Re: [R] Doing pairwise comparisons using either Duncan, Tukey or LSD
On 2/19/2009 11:51 AM, Saeed Ahmadi wrote: > Hi, > > I have a basic and simple question on how to code pairwise (multiple) mean > compariosn between levels of a factor using one of the Duncan, Tukey or LSD. Here is one approach: library(multcomp) summary(glht(lm(Petal.Width ~ Species, data = iris), linfct = mcp(Species = "Tukey"))) > Thanks in advance, > Saeed -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for nlm()
It seems to be in optimize.c Rgonzui has a very nice search facility for source of R or CRAN packages (however it is against R 2.8.0 source): http://rgonzui.nakama.ne.jp/R/markup/R-2.8.0/src/main/optimize.c?fm=c&q=nlm# l378 -Christos > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Ravi Varadhan > Sent: Thursday, February 19, 2009 1:00 PM > To: r-help@r-project.org > Subject: [R] Source code for nlm() > > Hi, > > Where can I find the source code for nlm()? I dowloaded the > R2.8.1.tar.gz file and looked at all the .c and .f files, but > couldn't find either nlm.c or nlm.f > > There is an nlm.r file, but that is not useful. > > Thanks for any help, > Ravi. > > -- > -- > --- > > Ravi Varadhan, Ph.D. > > Assistant Professor, The Center on Aging and Health > > Division of Geriatric Medicine and Gerontology > > Johns Hopkins University > > Ph: (410) 502-2619 > > Fax: (410) 614-9625 > > Email: rvarad...@jhmi.edu > > Webpage: > http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html > > > > -- > -- > > > > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for nlm()
On 19/02/2009 1:00 PM, Ravi Varadhan wrote: Hi, Where can I find the source code for nlm()? I dowloaded the R2.8.1.tar.gz file and looked at all the .c and .f files, but couldn't find either nlm.c or nlm.f There is an nlm.r file, but that is not useful. I don't see why you say it's not useful, because it's the starting point to find the code. See Ligges, U. (2006): R Help Desk: Accessing the Sources. R News 6 (4), 43-45. http://cran.r-project.org/doc/Rnews/ for the next steps. (To save you some time: look in src/main/optimize.c. But Uwe's article would have got you there pretty quickly). Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using R in Java?
nicro schrieb: Hi 2 questions- 1. Is there a package that will allow me to run R scripts (entirely) from Java? 2. If so, is there a way to capture the output of those scripts, (including images) and embed them in my SWT java app? My challenge is I have a java app that does some statistical chores- it would be fantastic if the users could use their R skills to modify a script in whatever R environment they like and then my app could use that script to calculate the results and display them in the app. I have found StatET and JavaGD with rJava/JRI and read through all the docs... its seems possible that some combination may give me what I want, but its not very clear. The JRI part from the rJava package does exactly what you want. Simple data types like numbers or strings are directly returned as java objects. But I'm afraid for the images you have to use the files system indirection. If needed I can post an example, Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Doing pairwise comparisons using either Duncan, Tukey or LSD
try: example(TukeyHSD) hth, Kingsford Jones On Thu, Feb 19, 2009 at 9:51 AM, Saeed Ahmadi wrote: > > Hi, > > I have a basic and simple question on how to code pairwise (multiple) mean > compariosn between levels of a factor using one of the Duncan, Tukey or LSD. > > Thanks in advance, > Saeed > -- > View this message in context: > http://www.nabble.com/Doing-pairwise-comparisons-using-either-Duncan%2C-Tukey-or-LSD-tp22104786p22104786.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using R in Java?
See also Biocep: http://biocep-distrib.r-forge.r-project.org/ -Roy M. On Feb 19, 2009, at 10:42 AM, Christian Ruckert wrote: nicro schrieb: Hi 2 questions- 1. Is there a package that will allow me to run R scripts (entirely) from Java? 2. If so, is there a way to capture the output of those scripts, (including images) and embed them in my SWT java app? My challenge is I have a java app that does some statistical chores- it would be fantastic if the users could use their R skills to modify a script in whatever R environment they like and then my app could use that script to calculate the results and display them in the app. I have found StatET and JavaGD with rJava/JRI and read through all the docs... its seems possible that some combination may give me what I want, but its not very clear. The JRI part from the rJava package does exactly what you want. Simple data types like numbers or strings are directly returned as java objects. But I'm afraid for the images you have to use the files system indirection. If needed I can post an example, Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Source code for nlm()
Thank you, Chris and Duncan. It never occurred to me to look in optimize.c since optimize() does univariate minimization. Furthermore, now I know that the underlying Fortran code (OPTIF9) is from the UNCMIN library (may be this should be mentioned in the help page, although once can get to this information from the second reference). Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch Sent: Thursday, February 19, 2009 1:17 PM To: Ravi Varadhan Cc: r-help@r-project.org Subject: Re: [R] Source code for nlm() On 19/02/2009 1:00 PM, Ravi Varadhan wrote: > Hi, > > Where can I find the source code for nlm()? I dowloaded the > R2.8.1.tar.gz file and looked at all the .c and .f files, but couldn't > find either nlm.c or nlm.f > > There is an nlm.r file, but that is not useful. I don't see why you say it's not useful, because it's the starting point to find the code. See Ligges, U. (2006): R Help Desk: Accessing the Sources. R News 6 (4), 43-45. http://cran.r-project.org/doc/Rnews/ for the next steps. (To save you some time: look in src/main/optimize.c. But Uwe's article would have got you there pretty quickly). Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using R in Java?
Wow, very interesting! The netbeans example looks similar to what I want, which is based on Eclipse RCP. I will explore this more, as well as the JRI indirect method suggested by Christian. Thanks! -Original Message- From: Roy Mendelssohn [mailto:roy.mendelss...@noaa.gov] Sent: Thursday, February 19, 2009 10:47 AM To: Christian Ruckert Cc: Bryan Coon; r-help@r-project.org Subject: Re: [R] Using R in Java? See also Biocep: http://biocep-distrib.r-forge.r-project.org/ -Roy M. On Feb 19, 2009, at 10:42 AM, Christian Ruckert wrote: > nicro schrieb: >> Hi 2 questions- >> 1. Is there a package that will allow me to run R scripts >> (entirely) from >> Java? >> 2. If so, is there a way to capture the output of those scripts, >> (including >> images) and embed them in my SWT java app? >> My challenge is I have a java app that does some statistical >> chores- it >> would be fantastic if the users could use their R skills to modify >> a script >> in whatever R environment they like and then my app could use that >> script to >> calculate the results and display them in the app. >> I have found StatET and JavaGD with rJava/JRI and read through all >> the >> docs... its seems possible that some combination may give me what I >> want, >> but its not very clear. > > The JRI part from the rJava package does exactly what you want. > Simple data types like numbers or strings are directly returned as > java objects. But I'm afraid for the images you have to use the > files system indirection. > > If needed I can post an example, > > Christian > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" THIS EMAIL MESSAGE IS FOR THE SOLE USE OF THE INTENDED RECIPIENT(S) AND MAY CONTAIN CONFIDENTIAL INFORMATION. ANY UNAUTHORIZED REVIEW, USE, DISCLOSURE OR DISTRIBUTION IS PROHIBITED. IF YOU ARE NOT THE INTENDED RECIPIENT, PLEASE CONTACT THE SENDER BY REPLY EMAIL AND DESTROY ALL COPIES OF THE ORIGINAL MESSAGE. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] modifying legend in scatterplot matrix R
Hello R users,
I have some troubles to modify the "per default" legend in the
scatterplot.matrix using the car package. Here is my code:
scatterplot.matrix(~ a + b + c,
groups=treatment,
by.groups=F,
data=newfile3,
smooth=T,
pch=c(16,4),
cex=1.3,
labels=label,
cex.labels=1.3,
font.labels=2,
col=c("black","dark grey","black","black"),
legend.plot=T,
)
legend("topright",c("fenced","unefenced"), fill=NULL,bty="o",cex=3)
In my dataset, the variable "treatment" contains two levels that are coded "N"
and "Y" (for No and Yes) and appear in my "per default" legend that is located
in the buttomright of my 3x3 scatterplot. I would like to replace N by a list
of character: "unfenced" and Y by "fenced", as well as moving the legend in
another place in my graphic... is someone know how to do that with a
scatterplot?
Thank's
Julien
--
Julien Beguin
Etudiant-chercheur au doctorat
Laboratoire d'analyse quantitative des paysages, local 2113
Faculté de Foresterie et de Géomatique
Université Laval
2405 rue de la Terrasse, G1V 0A6 Québec (Qc)
Tel: (418) 656-2131 poste 2620
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[R] using stepAIC with negative binomial regression - error message
Ben, I tried playing with the "na.action" but that didn't seem to help. I didn't know of the na.omit function. It made it much easier to get rid of all the missing values in the file, and now the regression model is running. I hadn't put interactions in the model yet since it wasn't even running. Cosday, sinday, and daylength are strongly collinear. The full model with interactions keeps all three in, plus all interactions between them. Thanks for your help! Tim [[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] colored maps again
The problem is that the order and number of polygons in map does not match your
data (most likely).
Try:
library(maps)
library(plotrix)
state.col<-color.scale(state.x77[,'HS Grad'],0,0,c(0,1))
map("state",fill=TRUE,col=state.col)
nms <- map('state', plot=FALSE)$names
nms <- sub(':.*$','',nms)
ind <- match(nms, tolower(state.name))
map('state', fill=TRUE, col=state.col[ind])
Now try it with your data, just replace state.name with the names of the states
in the order of your data if it is different (possibly the rownames).
You may also want to look at state.vbm in the TeachingDemos package (works with
maptools rather than maps) as another way to plot colored maps of the USA that
is less affected by geographical area.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
> project.org] On Behalf Of Alina Sheyman
> Sent: Thursday, February 19, 2009 9:46 AM
> To: r-help@r-project.org
> Subject: [R] colored maps again
>
> I'm trying to create a colored map that would show the number of
> students
> per state.
> My data frame consists of two columns - state and count.
> I'm using the following code
>
> library(maps)
> map("usa")
> library(plotrix)
> state.col<-color.scale(gre$count,0,0,c(0,1))
> map("state",fill=TRUE,col=state.col)
>
> I'm getting a map, but the values are not being mapped to correct
> states.
> What do I need to do to fix that?
>
> [[alternative HTML version deleted]]
>
> __
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> guide.html
> and provide commented, minimal, self-contained, reproducible code.
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[R] Roadmap for selecting an approach to analyzing repeated measures data
Dear Group, At http://biostat.mc.vanderbilt.edu/tmp/summary.pdf I have put a draft of a roadmap for choosing a method for analyzing serial (longitudinal) data. If anyone has feedback about this, including adding criteria for judging methods that I may have missed, I would appreciate hearing from you. Thanks Frank -- 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.
[R] Getting the difference between two data frames
Dear R users, I have the following data: x <- data.frame( myX = c(1,2,3,4,5,6,7,8,9) ) y <- data.frame( myX = c(1,2,3,4,5,6,7) ) How can I get the difference between data frame x and y? In this case, I want to get values 8 and 9 I know in SQL we can use minus operator, but I have no idea how to do so in R. I tried all.equal, diff, and identical, but they don't give me the actual data difference. Thank you beforehand, Ferry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] transform key value pair to column
Hi, is there a good way (instead of a time-consuming for loop) to transfer a key/value pair dataframe to a dataframe with key as column and value as row? For example, I have a dataframe with three columns: id, code, value: id,code,value 1,hi,10.3 1,lo,5.2 2,hi,19.4 3,hi,20 3,lo,12 4,lo,5.8 I want to get a dataframe like this: id,hi,lo 1,10.3,5.2 2,19.4,NA 3,20,12 4,NA,5.8 Thank you, Richard [[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] everybody loves R...
On Thu, Feb 19, 2009 at 5:29 PM, Gábor Csárdi wrote: > I don't want to be mean, I really like wikidot, but isn't it a better > solution to use the R wiki instead? > > http://wiki.r-project.org/rwiki/doku.php > Or even to contribute to existing well-structured sites such as Quick-R [1]? It would avoid doubling efforts, and dispersing similar information accross too many places. Liviu [1] http://www.statmethods.net/index.html -- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] transform key value pair to column
see ?stack, for example. vQ Tan, Richard wrote: > Hi, is there a good way (instead of a time-consuming for loop) to > transfer a key/value pair dataframe to a dataframe with key as column > and value as row? For example, I have a dataframe with three columns: > id, code, value: > > id,code,value > 1,hi,10.3 > 1,lo,5.2 > 2,hi,19.4 > 3,hi,20 > 3,lo,12 > 4,lo,5.8 > > I want to get a dataframe like this: > > id,hi,lo > 1,10.3,5.2 > 2,19.4,NA > 3,20,12 > 4,NA,5.8 > > Thank you, > Richard > > [[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] everybody loves R...
Liviu Andronic wrote: > On Thu, Feb 19, 2009 at 5:29 PM, Gábor Csárdi wrote: > >> I don't want to be mean, I really like wikidot, but isn't it a better >> solution to use the R wiki instead? >> >> http://wiki.r-project.org/rwiki/doku.php >> >> > Or even to contribute to existing well-structured sites such as > Quick-R [1]? It would avoid doubling efforts, and dispersing similar > information accross too many places. > > well, if the purpose is to have the message 'everybody loves r' imposed on as many as possible, dispersing similar information across places is one way to go ;) vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] transform key value pair to column
Try this: > dummy id code value 1 1 hi 10.3 2 1 lo 5.2 3 2 hi 19.4 4 3 hi 20.0 5 3 lo 12.0 6 4 lo 5.8 > reshape(dummy, idvar='id', timevar='code', direction='wide') id value.hi value.lo 1 1 10.3 5.2 3 2 19.4 NA 4 3 20.0 12.0 6 4 NA 5.8 Brian -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Wacek Kusnierczyk Sent: Thursday, February 19, 2009 5:39 PM To: Tan, Richard Cc: r-help@r-project.org Subject: Re: [R] transform key value pair to column see ?stack, for example. vQ Tan, Richard wrote: > Hi, is there a good way (instead of a time-consuming for loop) to > transfer a key/value pair dataframe to a dataframe with key as column > and value as row? For example, I have a dataframe with three columns: > id, code, value: > > id,code,value > 1,hi,10.3 > 1,lo,5.2 > 2,hi,19.4 > 3,hi,20 > 3,lo,12 > 4,lo,5.8 > > I want to get a dataframe like this: > > id,hi,lo > 1,10.3,5.2 > 2,19.4,NA > 3,20,12 > 4,NA,5.8 > > Thank you, > Richard > > [[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. -- This message w/attachments (message) may be privileged, confidential or proprietary, and if you are not an intended recipient, please notify the sender, do not use or share it and delete it. Unless specifically indicated, this message is not an offer to sell or a solicitation of any investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Merrill Lynch. Subject to applicable law, Merrill Lynch may monitor, review and retain e-communications (EC) traveling through its networks/systems. The laws of the country of each sender/recipient may impact the handling of EC, and EC may be archived, supervised and produced in countries other than the country in which you are located. This message cannot be guaranteed to be secure or error-free. References to "Merrill Lynch" are references to any company in the Merrill Lynch & Co., Inc. group of companies, which are wholly-owned by Bank of America Corporation. Secu! rities and Insurance Products: * Are Not FDIC Insured * Are Not Bank Guaranteed * May Lose Value * Are Not a Bank Deposit * Are Not a Condition to Any Banking Service or Activity * Are Not Insured by Any Federal Government Agency. Attachments that are part of this E-communication may have additional important disclosures and disclaimers, which you should read. This message is subject to terms available at the following link: http://www.ml.com/e-communications_terms/. By messaging with Merrill Lynch you consent to the foregoing. -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] transform key value pair to column
Thank you, works! -Original Message- From: Rowe, Brian Lee Yung (Portfolio Analytics) [mailto:b_r...@ml.com] Sent: Thursday, February 19, 2009 5:52 PM To: Wacek Kusnierczyk; Tan, Richard Cc: r-help@r-project.org Subject: RE: [R] transform key value pair to column Try this: > dummy id code value 1 1 hi 10.3 2 1 lo 5.2 3 2 hi 19.4 4 3 hi 20.0 5 3 lo 12.0 6 4 lo 5.8 > reshape(dummy, idvar='id', timevar='code', direction='wide') id value.hi value.lo 1 1 10.3 5.2 3 2 19.4 NA 4 3 20.0 12.0 6 4 NA 5.8 Brian -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Wacek Kusnierczyk Sent: Thursday, February 19, 2009 5:39 PM To: Tan, Richard Cc: r-help@r-project.org Subject: Re: [R] transform key value pair to column see ?stack, for example. vQ Tan, Richard wrote: > Hi, is there a good way (instead of a time-consuming for loop) to > transfer a key/value pair dataframe to a dataframe with key as column > and value as row? For example, I have a dataframe with three columns: > id, code, value: > > id,code,value > 1,hi,10.3 > 1,lo,5.2 > 2,hi,19.4 > 3,hi,20 > 3,lo,12 > 4,lo,5.8 > > I want to get a dataframe like this: > > id,hi,lo > 1,10.3,5.2 > 2,19.4,NA > 3,20,12 > 4,NA,5.8 > > Thank you, > Richard > > [[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. -- This message w/attachments (message) may be privileged, confidential or proprietary, and if you are not an intended recipient, please notify the sender, do not use or share it and delete it. Unless specifically indicated, this message is not an offer to sell or a solicitation of any investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Merrill Lynch. Subject to applicable law, Merrill Lynch may monitor, review and retain e-communications (EC) traveling through its networks/systems. The laws of the country of each sender/recipient may impact the handling of EC, and EC may be archived, supervised and produced in countries other than the country in which you are located. This message cannot be guaranteed to be secure or error-free. References to "Merrill Lynch" are references to any company in the Merrill Lynch & Co., Inc. group of companies, which are wholly-owned by Bank of America Corporation. Securities and Insurance Products: * Are Not FDIC Insured * Are Not Bank Guaranteed * May Lose Value * Are Not a Bank Deposit * Are Not a Condition to Any Banking Service or Activity * Are Not Insured by Any Federal Government Agency. Attachments that are part of this E-communication may have additional important disclosures and disclaimers, which you should read. This message is subject to terms available at the following link: http://www.ml.com/e-communications_terms/. By messaging with Merrill Lynch you consent to the foregoing. -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Getting the difference between two data frames
On 20/02/2009, at 11:23 AM, Ferry wrote:
Dear R users,
I have the following data:
x <- data.frame( myX = c(1,2,3,4,5,6,7,8,9) )
y <- data.frame( myX = c(1,2,3,4,5,6,7) )
How can I get the difference between data frame x and y? In this case,
I want to get values 8 and 9
I know in SQL we can use minus operator, but I have no idea how to
do so in R.
I tried all.equal, diff, and identical, but they don't give me the
actual data difference.
First of all, you ***don't*** want the ``difference between two data
frames''.
What you (apparently) want is the ***set difference*** between two
***vectors***
each of which is (irrelevantly) stored inside a different data frame.
You can get what you want using the function setdiff(). E.g.:
> setdiff(x$myX,y$myX)
[1] 8 9
Data frames as such do not come into it. You are just confusing the
issue
by referring to them. I.e. you could have much more simply said:
``
x <- c(1,2,3,4,5,6,7,8,9)
y <- c(1,2,3,4,5,6,7)
How do I get the difference c(8,9)?''
(Answer: setdiff(x,y).)
cheers,
Rolf
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[R] Detecting startup flags from within R.
Is there a way to detect from within R whether, e.g., R has been
started with the --no-restore-data flag set? So as to be able
to invoke code along the following lines:
if( --no-restore-data flag set) {
do something
} else {
do something else
}
Thanks for any assistance.
cheers,
Rolf Turner
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[R] Detecting startup flags from within R (never mind, I figured it out).
Just after sending my inquiry I found the answer myself:
Use commandArgs().
Duh! Sorry for wasting bandwidth.
cheers,
Rolf Turner
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Re: [R] Detecting startup flags from within R.
2009/2/19 Rolf Turner :
>
>
> Is there a way to detect from within R whether, e.g., R has been
> started with the --no-restore-data flag set? So as to be able
> to invoke code along the following lines:
>
>if( --no-restore-data flag set) {
>do something
>} else {
>do something else
>}
>
> Thanks for any assistance.
?commandArgs
> "--no-restore-data" %in% commandArgs()
[1] TRUE
or false if I hadn't started it with that arg...
Barry
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[R] change the label size when drawing trees with ape
Hi All,
I want to be able to change the labe size on a tree
when using ape package so that the graph can look
nicer, but don't know how. Playing with the "font"
doesn't seem to help. (Right now the labels barely
show.)
Thanks for your help!
Code I'm using now
#-
t1 = "(((1:77.37,2:77.37):9.4,4:86.77):7.56,3:94.33);"
t2 = "((1:12.56,(2:10.11,4:10.11):2.45):1.64,3:14.2);"
t3=
"(((1:57.54,3:57.54):11.54,4:69.08):4.13,2:73.21);"
t4 =
"(1:59.27,((2:34.77,3:34.77):6.99,4:41.76):17.51);"
t5 =
"(((1:22.26,4:22.26):3.4,3:25.66):15.81,2:41.47);"
t6 = "(((1:23.3,2:23.3):22.2,3:45.5):37.88,4:83.38);"
t7 =
"(((1:18.49,3:18.49):1.14,4:19.63):5.93,2:25.56);"
t8 =
"((1:40.26,2:40.26):31.51,(3:38.99,4:38.99):32.78);"
t9 =
"(1:60.72,((2:15.57,4:15.57):5.07,3:20.64):40.08);"
t10 =
"((1:54.81,3:54.81):13.81,(2:64.24,4:64.24):4.380001);"
t11 =
"((1:61.44,3:61.44):26.94,(2:26.52,4:26.52):61.86);"
t12 =
"((1:11.05,(3:10.15,4:10.15):0.9):68.71,2:79.76);"
t13 =
"(((1:39.53,3:39.53):6.25,4:45.78):3.09,2:48.87);"
t14 =
"((1:55.12,(2:37.99,3:37.99):17.13):18.28,4:73.4);"
t15 =
"((1:73.39,(2:54.24,4:54.24):19.15):20.58,3:93.97);"
library(ape)
ft = c(5,5,5,5)
postscript("test.ps")
par(mfrow=c(5,3))
plot(read.tree(text=t1),font=ft)
plot(read.tree(text=t2),font=ft)
plot(read.tree(text=t3),font=ft)
plot(read.tree(text=t4),font=ft)
plot(read.tree(text=t5),font=ft)
plot(read.tree(text=t6),font=ft)
plot(read.tree(text=t7),font=ft)
plot(read.tree(text=t8),font=ft)
plot(read.tree(text=t9),font=ft)
plot(read.tree(text=t10),font=ft)
plot(read.tree(text=t11),font=ft)
plot(read.tree(text=t12),font=ft)
plot(read.tree(text=t13),font=ft)
plot(read.tree(text=t14),font=ft)
plot(read.tree(text=t15),font=ft)
dev.off()
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[R] Arima bug?
I was looking at the 'R' code associated with arima. I see the following:
upARIMA <- function(mod, phi, theta) {
p <- length(phi)
q <- length(theta)
mod$phi <- phi
mod$theta <- theta
r <- max(p, q + 1)
if (p > 0)
mod$T[1:p, 1] <- phi
if (r > 1)
mod$Pn[1:r, 1:r] <- .Call(R_getQ0, phi, theta)
else if (p > 0)
mod$Pn[1, 1] <- 1/(1 - phi^2)
else mod$Pn[1, 1] <- 1
mod$a[] <- 0
mod
}
In particular the statement:
else if (p > 0)
mod$Pn[1, 1] <- 1/(1 - phi^2)
If p (the length of the phi vector) is greater than one then it looks like the
code is trying to assign a vector to a single element which will generate an
error in 'R'. Much like
x <- 1:3
x[1] <- 1:3
So I was wondering if there is something that I am missing that will
"guarantee" that the length of the phi vector in this case is always 1. If this
is not the case then it seems that this is a bug in the arima code.
Comments?
Kevin
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Re: [R] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009
Hi Kees,
No harm no foul. I'm glad you posted that anyway, because now anyone who's
trying to do the same thing and read this will know to seek your 1.1.9
version and stay away from 1.1.15.
Paul
chaogai-2 wrote:
>
> I do not know about the ubuntu instructions, they would not help me on
> Suse. The wine version is 1.1.9.
> I thought that was the latest,but when I checked latest is 1.1.15, which
> does indeed throw the blackbox error.
> So, now it does not work for me either
> Sorry I gave bad advise
>
> kees
>
> On Thu, 19 Feb 2009 01:38:15 +0100, Paul Heinrich Dietrich
> wrote:
>
>>
>> I went to this webpage (http://ubuntuforums.org/showthread.php?t=624644)
>> and
>> followed the instructions to the letter on getting the latest Wine. I
>> installed WinBUGS again, but this time I cannot open it in Wine. It says
>> Black Box, Trap #101, and some text I can't copy/paste here. Is this the
>> latest Wine that you have, or something different? Thanks.
>>
>>
>> chaogai-2 wrote:
>>>
>>> Hi,
>>>
>>> For me running winbugs through wine just works. Even when I do not
>>> specify
>>> any directories.
>>> The example they give in the bugs helpfile was my starting point.
>>> Setup is suse 11.1, latest Wine, R, R2WinBUGS & winbugs.
>>> I assume you first tried without specifying directories?
>>> The directories you use do not work for me, with WINEPATH the culprit.
>>> If you do not have the latest wine I advise to upgrade & not specify
>>> directories.
>>>
>>> Good luck,
>>> Kees
>>>
>>> On Wed, 18 Feb 2009 01:27:18 +0100, Paul Heinrich Dietrich
>>> wrote:
>>>
Hi Uwe,
Thank you for your guidance. I have installed R2WinBUGS and WinBUGS14
under
wine. Using ?bugs for help, it tells me:
useWINE: logical; attempt to use the Wine emulator to run 'WinBUGS',
defaults to 'FALSE' on Windows, and 'TRUE' otherwise. Not available in
S-PLUS.
WINE: character, path to 'wine' binary file, it is tried hard (by a
guess
and the utilities 'which' and 'locate') to get the information
automatically if not given.
newWINE: Use new versions of Wine that have 'winepath' utility
WINEPATH: character, path to 'winepath' binary file, it is tried hard
(by a
guess and the utilities 'which' and 'locate') to get the information
automatically if not given.
..and the following code is a simple Bayesian version of a t-test...
Directory Paths
MyModelPath <- "/home/me/Compound/R/WinBUGS/"
MyBUGSPath <- "/home/me/.wine/drive_c/Program Files/WinBUGS14/"
MyModelFile <- paste(MyModelPath, "model.bug", sep="")
WINEPATH <- "/usr/bin/wine"
Create Data Set
# Here is some fake data
n_draws <- 50
x <- round(runif(n_draws, 1, 2))
y <- ifelse(x == 1, rnorm(n_draws, 1, 1), rnorm(n_draws, 1.2, 0.8))
MyData <- as.data.frame(cbind(y, x))
y.n <- NROW(MyData$y)
x.j <- length(unique(x))
summary(MyData)
## Format Data for WinBUGS
##
MyBUGSData <- list(y=MyData$y, x=MyData$x, n=y.n, x.j=x.j)
MyBUGSData
## WinBUGS Model File
###
library(R2WinBUGS)
cat("model
{
for (i in 1:n)
{
y[i] ~ dnorm(mu[i], tau)
mu[i] <- alpha + beta[x[i]]
}
### STZ (Sum-To-Zero) Constraints
beta[1] <- -sum(beta[2:x.j])
### Priors
alpha ~ dnorm(0.0, 1.0E-4)
for (i in 2:x.j)
{
beta[i] ~ dnorm(0.0, 1.0E-4)
}
tau ~ dgamma(0.01, 0.01)
precision <- sqrt(1/tau)
}",
file=MyModelFile)
file.show(MyModelFile)
# WinBUGS Model
#
MyModel <- bugs(MyBUGSData, inits=NULL,
model.file=MyModelFile,
parameters.to.save=c("alpha", "beta", "precision"),
n.chains=3, n.iter=2000, n.burnin=1000, n.thin=1, codaPkg=TRUE,
bugs.directory = MyBUGSPath, working.directory=MyModelPath,
useWINE=TRUE, WINEPATH=WINEPATH, debug=TRUE)
The output says:
ERROR:
cannot open the connection
I'm wondering if I've misinterpreted how to set my paths with wine,
because
I can go to the following path, double-click on WinBUGS14.exe, and open
it
just fine: /home/me/.wine/drive_c/Program Files/WinBUGS14/
I can also go to Applications > Wine > Browse C:\ Drive and navigate to
WinBUGS.
Please help if I've done something wrong. Thanks.
>>>
>>>
>>>
>>> --
>>>
>>> __
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>>> https://stat.ethz.ch/mailman/listinf
[R] How to unload a dll loaded via library.dynam()?
Hello. To save the hassle of quitting and restarting R every time I rebuild the
package I'm working on (for the purposes of this question called "roots") I
would like to write a script cleanly remove the package from my R session and
then load it again. Of course detach("package:roots") works for the native R
objects in the package. However, the compiled C library remains loaded. Using
library.dynam.unload as documented results in:
Error in library.dynam.unload("roots.so",
"~/R/x86_64-pc-linux-gnu-library/2.8/roots/libs/") :
shared library 'roots' was not loaded
I also tried the above command with the file extension omitted and the last one
and two levels of the directory path omitted. In both cases I still get the
"not loaded" error. I've also Googled the list archives and while there were
several questions like mine, none of them were answered by the list. Am I to
believe that this is something hardly anybody does? Does this mean everybody
sits around waiting for R to start up everytime they make a minor change to the
C source?
If there is a tutorial for doing this, I'd much appreciate the link.
Thank you for your advice.
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Re: [R] Arima bug?
rkevinbur...@charter.net wrote:
I was looking at the 'R' code associated with arima. I see the following:
upARIMA <- function(mod, phi, theta) {
p <- length(phi)
q <- length(theta)
mod$phi <- phi
mod$theta <- theta
r <- max(p, q + 1)
if (p > 0)
mod$T[1:p, 1] <- phi
if (r > 1)
mod$Pn[1:r, 1:r] <- .Call(R_getQ0, phi, theta)
else if (p > 0)
mod$Pn[1, 1] <- 1/(1 - phi^2)
else mod$Pn[1, 1] <- 1
mod$a[] <- 0
mod
}
In particular the statement:
else if (p > 0)
mod$Pn[1, 1] <- 1/(1 - phi^2)
So I was wondering if there is something that I am missing that will
"guarantee" that the length of the phi vector in this case is always 1.
There is. You are only getting there if r > 1 is FALSE, and by the
definition of r, that can only happen if q==0 and (p==0 or p==1).
--
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c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907
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Re: [R] How to unload a dll loaded via library.dynam()?
On 19/02/2009 6:19 PM, Alex F. Bokov wrote:
Hello. To save the hassle of quitting and restarting R every time I rebuild the package I'm working
on (for the purposes of this question called "roots") I would like to write a script
cleanly remove the package from my R session and then load it again. Of course
detach("package:roots") works for the native R objects in the package. However, the
compiled C library remains loaded. Using library.dynam.unload as documented results in:
Error in library.dynam.unload("roots.so",
"~/R/x86_64-pc-linux-gnu-library/2.8/roots/libs/") :
shared library 'roots' was not loaded
I also tried the above command with the file extension omitted and the last one and two
levels of the directory path omitted. In both cases I still get the "not
loaded" error. I've also Googled the list archives and while there were several
questions like mine, none of them were answered by the list. Am I to believe that this is
something hardly anybody does? Does this mean everybody sits around waiting for R to
start up everytime they make a minor change to the C source?
If there is a tutorial for doing this, I'd much appreciate the link.
This is more of an R-devel question than R-help, so if this doesn't
answer your question, please follow up there.
On Windows, the following sort of works:
> library(rgl)
> .dynLibs()
Filename Dynamic.Lookup
1 F:/R/R-2.8.1/library/methods/libs/methods.dll FALSE
2 F:/R/R-2.8.1/library/grDevices/libs/grDevices.dll FALSE
3 F:/R/R-2.8.1/library/stats/libs/stats.dll FALSE
4 F:/R/R-2.8.1/library/rgl/libs/rgl.dll TRUE
> library.dynam.unload("rgl", "F:/R/R-2.8.1/library/rgl")
I say "sort of", in that I get no error messages and the dll is no
longer locked in use as it normally would be in Windows, but reloading
the package doesn't function properly. It's possible some combination of
detach() and unloadNamespace() would get a clean unload, but really, I
normally just quit R and restart. It's pretty quick to start up,
compared to the recompile time for the package.
Duncan Murdoch
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Re: [R] How to unload a dll loaded via library.dynam()?
Hmmm, I think restarting R is not a very good solution. It is rather
ugly in the first place. But perhaps even more importantly, it can be
rather inconvenient if one has a large data set in the memory and
needs to save/load it just to reload a package that was updated in the
meanwhile.
This happens to me quite often with 20-40Gb of data, so I would really
love to have a solution for proper detach/unload.
Best,
Gabor
On Fri, Feb 20, 2009 at 1:32 AM, Duncan Murdoch wrote:
> On 19/02/2009 6:19 PM, Alex F. Bokov wrote:
>>
>> Hello. To save the hassle of quitting and restarting R every time I
>> rebuild the package I'm working on (for the purposes of this question called
>> "roots") I would like to write a script cleanly remove the package from my R
>> session and then load it again. Of course detach("package:roots") works for
>> the native R objects in the package. However, the compiled C library remains
>> loaded. Using library.dynam.unload as documented results in:
>>
>> Error in library.dynam.unload("roots.so",
>> "~/R/x86_64-pc-linux-gnu-library/2.8/roots/libs/") :
>> shared library 'roots' was not loaded
>>
>> I also tried the above command with the file extension omitted and the
>> last one and two levels of the directory path omitted. In both cases I still
>> get the "not loaded" error. I've also Googled the list archives and while
>> there were several questions like mine, none of them were answered by the
>> list. Am I to believe that this is something hardly anybody does? Does this
>> mean everybody sits around waiting for R to start up everytime they make a
>> minor change to the C source?
>>
>> If there is a tutorial for doing this, I'd much appreciate the link.
>
>
> This is more of an R-devel question than R-help, so if this doesn't answer
> your question, please follow up there.
>
> On Windows, the following sort of works:
>
>> library(rgl)
>> .dynLibs()
> Filename Dynamic.Lookup
> 1 F:/R/R-2.8.1/library/methods/libs/methods.dll FALSE
> 2 F:/R/R-2.8.1/library/grDevices/libs/grDevices.dll FALSE
> 3 F:/R/R-2.8.1/library/stats/libs/stats.dll FALSE
> 4 F:/R/R-2.8.1/library/rgl/libs/rgl.dll TRUE
>
>> library.dynam.unload("rgl", "F:/R/R-2.8.1/library/rgl")
>
> I say "sort of", in that I get no error messages and the dll is no longer
> locked in use as it normally would be in Windows, but reloading the package
> doesn't function properly. It's possible some combination of detach() and
> unloadNamespace() would get a clean unload, but really, I normally just quit
> R and restart. It's pretty quick to start up, compared to the recompile
> time for the package.
>
> Duncan Murdoch
>
> __
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>
--
Gabor Csardi UNIL DGM
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[R] residuals from a fractional arima model and other questions
Dear list and Martin, I'm testing different approaches to fit an electricity demand time series and come upon the fracdiff package (v 1.3-1) for fitting fractional ARIMA models. The following questions are motivated by this package. 1. Despite having a help page, the residuals and fitted functions don't seem to have implementation, or did i miss something obvious? Alternatively, having a fitted fracdiff object, how do I calculate the residuals? (Please forgive me if this is totally obvious which I'm sure it may be. Is it just a matter of expanding out the (1-L)^d term?) 2. I don't have access to the cited Haslett & Raftery (1989) paper, but could someone explain to me the little cautionary note in the help page stating that "nar and nma should not be too large (say < 10) to avoid degeneracy in the model." I see that a different implementation of the FARIMA procedure in Splus could lead to an explosive, ie. non-stationary model when it's used to fit a log volatility data set (Zivot & Wang, p.291). Zivot explains that it might be due to canceling roots in the AR and MA polynomials. Is this a caution against a similar problem. Which leads to my next question, 3. Is the FARIMA procedure known to be unstable at time? Is there a better way (with a different package perhaps) to model long range dependence ? 4. When my model is fitted, i got a warning that it's unable to compute the correlation matrix. Output looks like, Call: fracdiff(x = res.iact.ts, nar = 9, nma = 9, M = 100) *** Warning during fit: unable to compute correlation matrix Coefficients: Estimate Std. Errorz value Pr(>|z|) d4.745e-01 0.000e+00Inf <2e-16 *** ar1 8.897e-01 0.000e+00Inf <2e-16 *** ar2 -3.386e-01 0.000e+00 -Inf <2e-16 *** ar3 3.339e-01 2.044e-17 1.634e+16 <2e-16 *** ar4 -4.406e-01 0.000e+00 -Inf <2e-16 *** ar5 3.924e-02 6.349e-18 6.182e+15 <2e-16 *** ar6 -5.184e-01 2.558e-17 -2.026e+16 <2e-16 *** ar7 8.988e-01 0.000e+00Inf <2e-16 *** ar8 -7.568e-01 3.112e-16 -2.432e+15 <2e-16 *** ar9 3.442e-01 2.175e-22 1.582e+21 <2e-16 *** ma1 -1.190e-01 1.470e-18 -8.097e+16 <2e-16 *** ma2 -9.343e-02 0.000e+00 -Inf <2e-16 *** ma3 2.140e-01 0.000e+00Inf <2e-16 *** ma4 -2.107e-01 0.000e+00 -Inf <2e-16 *** ma5 -2.892e-01 0.000e+00 -Inf <2e-16 *** ma6 -7.197e-01 2.888e-08 -2.492e+07 <2e-16 *** ma7 3.021e-01 0.000e+00Inf <2e-16 *** ma8 -1.395e-01 0.000e+00 -Inf <2e-16 *** ma9 -2.493e-02 3.013e-21 -8.274e+18 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 [d.tol = 0.0001221, M = 100, h = 0.004807] Log likelihood: -4.562e+05 ==> AIC = 912360.4 [1 deg.freedom] Last question : why are some of z-values infinite? Thanks in advance. Horace Tso [[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] equivalent function to MatLab 'step' ?
I have to admit I don't fully understand how MatLab's step() function works, but I'm learning that part. Can someone point me to equivalent&related functions in R? thanks Carl __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RODBC crashes connecting to Teradata
Received Fri 19 Dec 2008 7:38am +1100 from Prof Brian Ripley:
> On Thu, 18 Dec 2008, Francisco Javier Perez Caballero wrote:
>
>> Hi, I'm trying to connect to a Teradata database via RODBC on a Linux 64
>> machine (Red Hat Enterprise Linux 5).
[...]
>>> library(RODBC)
>>> conn = odbcConnect("thedsn", uid="theuid", pwd="thepass")
>>
>> *** caught segfault ***
>> address (nil), cause 'memory not mapped'
[...]
> Most likely a broken driver. It seems that several do not support
> GetInfo correctly: isql does not use it by default. Debugging will show
> you where the error actually was.
I came across the same problem recently and could not find any
discussion on the r-sig-db list solving this. Here's my solution.
I have a similar setup - Teradata ODBC driver on amd64 GNU/Linux
(Debian), using the RODBC package, and getting a segfault on
odbcConnect.
odbcConnect calls odbcDriverConnect which in turn .Call's
C_RODBCDriverConnect, which actually succeeds. Then there is a .Call
to C_RODBCGetInfo which results in the segfault.
I suspect underneath the Teradata driver is crashing on querying a
table that does not exists or that you may not have access to (for me
the default odbc GetInfo seems to try to access the table DBC.Table,
but our setup does not have that available, with DBC.TableX being used
instead!)
I dropped the GetInfo call from odbcDriverConnect and all is well,
until I query a table that does not exist, and once again the Teradata
driver crashes (also crashes in isql when typing "help" or querying a
table that does not exist).
Regards,
Graham
In case it helps, I use this to connect.
channel <- odbcDriverConnect("DSN=mydsn;UID=user;PWD=password")
with the following function.
odbcDriverConnect <- function (connection = "", case = "nochange",
believeNRows = TRUE,
colQuote, tabQuote = colQuote,
DBMSencoding = "", rows_at_time = 1000,
bulk_add = NULL)
{
id <- as.integer(1 + runif(1, 0, 1e+05))
stat <- .Call(RODBC:::C_RODBCDriverConnect,
as.character(connection),
id, as.integer(believeNRows))
if (stat < 0)
{
warning("ODBC connection failed")
return(stat)
}
### res <- .Call(C_RODBCGetInfo, attr(stat, "handle_ptr"))
### Also removed references to res in the following.
if (missing(colQuote)) colQuote <- "\""
if (missing(case)) case <- "nochange"
switch(case,
toupper = case <- 1,
oracle = case <- 1,
tolower = case <- 2,
postgresql = case <- 2,
nochange = case <- 0,
msaccess = case <- 0,
mysql = case <- ifelse(.Platform$OS.type == "windows", 2, 0),
stop("Invalid case parameter: nochange | toupper | tolower | common db
names"))
case <- switch(case + 1, "nochange", "toupper", "tolower")
### if (is.null(bulk_add))
### bulk_add <- .Call(RODBC:::C_RODBCCanAdd, attr(stat, "handle_ptr"))
structure(stat, class = "RODBC", case = case, id = id,
believeNRows = believeNRows,
bulk_add = bulk_add, colQuote = colQuote, tabQuote = tabQuote,
encoding = DBMSencoding, rows_at_time = rows_at_time)
}
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Re: [R] Build R-2.8.1 on AIX5.3
Thanks for Ej-ji's help. I have succesfully built R-2.8.1 on AIX,but I also found a problem in my build process-- the 783 line on patch file should be combined with 782 line. Thanks for Ei-ji again. Jin > Date: Thu, 19 Feb 2009 09:39:26 + > From: rip...@stats.ox.ac.uk > To: nak...@ki.rim.or.jp > CC: dna_...@hotmail.com > Subject: Re: [R] Build R-2.8.1 on AIX5.3 > > If you do test it, please let me know and I will merge it into the R > sources. > > Can we discuss such issues on R-devel, please (see the posting guide). > Most of the developers do not read R-help (at all, or in any detail). > > On Thu, 19 Feb 2009, Ei-ji Nakama wrote: > > > Hi Jin. > > > >> I found there is someone meet same problem when he build R-2.7.0 by > >> searching r-help, and he used a patch to resolve this issue. The > >> patch¡¯s location is http://prs.ism.ac.jp/~nakama/AIX/changefiles. But I > >> can not find a patch R-2.8.1 in this path. > >> > > > > Gnu patch is necessary.(AIX patch can't be used.) > > > > http://prs.ism.ac.jp/~nakama/AIX/AIX_R-2.8.1.patch > > > > However, this patch is not tried at all. > > -- > > EI-JI Nakama > > "\u4e2d\u9593\u6804\u6cbb" > > > > __ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 _ æ°çææºMSNï¼æ»¡è¶³ä½ å¤å½©éæ±ï¼åå æ¢é²ä½éªæ´»å¨ï¼é¢åç¹è²å¥åï¼ http://mobile.msn.com.cn/ [[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] Build R-2.8.1 on AIX5.3
> I have succesfully built R-2.8.1 on AIX,but I also found a problem in my > build process-- the 783 line on patch file should be combined with 782 > line. Oops, mended. http://prs.ism.ac.jp/~nakama/AIX/AIX_R-2.8.1_fix.patch Now, I do not have AIX that can be tested.:( Thank you Jin. -- EI-JI Nakama "\u4e2d\u9593\u6804\u6cbb" __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] importing data to SQLite database with sqldf
Hi all,
I am attempting to learn SQL through sqldf...
One task I am particularly interested in is merging separate
(presumably large) files into a single table without loading these
files into R as an intermediate step (by loading them into SQLite and
merging them there).
Taking a step back, I've considered these alternatives:
1) I know if I use straight SQLite commands I might use the 'IMPORT'
or 'INSERT INTO' command, which is not terribly flexible... (I can
read large files line-by-line in Python and use the 'INSERT INTO'
command, which is reasonably fast; I could do this in R as well but my
experience with R's input/output is that it's much slower...? and
sometimes setting up the table column definitions can be tedious if
there are many variables).
2) dbWriteTable() with append=TRUE is very convenient except that it
requires I load the data into R first...
3) sqldf's capability to put data directly into a database is
something I'd like to work out.
So in this case I have a series of tab-delimited text file with the
first line being a header.
For some reason I cannot seem to get it working. Combining examples 6
and 9 from the Google Code page (and R-help archives), I tried
source("http://sqldf.googlecode.com/svn/trunk/R/sqldf.R";)
(do I need it for SQLite?)
##
sqldf("attach 'mydb.db' as new")
f <- file("myexample.txt")
attr(f,"file.format") <- list(header=TRUE,sep="\t")
sqldf("create table myexample as select * from f",
stringsAsFactors=FALSE,
dbname="mydb.db")
## or
f <- file(fi)
sqldf("create table myexample as select * from f",
stringsAsFactors=FALSE,file.format=list(header=TRUE,sep="\t"),
dbname="mydb.db")
##
sqldf("select * from myexample",dbname="mydb.db")
gives me tables with 0 rows and 0 columns...
So in any case I have a few questions:
=== 1
Would this be scalable to files with few GBs of data in them (I guess
I am uncertain of the underlying mechanism for transporting data from
the .txt file to the .db file... I see there is a call the
dbWriteTable() internally in sqldf but through the connection)? And
is there anything obviously doing wrong above?
=== 2 ===
Since I cannot 'append' rows to existing tables in SQLite (or any SQL
database), I think what I would have to do is to load each of the
files into the database and then 'rbind' them into a new table using
'union all'? The following code is what I have (the part where I read
in each file before dumping into the database file would hopefully be
replaced by the method above, if it can be made to work).
## (1) create a database file
sqldf("attach 'alltables.db' as new")
## (2) convenience function
sql <- function(...) sqldf(...,dbname="alltables.db")
## (3) load data as separate tables
for( fi in list.files(".","txt$") ) {
mydata <- read.delim(fi)
sql(sprintf("create table %s as select * from mydata",sub("\\.txt","",fi)))
}
rm(fi,mydata)
## (4) merge tables
tablenames <- as.character(sql("select * from sqlite_master")$name)
sql(paste("create table myfulltable as",
paste(sprintf("select * from %s",tablenames),
collapse=" union all ")))
## (5) delete separate tables since we have a merged one
for( nm in tablenames ) sql(sprintf("drop table %s",nm))
=== 3 ===
The following command
sqldf("attach 'mydb.db' as new")
DF <- read.delim(fi)
sqldf("create table myexample as select * from DF",dbname="mydb.db")
will usually create a .db file twice the size of the .txt file (for
now I am playing with a files ~500KB so the .db files are around
~1MB). When I create a .db file using SQLite's 'import' command,
RSQLite's dbWriteTable(), or inserting values from the same .txt file
from Python's SQLite interface, I get .db files that are approximately
the same size as the .txt file (~500KB). Is the larger file size for
sqldf's method expected?
Many thanks in advance!
Stephen Tucker
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Re: [R] problem with comparing a part of string with whole string
Hi ,
i just attached one file to this mail which contains one modal of my data
and there i have to search for the rows which contains "SPECIMENTYP %in%
"ADIPOSE TISSUE""
and the rows which contains " "PRESERVED"in ORGCHARRES
for that i tried with
" r<-subset(rr,SPECIMENTYP %in% "ADIPOSE TISSUE" & grep("IN
DIAMETER",rr$ORGCHARRES),select=c(SPECIMENTYP,ORGCHARRES))"
but i got only the rows having "ADIPOSE TISSUE" in "SPECIMENTYP"
can anyone suggest any of the way for comparision of this type
thanks in advance
On Thu, Feb 19, 2009 at 6:26 PM, Petr PIKAL wrote:
> Hi
>
> r-help-boun...@r-project.org napsal dne 19.02.2009 13:39:42:
>
> > Hi all,
> >
> > I got one problem with comparing strings like if any string is like
> >
> > "*RIGHT, EPICARDIUM: FOCUS, GRAY-WHITE, SINGLE, APPROX 0.6 CM IN
> DIAMETER*."
> >
> > and i have to compare "*GRAY-WHITE*"with the above string
> >
> > or otherwise i have to compare " *TUMOR BENIGN*" this
> string
> > with
> >
> > "*MEDULLRY TUMOR BENIGN,TYP PHEOCHROMOCYTOMA*"
> >
> > i tried with split and compare but its not working
>
> Work for regular expressions?
>
> vec="*RIGHT, EPICARDIUM: FOCUS, GRAY-WHITE, SINGLE, APPROX 0.6 CM IN
> DIAMETER*."
> test="GRAY-WHITE"
> regexpr(test, vec)
> [1] 28
> attr(,"match.length")
> [1] 10
>
> Regards
> Petr
>
>
> >
> > can any one suggest how can i compare these type of Strings
> >
> > thanks in advance
> >
> >[[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.
>
>
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[R] log-minus-log plot
Dear experts, I would like to know how to plot the log-minus-log plot for survival analysis (to check the proportional assumption) in R. Using the AML example. fit <- survfit(Surv(time, status) ~ x, data=aml) length(fit$surv) #20 as the length of fit$surv is shorter than aml$x and aml$time. I don't know how to plot. Thank you. Regards, CH -- CH Chan Research Assistant - KWH http://www.macgrass.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] smoothing 2D vector field
Hi all, is there a function / package in R that provides a function like Matlab's conv2 or filter2 for smoothing a vector- / velocity- field. I unfortunately could not find anything. Thanks a lot. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] modifying legend in scatterplot matrix R
Julien Beguin ulaval.ca> writes:
> scatterplot.matrix(~ a + b + c,
>groups=treatment,
...
>legend.plot=T,
>)
> legend("topright",c("fenced","unefenced"), fill=NULL,bty="o",cex=3)
>
>
> In my dataset, the variable "treatment" contains two levels that are coded "N"
> and "Y" (for No and Yes) and appear in my "per default" legend that is located
> in the buttomright of my 3x3 scatterplot. I would like to replace N by a list
> of character: "unfenced" and Y by "fenced", as well as moving the legend in
> another place in my graphic... is someone know how to do that with a
> scatterplot?
In most cases it is easiest to assign new level to the factor;
a = as.factor(c("N","Y","Y","N"))
levels(a)=c("unfenced","fenced")
levels(ar)=c("unfenced","fenced") # if you want to keep orinale
legend has x,y coordinates.
Dieter
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[R] write.table
Hello, I tried to turn lists into vectors and then bind them together in order to create a dataframe but if, after this, I try to use the function write.table I get the following error message: Error in write.table(x, file, nrow(x), p, rnames, sep, eol, na, dec, as.integer(quote), : 'list' type not implemented in 'EncodeElement' Here is what I've done: as.vector(c(unique(portate$Anno)))->anno as.vector(loadListPO4)->loadPO4 as.vector(loadListPTG)->loadPTG as.vector(loadListNT)->loadNT as.vector(loadListNH4)->loadNH4 as.vector(loadListNO3)->loadNO3 as.vector(loadListBOD5)->loadBOD5 as.vector(loadListSiO2)->loadSiO2 cbind(anno,loadPTG,loadPO4,loadNT,loadNH4,loadNO3,loadBOD5,loadSiO2)->carichi as.data.frame(carichi)->carichi.annui #if I type carichi.annui #I get anno loadPTG loadPO4 loadNT loadNH4 loadNO3 loadBOD5 loadSiO2 1 2002 3.399518 1.382235 390.6959 22.07992 256.2244 492.9177 150.6505 2 2003 1.559606 0.6271712 202.9181 6.198592 145.9498 63.07578 68.08632 3 2004 2.363862 0.9493779 292.0841 12.21207 200.2545 141.0533 105.2409 4 2005 1.64 0.6570313 217.2192 6.58045 155.7393 66.44154 73.0394 5 2006 1.827174 0.7290634 235.7914 7.858396 166.8327 79.2474 80.92576 6 2007 1.742629 0.6891045 228.0253 7.130082 162.6692 71.91434 77.22507 7 2008 0.8382246 0.3612176 110.9079 2.024197 86.60459 25.46127 32.9733 #which looks lika a data frame #And if I type is.data.frame(carichi.annui) # I get this: [1] TRUE #but if I try write.table(carichi.annui, "carichi.annui.lav") #It doesn't work?!?!?! Does someone have an explanation? Thanks a lot for any help!! Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
