn't be too bad. good luck with it! Gerard Dieter Menne dieter.me...@men ne-biomed.de To Sent by: r-h...@stat.math.ethz.ch r-help-boun...@r- cc project.org Subject Re: [R] noise in time series 15/01/2009 07:54 David Riano driano at ucdavis.edu writes: I have two time series. Both measure the same thing and I would like to determine which one is noisier. Would it be a good measure of the noise in each time series the absolute lag difference? Is this a good measure? Any other measure I could use? You could fit an arima model and compare the residuals. It should be could enough to get an estimate, even if I see some theoretical problems in measure the same thing. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ** The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. It is the policy of the Department of Justice, Equality and Law Reform and the Agencies and Offices using its IT services to disallow the sending of offensive material. Should you consider that the material contained in this message is offensive you should contact the sender immediately and also mailminder[at]justice.ie. Is le haghaidh an duine nó an eintitis ar a bhfuil sí dírithe, agus le haghaidh an duine nó an eintitis sin amháin, a bheartaítear an fhaisnéis a tarchuireadh agus féadfaidh sé go bhfuil ábhar faoi rún agus/nó faoi phribhléid inti. Toirmisctear aon athbhreithniú, atarchur nó leathadh a dhéanamh ar an bhfaisnéis seo, aon úsáid eile a bhaint aisti nó aon ghníomh a dhéanamh ar a hiontaoibh, ag daoine nó ag eintitis seachas an faighteoir beartaithe. Má fuair tú é seo trí dhearmad, téigh i dteagmháil leis an seoltóir, le do thoil, agus scrios an t-ábhar as aon ríomhaire. Is é beartas na Roinne Dlí agus Cirt, Comhionannais agus Athchóirithe Dlí, agus na nOifígí agus na nGníomhaireachtaí a úsáideann seirbhísí TF na Roinne, seoladh ábhair cholúil a dhícheadú. Más rud é go measann tú gur ábhar colúil atá san ábhar atá sa teachtaireacht seo is ceart duit dul i dteagmháil leis an seoltóir láithreach agus le mailminder[ag]justice.ie chomh maith.
Re: [R] How to create a chromosome location map by locus ID
__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a chromosome location map by locus ID
Sorry list, I guess I sent an html reply. Hi Sake: If you do not find an answer within the list, MapChart will probably do what you want (without the fancy chromosomal bands, though). You can find it at http://www.biometris.wur.nl/uk/Software/MapChart/ Hope this helps Sake escribió: Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here: http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv I've tried some things, but nothing worked like I would like it to see. Maybe there is some kind of package that does this for you, but I did not find it yet. Thanx Sake -- *Pablo G Goicoechea* Bioteknología Saila / /Dpto Biotecnología/ NEIKER-Tecnalia Apdo 46 01080 Vitoria-Gasteiz (SPAIN) Phone: +34 902 540 546 Fax: +34 902 540 547 pgoikoet...@neiker.net mailto:pgoikoet...@neiker.net __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Linked count between matrix columns
Hello, I create this array: x - cbind(c(1:4, rep(0,10)), c(rep(0,4), 1:2, rep(3,6), 4,5)) [,1] [,2] [1,]10 [2,]20 [3,]30 [4,]40 [5,]01 [6,]02 [7,]03 [8,]03 [9,]03 [10,]03 [11,]03 [12,]03 [13,]04 [14,]05 I would like to do the following in vector syntax: for rows where the first column is not 0, put into the second column the number of times the value of the first column appears in the second column of rows where the value in the first row is 0 I'm not sure this sounds super clear, so I will show what I want to get: [,1] [,2] [1,]11 [2,]21 [3,]36 [4,]41 [5,]01 [6,]02 [7,]03 [8,]03 [9,]03 [10,]03 [11,]03 [12,]03 [13,]04 [14,]05 So for example, x[3,2] = 6, because length(x[x[,1]==0 x[,2]==3,2]) = 6 I have tried this: x[x[,1]!=0,2] - length(x[x[,1]==0 x[,2] %in% which(x[,1]!=0),2]) but it does not work correctly as it put the same value in the changed rows. Thanks for your help! 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] Linked count between matrix columns
Try this: x[,2][x[,1][x[,1] 0]] - table(x[,2])[as.character(x[,1][x[,1] 0])] On Thu, Jan 15, 2009 at 10:36 AM, Guillaume Chapron carnivorescie...@gmail.com wrote: Hello, I create this array: x - cbind(c(1:4, rep(0,10)), c(rep(0,4), 1:2, rep(3,6), 4,5)) [,1] [,2] [1,]10 [2,]20 [3,]30 [4,]40 [5,]01 [6,]02 [7,]03 [8,]03 [9,]03 [10,]03 [11,]03 [12,]03 [13,]04 [14,]05 I would like to do the following in vector syntax: for rows where the first column is not 0, put into the second column the number of times the value of the first column appears in the second column of rows where the value in the first row is 0 I'm not sure this sounds super clear, so I will show what I want to get: [,1] [,2] [1,]11 [2,]21 [3,]36 [4,]41 [5,]01 [6,]02 [7,]03 [8,]03 [9,]03 [10,]03 [11,]03 [12,]03 [13,]04 [14,]05 So for example, x[3,2] = 6, because length(x[x[,1]==0 x[,2]==3,2]) = 6 I have tried this: x[x[,1]!=0,2] - length(x[x[,1]==0 x[,2] %in% which(x[,1]!=0),2]) but it does not work correctly as it put the same value in the changed rows. Thanks for your help! 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] Linked count between matrix columns
Thank you! This is exactly what I wanted. Could you please explain the logic behind your code? x[,2][x[,1][x[,1] 0]] - table(x[,2])[as.character(x[,1][x[,1] 0])] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] logistic regression - exp(estimates)?
hello. I have a question on the interpretation of a logistic model. is it helpful to exponentiate the coefficients (estimates)? I think I once read something about that, but I cannot remember where. if so, how would be the interpretation of the exp(estimate) ? would there be a change of the interpretation of the ANOVA table (or is the ANOVA table not really helpful at all?). thanks for your time. cheers, gregor rolshausen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] misalignment of x-axis when overlaying two plots using latticeExtra
Hi Sean, as.layer() does not do what you think it does: it does not attempt to plot things on a common scale, it simply draws the panels of two lattice plots in the same space. Actually, it is not very useful on its own. What you want is doubleYScale() in the development version (0.5-5) of latticeExtra. You can install it with install.packages(latticeExtra, repos=http://R-Forge.R-project.org;) then doubleYScale(barchart.obj, dot.outcome) By the way, wise persons say plotting on multiple scales is often a bad idea. I would at least make sure both axes start from zero. -Felix 2009/1/15 Sean Zhang seane...@gmail.com: Dear R-helpers: I am an entry-level R user and have a question related to overlaying a barchart and and a xyplot using latticeExtra. My problem is that when I overlay them I fail to align their x-axes. I show my problem below through an example. #the example data frame is provided below vec -c(1,5.056656,0.5977967,0.06126587,0.08557778, 2,4.601049,0.5995989,0.05002188,0.11410027, 3,4.932008,0.5502283,0.06727938,0.12531825, 4,4.763798,0.5499489,0.06473846,0.10752641, 5,4.944967,0.5328129,0.05445327,0.13663951, 6,5.063504,0.5267245,0.06477738,0.12380332, 7,4.735251,0.5528205,0.06851714,0.12196075, 8,5.141733,0.5304151,0.07965567,0.15123277, 9,5.215678,0.5219224,0.06694207,0.16476356, 10,4.930439,0.5712519,0.08591549,0.09710933, 11,5.075990,0.5615573,0.05778996,0.15361845, 12,4.909847,0.5683740,0.08711699,0.11189277, 13,4.863164,0.5652511,0.0727,0.12071060, 14,5.173818,0.5564918,0.09830620,0.11831926, 15,4.762325,0.5345888,0.08792658,0.11738642, 16,5.046225,0.5268459,0.09574746,0.13254236, 17,4.902188,0.5370394,0.07194955,0.13164327, 18,4.865935,0.5446562,0.06894994,0.12645103, 19,5.204060,0.5650887,0.06726925,0.09242551, 20,5.208138,0.5765187,0.09282935,0.11053842) df-as.data.frame( t(matrix(vec,nrow=5,ncol=20))) names(df)-c(group,outcome,proportion_1,proportion_2,proportion_3) library(latticeExtra) library(lattice) #First generate barchart to plot the 3 proportions prop.data -subset(df,select=c(proportion_1,proportion_2,proportion_3)) prop.tab - as.table(as.matrix(prop.data)) barchart.obj-barchart(prop.tab, stack=TRUE, horizontal = FALSE) #Second, generate the dots of outcome (I could have used type=l but using type=p makes the #misalignment of x-axis more obvious. dot.outcome - xyplot(outcome~group,df,type=p, col=blue) #Last, overlay the two plots barchart.obj+ as.layer(dot.outcome,style=2,axes=c(y), outside=TRUE) #Now, you should be able to see the x-axis of the two plots are not matching. #i.e., a dot is not at the center of its correspoding bar. How can I fix this? Your help will be highly appreciated. Many thanks in advance. -Sean [[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. -- Felix Andrews / 安福立 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Linked count between matrix columns
Guillaume, # First, you need extract the values of x[,1] greater than 0: x[,1][x[,1] 0] # After, you want the number of times that appears in the second column: table(x2) # but only to values above: table(x2)[as.character(x[,1][x[,1] 0])] # Now, just put the values in column 2: x[,2][x[,1][x[,1] 0]] - table(x[,2])[as.character(x[,1][x[,1] 0])] On Thu, Jan 15, 2009 at 10:47 AM, Guillaume Chapron carnivorescie...@gmail.com wrote: Thank you! This is exactly what I wanted. Could you please explain the logic behind your code? x[,2][x[,1][x[,1] 0]] - table(x[,2])[as.character(x[,1][x[,1] 0])] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] radial.plot(plotrix) - plotting multiple polygons?
Dear List, Dear Jim, is it possible to draw multiple polygons with different line types? lty=c or line.lty=c do not work with radial.plot (in the matrix case) as well as add=TRUE. Stefan Jim Lemon schrieb, Am 14.11.2008 10:38: Jeremy Claisse wrote: Is it possible to plot multiple polygons on radial.plot(plotrix)? The new=FALSE argument (as used to add additional points or lines with the plot function to an existing plot) doesn't appear to work. I would like to overlay the outlines of multiple polygons of different colors on the same radial plot. Hi Jeremy, You can do this by passing a matrix or data frame of values to radial.plot. Look at the last example on the help page for radial.plot and check the Details section. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linked count between matrix columns
table(x2)[as.character(x[,1][x[,1] 0])] Why do I need as.character() here? I checked it does not work without, but I don't see why. The help says as.character attempts to coerce its argument to character type. Thanks very much! 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] Linked count between matrix columns
Because we want the values in table(x[,2]) where the **names** are as.character(x[,1][x[,1] 0])], not the positions x[,1][x[,1] 0])]. 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] Linked count between matrix columns
Because we want the values in table(x[,2]) where the **names** are as.character(x[,1][x[,1] 0])], not the positions x[,1][x[,1] 0])]. Best On Thu, Jan 15, 2009 at 10:59 AM, Guillaume Chapron carnivorescie...@gmail.com wrote: table(x2)[as.character(x[,1][x[,1] 0])] Why do I need as.character() here? I checked it does not work without, but I don't see why. The help says as.character attempts to coerce its argument to character type. Thanks very much! Guillaume -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] autocorrelation
Hi Is any multiple regression-like test with correction for autocorrelation ? Wojciech [[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] Precision in R
I'm not getting that difference: .Machine$double.eps [1] 2.220446e-16 # so I don't think that explains the different behavior. WB-as.matrix(read.table(file.choose())) tcp1 - tcrossprod(WB) tcp2 - crossprod(t(WB)) tcp1 [,1] [,2] [,3] [1,] 1916061939 2281366606 678696067 [2,] 2281366606 3098975504 1092911209 [3,] 678696067 1092911209 452399849 WBtWB [,1] [,2] [,3] [1,] 1916061939 2281366606 678696067 [2,] 2281366606 3098975504 1092911209 [3,] 678696067 1092911209 452399849 tcp2 [,1] [,2] [,3] [1,] 1916061939 2281366606 678696067 [2,] 2281366606 3098975504 1092911209 [3,] 678696067 1092911209 452399849 solve(tcp1) Error in solve.default(tcp1) : system is computationally singular: reciprocal condition number = 9.60696e-17 solve(tcp2) Error in solve.default(tcp2) : system is computationally singular: reciprocal condition number = 9.60696e-17 That is somewhat interesting since yesterday my machine solved my input version of your: WBtWB [,1] [,2] [,3] [1,] 1916061939 2281366606 678696067 [2,] 2281366606 3098975504 1092911209 [3,] 678696067 1092911209 452399849 I assume that despite those matrices being displayed as the same they are represented differently in the machine. Berry wrote: I suppose that it is possible that the difference between what you report and what I see lies in the numerical libraries (LINPACK/LAPACK) that R calls upon. That would seem to be a possibility. You are using an out-of-date version which may limit people's interest in investigating the problem. -- David Winsemius On Jan 15, 2009, at 12:47 AM, dos Reis, Marlon wrote: Hi, I attached the files I'm using, it may help. I'm using Windows XP sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Try for example: WB-as.matrix(read.table(WB.dat)) tcp1 - tcrossprod(WB) tcp2 - crossprod(t(WB)) solve(tcp1) [,1] [,2] [,3] [1,] -41692.80 58330.89 -78368.17 [2,] 58330.89 -81608.66 109642.09 [3,] -78368.17 109642.09 -147305.32 solve(tcp2) Error in solve.default(tcp2) : system is computationally singular: reciprocal condition number = 2.17737e-17 Marlon. -Original Message- From: Charles C. Berry [mailto:cbe...@tajo.ucsd.edu] Sent: Thursday, 15 January 2009 5:16 p.m. To: dos Reis, Marlon Cc: r-help@r-project.org Subject: Re: [R] Precision in R Marlon, Are you using a current version of R? sessionInfo()? It would help if you had something we could _fully_ reproduce. Taking the _printed_ values you have below (WBtWB) and adding or subtracting what you have printed as the difference of the two visually equal matrices ( say Delta ) , I am able to run solve( dat3 ) solve( WBtWB + Delta ) solve( WBtWB - Delta ) solve( WBtWB + 2*Delta ) solve( WBtWB - 2*Delta ) and get the results to agree to 3 significant digits. And perturbing things even more I still get solve() to return a value: for ( i in 1:1000 ) solve(WBtWB - tcrossprod(rnorm(3))) for ( i in 1:1000 ) solve(WBtWB + tcrossprod(rnorm(3))) And I cannot get condition numbers anything like what you report: range(replicate( 1, 1/kappa(dat3-tcrossprod(matrix(rnorm(9), 3) [1] 5.917764e-11 3.350445e-09 So I am very curious that you got the results that you print below. I suppose that it is possible that the difference between what you report and what I see lies in the numerical libraries (LINPACK/LAPACK) that R calls upon. This was done on a windows XP PC. Here is my sessionInfo() sessionInfo() R version 2.8.1 Patched (2008-12-22 r47296) 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 HTH, Chuck On Thu, 15 Jan 2009, dos Reis, Marlon wrote: Dear All, I'm preparing a simple algorithm for matrix multiplication for a specific purpose, but I'm getting some unexpected results. If anyone could give a clue, I would really appreciate. Basically what I want to do is a simple matrix multiplication: (WB) %*% t(WB). The WB is in the disk so I compared to approaches: - Load 'WB' using 'read.table' (put it in WB.tmp) and then to the simple matrix multiplication WB.tmp%*%t(WB.tmp) - Scan each row of WB and do the cross products 'sum(WB.i*WB.i)' and 'sum(WB.i*WB.j)', which proper arrangement leads to WBtWB. Comparing these two matrices, I get the very similar values, however when I tried their inverse, WBtWB leads to a singular system. I've tried different tests
Re: [R] power analyses for mixed effects lmer models
Greg and Ben, Thanks for the suggestions. I'll give it a try, and I'll also poke around to find the r-sig-mixed-models list. What a wonderful world we live in that such a thing exists! --Lee -- View this message in context: http://www.nabble.com/power-analyses-for-mixed-effects-lmer-models-tp21457651p21478011.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] how to get the signed distance in SVM?
Dear Qing, look at the file svminternals.txt in the /doc subdirectory of the installed e1071 package (or inst/doc in the source package), that should help. David In the svm() function in the package e1071, is there anyway to get the signed distance of a sample point to the separating hyperplane in the feature space? Namely, if the separating hyperplane is given by f(x) = h(x)^T * w - rho, is there any way to get f(x)? Also, in the returned values of the function svm(), what does $coefs mean? It is said to be the corresponding coefficients times the training labels, but I don't know what is that corresponding coefficients denoting? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] LCA (e1071 package): error
Hello, I will use the lca method in the e1071 package. But I get the following error: Error in pas[j, ] - drop(exp(rep(1, nvar) %*% log(mp))) : number of items to replace is not a multiple of replacement length Does anybody know this error and knows what this means? Kind regards, Tryntsje __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] quantile regression using SemiPar package
Hi everyone: I want to fit the truncated polynomial smoothing to the quantiles instead of means, does someone know how to do it? I am thinking that maybe I can use SemiPar package, but can not find how. Thanks so many, Suyan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] binary_matrix_to_ascii_dendrogram
Hi, I have a binary matrix and I would like from it make a cluster by agglomerative method (like agnes), and then generate a ascii art dendrogram. See the illustration: binary matrixascii art dendrogram ABCDEFGH P1 0101011101 +-P1 P2 1000101001 = (Agnes) = +--| P3 1001011101 | +-P3 P4 0101101110 +--| | +--P2 | +--P4 Someone could help-me??? Thanks Luciano [[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] Seemingly Unrelated Negative Binomial (SUNB) estimation
Elisa Lanzi elisa.lanzi at unive.it writes: Dear all, I am trying to estimate a system of equations with a Seemingly Unrelated Regression. However because of the characteristics of the data I'd like to do it with a negative binomial estimation. Would anybody know how to implement a Seemingly Unrelated Negative Binomial (SUNB) estimation in R? Thank you in advance for your help. Best regards, Elisa Lanzi This PhD thesis http://etd.library.arizona.edu/etd/metadata.jsp?id=urn:etd:azu_etd_1605_1_m gives a log-likelihood function (pp. 43-45) and GAUSS code (p. 112) that wouldn't be too hard to translate into R (using optim or mle). (Not too hard implies you already have some reasonable grasp of R/ statistical programming; if you're looking for a black box solution you will probably have to get some help ...) Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Time Series
If I want to make a numerical series, I can do so easily with: series.numbers - 1:10 But, I don't seem to be able to do the same with time. I want to create a vector with 480 points that corresponds to the 480 minutes in a 8 hour work day. Thus I want series.time to look something like this: 9:00 9:01 9:02 9:03 etc. Last night I managed to build this by concatenating a series of strings, and converting them to datetime format with as.Date() or strptime(), but my method seems overly complex. hour - 0:59 day - c(9, 10, 11, 12, 13, 14, 15, 16) hours - c(rep(9, 60), rep(10, 60), rep(11, 60), rep(12, 60), rep(1, 60), rep(2, 60), rep(3, 60), rep(4, 60)) one.day - paste(hours, :, hour, sep = ) strptime(one.day, %H:%M) # OR # as.Date(one.day, %H:%M) Is there any way to do something similar to: strptime(09:00, %H:%M) : strptime(11:00, %H:%M) When I try this, I get the following error: numerical expression has 9 elements: only the first used Thanks. --andy -- Insert something humorous here. :-) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] interpolation to abscissa
On 13/01/2009, David Winsemius dwinsem...@comcast.net wrote: It's fairly clear from the documentation that approxfun() will not extrapolate. help.search(extrapolate) library(Hmisc) ?approxExtrap Some sort of minimization approach: approxExtrap(x=c(0,5,10,15,20), y=c(16,45,77,101,125),xout=c(-4,0,4)) $x [1] -4 0 4 $y [1] -7.2 16.0 39.2 approxExtrap(x=c(0,5,10,15,20), y=c(16,45,77,101,125),xout=seq(-2.8,-2.6, by=0.01)) $x [1] -2.80 -2.79 -2.78 -2.77 -2.76 -2.75 -2.74 -2.73 -2.72 -2.71 -2.70 -2.69 -2.68 [14] -2.67 -2.66 -2.65 -2.64 -2.63 -2.62 -2.61 -2.60 $y [1] -0.240 -0.182 -0.124 -0.066 -0.008 0.050 0.108 0.166 0.224 0.282 0.340 [12] 0.398 0.456 0.514 0.572 0.630 0.688 0.746 0.804 0.862 0.920 How accurate do you need the answer? I tried Hmisc's inverseFunction(), but it returned 0 for an argument of zero: invF - inverseFunction(x=c(0,5,10,15,20), y=c(16,45,77,101,125)) invF(0) So I then hacked Harrell's inverseFunction by substituting approxExtrap in every in instance where approx appeared, creating invFunc2: then invF - invFunc2(x=c(0,5,10,15,20), y=c(16,45,77,101,125)) invF(0) [1] -2.758621 I have compared your answer to those obtained from gnuplot, scilab and qtiplot; all report a result of x=-3.28. Why is r different? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] About Tcl/Tk after command in R
Dear R-helpers, I have a problem with the tcl after instruction. When I send: library(tcltk) Loading Tcl/Tk interface ... done tcl(after,1000,cat(try tcl after\n)) try tcl after Tcl the tcl command works fine. Similarly, the tcl command: tcl(after,1000,plot(rnorm(100))) Tcl works fine. But, if I send the command: tcl(after,1000,10^2) Tcl after#0 appears a popup window which reports: Error: invalid command name 100 Why? Davide Massidda Università di Padova Dipartimento di Psicologia Generale Via Venezia, 8 - 35131 Padova - Italy QPLab http://qplab.psy.unipd.it/ tel. +39 049 8276905 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Confidence Intervals for Poisson
On Jan 15, 2009, at 1:10 AM, John Kerpel wrote:
Hi folks!
I run the following code to get a CI for a Poisson with lambda=12.73
library(MASS)
set.seed(125)
x - rpois(100,12.73)
lambda_hat-fitdistr(x, dpois, list(lambda=12))$estimate
#Confidence Intervals - Normal Approx.
alpha-c(.05,.025,.01)
for(n in 1:length(alpha)) {
LowerCI-mean(x)-(qnorm(1-alpha[n]/2, mean = 0, sd =
1)*sqrt(var(x)/length(x)))
UpperCI-mean(x)+(qnorm(1-alpha[n]/2, mean = 0, sd =
1)*sqrt(var(x)/length(x)))
cat(For
Alpha
=
,alpha
[n
],LowerCI
=,LowerCI,,Lambda=,mean(x),,UpperCI=,UpperCI,\n)
}
When I do something like:
qpois(.975, 12.73, lower.tail = TRUE, log.p = FALSE)
[1] 20
qpois(.025, 12.73, lower.tail = TRUE, log.p = FALSE)
[1] 6
I get quite a different result. Is this the difference between the
normal
approx and an (almost) exact Poisson CI?
Yes and no.
Using Byar's approximation, which is reasonably accurate at this
expected value, I get 6.2 and 20.9 so R's qpois seems pretty sensible.
Your results don't look like a proper creation of a Normal approx,
however. Weren't you worried that your code might not be performing as
desired when the upper CL for your alpha= 0.05, and 0.01 results were
only different by 0.3?
I would have thought a (much more simple) Normal approximation for the
Poisson 0.05 CL around an expected of E might be
E +/- 1.96* E^(.5). So 12 +/- 2* 3.4 (5.2, 18.8) might be an
eyeball estimate.
12 + 1.96*sqrt(12)
[1] 18.78964
12 - 1.96*sqrt(12)
[1] 5.210361
--
David Winsemius
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Re: [R] Time Series
Try this: library(chron) times(9:00:00) + 0:479/(24*60) Also see R News 4/1 and read the help pages in chron. If you eventually want to use these times with corresponding series data look at the zoo package. On Thu, Jan 15, 2009 at 10:01 AM, Andrew Choens andy.cho...@gmail.com wrote: If I want to make a numerical series, I can do so easily with: series.numbers - 1:10 But, I don't seem to be able to do the same with time. I want to create a vector with 480 points that corresponds to the 480 minutes in a 8 hour work day. Thus I want series.time to look something like this: 9:00 9:01 9:02 9:03 etc. Last night I managed to build this by concatenating a series of strings, and converting them to datetime format with as.Date() or strptime(), but my method seems overly complex. hour - 0:59 day - c(9, 10, 11, 12, 13, 14, 15, 16) hours - c(rep(9, 60), rep(10, 60), rep(11, 60), rep(12, 60), rep(1, 60), rep(2, 60), rep(3, 60), rep(4, 60)) one.day - paste(hours, :, hour, sep = ) strptime(one.day, %H:%M) # OR # as.Date(one.day, %H:%M) Is there any way to do something similar to: strptime(09:00, %H:%M) : strptime(11:00, %H:%M) When I try this, I get the following error: numerical expression has 9 elements: only the first used Thanks. --andy -- Insert something humorous here. :-) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] About Tcl/Tk after command in R
On 1/15/2009 10:18 AM, davide.massi...@unipd.it wrote: Dear R-helpers, I have a problem with the tcl after instruction. When I send: library(tcltk) Loading Tcl/Tk interface ... done tcl(after,1000,cat(try tcl after\n)) try tcl after Tcl the tcl command works fine. Similarly, the tcl command: tcl(after,1000,plot(rnorm(100))) Tcl works fine. But, if I send the command: tcl(after,1000,10^2) Tcl after#0 appears a popup window which reports: Error: invalid command name “100” Why? The value of cat(something) is NULL, the value of plot(something) is NULL, but the value of 10^2 is 100. You're trying to execute no Tcl command in the first two cases, but you're trying to execute the command 100 in the last, and that's not a legal Tcl command. 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] Summary of Total Object.Size in R Script
See also ll() in the R.oo package, e.g.
# To list all objects in .GlobalEnv:
ll()
member data.class dimension objectSize
1*tmp* Person 1 428
2 as.character.Person function NULL1208
3 country character 1 44
4equals.Person function NULL2324
5 filename character 1 84
6 getAge function NULL 372
7getAge.Person function NULL 612
8 getName.Person function NULL 628
9 hashCode.Person function NULL1196
10last.warning list 1 192
11 obj Person 1 428
12 Person Class NULL2292
13 setAge function NULL 372
14 setAge.Person function NULL2088
15 setName function NULL 372
16 setName.Person function NULL 760
17 staticCode.Person function NULL2372
# To list all functions in the methods package:
ll(mode=function, envir=methods)
# To list all numeric and character object in the base package:
ll(mode=c(numeric, character), envir=base)
# To list all objects in the base package greater than 40kb:
subset(ll(envir=base), objectSize 4)
ll() takes argument 'properties', which allows you to construct any
column property you ever like. There is also a 'sortBy' argument.
See help(ll) for more details.
/Henrik
On Thu, Jan 15, 2009 at 3:00 AM, Gundala Viswanath gunda...@gmail.com wrote:
Sorry for my late reply.
Thank you so much Jim. This script of yours
is very2 useful. I have used it.
- Gundala Viswanath
Jakarta - Indonesia
On Wed, Jan 14, 2009 at 12:17 AM, jim holtman jholt...@gmail.com wrote:
Here is a function I use to see how big the objects in my workspace are:
my.ls -
+ function (pos = 1, sorted = F)
+ {
+ .result - sapply(ls(pos = pos, all.names = TRUE), function(..x)
object.size(eval(as.symbol(..x
+ if (sorted) {
+ .result - rev(sort(.result))
+ }
+ .ls - as.data.frame(rbind(as.matrix(.result), `**Total` =
sum(.result)))
+ names(.ls) - Size
+ .ls$Size - formatC(.ls$Size, big.mark = ,, digits = 0,
+ format = f)
+ .ls$Mode - c(unlist(lapply(rownames(.ls)[-nrow(.ls)],
function(x) mode(eval(as.symbol(x),
+ ---)
+ .ls
+ }
my.ls()
SizeMode
.my.env 28 environment
.Random.seed 2,528 numeric
.required 72 character
my.ls6,712function
**Total 9,340 ---
On Tue, Jan 13, 2009 at 9:53 AM, Gundala Viswanath gunda...@gmail.com
wrote:
Dear all,
Is there a way we can find the total object.size of
all the objects in our R script?
The reason we want to do this because we want to know
how much memory does our R script require overall.
Rprofmem(), doesn't seem to do it.
and Unix 'top' command is dynamic and
it doesn't give the exact byte size.
- Gundala Viswanath
Jakarta - Indonesia
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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?
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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] LCA (e1071 package): error
I will use the lca method in the e1071 package. But I get the following
error:
Error in pas[j, ] - drop(exp(rep(1, nvar) %*% log(mp))) :
number of items to replace is not a multiple of replacement length
Does anybody know this error and knows what this means?
The error means that you are trying to assign a variable of one size to a
variable of another fixed size. An example that recreates it is:
x - matrix(1:6, nrow=3)
x[1,] - 1:10
x[1,] cannot be resized from 3 to 10 without affecting the rest of x, so
an error is thrown.
In your example, the jth row of the matrix pas is a different size from
drop(exp(rep(1, nvar) %*% log(mp))).
Since you haven't provided a reproducible example (tut tut, read the
posting guide) you'll have to do the debugging yourself.
To get you started, type traceback() to see where the problem occurs.
Now try options(error=recover), and call the lca function again. Now you
can examine the values of nvar, mp and pas to see what is going wrong.
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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[R] using R how to read a one column alone from a database table from MySQL
hello friends i have a created a database table in MYSQL consisting of 11 columns. throught RMYSQL i managed to read the entire table in R. but i have few qureries which i need solutions...here they are: 1. Using R how to read a one column alone from a database table from MYSQL. 2. Using R how to print on screen those column value. 3. Using R how to print one particular row (in this case row is X)value alone. 4. Using R how to read all the column (11) and print (X) value alone on screen. 5. Using R with logic print those (X) value which is/between say 20 to 30 degrees. as im very new to this R softwareits quite awkward for an experienced user to give me the solutions for my above queries...but i would be thankful if i get the solutions and it will also be an learning for me too...so i kindly request any people in this forum to give me solutions how to do it... BR sankar. -- View this message in context: http://www.nabble.com/using-R-how-to-read-a-one-column-alone-from-a-database-table-from-MySQL-tp21478288p21478288.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] rimage installation problem-ubuntu 8.10
(I'm quite afraid this is a dumb question, so sorry in advance) I am trying to install the package rimage to R version 2.8.1 with Ubuntu Intrepid. When I type sudo R CMD INSTALL I get the following error message (pasted below). I know the same problem appears here (http://www.r-project.org/nosvn/R.check/r-patched-linux-ix86/rimage-00install.html) but I do not know what its appearance there means. Thanks in advance for any help! Abbe g++ -I/usr/share/R/include -g -O2 -fpic -g -O2 -c matrix.cpp -o matrix.o /usr/include/c++/4.3/bits/stl_vector.h: In member function ‘void std::vector_Tp, _Alloc::_M_initialize_dispatch(_Integer, _Integer, std::__true_type) [with _Integer = int, _Tp = std::vectordouble, std::allocatordouble , _Alloc = std::allocatorstd::vectordouble, std::allocatordouble ]’: /usr/include/c++/4.3/bits/stl_vector.h:290: instantiated from ‘std::vector_Tp, _Alloc::vector(_InputIterator, _InputIterator, const _Alloc) [with _InputIterator = int, _Tp = std::vectordouble, std::allocatordouble , _Alloc = std::allocatorstd::vectordouble, std::allocatordouble ]’ matrix.cpp:31: instantiated from here /usr/include/c++/4.3/bits/stl_vector.h:932: error: no matching function for call to ‘std::vectorstd::vectordouble, std::allocatordouble , std::allocatorstd::vectordouble, std::allocatordouble ::_M_fill_initialize(size_t, int)’ /usr/include/c++/4.3/bits/stl_vector.h:974: note: candidates are: void std::vector_Tp, _Alloc::_M_fill_initialize(size_t, const _Tp) [with _Tp = std::vectordouble, std::allocatordouble , _Alloc = std::allocatorstd::vectordouble, std::allocatordouble ] make: *** [matrix.o] Error 1 -- View this message in context: http://www.nabble.com/rimage-installation-problem-ubuntu-8.10-tp21475502p21475502.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] R on Vista
Dear Sir/Madam, Thanks for the software. May I know that R can run on Vista system or not? Cause i donwload but cant install.. =( Thanks s much!! -- Best Regards, Ivy [[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] interpolation to abscissa
On Jan 15, 2009, at 10:04 AM, e-letter wrote: On 13/01/2009, David Winsemius dwinsem...@comcast.net wrote: It's fairly clear from the documentation that approxfun() will not extrapolate. help.search(extrapolate) library(Hmisc) ?approxExtrap Some sort of minimization approach: approxExtrap(x=c(0,5,10,15,20), y=c(16,45,77,101,125),xout=c(-4,0,4)) $x [1] -4 0 4 $y [1] -7.2 16.0 39.2 approxExtrap(x=c(0,5,10,15,20), y=c(16,45,77,101,125),xout=seq(-2.8,-2.6, by=0.01)) $x [1] -2.80 -2.79 -2.78 -2.77 -2.76 -2.75 -2.74 -2.73 -2.72 -2.71 -2.70 -2.69 -2.68 [14] -2.67 -2.66 -2.65 -2.64 -2.63 -2.62 -2.61 -2.60 $y [1] -0.240 -0.182 -0.124 -0.066 -0.008 0.050 0.108 0.166 0.224 0.282 0.340 [12] 0.398 0.456 0.514 0.572 0.630 0.688 0.746 0.804 0.862 0.920 How accurate do you need the answer? I tried Hmisc's inverseFunction(), but it returned 0 for an argument of zero: invF - inverseFunction(x=c(0,5,10,15,20), y=c(16,45,77,101,125)) invF(0) So I then hacked Harrell's inverseFunction by substituting approxExtrap in every in instance where approx appeared, creating invFunc2: then invF - invFunc2(x=c(0,5,10,15,20), y=c(16,45,77,101,125)) invF(0) [1] -2.758621 I have compared your answer to those obtained from gnuplot, scilab and qtiplot; all report a result of x=-3.28. Why is r different? Perhaps a coding error on my part (or on your part). Perhaps different methods (none of which you describe)? I suspect that my method only used the first two points (I just checked by plotting and -2.7 is closer to the paper and pen result I get than is -3.28. Perhaps you made an extrapolation from a linear fit of a dataset that is not co-linear? lm(c(0,5) ~ c(16,45)) Call: lm(formula = c(0, 5) ~ c(16, 45)) Coefficients: (Intercept)c(16, 45) -2.7586 0.1724 It not that R is different, it is merely that I used it differently than you used your other tools. Here's another method ( using all points and again reversing the roles of x and y) : lm(c(0,5,10,15,20) ~ c(16,45,77,101,125)) Call: lm(formula = c(0, 5, 10, 15, 20) ~ c(16, 45, 77, 101, 125)) Coefficients: (Intercept) c(16, 45, 77, 101, 125) -3.2332 0.1818 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] About Tcl/Tk after command in R
Duncan Murdoch wrote:
On 1/15/2009 10:18 AM, davide.massi...@unipd.it wrote:
Dear R-helpers,
I have a problem with the tcl after instruction. When I send:
library(tcltk)
Loading Tcl/Tk interface ... done
tcl(after,1000,cat(try tcl after\n))
try tcl after
Tcl
the tcl command works fine. Similarly, the tcl command:
tcl(after,1000,plot(rnorm(100)))
Tcl
works fine. But, if I send the command:
tcl(after,1000,10^2)
Tcl after#0
appears a popup window which reports:
Error: invalid command name “100”
Why?
The value of cat(something) is NULL, the value of plot(something) is
NULL, but the value of 10^2 is 100. You're trying to execute no Tcl
command in the first two cases, but you're trying to execute the command
100 in the last, and that's not a legal Tcl command.
Yes. Notice also that the argument is intended to be something to do
*after* the period of time has elapsed, and as written, it happens
immediately. You can use an R expression there, but it needs to be an
unevaluated call, usually created by
quote() or expression().
tcl(after,5000,quote(cat(try tcl after\n))) ; for (i in
1:10){print(i);Sys.sleep(1)}
Tcl after#4
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
try tcl after
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] interpolation to abscissa
Perhaps a coding error on my part (or on your part). Perhaps different methods (none of which you describe)? I suspect that my method only used the first two points (I just checked by plotting and -2.7 is closer to the paper and pen result I get than is -3.28. Perhaps you made an extrapolation from a linear fit of a dataset that is not co-linear? lm(c(0,5) ~ c(16,45)) Call: lm(formula = c(0, 5) ~ c(16, 45)) Coefficients: (Intercept)c(16, 45) -2.7586 0.1724 It not that R is different, it is merely that I used it differently than you used your other tools. Here's another method ( using all points and again reversing the roles of x and y) : lm(c(0,5,10,15,20) ~ c(16,45,77,101,125)) Call: lm(formula = c(0, 5, 10, 15, 20) ~ c(16, 45, 77, 101, 125)) Coefficients: (Intercept) c(16, 45, 77, 101, 125) -3.2332 0.1818 My understanding from gnuplot manual is that a marquart-levenberg algorithm is used, which I applied to the data to perform a least squares best fit linear curve. Gnuplot returns values for the intercept and gradient which I then apply to solve the linear equation y=mx+c. Similarly with scilab, where the regress(ion?) function was applied. Qtiplot performed non-weighted linear regression to output values similar to those from gnuplot. Why reverse the roles of x and y in your method? Although your revised value is closer to those from other programs, how do I understand and explain the discrepancy? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Vista
On 1/15/2009 6:53 AM, Ziqi wrote: Dear Sir/Madam, Thanks for the software. May I know that R can run on Vista system or not? Cause i donwload but cant install.. =( Thanks s much!! R can run on Vista. See the FAQ (online at http://cran.r-project.org/bin/windows/base/rw-FAQ.html, you want question 2.24) for details on what's different from earlier Windows systems. 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.
[R] problems with extractPrediction in package caret
Hi list, I´m working on a predictive modeling task using the caret package. I found the best model parameters using the train() and trainControl() command. Now I want to evaluate my model and make predictions on a test dataset. I tried to follow the instructions in the manual and the vignettes but unfortunately I´m getting an error message I can`t figure out. Here is my code: rfControl - trainControl(method = oob, returnResamp = all, returnData=TRUE, verboseIter = TRUE) rftrain - train(x=train_x, y=trainclass, method=rf, tuneGrid=tuneGrid, tr.control=rfControl) pred - predict(rftrain) pred# this works fine expred - extractPrediction(rftrain) Error in models[[1]]$trainingData : $ operator is invalid for atomic vectors My predictors are 28 numeric attributes and one factor. I`m working with the latest version of caret and R 2.7.2 on WinXP. Any advice is very welcome. Thanks. TIM --- Dipl.-Geogr. Tim Häring Sachgebiet Standort und Bodenschutz (SG 2.1) Bayerische Landesanstalt für Wald und Forstwirtschaft Am Hochanger 11 D-85354 Freising Tel.: +49-(0)8161/71-4769 E-Mail: tim.haer...@lwf.bayern.de http://www.lwf.bayern.de [[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] Using fortran code which call LAPACK subroutines
Prof Brian Ripley a écrit :
On Tue, 13 Jan 2009, Charles C. Berry wrote:
On Tue, 13 Jan 2009, Matthieu Stigler wrote:
Hello
I'm trying to run a fortran code which use LAPACK subroutines. I
think I should use some points shown in the manual 5.5 Creating
shared objects but it is too technical for me :-(...
Be sure to look over section 6, esp. 6.17
The headers for DGEQRF, DLASR, DROT, DROTG are all in Blas.h or
Lapack.h (although you will see them in lower case).
XERBLA in libRBlas.so but is not in the R API, so if your code needs
to use it you'll have to add a header like the one in main.c or add
your own version.
Not in Fortran code, though: see below
I think Matthieu had not read quite a lot of the documentation: given
how carefully it was written, that was disrespectful (as was the lack
of a proper signature: see the posting guide: Charles aka Chuck has
been exemplary).
Sorry if this could be seen as disrespectful, I nevertheless don't think
that having difficulties to read a good but complex (and difficult for a
newbie) documentation is a sign of disrespect.
To put it simply: if you are ashamed of who you are, so are the most
prolific helpers here. Some people resent being milked for free
consultancy for commercial firms, and many of us will go many miles
out of our way for third-world NGOs/academia.
Oh, I forgot to write my name... I'm sorry, well even if you could see
it from my address I should have written. I understand your worry about
commercial firms, personnaly, I'm trying to contribute myself to R
through extensions of package tsDyn
http://code.google.com/p/tsdyn/wiki/ThresholdCointegration
I think you can probably do what you want with just
PKG_LIBS=${LAPACK_LIBS} $(BLAS_LIBS) ${FLIBS}
in Makevars
and
R CMD INSTALL your-package
with just the default settings.
This did the job (just had to copy/paste the xerbla in a proper .f file
in src)!
Thank you so much!
Agreed.
HTH,
Chuck
Could anyone help me for the procedure to do:
-which part of the manual is relevant for this type of question?
actually I'm speaking from writing R extensions, should I read R admin?
-point 1.2 says: /Recent versions of Autoconf in fact allow an
already set |FLIBS| to override the test for the FORTRAN linker
flags. Also, recent versions of R can detect external BLAS and
LAPACK libraries./
but nevertheless I have to include something more? or modify the
script?
-should I compile from SHLIB with other options or include it
directly into a package and cretae a makevars or PACKAGE_LIBS...?
I'm lost...
The subroutine I try to use is delcols.f
(http://www.maths.manchester.ac.uk/~clucas/updating/addcols.f) which
calls
* .. External Subroutines ..
EXTERNAL DGEQRF, DLASR, DROT, DROTG, XERBLA
Thank you very much!!
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:cbe...@tajo.ucsd.eduUC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
92093-0901
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and provide commented, minimal, self-contained, reproducible code.
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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] interpolation to abscissa
On Jan 15, 2009, at 11:31 AM, e-letter wrote: Perhaps a coding error on my part (or on your part). Perhaps different methods (none of which you describe)? I suspect that my method only used the first two points (I just checked by plotting and -2.7 is closer to the paper and pen result I get than is -3.28. Perhaps you made an extrapolation from a linear fit of a dataset that is not co-linear? lm(c(0,5) ~ c(16,45)) Call: lm(formula = c(0, 5) ~ c(16, 45)) Coefficients: (Intercept)c(16, 45) -2.7586 0.1724 It not that R is different, it is merely that I used it differently than you used your other tools. Here's another method ( using all points and again reversing the roles of x and y) : lm(c(0,5,10,15,20) ~ c(16,45,77,101,125)) Call: lm(formula = c(0, 5, 10, 15, 20) ~ c(16, 45, 77, 101, 125)) Coefficients: (Intercept) c(16, 45, 77, 101, 125) -3.2332 0.1818 My understanding from gnuplot manual is that a marquart-levenberg algorithm is used, which I applied to the data to perform a least squares best fit linear curve. Gnuplot returns values for the intercept and gradient which I then apply to solve the linear equation y=mx+c. Similarly with scilab, where the regress(ion?) function was applied. Qtiplot performed non-weighted linear regression to output values similar to those from gnuplot. Why reverse the roles of x and y in your method? I accidentally switched x and y ad then realized I could get an intercept value without the labor of solving by hand. Although your revised value is closer to those from other programs, how do I understand and explain the discrepancy? The regression line for x ~ y is *not* the same as the regression line for y ~ x. If you want to check that the numbers from R agree with your other solutions, then take the regression equation from lmmod Call: lm(formula = c(16, 45, 77, 101, 125) ~ c(0, 5, 10, 15, 20)) Coefficients: (Intercept) c(0, 5, 10, 15, 20) 18.00 5.48 ... and then solve for x = 0 as you apparently did with the other systems. -- David Winsemius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 R how to read a one column alone from a database table from MySQL
sankar82 sankar.arughadhoss at tkk.fi writes: i have a created a database table in MYSQL consisting of 11 columns. throught RMYSQL i managed to read the entire table in R. but i have few qureries which i need solutions...here they are: 1. Using R how to read a one column alone from a database table from MYSQL. 2. Using R how to print on screen those column value. 3. Using R how to print one particular row (in this case row is X)value alone. 4. Using R how to read all the column (11) and print (X) value alone on screen. 5. Using R with logic print those (X) value which is/between say 20 to 30 degrees. Have you tried the examples in Rmysql-package? For 5., you could use something like: dbSendQuery(con, select * from WL where width\_nm between 0.5 and 1) Ok, here we let SQL do the job, and you homework want it to be done in R. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] rimage installation problem-ubuntu 8.10
On 15 January 2009 at 03:06, abbethesieyes wrote: | | (I'm quite afraid this is a dumb question, so sorry in advance) | I am trying to install the package rimage to R version 2.8.1 with Ubuntu | Intrepid. When I type sudo R CMD INSTALL I get the following error | message (pasted below). I know the same problem appears here | (http://www.r-project.org/nosvn/R.check/r-patched-linux-ix86/rimage-00install.html) | but I do not know what its appearance there means. | | Thanks in advance for any help! | | Abbe | | g++ -I/usr/share/R/include -g -O2 -fpic -g -O2 -c matrix.cpp -o | matrix.o | /usr/include/c++/4.3/bits/stl_vector.h: In member function void | std::vector_Tp, _Alloc::_M_initialize_dispatch(_Integer, _Integer, | std::__true_type) [with _Integer = int, _Tp = std::vectordouble, | std::allocatordouble , _Alloc = std::allocatorstd::vectordouble, | std::allocatordouble ] : | /usr/include/c++/4.3/bits/stl_vector.h:290: instantiated from | std::vector_Tp, _Alloc::vector(_InputIterator, _InputIterator, const | _Alloc) [with _InputIterator = int, _Tp = std::vectordouble, | std::allocatordouble , _Alloc = std::allocatorstd::vectordouble, | std::allocatordouble ] | matrix.cpp:31: instantiated from here | /usr/include/c++/4.3/bits/stl_vector.h:932: error: no matching function for | call to std::vectorstd::vectordouble, std::allocatordouble , | std::allocatorstd::vectordouble, std::allocatordouble | ::_M_fill_initialize(size_t, int) | /usr/include/c++/4.3/bits/stl_vector.h:974: note: candidates are: void | std::vector_Tp, _Alloc::_M_fill_initialize(size_t, const _Tp) [with _Tp = | std::vectordouble, std::allocatordouble , _Alloc = | std::allocatorstd::vectordouble, std::allocatordouble ] | make: *** [matrix.o] Error 1 Nothing specific to Ubuntu here. The rimage package simply does not build under g++ 4.3 as constructors like m = new vector vector double (x, y); are not supported -- ie you cannot pass the (x,y) size information. Looks like that worked in the past. However, you do get m = new vector vector double ; though and could explicitly resize the matrix (ie once for rows and then in a loop for each column). May require some testing though. Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] interpolation to abscissa
It appears the answer to your goal after a discursive exploration of interpolation, which was really extrapolation, is that you need to look at the predict methods for linear (and other sorts as well) models. ?predict ?predict.lm y - c(16,45,77,101,125) x - c(0,5,10,15,20) lmmod - lm(y ~ x) plot(x,y, ylim = c(0,125), xlim =c(-4,22)) #defaults would not allow estimates from plot lines(x=seq(-4,22, by=.5), y=predict(lm(y ~ x), newdata = data.frame(x = seq(-4,22, by=. 5) ) ) ) -- David Winsemius On Jan 15, 2009, at 11:31 AM, e-letter wrote: snipped preceding excursion __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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, clinical trials and the FDA
On Sun, Jan 11, 2009 at 11:05 AM, Kingsford Jones kingsfordjo...@gmail.com wrote: I hope that Marc doesn't mind, but I felt that part of his recent post was important enough to deserve it's own subject line rather then being lost in a 60-msg-long thread... I also wanted to thank Marc for this wealth of information on using R in clinical trials. I particularly want to recommend the R: Regulatory Compliance and Validation Issues document at http://www.r-project.org/certification.html . Even if you're not looking to validate R for 21CFR11 compliance, this document is an excellent description of R's world-class software development process. With this, and the documented use of R by the FDA itself and within pharma companies for clinical trials, I hope we can settle the Is R Validated? question at long last. Thanks go to the authors (Marc Schwartz, Frank Harrell, Tony Rossini and Ian Francis) and the R Foundation generally for putting this together. By the way, if (or a skeptical colleague) needs a more detailed answer to the Is R Validated? question, I expand upon the information Marc provided here: http://blog.revolution-computing.com/2009/01/analyzing-clinical-trial-data-with-r.html # David Smith -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (Seattle, USA) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Precision in R
On Thu, 15 Jan 2009, dos Reis, Marlon wrote: I'm using: solve(a, b, tol, LINPACK = FALSE, ...) Therefore,tol ==.Machine$double.eps .Machine$double.eps [1] 2.220446e-16 It explains why 'solve' works for 'tcp1' but not for 'tcp2': eigen(tcp1)$values [1] 5.208856e+09 2.585816e+08 -3.660671e-06 -3.660671e-06/5.208856e+09 [1] -7.027783e-16 eigen(tcp2)$values [1] 5.208856e+09 2.585816e+08 -6.416393e-08 -6.416393e-08/5.208856e+09 [1] -1.231824e-17 My question would be why 'tcrossprod' and 'crossprod' leads to such difference? Thanks for posting your data, Marlon. This is what I get on windows XP: tcp1-tcp2 [,1] [,2] [,3] [1,] -2.861023e-06 -4.768372e-07 -4.768372e-07 [2,] -4.768372e-07 -3.814697e-06 2.622604e-06 [3,] -4.768372e-07 2.622604e-06 -5.960464e-08 but on my Gentoo Linux Intel Core 2 Duo: print(tcp1-tcp2,digits=20) [,1] [,2] [,3] [1,]000 [2,]000 [3,]000 So, it would seem to be that the floating point calcs on my Windows box, David's Mac, and whatever system you are using are not as accurate as they might be. It is well known that rounding error can play havoc with crossproducts (particularly when the range of magnitudes of the numbers is wide as it is here), which is why matrix decompositions are generally used for solving least squares problems. The internal code for crossprod and tcrossprod is different, so the computations are likely done in a different order, which would account for the difference in tcp1 and tcp2 . Ultimately, array.c and blas.f SUBROUTINE DSYRK have the code if you want to dig into it. So to summarize: the difference is not due to R per se, but in the limited accuracy of floating point calcs on the system used. HTH, Chuck Marlon. -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Thursday, 15 January 2009 6:04 p.m. To: Charles C. Berry Cc: dos Reis, Marlon; r-help@r-project.org Subject: Re: [R] Precision in R I am seeing different behavior than don Reis on my installation as well: mtx is the same as his WBtWB mtx - matrix(c(1916061939, 2281366606, 678696067, 2281366606, 3098975504, 1092911209, 678696067, 1092911209, 452399849), ncol=3) mtx [,1] [,2] [,3] [1,] 1916061939 2281366606 678696067 [2,] 2281366606 3098975504 1092911209 [3,] 678696067 1092911209 452399849 eigen(mtx) $values [1] 5.208856e+09 2.585816e+08 -4.276959e-01 $vectors [,1] [,2] [,3] [1,] -0.5855545 -0.7092633 0.3925195 [2,] -0.7678140 0.3299775 -0.5491599 [3,] -0.2599763 0.6229449 0.7378021 rcond(mtx) [1] 5.33209e-11 Despite a very ill-conditioned matrix, solve still proceeds solve(mtx) [,1] [,2] [,3] [1,] -0.3602361 0.5039933 -0.6771204 [2,] 0.5039933 -0.7051189 0.9473348 [3,] -0.6771204 0.9473348 -1.2727543 sessionInfo() R version 2.8.1 Patched (2009-01-07 r47515) i386-apple-darwin9.6.0 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 snipped package info -- David Winsemius On Jan 14, 2009, at 11:15 PM, Charles C. Berry wrote: Marlon, Are you using a current version of R? sessionInfo()? It would help if you had something we could _fully_ reproduce. Taking the _printed_ values you have below (WBtWB) and adding or subtracting what you have printed as the difference of the two visually equal matrices ( say Delta ) , I am able to run solve( dat3 ) solve( WBtWB + Delta ) solve( WBtWB - Delta ) solve( WBtWB + 2*Delta ) solve( WBtWB - 2*Delta ) and get the results to agree to 3 significant digits. And perturbing things even more I still get solve() to return a value: for ( i in 1:1000 ) solve(WBtWB - tcrossprod(rnorm(3))) for ( i in 1:1000 ) solve(WBtWB + tcrossprod(rnorm(3))) And I cannot get condition numbers anything like what you report: range(replicate( 1, 1/kappa(dat3-tcrossprod(matrix(rnorm(9), 3) [1] 5.917764e-11 3.350445e-09 So I am very curious that you got the results that you print below. I suppose that it is possible that the difference between what you report and what I see lies in the numerical libraries (LINPACK/ LAPACK) that R calls upon. This was done on a windows XP PC. Here is my sessionInfo() sessionInfo() R version 2.8.1 Patched (2008-12-22 r47296) 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 HTH, Chuck On Thu, 15 Jan 2009, dos Reis, Marlon wrote: Dear All, I'm preparing a simple algorithm for matrix multiplication for a specific purpose, but I'm getting some unexpected results. If anyone could give a clue, I would really appreciate. Basically what I want to do is a simple matrix multiplication: (WB) %*% t(WB). The WB is
[R] user library help functionality (packages.html)
Here's another help file question. Some context: University setting wherein R is installed for availability to students and course instructors across campus in various PC labs. Windows Vista environment. Goal: To maximize flexibility and functionality of installing add-on packages and associated help files among different users, while avoiding conflicts across different user libraries. (I could have my difficult-to-access sysadmin install _all_ libraries, but this seems wasteful, and would seem to present problems when my colleague or I want to update a package or install a newly available package but do not have time to wait a week or two for our sysadmin.) Problem (?): As a course instructor, I want flexibility to install add- on libraries to a user (not site) library, and I don't want to step on my colleagues' toes (or vice-versa) when it comes to add-on packages and associated help files for use in classes. I have no problem installing add-on packages to a user library, with one exception: I do not have permission to update the file $RHOME/doc/html/packages.html, as evidenced by a permission error upon installing a package to a user library using update.packages (not to the default site library, which is also restricted). The installed add-on packages work fine, with the exception of some of the help functionality. I find myself having to use browseURL() to point to the html files in the package's file structure. I cannot expect the average student (or senior colleague) to tolerate this situation. I'm thinking that I simply need to have my sysadmin give me and my colleagues (all users who want to install add-ons packages?) permission to read/write packages.html, and the problem will go away. But, before I ask my sysadmin to give permission, I want to know, does this create another problem? For example, my colleague creates a library for STAT3000BC, which, I assume, will modify packages.html (assuming my sysadmin gives permission), then I create a library for STAT2010, which also modifies packages.html. See my concern? Does R somehow allow harmonious help functionality in such cases (by, for example, maintaining separate copies of packages.html for different users)? Suggestions? Thanks. Jarrett -- Jarrett Barber Assistant Professor Ross Hall Room 333 Department of Statistics Dept. 3332 University of Wyoming 1000 E. University Ave. Office: (307) 766-3341 Mobile: (307) 399-7759 FAX: (307) 766-3927 Reply To: jbarber8[ATT]uwyo.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bar Plot ggplot2 Filling bars with cross hatching
Hi Stephen, #I am putting a test together for an introductory biology class and I would like to put different cross hatching inside of each bar for the bar plot below ggplot2 uses the grid package to do all the drawing, and currently grid doesn't support cross-hatching, so unfortunately there's no way to do this in ggplot2. Regards, 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] Bar Plot ggplot2 Filling bars with cross hatching
This will be fixed in the next version, but until then you can do title = Aquarium\n Hadley On Wed, Jan 14, 2009 at 9:24 PM, stephen sefick ssef...@gmail.com wrote: Also notice that the q in Aquarium is hidden. Is there a way to make this not happen? thanks Stephen Sefick On Wed, Jan 14, 2009 at 10:18 PM, stephen sefick ssef...@gmail.com wrote: #I am putting a test together for an introductory biology class and I would like to put different cross hatching inside of each bar for the bar plot below color - c(Brightly Colored, Dull, Neither) lizards - c(277, 70, 3) liz.col - data.frame(color, lizards) qplot(color, lizards, data=liz.col, geom=bar, ylab=Observed Matings, main=Counts Out of 350 Aquariums, ylim=c(0,400), fill=color)+scale_y_continuous(breaks=c(0, 70, 277, 350)) Thanks -- 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 -- 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. -- 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.
[R] Warning on assignment.
I have a question on whether a warning message is valid or if I just don't understand the process. Let me illustrate via some R code: x - 1:20 i - x %% 2 0 y - rep(1,20) x[i] - y Warning message: In x[i] - y : number of items to replace is not a multiple of replacement length But it still does what I would expect for the assignment: x [1] 1 2 1 4 1 6 1 8 1 10 1 12 1 14 1 16 1 18 1 20 What don't I understand? Thank you. Kevin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Warning on assignment.
The lengths are different, particularly the length of subsetted x[i] x - 1:20 i - x %% 2 0 y - rep(1,20) length(x) [1] 20 length(i) [1] 20 length(x[i]) [1] 10 length(y) [1] 20 You happened to be lucky and got what you wanted, but a more reliable approach is: x[i] - y[i] Sarah On Thu, Jan 15, 2009 at 1:08 PM, rkevinbur...@charter.net wrote: I have a question on whether a warning message is valid or if I just don't understand the process. Let me illustrate via some R code: x - 1:20 i - x %% 2 0 y - rep(1,20) x[i] - y Warning message: In x[i] - y : number of items to replace is not a multiple of replacement length But it still does what I would expect for the assignment: x [1] 1 2 1 4 1 6 1 8 1 10 1 12 1 14 1 16 1 18 1 20 What don't I understand? Thank you. Kevin -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning on assignment.
This was just an illustration. It is the warning message that I don't understand. The warning says number of items to replace is not a multiple of replacement length. The way I look at it 10 is a multiple of 20. Kevin Sarah Goslee sarah.gos...@gmail.com wrote: The lengths are different, particularly the length of subsetted x[i] x - 1:20 i - x %% 2 0 y - rep(1,20) length(x) [1] 20 length(i) [1] 20 length(x[i]) [1] 10 length(y) [1] 20 You happened to be lucky and got what you wanted, but a more reliable approach is: x[i] - y[i] Sarah On Thu, Jan 15, 2009 at 1:08 PM, rkevinbur...@charter.net wrote: I have a question on whether a warning message is valid or if I just don't understand the process. Let me illustrate via some R code: x - 1:20 i - x %% 2 0 y - rep(1,20) x[i] - y Warning message: In x[i] - y : number of items to replace is not a multiple of replacement length But it still does what I would expect for the assignment: x [1] 1 2 1 4 1 6 1 8 1 10 1 12 1 14 1 16 1 18 1 20 What don't I understand? Thank you. Kevin -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning on assignment.
rkevinbur...@charter.net wrote: This was just an illustration. It is the warning message that I don't understand. The warning says number of items to replace is not a multiple of replacement length. The way I look at it 10 is a multiple of 20. Um, with a multiplier of 0.5 ? You're trying to put 20 things in 10 boxes. R will allow 10 things in 20 boxes (by recycling) without complaining. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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, clinical trials and the FDA
on 01/15/2009 11:42 AM David M Smith wrote: On Sun, Jan 11, 2009 at 11:05 AM, Kingsford Jones kingsfordjo...@gmail.com wrote: I hope that Marc doesn't mind, but I felt that part of his recent post was important enough to deserve it's own subject line rather then being lost in a 60-msg-long thread... I also wanted to thank Marc for this wealth of information on using R in clinical trials. I particularly want to recommend the R: Regulatory Compliance and Validation Issues document at http://www.r-project.org/certification.html . Even if you're not looking to validate R for 21CFR11 compliance, this document is an excellent description of R's world-class software development process. With this, and the documented use of R by the FDA itself and within pharma companies for clinical trials, I hope we can settle the Is R Validated? question at long last. Thanks go to the authors (Marc Schwartz, Frank Harrell, Tony Rossini and Ian Francis) and the R Foundation generally for putting this together. Thanks kindly David. On the R Foundation side, I want to ensure appropriate credit and note the tremendous assistance specifically provided by Doug Bates, Martin Maechler, Peter Dalgaard, Kurt Hornik and John Fox. Over the past couple of years their time, support, review and edits of the document ensured that the light at the end of the tunnel was not an oncoming train and ensured the accuracy of the content in documenting the R development process. In addition, their critical facilitation of the R Foundation review and approval process has enabled us to have these recent discussions predicated upon a base of formal and publicly available information that should put to rest any concerns over R's quality development procedures. R is developed and maintained using a world class process, implemented by a world class team. Importantly and so that we never forget, that Core team is comprised of volunteers who have donated of their time and careers to bring us R and to enable this wonderful community. Regards, Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] number of Mondays
dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. i appreciate any hint you could give, thanks. Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] number of Mondays
?chron() in particular day.of.week -Roy On Jan 15, 2009, at 11:28 AM, Carlos Hernandez wrote: dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. i appreciate any hint you could give, thanks. Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ** The contents of this message do not reflect any position of the U.S. Government or NOAA. ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ Old age and treachery will overcome youth and skill. From those who have been given much, much will be expected __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] number of Mondays
On Jan 15, 2009, at 2:28 PM, Carlos Hernandez wrote: dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. The chron package has a wide assortment of functions of that sort. Looks like Mondays would be 1 day.of.week(1,15,2009) # a Thursday [1] 4 day.of.week(1,18,2009) #Saturday [1] 0 day.of.week(1,17,2009) #Sunday [1] 6 -- David Winsemius __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] number of Mondays
Try this: library(zoo) # as.yearmon dd - seq(as.Date(2000-01-01), as.Date(2004-12-31), day) dow - as.numeric(format(dd, %w)) ym - as.yearmon(dd) tab - do.call(rbind, tapply(dow, ym, table)) rownames(tab) - format(as.yearmon(as.numeric(rownames(tab head(tab) 0 1 2 3 4 5 6 Jan 2000 5 5 4 4 4 4 5 Feb 2000 4 4 5 4 4 4 4 Mar 2000 4 4 4 5 5 5 4 Apr 2000 5 4 4 4 4 4 5 May 2000 4 5 5 5 4 4 4 Jun 2000 4 4 4 4 5 5 4 On Thu, Jan 15, 2009 at 2:28 PM, Carlos Hernandez carlos.u...@gmail.com wrote: dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. i appreciate any hint you could give, thanks. Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] number of Mondays
Carlos Hernandez wrote: dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. i appreciate any hint you could give, This is where POSIXlt objects are useful: unlist(unclass(as.POSIXlt(ISOdate(1959,3,11 sec min hour mday mon year wday yday isdst 0 01211 259 369 0 Which means that I was born on a Wednesday (wday==3) in March (mon==2) (some of the fields count from 0 and others, like mday, from 1; presumably some UNIX vendor back in the Stone Age got their implementation turned into a standard...). This allows you to do stuff like: dd - seq(Sys.Date(),as.Date(2009-3-11),1) dd - as.POSIXlt(dd) with(dd, table(mon,wday)) wday mon 0 1 2 3 4 5 6 0 2 2 2 2 3 3 3 1 4 4 4 4 4 4 4 2 2 2 2 2 1 1 1 which I think is pretty much what you were looking for. thanks. Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: Moving a Data Frame Column
Thanks, I knew it was something simple :) Petr Pikal wrote: Hi r-help-boun...@r-project.org napsal dne 15.01.2009 04:47:39: Dear R-Users if I have a data frame (or zoo data) as follows: Run Bike Walk Drive 1 2 7 5 5 2 4 2 8 3 2 1 How can I re-order it so that it reads: Drive Run Bike Walk 5 1 2 7 2 5 2 4 1 8 3 2 i.e. Drive has been copied and pasted to the left most column. test Run Bike Walk Drive 1 127 5 2 524 2 3 832 1 test2 - test[, c(4,1,2,3)] Drive Run Bike Walk 1 5 127 2 2 524 3 1 832 if you want it in new data frame or test - test[, c(4,1,2,3)] if you want to overwrite it. Regards Petr Thanks for your help. James -- View this message in context: http://www.nabble.com/Moving-a-Data-Frame- Column-tp21470798p21470798.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. -- View this message in context: http://www.nabble.com/Moving-a-Data-Frame-Column-tp21470798p21485810.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] user library help functionality (packages.html)
This helps a lot. I have options(htmlhelp=TRUE) and options(chmhelp=FALSE) (else problems). Now, ?, help(), and help.search() seem to work well. But, help.start() appears restricted to packages in the site library. I see, in the Help/FAQ on R for Windows/ Sections 4.3 and 4.4, that I cannot expect more from help.start() unless I have write permission to $RHOME/library, which I do not (package does have a CONTENTS file however). I assume that, if I want my students to have this functionality, they, too, would need write access to $RHOME/library, correct? But, this does not seem a wise thing to give. Am I missing something here, barring permission changes, that would allow help.search() to see user libraries? This would be ideal, but your suggestions seems to give us nice help functionality, and I think we can implement an R installation campus- wide without the full functionality of help.seach(). Thanks very much. Jarrett R Session: R version 2.7.0 (2008-04-22) ...snip... personalLib- .libPaths()[1]; personalLib [1] H:\\Desktop\\RFiles\\Library getOption(htmlhelp) [1] TRUE getOption(chmhelp) [1] FALSE install.packages(UsingR, + lib=personalLib, + depend=TRUE) trying URL 'http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/2.7/UsingR_0.1-10.zip' Content type 'application/zip' length 1433201 bytes (1.4 Mb) opened URL downloaded 1.4 Mb package 'UsingR' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Temp\RtmpQr4t3E\downloaded_packages updating HTML package descriptions Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/packages.html', reason 'Permission denied' ## PERMISSION PROBLEM library(UsingR) Warning message: package 'UsingR' was built under R version 2.7.2 help(UsingR) ## works! Help for ëUsingRí is shown in the browser help.start() ## restricted to site library updating HTML package listing updating HTML search index fixing URLs in non-standard libraries If nothing happens, you should open 'C:\PROGRA~1\R\R-27~1.0\doc\html \index.html' yourself Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/packages.html', reason 'Permission denied' ## SAME PERMISSION PROBLEM help.search(UsingR) ## works! ?UsingR ## works! Help for ëUsingRí is shown in the browser q() On Jan 15, 2009, at 11:42 AM, Duncan Murdoch wrote: On 1/15/2009 12:50 PM, Jarrett Barber wrote: Here's another help file question. Some context: University setting wherein R is installed for availability to students and course instructors across campus in various PC labs. Windows Vista environment. Goal: To maximize flexibility and functionality of installing add- on packages and associated help files among different users, while avoiding conflicts across different user libraries. (I could have my difficult-to-access sysadmin install _all_ libraries, but this seems wasteful, and would seem to present problems when my colleague or I want to update a package or install a newly available package but do not have time to wait a week or two for our sysadmin.) Problem (?): As a course instructor, I want flexibility to install add- on libraries to a user (not site) library, and I don't want to step on my colleagues' toes (or vice-versa) when it comes to add- on packages and associated help files for use in classes. I have no problem installing add-on packages to a user library, with one exception: I do not have permission to update the file $RHOME/doc/ html/packages.html, as evidenced by a permission error upon installing a package to a user library using update.packages (not to the default site library, which is also restricted). The installed add-on packages work fine, with the exception of some of the help functionality. I find myself having to use browseURL() to point to the html files in the package's file structure. I cannot expect the average student (or senior colleague) to tolerate this situation. A simpler way to get to the HTML man pages is to run options(htmlhelp=TRUE) and then the regular ?topic or help(topic) will find the HTML help pages in your local library. I'm thinking that I simply need to have my sysadmin give me and my colleagues (all users who want to install add-ons packages?) permission to read/write packages.html, and the problem will go away. But, before I ask my sysadmin to give permission, I want to know, does this create another problem? For example, my colleague creates a library for STAT3000BC, which, I assume, will modify packages.html (assuming my sysadmin gives permission), then I create a library for STAT2010, which also modifies packages.html. See my concern? Does R somehow allow harmonious help functionality in such cases (by, for example, maintaining separate copies of packages.html for different users)? You will likely
Re: [R] user library help functionality (packages.html)
On 1/15/2009 3:17 PM, Jarrett Barber wrote: This helps a lot. I have options(htmlhelp=TRUE) and options(chmhelp=FALSE) (else problems). Now, ?, help(), and help.search() seem to work well. But, help.start() appears restricted to packages in the site library. I see, in the Help/FAQ on R for Windows/ Sections 4.3 and 4.4, that I cannot expect more from help.start() unless I have write permission to $RHOME/library, which I do not (package does have a CONTENTS file however). I assume that, if I want my students to have this functionality, they, too, would need write access to $RHOME/library, correct? But, this does not seem a wise thing to give. Am I missing something here, barring permission changes, that would allow help.search() to see user libraries? You mean help.start() here, don't you? help.search() does see everything in the libraries listed in .libPaths(). This would be ideal, but your suggestions seems to give us nice help functionality, and I think we can implement an R installation campus- wide without the full functionality of help.seach(). Thanks very much. As far as I know on Windows there's currently no way to get help.start() to go to a personalized page. The stuff that it refers to all lives in RHOME/doc/html, and many of the links in the files it works with assume that they are installed in the same hierarchy. I'm not sure if things are different on Unix, where we use soft links to make all the package directories appear to be under one parent. Duncan Murdoch Jarrett R Session: R version 2.7.0 (2008-04-22) ...snip... personalLib- .libPaths()[1]; personalLib [1] H:\\Desktop\\RFiles\\Library getOption(htmlhelp) [1] TRUE getOption(chmhelp) [1] FALSE install.packages(UsingR, + lib=personalLib, + depend=TRUE) trying URL 'http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/2.7/UsingR_0.1-10.zip' Content type 'application/zip' length 1433201 bytes (1.4 Mb) opened URL downloaded 1.4 Mb package 'UsingR' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Temp\RtmpQr4t3E\downloaded_packages updating HTML package descriptions Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/packages.html', reason 'Permission denied' ## PERMISSION PROBLEM library(UsingR) Warning message: package 'UsingR' was built under R version 2.7.2 help(UsingR) ## works! Help for ëUsingRí is shown in the browser help.start() ## restricted to site library updating HTML package listing updating HTML search index fixing URLs in non-standard libraries If nothing happens, you should open 'C:\PROGRA~1\R\R-27~1.0\doc\html \index.html' yourself Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/packages.html', reason 'Permission denied' ## SAME PERMISSION PROBLEM help.search(UsingR) ## works! ?UsingR ## works! Help for ëUsingRí is shown in the browser q() On Jan 15, 2009, at 11:42 AM, Duncan Murdoch wrote: On 1/15/2009 12:50 PM, Jarrett Barber wrote: Here's another help file question. Some context: University setting wherein R is installed for availability to students and course instructors across campus in various PC labs. Windows Vista environment. Goal: To maximize flexibility and functionality of installing add- on packages and associated help files among different users, while avoiding conflicts across different user libraries. (I could have my difficult-to-access sysadmin install _all_ libraries, but this seems wasteful, and would seem to present problems when my colleague or I want to update a package or install a newly available package but do not have time to wait a week or two for our sysadmin.) Problem (?): As a course instructor, I want flexibility to install add- on libraries to a user (not site) library, and I don't want to step on my colleagues' toes (or vice-versa) when it comes to add- on packages and associated help files for use in classes. I have no problem installing add-on packages to a user library, with one exception: I do not have permission to update the file $RHOME/doc/ html/packages.html, as evidenced by a permission error upon installing a package to a user library using update.packages (not to the default site library, which is also restricted). The installed add-on packages work fine, with the exception of some of the help functionality. I find myself having to use browseURL() to point to the html files in the package's file structure. I cannot expect the average student (or senior colleague) to tolerate this situation. A simpler way to get to the HTML man pages is to run options(htmlhelp=TRUE) and then the regular ?topic or help(topic) will find the HTML help pages in your local library. I'm thinking that I simply need to have my sysadmin give me and my colleagues (all users who want to install add-ons
Re: [R] user library help functionality (packages.html)
Whoops! Yes, my last help.search() should have been help.start(). Thanks again. -- Jarrett On Jan 15, 2009, at 1:27 PM, Duncan Murdoch wrote: On 1/15/2009 3:17 PM, Jarrett Barber wrote: This helps a lot. I have options(htmlhelp=TRUE) and options(chmhelp=FALSE) (else problems). Now, ?, help(), and help.search() seem to work well. But, help.start() appears restricted to packages in the site library. I see, in the Help/ FAQ on R for Windows/ Sections 4.3 and 4.4, that I cannot expect more from help.start() unless I have write permission to $RHOME/ library, which I do not (package does have a CONTENTS file however). I assume that, if I want my students to have this functionality, they, too, would need write access to $RHOME/ library, correct? But, this does not seem a wise thing to give. Am I missing something here, barring permission changes, that would allow help.search() to see user libraries? You mean help.start() here, don't you? help.search() does see everything in the libraries listed in .libPaths(). This would be ideal, but your suggestions seems to give us nice help functionality, and I think we can implement an R installation campus- wide without the full functionality of help.seach(). Thanks very much. As far as I know on Windows there's currently no way to get help.start() to go to a personalized page. The stuff that it refers to all lives in RHOME/doc/html, and many of the links in the files it works with assume that they are installed in the same hierarchy. I'm not sure if things are different on Unix, where we use soft links to make all the package directories appear to be under one parent. Duncan Murdoch Jarrett R Session: R version 2.7.0 (2008-04-22) ...snip... personalLib- .libPaths()[1]; personalLib [1] H:\\Desktop\\RFiles\\Library getOption(htmlhelp) [1] TRUE getOption(chmhelp) [1] FALSE install.packages(UsingR, + lib=personalLib, + depend=TRUE) trying URL 'http://streaming.stat.iastate.edu/CRAN/bin/windows/contrib/2.7/UsingR_0.1-10.zip' Content type 'application/zip' length 1433201 bytes (1.4 Mb) opened URL downloaded 1.4 Mb package 'UsingR' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Temp\RtmpQr4t3E\downloaded_packages updating HTML package descriptions Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/ packages.html', reason 'Permission denied' ## PERMISSION PROBLEM library(UsingR) Warning message: package 'UsingR' was built under R version 2.7.2 help(UsingR) ## works! Help for ëUsingRí is shown in the browser help.start() ## restricted to site library updating HTML package listing updating HTML search index fixing URLs in non-standard libraries If nothing happens, you should open 'C:\PROGRA~1\R\R-27~1.0\doc \html \index.html' yourself Warning message: In file.create(f.tg) : cannot create file 'C:\PROGRA~1\R\R-27~1.0/doc/html/ packages.html', reason 'Permission denied' ## SAME PERMISSION PROBLEM help.search(UsingR) ## works! ?UsingR ## works! Help for ëUsingRí is shown in the browser q() On Jan 15, 2009, at 11:42 AM, Duncan Murdoch wrote: On 1/15/2009 12:50 PM, Jarrett Barber wrote: Here's another help file question. Some context: University setting wherein R is installed for availability to students and course instructors across campus in various PC labs. Windows Vista environment. Goal: To maximize flexibility and functionality of installing add- on packages and associated help files among different users, while avoiding conflicts across different user libraries. (I could have my difficult-to-access sysadmin install _all_ libraries, but this seems wasteful, and would seem to present problems when my colleague or I want to update a package or install a newly available package but do not have time to wait a week or two for our sysadmin.) Problem (?): As a course instructor, I want flexibility to install add- on libraries to a user (not site) library, and I don't want to step on my colleagues' toes (or vice-versa) when it comes to add- on packages and associated help files for use in classes. I have no problem installing add-on packages to a user library, with one exception: I do not have permission to update the file $RHOME/doc/ html/packages.html, as evidenced by a permission error upon installing a package to a user library using update.packages (not to the default site library, which is also restricted). The installed add-on packages work fine, with the exception of some of the help functionality. I find myself having to use browseURL() to point to the html files in the package's file structure. I cannot expect the average student (or senior colleague) to tolerate this situation. A simpler way to get to the HTML man pages is to run options(htmlhelp=TRUE) and then the regular ?topic or help(topic) will find
Re: [R] number of Mondays
Or for those not allergic to reading help, see ?weekdays . Just how hard do you have to work to miss that? E.g. ??day works. On Thu, 15 Jan 2009, Peter Dalgaard wrote: Carlos Hernandez wrote: dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. i appreciate any hint you could give, This is where POSIXlt objects are useful: unlist(unclass(as.POSIXlt(ISOdate(1959,3,11 sec min hour mday mon year wday yday isdst 0 01211 259 369 0 Which means that I was born on a Wednesday (wday==3) in March (mon==2) (some of the fields count from 0 and others, like mday, from 1; presumably some UNIX vendor back in the Stone Age got their implementation turned into a standard...). This allows you to do stuff like: dd - seq(Sys.Date(),as.Date(2009-3-11),1) dd - as.POSIXlt(dd) with(dd, table(mon,wday)) wday mon 0 1 2 3 4 5 6 0 2 2 2 2 3 3 3 1 4 4 4 4 4 4 4 2 2 2 2 2 1 1 1 which I think is pretty much what you were looking for. thanks. Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Precision in R
On 1/15/2009 1:32 PM, David Winsemius wrote: On Jan 15, 2009, at 12:25 PM, Charles C. Berry wrote: This is what I get on windows XP: tcp1-tcp2 [,1] [,2] [,3] [1,] -2.861023e-06 -4.768372e-07 -4.768372e-07 [2,] -4.768372e-07 -3.814697e-06 2.622604e-06 [3,] -4.768372e-07 2.622604e-06 -5.960464e-08 but on my Gentoo Linux Intel Core 2 Duo: print(tcp1-tcp2,digits=20) [,1] [,2] [,3] [1,]000 [2,]000 [3,]000 So, it would seem to be that the floating point calcs on my Windows box, David's Mac, and whatever system you are using are not as accurate as they might be. For the record; on an Intel Mac (Leopard) with Urbanek's compilation of R 2.8.1 print(tcp1-tcp2,digits=20) [,1] [,2] [,3] [1,]000 [2,]000 [3,]000 I haven't debugged these, but I would guess this is because we have the Windows libraries set to use extended precision (64 bit mantissas) on intermediate results, whereas once things get stored to RAM, they are rounded to double precision (53 bit mantissas). This has the benefit of giving a more accurate answer in many circumstances, but the disadvantage that the final results are more dependent on the order of calculations. I think the other platforms never do the full extended precision calculations, so their results are consistent (but probably less accurate sometimes). 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] number of Mondays
Indeed, i overlooked weekdays. Thank you all for your replies! On Jan 15, 2009, at 21:23 , Prof Brian Ripley wrote: Or for those not allergic to reading help, see ?weekdays . Just how hard do you have to work to miss that? E.g. ??day works. On Thu, 15 Jan 2009, Peter Dalgaard wrote: Carlos Hernandez wrote: dear All, i'm trying to calculate the number of Mondays, Tuesdays, etc that each month within a date range has. I have time series data that spans 60 months and i want to calculate the number of Mondays, Tuesdays, Wed, etc of each month. (I want to control for weekly seasonality but my data is monthly). Is there an easy way to to this in R? or is there a package i could use? i did some quick search in the help files and R sites but could not find any answers. i appreciate any hint you could give, This is where POSIXlt objects are useful: unlist(unclass(as.POSIXlt(ISOdate(1959,3,11 sec min hour mday mon year wday yday isdst 0 01211 259 369 0 Which means that I was born on a Wednesday (wday==3) in March (mon==2) (some of the fields count from 0 and others, like mday, from 1; presumably some UNIX vendor back in the Stone Age got their implementation turned into a standard...). This allows you to do stuff like: dd - seq(Sys.Date(),as.Date(2009-3-11),1) dd - as.POSIXlt(dd) with(dd, table(mon,wday)) wday mon 0 1 2 3 4 5 6 0 2 2 2 2 3 3 3 1 4 4 4 4 4 4 4 2 2 2 2 2 1 1 1 which I think is pretty much what you were looking for. thanks. Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Precision in R
On Jan 15, 2009, at 12:25 PM, Charles C. Berry wrote: This is what I get on windows XP: tcp1-tcp2 [,1] [,2] [,3] [1,] -2.861023e-06 -4.768372e-07 -4.768372e-07 [2,] -4.768372e-07 -3.814697e-06 2.622604e-06 [3,] -4.768372e-07 2.622604e-06 -5.960464e-08 but on my Gentoo Linux Intel Core 2 Duo: print(tcp1-tcp2,digits=20) [,1] [,2] [,3] [1,]000 [2,]000 [3,]000 So, it would seem to be that the floating point calcs on my Windows box, David's Mac, and whatever system you are using are not as accurate as they might be. For the record; on an Intel Mac (Leopard) with Urbanek's compilation of R 2.8.1 print(tcp1-tcp2,digits=20) [,1] [,2] [,3] [1,]000 [2,]000 [3,]000 -- David Winsemius It is well known that rounding error can play havoc with crossproducts (particularly when the range of magnitudes of the numbers is wide as it is here), which is why matrix decompositions are generally used for solving least squares problems. The internal code for crossprod and tcrossprod is different, so the computations are likely done in a different order, which would account for the difference in tcp1 and tcp2 . Ultimately, array.c and blas.f SUBROUTINE DSYRK have the code if you want to dig into it. So to summarize: the difference is not due to R per se, but in the limited accuracy of floating point calcs on the system used. HTH, Chuck snip __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] logistic regression - exp(estimates)?
On 16/01/2009, at 1:50 AM, gregor rolshausen wrote:
hello.
I have a question on the interpretation of a logistic model.
is it helpful to exponentiate the coefficients (estimates)? I think I
once read something about that, but I cannot remember where.
if so, how would be the interpretation of the exp(estimate) ?
exp(beta_i) is the odds ratio for success when the i-th predictor
x_i is incremented by 1.
In particular if x_i is a 0-1 indicator variable then exp(beta_i) is
the odds ratio for comparing the odds of success when x_i = 1 with
the odds of success when x_i = 0.
E.g. if x_i = 0 for Male and x_i = 1 for Female, and exp(beta_i) = 2,
then the odds of success for Females are twice as great as the odds
of success for Males. I.e. Females are ``twice as likely'' to succeed
as Males, all other things being equal. (Which may or may not be a
Good
Thing, depending on what ``success'' really means. :-) )
would there be a change of the interpretation of the ANOVA table
(or is
the ANOVA table not really helpful at all?).
ANOVA tables are ***so*** 20th century!
cheers,
Rolf Turner
##
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Re: [R] Warning on assignment.
It's the other way around. You are trying to replace 10 elements (x[i]) with 20 elements (y). R makes a best guess as to how you want to do that. 10 is not a multiple of 20. If you were trying to replace 20 elements with 10, then R would recycle them because 20 _is_ a multiple of 10. The safest course is always to make sure you are replacing with equal numbers. Sarah On Thu, Jan 15, 2009 at 1:20 PM, rkevinbur...@charter.net wrote: This was just an illustration. It is the warning message that I don't understand. The warning says number of items to replace is not a multiple of replacement length. The way I look at it 10 is a multiple of 20. Kevin Sarah Goslee sarah.gos...@gmail.com wrote: The lengths are different, particularly the length of subsetted x[i] x - 1:20 i - x %% 2 0 y - rep(1,20) length(x) [1] 20 length(i) [1] 20 length(x[i]) [1] 10 length(y) [1] 20 You happened to be lucky and got what you wanted, but a more reliable approach is: x[i] - y[i] Sarah On Thu, Jan 15, 2009 at 1:08 PM, rkevinbur...@charter.net wrote: I have a question on whether a warning message is valid or if I just don't understand the process. Let me illustrate via some R code: x - 1:20 i - x %% 2 0 y - rep(1,20) x[i] - y Warning message: In x[i] - y : number of items to replace is not a multiple of replacement length But it still does what I would expect for the assignment: x [1] 1 2 1 4 1 6 1 8 1 10 1 12 1 14 1 16 1 18 1 20 What don't I understand? Thank you. Kevin -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Partial function application in R
Hello,
in a desperate desire of using partial function application in R I fried out
the following piece of code:
bind - function( f, ... ) {
args - list(...)
function(...) f( ..., unlist(args) )
}
Its purpose, if not clear, is to return a function with part of its
arguments bound to specific values, so that I can for example create and use
functions like this:
q1 - bind( quantile, 0.25 )
lapply( some_list, q1 )
It's been a lot of work and unfortunately is not perfect. My bind applies
arguments only using positional rule. What I dream of is a function bind2
that would apply keyword arguments, like:
plot_lines - bind2( plot, type=l )
which would return
function(...) plot( type=l, ... )
How to do this in R?
Regards,
nosek
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] user library help functionality (packages.html)
On 1/15/2009 12:50 PM, Jarrett Barber wrote: Here's another help file question. Some context: University setting wherein R is installed for availability to students and course instructors across campus in various PC labs. Windows Vista environment. Goal: To maximize flexibility and functionality of installing add-on packages and associated help files among different users, while avoiding conflicts across different user libraries. (I could have my difficult-to-access sysadmin install _all_ libraries, but this seems wasteful, and would seem to present problems when my colleague or I want to update a package or install a newly available package but do not have time to wait a week or two for our sysadmin.) Problem (?): As a course instructor, I want flexibility to install add- on libraries to a user (not site) library, and I don't want to step on my colleagues' toes (or vice-versa) when it comes to add-on packages and associated help files for use in classes. I have no problem installing add-on packages to a user library, with one exception: I do not have permission to update the file $RHOME/doc/html/packages.html, as evidenced by a permission error upon installing a package to a user library using update.packages (not to the default site library, which is also restricted). The installed add-on packages work fine, with the exception of some of the help functionality. I find myself having to use browseURL() to point to the html files in the package's file structure. I cannot expect the average student (or senior colleague) to tolerate this situation. A simpler way to get to the HTML man pages is to run options(htmlhelp=TRUE) and then the regular ?topic or help(topic) will find the HTML help pages in your local library. I'm thinking that I simply need to have my sysadmin give me and my colleagues (all users who want to install add-ons packages?) permission to read/write packages.html, and the problem will go away. But, before I ask my sysadmin to give permission, I want to know, does this create another problem? For example, my colleague creates a library for STAT3000BC, which, I assume, will modify packages.html (assuming my sysadmin gives permission), then I create a library for STAT2010, which also modifies packages.html. See my concern? Does R somehow allow harmonious help functionality in such cases (by, for example, maintaining separate copies of packages.html for different users)? You will likely have strange problems if you do that. The doc/html/packages.html file is intended to talk about what is available to everyone; I suspect in your scenario, it would be updated to show your packages (but not your colleague's) whenever you added one, and then updated to show your colleague's packages (but not yours) when he added one, and would almost never be right for both of you. The good news is that it looks as though sometime this year we will make quite substantial changes to the way the help system is stored, so a lot of things like packages.html could be generated on the fly. 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] Partial function application in R
How is function() not the correct approach?
plot_lines - function(x, ...) plot(x, type=l, ...)
plot_lines(1:10, xlim = c(1,5))
plot_lines(1:10, 11:20, xlim = c(1,5))
Still seems to get the unnamed optional y argument to the plotting
machinery.
--
David Winsemius
On Jan 15, 2009, at 4:25 PM, nosek wrote:
Hello,
in a desperate desire of using partial function application in R I
fried out
the following piece of code:
bind - function( f, ... ) {
args - list(...)
function(...) f( ..., unlist(args) )
}
Its purpose, if not clear, is to return a function with part of its
arguments bound to specific values, so that I can for example create
and use
functions like this:
q1 - bind( quantile, 0.25 )
lapply( some_list, q1 )
It's been a lot of work and unfortunately is not perfect. My bind
applies
arguments only using positional rule. What I dream of is a function
bind2
that would apply keyword arguments, like:
plot_lines - bind2( plot, type=l )
which would return
function(...) plot( type=l, ... )
How to do this in R?
Regards,
nosek
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Re: [R] Partial function application in R
Have a look at the setDefaults package. It will set the default
arguments of a function to whatever you specify so that
if you omit them then those are the values you get for them.
On Thu, Jan 15, 2009 at 4:25 PM, nosek nospa...@interia.pl wrote:
Hello,
in a desperate desire of using partial function application in R I fried out
the following piece of code:
bind - function( f, ... ) {
args - list(...)
function(...) f( ..., unlist(args) )
}
Its purpose, if not clear, is to return a function with part of its
arguments bound to specific values, so that I can for example create and use
functions like this:
q1 - bind( quantile, 0.25 )
lapply( some_list, q1 )
It's been a lot of work and unfortunately is not perfect. My bind applies
arguments only using positional rule. What I dream of is a function bind2
that would apply keyword arguments, like:
plot_lines - bind2( plot, type=l )
which would return
function(...) plot( type=l, ... )
How to do this in R?
Regards,
nosek
--
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__
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Re: [R] Partial function application in R
Well,
it looks like it's a perfectly correct approach to bind functions writing
their wrappers by hand.
But I don't want to write them by hand every time I need them.
Being lambda expression, function() is most general, but there must be some
kind of shorter way for such a common task as partial application.
David Winsemius wrote:
How is function() not the correct approach?
plot_lines - function(x, ...) plot(x, type=l, ...)
plot_lines(1:10, xlim = c(1,5))
plot_lines(1:10, 11:20, xlim = c(1,5))
Still seems to get the unnamed optional y argument to the plotting
machinery.
--
David Winsemius
On Jan 15, 2009, at 4:25 PM, nosek wrote:
Hello,
in a desperate desire of using partial function application in R I
fried out
the following piece of code:
bind - function( f, ... ) {
args - list(...)
function(...) f( ..., unlist(args) )
}
Its purpose, if not clear, is to return a function with part of its
arguments bound to specific values, so that I can for example create
and use
functions like this:
q1 - bind( quantile, 0.25 )
lapply( some_list, q1 )
It's been a lot of work and unfortunately is not perfect. My bind
applies
arguments only using positional rule. What I dream of is a function
bind2
that would apply keyword arguments, like:
plot_lines - bind2( plot, type=l )
which would return
function(...) plot( type=l, ... )
How to do this in R?
Regards,
nosek
--
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and provide commented, minimal, self-contained, reproducible code.
__
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[R] Security Data extraction
Hi, Today I came across the R application and I will admit I am not a Statistician. However, I think this application will be useful for me at work. I am a Network/System Security Engineer trying to make sense of the huge security data I collect. I am trying to visualize the traffic on our network. The data in the packet header (captured by tcpdump) has all the information about the systems on the network. There are lots of visual tools that can present the data in a meaningful way. Each tool seems to have a different data format while most tools seem to understand CSV format? How do I select the subset of the network data or syslog data and create a CSV file? How else can the R application help me present the security data in a meaningful way to the management? Please excuse my ignorance. Thank you. Subba Rao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Partial function application in R
One other idea. The proto package also does currying. If f a method
(i.e. an R function
that takes an object as arg1 then p$f, i.e. the $.proto function,
returns function(...) f(p, ...).
Looking at the code for setDefaults as in my prior response and/or
proto should give
you some ideas.
On Thu, Jan 15, 2009 at 6:43 PM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
Have a look at the setDefaults package. It will set the default
arguments of a function to whatever you specify so that
if you omit them then those are the values you get for them.
On Thu, Jan 15, 2009 at 4:25 PM, nosek nospa...@interia.pl wrote:
Hello,
in a desperate desire of using partial function application in R I fried out
the following piece of code:
bind - function( f, ... ) {
args - list(...)
function(...) f( ..., unlist(args) )
}
Its purpose, if not clear, is to return a function with part of its
arguments bound to specific values, so that I can for example create and use
functions like this:
q1 - bind( quantile, 0.25 )
lapply( some_list, q1 )
It's been a lot of work and unfortunately is not perfect. My bind applies
arguments only using positional rule. What I dream of is a function bind2
that would apply keyword arguments, like:
plot_lines - bind2( plot, type=l )
which would return
function(...) plot( type=l, ... )
How to do this in R?
Regards,
nosek
--
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http://www.nabble.com/Partial-function-application-in-R-tp21487269p21487269.html
Sent from the R help mailing list archive at Nabble.com.
__
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and provide commented, minimal, self-contained, reproducible code.
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[R] PDF slided (beamer or prosper) to an editable PPT
Hello, I am getting requests to place our PDF slides (output from beamer) into Microsoft Powerpoint formats (.ppt). What's the best practice or any recommended software packages (any success with open or commercial) that we can use to convert PDF slides into an EDITABLE powerpoint deck? Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] XYplot in Lattice Package
Dear R-Users
I have 2 questions to do with XYplot.
1)
I am trying to use the XYplot function to generate multiple line graphs with
the legend outside the plot.
I am using the following loop for each graph:
library(lattice)
for (i in x.sp){
xyplot(Catch~Year, df, groups = Stock, type=a,auto.key =
list(space = top, points = FALSE, lines = TRUE,columns = 4))
}
When I run the script I don't get any output graphs, however if I change
'XYplot' to 'plot', or generate the plots manually using XYplot, It seems to
work. Is there a bug of some sort or is it me?
2)
How do I remove the top and right axis from a plot? If I add 'axis(side
= c(bottom, left)' to the xyplot call it comes up with the message:
Error in axis(side = c(bottom, left)) :
plot.new has not been called yet
Any help is much appreciated :)
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Security Data extraction
Subba Rao wrote: Hi, Today I came across the R application and I will admit I am not a Statistician. However, I think this application will be useful for me at work. I am a Network/System Security Engineer trying to make sense of the huge security data I collect. I am trying to visualize the traffic on our network. The data in the packet header (captured by tcpdump) has all the information about the systems on the network. There are lots of visual tools that can present the data in a meaningful way. Each tool seems to have a different data format while most tools seem to understand CSV format? How do I select the subset of the network data or syslog data and create a CSV file? Sniff is a good tool: http://www.thedumbterminal.co.uk/software/sniff.shtml How else can the R application help me present the security data in a meaningful way to the management? Depends on what you want to present Please excuse my ignorance. Thank you. Subba Rao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Project Robust Linier Regresssion
Hello, I'm EDWIN, I create (make) GUI, with call many function
but I don't know why when I call function I can't. if without function, Yes
I can..
can you help me ? can you make this, become true with full code?
Can you help me to
create data.entry with interface
LM - BETA1.HAT - BETA2.HAT SD.BETA1.HAT HAT SD.BETA2.HAT RLM - BETA1.HAT
- BETA2.HAT SD.BETA1.HAT HAT SD.BETA2.HAT
2
10 value
100
Thx
Edwwin
library(boot)
library(bootstrap)
library(MASS) # MASS berisi tools untuk fitting robust regression
library(tcltk)
library(stats)
library(rpanel)
#
ambil-function() {
data - read.csv(F:/data.csv)
plot-plot(data[,2],data[,3], xlab=Euro,ylab=Rupiah,main=Plot Euro, dan
Rupiah)
}
data - read.csv(F:/data.csv)
x - data[,2]
y - data[,3]
#
function seluruhlinier(){
plot(x, y)
fred - lm(y ~ x)
curve(predict(fred, data.frame(x = x)), add = TRUE)
beta1.hat - coefficients(fred)[1]
beta2.hat - coefficients(fred)[2]
n - length(x)
beta1.star - double(nboot)
beta2.star - double(nboot)
for (i in 1:nboot) {
k.star - sample(n, replace = TRUE)
x.star - x[k.star]
y.star - y[k.star]
sally - lm(y.star ~ x.star )
curve(predict(sally, data.frame(x.star = x)),
add = TRUE, col = plum)
beta1.star[i] - coefficients(sally)[1]
beta2.star[i] - coefficients(sally)[2]
}
points(x, y, pch = 16)
curve(predict(fred, data.frame(x = x)),
add = TRUE, lwd = 2)
data.frame (beta1.hat,sd(beta1.star),beta2.hat,sd(beta2.star),beta2.hat /
sd(beta2.star))
}
#
function seluruhrobust(){
plot(x, y)
fred - rlm(y ~ x)
curve(predict(fred, data.frame(x = x)), add = TRUE)
beta1.hat - coefficients(fred)[1]
beta2.hat - coefficients(fred)[2]
n - length(x)
beta1.star - double(nboot)
beta2.star - double(nboot)
for (i in 1:nboot) {
k.star - sample(n, replace = TRUE)
x.star - x[k.star]
y.star - y[k.star]
sally - rlm(y.star ~ x.star )
curve(predict(sally, data.frame(x.star = x)),
add = TRUE, col = plum)
beta1.star[i] - coefficients(sally)[1]
beta2.star[i] - coefficients(sally)[2]
}
points(x, y, pch = 16)
curve(predict(fred, data.frame(x = x)),
add = TRUE, lwd = 2)
data.frame (beta1.hat,sd(beta1.star),beta2.hat,sd(beta2.star),beta2.hat /
sd(beta2.star))
}
#
function linier2(){
nboot - 2
seluruhlinier()
}
#
function linier30(){
nboot - 30
seluruhlinier()
}
###
function linier100(){
nboot - 100
seluruhlinier()
}
function robust2(){
nboot - 2
seluruhrobust()
}
#
function linier30(){
nboot - 30
seluruhrobust()
}
###
function linier100(){
nboot - 100
seluruhrobust()
}
###
hitungan-function()
{
#data.entry(y_hat_linier,y_hat_robust,Residual_linier,Residual_robust)
}
kesimpulan-function()
{
m4 - tktoplevel()
tkwm.geometry(m4, +0+0)
tkpack(fr - tkframe(m4), side = top)
tkwm.title(m4, Kesimpulan)
tkpack(tklabel(fr, text = Semakin besar bootstrap, semakin besar nilai beta1*,
dan beta2*, Beta1 topi dan Beta topi2 akan tetap sama jika diulang terus
menerus, width = 120), side = left)
tkpack(fr - tkframe(m4), side = top)
tkpack(tkbutton(m4, text = OK, command = function() tkdestroy(m4)),
side = right)
}
linier-function ()
{
m2 - tktoplevel()
tkwm.geometry(m2, +0+0)
tkpack(fr - tkframe(m2), side = top)
tkwm.title(m2, Regresi Linier)
tkpack(tklabel(fr, text = OUTPUT, width = 50), side = left)
tkpack(tkbutton(m2, text = Regresi Linier B = 2,command=linier2), side =
left)
tkpack(tkbutton(m2, text = Regresi Linier B = 30,command=linier30), side =
left)
tkpack(tkbutton(m2, text = Regresi Linier B = 100,command=linier100), side =
left)
tkpack(fr - tkframe(m2), side = top)
tkpack(tkbutton(m2, text = Kembali, command = function() tkdestroy(m2)),
side = right)
}
robust-function()
{
m3 - tktoplevel()
tkwm.geometry(m3, +0+0)
tkpack(fr - tkframe(m3), side = top)
tkwm.title(m3, Regresi Robust)
tkpack(tklabel(fr, text = OUTPUT, width = 50), side = left)
tkpack(tkbutton(m3, text = Regresi robust B = 2,command=robust2), side =
left)
tkpack(tkbutton(m3, text = Regresi robust B =
Re: [R] XYplot in Lattice Package
On Jan 15, 2009, at 9:27 PM, jimdare wrote:
Dear R-Users
I have 2 questions to do with XYplot.
1)
I am trying to use the XYplot function to generate multiple line
graphs with
the legend outside the plot.
I am using the following loop for each graph:
library(lattice)
for (i in x.sp){
xyplot(Catch~Year, df, groups = Stock, type=a,auto.key =
list(space = top, points = FALSE, lines = TRUE,columns = 4))
}
From the help on package lattice:
Note
High level Lattice functions (like xyplot) are different from
conventional R graphics functions because they don't actually draw
anything. Instead, they return an object of class trellis which has
to be then printed or plotted to create the actual plot. This is
normally done automatically, but not when the high level functions are
called inside another function (most often source) or other contexts
where automatic printing is suppressed (e.g. for or while loops). In
such situations, an explicit call to print or plot is required.
Or the FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
When I run the script I don't get any output graphs, however if I
change
'XYplot' to 'plot', or generate the plots manually using XYplot, It
seems to
work. Is there a bug of some sort or is it me?
It's you.
2)
How do I remove the top and right axis from a plot? If I add
'axis(side
= c(bottom, left)' to the xyplot call it comes up with the
message:
Error in axis(side = c(bottom, left)) :
plot.new has not been called yet
see at the top of the axis help page:
axis {graphics} so axis is not part of lattice
Had you continued reading the next sentence in the lattice intro help
page, you would have seen:
Lattice plots are highly customizable via user-modifiable settings.
However, these are completely unrelated to base graphics settings; in
particular, changing par() settings usually have no effect on lattice
plots.
Try:
http://stat.ethz.ch/R-manual/R-patched/library/lattice/html/axis.default.html
And chapter 8 of:
http://lmdvr.r-forge.r-project.org/figures/figures.html
Best of luck and buy Sarkar's book.
David Winsemius
Any help is much appreciated :)
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[R] New Statistical Learning and Data Mining Course
Short course: Statistical Learning and Data Mining III: Ten Hot Ideas for Learning from Data Trevor Hastie and Robert Tibshirani, Stanford University Sheraton Hotel Palo Alto, CA March 16-17, 2009 This two-day course gives a detailed overview of statistical models for data mining, inference and prediction. With the rapid developments in internet technology, genomics, financial risk modeling, and other high-tech industries, we rely increasingly more on data analysis and statistical models to exploit the vast amounts of data at our fingertips. In this course we emphasize the tools useful for tackling modern-day data analysis problems. From the vast array of tools available, we have selected what we consider are the most relevant and exciting. Our top-ten list of topics are: * Regression and Logistic Regression (two golden oldies), * Lasso and Related Methods, * Support Vector and Kernel Methodology, * Principal Components (SVD) and Variations: sparse SVD, supervised PCA, Multidimensional Scaling and Isomap, Nonnegative Matrix Factorization, and Local Linear Embedding, * Boosting, Random Forests and Ensemble Methods, * Rule based methods (PRIM), * Graphical Models, * Cross-Validation, * Bootstrap, * Feature Selection, False Discovery Rates and Permutation Tests. Our earlier courses are not a prerequisite for this new course. Although there is some overlap with past courses, our new course contains many topics not covered by us before. The material is based on recent papers by the authors and other researchers, as well as the new second edition of our best selling book: Statistical Learning: data mining, inference and prediction Hastie, Tibshirani Friedman, Springer-Verlag, 2008 http://www-stat.stanford.edu/ElemStatLearn/ A copy of this book will be given to all attendees. ### The lectures will consist of video-projected presentations and discussion. Go to the site http://www-stat.stanford.edu/~hastie/sldm.html for more information and online registration. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Partial function application in R
czesc,
looks like you want some sort of currying, or maybe partial currying,
right? anyway, here's a quick guess at how you can modify your bind,
and it seems to work, as far as i get your intentions, with the plot
example you gave:
bind = function(f, ...) {
args = list(...)
function(...) do.call(f, c(list(...), args)) }
plotlines = bind(plot, type='l')
plotlines(1:10, runif(10))
plotredlines = bind(plotlines, col=red)
plotredlines(runif(10))
# careful about not overriding a named argument
plotredpoints = bind(plotredlines, type=p)
plotredpoints(runif(10))
you may want to figure out how to get rid of the smart y-axis title.
is this what you wanted?
pzdr,
vQ
nosek wrote:
Well,
it looks like it's a perfectly correct approach to bind functions writing
their wrappers by hand.
But I don't want to write them by hand every time I need them.
Being lambda expression, function() is most general, but there must be some
kind of shorter way for such a common task as partial application.
David Winsemius wrote:
How is function() not the correct approach?
plot_lines - function(x, ...) plot(x, type=l, ...)
plot_lines(1:10, xlim = c(1,5))
plot_lines(1:10, 11:20, xlim = c(1,5))
Still seems to get the unnamed optional y argument to the plotting
machinery.
--
David Winsemius
On Jan 15, 2009, at 4:25 PM, nosek wrote:
Hello,
in a desperate desire of using partial function application in R I
fried out
the following piece of code:
bind - function( f, ... ) {
args - list(...)
function(...) f( ..., unlist(args) )
}
Its purpose, if not clear, is to return a function with part of its
arguments bound to specific values, so that I can for example create
and use
functions like this:
q1 - bind( quantile, 0.25 )
lapply( some_list, q1 )
It's been a lot of work and unfortunately is not perfect. My bind
applies
arguments only using positional rule. What I dream of is a function
bind2
that would apply keyword arguments, like:
plot_lines - bind2( plot, type=l )
which would return
function(...) plot( type=l, ... )
How to do this in R?
Regards,
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