Re: [R] Bug in levels() function?
Hello all, Thank you for all the responses. It is clear to me now. However, if the drop possibility was also mentioned in the help text (in R, so ?levels) I wouldn't have asked this question at all! Regards, Philip From: Thomas Lumley [mailto:[EMAIL PROTECTED] Sent: Mon 28-1-2008 20:03 To: Groot, Philip de Cc: [EMAIL PROTECTED] Subject: Re: [R] Bug in levels() function? This is not a bug; it is deliberately designed this way. There are circumstances when you want to drop levels on subsetting and other circumstances where you don't, so the default behaviour can't make everyone happy. However, there is an option to get the behaviour you want x-as.factor(LETTERS) levels(x[1]) [1] A B C D E F G H I J K L M N O P Q R S [20] T U V W X Y Z levels(x[1,drop=TRUE]) [1] A On Mon, 28 Jan 2008, Groot, Philip de wrote: Hello all, I am not sure whether it actually is a bug, but it is not the behaviour I would expect. Please consider this: Sibships [1] Patient_2400 Patient_2400 Patient_345 Patient_345 Patient_8901 [6] Patient_8901 Patient_4008 Patient_4008 Patient_7991 Patient_7991 [11] Patient_8353 Patient_8353 Patient_1212 Patient_1212 Patient_2168 [16] Patient_2168 Patient_2760 Patient_2760 Patient_4726 Patient_4726 [21] Patient_6699 Patient_6699 Patient_7641 Patient_7641 Patient_8263 [26] Patient_8263 Patient_1389 Patient_1389 Patient_1618 Patient_1618 [31] Patient_2410 Patient_2410 Patient_2612 Patient_2612 Patient_2721 [36] Patient_2721 Patient_5053 Patient_5053 Patient_8458 Patient_8458 [41] Patient_211 Patient_211 Patient_9004 Patient_9004 Patient_3423 [46] Patient_3423 Patient_7413 Patient_7413 Patient_7815 Patient_7815 [51] Patient_9232 Patient_9232 Patient_2267 Patient_2267 Patient_468 [56] Patient_468 28 Levels: Patient_1212 Patient_1389 Patient_1618 Patient_211 ... Patient_9232 Comparison_Indices [1] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE Sibships[Comparison_Indices] [1] Patient_2400 Patient_2400 Patient_345 Patient_345 Patient_8901 [6] Patient_8901 Patient_7413 Patient_7413 28 Levels: Patient_1212 Patient_1389 Patient_1618 Patient_211 ... Patient_9232 The problem with this last command is that I would expect 4 levels (because only 8 Comparison_Indices are true, which is equal to 4 sibships. So: levels() does not take array indices into account or stated otherwise: if you use a subset in an array (vector), the levels() are not properly updated (to my opinion). What I additionally found is the following: small_test - factor(x=c(a, b, c)) typeof(small_test) [1] integer The same happens to the Sibships that I defined as a factor? Why is it of type integer? This is the version() output: version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 6.1 year 2007 month 11 day26 svn rev43537 language R version.string R version 2.6.1 (2007-11-26) So: should I submit a Bug report? Regards, Dr. Philip de Groot Wageningen University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED]University of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] matrix creation -- answer: data.matrix()
GS == Gavin Simpson [EMAIL PROTECTED] on Tue, 29 Jan 2008 00:09:05 + writes: GS hits=-2.6 tests=BAYES_00 GS X-USF-Spam-Flag: NO GS On Mon, 2008-01-28 at 12:17 -0700, Michelle DePrenger-Levin wrote: I was asked for the following information and hope it might help those who could answer my question... GS That looks fine to me Michelle. GS You will have problems with as.matrix on this though as a matrix in R GS has to contain *all* elements of the same kind, text or numeric. As $X GS is a factor, the matrix ends up as a character matrix, as this example GS shows: GS my.dat - data.frame(X = gl(4,5), Vegetative = runif(20), Dormant = GS runif(20)) GS str(my.dat) GS as.matrix(my.dat) [...] GS You could convert the factor column to its numeric representation and GS then you can produce a matrix that is numeric GS my.dat$X - as.numeric(my.dat$X) GS str(my.dat) GS as.matrix(my.dat) That's exactly what the --- seemlingy much underused --- function data.matrix() is for ! my.dat - data.frame(X = gl(4,5), Veg = runif(20), Dorm = runif(20)) my.mat - data.matrix(my.dat) str(my.mat) # all numeric In short: Use data.matrix(d), not as.matrix(d) if d potentially is a data frame !! Regards, Martin GS *But* you should read the help for popbio to see what you are required GS to provide as what I show is only a workaround for the matrix issue - I GS have no idea what a projection matrix is in the sense of popbio or how GS to use the functions in that package. GS HTH GS G To import the table I used: AsMi05test=read.csv(C:/AsMi_Site05_1998.csv) str(AsMi05test) `data.frame': 12 obs. of 8 variables: $ X : Factor w/ 6 levels Dead,Dormant,..: 5 6 3 4 2 1 5 6 3 4 ... $ Vegetative : num 0.25 0.50 0.17 0.08 0.00 ... $ Vegetative.with.Herbivory : num 0.13 0.5 0.33 0.67 0 0 0.41 0.5 0 0 ... $ Reproductive : num 0 0 0 0 0 0 0 0 0 0 ... $ Reproductive.with.Herbivory: num 0 0 0 0 0 ... $ Dormant: num 0.08 0 0.33 0.08 1 0 0.06 0 0 0 ... $ Dead : num 0.42 0.00 0.33 0.17 0.00 ... $ End.Date : int 1998 1998 1998 1998 1998 1998 1999 1999 1999 1999 ... From: Michelle DePrenger-Levin Sent: Monday, January 28, 2008 11:35 AM To: 'r-help@r-project.org' Subject: matrix creation Hello, I am trying to create multiple matrices (to run a PVA) but can't import all of them from a .csv without the numbers treated as labels and not factors. I can enter the matrix slowly: Site05_96 - matrix(c(0.07,0,0.03,0.00,NA,0.00, 0.09,0.16667,0.31,0.42,NA,0.00, 0.00,0,0.00,0.00,NA,0.00, 0.00,0,0.00,0.00,NA,0.00, 0.26,0.16667,0.19,0.00,NA,0.00, 0.58,0.7,0.47,0.58,0,0.00), nrow = 6, ncol = 6, dimnames = list(c(Vegetative, Vegetative with herbivory, Reproductive, Reproductive with herbivory, Dormant, Dead), c(Vegetative, Vegetative with herbivory, Reproductive, Reproductive with herbivory, Dormant, Dead))) I would like to list all matrices (for all 12 years and all 4 sites) in one Excel sheet (.csv) and then read each matrix as chucks of 6 rows. However, when I try this I either get all the values (the %) in quotes (not as factors) and if I try to force them with as.factor, it no longer seems to be a matrix. AsMi0598test2 - as.matrix(AsMi05test[1:6,1:6]) X Vegetative Vegetative.with.Herbivory Reproductive Reproductive.with.Herbivory Dormant 1 Vegetative 0.25 0.130 0 0.08 2 Vegetative with Herbivory 0.50 0.500 0 0.00 3 Reproductive0.17 0.330 0 0.33 4 Reproductive with Herbivory 0.08 0.670 0 0.08 5 Dormant 0.00 0.000 0 1.00 6 Dead0.00 0.000 0 0.00 When I add AsMi0598test2 - as.factor(as.matrix(AsMi05test[1:6,1:6])) I get this: [1] Vegetative Vegetative with Herbivory Reproductive Reproductive with Herbivory
Re: [R] Expert systems
Hans W. Borchers wrote: Ralf Finne Ralf.Finne at syh.fi writes: Hi R-users Is there any functions in R that can implement expert systems? The aim of an expert system is to produce a probable diagnosis for a patient with certain symptoms. In the classical expert system a mumber of experts are asked to make statements on the probabilities for different diseases when a combination of systems would appear. One typical expert system uses Fuzzy Logic to suggest the diagnosis. In more modern systems one tends to make the system self learning to improve the system. What you are describing here is just one of several ways to realize an expert systems. And the question is also what kind of technique you would like to implement such a system in, e.g., rule-based, fuzzy sets, (Bayesian) networks, constraints, case bases, etc. The closest R may come to expert system techniques is through Weka in the RWeka package (I should also mention 'deal' for graphical networks). R as statistical software focuses more on the learning aspect, not on explicitly representing 'knowledge' in whatever form. There are commercial and free expert system shells one could utilize. CLIPS http://clipsrules.sourceforge.net/ is a bit old-fashioned, but could easily be integrated with R; JESS http://www.jessrules.com/ being another one. Also Prolog systems (especially if they include CSP solvers) such as BProlog or SWI Prolog are free and could be combined (at least through file or pipe transfer) with R to generate complete applications. Regards, Hans Werner Borchers You might also want to look at gRain which Søren Højsgaard announced yesterday. Hoping for comments Ralf Finne Swenska yrkeshögskolan Vasa Finland __ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. -- 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 ~~ - ([EMAIL PROTECTED]) 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.
[R] Expert systems
Hi R-users Is there any functions in R that can implement expert systems? The aim of an expert system is to produce a probable diagnosis for a patient with certain symptoms. In the classical expert system a mumber of experts are asked to make statements on the probabilities for different diseases when a combination of systems would appear. One typical expert system uses Fuzzy Logic to suggest the diagnosis. In more modern systems one tends to make the system self learning to improve the system. Hoping for comments Ralf Finne Swenska yrkeshögskolan Vasa Finland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] package.skeleton from within function: objects not found
Hi all,
sorry to bother you all once more, but I still haven't solved this
problem. Is there anyone who knows how to pass an environment as an
argument to package.skeleton from within function, so that this
environment can be saved into a newly build source package? See
example script below.
Many thanks in advance,
Kindest regards,
tine
On Jan 28, 2008 12:38 PM, Tineke Casneuf [EMAIL PROTECTED] wrote:
Professor Ripley,
do you have an idea why it works for me to save different types of
objects, but not for the environment object I construct in the
function:
### Example of a function that works without error:
fun2 - function(myname){
f - function(x,y) x+y
g - function(x,y) x-y
d - data.frame(a=1, b=2)
e - hello
env - sys.frames()[[sys.nframe()]]
package.skeleton(list=c(f,g,d,e), name=myname,env=env)
}
fun2(mypkg)
fun3 - function(myname){
myenv - new.env()
apply(x, 1, function(row){
assign(row[1], row[2], envir=myenv)
})
f - function(x,y) x+y
g - function(x,y) x-y
d - data.frame(a=1, b=2)
e - hello
env - sys.frames()[[sys.nframe()]]
package.skeleton(list=c(f,g,d,e,myenv), name=myname,env=env)
}
fun3(mypkg)
###
For the second example, 'fun3', I get this error message:
Error in save(list = item, file = file.path(data_dir, sprintf(%s.rda, :
object 'myenv' not found
Thanks in advance!
On Jan 28, 2008 9:30 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote:
You need to set the 'environment' argument (the help file is incomplete).
e.g.
env - sys.frames()[[sys.nframe()]]
package.skeleton(name = pkgName, list=c(f,e, myenv), env=env)
On Mon, 28 Jan 2008, Tineke Casneuf wrote:
Hi all,
I ran into a strange error: I am trying to create a package skeleton for a
new source package from within a function. Objects that are created in
this
function are to be included in my package, but for some reason, I get an
error message saying that these objects cannot be found.
Here is the code:
##
myfun - function(pkgName,x){
myenv - new.env()
apply(x, 1, function(row){
assign(row[1], row[2], envir=myenv)
})
f - function(x,y) x+y
e - rnorm(1000)
# browser()
package.skeleton(name = pkgName, list=c(f,e, myenv))
return(myenv)
}
x - data.frame(keys = LETTERS[1:5], values = 1:5)
myfun(test, x)
##
And my sessionInfo:
sessionInfo()
R version 2.6.1 (2007-11-26)
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
I did not find anything referring to this problem in the help page, on
the R
mailing list or wiki. Has anyone noticed this or can someone explain to me
why my objects cannot be found?
Many thanks in advance,
best wishes,
Tine
[[alternative HTML version deleted]]
__
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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.
--
Brian D. Ripley, [EMAIL PROTECTED]
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
__
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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] Expert systems
Ralf Finne Ralf.Finne at syh.fi writes: Hi R-users Is there any functions in R that can implement expert systems? The aim of an expert system is to produce a probable diagnosis for a patient with certain symptoms. In the classical expert system a mumber of experts are asked to make statements on the probabilities for different diseases when a combination of systems would appear. One typical expert system uses Fuzzy Logic to suggest the diagnosis. In more modern systems one tends to make the system self learning to improve the system. What you are describing here is just one of several ways to realize an expert systems. And the question is also what kind of technique you would like to implement such a system in, e.g., rule-based, fuzzy sets, (Bayesian) networks, constraints, case bases, etc. The closest R may come to expert system techniques is through Weka in the RWeka package (I should also mention 'deal' for graphical networks). R as statistical software focuses more on the learning aspect, not on explicitly representing 'knowledge' in whatever form. There are commercial and free expert system shells one could utilize. CLIPS http://clipsrules.sourceforge.net/ is a bit old-fashioned, but could easily be integrated with R; JESS http://www.jessrules.com/ being another one. Also Prolog systems (especially if they include CSP solvers) such as BProlog or SWI Prolog are free and could be combined (at least through file or pipe transfer) with R to generate complete applications. Regards, Hans Werner Borchers Hoping for comments Ralf Finne Swenska yrkeshögskolan Vasa Finland __ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] remove similar values
Hi, Not sure I understand the question, but maybe you need ?unique or ?duplicated Cheers, Romain mohamed nur anisah wrote: hello!! say that i have the values of x1 and x2. my x1 has longer length than x2. how am i going to remove the similar values of x1 and x2. Any suggestion?? Thanks in advance!! Cheers, Anisah e f [1,] 17358865 17906353 [2,] 17966995 21295547 [3,] 21306539 27880531 [4,] 27880531 34118702 [5,] 34166504 35395488 [6,] 36111044 36132622 [7,] 36266288 37916920 [8,] 36854306 43786190 [9,] 43786190 44322336 [10,] 44322336 46302360 [11,] 45529444 53494622 [12,] 46302360 62105336 [13,] 53479132 63817440 [14,] 58567262 72637088 [15,] 60564442 79875476 [16,] 72637088 94545992 [17,] 79875476 96506368 [18,] 93155112 103123936 [19,] 94372260 116908456 [20,] 96643396 126190072 [21,] 103123936 127446552 [22,] 116908456 131781664 [23,] 131781664 154658264 [24,] 132968364 176302744 [25,] 135945080 181670472 [26,] 141788832 182625272 [27,] 149924864 182878168 [28,] 156539568 183946152 [29,] 157817896NA [30,] 162399496 [31,] 168344072 [32,] 173146584 [33,] 176302744 [34,] 182878168 [35,] 183946152 [36,] 185068720 [37,] 190791232 [38,]NA -- Introduction to R training course :: London :: 06-07 March 2008 http://www.mango-solutions.com/services/rtraining/r_intro.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] remove similar values
Romain Francois wrote: Hi, Not sure I understand the question, but maybe you need ?unique or ?duplicated Or maybe ?union, ?setdiff, ?intersection. Or ?merge. Cheers, Romain mohamed nur anisah wrote: hello!! say that i have the values of x1 and x2. my x1 has longer length than x2. how am i going to remove the similar values of x1 and x2. Any suggestion?? Thanks in advance!! Cheers, Anisah e f [1,] 17358865 17906353 [2,] 17966995 21295547 [3,] 21306539 27880531 [4,] 27880531 34118702 [5,] 34166504 35395488 [6,] 36111044 36132622 [7,] 36266288 37916920 [8,] 36854306 43786190 [9,] 43786190 44322336 [10,] 44322336 46302360 [11,] 45529444 53494622 [12,] 46302360 62105336 [13,] 53479132 63817440 [14,] 58567262 72637088 [15,] 60564442 79875476 [16,] 72637088 94545992 [17,] 79875476 96506368 [18,] 93155112 103123936 [19,] 94372260 116908456 [20,] 96643396 126190072 [21,] 103123936 127446552 [22,] 116908456 131781664 [23,] 131781664 154658264 [24,] 132968364 176302744 [25,] 135945080 181670472 [26,] 141788832 182625272 [27,] 149924864 182878168 [28,] 156539568 183946152 [29,] 157817896NA [30,] 162399496 [31,] 168344072 [32,] 173146584 [33,] 176302744 [34,] 182878168 [35,] 183946152 [36,] 185068720 [37,] 190791232 [38,]NA -- Introduction to R training course :: London :: 06-07 March 2008 http://www.mango-solutions.com/services/rtraining/r_intro.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 ~~ - ([EMAIL PROTECTED]) 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] maptools no such file
-- X-USF-Spam-Status: hits=-2.5 tests=BAYES_00,FORGED_RCVD_HELO X-USF-Spam-Flag: NO Am 29.01.2008 00:04 (UTC+1) schrieb Roger Bivand: On Mon, 28 Jan 2008, Rainer Hurling wrote: Roger, I tried your suggestions and ran into same problems as Pieter did before. Rainer: I don't think that we know what platform Pieter was using, apart from the working directory that looked like Windows, and where the problem could not be reproduced. I note that yours is FreeBSD 8, and I agree, the .C() interface to the small helper function should most likely be replaced by a .Call() to make handling the file name more robust. Can I send a modified version off-list tomorrow, since I have no access to your platform otherwise? Is readOGR() in rgdal working, by the way? Roger, cities - readOGR(./R\ scripts, cities) works well for me. Rainer Roger On 28.01.2008 12:35 (UTC+1), Roger Bivand wrote: pieterprovoost at gmail.com writes: No, I get the same error message there... Please do not needlesly delete the thread content. Your original question was: I'm having problems reading a shapefile with read.shape (maptools). I'm absolutely sure my file is there, but I get no such file. The wd is ok, since read.table for example does find the file. For testing I copied /usr/local/lib/R/library/rgdal/vectors/cities.shp into /usr/home/rhurlin/TEMP/Rscripts/ getwd() [1] D:/somedirectory/R scripts [1] /usr/home/rhurlin/TEMP/Rscripts read.table(cities.shp) Error in read.table(cities.shp) : empty beginning of file In addition: Warning message: In read.table(cities.shp) : incomplete final line found by readTableHeader on 'cities.shp' which is self-explanatory, because you were not using read.shape() anyway. You continued: read.shape(cities.shp) Error in getinfo.shape(filen) : No such file Fehler in getinfo.shape(filen) : No such file but did not respond to the suggestion from an R-helper with the output from: readShapePoly(cities.shp) Fehler in getinfo.shape(filen) : No such file Try list.files(pattern=shp$) to see whether your assumption that the files are where you think they are, is justified. [1] cities.shp Then get back with the output of getinfo.shape(cities.shp) Fehler in getinfo.shape(cities.shp) : No such file If you want to, you can use file.choose() to choose the file interactively. If you haven't solved this yourself by then (found the files youself), do remember to include the verbatim output of sessionInfo() too. R version 2.6.1 (2007-11-26) i386-unknown-freebsd8.0 # This is 8.0-CURRENT from yesterday locale: de_DE.ISO8859-15/de_DE.ISO8859-15/de_DE.ISO8859-15/C/de_DE.ISO8859-15/de_DE.ISO8859-15 attached base packages: [1] stats graphics grDevices utils datasets grid methods [8] base other attached packages: [1] maptools_0.7-4 sp_0.9-19 foreign_0.8-23 proto_0.3-8 loaded via a namespace (and not attached): [1] ggplot2_0.5.7 lattice_0.17-4 rcompgen_0.1-17 Roger Bivand It seems, that the C call of 'Rshapeinfo' makes trouble on my system. Rshapeinfo.c tries to open the shapefile with the following code: hSHP = SHPOpen( shpnm[0], rb ); If I did not misunderstood, this returns NULL on my system. I have almost no C programming skills, so I am not able to understand the code enough. Could something be wrong in using 'gettext'? (GNU gettext-runtime 0.16.1) Hope this helps a bit, Rainer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Correlation matrix for data in long format
Hello, I cannot figure out how to use tapply to compute the correlation matrix in the variable x between the states? The data is in long format, e.g.: state,year,x Alabama,2001,0.45 Alabama,2002,0.47 Alabama,2003,0.48 Alabama,2004,0.44 Arizona,2001,0.34 Arizona,2002,0.32 Arizona,2003,0.38 Arizona,2004,0.36 Thank you in advance for your help, Serguei Kaniovski __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] sqldf error
Hi, sqldf sounds like a very useful package but I don't even get the example to run: a1s - sqldf(select * from warpbreaks limit 6) Error in combine(FUN(...)) : argument value is missing, with no default I am using R 2.6.1 on Windows Vista Business and have updated all packages. Some help would be very much appreciated. Many thanks, Werner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] sqldf error
I can't reproduce your error: library(sqldf) sqldf(select * from warpbreaks limit 6) breaks wool tension 1 26A L 2 30A L 3 54A L 4 25A L 5 70A L 6 52A L R.version.string # Vista [1] R version 2.6.2 alpha (2008-01-26 r44181) A few things to try: 1. maybe you have some other package loaded that is interfering? The error occurs in 'combine' but combine is not a function in sqldf nor in RSQLite, DBI or proto -- the packages on which it depends. Try it from a new session. Be sure you don't have an .Rprofile file that is loading other packages. Rgui --vanilla library(sqldf) sqldf(...command...) 2. Try issuing the source statement in example 6 on the sqldf home page first (that will get you the development version) and try that. I doubt that will solve it but its worth a try. http://sqldf.googlecode.com On Jan 29, 2008 5:58 AM, Werner Wernersen [EMAIL PROTECTED] wrote: Hi, sqldf sounds like a very useful package but I don't even get the example to run: a1s - sqldf(select * from warpbreaks limit 6) Error in combine(FUN(...)) : argument value is missing, with no default I am using R 2.6.1 on Windows Vista Business and have updated all packages. Some help would be very much appreciated. Many thanks, Werner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] pivot table in R
A = read.table(clipboard, header=TRUE) A sex age region no_of_accidents 1 F young north 10 2 F young south 12 3 F old north 5 4 F old south 7 5 M young north 24 6 M young south 30 7 M old north 12 8 M old south 17 sum(A$no_of_accidents[which( A$sex==F)]) should give you the required sum. You have to remember that sex, age and region are Factors with their respective levels and no_of_accidents is a numeric vector. Do str( A) to see their type. Hope that helps. Mama - Mama Attiglah, PhD Advanced Research Center Quantitative Research Analyst State Street Bank +44(0)20 7698 6290 (Direct Line) +44 (0)207 004 2968 (Direct Fax) Please visit our Web site at www.ssga.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: 29 January 2008 12:05 To: r-help@r-project.org Subject: [R] pivot table in R Hello, I'm struggling with an elementary problem with R. I have a simple data frame such as this one giving the number of accidents subdivided by sex, age and region. sex age region no_of_accidents F young north 10 F young south 12 F old north 5 F old south 7 M young north 24 M young south 30 M old north 12 M old south 17 and I would like to build a pivot table, e.g. obtaining the sum of the number of accidents for each sex: sex age region no_of_accidents F (any) (any) 34 M (any) (any) 83 but I can't seem to obtain this result simply in R, except by embarking in complicated for loops. I have checked the documentation on such functions as table() and the documentation on An introduction to R but couldn't solve the problem. Could you please help me with this? Cheers Pete PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS E-MAIL For Aon's standard conditions associated with this e-mail please visit http://www.aon.com/uk/en/email-footer/aon-limited.jsp Aon Limited Registered Office: 8 Devonshire Square, London EC2M 4PL Registered in London No. 210725 . VAT Registration No. 480 8401 48 Aon Limited is authorised and regulated by the Financial Services Authority in respect of insurance mediation activities only. [[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] pivot table in R
Hi Pietro, Depending on the actual structure you want in the output, you can use some of the functions in the apply family, particularly tapply, aggregate, or by. Something like : R tapply( d[[no_of_accidents ]], d[[ sex ]], sum ) F M 34 83 R aggregate( d[no_of_accidents ], d[ sex ], sum ) sex no_of_accidents 1 F 34 2 M 83 R by( d[[no_of_accidents ]], d[[ sex ]], sum ) INDICES: F [1] 34 INDICES: M [1] 83 Cheers, Romain -- Mango Solutions data analysis that delivers R for finance training course :: 3 days :: London (27-29/02/2008) http://www.mango-solutions.com/services/rtraining/r_finance.html [EMAIL PROTECTED] wrote: Hello, I'm struggling with an elementary problem with R. I have a simple data frame such as this one giving the number of accidents subdivided by sex, age and region. sex age region no_of_accidents F young north 10 F young south 12 F old north 5 F old south 7 M young north 24 M young south 30 M old north 12 M old south 17 and I would like to build a pivot table, e.g. obtaining the sum of the number of accidents for each sex: sex age region no_of_accidents F (any) (any) 34 M (any) (any) 83 but I can't seem to obtain this result simply in R, except by embarking in complicated for loops. I have checked the documentation on such functions as table() and the documentation on An introduction to R but couldn't solve the problem. Could you please help me with this? Cheers Pete PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS E-MAIL For Aon’s standard conditions associated with this e-mail please visit http://www.aon.com/uk/en/email-footer/aon-limited.jsp Aon Limited Registered Office: 8 Devonshire Square, London EC2M 4PL Registered in London No. 210725 . VAT Registration No. 480 8401 48 Aon Limited is authorised and regulated by the Financial Services Authority in respect of insurance mediation activities only. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how do i creat multiple back to back histograms?
dear R-ussers,
I would like to creeate a graph, i wich my data is presented as verticaly
oriented histograms, wich give the frequency of the measured values,
grouped per used measurement methode.
So the X axis should hold the grouping variable and the Y axis a continuos
variable. well not realy continouse, but it should show the values,
representing the clase intervals.
small example to clarify this:
This one i can create: graph 1
only the positive results per test
5 | ##|#|##
| # |## |#
4 | ### | |
| |## |##
3 | ### |#|
| # |###|#
2 | | |##
| ### |## |#
1 | # |#|##
|_|_|_
0test 1test2test3
Tihs is what i want to create: graph 2
a back to back histogram plot of the pos/negative results, grouped per
test
5 | |## |#
|##
| |#|##
#|#
4 | |###| ##|
| .|..|##
...#|##..
3 |#|### #|#|
| ##|###|#####|#
2
|#|..|..##|##..
|###|#####|#####|#
1 | ##|# #|#|##
|___|__#|#|_
0test 1test2test3
Neg. | Pos.Neg. | Pos. Neg. | Pos.
I 'd like to creat the figure of graph 2, a back to back plot of the pos/
and negative results of a test,
and this with the 3 tests in one graf.
I have been searching for examples, the only trouble is that it is way to
complex.
(http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=109)
Here is one other example of a back to back plot (graph 2) .
(histbackback(fool)
After trying to understand wath happens in the complex example, i
identified a part that does what i need.
It does creat the graph similar to what i want (graph 1). see code
below
Yet i do not understand it wel enough,so i can't creat the more complex
graph 2.
What can i do to understand this graph functions beter, without spending
to much time on them?
Kind regards,
Tom.
this is the code, wich i use to creat graph 1
# data for plot:
freqs - data.frame(value= c(
0.000,1.204,1.301,1.362,1.447,1.505,1.602,1.653,1.756,1.806,1.903,1.959,
2.053,2.107,2.204,2.258,2.354,2.408,2.505,2.559,2.656,2.709,2.806) ,
tp1= c( 8,1,0,13,0,6,0,25,0,5,0,15,0,4,0,7,0,0,0,1,0,0,0) ,
tn1= c( 17,0,0,2,0,0,0,1,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0),
tp2= c( 10,0,2,0,9,0,8,0,19,0,4,0,5,0,2,0,5,0,2,0,1,0,2) ,
tn2= c( 13,0,1,0,1,0,2,0,2,0,0,0,2,0,0,0,0,0,0,0,0,0,0),
tp3= c( 9,0,0,0,0,0,0,0,0,10,0,10,0,21,0,10,0,11,0,8,0,5,0),
tn3= c( 15,0,0,0,0,0,0,0,0,3,0,2,0,2,0,1,0,0,0,0,0,0,0))
test-c(1,2,3,4,5,6)
testname -c('test1 p','test1 n','test2 p','test2 n','test3 p','test3 n')
# parameters for plot
xlim = c(min(test),max(test))
ylim = c(0,length(freqs$value))
barscale = 0.2
barcol = 8
# plot
win.graph()
for (i in 1:length(freqs))
{
par(new = TRUE)
xmin - -test[i] + xlim[1]
xmax - xlim[2] - test[i]
ser - freqs[, i+1]
ser - ser/max(ser) * barscale
barplot(ser, horiz = TRUE, axes = FALSE, xlim = c(xmin,
xmax),
ylim = ylim, col = barcol, space = 0)
}
axis(1,labels=testname,at=c(0,0.2,0.4,0.6,0.8,1))
axis(2,labels=freqs$value ,at=c((0:22)/23) )
this is the code, wich i hoped would creat graph 2 but it doesn't work
for (i in 1:length(freqs))
{
par(new = TRUE)
xmin - -test[i] + xlim[1]
xmax - xlim[2] - test[i]
serx - freqs[, i+1]
sery - freqs[, i+2]
ser - list((serx/sum(serx) * barscale),(sery/sum(sery) *
barscale))
histbackback(ser,axes=FALSE ,xlim = c(xmin, xmax), ylim =
ylim)
}
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Re: [R] Form Pairs of Variables for a paired t-test
Thanks a lot! Its working fine Pratap Henrique Dallazuanna [EMAIL PROTECTED] wrote: Try this: lapply(apply(combn(ncol(x),2), 2, function(y)x[,y]), function(z)t.test(z[,1], z[,2])) On 29/01/2008, nalluri pratap wrote: Hi Users, This is regarding the paired t-test. I have 5 variables (say) Data$v1,Data$v2,Data$v3,Data$v4,Data$v5 in my data frame. Now, I need to perform a paired t-test on all the possible 10 pairs.How do I set up the pairs table directly and pass those variables in to t-test. Thanks in advance, Pratap - Now you can chat without downloading messenger. Click here to know how. [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O - Bring your gang together - do your thing. Start your group. [[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] Fortunes - was Re: [OT] vernacular names for circular diagrams
Gabor Grothendieck [EMAIL PROTECTED] 29/01/2008 12:35:27
As is common in human affairs, even
the illusion of understanding is preferred to a lofty digression
upon
why the audience does not understand.
Gabor,
This should be in fortunes; it is depressingly accurate.
But it doesn't have to be a lofty digression.
S
***
This email and any attachments are confidential. Any use...{{dropped:8}}
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[R] How to get two y-axises in a bar plot?
Hi, I have measured two response variables (y1, y2) at each treatment level (x = 0, 1.5 or 3). Now I would like to show the y1 and y2 against x in a bar plot. However, y1 and y2 differ in scale so I need two y-axises, one on the left side and one on the right side (and I dont want to standardize my responses). This is fairly easy if you want to show points,lines etc, but gets more complicated with bars.Although these kind of bar graphs are quite common, I have found very limited information about how to do them in R. I have been struggling with the barplot() command. My problem is that the bars for y1 and y2 end up at the same place (blocking each other) and not beside each other when I use par(new=TRUE). Is there a way to separate them so y1 and y2 are placed beside each other at each x level, or is this easier to do this with lattice?? I would also like to add error bars but I guess that should not be a problem. For code and data, see below. Cheers, Gustaf Granath, phd student My code so far: #Creating data c(6.34,13.38,17.87)-y1 c(0.85,1.88,2.33)-y2 c(0,1.5,3)-x cbind(y1,y2,x)-mydata data.frame(mydata)-mydata with(mydata, tapply(y1,x,mean))-mean.y1 with(mydata, tapply(y2,x,mean))-mean.y2 #Barplot par(mar=c(5,4,4,4)+0,1) barplot(mean.y1,density=1,las=1) par(new=T) barplot(mean.y2,density=3,angle=3,axes=F) axis(4,las=1) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] pivot table in R
Have a look at the reshape package. With your data as data.frame xx : library(reshape) dd - melt(xx, id=c(sex, age, region),measured=c(no_of_accidents)); dd cast(dd, sex~variable, sum) --- [EMAIL PROTECTED] wrote: Hello, I'm struggling with an elementary problem with R. I have a simple data frame such as this one giving the number of accidents subdivided by sex, age and region. sex age region no_of_accidents F young north 10 F young south 12 F old north 5 F old south 7 M young north 24 M young south 30 M old north 12 M old south 17 and I would like to build a pivot table, e.g. obtaining the sum of the number of accidents for each sex: sex age region no_of_accidents F (any) (any) 34 M (any) (any) 83 but I can't seem to obtain this result simply in R, except by embarking in complicated for loops. I have checked the documentation on such functions as table() and the documentation on An introduction to R but couldn't solve the problem. Could you please help me with this? Cheers Pete PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS E-MAIL For Aons standard conditions associated with this e-mail please visit http://www.aon.com/uk/en/email-footer/aon-limited.jsp Aon Limited Registered Office: 8 Devonshire Square, London EC2M 4PL Registered in London No. 210725 . VAT Registration No. 480 8401 48 Aon Limited is authorised and regulated by the Financial Services Authority in respect of insurance mediation activities only. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] number of rescaling cycles in decorana
How do one dertermine the optimal number of rescaling cycles to use when performing DCA using the decorana function (library vegan)? Thanks for your time, Marc === Marc Bélisle Professeur adjoint Chaire de recherche du Canada en écologie spatiale et en écologie du paysage Département de biologie Université de Sherbrooke 2500 Boul. de l'Université Sherbrooke, Québec J1K 2R1 Canada Tél: +1-819-821-8000 poste 61313 Fax: +1-819-821-8049 Courriél: [EMAIL PROTECTED] [[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] pivot table in R
Also, see ?aggregate: with(A, aggregate(no_of_accidents, by=list(SEX=sex), FUN='sum')) SEX x 1 F 34 2 M 83 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Attiglah, Mama Sent: Tuesday, January 29, 2008 7:21 AM To: [EMAIL PROTECTED]; r-help@r-project.org Subject: Re: [R] pivot table in R A = read.table(clipboard, header=TRUE) A sex age region no_of_accidents 1 F young north 10 2 F young south 12 3 F old north 5 4 F old south 7 5 M young north 24 6 M young south 30 7 M old north 12 8 M old south 17 sum(A$no_of_accidents[which( A$sex==F)]) should give you the required sum. You have to remember that sex, age and region are Factors with their respective levels and no_of_accidents is a numeric vector. Do str( A) to see their type. Hope that helps. Mama - Mama Attiglah, PhD Advanced Research Center Quantitative Research Analyst State Street Bank +44(0)20 7698 6290 (Direct Line) +44 (0)207 004 2968 (Direct Fax) Please visit our Web site at www.ssga.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: 29 January 2008 12:05 To: r-help@r-project.org Subject: [R] pivot table in R Hello, I'm struggling with an elementary problem with R. I have a simple data frame such as this one giving the number of accidents subdivided by sex, age and region. sex age region no_of_accidents F young north 10 F young south 12 F old north 5 F old south 7 M young north 24 M young south 30 M old north 12 M old south 17 and I would like to build a pivot table, e.g. obtaining the sum of the number of accidents for each sex: sex age region no_of_accidents F (any) (any) 34 M (any) (any) 83 but I can't seem to obtain this result simply in R, except by embarking in complicated for loops. I have checked the documentation on such functions as table() and the documentation on An introduction to R but couldn't solve the problem. Could you please help me with this? Cheers Pete PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS E-MAIL For Aon's standard conditions associated with this e-mail please visit http://www.aon.com/uk/en/email-footer/aon-limited.jsp Aon Limited Registered Office: 8 Devonshire Square, London EC2M 4PL Registered in London No. 210725 . VAT Registration No. 480 8401 48 Aon Limited is authorised and regulated by the Financial Services Authority in respect of insurance mediation activities only. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] on trellis.par.set/get (reproducing figures from Pinheiro Bates)
Dear R users, I would like to exactly reproduce a figure like the 1.5 or 1.9 or 4.13 from the book Mixed effects models in S and S-Plus. Not for the sake of it, but because I have my own data I would like to plot in that fashion (no colors) If I write plot(ergoStool) I can get a good informative plot with colors, but I would like to have a BW one instead. I've played a little with trellis.par.set managing to change some aspect of the appearance of the plot, for example with prove.theme- list( dot.line = list(col = 1, lty = 3, lwd = 1), fontsize = list(text = 12, points = 10) ) trellis.par.set(prove.theme) plot(ergoStool) I also queried trellis.par.get by names(trellis.par.get()) but still I'm not able to figure out which are the parameters, if any, that control pch and col of the symbols. Any help is highly appreciated. -- Ottorino-Luca Pantani, Università di Firenze Dip. Scienza del Suolo e Nutrizione della Pianta P.zle Cascine 28 50144 Firenze Italia Tel 39 055 3288 202 (348 lab) Fax 39 055 333 273 [EMAIL PROTECTED] http://www4.unifi.it/dssnp/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 generate sequence a - z
Bernd Weiss wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
skestin schrieb:
| I suppose it's very simple but I can't find the way to generate a
sequence of
| characters, e.g. from a to z.
| Could you please help me with this?
?letters
letters
letters is okay for just that sequence, or parts of it, but might
not be general enough for the original poster...
I just discovered 'charToInt' and 'intToChar' in the R.oo package:
intToChar(65:68)
[1] A B C D
Then you can define cseq:
cseq =
function(from,to,by=1){
from=charToInt(from)
to=charToInt(to)
intToChar(seq(from,to,by))
}
and do:
cseq('A','G')
[1] A B C D E F G
cseq('A','G',2)
[1] A C E G
cseq('a','A',-2)
[1] a _ ] [ Y W U S Q O M K I G E C A
Note this uses ASCII codes and not whatever your language alphabet is.
I'd overload ':' for this and then you could do 'a':'z', but ':' heads
into .Primitive territory...
Barry
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Re: [R] how to generate sequence a - z
On 1/29/2008 7:39 AM, skestin wrote:
I suppose it's very simple but I can't find the way to generate a sequence of
characters, e.g. from a to z.
Could you please help me with this?
If you want the standard collation sequence, use the letters variable,
as others have said.
If you want the sequence that applies in your locale (where does ü
fall?), it's harder. I don't know a simple way, but this gives you
collation order in the German locale in Windows:
x - as.raw(32:255)
y - readChar(x, rep(1, 224))
Sys.setlocale(LC_COLLATE, German)
[1] German_Germany.1252
sort(y)
[1] \177 �����'-–
[11] — !\ #$%(
[21] )*,./:;?@[
[31] \\ ]^ˆ_`{|}~
[41] ¡¦¨¯´¸¿˜‘’
[51] ‚“”„‹›+=
[61] ±«»×÷¢£¤¥§
[71] ©¬®°µ¶·†‡•
[81] …‰€0¼½¾1¹2
[91] ²3³456789a
[101] AªáÁàÀâÂäÄ
[111] ãÃåÅæÆbBcC
[121] çÇdDðÐeEéÉ
[131] èÈêÊëËfFƒg
[141] GhHiIíÍìÌî
[151] ÎïÏjJkKlLm
[161] MnNñÑoOºóÓ
[171] òÒôÔöÖõÕøØ
[181] œŒpPqQrRsS
[191] šŠßtTþÞ™uU
[201] úÚùÙûÛüÜvV
[211] wWxXyYýÝÿŸ
[221] zZžŽ
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[R] Convert string for expression in plot
Hi,
Although I understand how to use expression and paste to add
superscripts and symbols to my graphs, I have a problem with adding
superscripts to an existing string.
For example, I read in the following from a separate file:
25Mg(p,g)
I want to convert that to superscripts etc. (in LaTex format):
$^{25}$Mg(p,$\gamma$)
This needs to then be put into a graph title.
Any ideas? I know that I can just write it in using expression and
paste, but the title is read in from a separate file.
Cheers for the help,
Richard longland
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[R] Scale function
Hello everybody, There is something that I do not get with scale function. Say that I have a vector v - c(1,2,3,4,5,6), scale(v,center=TRUE,scale=TRUE) gives a new vector with 0 as mean and 1 as standard deviation. but, scale(v, center=FALSE,scale=TRUE) gives a new vector with a standard deviation different from 1. I would also expect a standard deviation of 1 in that case. am I wrong ? thanks Eric Pellegrini __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Guidance for reporting results from lme test?
Hello, I have sucsessfully used a linear mixed effect model, lme, (REML). The results are satisfactory, but I have problems with sorting out how to report the result in a scientific paper. Is there a genearal guidance for reporting lme results available (web page, book or article)? Best regards Ronny _ [[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] pivot table in R
[EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED] k: Three or four solutions have already been offered. Here is (yet) another: Atxt - + sex age region no_of_accidents + 1 F young north 10 + 2 F young south 12 + 3 F old north 5 + 4 F old south 7 + 5 M young north 24 + 6 M young south 30 + 7 M old north 12 + 8 M old south 17 A - read.table(textConnection(Atxt), header=TRUE) Asex - xtabs(no_of_accidents ~ sex, data=A) Asex sex F M 34 83 xtabs() returns an object of class = contingency table. This may have added advantage if you are using statistical function which expect such an object. Using a formula based function also lets you quickly expand the analysis. Asexreg - xtabs(no_of_accidents ~ sex+region, data=A) Asexreg region sex north south F1519 M3647 -- David Winsemius Hello, I'm struggling with an elementary problem with R. I have a simple data frame such as this one giving the number of accidents subdivided by sex, age and region. sex age region no_of_accidents F young north 10 F young south 12 F old north 5 F old south 7 M young north 24 M young south 30 M old north 12 M old south 17 and I would like to build a pivot table, e.g. obtaining the sum of the number of accidents for each sex: sex age region no_of_accidents F (any) (any) 34 M (any) (any) 83 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] sqldf error
I cleaned up the environment and restarted everything and it does work. But I have no idea what it is what is different now. Anyway, it works! Thanks a lot Gabor! Best, Werner I can't reproduce your error: library(sqldf) sqldf(select * from warpbreaks limit 6) breaks wool tension 1 26A L 2 30A L 3 54A L 4 25A L 5 70A L 6 52A L R.version.string # Vista [1] R version 2.6.2 alpha (2008-01-26 r44181) A few things to try: 1. maybe you have some other package loaded that is interfering? The error occurs in 'combine' but combine is not a function in sqldf nor in RSQLite, DBI or proto -- the packages on which it depends. Try it from a new session. Be sure you don't have an .Rprofile file that is loading other packages. Rgui --vanilla library(sqldf) sqldf(...command...) 2. Try issuing the source statement in example 6 on the sqldf home page first (that will get you the development version) and try that. I doubt that will solve it but its worth a try. http://sqldf.googlecode.com On Jan 29, 2008 5:58 AM, Werner Wernersen [EMAIL PROTECTED] wrote: Hi, sqldf sounds like a very useful package but I don't even get the example to run: a1s - sqldf(select * from warpbreaks limit 6) Error in combine(FUN(...)) : argument value is missing, with no default I am using R 2.6.1 on Windows Vista Business and have updated all packages. Some help would be very much appreciated. Many thanks, Werner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 needed on Normality test
Hi all T gurus, I would like to test if my dataset is indeed from N(0, 0.011908969). K.S. test gives following result: ks.test(data, pnorm, 0, 0.011908969) One-sample Kolmogorov-Smirnov test data: data D = 0.1092, p-value = 1.318e-05 alternative hypothesis: two-sided How ever Shapiro-Wilk test give following : shapiro.test(data) Shapiro-Wilk normality test data: data W = 0.9946, p-value = 0.07562 also, sd(data) [1] 0.01625074 2nd test saying data is from normal however 1st isnot. Which one is correct? Am I missing something? Regards, - [[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] Form Pairs of Variables for a paired t-test
Hi Users, This is regarding the paired t-test. I have 5 variables (say) Data$v1,Data$v2,Data$v3,Data$v4,Data$v5 in my data frame. Now, I need to perform a paired t-test on all the possible 10 pairs.How do I set up the pairs table directly and pass those variables in to t-test. Thanks in advance, Pratap - Now you can chat without downloading messenger. Click here to know how. [[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] regression - cluster option in STATA - what in R?
My phd-student works in stata using cluster option in a regression model like this example: (from link: http://www.ats.ucla.edu/stat/stata/faq/clusterreg.htm) /* model 2 -- same as svy: regress with psu */ regress math homework, cluster(schid) I need to put som extra blinded data into the same model using R. This cluster option. Is there something in R for this? /Thanks Niels Steen Krogh Konsulent ZiteLab ApS Mail: -- [EMAIL PROTECTED] Telefon: --- +45 38 88 86 13 Mobil: - +45 22 67 37 38 Adresse: --- ZiteLab ApS Solsortvej 44 dk - 2000 F. --- og --- ZiteLab ApS Refshalevej 110a dk - 1432 københavn k Web: --- www.zitelab.dk CVR: --- 29178364 Bank: -- Sparbank Vest Ejer: -- ZSRK Group Holding __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] pivot table in R
Hello, I'm struggling with an elementary problem with R. I have a simple data frame such as this one giving the number of accidents subdivided by sex, age and region. sex age region no_of_accidents F young north 10 F young south 12 F old north 5 F old south 7 M young north 24 M young south 30 M old north 12 M old south 17 and I would like to build a pivot table, e.g. obtaining the sum of the number of accidents for each sex: sex age region no_of_accidents F (any) (any) 34 M (any) (any) 83 but I can't seem to obtain this result simply in R, except by embarking in complicated for loops. I have checked the documentation on such functions as table() and the documentation on An introduction to R but couldn't solve the problem. Could you please help me with this? Cheers Pete PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS E-MAIL For Aons standard conditions associated with this e-mail please visit http://www.aon.com/uk/en/email-footer/aon-limited.jsp Aon Limited Registered Office: 8 Devonshire Square, London EC2M 4PL Registered in London No. 210725 . VAT Registration No. 480 8401 48 Aon Limited is authorised and regulated by the Financial Services Authority in respect of insurance mediation activities only. [[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] [OT] vernacular names for circular diagrams
Rolf Turner wrote: ... I have been for many years under the impression that the pie chart was invented by Florence Nightingale. Am I misinformed? Hi Rolf, Yes, you have been misled. Dear old Florence invented a related illustration now usually referred to as a polar area diagram. It was an ingenious way of representing quantities as areas, but probably had to be explained at length to those subjected to it. The principal advantage of the pie chart is that most people think they understand it upon seeing it, even if they don't. As is common in human affairs, even the illusion of understanding is preferred to a lofty digression upon why the audience does not understand. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [OT] vernacular names for circular diagrams
http://en.wikipedia.org/wiki/Pie_chart cites papers using the polar area diagram prior to Nightengale although it does say that many sources credit it to her. On Jan 29, 2008 6:16 AM, Jim Lemon [EMAIL PROTECTED] wrote: Rolf Turner wrote: ... I have been for many years under the impression that the pie chart was invented by Florence Nightingale. Am I misinformed? Hi Rolf, Yes, you have been misled. Dear old Florence invented a related illustration now usually referred to as a polar area diagram. It was an ingenious way of representing quantities as areas, but probably had to be explained at length to those subjected to it. The principal advantage of the pie chart is that most people think they understand it upon seeing it, even if they don't. As is common in human affairs, even the illusion of understanding is preferred to a lofty digression upon why the audience does not understand. 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] Convert string for expression in plot
Richard Longland wrote:
Hi,
Although I understand how to use expression and paste to add
superscripts and symbols to my graphs, I have a problem with adding
superscripts to an existing string.
For example, I read in the following from a separate file:
25Mg(p,g)
I want to convert that to superscripts etc. (in LaTex format):
$^{25}$Mg(p,$\gamma$)
This needs to then be put into a graph title.
Any ideas? I know that I can just write it in using expression and
paste, but the title is read in from a separate file.
If you explain what the rules are to use superscript or greek letters
(why is the p not converted to pi but the g to gamma, etc?), we ca help,
as an example if you read just the number from a file:
#number - scan(that_file)
# say you read
number - 25
plot(1:10, main=substitute(phantom()^number * Mg(p, gamma),
list(number=number)))
See ?plotmath and for automating things like this my article in R News
might help:
Ligges, U. (2002): R Help Desk: Automation of Mathematical Annotation in
Plots. R News 2 (3), 32-34.
Best,
Uwe Ligges
Cheers for the help,
Richard longland
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[R] q about efficient cross-classification/creating tables
Dear R Users,
I am posting a smaller portion of a question I posted last week. Code I have
written
takes weeks to run, and I am trying to make all the lines as efficient as
possible. Here is
one part of the code.
I have some data that looks like
[,1] [,2] [,3] [,4]
[1,]1313
[2,]3323
[3,]1333
and a binary response. I am trying to obtain a vector of counts for all
cross classifications of the response
and each pair of columns from the data.
Have I coded this in an efficient manner?
library(combinat)
# some example data
myData - matrix(sample(c(1:3),500,replace=TRUE),nrow=100,ncol=4)
response - c(rep(1,50),rep(0,50))
#initialize result matrix
count.matrix - matrix(-1,ncol=6,nrow=18);
# indices of all pairs of columns
all.pairs - combn2(1:ncol(myData))
getCounts - function(index)
{
counts - as.vector(table(myData[,index[1]],myData[,index[2]],response));
}
count.matrix - apply(all.pairs, 1, getCounts)
Thanks,
Juliet
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[R] [R-pkgs] New package: dtw - Dynamic Time Warping
Dear R community,
I would like to introduce the package dtw for computing Dynamic Time
Warping (DTW) alignments and related algorithms on timeseries.
The DTW algorithm computes the time axis stretch which optimally maps one
timeseries (query) onto another (template); it outputs the resulting
cumulative distance between the two inputs, which is frequently used for
classification and clustering.
The R implementation in package dtw is fairly comprehensive, allowing
choice of:
* windowing functions (global constraints), eg. the Sakoe-Chiba band
* 26 transition types (local constraints), incl.
- symmetric and asymmetric
- smoothed
- slope-constrained
- step patterns found in Sakoe-Chiba and Rabiner-Myers;
* any definition for a local distance can be used for multivariate
timeseries, thanks to the {proxy}distance function.
Besides alignment computations, the package also provides:
* plot methods for warping functions with several visualization styles;
* methods for applying a warping function (direct or inverse);
* native and interpreted implementations.
DTW itself registers as a distance function with {proxy}distance;
Package dtw is hosted on CRAN (stable) and R-forge (testing: recommended).
Current package version is 1.4-3 (this is the first announcement on
r-packages).
Please find more information at the project home page:
http://dtw.r-forge.r-project.org , providing repository locations and a
gallery of sample plots. A companion paper is upcoming.
Best regards,
Toni Giorgino
--
Toni Giorgino, PhD [EMAIL PROTECTED]
Laboratorio di Informatica Biomedica tel +39 0382 985981
Dip. Informatica e Sistemistica fax +39 0382 526088
via Ferrata 1 I-27100 Pavia
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Re: [R] Correlation matrix for data in long format
If I understand your question, you can try something like this: cor(data.frame(lapply(split(x, x$state), [, 3))) On 29/01/2008, Serguei Kaniovski [EMAIL PROTECTED] wrote: Hello, I cannot figure out how to use tapply to compute the correlation matrix in the variable x between the states? The data is in long format, e.g.: state,year,x Alabama,2001,0.45 Alabama,2002,0.47 Alabama,2003,0.48 Alabama,2004,0.44 Arizona,2001,0.34 Arizona,2002,0.32 Arizona,2003,0.38 Arizona,2004,0.36 Thank you in advance for your help, Serguei Kaniovski __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Integer vs numeric
Seems strange to me to define an operator relatively to a very special case.
I have to admit that I do not use 1:1e7 every day :-)
Wouldn't it be more appropriate to define a a:b operator numeric (that
is preserving the initial class of a and b) and in specific case that
need optimization, changing the type?
for i in as.integer(1:1e7)
That might appears as a minor point, but when using S4, for what I
know, if you define a class that can take either 1:3 or c(1,3,4), one
is integer, the other numeric, one of those will not be accepted by the
class...
Christophe
On 28-Jan-08 22:40:02, Peter Dalgaard wrote:
[...]
AFAIR, space is/was more of an issue. If you do something like
for i in 1:1e7
some.silly.simulation()
then you have 40 MB sitting there doing nothing, and 80 MB if
it had been floating point.
Hmmm ... there's something to be said for good old
for(i=1,i=1e7,i++){}
As pointed out in ?for, when you do
for(i in X){...} #(e.g. X=(1:1e7))
the object X is created (or is already there) in full
at the start and sits there, as you say doing nothing,
until you end the loop. Whereas the C code just keeps
track of i and of the condition.
At least on a couple of my machines (64MB and 184MB RAM)
knocking out 40MB would inflict severe trauma! Let alone 80MB.
Mind you, the little one is no longer allowed to play with
big boys like R, though the other one is still used for
moderate-sized games.
Would there be much of a time penalty in implementing
a 'for' loop, C-style, as
i-1
while(i=1e7){
...
i-i+1
}
??
It looks as though there might be:
system.time(for(i in (1:1e7)) x-cos(3) )
#[1] 13.521 0.132 13.355 0.000 0.000
system.time({i-1;while(i=1e7){x-cos(3);i-i+1}})
#[1] 38.270 0.076 37.629 0.000 0.000
which suggests that the latter is about 3 times as slow.
(And no, this wasn't done on either of my puny babes).
(And this isn't the first time I've wished for an R
implementation of ++ as a CPU-level incrementation,
as opposed to the R-arithmetic implementation which
treats adding 1 to a variable as a full-dress
arithmetic parade!
Best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 28-Jan-08 Time: 23:34:52
-- XFMail --
Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
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Re: [R] how to generate sequence a - z
letters [1] a b c d e f g h i j k l m n o p q r s t u v w x y z LETTERS [1] A B C D E F G H I J K L M N O P Q R S T U V W X Y Z Hope that will help. Mama - Mama Attiglah, PhD Advanced Research Center Quantitative Research Analyst State Street Bank +44(0)20 7698 6290 (Direct Line) +44 (0)207 004 2968 (Direct Fax) Please visit our Web site at www.ssga.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernd Weiss Sent: 29 January 2008 12:43 To: skestin; [EMAIL PROTECTED] Subject: Re: [R] how to generate sequence a - z -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 skestin schrieb: | I suppose it's very simple but I can't find the way to generate a sequence of | characters, e.g. from a to z. | Could you please help me with this? ?letters letters HTH, B. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.7 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHnx9IUsbvfbd00+ERAuasAKCYIZ9KC4c3NoDFfkdDP0MyZckinwCbBQv7 CX249me9JFbVlWNPy/mDtV0= =Vaea -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.
Re: [R] Logit Regressions, Clustering etc
Hi Sorry to bother the list again, but no-one has so far been able to suggest any help for the query below. As an added incentive, I have been asked why don't you do this in Stata? It's just a case of adding a flag in the regression... I'm loathe to start learning another stats package, so if anyone is able to help...! Thanks Paul Hi I am carrying out some logit regressions and want to (a) make sure I'm taking the right approach and (b) work out how to carry out some additional analysis. So, to carry out a logit regression where the dependent variable is a factor db, I use something like: res1_l - glm(formula = db ~ y1 + + y5, family = binomial(link = logit)) summary(res1_l) ...which is, I hope correct. I also need to carry out an ordered logit regression. Is this as simple as: res1_l - polr(formula = db ~ y1 + + y5) summary(res1_l) ..with db being a factor which has more levels than just 0 and 1? Assuming it is, the part I am really struggling with is the calculation of robust standard errors to allow for clustering. In an ordinary regression, Ive used survreg, where the data has also been censored, e.g.: res1 - survreg(formula = Surv(ip, db_Censor) ~ y1 + y5 + cluster(db_ID), dist = gaussian) summary(res1) This has the benefit of giving a nice clear display of the naïve standard error as well as the robust one - is there any way of getting similar output for a logit and an ordered logit regression Thanks in advance for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 generate sequence a - z
I suppose it's very simple but I can't find the way to generate a sequence of characters, e.g. from a to z. Could you please help me with this? -- View this message in context: http://www.nabble.com/how-to-generate-sequence-%22a%22---%22z%22-tp15158509p15158509.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] Expert systems
I know that there are packages implementings the probabilistic expert systems (the so-called probabilistic networks or bayesian networks). You find (at least) the following packages: bnlearn (bayesian network structure learning) deal (learning bayesian networks with mixed variables) G1DBN (for dynamic bayesian network inference) Ciao, domenico Ralf Finne wrote: Hi R-users Is there any functions in R that can implement expert systems? The aim of an expert system is to produce a probable diagnosis for a patient with certain symptoms. In the classical expert system a mumber of experts are asked to make statements on the probabilities for different diseases when a combination of systems would appear. One typical expert system uses Fuzzy Logic to suggest the diagnosis. In more modern systems one tends to make the system self learning to improve the system. Hoping for comments Ralf Finne Swenska yrkeshögskolan Vasa Finland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Logit Regressions, Clustering etc
The 'sandwich' package has sandwich standard errors of various sorts for a generalized linear models. I don't know if it handles the proportional odds model. -thomas On Tue, 29 Jan 2008, Paul Sweeting wrote: Hi Sorry to bother the list again, but no-one has so far been able to suggest any help for the query below. As an added incentive, I have been asked why don't you do this in Stata? It's just a case of adding a flag in the regression... I'm loathe to start learning another stats package, so if anyone is able to help...! Thanks Paul Hi I am carrying out some logit regressions and want to (a) make sure I'm taking the right approach and (b) work out how to carry out some additional analysis. So, to carry out a logit regression where the dependent variable is a factor db, I use something like: res1_l - glm(formula = db ~ y1 + + y5, family = binomial(link = logit)) summary(res1_l) ...which is, I hope correct. I also need to carry out an ordered logit regression. Is this as simple as: res1_l - polr(formula = db ~ y1 + + y5) summary(res1_l) ..with db being a factor which has more levels than just 0 and 1? Assuming it is, the part I am really struggling with is the calculation of robust standard errors to allow for clustering. In an ordinary regression, Ive used survreg, where the data has also been censored, e.g.: res1 - survreg(formula = Surv(ip, db_Censor) ~ y1 + y5 + cluster(db_ID), dist = gaussian) summary(res1) This has the benefit of giving a nice clear display of the naïve standard error as well as the robust one - is there any way of getting similar output for a logit and an ordered logit regression Thanks in advance for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 do i creat multiple back to back histograms?
Is
?pyramid.plot
in the plotrix package of any help?
Plotting three of these on the same device is possible after
par(mfrow=c(1,3))
Tom Willems [EMAIL PROTECTED] 29/01/2008 11:43:46
dear R-ussers,
I would like to creeate a graph, i wich my data is presented as
verticaly
oriented histograms, wich give the frequency of the measured values,
grouped per used measurement methode.
So the X axis should hold the grouping variable and the Y axis a
continuos
variable. well not realy continouse, but it should show the values,
representing the clase intervals.
small example to clarify this:
This one i can create: graph 1
only the positive results per test
5 | ##|#|##
| # |## |#
4 | ### | |
| |## |##
3 | ### |#|
| # |###|#
2 | | |##
| ### |## |#
1 | # |#|##
|_|_|_
0test 1test2test3
Tihs is what i want to create: graph 2
a back to back histogram plot of the pos/negative results, grouped per
test
5 | |## |#
|##
| |#|##
#|#
4 | |###| ##|
| .|..|##
...#|##..
3 |#|### #|#
|
| ##|###|#####|#
2
|#|..|..##|##..
|###|#####|#####|#
1 | ##|# #|#|##
|___|__#|#|_
0test 1test2
test3
Neg. | Pos.Neg. | Pos. Neg. | Pos.
I 'd like to creat the figure of graph 2, a back to back plot of the
pos/
and negative results of a test,
and this with the 3 tests in one graf.
I have been searching for examples, the only trouble is that it is way
to
complex.
(http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=109)
Here is one other example of a back to back plot (graph 2) .
(histbackback(fool)
After trying to understand wath happens in the complex example, i
identified a part that does what i need.
It does creat the graph similar to what i want (graph 1). see
code
below
Yet i do not understand it wel enough,so i can't creat the more complex
graph 2.
What can i do to understand this graph functions beter, without
spending
to much time on them?
Kind regards,
Tom.
this is the code, wich i use to creat graph 1
# data for plot:
freqs - data.frame(value= c(
0.000,1.204,1.301,1.362,1.447,1.505,1.602,1.653,1.756,1.806,1.903,1.959,
2.053,2.107,2.204,2.258,2.354,2.408,2.505,2.559,2.656,2.709,2.806) ,
tp1= c( 8,1,0,13,0,6,0,25,0,5,0,15,0,4,0,7,0,0,0,1,0,0,0)
,
tn1= c( 17,0,0,2,0,0,0,1,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0)
,
tp2= c( 10,0,2,0,9,0,8,0,19,0,4,0,5,0,2,0,5,0,2,0,1,0,2)
,
tn2= c( 13,0,1,0,1,0,2,0,2,0,0,0,2,0,0,0,0,0,0,0,0,0,0)
,
tp3= c( 9,0,0,0,0,0,0,0,0,10,0,10,0,21,0,10,0,11,0,8,0,5,0)
,
tn3= c( 15,0,0,0,0,0,0,0,0,3,0,2,0,2,0,1,0,0,0,0,0,0,0)
)
test-c(1,2,3,4,5,6)
testname -c('test1 p','test1 n','test2 p','test2 n','test3 p','test3
n')
# parameters for plot
xlim = c(min(test),max(test))
ylim = c(0,length(freqs$value))
barscale = 0.2
barcol = 8
# plot
win.graph()
for (i in 1:length(freqs))
{
par(new = TRUE)
xmin - -test[i] + xlim[1]
xmax - xlim[2] - test[i]
ser - freqs[, i+1]
ser - ser/max(ser) * barscale
barplot(ser, horiz = TRUE, axes = FALSE, xlim =
c(xmin,
xmax),
ylim = ylim, col = barcol, space = 0)
}
axis(1,labels=testname,at=c(0,0.2,0.4,0.6,0.8,1))
axis(2,labels=freqs$value ,at=c((0:22)/23) )
this is the code, wich i hoped would creat graph 2 but it doesn't work
for (i in 1:length(freqs))
{
par(new = TRUE)
xmin - -test[i] + xlim[1]
xmax - xlim[2] - test[i]
serx - freqs[, i+1]
sery - freqs[, i+2]
ser - list((serx/sum(serx) *
barscale),(sery/sum(sery) *
barscale))
histbackback(ser,axes=FALSE ,xlim = c(xmin, xmax),
ylim =
ylim)
Re: [R] how to generate sequence a - z
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 skestin schrieb: | I suppose it's very simple but I can't find the way to generate a sequence of | characters, e.g. from a to z. | Could you please help me with this? ?letters letters HTH, B. -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.7 (MingW32) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHnx9IUsbvfbd00+ERAuasAKCYIZ9KC4c3NoDFfkdDP0MyZckinwCbBQv7 CX249me9JFbVlWNPy/mDtV0= =Vaea -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.
Re: [R] how to generate sequence a - z
-- X-USF-Spam-Status: hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO Hello, Sequences of letters can be generated by typing LETTERS #for capital letters or letters #for small letters Best wishes Christoph skestin schrieb: I suppose it's very simple but I can't find the way to generate a sequence of characters, e.g. from a to z. Could you please help me with this? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 do i creat multiple back to back histograms?
Maybe this is what you'd like. library(ggplot2) freqs - data.frame(value= c( 0.000,1.204,1.301,1.362,1.447,1.505,1.602,1.653,1.756,1.806,1.903,1.959, 2.053,2.107,2.204,2.258,2.354,2.408,2.505,2.559,2.656,2.709,2.806) , tp1= c( 8,1,0,13,0,6,0,25,0,5,0,15,0,4,0,7,0,0,0,1,0,0,0) , tn1= c( 17,0,0,2,0,0,0,1,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0) , tp2= c( 10,0,2,0,9,0,8,0,19,0,4,0,5,0,2,0,5,0,2,0,1,0,2) , tn2= c( 13,0,1,0,1,0,2,0,2,0,0,0,2,0,0,0,0,0,0,0,0,0,0) , tp3= c( 9,0,0,0,0,0,0,0,0,10,0,10,0,21,0,10,0,11,0,8,0,5,0) , tn3= c( 15,0,0,0,0,0,0,0,0,3,0,2,0,2,0,1,0,0,0,0,0,0,0) ) freqsMelt - melt(freqs, id = value, measure.var = 2:7) colnames(freqsMelt)[3] - n freqsMelt$test - factor(paste(test, substr(freqsMelt$variable, 3, 3))) freqsMelt$posneg - factor(substr(freqsMelt$variable, 2, 2)) freqsMelt$n[freqsMelt$posneg == n] - - freqsMelt$n[freqsMelt$posneg == n] ggplot(freqsMelt, aes(x = factor(value), y = n, fill = posneg)) + geom_bar(stat= identity, position = identity) + facet_grid(. ~test) + coord_flip() HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Tom Willems Verzonden: dinsdag 29 januari 2008 12:44 Aan: r-help@r-project.org Onderwerp: [R] how do i creat multiple back to back histograms? dear R-ussers, I would like to creeate a graph, i wich my data is presented as verticaly oriented histograms, wich give the frequency of the measured values, grouped per used measurement methode. So the X axis should hold the grouping variable and the Y axis a continuos variable. well not realy continouse, but it should show the values, representing the clase intervals. small example to clarify this: This one i can create: graph 1 only the positive results per test 5 | ##|#|## | # |## |# 4 | ### | | | |## |## 3 | ### |#| | # |###|# 2 | | |## | ### |## |# 1 | # |#|## |_|_|_ 0test 1test2test3 Tihs is what i want to create: graph 2 a back to back histogram plot of the pos/negative results, grouped per test 5 | |## |# |## | |#|## #|# 4 | |###| ##| | .|..|## ...#|##.. 3 |#|### #|#| | ##|###|#####|# 2 |#|..|..##|##... ... |###|#####|#####|# 1 | ##|# #|#|## |___|__#|#|_ 0test 1test2 test3 Neg. | Pos.Neg. | Pos. Neg. | Pos. I 'd like to creat the figure of graph 2, a back to back plot of the pos/ and negative results of a test, and this with the 3 tests in one graf. I have been searching for examples, the only trouble is that it is way to complex. (http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=109) Here is one other example of a back to back plot (graph 2) . (histbackback(fool) After trying to understand wath happens in the complex example, i identified a part that does what i need. It does creat the graph similar to what i want (graph 1). see code below Yet i do not understand it wel enough,so i can't creat the more complex graph 2. What can i do to understand this graph functions beter, without spending to much time on them? Kind regards, Tom. this is the code, wich i use to creat graph 1 # data for plot: freqs - data.frame(value= c( 0.000,1.204,1.301,1.362,1.447,1.505,1.602,1.653,1.756,1.806,1.903,1.959,
[R] Compiling R code
Hi all, I am struggling to compile a massive R code that I have written through some years, aiming to provide automated investment strategies to my Portfolio Managers. You may ask me why do I not rewrite the code in C or C++; the answer is it is really massive and that will take me lots of time. The pb is I will be moving from one team to another therefore I want to make it an exec program that the PMs can run in their investment universe without my help. I am using the very long method described in the R extension doc which is taking me time as each block of the code needs to be carefully evaluated. I researched about the RCC project aiming to do the job but it seems to me that the compiler is not yet available. Is anyone experienced in compiling R code to an exec file or had a similar experience in the past? Thanks Mama - Mama Attiglah, PhD Advanced Research Center Quantitative Research Analyst State Street Bank +44(0)20 7698 6290 (Direct Line) +44 (0)207 004 2968 (Direct Fax) Please visit our Web site at www.ssga.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Integer vs numeric
x[1:n]
/H
On Jan 29, 2008 5:07 AM, [EMAIL PROTECTED] wrote:
Seems strange to me to define an operator relatively to a very special case.
I have to admit that I do not use 1:1e7 every day :-)
Wouldn't it be more appropriate to define a a:b operator numeric (that
is preserving the initial class of a and b) and in specific case that
need optimization, changing the type?
for i in as.integer(1:1e7)
That might appears as a minor point, but when using S4, for what I
know, if you define a class that can take either 1:3 or c(1,3,4), one
is integer, the other numeric, one of those will not be accepted by the
class...
Christophe
On 28-Jan-08 22:40:02, Peter Dalgaard wrote:
[...]
AFAIR, space is/was more of an issue. If you do something like
for i in 1:1e7
some.silly.simulation()
then you have 40 MB sitting there doing nothing, and 80 MB if
it had been floating point.
Hmmm ... there's something to be said for good old
for(i=1,i=1e7,i++){}
As pointed out in ?for, when you do
for(i in X){...} #(e.g. X=(1:1e7))
the object X is created (or is already there) in full
at the start and sits there, as you say doing nothing,
until you end the loop. Whereas the C code just keeps
track of i and of the condition.
At least on a couple of my machines (64MB and 184MB RAM)
knocking out 40MB would inflict severe trauma! Let alone 80MB.
Mind you, the little one is no longer allowed to play with
big boys like R, though the other one is still used for
moderate-sized games.
Would there be much of a time penalty in implementing
a 'for' loop, C-style, as
i-1
while(i=1e7){
...
i-i+1
}
??
It looks as though there might be:
system.time(for(i in (1:1e7)) x-cos(3) )
#[1] 13.521 0.132 13.355 0.000 0.000
system.time({i-1;while(i=1e7){x-cos(3);i-i+1}})
#[1] 38.270 0.076 37.629 0.000 0.000
which suggests that the latter is about 3 times as slow.
(And no, this wasn't done on either of my puny babes).
(And this isn't the first time I've wished for an R
implementation of ++ as a CPU-level incrementation,
as opposed to the R-arithmetic implementation which
treats adding 1 to a variable as a full-dress
arithmetic parade!
Best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 28-Jan-08 Time: 23:34:52
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Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
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Re: [R] Fortunes - was Re: [OT] vernacular names for circular diagrams
I did not write that.
On Jan 29, 2008 9:05 AM, S Ellison [EMAIL PROTECTED] wrote:
Gabor Grothendieck [EMAIL PROTECTED] 29/01/2008 12:35:27
As is common in human affairs, even
the illusion of understanding is preferred to a lofty digression
upon
why the audience does not understand.
Gabor,
This should be in fortunes; it is depressingly accurate.
But it doesn't have to be a lofty digression.
S
***
This email and any attachments are confidential. Any u...{{dropped:9}}
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Re: [R] Form Pairs of Variables for a paired t-test
Try this: lapply(apply(combn(ncol(x),2), 2, function(y)x[,y]), function(z)t.test(z[,1], z[,2])) On 29/01/2008, nalluri pratap [EMAIL PROTECTED] wrote: Hi Users, This is regarding the paired t-test. I have 5 variables (say) Data$v1,Data$v2,Data$v3,Data$v4,Data$v5 in my data frame. Now, I need to perform a paired t-test on all the possible 10 pairs.How do I set up the pairs table directly and pass those variables in to t-test. Thanks in advance, Pratap - Now you can chat without downloading messenger. Click here to know how. [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] B-W stacked area chart with pattern
Dear all, I would like to create a stacked area chart to show the development of species biomass over time. Since it is intended for publication I need to prepare in black and white. I have tried to modify the stackedPlot function submitted to this list by Christian Lasarczyk on Tue, 16 Aug 2005 using shading lines rather than colors to distinguish between the species. Unfortunately, the result was not very satisfying as the options using different angles and densities for the shading lines was not sufficient to clearly distinguish between species. I would thus like to use different pattern (or texture) for this purpose. I have searched the various help lists on graphics in R but was unable to find something appropriate. Thanks, Markus -- Markus Didion WaldökologieForest Ecology Inst. f. Terrestrische Oekosysteme Inst. of Terrestrial Ecosystems Departement UmweltwissenschaftenDept. of Environmental Sciences Eidg. Technische Hochschule Swiss Fed. Inst. of Technology ETH-Zentrum CHN G78 ETH-Zentrum CHN G78 Universitätstr. 22 Universitaetstr. 22 CH-8092 Zürich CH-8092 Zurich Schweiz Switzerland Tel +41 (0)44 632 5629 Fax +41 (0)44 632 1358 Email [EMAIL PROTECTED] homepage: http://www.fe.ethz.ch/people/didionm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] B-W stacked area chart with pattern
On Jan 29, 2008 9:12 AM, Markus Didion [EMAIL PROTECTED] wrote: Dear all, I would like to create a stacked area chart to show the development of species biomass over time. Since it is intended for publication I need to prepare in black and white. I have tried to modify the stackedPlot function submitted to this list by Christian Lasarczyk on Tue, 16 Aug 2005 using shading lines rather than colors to distinguish between the species. Unfortunately, the result was not very satisfying as the options using different angles and densities for the shading lines was not sufficient to clearly distinguish between species. I would thus like to use different pattern (or texture) for this purpose. I have searched the various help lists on graphics in R but was unable to find something appropriate. How many species do you have? Coming about with a good (distinguishable) set of patterns is a difficult task. Have you tried just using different greys? 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] B-W stacked area chart with pattern
Thanks Hadley for your comment. I've got a minimum of 12 species and thus just using different greys won't do it. I've tried it with two background fills, i.e. white and a medium grey, and then used various angles for the shading lines, even plotted it twice to obtain some sort of cross shading. For good, distinguishable patterns I've been hoping to be able to fill an area with different symbols. Markus hadley wickham wrote: On Jan 29, 2008 9:12 AM, Markus Didion [EMAIL PROTECTED] wrote: Dear all, I would like to create a stacked area chart to show the development of species biomass over time. Since it is intended for publication I need to prepare in black and white. I have tried to modify the stackedPlot function submitted to this list by Christian Lasarczyk on Tue, 16 Aug 2005 using shading lines rather than colors to distinguish between the species. Unfortunately, the result was not very satisfying as the options using different angles and densities for the shading lines was not sufficient to clearly distinguish between species. I would thus like to use different pattern (or texture) for this purpose. I have searched the various help lists on graphics in R but was unable to find something appropriate. How many species do you have? Coming about with a good (distinguishable) set of patterns is a difficult task. Have you tried just using different greys? Hadley -- Markus Didion WaldökologieForest Ecology Inst. f. Terrestrische Oekosysteme Inst. of Terrestrial Ecosystems Departement UmweltwissenschaftenDept. of Environmental Sciences Eidg. Technische Hochschule Swiss Fed. Inst. of Technology ETH-Zentrum CHN G78 ETH-Zentrum CHN G78 Universitätstr. 22 Universitaetstr. 22 CH-8092 Zürich CH-8092 Zurich Schweiz Switzerland Tel +41 (0)44 632 5629 Fax +41 (0)44 632 1358 Email [EMAIL PROTECTED] homepage: http://www.fe.ethz.ch/people/didionm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 get two y-axises in a bar plot?
Try this X = rbind(y1, y2) colnames(X) = as.character(x) barplot( X, density=c(35,40), col=c(red,blue), beside=FALSE) barplot( X, density=c(35,40), col=c(red,blue), beside=TRUE) Alternatively, barplot( y1, ylim = c(0, max(y1,y2)), col=blue, beside=FALSE) par(new=TRUE) barplot( y2, ylim = c(0, max(y1,y2)), col=red, beside=FALSE, names.arg=as.character(x)) Mama - Mama Attiglah, PhD Advanced Research Center Quantitative Research Analyst State Street Bank +44(0)20 7698 6290 (Direct Line) +44 (0)207 004 2968 (Direct Fax) Please visit our Web site at www.ssga.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gustaf Granath Sent: 29 January 2008 16:15 To: r-help@r-project.org Subject: [R] How to get two y-axises in a bar plot? Hi, I have measured two response variables (y1, y2) at each treatment level (x = 0, 1.5 or 3). Now I would like to show the y1 and y2 against x in a bar plot. However, y1 and y2 differ in scale so I need two y-axises, one on the left side and one on the right side (and I dont want to standardize my responses). This is fairly easy if you want to show points,lines etc, but gets more complicated with bars.Although these kind of bar graphs are quite common, I have found very limited information about how to do them in R. I have been struggling with the barplot() command. My problem is that the bars for y1 and y2 end up at the same place (blocking each other) and not beside each other when I use par(new=TRUE). Is there a way to separate them so y1 and y2 are placed beside each other at each x level, or is this easier to do this with lattice?? I would also like to add error bars but I guess that should not be a problem. For code and data, see below. Cheers, Gustaf Granath, phd student My code so far: #Creating data c(6.34,13.38,17.87)-y1 c(0.85,1.88,2.33)-y2 c(0,1.5,3)-x cbind(y1,y2,x)-mydata data.frame(mydata)-mydata with(mydata, tapply(y1,x,mean))-mean.y1 with(mydata, tapply(y2,x,mean))-mean.y2 #Barplot par(mar=c(5,4,4,4)+0,1) barplot(mean.y1,density=1,las=1) par(new=T) barplot(mean.y2,density=3,angle=3,axes=F) axis(4,las=1) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] coherency and phase plots
spec.pgram does accept multivariate time series, and I have used this with success. I just don't know if there is an implementation of cross-spectrum in R. Or what exactley Phase vs frequency is telling me. On Jan 29, 2008 2:06 PM, Donald McKenzie [EMAIL PROTECTED] wrote: See the help for spec.pgram(). It accepts a multivariate time series as an argument. Don McKenzie, Research Ecologist Fire and Environmental Research Applications (FERA) Pacific Wildland Fire Sciences Lab, USDA Forest Service Affiliate Assistant Professor College of Forest Resources JISAO / CSES Climate Impacts Group University of Washington [EMAIL PROTECTED] [EMAIL PROTECTED] (206)732-7824; fax (206)732-7801 On Tue, 29 Jan 2008, stephen sefick wrote: I am having a hard time interpreting the phase and coherency plots. x is two timeseries that occur at the same time i.e. a b 1 11.2 12.3 16 11.3 12.4 31 11.4 12.5 46 11.5 12.6 ...etc even though my example is does not show this they are oscillating at more or less the same frequency just shifted by t=x (imagine two sine waves offset with the 2nd sine wave starting at the peak of the first). I would like to know what x is. I think I am looking for the phase shift? The coherency? Cross-spectrum? And I have read the help files, Shumway and Stoffer has a small section on this, I don't have journal access, and I am having trouble finding anything on the internet. s = spec.pgram(x) par(mfrow = c(2,1)) plot(s, plot.type = coh) plot(s, plot.type = pha) Can R do the cross-spectrum of two timeseries? How? -- 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. -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fortunes - was Re: [OT] vernacular names for circular diagrams
Search the archives and find who posted it.
On Jan 29, 2008 1:52 PM, John Kane [EMAIL PROTECTED] wrote:
Any idea who did? I have it in my list of quotes and
attributed to you.
Anon is so boring as a source.
--- Gabor Grothendieck [EMAIL PROTECTED]
wrote:
I did not write that.
On Jan 29, 2008 9:05 AM, S Ellison
[EMAIL PROTECTED] wrote:
Gabor Grothendieck [EMAIL PROTECTED]
29/01/2008 12:35:27
As is common in human affairs, even
the illusion of understanding is preferred to a
lofty digression
upon
why the audience does not understand.
Gabor,
This should be in fortunes; it is depressingly
accurate.
But it doesn't have to be a lofty digression.
S
***
This email and any attachments are confidential.
Any u...{{dropped:9}}
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Re: [R] Expert systems
I can add that I've recently uploaded the gRain package for gRAphical Independence Networks, aka probabilistic networks/Bayesian networks. Regards Søren Fra: [EMAIL PROTECTED] på vegne af Domenico Vistocco Sendt: ti 29-01-2008 19:07 Til: Ralf Finne Cc: r-help@r-project.org Emne: Re: [R] Expert systems I know that there are packages implementings the probabilistic expert systems (the so-called probabilistic networks or bayesian networks). You find (at least) the following packages: bnlearn (bayesian network structure learning) deal (learning bayesian networks with mixed variables) G1DBN (for dynamic bayesian network inference) Ciao, domenico Ralf Finne wrote: Hi R-users Is there any functions in R that can implement expert systems? The aim of an expert system is to produce a probable diagnosis for a patient with certain symptoms. In the classical expert system a mumber of experts are asked to make statements on the probabilities for different diseases when a combination of systems would appear. One typical expert system uses Fuzzy Logic to suggest the diagnosis. In more modern systems one tends to make the system self learning to improve the system. Hoping for comments Ralf Finne Swenska yrkeshögskolan Vasa Finland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Help needed on Normality test
The 2 tests are testing different hypotheses. The KS test is testing the null that the data comes from a normal with mean 0 and sd 0.11908969, this can be false if the data is not normal or if the mean is not 0 or if the sd is not 0.0119 or any combination of the 3. The Shapiro test was not given a specific mean and sd so it is just testing normality, not mean or sd. You should really be asking the question of why do you want to know if the data is normal? If your sample size is small then these tests don't have enough power to truly distinguish between distributions (and 1 outlier can cause you to falsly reject normality if it is true). If your sample size is large then the CLT comes into play in many common analyses and it does not matter if the population is normal or not. In many cases the better question is Is this data close enough to normal? and that question is often better answered by a qq normal plot than a p-value. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Megh Dal Sent: Tuesday, January 29, 2008 7:57 AM To: [EMAIL PROTECTED] Subject: [R] Help needed on Normality test Hi all T gurus, I would like to test if my dataset is indeed from N(0, 0.011908969). K.S. test gives following result: ks.test(data, pnorm, 0, 0.011908969) One-sample Kolmogorov-Smirnov test data: data D = 0.1092, p-value = 1.318e-05 alternative hypothesis: two-sided How ever Shapiro-Wilk test give following : shapiro.test(data) Shapiro-Wilk normality test data: data W = 0.9946, p-value = 0.07562 also, sd(data) [1] 0.01625074 2nd test saying data is from normal however 1st isnot. Which one is correct? Am I missing something? Regards, - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fortunes - was Re: [OT] vernacular names for circular di
On 29-Jan-08 18:52:30, John Kane wrote:
Any idea who did? I have it in my list of quotes and
attributed to you.
Anon is so boring as a source.
It was Jim Lemon, earlier in this thread:
Date: Tue, 29 Jan 2008 22:16:55 +1100
Ted.
--- Gabor Grothendieck [EMAIL PROTECTED]
wrote:
I did not write that.
On Jan 29, 2008 9:05 AM, S Ellison
[EMAIL PROTECTED] wrote:
Gabor Grothendieck [EMAIL PROTECTED]
29/01/2008 12:35:27
As is common in human affairs, even
the illusion of understanding is preferred to a
lofty digression
upon
why the audience does not understand.
Gabor,
This should be in fortunes; it is depressingly
accurate.
But it doesn't have to be a lofty digression.
S
***
This email and any attachments are confidential.
Any u...{{dropped:9}}
__
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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.
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E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 29-Jan-08 Time: 21:24:29
-- XFMail --
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[R] rpart Error in yval[, 1] : incorrect number of dimensions
I am trying to make a decision tree using rpart. The function runs very quickly considering the size of the data (1742, 163). When I call the summary command I get this: summary(bookings.cart) Call: rpart(formula = totalRev ~ ., data = bookings, method = class) n=1741 (1 observation deleted due to missingness) CP nsplit rel error 1 0 0 1 Error in yval[, 1] : incorrect number of dimensions note: dim(bookings) [1] 1742 163 I have run rpart on past projects without any problems. I have used a catagorical version of the variable totalRev that was partitioned into four levels (and coded as a factor). Does anyone have any ideas that might help? [[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] B-W stacked area chart with pattern
I would question if a stacked area chart is really the best way to display information on 12 groups. You can put a lot of information into the plot, but the viewer will probably experience information overload and not be able to get much useful information out of the plot. Stacked area plots rely on people being able to compare areas and lengths, which we don't do as well as we compare positions in a graph. If your viewer is needing to go back and forth between the legend and the graph, then the information will be harder to assimilate. It may be better to use lattice/trellis graphs and plot each line in its own panel (on the same scale and possibly with a light background grid to make comparison easier). If there are specific comparisons that you want to point out, then make a separate graph with just those comparisons leaving out the extra information that will just distract. If you give us a better idea of what information you are trying to convey, we may be able to give you some better options for graphs to use. If you really want to go the pattern route then you may want to look at the discussion from october that started with: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/111226.html and/or the discussion from earlier this week started by yaosheng CHEN with the subject How to fill bar plot with textile rather than color. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Markus Didion Sent: Tuesday, January 29, 2008 8:42 AM To: hadley wickham Cc: r-help@r-project.org Subject: Re: [R] B-W stacked area chart with pattern Thanks Hadley for your comment. I've got a minimum of 12 species and thus just using different greys won't do it. I've tried it with two background fills, i.e. white and a medium grey, and then used various angles for the shading lines, even plotted it twice to obtain some sort of cross shading. For good, distinguishable patterns I've been hoping to be able to fill an area with different symbols. Markus hadley wickham wrote: On Jan 29, 2008 9:12 AM, Markus Didion [EMAIL PROTECTED] wrote: Dear all, I would like to create a stacked area chart to show the development of species biomass over time. Since it is intended for publication I need to prepare in black and white. I have tried to modify the stackedPlot function submitted to this list by Christian Lasarczyk on Tue, 16 Aug 2005 using shading lines rather than colors to distinguish between the species. Unfortunately, the result was not very satisfying as the options using different angles and densities for the shading lines was not sufficient to clearly distinguish between species. I would thus like to use different pattern (or texture) for this purpose. I have searched the various help lists on graphics in R but was unable to find something appropriate. How many species do you have? Coming about with a good (distinguishable) set of patterns is a difficult task. Have you tried just using different greys? Hadley -- Markus Didion Waldökologie Forest Ecology Inst. f. Terrestrische OekosystemeInst. of Terrestrial Ecosystems Departement Umweltwissenschaften Dept. of Environmental Sciences Eidg. Technische Hochschule Swiss Fed. Inst. of Technology ETH-Zentrum CHN G78 ETH-Zentrum CHN G78 Universitätstr. 22Universitaetstr. 22 CH-8092 ZürichCH-8092 Zurich Schweiz Switzerland Tel +41 (0)44 632 5629Fax +41 (0)44 632 1358 Email [EMAIL PROTECTED] homepage: http://www.fe.ethz.ch/people/didionm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Convert string for expression in plot
Richard Longland wrote:
Thanks for the help. This substitute command might be what I'm after,
but, the whole string is being read in from a file. So I can't
explicitly write the thing out as you did in your example, as with your
example in R-news.
My rules are:
Convert any ,g or g, to ,gamma or gamma,
(This comma search avoids converting the Mg to Mgamma!)
Make ANY number a superscript.
Currently, this is what I do:
# Read in the reaction name, not very elegant I know
ReacName -
as.character(read.table(file.dat,skip=0,header=FALSE,nrows=1)$V1)
print(ReacName)
# convert and numbers and g
ReacName - sub(,g,,gamma,ReacName)
ReacName - sub(g,,gamma,,ReacName)
ReacName - gsub(([1-9]),phantom()^\\1,ReacName)
replace the last line by
ReacName - gsub(([[:digit:]]+), phantom()^{\\1}*, ReacName)
and later perhaps something ugly like
plot(1:10, main=parse(text=ReacName)))
Uwe Ligges
print(ReacName)
This results in:
25Mg(p,g)
phantom()^2phantom()^5Mg(p,gamma)
Just to clarify quickly, The text will always be different. The Mg could
be Al, S etc. The p could be different also. So the whole name has to be
automated into the plot title.
I imagine it's possible to split this string into pieces... but there
must be a better and easier way to do this.
Thanks again for the help,
Richard
On Tue, 2008-01-29 at 18:54 +0100, Uwe Ligges wrote:
Richard Longland wrote:
Hi,
Although I understand how to use expression and paste to add
superscripts and symbols to my graphs, I have a problem with adding
superscripts to an existing string.
For example, I read in the following from a separate file:
25Mg(p,g)
I want to convert that to superscripts etc. (in LaTex format):
$^{25}$Mg(p,$\gamma$)
This needs to then be put into a graph title.
Any ideas? I know that I can just write it in using expression and
paste, but the title is read in from a separate file.
If you explain what the rules are to use superscript or greek letters
(why is the p not converted to pi but the g to gamma, etc?), we ca help,
as an example if you read just the number from a file:
#number - scan(that_file)
# say you read
number - 25
plot(1:10, main=substitute(phantom()^number * Mg(p, gamma),
list(number=number)))
See ?plotmath and for automating things like this my article in R News
might help:
Ligges, U. (2002): R Help Desk: Automation of Mathematical Annotation in
Plots. R News 2 (3), 32-34.
Best,
Uwe Ligges
Cheers for the help,
Richard longland
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[R] for loop help
Hi,
I have written the following code which works fine
step-5
numSim-15
N-double(numSim)
A-double(numSim)
F-double(numSim)
M-double(numSim)
genx-double(numSim)
for (i in 1:numSim) {
N[i]-20
PN-(runif(N[i], 0, 1))
A[i]-sum(ifelse(PN0.2, 1, 0))
PF- runif((A[i]*0.5), 0, 1)
F[i]-sum(ifelse(PF0.2, 1, 0))
PM- runif((A[i]*0.5), 0, 1)
M[i]-sum(ifelse(PM0.2, 1, 0))
genx[i]- (min(F[i], M[i])*12)
}
data-data.frame(N, A, F, M, genx)
What I would like to do next is to make 'genx' from step '1' the seed for N
in step '2'- run the above code 15 times (numSim), make 'genx' from step '2'
the seed for N in step '3'- run the above code 15 times (numSim) etc
How do I do that?. Any advice would be greatly appreciated
Adriana (R-beginner)
[[alternative HTML version deleted]]
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Re: [R] heatmap and legend
Ng Stanley [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] This should be elementary, but I can't find any resource on creating a legend for heatmap. Please help. Take a look at: * heatmap.2 in gplots package * heatplot in made4 Bioconductor package * heatmap_2 in Heatplus Bioconductor package efg Earl F. Glynn Bioinformatics Stowers Institute for Medical Research __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
On Sun, 27-Jan-2008 at 07:38PM -0500, Gabor Grothendieck wrote:
| On the PC there is a builtin GUI but not on UNIX and there are
| some packages that are OS specific in which case you might
| get more or less selection but probably more. Also depending
| on the specific system you may have greater difficulty installing
| certain packages due to the need to compile them on UNIX
| and the possibility exists that you don't quite have the right
| libraries. On Windows you get binaries so this is not a problem.
| I have repeatedly found that common packages that I took
| for granted on Windows had some problem with installation
| on UNIX and I had to hunt around and figure out what the problem
| was with my UNIDX libraries or possibly some other problem.
| For all R packages this won't be a problem but for packages
| that use C and FORTRAN this can be. Although I am lumping
| all UNIX systems together I think this varies quite a bit from
| one particular type/distro of UNIX/Linux to another and I suspect if you
| are careful in picking out the right one (if you have a choice) you
| will actually have zero problems.
I've had a fair bit of experience with Redhat/Fedora/CentOS and with
Mepis distros. I've had zero problems compiling R or packages.
The only problem I've had is with *using* a package which uses R code
to hard-wire graphic options that don't suit X11, postscript or pdf
devices. Virually every other package I've used doesn't hard-wire
graphic options, so that problem never arises.
YMMV
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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Re: [R] Fortunes - was Re: [OT] vernacular names for circular diagrams
Any idea who did? I have it in my list of quotes and
attributed to you.
Anon is so boring as a source.
--- Gabor Grothendieck [EMAIL PROTECTED]
wrote:
I did not write that.
On Jan 29, 2008 9:05 AM, S Ellison
[EMAIL PROTECTED] wrote:
Gabor Grothendieck [EMAIL PROTECTED]
29/01/2008 12:35:27
As is common in human affairs, even
the illusion of understanding is preferred to a
lofty digression
upon
why the audience does not understand.
Gabor,
This should be in fortunes; it is depressingly
accurate.
But it doesn't have to be a lofty digression.
S
***
This email and any attachments are confidential.
Any u...{{dropped:9}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
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and provide commented, minimal, self-contained, reproducible code.
[R] coherency and phase plots
I am having a hard time interpreting the phase and coherency plots. x is two timeseries that occur at the same time i.e. a b 1 11.2 12.3 16 11.3 12.4 31 11.4 12.5 46 11.5 12.6 ...etc even though my example is does not show this they are oscillating at more or less the same frequency just shifted by t=x (imagine two sine waves offset with the 2nd sine wave starting at the peak of the first). I would like to know what x is. I think I am looking for the phase shift? The coherency? Cross-spectrum? And I have read the help files, Shumway and Stoffer has a small section on this, I don't have journal access, and I am having trouble finding anything on the internet. s = spec.pgram(x) par(mfrow = c(2,1)) plot(s, plot.type = coh) plot(s, plot.type = pha) Can R do the cross-spectrum of two timeseries? How? -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] on trellis.par.set/get (reproducing figures from Pinheiro Bates)
On 1/29/08, Dr. Ottorino-Luca Pantani [EMAIL PROTECTED] wrote: Dear R users, I would like to exactly reproduce a figure like the 1.5 or 1.9 or 4.13 from the book Mixed effects models in S and S-Plus. Not for the sake of it, but because I have my own data I would like to plot in that fashion (no colors) If I write plot(ergoStool) I can get a good informative plot with colors, but I would like to have a BW one instead. Have you tried trellis.device(color = FALSE) plot(ergoStool) -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bootstrap sampling using sample
Hello All, I used sample(..., replace = TRUE) repeatedly to generate 100 bootstrap samples of a data that I'm working with. If I re-run my codes, it'll generate a different set of 100 bootstrap samples. Is there any way that I can get the same set of 100 bootstrap re-samples at each re-run of my codes? Something like setting the seed in a random number generator... Any help is very much appreciated. Thanks, Majnu [[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] bootstrap sampling using sample
see ?set.seed On 29/01/2008, Majnu John [EMAIL PROTECTED] wrote: Hello All, I used sample(..., replace = TRUE) repeatedly to generate 100 bootstrap samples of a data that I'm working with. If I re-run my codes, it'll generate a different set of 100 bootstrap samples. Is there any way that I can get the same set of 100 bootstrap re-samples at each re-run of my codes? Something like setting the seed in a random number generator... Any help is very much appreciated. Thanks, Majnu [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Linux, UNIX, XP32, Vista X64 or ...? [SEC=UNCLASSIFIED]
On Jan 29, 2008 2:30 PM, Patrick Connolly [EMAIL PROTECTED] wrote: On Sun, 27-Jan-2008 at 07:38PM -0500, Gabor Grothendieck wrote: | On the PC there is a builtin GUI but not on UNIX and there are | some packages that are OS specific in which case you might | get more or less selection but probably more. Also depending | on the specific system you may have greater difficulty installing | certain packages due to the need to compile them on UNIX | and the possibility exists that you don't quite have the right | libraries. On Windows you get binaries so this is not a problem. | I have repeatedly found that common packages that I took | for granted on Windows had some problem with installation | on UNIX and I had to hunt around and figure out what the problem | was with my UNIDX libraries or possibly some other problem. | For all R packages this won't be a problem but for packages | that use C and FORTRAN this can be. Although I am lumping | all UNIX systems together I think this varies quite a bit from | one particular type/distro of UNIX/Linux to another and I suspect if you | are careful in picking out the right one (if you have a choice) you | will actually have zero problems. I've had a fair bit of experience with Redhat/Fedora/CentOS and with Mepis distros. I've had zero problems compiling R or packages. The only problem I've had is with *using* a package which uses R code to hard-wire graphic options that don't suit X11, postscript or pdf devices. Virually every other package I've used doesn't hard-wire graphic options, so that problem never arises. I assume you are referring to 32 bit FC because I certainly have had library problelms on 64 bit FC. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Logit Regressions, Clustering etc
Paul Sweeting wrote: Hi Sorry to bother the list again, but no-one has so far been able to suggest any help for the query below. As an added incentive, I have been asked why don't you do this in Stata? It's just a case of adding a flag in the regression... I'm loathe to start learning another stats package, so if anyone is able to help...! Thanks Paul library(Design) f - lrm(Y ~ x1 + x2 + ..., x=TRUE, y=TRUE) g - robcov(f, subjectID) anova(g) summary(g) etc. Frank Hi I am carrying out some logit regressions and want to (a) make sure I'm taking the right approach and (b) work out how to carry out some additional analysis. So, to carry out a logit regression where the dependent variable is a factor db, I use something like: res1_l - glm(formula = db ~ y1 + … + y5, family = binomial(link = logit)) summary(res1_l) ...which is, I hope correct. I also need to carry out an ordered logit regression. Is this as simple as: res1_l - polr(formula = db ~ y1 + … + y5) summary(res1_l) ..with db being a factor which has more levels than just 0 and 1? Assuming it is, the part I am really struggling with is the calculation of robust standard errors to allow for clustering. In an ordinary regression, I’ve used survreg, where the data has also been censored, e.g.: res1 - survreg(formula = Surv(ip, db_Censor) ~ y1 + … y5 + cluster(db_ID), dist = gaussian) summary(res1) This has the benefit of giving a nice clear display of the naïve standard error as well as the robust one - is there any way of getting similar output for a logit and an ordered logit regression Thanks in advance for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] B-W stacked area chart with pattern
I would support this advice. Stacked bar charts are generally not recommended because comparisons are difficult. Having 12 groups increases the difficulty. Best have a look at Cleveland's work before you go down your currently intended path. Try delving into Elements of Graphing Data and Visualizing Data. David Scott On Tue, 29 Jan 2008, Greg Snow wrote: I would question if a stacked area chart is really the best way to display information on 12 groups. You can put a lot of information into the plot, but the viewer will probably experience information overload and not be able to get much useful information out of the plot. Stacked area plots rely on people being able to compare areas and lengths, which we don't do as well as we compare positions in a graph. If your viewer is needing to go back and forth between the legend and the graph, then the information will be harder to assimilate. It may be better to use lattice/trellis graphs and plot each line in its own panel (on the same scale and possibly with a light background grid to make comparison easier). If there are specific comparisons that you want to point out, then make a separate graph with just those comparisons leaving out the extra information that will just distract. If you give us a better idea of what information you are trying to convey, we may be able to give you some better options for graphs to use. If you really want to go the pattern route then you may want to look at the discussion from october that started with: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/111226.html and/or the discussion from earlier this week started by yaosheng CHEN with the subject How to fill bar plot with textile rather than color. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Markus Didion Sent: Tuesday, January 29, 2008 8:42 AM To: hadley wickham Cc: r-help@r-project.org Subject: Re: [R] B-W stacked area chart with pattern Thanks Hadley for your comment. I've got a minimum of 12 species and thus just using different greys won't do it. I've tried it with two background fills, i.e. white and a medium grey, and then used various angles for the shading lines, even plotted it twice to obtain some sort of cross shading. For good, distinguishable patterns I've been hoping to be able to fill an area with different symbols. Markus hadley wickham wrote: On Jan 29, 2008 9:12 AM, Markus Didion [EMAIL PROTECTED] wrote: Dear all, I would like to create a stacked area chart to show the development of species biomass over time. Since it is intended for publication I need to prepare in black and white. I have tried to modify the stackedPlot function submitted to this list by Christian Lasarczyk on Tue, 16 Aug 2005 using shading lines rather than colors to distinguish between the species. Unfortunately, the result was not very satisfying as the options using different angles and densities for the shading lines was not sufficient to clearly distinguish between species. I would thus like to use different pattern (or texture) for this purpose. I have searched the various help lists on graphics in R but was unable to find something appropriate. How many species do you have? Coming about with a good (distinguishable) set of patterns is a difficult task. Have you tried just using different greys? Hadley -- Markus Didion WaldökologieForest Ecology Inst. f. Terrestrische Oekosysteme Inst. of Terrestrial Ecosystems Departement UmweltwissenschaftenDept. of Environmental Sciences Eidg. Technische Hochschule Swiss Fed. Inst. of Technology ETH-Zentrum CHN G78 ETH-Zentrum CHN G78 Universitätstr. 22 Universitaetstr. 22 CH-8092 Zürich CH-8092 Zurich Schweiz Switzerland Tel +41 (0)44 632 5629 Fax +41 (0)44 632 1358 Email [EMAIL PROTECTED] homepage: http://www.fe.ethz.ch/people/didionm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. _ David Scott Department of Statistics, Tamaki Campus The University of Auckland, PB 92019 Auckland 1142,NEW ZEALAND Phone: +64 9 373 7599 ext 86830 Fax: +64
Re: [R] for loop help
Is this what you want?
numSim - 15
genx-double(numSim)
N - rep(20, numSim)
A - F - M - numeric(numSim)
result - lapply(1:5, function(.x){
+ for (i in 1:numSim) {
+ PN-(runif(N[i], 0, 1))
+ A[i]-sum(ifelse(PN0.2, 1, 0))
+ PF- runif((A[i]*0.5), 0, 1)
+ F[i]-sum(ifelse(PF0.2, 1, 0))
+ PM- runif((A[i]*0.5), 0, 1)
+ M[i]-sum(ifelse(PM0.2, 1, 0))
+ genx[i]- (min(F[i], M[i])*12)
+ }
+
+ data - data.frame(N, A, F, M, genx)
+ N - genx # assign at the top level
+ data # return the data frame
+ })
result
[[1]]
N A F M genx
1 20 16 6 7 72
2 20 12 6 4 48
3 20 16 5 8 60
4 20 18 7 6 72
5 20 14 6 7 72
6 20 18 8 8 96
7 20 15 3 7 36
8 20 13 5 6 60
9 20 15 7 5 60
10 20 15 6 7 72
11 20 16 6 5 60
12 20 13 5 6 60
13 20 15 6 6 72
14 20 15 6 7 72
15 20 20 8 8 96
[[2]]
N A F M genx
1 72 60 21 25 252
2 48 39 17 15 180
3 60 50 18 22 216
4 72 55 20 18 216
5 72 57 22 25 264
6 96 72 29 25 300
7 36 28 12 8 96
8 60 51 18 22 216
9 60 49 19 20 228
10 72 56 24 21 252
11 60 47 19 17 204
12 60 44 18 20 216
13 72 59 21 26 252
14 72 56 24 21 252
15 96 75 33 32 384
[[3]]
N A F M genx
1 252 209 81 84 972
2 180 137 54 59 648
3 216 172 66 69 792
4 216 166 59 65 708
5 264 226 92 93 1104
6 300 246 106 93 1116
7 96 74 29 28 336
8 216 171 68 70 816
9 228 183 74 75 888
10 252 207 83 77 924
11 204 166 65 63 756
12 216 169 69 67 804
13 252 195 74 79 888
14 252 200 88 89 1056
15 384 297 118 119 1416
[[4]]
NA F M genx
1 972 799 313 316 3756
2 648 523 213 217 2556
3 792 646 259 256 3072
4 708 575 242 231 2772
5 1104 888 372 351 4212
6 1116 913 365 353 4236
7 336 272 114 100 1200
8 816 650 250 262 3000
9 888 718 285 296 3420
10 924 741 302 291 3492
11 756 603 260 245 2940
12 804 637 249 245 2940
13 888 720 288 281 3372
14 1056 847 343 353 4116
15 1416 438 446 5256
[[5]]
NAFM genx
1 3756 3021 1229 1232 14748
2 2556 2057 830 793 9516
3 3072 2463 1009 982 11784
4 2772 2214 884 884 10608
5 4212 3385 1355 1361 16260
6 4236 3380 1329 1368 15948
7 1200 986 376 400 4512
8 3000 2407 966 960 11520
9 3420 2702 1091 1090 13080
10 3492 2778 1130 1133 13560
11 2940 2361 932 952 11184
12 2940 2289 932 903 10836
13 3372 2680 1045 1054 12540
14 4116 3279 1305 1304 15648
15 5256 4233 1713 1715 20556
On Jan 29, 2008 2:23 PM, Adriana Bejarano [EMAIL PROTECTED] wrote:
Hi,
I have written the following code which works fine
step-5
numSim-15
N-double(numSim)
A-double(numSim)
F-double(numSim)
M-double(numSim)
genx-double(numSim)
for (i in 1:numSim) {
N[i]-20
PN-(runif(N[i], 0, 1))
A[i]-sum(ifelse(PN0.2, 1, 0))
PF- runif((A[i]*0.5), 0, 1)
F[i]-sum(ifelse(PF0.2, 1, 0))
PM- runif((A[i]*0.5), 0, 1)
M[i]-sum(ifelse(PM0.2, 1, 0))
genx[i]- (min(F[i], M[i])*12)
}
data-data.frame(N, A, F, M, genx)
What I would like to do next is to make 'genx' from step '1' the seed for N
in step '2'- run the above code 15 times (numSim), make 'genx' from step '2'
the seed for N in step '3'- run the above code 15 times (numSim) etc…
How do I do that?. Any advice would be greatly appreciated
Adriana (R-beginner)
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
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+1 513 646 9390
What is the problem 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.
[R] drawing arrows with rgl
Hi, I am looking for a package which allows me to draw arrows (cylinders with cones on them, basically) in 3d images produced with rgl. Is such a thing available? I did notice the 'compositions' package, which contains 'arrow3D'. However, it relies on 'tensorA', which fails to install on my machine with the error message copied below. If anyone can help me fix this problem, that would do the trick too. Best, Kasper trying URL 'http://www.sourcekeg.co.uk/cran/src/contrib/tensorA_0.31.tar.gz' Content type 'application/x-tar' length 45248 bytes opened URL == downloaded 44Kb * Installing *source* package 'tensorA' ... ** libs gcc -I/usr/lib/R/include -fPIC -g -O2 -c tensora.c -o tensora.o gcc -shared -o tensorA.so tensora.o -L/usr/lib/R/lib -lR ** R ** preparing package for lazy loading Error in gettext(domain, unlist(args)) : invalid 'domain' value Execution halted ERROR: lazy loading failed for package 'tensorA' ** Removing '/usr/local/lib/R/site-library/tensorA' The downloaded packages are in /tmp/RtmpikOKjt/downloaded_packages Warning message: installation of package 'tensorA' had non-zero exit status in: install.packages tensorA) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Direct adjusted survival?
Hello, I am trying to find an R function to compute 'direct adjusted survival' with standard errors. A SAS-macro to do this is presented in Zhang X, Loberiza FR, Klein JP, Zhang MJ. A SAS macro for estimation of direct adjusted survival curves based on a stratified Cox regression model. Comput Methods Programs Biomed 2007;88:95-101. It appears that this method is not implemented in R. Can anyone prove me wrong? Thank you for your time and assistance, Peter. [[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] Compiling R code
One suggestion you have probably already considered, but: why not R CMD BATCH the script? You can set up an executable to do that. No need to compile the actual R code. If you want to hide the code and/or it has interaction, you can also set it up on a web or intranet server for them, calling the R.so or R.dll from a simple .NET or python script or something like that.. just some ideas, daniel On Jan 29, 2008 1:01 PM, Attiglah, Mama [EMAIL PROTECTED] wrote: Hi all, I am struggling to compile a massive R code that I have written through some years, aiming to provide automated investment strategies to my Portfolio Managers. You may ask me why do I not rewrite the code in C or C++; the answer is it is really massive and that will take me lots of time. The pb is I will be moving from one team to another therefore I want to make it an exec program that the PMs can run in their investment universe without my help. I am using the very long method described in the R extension doc which is taking me time as each block of the code needs to be carefully evaluated. I researched about the RCC project aiming to do the job but it seems to me that the compiler is not yet available. Is anyone experienced in compiling R code to an exec file or had a similar experience in the past? Thanks Mama - Mama Attiglah, PhD Advanced Research Center Quantitative Research Analyst State Street Bank +44(0)20 7698 6290 (Direct Line) +44 (0)207 004 2968 (Direct Fax) Please visit our Web site at www.ssga.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] drawing arrows with rgl
On 1/29/2008 6:23 PM, Kasper Peeters wrote: Hi, I am looking for a package which allows me to draw arrows (cylinders with cones on them, basically) in 3d images produced with rgl. Is such a thing available? The shapes3d demo in rgl draws cones. You could use the same ideas to draw cylinders. Once you have instructions to draw one prototypical arrow, you can use the scale3d, translate3d and rotate3d functions to reshape it and move it. I've never found such arrows very visually pleasing, but if you do find a way to draw nice ones, please post the code here. Duncan Murdoch I did notice the 'compositions' package, which contains 'arrow3D'. However, it relies on 'tensorA', which fails to install on my machine with the error message copied below. If anyone can help me fix this problem, that would do the trick too. Best, Kasper trying URL 'http://www.sourcekeg.co.uk/cran/src/contrib/tensorA_0.31.tar.gz' Content type 'application/x-tar' length 45248 bytes opened URL == downloaded 44Kb * Installing *source* package 'tensorA' ... ** libs gcc -I/usr/lib/R/include -fPIC -g -O2 -c tensora.c -o tensora.o gcc -shared -o tensorA.so tensora.o -L/usr/lib/R/lib -lR ** R ** preparing package for lazy loading Error in gettext(domain, unlist(args)) : invalid 'domain' value Execution halted ERROR: lazy loading failed for package 'tensorA' ** Removing '/usr/local/lib/R/site-library/tensorA' The downloaded packages are in /tmp/RtmpikOKjt/downloaded_packages Warning message: installation of package 'tensorA' had non-zero exit status in: install.packages tensorA) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Package simex
Dear Michael If I understand you correctly, you already have an estimate of the measurement error? It would seem that if you can estimate the error, then this estimate comes with a standard error. For example, suppose that you have a nonlinear model where one of the predictors is a sum of two variables, which has been measured with error. You then want to use simex to extrapolate the value the estimator of the nonlinear model would have if there were no error. If these two variables are related according to a factor model, then the measurement error estimate would be the correlation between the variables, with the corresponding s.e. (assuming the reliabilities of the variables are equal). It depends of course what the measurement model and corresponding estimates are but you usually get a standard error with the estimate. If you want to take into account the variability in this estimate, in the case of simex an approach would be to simulate values of the measurement error estimates from its distribution using the standard error, and repeat the simex procedure each time. You are then in the framework of multiple imputation. So you need to record the between- and within- variance and covariance of the estimates, and then combine them according to the rules laid out by Rubin to get the final variance of the nonlinear model's estimates. The between covariance matrix you get from the simulations. The within covariance matrix as I understood from the book needs to be bootstrapped. So it is quite a process but certainly possible! -daniel P.S. Note that simex is an approximate method; if you possibly can use them, the alternative likelihood based or estimating equations approaches provide a method of correcting the standard errors for uncertainty in the measurement error estimates. This is explained in the book by Carroll, Ruppert Stefanski, in the appendix. On Jan 28, 2008 2:36 AM, Michael Kubovy [EMAIL PROTECTED] wrote: Dear R-helpers, It is not clear to me how you get measurement.error SD when you have a single dataset, and it is not clear to me how sensitive SIMEX is to errors in the estimates of measurement error. Could someone please point me to the relevant literature? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/http://www.people.virginia.edu/%7Emk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Direct adjusted survival?
On Wed, 30 Jan 2008, Peter Jepsen wrote: I am trying to find an R function to compute 'direct adjusted survival' with standard errors. A SAS-macro to do this is presented in Zhang X, Loberiza FR, Klein JP, Zhang MJ. A SAS macro for estimation of direct adjusted survival curves based on a stratified Cox regression model. Comput Methods Programs Biomed 2007;88:95-101. It appears that this method is not implemented in R. Can anyone prove me wrong? This looks like what survexp() does. It's hard to be sure, since I can only find the abstract online. -thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] assign column classes when creating a data frame from several vectors
R-helpers, Thanks in advance for your help. I am an R newbie and I am having trouble figuring out the easiest/most efficient way to assign classes to columns in a newly created data frame. R seems to want to convert everything to a factor when I use the cbind function to compile vectors into a data frame. ID-seq(1,10,1) TREAT-c(rep(B,5),rep(G,5)) T1-rnorm(10,50,10) T2-rnorm(10,15,10) data-as.data.frame(cbind(ID,TREAT,T1,T2)) data ID TREAT T1T2 1 1 B 41.506987139726 20.0964019326073 2 2 B 53.7814271299636 4.9049787919397 3 3 B 54.118333111305 18.2182330777312 4 4 B 48.8591282265369 12.4561774992591 5 5 B 32.3160291908524 23.6665858869752 6 6 G 52.3181626145907 -4.60173207209386 7 7 G 53.4170845444393 2.30744010208809 8 8 G 60.4200675102018 10.9954680147326 9 9 G 42.6264529901835 9.22980548637643 10 10 G 40.2748346897501 14.2458580129253 sapply(data,class) IDTREAT T1 T2 factor factor factor factor The only way I can find to get around this is to use stringsAsFactors=FALSE and then assign classes to each of the columns individually. data-as.data.frame(cbind(ID,TREAT,T1,T2), stringsAsFactors=F) data$ID-as.factor(data$ID) data$TREAT-as.factor(data$TREAT) data$T1-as.numeric(data$T1) data$T2-as.numeric(data$T2) sapply(data,class) ID TREATT1T2 factor factor numeric numeric Is there a more efficient way to do the same thing. Thanks for your help. -- View this message in context: http://www.nabble.com/assign-column-classes-when-creating-a-data-frame-from-several-vectors-tp15174042p15174042.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] Scale function
pellegrini [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: There is something that I do not get with scale function. Say that I have a vector v - c(1,2,3,4,5,6), scale(v,center=TRUE,scale=TRUE) gives a new vector with 0 as mean and 1 as standard deviation. but, scale(v, center=FALSE,scale=TRUE) gives a new vector with a standard deviation different from 1. I would also expect a standard deviation of 1 in that case. am I wrong ? Appears that you are. From the help page: If scale is TRUE then scaling is done by dividing the (centered) columns of x by their root-mean-square. The root-mean-square for a column is obtained by computing the square- root of the sum-of-squares of the non-missing values in the column divided by the number of non-missing values minus one. sd(scale(warpbreaks$breaks, scale=TRUE)) #default is center=TRUE [1] 1 sd(scale(warpbreaks$breaks, center=FALSE, scale=TRUE)) [1] 0.4212988 -- 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] Guidance for reporting results from lme test?
Dear Ronny, I have sucsessfully used a linear mixed effect model, lme, (REML). The results are satisfactory, but I have problems with sorting out how to report the result in a scientific paper. Is there a genearal guidance for reporting lme results available (web page, book or article)? This is likely to depend on the specific subject area that you are working in. I minimally report F-values and their degrees of freedom plus the p-value in applied biology. This is sometimes complemented by reporting the parameter estimates (and either their estimated standard error or a confidence interval) or by a figure including the model fit. Mostly, the random effects are described in the methods section as how they reflect experimental design but often no specific details are reported. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat., postdoc Federal Veterinary Office Centre for proper housing of ruminants and pigs Agroscope Reckenholz-Tänikon Research Station ART Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Concatenate xyplots
Dear R-community, I created 5 different xyplots and graphed all of them with the print command on one page (e.g. print(graph1, split=c(1,1,1,5), more = T) ... print(graph5, split=c(1,5,1,5), more =T) Using the above commands separates each graph by a white space. However, since the graphs do share the same x-axis, I was wondering if there is a way to concatenate graph1 through 5 so that the white space disappears? Thanks for your time and help Best, Jan Jan EitelPhD Candidate of Remote Sensing Room 12 CNRCollege of Natural ResourcesUniversity of IdahoMoscow, ID 83844-1133Phone: (208)596-9277Em: [EMAIL PROTECTED]://www.cnrhome.uidaho.edu/default.aspx?pid=68846 [[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] Integer vs numeric
x[c(2,4)] work as well
Henrik Bengtsson a écrit :
x[1:n]
/H
On Jan 29, 2008 5:07 AM, [EMAIL PROTECTED] wrote:
Seems strange to me to define an operator relatively to a very special case.
I have to admit that I do not use 1:1e7 every day :-)
Wouldn't it be more appropriate to define a a:b operator numeric (that
is preserving the initial class of a and b) and in specific case that
need optimization, changing the type?
for i in as.integer(1:1e7)
That might appears as a minor point, but when using S4, for what I
know, if you define a class that can take either 1:3 or c(1,3,4), one
is integer, the other numeric, one of those will not be accepted by the
class...
Christophe
On 28-Jan-08 22:40:02, Peter Dalgaard wrote:
[...]
AFAIR, space is/was more of an issue. If you do something like
for i in 1:1e7
some.silly.simulation()
then you have 40 MB sitting there doing nothing, and 80 MB if
it had been floating point.
Hmmm ... there's something to be said for good old
for(i=1,i=1e7,i++){}
As pointed out in ?for, when you do
for(i in X){...} #(e.g. X=(1:1e7))
the object X is created (or is already there) in full
at the start and sits there, as you say doing nothing,
until you end the loop. Whereas the C code just keeps
track of i and of the condition.
At least on a couple of my machines (64MB and 184MB RAM)
knocking out 40MB would inflict severe trauma! Let alone 80MB.
Mind you, the little one is no longer allowed to play with
big boys like R, though the other one is still used for
moderate-sized games.
Would there be much of a time penalty in implementing
a 'for' loop, C-style, as
i-1
while(i=1e7){
...
i-i+1
}
??
It looks as though there might be:
system.time(for(i in (1:1e7)) x-cos(3) )
#[1] 13.521 0.132 13.355 0.000 0.000
system.time({i-1;while(i=1e7){x-cos(3);i-i+1}})
#[1] 38.270 0.076 37.629 0.000 0.000
which suggests that the latter is about 3 times as slow.
(And no, this wasn't done on either of my puny babes).
(And this isn't the first time I've wished for an R
implementation of ++ as a CPU-level incrementation,
as opposed to the R-arithmetic implementation which
treats adding 1 to a variable as a full-dress
arithmetic parade!
Best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 28-Jan-08 Time: 23:34:52
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Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
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Re: [R] Random and fixed effect model with a covariate
Dear Sophie, I wonder if anyone can please offer any advice on a model including 2 fixed effects and 1 random effect, as well as a covariate? The experimental design is as follows: I have a two by two factor design, where the two factors, Age (A) and Group size (G), both have 2 levels (old or young, and 1 or 3 respectively), and I am interested in the effect of these factors upon a continuous Response variable (R). The data is from social insects, so the above design is repeated for several colonies. I think that Colony (C) should be a random factor, as they were taken from a larger pool of available colonies. Identification number (I) is different for each individual. Furthermore, I have a covariate, Mass (M), which could have an effect upon R. This sounds all quite reasonable. Do you know which of the below (if any) would be the most appropriate model please? model-lme(R~A*G*M,random=~1|C/I) model-lme(R~A*G+M,random=~1|C/I) Well, this depends on your research question and whether or not interactions between A:M, A:G and A:G:M can be interpreted meaningfully, I would say. or is it necessary to state that A and G are factors as below: model-lme(R~as.factor(A)*as.factor(G)*M,random= ~1|C/I) model-lme(R~as.factor(A)*as.factor(G)+M,random= ~1|C/I) Yes, indeed, you need to specify factors as such. If they are factors it possibly makes sense to change their type in the data frame as many other functions (e.g. plotting functions) do different things with factors rather than continuous variables. If your factor levels include letters then R automatically turns these variables into factors while you read the data. A two-level factor can be coded numerically with 0 and 1s instead of explicitly turning it into a factor variable. Do you also please have any advice upon the effect it would have to change the order in which the factors and covariate are placed in the model? When I tried moving them around in the above models it changed the test statistics slightly. Well, the standard anova output follows a type I sum-of-squares logic, i.e. each addditional variable (lower down in the list) is tested for a significant improvement of the model so far. Thus, the seuquence has some importance. If you use anova (..., type= 'marginal') you can follow a type III sum-of-squares logic, i.e. it is tested whether dropping a specific variable from the full model leads to a significant deterioration of the model or not. In my perception, there are different schools of thought that either prefer the one or the other. Thus, perhaps you should use what is commonly used in your field. Regards, Lorenz - Lorenz Gygax, Dr. sc. nat., postdoc Federal Veterinary Office Centre for proper housing of ruminants and pigs Agroscope Reckenholz-Tänikon Research Station ART Tänikon, CH-8356 Ettenhausen / Switzerland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Multiplying each row of a big matrix with a vector
I have a big matrix 'ret'. I want to multiply each row of it with a 2nd vector
'pos', resulting result, I want to save in a vector named 'port'. I wrote
following code:
pos
[1] 2593419 2130220 6198197 1673888 198 1784732 2052120 -7490228
-5275000
dim(ret)
[1] 500 9
fu# user defined function
function(x)
{
fu = x %*% t(pos)
}
port = apply(ret, 1, fu)
dim(port)
[1] 81 500
My desire is to get port as a vector with length 500. However I am not
getting that?
Can anyone tell me how to correct that?
Regards,
-
[[alternative HTML version deleted]]
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Re: [R] Multiplying each row of a big matrix with a vector
port - as.vector(ret %*% port)
should do it.
Bill Venables
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Megh Dal
Sent: Wednesday, 30 January 2008 5:20 PM
To: [EMAIL PROTECTED]
Subject: [R] Multiplying each row of a big matrix with a vector
I have a big matrix 'ret'. I want to multiply each row of it with a 2nd
vector 'pos', resulting result, I want to save in a vector named 'port'.
I wrote following code:
pos
[1] 2593419 2130220 6198197 1673888 198 1784732 2052120
-7490228 -5275000
dim(ret)
[1] 500 9
fu# user defined function
function(x)
{
fu = x %*% t(pos)
}
port = apply(ret, 1, fu)
dim(port)
[1] 81 500
My desire is to get port as a vector with length 500. However I am not
getting that?
Can anyone tell me how to correct that?
Regards,
-
[[alternative HTML version deleted]]
__
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] [OT] vernacular names for circular diagrams
On Mon, 28 Jan 2008 13:38:51 -0600, Roger Koenker wrote: Howard Wainer (Graphical Discovery, PUP, 2005, p 20) gives this dubious honor to Playfair (1759- 1823). Nightingale (1820- 1910) was far too enlightened for this sort of thing, see for example her letter to Galton about endowing an Oxford professorship in social statistics (reprinted in Karl Pearson's bio of Galton: http://galton.org/cgi-bin/searchImages/search/pearson/vol2/pages/vol2_0482.htm It sets a very ambitious agenda that we have not yet made much progress on... So, if the pie chart was invented by Florence Nightingale (1820-1910), then William Playfair (1759-1823) would be guilty of what the surrealists called a plagiarism by anticipation. Best, -- Jean R. Lobry([EMAIL PROTECTED]) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 27 56 fax: +33 472 43 13 88 http://pbil.univ-lyon1.fr/members/lobry/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: Multiplying each row of a big matrix with a vector
I am not sure if you really want what you explain that you want
To multiply each row with a vector you can use e.g.
t(apply(ret,1, function(y) pos*y))
or
t(t(ret)*pos)
but then you will get the same matrix just multiplied by a vector.
If you want to perform matrix multiplication then just
ret %*% pos will do it for you
Petr Pikal
[EMAIL PROTECTED]
[EMAIL PROTECTED] napsal dne 30.01.2008 08:20:21:
I have a big matrix 'ret'. I want to multiply each row of it with a 2nd
vector
'pos', resulting result, I want to save in a vector named 'port'. I
wrote
following code:
pos
[1] 2593419 2130220 6198197 1673888 198 1784732 2052120
-7490228 -5275000
dim(ret)
[1] 500 9
fu# user defined function
function(x)
{
fu = x %*% t(pos)
}
port = apply(ret, 1, fu)
dim(port)
[1] 81 500
My desire is to get port as a vector with length 500. However I am not
getting that?
Can anyone tell me how to correct that?
Regards,
-
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
