Re: [R] Help creating a correlation matrix
Hi,
I tried the following one:
z - outer(1:14,1:14,function(i,j)
eval(parse(text=paste(cor(D2_,i,,D2_,j,),sep=
but this doen not work (why?).
Two alternatives which work are either
x - matrix(0,length(D2_1,14)
for (i in 1:14) x[,i] -
eval(parse(text=paste(D2_,i,sep=)))
z - cor(x)
or
z - diag(14)
for (i in 1:14) for (j in 1:14) z[i,j] -
eval(parse(text=paste(cor(D2_,i,,D2_,j,),sep=)))
--- Robert O'Brien [EMAIL PROTECTED]
wrote:
Hello all. I have 14 variables, named D2_1,
D2_2,...,D2_14 (inherited from a data set). I would
like to create a matrix of correlations, although I
would be content in just learning how to create a
proper do loop. I tried something like this:
(for i in 1:14){cor(D2_[i],D2_[i], use =
complete.obs)}
This is wrong, of course, but I don't know how to
tell R to run through D2_1, D2_2,...,D2_14 giving
me
the correlations for each pair.
Any help or hints would be appreciated.
Sincerely,
Robert O'Brien
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[R] an unknown error message when using gamm function
Dear everyone, I'm encountering an unknown error message when using gamm function: fitoutput - gamm(cvd~as.factor(dow)+pm10+s(time,bs=cr,k=15,fx=TRUE)+s(tmean,bs=cr,k=7,fx=TRUE) + ,correlation=corAR1(form=~1|city),family=poisson,random=list(city=~pm10),data=mimp) Maximum number of PQL iterations: 20 iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6 Error in `*tmp*`[[k]] : attempt to select less than one element I never saw this error message before, and there is also no related information about this error from the Internet. Hope some people who once encountered this problem can tell me what's wrong. Many thanks, LC -- Lung-Chang Chien Doctoral candidate, Department of Biostatistics Statistical assistant, School of Nursing University of North Carolina at Chapel Hill Office: Carrington Hall, RSC, Room 2014 TEL: 919-843-2480 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R help needed
Dear Sir/Madam, I have tried to upload data in R but it showing some error in command window. It's should be noted that I am using Mac version of R. I am using Mac-text for writing my data. I am getting following message on the command window. source(/Users/kamleshkumar/Desktop/DS1.txt) Error in source(/Users/kamleshkumar/Desktop/DS1.txt) : /Users/kamleshkumar/Desktop/DS1.txt: unexpected symbol at 1: x y I am attaching the the DS1.txt file also with this mail. Please go through it and guide me about this. I am waiting for a reply from your side. Thanking you. Yours Sincerely, Kamlesh Kumar -- Kamlesh kumar QEM1, Universität Bielefeld Appt. No.- 313A, 29, Morganbreede, 33615 Bielefeld, Germany. x y 0.43678295 -3.28526227 0.13718621 -4.92480568 0.17818460 -4.05188084 0.16101891 -4.67132656 0.07748958 -4.57308386 0.07665154 -4.65652237 0.93462605 -2.43577939 0.08393081 -4.77342552 0.21957806 -4.30777061 0.72091525 -2.40654408 0.78820620 -2.48382294 0.03020949 -5.13427708 0.68054097 -3.29446962 0.30986188 -4.27261703 0.95362188 -1.95420377 0.55720882 -2.97490588 0.43290669 -3.89988872 0.70655859 -2.80856040 0.27899269 -4.53354360 0.86257070 -2.01097646 0.05536443 -5.25322277 0.63851330 -3.29444349 0.61166177 -3.16909365 0.53661890 -3.47439468 0.04897602 -4.94514890 0.40846848 -3.55536513 0.48529544 -3.33571965 0.62426309 -3.15729236 0.51640396 -3.52697121 0.48633149 -3.48081848 0.56278950 -3.21171279 0.84846483 -2.84878605 0.78607647 -2.49938705 0.08552248 -4.66611865 0.27222455 -3.68753951 0.52786212 -3.18143578 0.42516159 -3.52162673 0.79234991 -2.31155140 0.84189899 -2.45189562 0.23900177 -4.47138986 0.91564840 -2.09537746 0.67030122 -2.52637849 0.94819300 -1.98333241 0.18291447 -4.89865053 0.52996478 -3.87409080 0.50593282 -3.79463028 0.73293227 -2.53096580 0.47889233 -3.83944563 0.10962530 -5.09931633 0.28968145 -3.91778725 0.51736481 -4.18277038 0.51200367 -3.47252783 0.69443868 -2.93954049 0.85456938 -2.66937293 0.85227096 -2.00744394 0.39924035 -3.81892375 0.76328850 -2.97426388 0.26705593 -4.64157081 0.78798635 -2.52137869 0.08613956 -4.91270415 0.50749160 -3.41245218 0.88808879 -2.31015263 0.93046255 -1.91780699 0.61369620 -3.20740210 0.62948767 -3.12272095 0.14147349 -4.09641126 0.46920070 -3.66767757 0.35005896 -3.78436370 0.55357248 -3.22255576 0.04723303 -4.60194879 0.52039850 -3.51374627 0.06786648 -5.10241809 0.98168950 -1.97958974 0.01757815 -5.06735833 0.36243887 -3.84462984 0.42420613 -3.13386319 0.22285663 -4.71020127 0.08062803 -4.36007637 0.36207742 -4.06609100 0.13193842 -5.10268694 0.69752291 -3.03723431 0.22458552 -3.76104542 0.76745054 -2.51812578 0.58135253 -2.69485523 0.90282985 -2.11135506 0.96344637 -2.13711582 0.74533493 -3.14761947 0.41475951 -4.37647029 0.80989250 -2.44450728 0.18761541 -4.28119680 0.86392396 -2.75540153 0.86466167 -2.45686213 0.03874840 -4.62795990 0.70687607 -2.89780500 0.36910319 -4.2300 0.04626376 -5.21006098 0.32207711 -4.36650935 0.18580701 -5.27752600 0.65028098 -3.37388899 0.66456437 -3.07719445 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R help needed
Try: dat - read.table(/Users/kamleshkumar/Desktop/DS1.txt, header=TRUE) Please also read the F documentation. The use of read.table is in An Introduction to R for example. Simon. On Wed, 2008-05-21 at 08:13 +0200, Kamlesh Kumar wrote: Dear Sir/Madam, I have tried to upload data in R but it showing some error in command window. It's should be noted that I am using Mac version of R. I am using Mac-text for writing my data. I am getting following message on the command window. source(/Users/kamleshkumar/Desktop/DS1.txt) Error in source(/Users/kamleshkumar/Desktop/DS1.txt) : /Users/kamleshkumar/Desktop/DS1.txt: unexpected symbol at 1: x y I am attaching the the DS1.txt file also with this mail. Please go through it and guide me about this. I am waiting for a reply from your side. Thanking you. Yours Sincerely, Kamlesh Kumar __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Converting Data Types
EW == Edward Wijaya [EMAIL PROTECTED] on Wed, 21 May 2008 11:52:17 +0900 writes: EW Hi Peter, EW Thanks. EW as.matrix() does the trick. and ... again my perennial remark to the above trick : Do use data.matrix(dd) instead of as.matrix(dd) if dd is a data frame ... it will also produce a numeric matrix when dd contains factor (and similar) columns. Martin Maechler, ETH Zurich EW - Edward EW On Wed, May 21, 2008 at 11:31 AM, Peter Alspach EW [EMAIL PROTECTED] wrote: Edward Are you sure mymatrix is, in fact, a matrix and note a dataframe (which is a list)? I get: is.matrix(mymatrix) [1] FALSE is.data.frame(mymatrix) [1] TRUE samples - mymatrix[1,] llgm - dgamma(samples, scale=1, shape=2, log = TRUE) Error in dgamma(x, shape, scale, log) : Non-numeric argument to mathematical function That is, the same error as you when mymatrix is a dataframe. But convert it to a matrix and: mymatrix - as.matrix(mymatrix) is.matrix(mymatrix) [1] TRUE is.data.frame(mymatrix) [1] FALSE samples - mymatrix[1,] llgm - dgamma(samples, scale=1, shape=2, log = TRUE) llgm V1 V2 V3 V4 V5 V6 -99.25657 -84.01700 -237.40735 -201.26922 -170.53122 -159.29770 HTH Peter Alspach -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Edward Wijaya Sent: Wednesday, 21 May 2008 2:17 p.m. To: r-help@r-project.org Subject: [R] Converting Data Types Hi, How can I convert the matrices to list. For example I have this snippet: samples-mymatrix[1,] print(samples) which prints: V1 V2V3V4V5V6 1 103.9 88.5 242.9 206.6 175.7 164.4 How can I convert the object samples such that it prints: [1] 103.9 88.5 242.9 206.6 175.7 164.4 The reason I ask this because I can't use the former samples object with this function: llgm - dgamma(samples, scale=1, shape=2, log = TRUE) which gives this error: e 1374Error in dgamma(x, shape, scale, log) : Non-numeric argument to mathematical function Regards, Edward __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. EW __ EW R-help@r-project.org mailing list EW https://stat.ethz.ch/mailman/listinfo/r-help EW PLEASE do read the posting guide http://www.R-project.org/posting-guide.html EW 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] Insufficient memory
Dear Sir/Madam,
I have only started using a R-written script for modeling the distribution of
disease vector species. Part of the script is to make a large GIS grid for use
with GIS software, but it seems I have a memory problem. I get the following
message:
Reached total allocation of 1535Mb: see help(memory.size)
My hard disk has more than 100 gigabytes available, I just have to increase the
allocated memory - sofar unsuccesful. I've used the code:
memory.limit(4094) which returns: NULL.
When I then use the code: memory.limit(size = NA) it returns: [1] 4094. But
then when I run the code to produce the large grid, I still get the same error
message as above.
How do I go about to increase the memory to the maximum?
Your help is much appreciated.
Regards
Roy Williams
Dr R Williams
Diagnostic Products GIS
ARC-Onderstepoort Vet Institute
Tel: +27 12 529-9107
Fax: +27 12 529-9285
Cell: 072 200 0024
[EMAIL PROTECTED]
Visit us at: www.arc.agric.za
Disclaimer\ \ This message is confidential and may be co...{{dropped:20}}
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and provide commented, minimal, self-contained, reproducible code.
[R] Problem in converting natural numbers to bits and others
Hi, I just started using R for about one week and I have few problems. i)I have a problem in finding right function to convert a table of natural numbers to bitwise. For a simple example; I have the below table:- Column Col1 Col2 Col3 Sample1 57 10 Sample2 02 1 Sample3 4 0 0 Supposedly i wanted to convert to :- Column Col1 Col2 Col3 Sample1 11 1 Sample2 01 1 Sample3 1 0 0 ii)Besides, I would like to create a formula of Sum(3*(Element in each column for a row))..does it equivalent to 3*(data[1:3,1:2]) in this case?or I need to have Sum(3*(data[1:3,1:2])). Basically I wanted to mutliply each element of column table of a row and sum it up. iii)I would also like to know how to insert an if else statement where in the above case, I wanted to check if data[1:3,] returns me 1 or 0, it will execute some calculations. I refer to the R intro pdf and it mentioned using if (expr_1 ) expr_2 else expr_3. Does that mean if(data[1:3,1:2])0 output[1:3,1:2]=0 else output[1:3,1:2]=100. If I did this command, how does R knows which row and column to map the output with? Please advise. Appreciate alot. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] an unknown error message when using gamm function
What version of mgcv are you using, please? On Wednesday 21 May 2008 06:16, Lung-Chang Chien wrote: Dear everyone, I'm encountering an unknown error message when using gamm function: fitoutput - gamm(cvd~as.factor(dow)+pm10+s(time,bs=cr,k=15,fx=TRUE)+s(tmean,bs=cr,k =7,fx=TRUE) + ,correlation=corAR1(form=~1|city),family=poisson,random=list(city=~pm10),da ta=mimp) Maximum number of PQL iterations: 20 iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6 Error in `*tmp*`[[k]] : attempt to select less than one element I never saw this error message before, and there is also no related information about this error from the Internet. Hope some people who once encountered this problem can tell me what's wrong. Many thanks, LC -- Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Problem in converting natural numbers to bits and others
Hallo [EMAIL PROTECTED] napsal dne 21.05.2008 09:42:40: Hi, I just started using R for about one week and I have few problems. i)I have a problem in finding right function to convert a table of natural numbers to bitwise. For a simple example; I have the below table:- Column Col1 Col2 Col3 Sample1 57 10 Sample2 02 1 Sample3 4 0 0 Supposedly i wanted to convert to :- Column Col1 Col2 Col3 Sample1 11 1 Sample2 01 1 Sample3 1 0 0 data-read.table(clipboard, header=T If data is your data frame, data.bit-data.frame(column=data[,1],(data[,-1]0)*1) ii)Besides, I would like to create a formula of Sum(3*(Element in each column for a row))..does it equivalent to 3*(data[1:3,1:2]) in this case?or I need to have Sum(3*(data[1:3,1:2])). Basically I wanted to mutliply each element of column table of a row and sum it up. Rather complicated. 3*(data[1:3,2:3]) Col1 Col2 1 15 21 206 3 120 sum(3*(data[1:3,2:3])) [1] 54 Works but I am suspicious that you wont something else. iii)I would also like to know how to insert an if else statement where in the above case, I wanted to check if data[1:3,] returns me 1 or 0, it will execute some calculations. I refer to the R intro pdf and it mentioned using if (expr_1 ) expr_2 else expr_3. Does that mean if(data[1:3,1:2])0 output[1:3,1:2]=0 else output[1:3,1:2]=100. If I did this command, how does R knows which row and column to map the output with? If ... else ... is usually for working as programming steps ifelse(..., ..., ...) works with objects and is parts. You shall think first how to do your calculations with whole objects, it is usually more effective. Regards Petr Please advise. Appreciate alot. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Proportional axes
Hi! If I'm plotting 2 variables with the same units (i.e. wing length of 2 species), how can I force that X and Y axes have the same size for length unit? For example, if X ranges from 0 to 10 and Y ranges from 10 to 30, I want Y axis to be twice as long as X axis. I know I can just put xlim and ylim from 0 to 30, i.e., plot(runif(10,0,10),runif(10,10,30),xlim=c(0,30),ylim=c(0,30)) but this is a waste of space. Thanks -- Dr. Agustin Lobo Institut de Ciencies de la Terra Jaume Almera (CSIC) LLuis Sole Sabaris s/n 08028 Barcelona Spain Tel. 34 934095410 Fax. 34 934110012 email: [EMAIL PROTECTED] http://www.ija.csic.es/gt/obster __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] need some help in plotting xy graph
fdf dataframe contains the data as follows bin rate overlay x 1 90 Assign First/cc _from_SN_53 RNC_20_to_SN_50 RNC_21_Success Rate (04/01/08 16:02:30) 2 93 Assign First/cc _from_SN_53 RNC_20_to_SN_50 RNC_21_Success Rate (04/01/08 16:07:30) 1 90 Assign First/cc _from_SN_50 RNC_21_to_SN_53 RNC_20_Success Rate (04/01/08 16:02:30) 2 94 Assign First/cc _from_SN_50 RNC_21_to_SN_53 RNC_20_Success Rate (04/01/08 16:07:30) I want to plot a xygraph on xaxis-x on y-axis-rate groups=overlay formd-rate ~ as.numeric(x) groups-overlay lgnd.txt-levels(df$overlay) print(xyplot(formula(formd),data = fdf, groups = overlay, type = b, as.table = TRUE, cex=0.20,main = this is my first plot, xlab = Time, ylab = session transfer,scales = c(xscales,yscales),key = simpleKey(text = lgnd.txt, cex = 3/4,points = FALSE, lines = TRUE), layout = c(1,1))) but I didn't get any o/p so can u tel how can I get the desired xygraph from fdf dataframe -Original Message- From: Deepayan Sarkar [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 21, 2008 10:43 AM To: Kurapati, Ravichandra (Ravichandra) Cc: [EMAIL PROTECTED] Subject: Re: [Rd] need some help in plotting xy graph On 5/20/08, Kurapati, Ravichandra (Ravichandra) [EMAIL PROTECTED] wrote: Dataframedf contains bin rate overlay 1 1 90 Assign First/cc _from_SN_53 RNC_20_to_SN_50 RNC_21_Success Rate 2 2 93 Assign First/cc _from_SN_53 RNC_20_to_SN_50 RNC_21_Success Rate 3 1 90 Assign First/cc _from_SN_50 RNC_21_to_SN_53 RNC_20_Success Rate 4 2 94 Assign First/cc _from_SN_50 RNC_21_to_SN_53 RNC_20_Success Rate time 1 (04/01/08 16:02:30) 2 (04/01/08 16:07:30) 3 (04/01/08 16:02:30) 4 (04/01/08 16:07:30) It would be more work to read in your data than I have time for. Could you post it in a more convenient format? (The output of dput(fdf) should be fine.) -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Insufficient memory
Presumably you are using Windows without telling us. Please study the
appropriate section of the rw-FAQ (and also the posting guide).
On Wed, 21 May 2008, Roy Williams wrote:
Dear Sir/Madam,
I have only started using a R-written script for modeling the
distribution of disease vector species. Part of the script is to make a
large GIS grid for use with GIS software, but it seems I have a memory
problem. I get the following message:
Reached total allocation of 1535Mb: see help(memory.size)
My hard disk has more than 100 gigabytes available, I just have to increase the
allocated memory - sofar unsuccesful. I've used the code:
memory.limit(4094) which returns: NULL.
When I then use the code: memory.limit(size = NA) it returns: [1] 4094. But
then when I run the code to produce the large grid, I still get the same error
message as above.
How do I go about to increase the memory to the maximum?
Tell your unstated OS that you want more of the address space? See the
rw-FAQ.
Your help is much appreciated.
Regards
Roy Williams
Dr R Williams
Diagnostic Products GIS
ARC-Onderstepoort Vet Institute
Tel: +27 12 529-9107
Fax: +27 12 529-9285
Cell: 072 200 0024
[EMAIL PROTECTED]
Visit us at: www.arc.agric.za
Disclaimer\ \ This message is confidential and may be co...{{dropped:20}}
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Proportional axes
Hello. Try the to set asp=1 (aspect ratio between y- and x-axis): plot(runif(10, 0, 10), runif(10, 10, 30), asp=1) Best Ivar Herfindal Agustin Lobo skrev: Hi! If I'm plotting 2 variables with the same units (i.e. wing length of 2 species), how can I force that X and Y axes have the same size for length unit? For example, if X ranges from 0 to 10 and Y ranges from 10 to 30, I want Y axis to be twice as long as X axis. I know I can just put xlim and ylim from 0 to 30, i.e., plot(runif(10,0,10),runif(10,10,30),xlim=c(0,30),ylim=c(0,30)) but this is a waste of space. Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Proportional axes
Thanks, I looked into the man pages of par() and did not into the ones of plot() Sorry about it, Agus Richard Rowe escribió: plot(runif(10,0,10),runif(10,10,30),xlim=c(0,10),ylim=c(10,30), asp=1) asp is the aspect parameter and ensures x y metrics are the same (try the plot without it). To save more space you will need to inform the plotting system you want a portrait perspective plot and control the size of the canvas. You can also drag the handles of the plot as the asp = 1 will maintain the metric relationship ... and rely on Brian Ripley's graphics drivers to deliver the information you want into a form you can incorporate elsewhere, Richard Agustin Lobo wrote: Hi! If I'm plotting 2 variables with the same units (i.e. wing length of 2 species), how can I force that X and Y axes have the same size for length unit? For example, if X ranges from 0 to 10 and Y ranges from 10 to 30, I want Y axis to be twice as long as X axis. I know I can just put xlim and ylim from 0 to 30, i.e., plot(runif(10,0,10),runif(10,10,30),xlim=c(0,30),ylim=c(0,30)) but this is a waste of space. Thanks -- Dr. Agustin Lobo Institut de Ciencies de la Terra Jaume Almera (CSIC) LLuis Sole Sabaris s/n 08028 Barcelona Spain Tel. 34 934095410 Fax. 34 934110012 email: [EMAIL PROTECTED] http://www.ija.csic.es/gt/obster __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Search a string and modify it in a .txt file
Hi there,
I use R and I would like to be able to modify a file .txt init_file like this
one :
# #
# Parameters A
# #
# Parameter 1
PA1 = 15
# Parameter 2
PA2 = 3
# Parameter 3
PA3 = 2
# #
# #
# Parameters B
# #
# Parameter 1
PB1 = 6
...
I have in a first time stocked the values I want to attribute to each parameter
and so I would like to create several config files like the first one but with
different values for each parameter. I have an array like this one
PA1 PA2 PA3 PB1
j=1 122 15
j=2 103 24
j=3 114 36
...
To create each file I use :
for (j in 1:Nb_config_file)
{
file.copy(fichier_init,paste(Config_file,j,sep=))
}
How can I do to search in each config file j created to modify the values of
the parameters according to the j-th row of the array?
I thought about looking for the lines 'Parameter' = Value and modify this
line in 'Parameter' = New_value but I don't find any function to know the
location of each string in my config_file...
I could also use such a function to modify the format of the date to replace
the : by something which can be used in a Directory/file name.
Thanks you for your time and for your future help =)
Cheers
Romain
Vous aussi bénéficiez d'1 Go de stockage gratuit en ligne avec Voila
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and provide commented, minimal, self-contained, reproducible code.
[R] number of trading days
Hi, I work on the date format: mmdd. I would like to calculate the number of (working or trading) days between two of such specified dates in specific year at US stock exchange OR at least with respect to 252-days year. What I did so far was the conversion (example): x-20060213; y-20060402 # refering to January 13 and April 2, 2006 x1 - as.Date(as.character(x), %Y%m%d) y1 - as.Date(as.character(y), %Y%m%d) # nuber of calendar days nr_cal-diff(rbind(x1,y1)) best regards, robert -- View this message in context: http://www.nabble.com/number-of-trading-days-tp17364148p17364148.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] number of trading days
On Wed, May 21, 2008 at 04:44:32AM -0700, threshold wrote: Hi, I work on the date format: mmdd. I would like to calculate the number of (working or trading) days between two of such specified dates in specific year at US stock exchange OR at least with respect to 252-days year. What I did so far was the conversion (example): x-20060213; y-20060402 # refering to January 13 and April 2, 2006 x1 - as.Date(as.character(x), %Y%m%d) y1 - as.Date(as.character(y), %Y%m%d) # nuber of calendar days nr_cal-diff(rbind(x1,y1)) Have a look at the fCalendar package on CRAN. Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave / Latex per-chapter output
Anne-Marie Ternes [EMAIL PROTECTED] writes:
What I would like to do, is to be able to get 2 types of output with
the same code (I'm lazy ;-) ):
...
2. a PDF and HTML file *per chapter*, for displaying on our website
and allowing people to download individual chapters
...
BTW, I'm working on Ubuntu Linux.
I'm assuming that you are using pdflatex to process the latex file(s)
produced by Sweave.
Assuming also that you are using latex's \include command (e.g.,
\include{chap1}, \include{chap2}, etc.) inside your master file, you
could add a line like
\includeonly{chap2}
in the preamble to just create a pdf file containing only Chapter 2.
The easiest way to do this is probably to edit the master latex file
by hand, after having run pdflatex a few times to produce the full
document (you need to do this to get all the pagination and
cross-referencing information into the .aux, .toc, and other files).
Another way to accomplish 2 is to install Ubuntu's pdftk package then
use the pdftk command with the cat option to extract whatever pages
you want.
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Re: [R] mixed effects models with nested factors
Thanks for the help provided to fit the model. I still have two questions: 1) What is the syntax for nested fixed and random factors. I have tried using the %in% operator but it does not work. The model I want to fit would be as follow: lmer 1 - lmer(Growing ~ Seed + Species%in%Seed + Treatment + (1|Block%in%Treatment), data) 2) Seed, Species and Treatment are intra-subject factors. This means that an ANOVA of repeated measure should apply here. How should this be specified in the model? Or should I assume that this is incorporated by specifying the Block as a random factor? All the best, Luis Luis Cayuela Departamento de Ecología Universidad de Alcalá Crta. de Barcelona km. 33,600 E-28871 Alcalá de Henares Madrid España Tlf: (+0034) 918856407 Fax: (+0034) 918854929 - Original Message - From: Douglas Bates [EMAIL PROTECTED] To: Luis Cayuela [EMAIL PROTECTED] Cc: r-help@r-project.org Sent: Thursday, May 15, 2008 5:22 PM Subject: Re: [R] mixed effects models with nested factors On Thu, May 15, 2008 at 9:22 AM, Luis Cayuela [EMAIL PROTECTED] wrote: Hi everybody, I am trying to fit a model with the lmer function for mixed effects. I have an experimental design consisting of 5 field plots. Each plot is divided in 12 subplots where the influence of three factors on the growing of tree seedlings is tested: (1) seed (1 = presence; 0 = absence); (2) seedling species (oak holm vs. pine); (3) treatment (three different treatments). In each of these subplots we planted 13 seedlings. Therefore I would have a model with three fixed factors and one random factor (a block?). If I´m not wrong the model would be as follows: model2 - lmer(Growing ~ Seed + Species + Treatment +(Seed + Species + Treatment|Block), data) That's unlikely. This specification would fit 5 fixed effects parameters and 5, possibly correlated, random effects for each level of the Block factor. This would require estimating a total of 15 variance-covariance parameters for the random effects from the 5 blocks. Can you indicate how many random effects you expect to obtain and how many variance-covariance parameters would be involved? For example, a model with a simple random effect would be expressed as lmer(Growing ~ Seed + Species + Treatment + (1|Block), data) and would involve estimating the 5 fixed effects and one variance for the random effects. My first question is: if the three fixed factors occur within-subjects (considering the plot as a subject), is the model correctly defined (assuming no interactions)? Should I specify the model in some other way? I second problem I had is that the factors are not crossed because some of the seedling died during the experiment. This means that some factors are nested. Specifically Species is nested within Seed and Block would be nested within Treatment. I have tried to use the %in% specification for nested designs but it does not work. model2 - lmer(Growing ~ Seed + Species%in%Seed + Treatment +(Seed + Species + Treatment|Block%in%Treatment), data) I get the following error: Error en lmer(Growing ~ Seed + Species %in% Seed + Treatment + : .. Leading minor of order 5 in downdated X'X is not positive definite I would appreciate some help to fit this model. Thanks to everybody, Luis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] scheduling - algorithm solution or iterate?
Our final year students rank 5 classes (1st, 2nd, ..., 5th), and are allocated 3, based on their choices and a minimum class size. We want to maximise satisfaction (students getting their higher preferences), but have a minimum viable class size. Is there an algorithm out there to help, in R (like TSP for the travelling salesman prob) or elsewhere, or must I just iterate and locate the highest scoring ??? Thanks! -- View this message in context: http://www.nabble.com/scheduling---algorithm-solution-or-iterate--tp17364154p17364154.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] 'Extracting' plot area
Hi! Does anyone know hot to save (to png, pdf, ...) only plot area. That is without box around, titles, axis, ... I tried: par(mar=c(0,0,0,0)) and it works for internal viewer (linux and windows). But when I save the image in png it adds that annoying margin around plot area. Any ideas? by, Tine __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 'Extracting' plot area
on 05/21/2008 08:02 AM Tine wrote: Hi! Does anyone know hot to save (to png, pdf, ...) only plot area. That is without box around, titles, axis, ... I tried: par(mar=c(0,0,0,0)) and it works for internal viewer (linux and windows). But when I save the image in png it adds that annoying margin around plot area. Any ideas? by, Tine Is this what you want? pdf(plot.pdf, height = 4, width = 4) par(mar = c(0, 0, 0, 0)) plot(1:10, ann = FALSE, axes = FALSE) dev.off() See ?plot.default for more information on the 'ann' and 'axes' arguments. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 'Extracting' plot area
On 5/21/2008 9:02 AM, Tine wrote: Hi! Does anyone know hot to save (to png, pdf, ...) only plot area. That is without box around, titles, axis, ... I tried: par(mar=c(0,0,0,0)) and it works for internal viewer (linux and windows). But when I save the image in png it adds that annoying margin around plot area. Any ideas? Set up the options for no margins after opening the device. (If you are copying from the screen device in Windows, you don't need to do it again; presumably the same is true in Linux. But if you use png() to open a png device it will start up with default par settings. You need to set the margins after that.) For example, png(test.png) par(mar=c(0,0,0,0), xaxs=i, yaxs=i) plot(runif(1)) dev.off() produces a big ugly plot without those nice margins. 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] Rank Values in a Matrix
On 05/19/08 13:46, Jens Oldeland wrote: Dear All, a short and maybe simple question: I have to rank all values in a matrix from 0 to X, [1] [2] [3] [4] [1] 0.1 2 03 [2] 50 3 31 [3] 100 1 10 [4] 100 2 20 0-0 0.1-1 2-2 3-3 50-4 100-5 (X=5) Does this do what you want? x - matrix(c(3,100,0.1,3,100,2,5,0,0,50),5) y - as.data.frame(table(x)) y$Rank - rank(y$x) m. -- Marianne Promberger Graduate student in Psychology http://www.psych.upenn.edu/~mpromber __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Search a string and modify it in a .txt file
Instead of trying to modify the file, why not generate it from the data that
you have. Is the array in your mail an example of one of many that have the
configuration data? If so, why don't you just create the output file from
that data. You can just loop through and do 'writeLines' to create the
init_file.
On Wed, May 21, 2008 at 7:05 AM, Romain [EMAIL PROTECTED] wrote:
Hi there,
I use R and I would like to be able to modify a file .txt init_file like
this one :
#
#
# Parameters A
#
#
# Parameter 1
PA1 = 15
# Parameter 2
PA2 = 3
# Parameter 3
PA3 = 2
#
#
#
#
# Parameters B
#
#
# Parameter 1
PB1 = 6
...
I have in a first time stocked the values I want to attribute to each
parameter and so I would like to create several config files like the first
one but with different values for each parameter. I have an array like this
one
PA1 PA2 PA3 PB1
j=1 122 15
j=2 103 24
j=3 114 36
...
To create each file I use :
for (j in 1:Nb_config_file)
{
file.copy(fichier_init,paste(Config_file,j,sep=))
}
How can I do to search in each config file j created to modify the values
of the parameters according to the j-th row of the array?
I thought about looking for the lines 'Parameter' = Value and modify this
line in 'Parameter' = New_value but I don't find any function to know the
location of each string in my config_file...
I could also use such a function to modify the format of the date to
replace the : by something which can be used in a Directory/file name.
Thanks you for your time and for your future help =)
Cheers
Romain
Vous aussi bénéficiez d'1 Go de stockage gratuit en ligne avec Voila
http://macle.voila.fr
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[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.
Re: [R] Odp: Problem in converting natural numbers to bits and others
Le mer. 21 mai à 04:38, Petr PIKAL a écrit : Hallo [EMAIL PROTECTED] napsal dne 21.05.2008 09:42:40: Hi, I just started using R for about one week and I have few problems. i)I have a problem in finding right function to convert a table of natural numbers to bitwise. For a simple example; I have the below table:- Column Col1 Col2 Col3 Sample1 57 10 Sample2 02 1 Sample3 4 0 0 Supposedly i wanted to convert to :- Column Col1 Col2 Col3 Sample1 11 1 Sample2 01 1 Sample3 1 0 0 data-read.table(clipboard, header=T If data is your data frame, data.bit-data.frame(column=data[,1],(data[,-1]0)*1) sign(data) will also do. Vincent ii)Besides, I would like to create a formula of Sum(3*(Element in each column for a row))..does it equivalent to 3*(data[1:3,1:2]) in this case?or I need to have Sum(3*(data[1:3,1:2])). Basically I wanted to mutliply each element of column table of a row and sum it up. Rather complicated. 3*(data[1:3,2:3]) Col1 Col2 1 15 21 206 3 120 sum(3*(data[1:3,2:3])) [1] 54 Works but I am suspicious that you wont something else. iii)I would also like to know how to insert an if else statement where in the above case, I wanted to check if data[1:3,] returns me 1 or 0, it will execute some calculations. I refer to the R intro pdf and it mentioned using if (expr_1 ) expr_2 else expr_3. Does that mean if(data[1:3,1:2])0 output[1:3,1:2]=0 else output[1:3,1:2]=100. If I did this command, how does R knows which row and column to map the output with? If ... else ... is usually for working as programming steps ifelse(..., ..., ...) works with objects and is parts. You shall think first how to do your calculations with whole objects, it is usually more effective. Regards Petr Please advise. Appreciate alot. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Search a string and modify it in a .txt file
Here is an example of how to create the init files:
x - read.table(textConnection( PA1 PA2 PA3 PB1
j=1 122 15
j=2 103 24
j=3 114 36), header=TRUE)
closeAllConnections()
for (i in 1:nrow(x)){
outfile - file(paste(init., i, .txt, sep=''), w)
for (j in colnames(x)){
writeLines(paste(j, '=', x[i,j], sep=''), outfile)
}
close(outfile)
}
This will create a file that will look like this:
readLines('init.1.txt')
[1] PA1=12 PA2=2 PA3=1 PB1=5
On Wed, May 21, 2008 at 7:05 AM, Romain [EMAIL PROTECTED] wrote:
Hi there,
I use R and I would like to be able to modify a file .txt init_file like
this one :
#
#
# Parameters A
#
#
# Parameter 1
PA1 = 15
# Parameter 2
PA2 = 3
# Parameter 3
PA3 = 2
#
#
#
#
# Parameters B
#
#
# Parameter 1
PB1 = 6
...
I have in a first time stocked the values I want to attribute to each
parameter and so I would like to create several config files like the first
one but with different values for each parameter. I have an array like this
one
PA1 PA2 PA3 PB1
j=1 122 15
j=2 103 24
j=3 114 36
...
To create each file I use :
for (j in 1:Nb_config_file)
{
file.copy(fichier_init,paste(Config_file,j,sep=))
}
How can I do to search in each config file j created to modify the values
of the parameters according to the j-th row of the array?
I thought about looking for the lines 'Parameter' = Value and modify this
line in 'Parameter' = New_value but I don't find any function to know the
location of each string in my config_file...
I could also use such a function to modify the format of the date to
replace the : by something which can be used in a Directory/file name.
Thanks you for your time and for your future help =)
Cheers
Romain
Vous aussi bénéficiez d'1 Go de stockage gratuit en ligne avec Voila
http://macle.voila.fr
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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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] Sweave / Latex per-chapter output
Dear Anne-Marie,
we had a similar problem to handle the LaTeX book that ships with the
seqinr package (http://pbil.univ-lyon1.fr/software/seqinr/seqinr_1_1-5.pdf).
Here is basically the approach we have used:
o Each book chapter is written first as a LaTeX article produced by Sweaving
its corresponding *.rnw file. They are therefore available as individual
articles in PDF.
o The book itself is produced by collating the core of each LaTeX source
files and turning articles titles into chapter titles (among other things
such as computing the full author list from article authors). The book is
therefore also available in PDF without changing the *.rnw files.
There are of course some constraints for this to work (e.g. all articles
are sharing the same *.bib file, all figures are in the same folder and
we are using the following (ugly) construct:
hack, echo=FALSE, fig=FALSE, results=hide, eval=TRUE=
.CurFileName - get(file, env = parent.frame(3))
.PrefixName - strsplit(.CurFileName, \\.)[[1]][1]
@
\SweaveOpts{prefix.string = ../figs/\Sexpr{.PrefixName} }
to avoid collisions between figures names produced by Sweave by prefixing
them with the current *.rnw file name, etc.)
If you want to know more the source code for the book is distributed with
the seqinr package in the /doc/src folder, see /doc/src/template/template.pdf
file as a starter. Please send an e-mail to the seqinr diffusion list if you
have more questions.
HTH,
Jean
--
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/
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and provide commented, minimal, self-contained, reproducible code.
[R] problems with data frames, factors and lists
I have a function that creates a list based on some clustered data:
mix - function(Y, pid) {
hc = gethc(Y,pid)
maxheight = max(hc$height)
noingrp = processhc(hc)
one = noingrp$one
two = noingrp$two
twoisone = one
if (two != 1)
twoisone = more
out = list(pid = pid,one = noingrp$one, two = noingrp$two, diff = maxheight,
noseqs = length(hc$labels), twogrp = twoisone)
return(out)
}
example result:
mix(tsus_same, 77)
$pid
[1] 77
$one
[1] 9
$two
[1] 2
$diff
[1] 8.577195
$noseqs
[1] 11
$twogrp
[1] more
I then use this function in another function that just runs this
function through a lot of data:
doset - function(sameset) {
pids = unique(c(sameset$APID, sameset$BPID))
for (f in pids) {
oputframe = data.frame(rbind(oputframe, mix(sameset, f)))
}
return(oputframe)
}
All values except $twogrp are numbers. There are two possible values
for $twogrp, one and more. the first one is more common and gets
added to the data frame first. The result is that I cannot add the
rows where this is more without getting
38: In `[-.factor`(`*tmp*`, ri, value = more) :
invalid factor level, NAs generated
Now, this is a pain in the neck. How can I merge these lists to the
data frame and still have the value $twogrp as a factor?
Thanks, and I hope my code makes some sense!
Karin
--
Karin Lagesen, PhD student
[EMAIL PROTECTED]
http://folk.uio.no/karinlag
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Re: [R] an unknown error message when using gamm function
The version is mgcv 1.3-27. Last night, I dropped out many arguments from my program to test which part might be the source of causing this error message, and found that the program works when just using corAR1(). This program has no this kind of problem in the beginning, but doesn't work after I impute some missing data in PM10 and tmean by multiple imputation approach. Hope this information can also help identify the element of this problem. LC From: Simon Wood [EMAIL PROTECTED] To: r-help@r-project.org Date: Wed, 21 May 2008 08:55:02 +0100 Subject: Re: [R] an unknown error message when using gamm function What version of mgcv are you using, please? On Wednesday 21 May 2008 06:16, Lung-Chang Chien wrote: Dear everyone, I'm encountering an unknown error message when using gamm function: fitoutput - gamm(cvd~as.factor(dow)+pm10+s (time,bs=cr,k=15,fx=TRUE)+s(tmean,bs=cr,k =7,fx=TRUE) + ,correlation=corAR1(form=~1|city),family=poisson,random=list(city=~pm10),da ta=mimp) Maximum number of PQL iterations: 20 iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6 Error in `*tmp*`[[k]] : attempt to select less than one element I never saw this error message before, and there is also no related information about this error from the Internet. Hope some people who once encountered this problem can tell me what's wrong. Many thanks, LC -- Lung-Chang Chien Doctoral candidate, Department of Biostatistics Statistical assistant, School of Nursing University of North Carolina at Chapel Hill Office: Carrington Hall, RSC, Room 2014 TEL: 919-843-2480 [[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] split character string in matrix into character vector and numeric vector
Hello, I've got a matrix consisting of one column with n rows. Each field in the matrix is filled with a character vector. I would like to convert this matrix into a character vector containing the B03_MAH-type entries from the beginning of each row and a data.frame that contains the numeric data, but I am stuck. I have tried to use textConnection with sep =but since there is sometimes more than two spaces separating the entries, I obtain a result with columns full of NAs. Then I tried sub() to replace the all multi-spaces to get only one space that separates each entry but that didn't work either. Do you know a good way to convert this matrix? Thanks already, Kim taxa.vec B03_MAH 0.2115 0.2087 0.2087 0.2147 0.2115 0.2176 taxa.vec F02_SSBH0.2162 0.2191 0.2133 0.2130 0.2220 0.2158 taxa.vec G04_MAH 0.2083 0.2111 0.2055 0.2115 0.2140 0.2087 taxa.vec A04_MAH 0.2097 0.2126 0.2069 0.2065 0.2097 0.2037 taxa.vec E03_MAH 0.2097 0.2069 0.2069 0.2130 0.2155 0.2101 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] split character string in matrix into character vector and numeric vector
x - B03_MAH 0.2115 0.2087 0.2087 0.2147 0.2115 0.2176 strsplit(x, +) [[1]] [1] B03_MAH 0.2115 0.2087 0.2087 0.2147 0.2115 0.2176 -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kim Milferstedt Sent: Wednesday, May 21, 2008 1:11 PM To: [EMAIL PROTECTED] Subject: [R] split character string in matrix into character vector and numeric vector Hello, I've got a matrix consisting of one column with n rows. Each field in the matrix is filled with a character vector. I would like to convert this matrix into a character vector containing the B03_MAH-type entries from the beginning of each row and a data.frame that contains the numeric data, but I am stuck. I have tried to use textConnection with sep =but since there is sometimes more than two spaces separating the entries, I obtain a result with columns full of NAs. Then I tried sub() to replace the all multi-spaces to get only one space that separates each entry but that didn't work either. Do you know a good way to convert this matrix? Thanks already, Kim taxa.vec B03_MAH 0.2115 0.2087 0.2087 0.2147 0.2115 0.2176 taxa.vec F02_SSBH0.2162 0.2191 0.2133 0.2130 0.2220 0.2158 taxa.vec G04_MAH 0.2083 0.2111 0.2055 0.2115 0.2140 0.2087 taxa.vec A04_MAH 0.2097 0.2126 0.2069 0.2065 0.2097 0.2037 taxa.vec E03_MAH 0.2097 0.2069 0.2069 0.2130 0.2155 0.2101 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to do pairwise sums in a matrix
Try this: t(rowsum(t(Mat), substr(colnames(Mat), 1, 1))) On Wed, May 21, 2008 at 2:22 PM, Gregory Gentlemen [EMAIL PROTECTED] wrote: I am looking for an efficient way to solve the following problem. I have a large matrix of continuous values with a small proportion of missing values. Columns correspond to variables where each variable has two measurements, call them A and B. The matrix is such that the columns are in sequence with respect to the variables. I would like to sum up the two measurements for each variable and each observation (the rows) for the whole matrix. Here is an example of such a matrix with 5 variables (R, S, T, U, V) and 50 observations: set.seed(27) Mat - matrix(rnorm(500), nrow=50, ncol=10) dimnames(Mat)[[2]] - c(R.A,R.B,S.A,S.B,T.A,T.B,U.A,U.B,V.A,V.B) miss.ind - rbinom(500,1,prob=0.98) Mat[!as.logical(miss.ind)] - NA So I would like to produce 50 by 5 matrix where the columns are the sums of A+B measurements for each of the 5 variables. Thanks for any help. Gregory Gentlemen - [[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 [[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] Labeling a plot's x-axis with 12 strings, vertically oriented.
Hello, I really enjoy using R for my plotting. I have a modest plot, containing 24 data points, across 2 lines,12 points each. Ideally, the x-axis would be labeled with a series of strings, oriented vertically. Here is the R container holding the Search strings: Search [1] Route To: NCENGR Status: Open CR Route To: NCENGR [3] Status: Cancel Route To: TEST1 Status: ENG REQ Route To: TDELLE [5] (*) Customer Name: *(*) Customer Name: S*IT* [7] (*) Customer Name: SMITH (*) Address: 1*** [9] (*) Address: 1** S ST Route To: NCS [11] Route To: NCS From Date: 01/01/2000 Name: SMITH 12 Levels: (*) Address: 1** S ST(*) Address: 1*** ... Status: Open CR Route To: NCENGR Is there a function to define the x-axis, using the above 12 strings as axis tick labels, from 1 - 12, vertically oriented? Any help would be appreciated, as my current work around is tedious, and not asthetically pleasing. Cheers, John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Labeling a plot's x-axis with 12 strings, vertically oriented.
Here is one example: y - rnorm(12) x - 1:12 par(mar=c(10, 4, 4, 1)+0.1) plot(x,y, xlab='', xaxt='n') axis(1, at=x, labels=month.name, las=2) See help on par and axis for details. -- 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 John Sent: Wednesday, May 21, 2008 12:56 PM To: r-help@r-project.org Subject: [R] Labeling a plot's x-axis with 12 strings, vertically oriented. Hello, I really enjoy using R for my plotting. I have a modest plot, containing 24 data points, across 2 lines,12 points each. Ideally, the x-axis would be labeled with a series of strings, oriented vertically. Here is the R container holding the Search strings: Search [1] Route To: NCENGR Status: Open CR Route To: NCENGR [3] Status: Cancel Route To: TEST1 Status: ENG REQ Route To: TDELLE [5] (*) Customer Name: *(*) Customer Name: S*IT* [7] (*) Customer Name: SMITH (*) Address: 1*** [9] (*) Address: 1** S ST Route To: NCS [11] Route To: NCS From Date: 01/01/2000 Name: SMITH 12 Levels: (*) Address: 1** S ST(*) Address: 1*** ... Status: Open CR Route To: NCENGR Is there a function to define the x-axis, using the above 12 strings as axis tick labels, from 1 - 12, vertically oriented? Any help would be appreciated, as my current work around is tedious, and not asthetically pleasing. Cheers, John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Labeling a plot's x-axis with 12 strings, vertically oriented.
On 5/21/2008 2:56 PM, John wrote:
Hello,
I really enjoy using R for my plotting. I have a modest plot, containing
24 data points, across 2 lines,12 points each. Ideally, the x-axis would
be labeled with a series of strings, oriented vertically. Here is the R
container holding the Search strings:
Search
[1] Route To: NCENGR Status: Open
CR Route To: NCENGR
[3] Status: Cancel Route To: TEST1 Status: ENG REQ
Route To: TDELLE
[5] (*) Customer Name: *(*)
Customer Name: S*IT*
[7] (*) Customer Name: SMITH (*) Address:
1***
[9] (*) Address: 1** S ST Route To:
NCS
[11] Route To: NCS From Date: 01/01/2000 Name:
SMITH
12 Levels: (*) Address: 1** S ST(*) Address:
1*** ... Status: Open CR Route To: NCENGR
Is there a function to define the x-axis, using the above 12 strings as
axis tick labels, from 1 - 12, vertically oriented? Any help would be
appreciated, as my current work around is tedious, and not asthetically
pleasing.
plot(1:12, axes=F)
axis(1, at=1:12, labels=c('one','two','three','four','five','six',
'seven', 'eight', 'nine','ten','eleven','twelve'), las=2)
axis(2)
box()
You'll probably need bigger margins for your longer strings.
Duncan Murdoch
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[R] how to write fac.design (S-plus) in R
hi, Anyone here know well of the fac.design of S-plus? I need to rewrite the following code in R code in S-plus *pt.design = fac.design( c(2,2,3,2),factor.names = list(Hs=c(I,II),lef = c(0,1),lep = c(0,1,2),Type=c(gt,sy))) c.design=fac.design( levels=c(2,2,2,2),factor=list(A=lohi,B=lohi,C=lohi,D=lohi),fraction=1/2) f.design=fac.design( rep(2,6),factor.names=c(XF,XE,XD,XC,XB,XA),fraction=~XA:XB:XC:XD+XB:XC:XE:XF) * I need to rewrite the above in R, but I have no idea what the results look like under S-plus since I don't have such platform. So could some one here help me out, or just give the result under S-plus will also be appreciated. Best Wishes, Becky -- + Be not afraid of growing slowly, be afraid only of standing still. $B!]!](BChinese Proverb + [[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] Course of R in Brazil
Hello! I´m Ana Carolina from UNICAMP (Campinas - SP - Brazil) and wonders, if there is someone interested and qualified, to give a course of R during one week in UNICAMP for the Department of Social and Preventive Medicine. We need to be some lessons on use of mgcv, gam and VGAM packages. If there is interest, please contact us. We have some urgency! The course would be for June / 08. Thanks, Ana Carolina [[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] fac.design in R
hi, Anyone here know well of the fac.design of S-plus? I need to rewrite the following code in R code in S-plus *pt.design = fac.design( c(2,2,3,2),factor.names = list(Hs=c(I,II),lef = c(0,1),lep = c(0,1,2),Type=c(gt,sy))) c.design=fac.design( levels=c(2,2,2,2),factor=list(A=lohi,B=lohi,C=lohi,D=lohi),fraction=1/2) f.design=fac.design( rep(2,6),factor.names=c(XF,XE,XD,XC,XB,XA),fraction=~XA:XB:XC:XD+XB:XC:XE:XF) * I need to rewrite the above in R, but I have no idea what the results look like under S-plus since I don't have such platform. So could some one here help me out, or just give the result under S-plus will also be appreciated. Best Wishes, Becky [[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] Converting a 'difftime' to integer - How to???
I want to find the DOY (Day of Year) of some dates. I think to substract the date 1. January from the data to achive this. Something like: d - as.Date(2006-03-13) - as.Date(2006-01-01) +1 d Time difference of 72 days So far so good. But d is a 'difftime' object. How do I get an Integer value from that? I tried severel things, incuding the following: dd - as(d,numeric) Error in .classEnv(thisClass) : unable to find an environment containing class difftime Sugestions appriciated... :-) [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Converting a 'difftime' to integer - How to???
Try : as.numeric(d) or also: unclass(d) On Wed, May 21, 2008 at 5:04 PM, Martin Hvidberg [EMAIL PROTECTED] wrote: I want to find the DOY (Day of Year) of some dates. I think to substract the date 1. January from the data to achive this. Something like: d - as.Date(2006-03-13) - as.Date(2006-01-01) +1 d Time difference of 72 days So far so good. But d is a 'difftime' object. How do I get an Integer value from that? I tried severel things, incuding the following: dd - as(d,numeric) Error in .classEnv(thisClass) : unable to find an environment containing class difftime Sugestions appriciated... :-) [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting a 'difftime' to integer - How to???
Or, convert your object of class Date to POSIXlt, and then use the yday element of the resulting list. Example: today - Sys.Date() as.POSIXlt(today)$yday Erik Martin Hvidberg wrote: I want to find the DOY (Day of Year) of some dates. I think to substract the date 1. January from the data to achive this. Something like: d - as.Date(2006-03-13) - as.Date(2006-01-01) +1 d Time difference of 72 days So far so good. But d is a 'difftime' object. How do I get an Integer value from that? I tried severel things, incuding the following: dd - as(d,numeric) Error in .classEnv(thisClass) : unable to find an environment containing class difftime Sugestions appriciated... :-) [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Converting a 'difftime' to integer - How to???
Martin Hvidberg wrote: I want to find the DOY (Day of Year) of some dates. I think to substract the date 1. January from the data to achive this. Something like: d - as.Date(2006-03-13) - as.Date(2006-01-01) +1 d Time difference of 72 days So far so good. But d is a 'difftime' object. How do I get an Integer value from that? I tried severel things, incuding the following: dd - as(d,numeric) Error in .classEnv(thisClass) : unable to find an environment containing class difftime Sugestions appriciated... The canonical way is as.numeric(d, units=days) [1] 72 In fact, you can leave out the units when dealing with differences between Date objects, because it is always days, but that is an undocumented implementation detail. If you have differences between POSIXt objects, real confusion can arise: ISOdatetime(2008,1,1,12,0,2) - ISOdatetime(2008,1,1,12,0,0) Time difference of 2 secs ISOdatetime(2008,1,1,12,2,0) - ISOdatetime(2008,1,1,12,0,0) Time difference of 2 mins ISOdatetime(2008,1,1,14,0,0) - ISOdatetime(2008,1,1,12,0,0) Time difference of 2 hours -- 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] generating help files
Hi R People! Is there a quick way to generate help files for functions, please? I know that if you use package.skeleton, that will work. However, I'm not using that for a new package. (Hope this make sense) this is for SUSE10.1, please. thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] generating help files
Hi, try prompt(yourFunction) hope thus helps, baptiste On 21 May 2008, at 21:40, Erin Hodgess wrote: Hi R People! Is there a quick way to generate help files for functions, please? I know that if you use package.skeleton, that will work. However, I'm not using that for a new package. (Hope this make sense) this is for SUSE10.1, please. thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. _ Baptiste Auguié Physics Department University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag http://projects.ex.ac.uk/atto __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Converting qqplot2 qplot() to grammar?
Now that this part is working there are two more aspects of the plot I would like to remove: (in order of importance) * The row/column facetting labels. You should be able to find that using grid.ls() * the whitespace that surrounds the plot. I'd like the ggsave output to resemble the cropped.png file rather than the ggplot.png file (attached). That's not easy to do at the moment, because you need to modify properties of the viewports, which you can't currently do with grid. I'm working on a better customisation solution that should allow you to do this. (And to package everything up into a theme that can easily be applied to other plots) * the gaps between the subplots (or the ability to change the colour of the subplot border?, looks to be grey50.) As above. Hmm, I just get the generic R help for ggplot that says go to the website for complete documentation. That's weird - you might need to upgrade your R to get the latest version of ggplot2. 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] xlab at top in xyplot()
On 5/21/08, Michael Kubovy [EMAIL PROTECTED] wrote:
Dear R-helpers,
(1) How do I add a 'top' label symmetric with the 'bottom' label' in:
axis.td -
function(side, ...)
{
ylim - current.panel.limits()$ylim
switch(side,
bottom = {
panel.axis(side = side, outside = TRUE, rot = 0,
at = 1:3, labels = c(2.0, 3.5, 5.0))
},
top = {
panel.axis(side = side, outside = TRUE, rot = 45,
at = 1:3, labels = c(0.143, 0.250, 0.357))
},
axis.default(side = side, ...))
}
xyplot(1:3 ~ 1:3, type = 'b', axis = axis.td, xlab = 'bottom', ylab =
'left', aspect = 'xy')
No good way ('main' will be centered differently). I will consider
adding a new row for something like xlab.top (and a column for a
ylab.right).
(2) Is there a simpler way to create the two axes?
Simpler? Probably not. ?axis.default has this and another approach as
examples; in theory, the other method is better because it gives
lattice a chance to automatically allocate space for the labels, but
that doesn't happen yet in practice.
(3) A bit more complex:
df - data.frame(x = rep(1:3, 3), y = 1:9, z = factor(rep(1:3, each =
3)))
xyplot(y ~ x | z, df, axis = axis.td, xlab = 'bottom', ylab = 'left',
layout = c(3, 1), aspect = 'xy', type = 'b')
Here I would like to have a different pair of top and bottom axes for
each panel (i.e., different labels at 1:3), and a different top and
bottom label.
You could use current.column() and current.row() inside axis.td().
The different bottom labels are easy: xlab = c(one, two, three),
but labels on the top are not. Of course, you could add a label from
inside each axis.td call, and add some space for them manually.
-Deepayan
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[R] automation of R? running an R script at a certain time each night?
I am using R in a Windows environment. I store my data in a Microsoft SQL database that gets updated automatically nightly. Once my SQL db is updated, I wish to automatically run an R script Any tips on good ways to approach this task? Is there an easy way to launch an R script using the Windows or other scheduler? Can I have an R-script run every hour, and within the script check to determine if my database is updated, and proceed only if it is updated? [[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] automation of R? running an R script at a certain time each night?
You might try cron job under Windows. http://drupal.org/node/31506 HTH. - Edward On Thu, May 22, 2008 at 8:51 AM, Thomas Pujol [EMAIL PROTECTED] wrote: I am using R in a Windows environment. I store my data in a Microsoft SQL database that gets updated automatically nightly. Once my SQL db is updated, I wish to automatically run an R script Any tips on good ways to approach this task? Is there an easy way to launch an R script using the Windows or other scheduler? Can I have an R-script run every hour, and within the script check to determine if my database is updated, and proceed only if it is updated? [[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] Computing Maximum Loglikelihood With nlm Problem
Hi,
I tried to compute maximum likelihood under gamma distribution,
using nlm function. The code is this:
__BEGIN__
vsamples- c(103.9, 88.5, 242.9, 206.6, 175.7, 164.4)
mlogl - function(alpha, x) {
if (length(alpha) 1) stop(alpha must be scalar)
if (alpha = 0) stop(alpha must be positive)
return(- sum(dgamma(x, shape = alpha, log = TRUE)))
}
mlogl_out - nlm(mlogl, mean(vsamples),vsamples=vsamples)
print(mlogl_out)
__END__
However, it gives the following error:
Error in f(x, ...) :
unused argument(s) (vsamples = c(103.9, 88.5, 242.9, 206.6, 175.7, 164.4))
Calls: nlm - Anonymous - f
Execution halted
What's wrong in my way of calling 'nlm function?
Please advice.
- Edward
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Re: [R] Cumulative average
Thank you! Your interpretation was correct. I'll remember to be more specific next time. Thank you for being patient and understanding. Jacques On 5/21/08, jim holtman [EMAIL PROTECTED] wrote: Not sure exactly what you want since you did not provide any data or an example of the expected out' Here is my interpretation of what you were asking: x - sample(1:20) x [1] 6 16 8 1 17 11 2 19 18 5 15 13 3 20 9 14 7 10 12 4 cumsum(x) / seq_along(x) [1] 6.00 11.00 10.00 7.75 9.60 9.83 8.714286 10.00 10.89 10.30 [11] 10.727273 10.916667 10.307692 11.00 10.87 11.062500 10.823529 10.78 10.842105 10.50 On Wed, May 21, 2008 at 9:48 PM, Jacques Wagnor [EMAIL PROTECTED] wrote: Dear List, Does there exist a function that calculates a cumulative average? Neither running() from library(gregmisc) nor running.mean() from library(igraph) seems to be able to give a cumulative average. Any help or pointers would be greatly appreciated. Jacques __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cumulative average
Jacques, you should be able to construct a solution from cumsum(). Cheers Andrew On Wed, May 21, 2008 at 08:48:29PM -0500, Jacques Wagnor wrote: Dear List, Does there exist a function that calculates a cumulative average? Neither running() from library(gregmisc) nor running.mean() from library(igraph) seems to be able to give a cumulative average. Any help or pointers would be greatly appreciated. Jacques __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-6410 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Computing Maximum Loglikelihood With nlm Problem
Try:
mlogl_out - nlm(mlogl, mean(vsamples), vsamples)
or
mlogl_out - nlm(mlogl, mean(vsamples), x=vsamples)
The argument vsamples=vsamples is passed to mlogl, since nlm does not
recognize it. But mlogl doesn't have a vsamples argument, only alpha
and x arguments. So you have to either leave mean(vsamples) and
vsamples unnamed, or else name them alpha and x respectively, as you
told mlogl. Or change the argument names in mlogl.
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On May 21, 2008, at 10:05 PM, Edward Wijaya wrote:
Hi,
I tried to compute maximum likelihood under gamma distribution,
using nlm function. The code is this:
__BEGIN__
vsamples- c(103.9, 88.5, 242.9, 206.6, 175.7, 164.4)
mlogl - function(alpha, x) {
if (length(alpha) 1) stop(alpha must be scalar)
if (alpha = 0) stop(alpha must be positive)
return(- sum(dgamma(x, shape = alpha, log = TRUE)))
}
mlogl_out - nlm(mlogl, mean(vsamples),vsamples=vsamples)
print(mlogl_out)
__END__
However, it gives the following error:
Error in f(x, ...) :
unused argument(s) (vsamples = c(103.9, 88.5, 242.9, 206.6,
175.7, 164.4))
Calls: nlm - Anonymous - f
Execution halted
What's wrong in my way of calling 'nlm function?
Please advice.
- Edward
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Computing Maximum Loglikelihood With nlm Problem
Thanks so much.
- Edward
On Thu, May 22, 2008 at 11:17 AM, Charilaos Skiadas [EMAIL PROTECTED] wrote:
Try:
mlogl_out - nlm(mlogl, mean(vsamples), vsamples)
or
mlogl_out - nlm(mlogl, mean(vsamples), x=vsamples)
The argument vsamples=vsamples is passed to mlogl, since nlm does not
recognize it. But mlogl doesn't have a vsamples argument, only alpha and x
arguments. So you have to either leave mean(vsamples) and vsamples unnamed,
or else name them alpha and x respectively, as you told mlogl. Or change the
argument names in mlogl.
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On May 21, 2008, at 10:05 PM, Edward Wijaya wrote:
Hi,
I tried to compute maximum likelihood under gamma distribution,
using nlm function. The code is this:
__BEGIN__
vsamples- c(103.9, 88.5, 242.9, 206.6, 175.7, 164.4)
mlogl - function(alpha, x) {
if (length(alpha) 1) stop(alpha must be scalar)
if (alpha = 0) stop(alpha must be positive)
return(- sum(dgamma(x, shape = alpha, log = TRUE)))
}
mlogl_out - nlm(mlogl, mean(vsamples),vsamples=vsamples)
print(mlogl_out)
__END__
However, it gives the following error:
Error in f(x, ...) :
unused argument(s) (vsamples = c(103.9, 88.5, 242.9, 206.6, 175.7,
164.4))
Calls: nlm - Anonymous - f
Execution halted
What's wrong in my way of calling 'nlm function?
Please advice.
- Edward
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
