Re: [R] R help on write.csv
IS there a way we can append row wise, so that it all stacks up
horizontally, the way you do it in xlswrite in matlab, where you can even
specify the cell number from where you want to write.
-Ashish
From: R. Michael Weylandt [mailto:michael.weyla...@gmail.com]
Sent: Thursday, September 22, 2011 12:03 AM
To: Jan van der Laan
Cc: r-help@r-project.org; ashish.ku...@esteeadvisors.com
Subject: Re: [R] R help on write.csv
Oh darn, I had that line and then when I copied it to gmail I thought I'd be
all slick and clean up my code: oh well...just not my day/thread...
It's possible to work around the repeated headers business (change to
something like Call$col.names - !append) but yeah, at this point I'm
thinking its perhaps better practice to direct the OP to the various
connection methods: sink() is nice, but he'll probably have to do something
to convert his object to a CSV like string before printing:
apply(OBJ, 1, paste, sep=,)
Michael Weylandt
On Wed, Sep 21, 2011 at 11:20 AM, Jan van der Laan e...@dds.nl wrote:
Michael,
You example doesn't seem to work. Append isn't passed on to the write.table
call. You will need to add a
Call$append- append
to the function. And even then there will be a problem with the headers that
are repeated when appending.
An easier solution is to use write.table directly (I am using Dutch/European
csv format):
data - data.frame(a=1:10, b=1, c=letters[1:10])
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,
col.names=TRUE)
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,
col.names=FALSE,
append=TRUE)
When first openening a file connection and passing that to write.csv or
write.table data is also appended. The problem with write.csv is that
writing the column names can not be suppressed which will result in repeated
column names:
con - file(d:test2.csv, wt)
write.csv2(data, file=con, row.names=FALSE)
write.csv2(data, file=con, row.names=FALSE)
close(con)
So one will still have to use write.table to avoid this:
con - file(d:test2.csv, wt)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
col.names=TRUE)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
col.names=FALSE,
append=TRUE)
close(con)
Using a file connection is probably also more efficient when doing a large
number of appends.
Jan
Quoting R. Michael Weylandt michael.weyla...@gmail.com:
Touche -- perhaps we could make one though?
write.csv.append - function(..., append = TRUE)
{
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
(!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn) !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name(write.table)
eval.parent(Call)
}
write.csv.append(1:5,test.csv, append = FALSE)
write.csv.append(1:15, test.csv)
Output seems a little sloppy, but might work for the OP.
Michael Weylandt
On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra ivan.calan...@uni-hamburg.de
wrote:
I don't think there is an append argument to write.csv() (well, actually
there is one, but set to FALSE).
There is however one to write.table()
Ivan
Le 9/21/2011 14:54, R. Michael Weylandt michael.weyla...@gmail.com a
écrit :
The append argument of write.csv()?
Michael
On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
esteeadvisors.com ashish.ku...@esteeadvisors.com wrote:
Hi,
I wanted to write the data created using R on existing csv file. However
everytime I use write.csv, it overwrites the values already there in the
existing csv file. Any workaround on this.
Thanks for your help
Ashish Kumar
Estee Advisors Pvt. Ltd.
Email: ashish.ku...@esteeadvisors.com
Cell: +91-9654072144 tel:%2B91-9654072144
Direct: +91-124-4637-713 tel:%2B91-124-4637-713
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Ivan CALANDRA
PhD Student
University of Hamburg
Biozentrum Grindel und Zoologisches Museum
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Martin-Luther-King-Platz 3
D-20146 Hamburg, GERMANY
+49(0)40 42838 6231 tel:%2B49%280%2940%2042838%206231
ivan.calan...@uni-hamburg.de
Re: [R] R help on write.csv
Rowwise is easy. The example code I gave does this: it appends the new
data /below/ the old. I'll repeat the example below:
con - file(d:test2.csv, wt)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
col.names=TRUE)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
col.names=FALSE, append=TRUE)
close(con)
Or do you mean columnwise where you append columns? This would be very
difficult in CSV. If you would like to do this you might have a look at
the various options for exporting to Excel directly. See for example
http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windows . I have
no experience in this.
Regards,
Jan
PS I am sorry for my previous triple post. I had a little fight with my
webmail client.
On 09/22/2011 06:14 AM, Ashish Kumar wrote:
IS there a way we can append row wise, so that it all stacks up
horizontally, the way you do it in xlswrite in matlab, where you can
even specify the cell number from where you want to write.
-Ashish
*From:*R. Michael Weylandt [mailto:michael.weyla...@gmail.com]
*Sent:* Thursday, September 22, 2011 12:03 AM
*To:* Jan van der Laan
*Cc:* r-help@r-project.org; ashish.ku...@esteeadvisors.com
*Subject:* Re: [R] R help on write.csv
Oh darn, I had that line and then when I copied it to gmail I thought
I'd be all slick and clean up my code: oh well...just not my day/thread...
It's possible to work around the repeated headers business (change to
something like Call$col.names - !append) but yeah, at this point
I'm thinking its perhaps better practice to direct the OP to the
various connection methods: sink() is nice, but he'll probably have to
do something to convert his object to a CSV like string before printing:
apply(OBJ, 1, paste, sep=,)
Michael Weylandt
On Wed, Sep 21, 2011 at 11:20 AM, Jan van der Laan e...@dds.nl
mailto:e...@dds.nl wrote:
Michael,
You example doesn't seem to work. Append isn't passed on to the
write.table call. You will need to add a
Call$append- append
to the function. And even then there will be a problem with the
headers that are repeated when appending.
An easier solution is to use write.table directly (I am using
Dutch/European csv format):
data - data.frame(a=1:10, b=1, c=letters[1:10])
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,
col.names=TRUE)
write.table(data, file=test.csv, sep=;, dec=,, row.names=FALSE,
col.names=FALSE,
append=TRUE)
When first openening a file connection and passing that to write.csv
or write.table data is also appended. The problem with write.csv is
that writing the column names can not be suppressed which will result
in repeated column names:
con - file(d:test2.csv, wt)
write.csv2(data, file=con, row.names=FALSE)
write.csv2(data, file=con, row.names=FALSE)
close(con)
So one will still have to use write.table to avoid this:
con - file(d:test2.csv, wt)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
col.names=TRUE)
write.table(data, file=con, sep=;, dec=,, row.names=FALSE,
col.names=FALSE,
append=TRUE)
close(con)
Using a file connection is probably also more efficient when doing a
large number of appends.
Jan
Quoting R. Michael Weylandt michael.weyla...@gmail.com
mailto:michael.weyla...@gmail.com:
Touche -- perhaps we could make one though?
write.csv.append - function(..., append = TRUE)
{
Call - match.call(expand.dots = TRUE)
for (argname in c(col.names, sep, dec, qmethod)) if
(!is.null(Call[[argname]]))
warning(gettextf(attempt to set '%s' ignored, argname),
domain = NA)
rn - eval.parent(Call$row.names)
Call$col.names - if (is.logical(rn) !rn)
TRUE
else NA
Call$sep - ,
Call$dec - .
Call$qmethod - double
Call[[1L]] - as.name http://as.name(write.table)
eval.parent(Call)
}
write.csv.append(1:5,test.csv, append = FALSE)
write.csv.append(1:15, test.csv)
Output seems a little sloppy, but might work for the OP.
Michael Weylandt
On Wed, Sep 21, 2011 at 9:03 AM, Ivan Calandra
ivan.calan...@uni-hamburg.de mailto:ivan.calan...@uni-hamburg.de
wrote:
I don't think there is an append argument to write.csv()
(well, actually
there is one, but set to FALSE).
There is however one to write.table()
Ivan
Le 9/21/2011 14:54, R. Michael Weylandt
michael.weyla...@gmail.com mailto:michael.weyla...@gmail.com a
écrit :
The append argument of write.csv()?
Michael
On Sep 21, 2011, at 8:01 AM, Ashish Kumarashish.kumar@**
esteeadvisors.com http://esteeadvisors.com
ashish.ku...@esteeadvisors.com
mailto:ashish.ku...@esteeadvisors.com wrote:
Hi,
I wanted to write the data created using R on existing
csv file. However
everytime I use write.csv, it overwrites the values
Re: [R] Error: cannot allocate vector of size xxx
On 09/22/2011 04:00 AM, R. Michael Weylandt michael.weyla...@gmail.com wrote: Are you running a 32bit or 64bit version of R? Type sessionInfo() to see. Michael ...in addition, how large is your dataset? Please provide us with a self contained example which reproduces this problem. You could take a look at the biglm package. regards, Paul On Sep 21, 2011, at 10:41 PM, Mario Montecinos Carvajal mariomonteci...@gmail.com wrote: Hi I am a new user of the mail list. Mi problem occurs when I try to test a lineal model (lm), becouse appear the messaje Error: cannot allocate vector of size xxx The data frame whit I am working, Have dim(d) [1] 7017411 and the function i am test is: lm(length~as.factor(age)*as.factor(year)*as.factor(sex)*soi*k,data=d[d$age %in% minage:maxage,]) I tried with a diferent options for solve this problem, but any one give me results. I tried with: Change in Function: memory.limit(size=4000) Change the setting in Windows using BCDEdit /set Change in the memory availability for R, change the path of the program (suggested for other user) My computer have 4GB RAM, Have 20 GB of Virtual Memory, HDD 300 GB with 200 GB of free space and Windows 7 as OS and my R version is 2.11.1 I need solve this problem, any help or suggestion will be very well received. I've been thinking in change the OS, but this is may last option. Regards I read -- Mario Montecinos C. Biologo Marino Dr (c) en Ciencias Universidad Austral de Chile Los acentos han sido omitidos voluntariamente para evitar incompatibilidades Evite enviar cartas impresas, cuidemos el medio ambiente y evitemos el uso innecesario de papel. [[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. -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Limitations of audio processing in R
Or if people want to do it the R way: Use the tuneR package and its readWave function that supports reading parts of Wave files if the whole file is not relevant. You can specify it in many units, see its help page. tuneR has also the tools to cut, merge etc. Wave files and analyse it with basic tools. If you want to deal with the whole thing in R: In CD quality this is roughly 2GB: 3 hours x 60 minutes x 60 seconds x 44100 samples x 2 channels x 2 bytes and you need at least 6 GB to do sensible things with it. Best, Uwe Ligges On 22.09.2011 00:26, Ulisses Camargo wrote: Dear Ted, Thank you very much about your answer, it really helped. Now I am working on the function that will do all the job with sox help. All the best, Ulisses 2011/9/21 Ted Hardingted.hard...@wlandres.net Hi Ulisses! Yes, get more creative -- or get more memory! On the creative side, it may be worth thinking about using an independent (non-R) audio file editor. I'm writing from the standpoint of a Linux/Unixoid user here -- I wouldn;t know how to set ebout this in WIndows. You could use R to create a shell script which would run the editor in such a way as to extract your 6 random samples, and save them, where the script would be fed with the randomly-chosen 5-minute intervals decided by R. This could be done under the control of R, so you could set it up for your 1500 or so sets of samples, which (with the right editing program) could be done quite quickly. On Linux (also available for Windows) a flexible audio editor is 'sox' -- see: http://en.wikipedia.org/wiki/SoX To take, say, a 5-minute sample starting at 1 hour, 10 min and 35sec into the audio file infile.wav, and save this as outfile.wav, you can execute sox infile.wav outfile.wav trim 01:10:35 00:05:00 and such a command could easily be generated by R and fed to a shell script (or simply executed from R by using the system() command). My test just now with a 5-minute long sample from a .wav file was completed in about 5 seconds, so it is quite efficient. There is a huge number of options for 'sox', allowing you to manipulate almost any aspect of the editing. Hoping this helps, Ted. On 21-Sep-11 19:55:22, R. Michael Weylandt wrote: If you are running Windows it may be as simple as using memory.limit() to allow R more memory -- if you are on another OS, it may be possible to get the needed memory by deleting various things in your workspace and running gc() Of course, if your computer's memory is3GB, you are probably going to have trouble with R's keeping all objects in memory and will have to get more creative. Michael On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo moliterno.cama...@gmail.com wrote: Hello everybody I am trying to process audio files in R and had some problems with files size. I惴 using R packages 'audio' and 'sound'. I惴 trying a really simple thing and it is working well with small sized .wav files. When I try to open huge audio files I received this error message: cannot allocate vector of size 2.7 Gb. My job is open in R a 3-hour .wav file, make six 5-minute random audio subsamples, and than save these new files. I have to do the same process +1500 times. My problems is not in build the function to do the job, but in oppening the 3-hour files. Does anybody knows how to handle big audio files in R? Another package that allows me to do this work? I believe this is a really simple thing, but I really don愒 know what to do to solve that memory problem. Thank you very much for your answers, all the best! Ulisses E-Mail: (Ted Harding)ted.hard...@wlandres.net Fax-to-email: +44 (0)870 094 0861 Date: 21-Sep-11 Time: 22:05:55 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] comparing mixed binomial model against the same model without random effect
Hi everybody, If I am correct, you can compare a model with random effect with the same model without the random effect by using the nlme function, like this: no.random.model - gls(Richness ~ NAP * fExp, method = REML, data = RIKZ) random.model - lme(Richness ~NAP * fExp, data = RIKZ, random = ~1 | fBeach, method = REML) anova(no.random.model,random.model) But, nlme is valid only for the gaussian family, isn't it? In my case I have a mixed model with binomial family, like this: random.model - lme(sex ~hwp+hcp, data = mydata, random = ~1 | colony, method = REML) where sex is a binary variable, hwp and hcp are continuous variable and colony is a factor with two levels. I want to compare this model with another one without the random effect, I have tried with the lme4 but after this I cannot figure out how to build this same model without the random effect in order to make it comparable to the random effect model. Thanks for any help. Simone [[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] Quelplot
Hi Hadley, have a look at: http://www.riani.it/pub/zrc-csda98.pdf and some Gauss code: http://www.riani.it/Gauss/procedures/BOXPLOTB.G Best regards, Daniele 2011/9/21 Hadley Wickham had...@rice.edu: Hi all, Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307–320, 1992)? I'm struggling with the estimation of the asymmetry parameters. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Reading data in lisp format
Thanks David, The crx.data is a different database and I would like to use both. I have contacted with the developer but he has not answered me. Regards, Esteban De: David Winsemius [mailto:dwinsem...@comcast.net] Enviado el: mié 21/09/2011 17:08 Para: ESTEBAN ALFARO CORTES CC: r-help@r-project.org Asunto: Re: [R] Reading data in lisp format If you think that R is loosely typed, then examining LiSP code will change your mind, or at least give you a new data point further out on the Loose-Tight axis. I think you will need to do the processing by hand. The organization of the data is fairly clear. There are logical columns with values :neg and :pos, categorical columns with values in (id value) pairs, numeric ones and then a group of computed columns at the bottom. It also appears that after the first enumeration of ids with logical values that subsequent logical variables are defined possibly with pos: values only. So I guess the counter-question is: How important is this particular dataset to you?? And further question might be, are you sure that you don't want the dataset that is right next to it: ftp://ftp.ics.uci.edu/pub/machine-learning-databases/credit-screening/crx.data It is well-behaved comma-separated file. -- David. On Sep 21, 2011, at 6:39 AM, ESTEBAN ALFARO CORTES wrote: Hi, I am trying to read the credit.lisp file of the Japanese credit database in UCI repository, but it is in lisp format which I do not know how to read. I have not found how to do that in the foreign library http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening Could anyone help me? Best regards, Esteban Alfaro PS: This is my first time in r-help so I apologize for possible inconveniences. [[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. David Winsemius, MD West Hartford, CT [[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] R-help Digest, Vol 103, Issue 21
Szeptember 12-től 26-ig irodán kívül vagyok, és az emailjeimet nem érem el. Sürgős esetben kérem forduljon Kárpáti Edithez (karpati.e...@gyemszi.hu). Üdvözlettel, Mihalicza Péter I will be out of the office from 12 till 26 September with no access to my emails. In urgent cases please contact Ms. Edit Kárpáti (karpati.e...@gyemszi.hu). With regards, Peter Mihalicza __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Reading data in lisp format
Thanks Cesar, Any idea for this contents of the file? ;; positive examples represent people that were granted credit (def-pred credit_screening :type (:person) :pos ((s1) (s2) (s4) (s5) (s6) (s7) (s8) (s9) (s14) (s15) (s17) (s18) (s19) (s21) (s22) (s24) (s28) (s29) (s31) (s32) (s35) (s38) (s40) (s41) (s42) (s43) (s45) (s46) (s47) (s49) (s50) (s51) (s53) (s54) (s55) (s56) (s57) (s59) (s61) (s62) (s63) (s64) (s65) (s66) (s69) (s70) (s71) (s72) (s73) (s74) (s75) (s76) (s77) (s78) (s79) (s80) (s81) (s83) (s84) (s85) (s86) (s87) (s89) (s90) (s91) (s92) (s93) (s94) (s96) (s97) (s98) (s100) (s103) (s104) (s106) (s108) (s110) (s116) (s117) (s118) (s119) (s121) (s122) (s123) (s124)) :neg ((s3) (s10) (s11) (s12) (s13) (s16) (s20) (s23) (s25) (s26) (s27) (s30) (s33) (s34) (s36) (s37) (s39) (s44) (s48) (s52) (s58) (s60) (s67) (s68) (s82) (s88) (s95) (s99) (s101) (s102) (s105) (s107) (s109) (s111) (s112) (s113) (s114) (s115) (s120) (s125))) (def-pred jobless :type (:person) :pos ((s3) (s10) (s12) (s23) (s34) (s39) (s44) (s56) (s60) (s82) (s85) (s88) (s99) (s115))) ;; item purchased that loan is for. (def-pred purchase_item :type (:person :atom) :pos ((s1 pc) (s2 pc) (s3 pc) (s4 pc) (s5 pc) (s6 pc) (s7 pc) (s8 pc) (s9 pc) (s10 pc) (s11 car) (s12 car) (s13 car) (s14 car) (s15 car) (s16 car) (s17 car) (s18 car) (s19 car) (s20 car) (s21 stereo) (s22 stereo) (s23 stereo) (s24 stereo) (s25 stereo) (s26 stereo) (s27 stereo) (s28 stereo) (s29 stereo) (s30 stereo) (s31 stereo) (s32 stereo) (s33 stereo) (s34 stereo) (s35 stereo) (s36 stereo) (s37 stereo) (s38 stereo) (s39 stereo) (s40 stereo) (s41 stereo) (s42 jewel) (s43 jewel) (s44 jewel) (s45 jewel) (s46 jewel) (s47 jewel) (s48 jewel) (s49 jewel) (s50 jewel) (s51 jewel) (s52 jewel) (s53 jewel) (s54 jewel) (s55 jewel) (s56 jewel) (s57 jewel) (s58 jewel) (s59 jewel) (s60 jewel) (s61 jewel) (s62 jewel) (s63 medinstru) (s64 medinstru) (s65 medinstru) (s66 medinstru) (s67 medinstru) (s68 medinstru) (s69 medinstru) (s70 medinstru) (s71 medinstru) (s72 medinstru) (s73 medinstru) (s74 medinstru) (s75 medinstru) (s76 medinstru) (s77 medinstru) (s78 medinstru) (s79 medinstru) (s80 medinstru) (s81 medinstru) (s82 medinstru) (s83 medinstru) (s84 jewel) (s85 stereo) (s86 medinstru) (s87 stereo) (s88 stereo) (s89 stereo) (s90 stereo) (s91 stereo) (s92 medinstru) (s93 medinstru) (s94 medinstru) (s95 medinstru) (s96 jewel) (s97 jewel) (s98 jewel) (s99 jewel) (s100 jewel) (s101 jewel) (s102 jewel) (s103 jewel) (s104 jewel) (s105 jewel) (s106 bike) (s107 bike) (s108 bike) (s109 bike) (s110 bike) (s111 bike) (s112 bike) (s113 bike) (s114 bike) (s115 bike) (s116 furniture) (s117 furniture) (s118 furniture) (s119 furniture) (s120 furniture) (s121 furniture) (s122 furniture) (s123 furniture) (s124 furniture) (s125 furniture))) (def-pred male :type (:person) :pos ((s6) (s7) (s8) (s9) (s10) (s16) (s17) (s18) (s19) (s20) (s21) (s22) (s25) (s27) (s29) (s37) (s38) (s39) (s40) (s41) (s42) (s43) (s45) (s48) (s49) (s51) (s58) (s59) (s60) (s61) (s62) (s68) (s69) (s70) (s71) (s72) (s74) (s76) (s77) (s79) (s80) (s82) (s84) (s86) (s89) (s90) (s91) (s92) (s94) (s97) (s98) (s102) (s103) (s104) (s105) (s106) (s107) (s108) (s109) (s110) (s121) (s122) (s123) (s124) (s125))) (def-pred female :type (:person) :pos ((s1) (s2) (s3) (s4) (s5) (s11) (s12) (s13) (s14) (s15) (s23) (s24) (s26) (s28) (s30) (s31) (s32) (s33) (s34) (s35) (s36) (s44) (s46) (s47) (s50) (s52) (s53) (s54) (s55) (s56) (s57) (s63) (s64) (s65) (s66) (s67) (s73) (s75) (s78) (s81) (s83) (s85) (s87) (s88) (s93) (s95) (s96) (s99) (s100) (s101) (s111) (s112) (s113) (s114) (s115) (s116) (s117) (s118) (s119) (s120))) (def-pred unmarried :type (:person) :pos ((s1) (s2) (s5) (s6) (s7) (s11) (s13) (s14) (s16) (s18) (s22) (s25) (s26) (s28) (s30) (s31) (s32) (s33) (s34) (s37) (s41) (s43) (s46) (s48) (s50) (s52) (s53) (s54) (s55) (s59) (s60) (s63) (s68) (s70) (s74) (s75) (s76) (s78) (s82) (s84) (s86) (s87) (s90) (s93) (s95) (s96) (s97) (s100) (s101) (s102) (s104) (s105) (s106) (s107) (s108) (s109) (s114) (s118) (s123))) ;; people who live in a problematic region (def-pred problematic_region :type (:person) :pos ((s3) (s5) (s23) (s30) (s33) (s39) (s48) (s60) (s68) (s72) (s76) (s78) (s84) (s105))) (def-pred age :type (:person :number) :pos ((s1 18) (s2 20) (s3 25) (s4 40) (s5 50) (s6 18) (s7 22) (s8 28) (s9 40) (s10 50) (s11 18) (s12 20) (s13 25) (s14 38) (s15 50) (s16 19) (s17 21) (s18 25) (s19 38) (s20 50) (s21 42) (s22 28) (s23 55) (s24 21) (s25 81) (s26 23) (s27 35) (s28 47) (s29 98) (s30 68) (s31 27) (s32 19) (s33 23) (s34 25) (s35 31) (s36 34) (s37 20) (s38 32) (s39 38) (s40 45) (s41 57) (s42 25) (s43 42) (s44 61) (s45 48)
[R] Subsetting a zooreg object using window / subset
Dear R users, I am currently working in subsetting a zooreg() object using either window or subset. I have a solution but it may be a bit cumbersome when I start working with actual data. Your inputs would be greatly appreciated. Example: I have a zooreg() object that starts in 1997 and ends in 2001. This object contains daily data for the 4 years aa-zooreg(1:1825,start=as.Date(1997-01-01)) My aim is to subset the data according to seasons (Southern Hemisphere) for continuous years: December - January - February (DJF-Summer: 1997-2001), March - April - May (MAM-Autumn: 1997-2001), June - July - August (JJA-Winter: 1997-2001), September - October - November (SON-Spring: 1997-2001) thereby analysing the seasons data only for all years. The example below is only for DJF but I would like to replicate the analysis for each season. My solution so far uses subset to select the monthly data for each year and then rbind() the results. bb - subset(aa, index(aa)=as.Date(1998-12-01)index(aa)=as.Date(1999-02-28)) cc - subset(aa, index(aa)=as.Date(1999-12-01)index(aa)=as.Date(2000-02-28)) dd - subset(aa, index(aa)=as.Date(2000-12-01)index(aa)=as.Date(2001-02-28)) ee- rbind(bb,cc,dd) The method above appears to do the job just fine except that I have around 30 locations (catchments) each with varying data availability and some with over 20 years worth of data. Ideally I would like to combine the second set of commands into a single command where I specify the start and end year and the months that I am interested in. Any advice on this matter would be greatly appreciated. Many thanks and kind regards, Wesley Wesley Roberts PhD. Researcher: Earth Observation Natural Resources the Environment (NRE) CSIR Tel: +27 (0)21 888-2490 Fax: +27 (0)21 888-2693 skype: roberts-w -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Suggest workshops/short course in R programming
Hi Interested in learning R programming via workshop/short course in India. Request all to suggest any. [[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] Subsetting a zooreg object using window / subset
On Thu, Sep 22, 2011 at 6:48 AM, Wesley Roberts wrobe...@csir.co.za wrote: Dear R users, I am currently working in subsetting a zooreg() object using either window or subset. I have a solution but it may be a bit cumbersome when I start working with actual data. Your inputs would be greatly appreciated. Example: I have a zooreg() object that starts in 1997 and ends in 2001. This object contains daily data for the 4 years aa-zooreg(1:1825,start=as.Date(1997-01-01)) My aim is to subset the data according to seasons (Southern Hemisphere) for continuous years: December - January - February (DJF-Summer: 1997-2001), March - April - May (MAM-Autumn: 1997-2001), June - July - August (JJA-Winter: 1997-2001), September - October - November (SON-Spring: 1997-2001) thereby analysing the seasons data only for all years. The example below is only for DJF but I would like to replicate the analysis for each season. My solution so far uses subset to select the monthly data for each year and then rbind() the results. bb - subset(aa, index(aa)=as.Date(1998-12-01)index(aa)=as.Date(1999-02-28)) cc - subset(aa, index(aa)=as.Date(1999-12-01)index(aa)=as.Date(2000-02-28)) dd - subset(aa, index(aa)=as.Date(2000-12-01)index(aa)=as.Date(2001-02-28)) ee- rbind(bb,cc,dd) The method above appears to do the job just fine except that I have around 30 locations (catchments) each with varying data availability and some with over 20 years worth of data. Ideally I would like to combine the second set of commands into a single command where I specify the start and end year and the months that I am interested in. This gives the season (1 = djf, 2 = mam, 3 = jja, 5 = son): seas - as.numeric(format(as.yearqtr(as.yearmon(time(aa)) + 1/12), %q)) and this picks out djf: aa[seas == 1] -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading data in lisp format
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 22/09/11 10:13, ESTEBAN ALFARO CORTES wrote: Thanks David, The crx.data is a different database and I would like to use both. I have contacted with the developer but he has not answered me. I would suggest talk to folks using emacs, as emacs is written in lisp (well - elsisp)and particularly, especially the guys from org-mode (http://orgmode.org/), because they deal with all kinds of languages (including R) http://orgmode.org/worg/org-contrib/babel/. Very helpfull mailing list (http://orgmode.org/index.html#sec-5-2). I am quite sure, that somebody there should be able to help. Rainer Regards, Esteban De: David Winsemius [mailto:dwinsem...@comcast.net] Enviado el: mié 21/09/2011 17:08 Para: ESTEBAN ALFARO CORTES CC: r-help@r-project.org Asunto: Re: [R] Reading data in lisp format If you think that R is loosely typed, then examining LiSP code will change your mind, or at least give you a new data point further out on the Loose-Tight axis. I think you will need to do the processing by hand. The organization of the data is fairly clear. There are logical columns with values :neg and :pos, categorical columns with values in (id value) pairs, numeric ones and then a group of computed columns at the bottom. It also appears that after the first enumeration of ids with logical values that subsequent logical variables are defined possibly with pos: values only. So I guess the counter-question is: How important is this particular dataset to you?? And further question might be, are you sure that you don't want the dataset that is right next to it: ftp://ftp.ics.uci.edu/pub/machine-learning-databases/credit-screening/crx.data It is well-behaved comma-separated file. -- David. On Sep 21, 2011, at 6:39 AM, ESTEBAN ALFARO CORTES wrote: Hi, I am trying to read the credit.lisp file of the Japanese credit database in UCI repository, but it is in lisp format which I do not know how to read. I have not found how to do that in the foreign library http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening http://archive.ics.uci.edu/ml/datasets/Japanese+Credit+Screening Could anyone help me? Best regards, Esteban Alfaro PS: This is my first time in r-help so I apologize for possible inconveniences. [[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. David Winsemius, MD West Hartford, CT [[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. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk57JDwACgkQoYgNqgF2egrnOwCfaHw0ayhVoNlqkDfbwx8lXFVW AAcAnAwSyzlEK7eQJBnK0jMogIbLk64U =b961 -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subsetting a zooreg object using window / subset
On Thu, 22 Sep 2011, Gabor Grothendieck wrote: On Thu, Sep 22, 2011 at 6:48 AM, Wesley Roberts wrobe...@csir.co.za wrote: Dear R users, I am currently working in subsetting a zooreg() object using either window or subset. I have a solution but it may be a bit cumbersome when I start working with actual data. Your inputs would be greatly appreciated. Example: I have a zooreg() object that starts in 1997 and ends in 2001. This object contains daily data for the 4 years aa-zooreg(1:1825,start=as.Date(1997-01-01)) My aim is to subset the data according to seasons (Southern Hemisphere) for continuous years: December - January - February (DJF-Summer: 1997-2001), March - April - May (MAM-Autumn: 1997-2001), June - July - August (JJA-Winter: 1997-2001), September - October - November (SON-Spring: 1997-2001) thereby analysing the seasons data only for all years. The example below is only for DJF but I would like to replicate the analysis for each season. My solution so far uses subset to select the monthly data for each year and then rbind() the results. bb - subset(aa, index(aa)=as.Date(1998-12-01)index(aa)=as.Date(1999-02-28)) cc - subset(aa, index(aa)=as.Date(1999-12-01)index(aa)=as.Date(2000-02-28)) dd - subset(aa, index(aa)=as.Date(2000-12-01)index(aa)=as.Date(2001-02-28)) ee- rbind(bb,cc,dd) The method above appears to do the job just fine except that I have around 30 locations (catchments) each with varying data availability and some with over 20 years worth of data. Ideally I would like to combine the second set of commands into a single command where I specify the start and end year and the months that I am interested in. This gives the season (1 = djf, 2 = mam, 3 = jja, 5 = son): seas - as.numeric(format(as.yearqtr(as.yearmon(time(aa)) + 1/12), %q)) An alternative route might be to go via the mon component of POSIXlt, e.g., as.POSIXlt(time(aa))$mon %in% c(11, 0, 1) instead of seas == 1 etc. and this picks out djf: aa[seas == 1] -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Error in as.vector(data) optim() / fkf()
Dear R users,
When running the program below I receive the following error message:
fit - optim(parm, objective, yt = tyield, hessian = TRUE)
Error in as.vector(data) :
no method for coercing this S4 class to a vector
I can't figure out what the problem is exactly. I imagine that it has
something to do with tyield being a matrix. Any help on explaining what's
going on and how to solve this is much appreciated.
Thank you,
Kristian
library(FKF) #loading Fast Kalman Filter package
library(Matrix) # matrix exponential package
K_1 = 0.1156
K_2 = 0.17
sigma_1 = 0.1896
sigma_2 = 0.2156
lambda_1 = 0
lambda_2 = -0.5316
theta_1 = 0.1513
theta_2 = 0.2055
#test data
tyield - matrix(data = rnorm(200), nrow =2, ncol =100)
# defining dimensions
m - 2 # m is the number of state variables
n - 100 # is the length of the observed sample
d - 2 # is the number of observed variables.
theta - c(theta_1, theta_2)
h - t - 1/52 # time between observations
## creating state space representation of 2-factor CIR model follwing
Driessen and Geyer et al.
CIR2ss - function(K_1, K_2, sigma_1, sigma_2, lambda_1, lambda_2, theta_1,
theta_2){
## defining auxilary parameters
phi_11 - sqrt((K_1+lambda_1)^2+2*sigma_1^2)
phi_21 - sqrt((K_1+lambda_2)^2+2*sigma_2^2)
phi_12 - K_1+lambda_1+phi_11
phi_22 - K_2+lambda_2+phi_12
phi_13 - -2*K_1*theta_1/sigma_1^2
phi_23 - -2*K_2*theta_2/sigma_2^2
phi_14 - 2*phi_11+phi_21*(exp(phi_11*t)-1)
phi_24 - 2*phi_12+phi_22*(exp(phi_12*t)-1)
phi - array(c(phi_11, phi_21, phi_12, phi_22, phi_13, phi_23, phi_14,
phi_24), c(4,2))
a - array(0, c(d,n))
for(t in n:1){
a[,n-(t+1)] -
-phi_13/(n-(t+1))*log(2*phi_11*exp(phi_12*(n-(t+1))/2)/phi_14)-phi_23/(n-(t+1))*log(2*phi_21*exp(phi_22*(n-(t+1))/2)/phi_24)
}
b - array(c(1,0,0,1,0), c(d,m,n))
j - -array(c(K_1, 0, 0, K_2), c(2,2))*h
explh - expm(j)
Tt - array(explh, c(m,m,n)) #array giving the factor of the transition
equation
Zt - b #array giving the factor of the measurement equation
ct - a #matrix giving the intercept of the measurement equation
dt - (diag(m)-expm(-array(c(K_1, 0, 0, K_2), c(2,2))*h))*theta #matrix
giving the intercept of the transition equation
GGt - array(c(1,0,0,1), c(d,d,n)) #array giving the variance of the
disturbances of the measurement equation
HHt - array(c(1,0,0,1), c(m,m,n)) #array giving the variance of the
innovations of the transition equation
a0 - c(0, 0) #vector giving the initial value/estimation of the state
variable
P0 - matrix(1e6, nrow = 2, ncol = 2) # matrix giving the variance of a0
return(list(a0 = a0, P0 = P0, ct = ct, dt = dt, Zt = Zt, Tt = Tt, GGt =
GGt,
HHt = HHt))
}
## Objective function passed to optim
objective - function(parm, yt) {
sp - CIR2ss(parm[K_1], parm[K_2], parm[sigma_1], parm[sigma_2],
parm[lambda_1], parm[lambda_2],
parm[theta_1], parm[theta_2])
ans - fkf(a0 = sp$a0, P0 = sp$P0, dt = sp$dt, ct = sp$ct, Tt = sp$Tt,
Zt = sp$Zt, HHt = sp$HHt, GGt = sp$GGt, yt = yt)
return(-ans$loglik)
}
parm - c(K_1 = 0.1156, K_2 = 0.17, sigma_1 = 0.1896, sigma_2 = 0.2156,
lambda_1 = 0, lambda_2 = -0.5316, theta_1 = 0.1513, theta_2 =
0.2055) # initial parameters
##optimizing objective function
fit - optim(parm, objective, yt = tyield, hessian = TRUE)
print(fit)
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Re: [R] help in interpreting paired t-test
Late, I know, but if method comparison id the interest, the methcomp package on
CRAN does Bland-Altman plots and passing-Bablock regression, both clinical
chemistry staples for method comparison.
S Ellison
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Pedro Mardones
Sent: 21 September 2011 19:12
To: Marc Schwartz
Cc: R-help@r-project.org
Subject: Re: [R] help in interpreting paired t-test
Thanks for all the replies and comments. I've followed Marc's
suggestion of using the Bland-Altman's approach which I found
pretty clarifying for comparing data collected on the same subjects.
BR,
PM
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This email and any attachments are confidential. Any use...{{dropped:8}}
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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] help in interpreting paired t-test
On Sep 21, 2011, at 18:39 , Marc Schwartz wrote: Jeremy, Correlation alone is irrelevant when comparing two separate sets of measurements on the same specimen. Correlation does not mean good agreement, but good agreement tends to infer high correlation. Marc, I think Jeremy is well aware of that. He just said that the power to detect a (small) difference is higher when the correlation is higher. (Since V(X-Y) = 2*(1-rho)*sigma^2 if X and Y have the same variance sigma^2) -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re-installing R
Dear R users How does one completely uninstall R from their machine? Going to control panelprograms does not do it for me. After installing the new version it will still remember my previous workspace and all packages I've installed. Thank you. [[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] Header auslesen und bei Regression verwenden
Hi. First, a little preliminary observation: in this thread, it is indeed a (multiple linear) regression model, the real problem is but my opinion on general questions about R assign. So as I said, I want to do a regression analysis, however, for several target variables or data tables. This case, although the target variable is always the same, but the data comes from different sectors, ie, I have several data tables as covariates for different sectors, which can in size, better said the number of columns or different covariates. All of these tables but have a partially similar structure: in the first column gives the metric target variable, (n is fixed) in the next n are the metrical covariates and last m (m is variable) the categorical covariates can be found. The data is read from the csv-table in a matrix MX as follows: /MX - read.csv2(C://…/….csv, header=TRUE)/ The general R-code for stepwise linear regression is as follows: /step(regr - lm(Zielvariable~ Covariate_1 + Covariate_2 +… + Covariate_n +factor(Covariate_n+1) +factor(Covariate_n+2) +… +factor(Covariate_n+m) , data=MX))/ Here are the covariates, the column names and factor points to a categorical covariate. I would like to make my program so that it would be universally used for the analysis with each of these tables. To make it work, so my idea must first be read the column headings. R may provide for a more elegant, solution unknown to me, but I have it solved as follows: /heads - dimnames(MX)[[2]]/ Now, the individual head - values to get correct position as follows: /step(regr - lm(heads[1]~ heads[2] + heads[3] +… + heads[n] +factor(heads[n+1]) +factor(heads[n+2]) +… +factor(heads[n+m]) , data=Matrix))/ , where n is a fixed number, and m = length (head)-n-1. I can well imagine how I could implement in MATLAB, but in R I'm no professional and I hope for your help. Is there a way in the lm function a for loop to integrate, or possibly to create an appropriate string and then to take over the function? Or you may consider yourself, other alternative solutions? In any case, I am happy about every suggestion and thank you in advance. -- View this message in context: http://r.789695.n4.nabble.com/Header-auslesen-und-bei-Regression-verwenden-tp3833364p3833364.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] need help on melt/cast
Hello, I need to convert dataframe from: ID T0 T1 T2 A1 2 3 B4 5 6 C7 8 9 to: ID Variable Value A T0 1 A T1 2 A T2 3 B T0 4 B T1 5 B T2 6 C T0 7 C T1 8 C T2 9 i tried to use melt cast but it gives me all the time not exactly what I need. Thank you. [[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] Subsetting a zooreg object using window / subset
Many thanks Gabor, That is exactly what I needed. Regards, W. Gabor Grothendieck ggrothendi...@gmail.com 22/09/2011 13:52 On Thu, Sep 22, 2011 at 6:48 AM, Wesley Roberts wrobe...@csir.co.za wrote: Dear R users, I am currently working in subsetting a zooreg() object using either window or subset. I have a solution but it may be a bit cumbersome when I start working with actual data. Your inputs would be greatly appreciated. Example: I have a zooreg() object that starts in 1997 and ends in 2001. This object contains daily data for the 4 years aa-zooreg(1:1825,start=as.Date(1997-01-01)) My aim is to subset the data according to seasons (Southern Hemisphere) for continuous years: December - January - February (DJF-Summer: 1997-2001), March - April - May (MAM-Autumn: 1997-2001), June - July - August (JJA-Winter: 1997-2001), September - October - November (SON-Spring: 1997-2001) thereby analysing the seasons data only for all years. The example below is only for DJF but I would like to replicate the analysis for each season. My solution so far uses subset to select the monthly data for each year and then rbind() the results. bb - subset(aa, index(aa)=as.Date(1998-12-01)index(aa)=as.Date(1999-02-28)) cc - subset(aa, index(aa)=as.Date(1999-12-01)index(aa)=as.Date(2000-02-28)) dd - subset(aa, index(aa)=as.Date(2000-12-01)index(aa)=as.Date(2001-02-28)) ee- rbind(bb,cc,dd) The method above appears to do the job just fine except that I have around 30 locations (catchments) each with varying data availability and some with over 20 years worth of data. Ideally I would like to combine the second set of commands into a single command where I specify the start and end year and the months that I am interested in. This gives the season (1 = djf, 2 = mam, 3 = jja, 5 = son): seas - as.numeric(format(as.yearqtr(as.yearmon(time(aa)) + 1/12), %q)) and this picks out djf: aa[seas == 1] -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] negative binomial GAMM with variance structures
Hello, I am having some difficulty converting my gam code to a correct gamm code, and I'm really hoping someone will be able to help me. I was previously using this script for my overdispersed gam data: M30 -gam(efuscus~s(mic, k=7) +temp +s(date)+s(For3k, k=7) + pressure+ humidity, family=negbin(c(1,10)), data=efuscus) My gam.check gave me the attached result. In order to deal with my heterogeneity, I need to switch over to a gamm structure and use at least one, but possibly multiple, variance structures, and I am starting by applying varPower to my temperature covariate. (Efuscus is my square root transformed response variable). Here is the code I have for the gamm: K1 -(efuscus~s(mic, k=7) +temp +s(date)+s(For3k, k=7) + pressure+ humidity+ windspeed + year) M17.4A -gamm(K1, method=REML, family=negbin(c(1,10), data=efuscus, weights=varPower(form=~temp)) With my various versions of the script, the two error messages I have been getting repeatedly are: Error in eval(expr, envir, enclos) : object 'temp' not found, and Error: unexpected symbol in: M17.4A -gamm(K1, method=REML, family=negbin(c(1,10), data=efuscus, weights=varPower(form=~temp)) I know I must be missing something obvious that is causing my script not to work...I've been looking at both Wood (2006) and Zuur's Mixed Models book for examples but none of them are completely the same as my situation, which is causing me to get tripped up. Am I defining my negative binomial family correctly for the situation? Do I need to somehow define the variance term before I apply it? Thank you very much. I appreciate your time and patience. Meredith __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Re-installing R
You need to uninstall packages directly (they are kept independently of R, which is actually quite helpful when updating so you don't have to get them all anew): this can be done within R by combining remove.packages() and installed.packages(). To delete the workspace you need to manually remove the .Rdata folder in your start-up working directory. Hope this helps Michael On Thu, Sep 22, 2011 at 8:47 AM, Andrey A ava...@gmail.com wrote: Dear R users How does one completely uninstall R from their machine? Going to control panelprograms does not do it for me. After installing the new version it will still remember my previous workspace and all packages I've installed. Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re-installing R
On 22.09.2011 14:47, Andrey A wrote: Dear R users How does one completely uninstall R from their machine? Going to control panelprograms does not do it for me. After installing the new version it will still remember my previous workspace and all packages I've installed. This seems to be Windows? remove.packages() removes packages. You found the way to uninstall the part that got installed, The uninstaller won't install stuff you installed independently (such as packages, additional config files). The workspace is just a file called .RData in your working directory. Since it is user data, the user has to delete it himself. If you uninstall MS Word, it also won't remove all your .doc / .docx files - at least I hope so. Uwe Ligges Thank you. [[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] need help on melt/cast
?reshape From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Eugene Kanshin [kanshin...@gmail.com] Sent: Thursday, September 22, 2011 9:54 AM To: r-help@r-project.org Subject: [R] need help on melt/cast Hello, I need to convert dataframe from: ID T0 T1 T2 A1 2 3 B4 5 6 C7 8 9 to: ID Variable Value A T0 1 A T1 2 A T2 3 B T0 4 B T1 5 B T2 6 C T0 7 C T1 8 C T2 9 i tried to use melt cast but it gives me all the time not exactly what I need. Thank you. [[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] need help on melt/cast
You can use function reshape(), e.g., DF - data.frame(ID = LETTERS[1:3], T0 = c(1,4,7), T1 = c(2,5,8), T2 = c(3,6,9)) DF.new - reshape(DF, idvar = ID, direction = long, varying = list(2:4), times = names(DF[-1])) DF.new DF.new[order(DF.new$ID), ] I hope it helps. Best, Dimitris On 9/22/2011 3:54 PM, Eugene Kanshin wrote: Hello, I need to convert dataframe from: ID T0 T1 T2 A1 2 3 B4 5 6 C7 8 9 to: ID Variable Value A T0 1 A T1 2 A T2 3 B T0 4 B T1 5 B T2 6 C T0 7 C T1 8 C T2 9 i tried to use melt cast but it gives me all the time not exactly what I need. Thank you. [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/biostatistiek/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Header auslesen und bei Regression verwenden
If you explicitly convert your categorical covariates to factors before you regress, you can use the dot notation (see help on lm) to refer to the rest of the columns not otherwise specified in your formula. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. BiGBeN76 johann.ma...@gmx.de wrote: Hi. First, a little preliminary observation: in this thread, it is indeed a (multiple linear) regression model, the real problem is but my opinion on general questions about R assign. So as I said, I want to do a regression analysis, however, for several target variables or data tables. This case, although the target variable is always the same, but the data comes from different sectors, ie, I have several data tables as covariates for different sectors, which can in size, better said the number of columns or different covariates. All of these tables but have a partially similar structure: in the first column gives the metric target variable, (n is fixed) in the next n are the metrical covariates and last m (m is variable) the categorical covariates can be found. The data is read from the csv-table in a matrix MX as follows: /MX - read.csv2(C://â¦/â¦.csv, header=TRUE)/ The general R-code for stepwise linear regression is as follows: /step(regr - lm(Zielvariable~ Covariate_1 + Covariate_2 +⦠+ Covariate_n +factor(Covariate_n+1) +factor(Covariate_n+2) +⦠+factor(Covariate_n+m) , data=MX))/ Here are the covariates, the column names and factor points to a categorical covariate. I would like to make my program so that it would be universally used for the analysis with each of these tables. To make it work, so my idea must first be read the column headings. R may provide for a more elegant, solution unknown to me, but I have it solved as follows: /heads - dimnames(MX)[[2]]/ Now, the individual head - values ââto get correct position as follows: /step(regr - lm(heads[1]~ heads[2] + heads[3] +⦠+ heads[n] +factor(heads[n+1]) +factor(heads[n+2]) +⦠+factor(heads[n+m]) , data=Matrix))/ , where n is a fixed number, and m = length (head)-n-1. I can well imagine how I could implement in MATLAB, but in R I'm no professional and I hope for your help. Is there a way in the lm function a for loop to integrate, or possibly to create an appropriate string and then to take over the function? Or you may consider yourself, other alternative solutions? In any case, I am happy about every suggestion and thank you in advance. -- View this message in context: http://r.789695.n4.nabble.com/Header-auslesen-und-bei-Regression-verwenden-tp3833364p3833364.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. [[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] need help on melt/cast
I can never remember what melt, cast and all that means, hence I simpy use reshape() which does not even require any additional package: reshape(dat, direction=long, idvar = ID, varying=list(2:4), v.names=Value, times=names(dat)[2:4]) Uwe Ligges On 22.09.2011 15:54, Eugene Kanshin wrote: Hello, I need to convert dataframe from: ID T0 T1 T2 A1 2 3 B4 5 6 C7 8 9 to: ID Variable Value A T0 1 A T1 2 A T2 3 B T0 4 B T1 5 B T2 6 C T0 7 C T1 8 C T2 9 i tried to use melt cast but it gives me all the time not exactly what I need. Thank you. [[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] the opposite of lag() in panel data
Hi R-helpers I want a function that performs the opposite of lag() with panel data. I have transformed my data before with pdata.frame(mydata, index=c(groupindex, timeindex)) And then Ive done lag(mydata, -1) but it doesnt work. The error message was: Error in rep(1, ak) : invalid 'times' argument Thank you in advance, Cecília Carmo [[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] the opposite of lag() in panel data
Is there perhaps a particular package you are interested in here? I'm not aware of a pdata.frame function... This certainly works with the xts class. If you just mean a regular data.frame() perhaps some of the ideas in this old thread will work with a little tweaking: http://www.mail-archive.com/r-help@r-project.org/msg142805.html Michael Weylandt On Thu, Sep 22, 2011 at 10:36 AM, Cecilia Carmo cecilia.ca...@ua.pt wrote: Hi R-helpers I want a function that performs the opposite of lag() with panel data. I have transformed my data before with pdata.frame(mydata, index=c(groupindex, timeindex)) And then Ive done lag(mydata, -1) but it doesnt work. The error message was: Error in rep(1, ak) : invalid 'times' argument Thank you in advance, Cecília Carmo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] negative binomial GAMM with variance structures
gamm can't estimate the theta parameter for a negative binomial automatically. It can only work with fixed user supplied values for theta (i.e. negbin(2.3) should work, but negbin(c(1,10)) won't). Is negative binomial the only thing you can use here (it doesn't seem like the most natural choice for a variable that's been sqrt transformed)? Simon ps. Your checking plot didn't come through --- you can send it offline, if you want. On 09/22/2011 02:59 PM, Meredith Jantzen wrote: Hello, I am having some difficulty converting my gam code to a correct gamm code, and I'm really hoping someone will be able to help me. I was previously using this script for my overdispersed gam data: M30-gam(efuscus~s(mic, k=7) +temp +s(date)+s(For3k, k=7) + pressure+ humidity, family=negbin(c(1,10)), data=efuscus) My gam.check gave me the attached result. In order to deal with my heterogeneity, I need to switch over to a gamm structure and use at least one, but possibly multiple, variance structures, and I am starting by applying varPower to my temperature covariate. (Efuscus is my square root transformed response variable). Here is the code I have for the gamm: K1-(efuscus~s(mic, k=7) +temp +s(date)+s(For3k, k=7) + pressure+ humidity+ windspeed + year) M17.4A-gamm(K1, method=REML, family=negbin(c(1,10), data=efuscus, weights=varPower(form=~temp)) With my various versions of the script, the two error messages I have been getting repeatedly are: Error in eval(expr, envir, enclos) : object 'temp' not found, and Error: unexpected symbol in: M17.4A-gamm(K1, method=REML, family=negbin(c(1,10), data=efuscus, weights=varPower(form=~temp)) I know I must be missing something obvious that is causing my script not to work...I've been looking at both Wood (2006) and Zuur's Mixed Models book for examples but none of them are completely the same as my situation, which is causing me to get tripped up. Am I defining my negative binomial family correctly for the situation? Do I need to somehow define the variance term before I apply it? Thank you very much. I appreciate your time and patience. Meredith __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] NLS- check convergence
Hi there, I am having some trouble with NLS convergence for my function. I was wondering if there is a way to check the value of the indicator function for all the iterations to look at the surface of the likelihood function. Any help would be most appreciated. Thanks, Diviya [[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] the opposite of lag() in panel data
Yes, I want to it with plm package for panel data in dataframes. Thank you, Cecília Carmo De: R. Michael Weylandt [mailto:michael.weyla...@gmail.com] Enviada: quinta-feira, 22 de Setembro de 2011 16:06 Para: Cecilia Carmo Cc: r-help@r-project.org Assunto: Re: [R] the opposite of lag() in panel data Is there perhaps a particular package you are interested in here? I'm not aware of a pdata.frame function... This certainly works with the xts class. If you just mean a regular data.frame() perhaps some of the ideas in this old thread will work with a little tweaking: http://www.mail-archive.com/r-help@r-project.org/msg142805.html Michael Weylandt On Thu, Sep 22, 2011 at 10:36 AM, Cecilia Carmo cecilia.ca...@ua.pt wrote: Hi R-helpers I want a function that performs the opposite of lag() with panel data. I have transformed my data before with pdata.frame(mydata, index=c(groupindex, timeindex)) And then Ive done lag(mydata, -1) but it doesnt work. The error message was: Error in rep(1, ak) : invalid 'times' argument Thank you in advance, Cecília Carmo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nlm's Hessian update method
BFGS is actually Fletcher's (1970) variable metric code that I modified with him in January 1976 in Dundee and then modified very, very slightly (to insist that termination only occurred on a steepest descent search -- this messes up the approximated inverse Hessian, but I have an experimental Rvmminx in the optimization and solver project on R-forge for those interested). I haven't looked at the internals of nlm to judge the precise update used. However, the code is there in R-2.13.1 under src/appl/uncmin.c, where at first glance a simple finite difference approximation to the Hessian seems to be used. (numDeriv would likely do better, even without the analytic gradient, because it uses an extrapolation process to improve the approximation.) Given that you do not have a huge problem, it is likely safer to use numDeriv to compute the Hessian when you need it, preferably using the Jacobian function on the (analytic) gradient if the latter is available. That is what we do in optimx. Currently I am doing a back to basics refactoring of optimx. The updated version is working, but I expect it will be a few more weeks before I have a sufficiently comprehensive set of tests in place and run. However, if someone is eager, I can provide access to the code earlier. Contact me off-list. The existing version on CRAN works reasonably well, but the code was getting too heavily patched. John Nash Date: Thu, 22 Sep 2011 12:15:41 +1000 From: Amy Willis amy.wil...@anu.edu.au To: r-help@r-project.org Subject: [R] nlm's Hessian update method Message-ID: 343e6871-4564-4d9d-90f0-f2c9b30ea...@anu.edu.au Content-Type: text/plain; charset=us-ascii Hi R-help! I'm trying to understand how R's nlm function updates its estimate of the Hessian matrix. The Dennis/Schnabel book cited in the references presents a number of different ways to do this, and seems to conclude that the positive-definite secant method (BFGS) works best in practice (p201). However, when I run my code through the optim function with the method as BFGS, slightly different estimates are produced to that of nlm: optim(strt,jointll2,method=BFGS,hessian=T)$par -0.4016808 0.6057144 0.3744790-7.1819734 3.0230386 0.4446641 nlm(jointll2,strt,hessian=T)$estimate [1] -0.4016825 0.6057159 0.3744765 -7.1819737 3.0230386 0.4446623 Can anyone tell me if nlm employs the BFGS method for updating its estimates? Or does it use another algorithm? Thank you! -- On 09/22/2011 06:00 AM, r-help-requ...@r-project.org wrote: Date: Thu, 22 Sep 2011 12:15:41 +1000 From: Amy Willis amy.wil...@anu.edu.au To: r-help@r-project.org Subject: [R] nlm's Hessian update method Message-ID: 343e6871-4564-4d9d-90f0-f2c9b30ea...@anu.edu.au Content-Type: text/plain; charset=us-ascii Hi R-help! I'm trying to understand how R's nlm function updates its estimate of the Hessian matrix. The Dennis/Schnabel book cited in the references presents a number of different ways to do this, and seems to conclude that the positive-definite secant method (BFGS) works best in practice (p201). However, when I run my code through the optim function with the method as BFGS, slightly different estimates are produced to that of nlm: optim(strt,jointll2,method=BFGS,hessian=T)$par -0.4016808 0.6057144 0.3744790-7.1819734 3.0230386 0.4446641 nlm(jointll2,strt,hessian=T)$estimate [1] -0.4016825 0.6057159 0.3744765 -7.1819737 3.0230386 0.4446623 Can anyone tell me if nlm employs the BFGS method for updating its estimates? Or does it use another algorithm? Thank you! -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems with as.POSIXct
Hi R users: This is a very strange problem: Why this instruction shows me NA?, and any other date shows me that error! as.POSIXct(strptime(1992-5-3,format=%Y-%m-%d)) This is my R version on windows 7. R version 2.13.1 Patched (2011-08-25 r56794) Thank you for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R.oo: do work on data member at construction
Hello,
I'd like to 'do work' on data members upon construction (i.e. without
implementing it in a get method). Is this the best way to create data member
'z' upon construction? I'm thinking if .z=paste(x,y) below gets more complex
I'll run into issues.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=paste(x,y)
)
})
setMethodS3(getX, MyClass, function(this, ...) {
this$.x;
})
setMethodS3(getY, MyClass, function(this, ...) {
this$.y;
})
setMethodS3(getZ, MyClass, function(this, ...) {
this$.z;
})
mc = MyClass('a','b')
mc$x
[1] a
mc$y
[1] b
mc$z
[1] a b
Thanks,
ben
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[R] corrigendum on fixed effects and R2 in within models
Dear list, dear Cecilia and Daniel,
sorry for coming in ten days late, I've been very busy lately so I came
across this email only today.
This is just to make some points clearer re: fixed effects and r2 in
package 'plm', to both you and the list. In particular, to make you
aware of some additional features.
Please see my comments below, with '##'.
Best,
Giovanni
original thread --
Message: 49
Date: Mon, 5 Sep 2011 21:43:02 -0700 (PDT)
From: Daniel Malter dan...@umd.edu
To: r-help@r-project.org
Subject: Re: [R] plm package, R squared, dummies in panel data
Message-ID: 1315284182071-3792582.p...@n4.nabble.com
Content-Type: text/plain; charset=UTF-8
Hi, I answered this question before in this post:
http://r.789695.n4.nabble.com/Regressions-with-fixed-effect-in-R-td21733
14.html
, specifically in my message from May 11, 2010; 4:30pm.
However, I believe the newer version of plm shows an R-squared, which
should
be the within R-squared.
## it is, at least in the case of within models. Actually, for each
model it is the r-squared on the relevant transformed data.
Why the programmers of the package decided to not
show the others or to not provide a test of the significance of the
a(i)s, I
don't know.
## in fact we do, and we have done since mid-2010 (shortly after the
thread you reference in your post). See ?r.squared, and in particular be
aware of the 'model' argument. The a_i are there as well, see below. PS
as for the general reason for not doing something, lack of time is
always a good guess ;^)
As for your second question, the plm function has an option as to
whether
the FEs should be id, time, or twoways, i.e., for id and time. I
would
guess that then the time FEs are not estimated either but differenced
out,
too.
## sort of. The standard way for estimating one or two-ways FE models is
to demean the data. If you want the first-difference model, try plm(...,
model=fd).
## The fixed effects are nevertheless available, they can be recovered
later: see ?fixef and ?summary.fixef for t-tests for significance of
single effects. See ?pooltest for the joint test of significance of all
FEs.
This should affect the within/between variance and therefore the within
and between R-squareds.
## it is the (different flavours of-) r2s that are *defined* according
to the transformation used. Yet, as I said above, you can have them all,
just ask (-the software!).
HTH,
Daniel
Cecilia Carmo wrote:
Hi R-helpers,
I have two questions I hope you could help me with them:
In the plm package how can I calculate the R2 within, R2 between and
R2
overall? Is there any special reason to not display these values?
When using first differences do I need to have some special care with
dummies (both year dummies and industry dummies)?
(A friend who works with Stata told me that there is necessary to
construct
some ?accumulated dummies?.)
Thank you very much,
Cec?lia Carmo
(Universidade de Aveiro ? Portugal)
-- end original thread -
Giovanni Millo, PhD
Research Dept.,
Assicurazioni Generali SpA
Via Machiavelli 4,
34132 Trieste (Italy)
tel. +39 040 671184
fax +39 040 671160
Ai sensi del D.Lgs. 196/2003 si precisa che le informazi...{{dropped:12}}
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Re: [R] Problems with as.POSIXct
Didn't Columbia switch to a year of daylight savings time at what would have been midnight May 3, 1992 (so midnight did not exist that day)? Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of KENNETH R CABRERA Sent: Thursday, September 22, 2011 8:59 AM To: r-help@r-project.org Cc: krcab...@gmail.com Subject: [R] Problems with as.POSIXct Hi R users: This is a very strange problem: Why this instruction shows me NA?, and any other date shows me that error! as.POSIXct(strptime(1992-5-3,format=%Y-%m-%d)) This is my R version on windows 7. R version 2.13.1 Patched (2011-08-25 r56794) Thank you for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to adjust the y-axis range in barplot properly
Hello R-Users, it might be a rather simple problem I have, but I couldn't find any solution online. Thus, here is my problem: I would like to adjust the y-axis range in a barplot, since all my values are 70. Therefore I would like to only visualize the y-axis from 60-100 (example 1). The problem is, the range of the y-axis is adjusted, but the barsize stays the same and vanishes from the plot area. How can I cut the y-axis and the bars in a proper way. Unfortunatlely I dit not get gap.barplot function to work on the matrix in example 1. I would be very greatful for some ideas and help, cheers, Benedikt example 1: data - as.matrix(rbind(c(85:90), c(75:80))) barplot(data, beside=TRUE) barplot(data, ylim=c(60,90), beside=TRUE) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] image.plot for non-regular grid: round pixel
Hi,
I am very new to R so I hope this is not stupid. Here a small example:
(I use R version 2.13.1)
library(fields)
## round pixel
x=matrix(1:100,ncol=10)
y=matrix(1:100,ncol=10)
for(i in 1:10){
x[i,] - 1:10 + i
y[i,] - 1:10 + i/20
}
#x=1:10
#y=1:10
z=matrix(1:100,ncol=10)
pdf(test.pdf)
image.plot(x,y,z)
dev.off()
With that, the generated pixels have round corners. Uncommenting the
second assignements for x and y results in rectangular pixel.
For the actual data which I wanted to plot the round corners look much
worse. What can I do to get non-round pixels?
Thanks a lot!
Sebastian
signature.asc
Description: This is a digitally signed message part.
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Re: [R] Problems with as.POSIXct
What timezone is this?
In America/Bogota there was no midnight that day, so the time would be
invalid. The Olson database has
# Colombia
# Rule NAMEFROMTO TYPEIN ON AT SAVELETTER/S
RuleCO 1992only- May 3 0:001:00S
RuleCO 1993only- Apr 4 0:000
-
# Zone NAMEGMTOFF RULES FORMAT [UNTIL]
ZoneAmerica/Bogota -4:56:20 - LMT 1884 Mar 13
-4:56:20 - BMT 1914 Nov 23 # Bogota Mean Time
-5:00 CO CO%sT # Colombia Time
When all else fails, read the help:
Character input is first converted to class ‘POSIXlt’ by
‘strptime’: numeric input is first converted to ‘POSIXct’. Any
conversion that needs to go between the two date-time classes
requires a timezone: conversion from ‘POSIXlt’ to ‘POSIXct’
will validate times in the selected timezone. One issue is what
happens at transitions to and from DST, for example in the UK
as.POSIXct(strptime('2011-03-27 01:30:00', '%Y-%m-%d %H:%M:%S'))
as.POSIXct(strptime('2010-10-31 01:30:00', '%Y-%m-%d %H:%M:%S'))
are respectively invalid (the clocks went forward at 1:00 GMT to
2:00 BST) and ambiguous (the clocks went back at 2:00 BST to 1:00
GMT).
On Thu, 22 Sep 2011, KENNETH R CABRERA wrote:
Hi R users:
This is a very strange problem:
Why this instruction shows me NA?,
and any other date shows me that error!
as.POSIXct(strptime(1992-5-3,format=%Y-%m-%d))
This is my R version on windows 7.
R version 2.13.1 Patched (2011-08-25 r56794)
Thank you for your help.
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and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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Re: [R] How to adjust the y-axis range in barplot properly
This should do the trick: barplot(data, ylim=c(60,90), beside=TRUE, xpd = FALSE) As usual, check ?barplot first for clues on how to customize the plot to your specifications. On Thu, Sep 22, 2011 at 11:49 AM, Benedikt Drosse dro...@mpipz.mpg.de wrote: Hello R-Users, it might be a rather simple problem I have, but I couldn't find any solution online. Thus, here is my problem: I would like to adjust the y-axis range in a barplot, since all my values are 70. Therefore I would like to only visualize the y-axis from 60-100 (example 1). The problem is, the range of the y-axis is adjusted, but the barsize stays the same and vanishes from the plot area. How can I cut the y-axis and the bars in a proper way. Unfortunatlely I dit not get gap.barplot function to work on the matrix in example 1. I would be very greatful for some ideas and help, cheers, Benedikt example 1: data - as.matrix(rbind(c(85:90), c(75:80))) barplot(data, beside=TRUE) barplot(data, ylim=c(60,90), beside=TRUE) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- ___ Luke Miller Postdoctoral Researcher Marine Science Center Northeastern University Nahant, MA (781) 581-7370 x318 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.oo: do work on data member at construction
On Thu, Sep 22, 2011 at 9:06 AM, Ben qant ccqu...@gmail.com wrote:
Hello,
I'd like to 'do work' on data members upon construction (i.e. without
implementing it in a get method). Is this the best way to create data member
'z' upon construction? I'm thinking if .z=paste(x,y) below gets more complex
I'll run into issues.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=paste(x,y)
)
Looks good to me and is standard R procedure where you work with the
*arguments*. You can also work on the object after it's been
instantiated, e.g.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=NULL
)
# Assign z
this$.z - paste(this$.x, this$.y);
this;
})
Note that if .z always a function of .x and .y it is redundant. Then
an alternative is to create it on the fly, i.e.
setMethodS3(getZ, MyClass, function(this, ...) {
x - this$.x;
y - this$.;
z - paste(x, y);
z;
})
You can then make it clever and cache the results so that it is only
calculated once, e.g.
setMethodS3(getZ, MyClass, function(this, ...) {
z - this$.z;
if (is.null(z)) {
x - this$.x;
y - this$.;
z - paste(x, y);
this$.z - z;
}
z;
})
However, you then have to make sure to reset z (this$.z - NULL)
whenever .x or .y is changed.
/Henrik
})
setMethodS3(getX, MyClass, function(this, ...) {
this$.x;
})
setMethodS3(getY, MyClass, function(this, ...) {
this$.y;
})
setMethodS3(getZ, MyClass, function(this, ...) {
this$.z;
})
mc = MyClass('a','b')
mc$x
[1] a
mc$y
[1] b
mc$z
[1] a b
Thanks,
ben
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] ARIMA - Skipping intermediate lags
Dear Prof. Repley, may I know in details why ignoring intermediate lags are sin? How the statistical properties will be worse than not ignoring them? If I am correct then, ignoring some parameters means we know the population values for them. Therefore in this case, my MSE estimate should be smaller (or, my prediction will be more accurate) isn't it? Thanks and regards, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Prof Brian Ripley Sent: 21 September 2011 13:32 To: leighton155 Cc: r-help@r-project.org Subject: Re: [R] ARIMA - Skipping intermediate lags On Tue, 20 Sep 2011, leighton155 wrote: Hello, I am a new R user. I am trying to use the arima command, but I have a question on intermediate lags. I want to run in R the equivalent Stata command of ARIMA d.yyy, AR(5) MA(5 7). This would tell the program I am interested in AR lag 5, MA lag 5, and MA lag 7, all while skipping the intermediate lags of AR 1-4, and MA 1-4, 6. Is there any way to do this in R? Thank you. Yes. See the 'fixed' argument on the help page. Note that this is not recommended in general -- View this message in context: http://r.789695.n4.nabble.com/ARIMA-Skipping-intermediate-lags-tp38284 49p3828449.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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] need help on melt/cast
And I always have a problem with reshape(). Mind you I often have similar problems with melt() Anyway with the data.frame xx, try melt(xx, id=c(ID)) --- On Thu, 9/22/11, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: From: Uwe Ligges lig...@statistik.tu-dortmund.de Subject: Re: [R] need help on melt/cast To: Eugene Kanshin kanshin...@gmail.com Cc: r-help@r-project.org Received: Thursday, September 22, 2011, 10:30 AM I can never remember what melt, cast and all that means, hence I simpy use reshape() which does not even require any additional package: reshape(dat, direction=long, idvar = ID, varying=list(2:4), v.names=Value, times=names(dat)[2:4]) Uwe Ligges On 22.09.2011 15:54, Eugene Kanshin wrote: Hello, I need to convert dataframe from: ID T0 T1 T2 A 1 2 3 B 4 5 6 C 7 8 9 to: ID Variable Value A T0 1 A T1 2 A T2 3 B T0 4 B T1 5 B T2 6 C T0 7 C T1 8 C T2 9 i tried to use melt cast but it gives me all the time not exactly what I need. Thank you. [[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] need help on melt/cast
On Sep 22, 2011, at 12:28 PM, John Kane wrote: And I always have a problem with reshape(). Me too. Mind you I often have similar problems with melt() Many fewer, though. Anyway with the data.frame xx, try melt(xx, id=c(ID)) Just newdf - melt(xx) # would have succeeded here. -- David --- On Thu, 9/22/11, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: From: Uwe Ligges lig...@statistik.tu-dortmund.de Subject: Re: [R] need help on melt/cast To: Eugene Kanshin kanshin...@gmail.com Cc: r-help@r-project.org Received: Thursday, September 22, 2011, 10:30 AM I can never remember what melt, cast and all that means, hence I simpy use reshape() which does not even require any additional package: reshape(dat, direction=long, idvar = ID, varying=list(2:4), v.names=Value, times=names(dat)[2:4]) Uwe Ligges On 22.09.2011 15:54, Eugene Kanshin wrote: Hello, I need to convert dataframe from: ID T0 T1 T2 A1 2 3 B4 5 6 C7 8 9 to: ID Variable Value A T0 1 A T1 2 A T2 3 B T0 4 B T1 5 B T2 6 C T0 7 C T1 8 C T2 9 i tried to use melt cast but it gives me all the time not exactly what I need. Thank you. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.oo: do work on data member at construction
Thank you very much! I'm using the first example.
For others: there are two simple typos in Henrik's email below: pretty sure
y - this$.; should be y - this$.y;
Thanks again...
Corrected below...
Ben
Hello,
I'd like to 'do work' on data members upon construction (i.e. without
implementing it in a get method). Is this the best way to create data
member
'z' upon construction? I'm thinking if .z=paste(x,y) below gets more
complex
I'll run into issues.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=paste(x,y)
)
Looks good to me and is standard R procedure where you work with the
*arguments*. You can also work on the object after it's been
instantiated, e.g.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=NULL
)
# Assign z
this$.z - paste(this$.x, this$.y);
this;
})
Note that if .z always a function of .x and .y it is redundant. Then
an alternative is to create it on the fly, i.e.
setMethodS3(getZ, MyClass, function(this, ...) {
x - this$.x;
y - this$.y;
z - paste(x, y);
z;
})
You can then make it clever and cache the results so that it is only
calculated once, e.g.
setMethodS3(getZ, MyClass, function(this, ...) {
z - this$.z;
if (is.null(z)) {
x - this$.x;
y - this$.y;
z - paste(x, y);
this$.z - z;
}
z;
})
However, you then have to make sure to reset z (this$.z - NULL)
whenever .x or .y is changed.
/Henrik
On Thu, Sep 22, 2011 at 10:18 AM, Henrik Bengtsson h...@biostat.ucsf.eduwrote:
On Thu, Sep 22, 2011 at 9:06 AM, Ben qant ccqu...@gmail.com wrote:
Hello,
I'd like to 'do work' on data members upon construction (i.e. without
implementing it in a get method). Is this the best way to create data
member
'z' upon construction? I'm thinking if .z=paste(x,y) below gets more
complex
I'll run into issues.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=paste(x,y)
)
Looks good to me and is standard R procedure where you work with the
*arguments*. You can also work on the object after it's been
instantiated, e.g.
setConstructorS3(MyClass, function(x=NA,y=NA,...) {
this - extend(Object(), MyClass,
.x=x,
.y=y,
.z=NULL
)
# Assign z
this$.z - paste(this$.x, this$.y);
this;
})
Note that if .z always a function of .x and .y it is redundant. Then
an alternative is to create it on the fly, i.e.
setMethodS3(getZ, MyClass, function(this, ...) {
x - this$.x;
y - this$.;
z - paste(x, y);
z;
})
You can then make it clever and cache the results so that it is only
calculated once, e.g.
setMethodS3(getZ, MyClass, function(this, ...) {
z - this$.z;
if (is.null(z)) {
x - this$.x;
y - this$.;
z - paste(x, y);
this$.z - z;
}
z;
})
However, you then have to make sure to reset z (this$.z - NULL)
whenever .x or .y is changed.
/Henrik
})
setMethodS3(getX, MyClass, function(this, ...) {
this$.x;
})
setMethodS3(getY, MyClass, function(this, ...) {
this$.y;
})
setMethodS3(getZ, MyClass, function(this, ...) {
this$.z;
})
mc = MyClass('a','b')
mc$x
[1] a
mc$y
[1] b
mc$z
[1] a b
Thanks,
ben
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and provide commented, minimal, self-contained, reproducible code.
[R] create variables through a loop
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i -
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
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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] create variables through a loop
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather than
an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i -
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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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] create variables through a loop
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather
than an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i
-
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
[[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] Wrapper of linearHypothesis (car) for post-hoc of repeated measures ANOVA
For some time I have been looking for a convenient way of performing post-hoc analysis to Repeated Measures ANOVA, that would be acceptable if sphericity is violated (i.e. leaving aside post-hoc to lme models). The best solution I found was John Fox's proposal to similar requests in R-help: http://tolstoy.newcastle.edu.au/R/e2/help/07/09/26518.html http://tolstoy.newcastle.edu.au/R/e10/help/10/04/1663.html However, I think that using linearHypothesis() is not as straightforward as I would desire for testing specific contrasts between factor levels. The hypotheses must be defined as linear combinations of the model coefficients (subject to response transformations according to the intra-subjects design), which may need some involved calculations if one is thinking on differences between this and that factor levels (either between-subjects or intra-subjects), and the issue gets worse for post-hoc tests on interaction effects. For that reason, I have spent some time in writing a wrapper to linearHypothesis() that might be helpful in those situations. I copy the commented code at the end of this message, because although I have successfully used it in some cases, I would like more knowledgeable people to put it to test (and eventually help me create a worthwile contribution for other people that could find it useful). This function (which I have called factorltest.mlm) needs the multivariate linear model and the intrasubject-related arguments (idata, idesign...) that would be passed on to Anova() (from car) for a repeated measures analysis, or directly the Anova.mlm object returned by Anova() instead of idata, idesign... (I have tried to explain it clearly in the commentaries to the code.) Moreover, it needs an argument levelcomb: a list that represents the level combinations of factors to be tested. There are different ways of representing those combinations (through names of factor levels, or coefficient vectors/matrices), and depending on the elements of that list the test is made for main effects, simple effects, interaction contrasts, etc. For instance, let me use an example with the OBrienKaiser data set (as in the help documentation for Anova() and linearHypothesis()). The calculation of the multivariate linear model and Anova is copied from those help files: phase - factor(rep(c(pretest, posttest, followup), c(5, 5, 5)), + levels=c(pretest, posttest, followup)) hour - ordered(rep(1:5, 3)) idata - data.frame(phase, hour) mod.ok - lm(cbind(pre.1, pre.2, pre.3, pre.4, pre.5, +post.1, post.2, post.3, post.4, post.5, +fup.1, fup.2, fup.3, fup.4, fup.5) ~ treatment*gender, + data=OBrienKaiser) av.ok - Anova(mod.ok, idata=idata, idesign=~phase*hour) Then, let's suppose that I want to test pairwise comparisons for the significant main effect treatment (whose levels are c(control,A,B)). For the specific contrast between treatment A and the control group I can define levelcomb in the following (equivalent) ways: levelcomb - list(treatment=c(A,control)) levelcomb - list(treatment=c(A=1,control=-1)) levelcomb - list(treatment=c(-1,1,0)) Now, let's suppose that I am interested in the (marginally) significant interaction between treatment and phase. First I test the simple main effect of phase for different levels of treament (e.g. for the control group). To do this, levelcomb must have one variable for each interacting factor (treatment and phase): levelcomb$treatment will specify the treatment that I want to fix for the simple main effects test (control), and levelcomb$phase will have a NA value to represent that I want to test all orthogonal contrasts within that factor: levelcomb - list(treatment=control,phase=NA) I could also use numeric vectors to define the levels of treatment that I want to fix, as in the previous example, or if I want a more complicated combination (e.g. if I want to test the phase effect for pooled treatments A and B): levelcomb - list(treatment=c(A=1,B=1),phase=NA) The NA value can be replaced by the specific contrast matrix that I would like to use. For instance, the previous statement is equivalent to the following one: levelcomb - list(treatment=c(0,1,1),phase=contr.sum(levels(phase))) And then, let's see an example of interaction contrast: I want to see if the difference between the pre-test phase and the following two, itself differs between the control group and the two treatments. This would be levelcomb - list(treatment=c(2,-1,-1),phase=c(2,-1,-1)) or levelcomb - list(treatment=c(control=2,A=-1,B=-1),phase=c(pretest=2,posttest=-1,followup=-1)) etc. Now, to perform the test I just use this levelcomb list object with the model and ANOVA previously performed, in the following way: factorltest.mlm(mod.ok,levelcomb,av.ok) Or if I want to use idata and idesign directly: factorltest.mlm(mod.ok,levelcomb,idata=idata,idesign=~phase*hour) Of course, this function only performs one test at a
Re: [R] create variables through a loop
There are a few ways to proceed from here. If you are really committed to
this loop + assign idea, I'd provide the following code:
for( i in 2:3) {
label - paste(array, i, sep=)
assign(label, value = result.fun[[i-1]] )
first - cbind(first, get(label))
}
However, this is generally pretty inefficient. Why not something more like
the following?
first.out - do.call(cbind, list(first, result.fun))
If you need the names to be arrayi you can add this line:
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
I'm unable to test this on your (unprovided) data, but here's an example of
how this works:
first = data.frame(x = 1:3, y = 6:8, z = 11:13)
a = data.frame(a = 1:3)
b = data.frame(b = 4:6)
result.fun = list(a,b)
first.out - do.call(cbind, list(first, result.fun))
print(first.out)
which provides this output.
x y z a b
1 1 6 11 1 4
2 2 7 12 2 5
3 3 8 13 3 6
More generally, you really should read about how arguments and assignments
work in R. See, e.g., 8.2.26 in the R inferno.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:21 PM, Changbin Du changb...@gmail.com wrote:
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I
expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather
than an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i
-
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
[[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] create variables through a loop
Actually, I think you can make that even easier:
first.out - cbind(first, result.fun)
Michael Weylandt
On Thu, Sep 22, 2011 at 1:37 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There are a few ways to proceed from here. If you are really committed to
this loop + assign idea, I'd provide the following code:
for( i in 2:3) {
label - paste(array, i, sep=)
assign(label, value = result.fun[[i-1]] )
first - cbind(first, get(label))
}
However, this is generally pretty inefficient. Why not something more like
the following?
first.out - do.call(cbind, list(first, result.fun))
If you need the names to be arrayi you can add this line:
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
I'm unable to test this on your (unprovided) data, but here's an example of
how this works:
first = data.frame(x = 1:3, y = 6:8, z = 11:13)
a = data.frame(a = 1:3)
b = data.frame(b = 4:6)
result.fun = list(a,b)
first.out - do.call(cbind, list(first, result.fun))
print(first.out)
which provides this output.
x y z a b
1 1 6 11 1 4
2 2 7 12 2 5
3 3 8 13 3 6
More generally, you really should read about how arguments and assignments
work in R. See, e.g., 8.2.26 in the R inferno.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:21 PM, Changbin Du changb...@gmail.com wrote:
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I
expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather
than an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.comwrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value =
result.fun[[i -
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
[[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] Problem with error message in Rcmdr
Hello, I just upgraded to R version 2.13.1 and am running Rcmdr version 1.7-0. Prior to the upgrade, Rcmdr returned descriptive error messages. However, since the upgrade the only error message Rcmdr supplies is: ERROR: text How can I convince Rcmdr to return useful error messages again? Thanks, Jake B [[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] Quelplot
Hadley, I forwarded your request to Boris and Ken. Here is Boris' response. Rich Dear Richard: I looked a bit more and found the second edition of book referenced, Rand R Wilcox, Introduction to Robust Estimation and Hypothesis Testing, Second Edition, Academic Press, 2005. It has over 600 quotes on google scholar. If my memory is correct, Wilcox developed code for relplots and possibly quelplots. Best Wishes, Boris On Wed, Sep 21, 2011 at 3:11 PM, Hadley Wickham had...@rice.edu wrote: Hi all, Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307320, 1992)? I'm struggling with the estimation of the asymmetry parameters. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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. [[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] create variables through a loop
Hi,
It's hard to provide you with working code when you don't provide a
reproducible example, but do you really need to create variables? What
about (untested):
for (i in 1:2) {
first -cbind(first, result.fun[[i]])
}
you will then have to look at
names(first)
and change the last part of it to
paste(array,2:3,sep=)
Hope that works!
JC
2011/9/22 Changbin Du changb...@gmail.com:
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3 were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather
than an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1 C-7SARK 1 849467 10
2 C-4WYLN 1 854278 10
3 C-3BFNY 1 854471 10
4 C-7ONNE 1 874460 10
5 C-6HYCN 1 874571 10
6 C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1 C-7SARK 1 849467 10 10 10
2 C-4WYLN 1 854278 10 10 10
3 C-3BFNY 1 854471 10 10 10
4 C-7ONNE 1 874460 10 10 10
5 C-6HYCN 1 874571 10 10 10
6 C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i
-
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
[[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] create variables through a loop
On how to use named vs. positional arguments, you can also have a look
at section 2.3 of an introduction to R.
2011/9/22 Jean-Christophe BOUËTTÉ jcboue...@gmail.com:
Hi,
It's hard to provide you with working code when you don't provide a
reproducible example, but do you really need to create variables? What
about (untested):
for (i in 1:2) {
first -cbind(first, result.fun[[i]])
}
you will then have to look at
names(first)
and change the last part of it to
paste(array,2:3,sep=)
Hope that works!
JC
2011/9/22 Changbin Du changb...@gmail.com:
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3 were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather
than an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1 C-7SARK 1 849467 10
2 C-4WYLN 1 854278 10
3 C-3BFNY 1 854471 10
4 C-7ONNE 1 874460 10
5 C-6HYCN 1 874571 10
6 C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1 C-7SARK 1 849467 10 10 10
2 C-4WYLN 1 854278 10 10 10
3 C-3BFNY 1 854471 10 10 10
4 C-7ONNE 1 874460 10 10 10
5 C-6HYCN 1 874571 10 10 10
6 C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i
-
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Sincerely,
Changbin
--
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Re: [R] Quelplot
Thanks Rich - unfortunately, as far as I can, tell Rand Wilcox only developed relplot code. Hadley On Thu, Sep 22, 2011 at 12:52 PM, Richard M. Heiberger r...@temple.edu wrote: Hadley, I forwarded your request to Boris and Ken. Here is Boris' response. Rich Dear Richard: I looked a bit more and found the second edition of book referenced, Rand R Wilcox, Introduction to Robust Estimation and Hypothesis Testing, Second Edition, Academic Press, 2005. It has over 600 quotes on google scholar. If my memory is correct, Wilcox developed code for relplots and possibly quelplots. Best Wishes, Boris On Wed, Sep 21, 2011 at 3:11 PM, Hadley Wickham had...@rice.edu wrote: Hi all, Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307–320, 1992)? I'm struggling with the estimation of the asymmetry parameters. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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. -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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] create variables through a loop
Thank, Jean, appreciated your help!
On Thu, Sep 22, 2011 at 10:52 AM, Jean-Christophe BOUËTTÉ
jcboue...@gmail.com wrote:
Hi,
It's hard to provide you with working code when you don't provide a
reproducible example, but do you really need to create variables? What
about (untested):
for (i in 1:2) {
first -cbind(first, result.fun[[i]])
}
you will then have to look at
names(first)
and change the last part of it to
paste(array,2:3,sep=)
Hope that works!
JC
2011/9/22 Changbin Du changb...@gmail.com:
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I
expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did someone
provide you with example code that suggested such a thing? remove lab=
entirely or replace it with x= to make your code work. More generally
type
?assign or args(assign) to see what the arguments for a function are.
More generally, this sort of thing may be best handled in a list rather
than an set of independent variables.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:07 PM, Changbin Du changb...@gmail.com
wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through
a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value =
result.fun[[i
-
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
Changbin Du
Data Analysis Group, Affymetrix Inc
6550 Emeryville, CA, 94608
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] create variables through a loop
HI, Michael,
The following codes are great!
first.out - do.call(cbind, list(first, result.fun))
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
head(first.out)
probe_name chr_id position array1 array2 array3 array4 array5 array6
array7
1C-7SARK 1 849467 10 10 10 10 10 10
10
2C-4WYLN 1 854278 10 10 10 10 10 10
10
3C-3BFNY 1 854471 10 10 10 10 10 10
10
4C-7ONNE 1 874460 10 10 10 10 10 10
10
5C-6HYCN 1 874571 10 10 10 10 10 10
10
6C-7SCGC 1 874609 10 10 10 10 10 10
10
array8 array9 array10 array11 array12 array13 array14 array15 array16
array17
1 10 10 10 10 10 10 10 10 10
10
2 10 10 10 10 10 10 10 10 10
10
3 10 10 10 10 10 10 10 10 10
10
4 10 10 10 10 10 10 10 10 10
10
5 10 10 10 10 10 10 10 10 10
10
6 10 10 10 10 10 10 10 10 10
10
array18 array19 array20 array21 array22 array23 array24 array25 array26
1 10 10 10 10 10 10 10 10 10
2 10 10 10 10 10 10 10 10 10
3 10 10 10 10 10 10 10 10 10
4 10 10 10 10 10 10 10 10 10
5 10 10 10 10 10 10 10 10 10
6 10 10 10 10 10 10 10 10 10
array27 array28 array29 array30 array31 array32 array33 array34 array35
1 10 10 10 10 10 10 10 10 10
2 10 10 10 10 10 10 10 10 10
3 10 10 10 10 10 10 10 10 10
4 10 10 10 10 10 10 10 10 10
5 10 10 10 10 10 10 10 10 10
6 10 10 10 10 10 10 10 10 10
array36 array37 array38 array39 array40 array41 array42 array43 array44
1 10 10 10 10 10 10 10 10 10
2 10 10 10 10 10 10 10 10 10
3 10 10 10 10 10 10 10 10 10
4 10 10 10 10 10 10 10 10 10
5 10 10 10 10 10 10 10 10 10
6 10 10 10 10 10 10 10 10 10
array45 array46 array47 array48
1 10 10 10 10
2 10 10 10 10
3 10 10 10 10
4 10 10 10 10
5 10 10 10 10
6 10 10 10 10
Appreciated your great helps!
On Thu, Sep 22, 2011 at 10:55 AM, Changbin Du changb...@gmail.com wrote:
Thanks so much, Michael!
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
for( i in 2:3) {
+ label - paste(array, i, sep=)
+ assign(label, value = result.fun[[i-1]] )
+ first - cbind(first, get(label))
+ }
head(first)
probe_name chr_id position array1 get(label) get(label)
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
**
I can use the codes to change the columns names.
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
I am running:
first.out - do.call(cbind, list(first, result.fun))
and
first.out - cbind(first, result.fun)
IT has been 10 mins, and I will let you know the results.
Thanks so much for the great helps!
On Thu, Sep 22, 2011 at 10:37 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There are a few ways to proceed from here. If you are really committed to
this loop + assign idea, I'd provide the following code:
for( i in 2:3) {
label - paste(array, i, sep=)
assign(label, value = result.fun[[i-1]] )
first - cbind(first, get(label))
}
However, this is generally pretty inefficient. Why not something more like
the following?
first.out - do.call(cbind, list(first, result.fun))
If you need the names to be arrayi you can add this line:
colnames(first.out) -
Re: [R] create variables through a loop
On Sep 22, 2011, at 2:06 PM, Changbin Du wrote:
HI, Michael,
The following codes are great!
first.out - do.call(cbind, list(first, result.fun))
Would this have been easier?
dat[ , c(1:3, rep(4, 5))]
probe_name chr_id position array1 array1.1 array1.2 array1.3
1C-7SARK 1 849467 10 10 10 10
2C-4WYLN 1 854278 10 10 10 10
3C-3BFNY 1 854471 10 10 10 10
4C-7ONNE 1 874460 10 10 10 10
5C-6HYCN 1 874571 10 10 10 10
6C-7SCGC 1 874609 10 10 10 10
array1.4
1 10
2 10
3 10
4 10
5 10
6 10
With the obvious substitution of 45 as the second argument to `rep`
where you currently see 5.
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
They may or may not need to be renamed.
--
David.
head(first.out)
probe_name chr_id position array1 array2 array3 array4 array5 array6
array7
1C-7SARK 1 849467 10 10 10 10 10 10
10
2C-4WYLN 1 854278 10 10 10 10 10 10
10
3C-3BFNY 1 854471 10 10 10 10 10 10
10
4C-7ONNE 1 874460 10 10 10 10 10 10
10
5C-6HYCN 1 874571 10 10 10 10 10 10
10
6C-7SCGC 1 874609 10 10 10 10 10 10
10
array8 array9 array10 array11 array12 array13 array14 array15 array16
array17
1 10 10 10 10 10 10 10 10
10
10
2 10 10 10 10 10 10 10 10
10
snipped extraneous output.
Appreciated your great helps!
On Thu, Sep 22, 2011 at 10:55 AM, Changbin Du changb...@gmail.com
wrote:
Thanks so much, Michael!
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
for( i in 2:3) {
+ label - paste(array, i, sep=)
+ assign(label, value = result.fun[[i-1]] )
+ first - cbind(first, get(label))
+ }
head(first)
probe_name chr_id position array1 get(label) get(label)
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
**
I can use the codes to change the columns names.
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
I am running:
first.out - do.call(cbind, list(first, result.fun))
and
first.out - cbind(first, result.fun)
IT has been 10 mins, and I will let you know the results.
Thanks so much for the great helps!
On Thu, Sep 22, 2011 at 10:37 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There are a few ways to proceed from here. If you are really
committed to
this loop + assign idea, I'd provide the following code:
for( i in 2:3) {
label - paste(array, i, sep=)
assign(label, value = result.fun[[i-1]] )
first - cbind(first, get(label))
}
However, this is generally pretty inefficient. Why not something
more like
the following?
first.out - do.call(cbind, list(first, result.fun))
If you need the names to be arrayi you can add this line:
colnames(first.out) - c(colnames(first), paste(array,
seq(length(result.fun)), sep=))
I'm unable to test this on your (unprovided) data, but here's an
example
of how this works:
first = data.frame(x = 1:3, y = 6:8, z = 11:13)
a = data.frame(a = 1:3)
b = data.frame(b = 4:6)
result.fun = list(a,b)
first.out - do.call(cbind, list(first, result.fun))
print(first.out)
which provides this output.
x y z a b
1 1 6 11 1 4
2 2 7 12 2 5
3 3 8 13 3 6
More generally, you really should read about how arguments and
assignments
work in R. See, e.g., 8.2.26 in the R inferno.
Michael Weylandt
On Thu, Sep 22, 2011 at 1:21 PM, Changbin Du changb...@gmail.com
wrote:
HI, Michael,
I tried use x and got the following:
for (i in 2:3) {
+
+ assign(x=paste(array, i, sep=), value=result.fun[[i-1]])
+
+ first -cbind(first, x)
+
+ }
*Error in cbind(first, x) : object 'x' not found
*
But I checked the
ls()
array2 array3were created.
Can I put them into the first data set by loop, or manually?
Thanks!
P.S I search the similar codes from google and can not work as I
expected.
Thanks!
On Thu, Sep 22, 2011 at 10:11 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
There is no lab= argument for assign() hence the error. Did
someone
provide you with example code that suggested such a
[R] suggestions argument in rbga function in genalg package
Would someone be so kind as to provide example code where they use the suggestions argument in the rgba function In genalg? I can't get it to work. The following code works just fine: GenFit -rbga(Lower, Upper, evalFunc = evaluate) Lower and Upper are each numeric vectors with 7 elements. Evaluate is an objective function. However, when I want to use a suggested chromosome, I get an error message. My code is start - c(1,0.1,10, 100,1,100,1) suggestions - list(start) GenFit -rbga(Lower, Upper, suggestions = suggestions, evalFunc = evaluate) The error message is: Error in 1:suggestionCount : argument of length 0 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] Quelplot
On 9/21/2011 3:11 PM, Hadley Wickham wrote: Hi all, Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307–320, 1992)? I'm struggling with the estimation of the asymmetry parameters. Do you have some code you have tried or don't you know how to calculate P_1 and P_2? The description is not particularly explicit, but the major/minor axes of the ellipse are defined in terms of standard scores for X and Y as Z1 = Y + X Z2 = Y - X If you can figure out what they mean by proportion of the total standard deviation due to residuals..., then something like P_1 = sum(Z_10) / n P_2 = sum(Z_20) / n Maybe Boris can help. Thanks for bringing this to our attention. If the bagplot is a totally non-parametric analog of a bivariate boxplot, the quelplot might be a 2df parametric version. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Proportions of a vector
Hi all, I have a vector xm say: xm = c(1,2,3,4,5,5,5,6,6) I want to return a vector with the corresponding probabilities based on the amount of times the numbers occurred. For example, I should get the following vector for xm: prob.xm = c(1/9, 1/9, 1/9, 1/9, 3/9, 3/9, 3/9, 2/9, 2/9) Using prop.table gives: Usage (with table) prob.xm - round( prop.table(table(xm)), digits=3) prob.xm xm 1 2 3 4 5 6 0.111 0.111 0.111 0.111 0.333 0.222 But I want the entire length of probabilities, not just a condensed version. Any help is greatl appreciated. -- Thanks, Jim. [[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] Proportions of a vector
If the values in xm are always going to be consecutive integers 1:n, then this: prob.xm[xm] xm 1 2 3 4 5 5 5 6 6 0.111 0.111 0.111 0.111 0.333 0.333 0.333 0.222 0.222 otherwise: prob.xm[as.numeric(as.factor(xm))] xm 1 2 3 4 5 5 5 6 6 0.111 0.111 0.111 0.111 0.333 0.333 0.333 0.222 0.222 (equivalent in this case). Sarah On Thu, Sep 22, 2011 at 3:41 PM, Jim Silverton jim.silver...@gmail.com wrote: Hi all, I have a vector xm say: xm = c(1,2,3,4,5,5,5,6,6) I want to return a vector with the corresponding probabilities based on the amount of times the numbers occurred. For example, I should get the following vector for xm: prob.xm = c(1/9, 1/9, 1/9, 1/9, 3/9, 3/9, 3/9, 2/9, 2/9) Using prop.table gives: Usage (with table) prob.xm - round( prop.table(table(xm)), digits=3) prob.xm xm 1 2 3 4 5 6 0.111 0.111 0.111 0.111 0.333 0.222 But I want the entire length of probabilities, not just a condensed version. Any help is greatl appreciated. -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Proportions of a vector
Try this:
long.prop.table - function(x) {
x - as.factor(x)
p = tabulate(x)/length(x)
p[x]
}
Michael Weylandt
On Thu, Sep 22, 2011 at 3:41 PM, Jim Silverton jim.silver...@gmail.comwrote:
Hi all,
I have a vector xm say: xm = c(1,2,3,4,5,5,5,6,6)
I want to return a vector with the corresponding probabilities based on
the
amount of times the numbers occurred. For example, I should get the
following vector for xm:
prob.xm = c(1/9, 1/9, 1/9, 1/9, 3/9, 3/9, 3/9, 2/9, 2/9)
Using prop.table gives:
Usage (with table)
prob.xm - round( prop.table(table(xm)), digits=3)
prob.xm
xm
1 2 3 4 5 6
0.111 0.111 0.111 0.111 0.333 0.222
But I want the entire length of probabilities, not just a condensed
version.
Any help is greatl appreciated.
--
Thanks,
Jim.
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] solving linear equations
Hi Bolker, Sorry for the late reply and thank you very much. The code works fine. I am indeed sorry for telling you it was a linear equation. I am just trying to use the R code to perform the curve fitting problem for the team of biologists. The data given to me was a sample data and they told me they use the 4 parameter and 5 parameter log logistic functions, they haven't exactly given me anything else. Is there a more general way to find the parameters and hence perform curve fitting on a given set of data. I just want to know how you came up with the initial values of a and d. I would also like to know if there is a formula or an approximation, given the data, to find the same, as they want the process to be automated. Please do let me know, and I am much obliged to whatever help I get. Varun -- View this message in context: http://r.789695.n4.nabble.com/solving-linear-equations-tp3811144p3834421.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] Quelplot
Hi Hadley, Thank-you for your interest in the quelplot. I agree that Rand Wilcox only published relplot code. I do not know of any other R or S implementations. I wrote all of my code in HTBasic (Rocky Mountain BASIC) originally. I later copied some of it to SAS proc iml, but I think that was just the multivariate analog of the relplot (including the bivariate relplot). I wonder if there is a typo in the Technometrics article, because the quelplot always worked fine for me but I recall somebody else having trouble with programming it. I think I sent that person my HTBasic code back in the early 1990's. Perhaps that was Rand. I think I did send it to somebody who asked for it in Australia. I will have to search for my code. I know I have it on my PC in HTBasic format, but it has been a long time since I used it and may have to work a bit even to print it or to get it out into a DOS text file. I may have a DOS text file of it at home on a 3.5 diskette, but even if I could find it, I doubt if I could find a disk drive to read it! When I get it in a useable format, I can send you that code, or at least the parts of it relevant to the quelplot, if you would like it. Perhaps just browsing it would show the problem you are having with my Technometrics article, whether it was a typo or just something that I wrote poorly. There may just be a few subroutines that would need translating from HTBasic into R, and that when added to Rand Wilcox's library would give his software the quelplot capacity. Hadley, I took your R/Splus Fundamentals and Programming Techniques course 5 years ago in Washington DC, but have used R just a couple of times since. I've rarely programmed in R, but this would be a good project for me to start with. It may be a few weeks though until I can get started on any of this though, but I will keep you informed. Regards, Ken Kenneth M. Goldberg, Ph.D. Associate Director, Nonclinical Statistics Johnson Johnson Pharmaceutical Research Development, LLC 965 Chesterbrook Boulevard, Mailstop C-4-1 Wayne, PA 19087 Tel 610-651-6924 Fax 610-651-6717 kgold...@its.jnj.com Confidentiality Notice: This e-mail transmission may contain confidential or legally privileged information that is intended only for the individual or entity named in the e-mail address. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or reliance upon the contents of this e-mail is strictly prohibited. If you have received this e-mail transmission in error, please reply to the sender, so that Centocor can arrange for proper delivery, and then please delete the message from your inbox. Thank you. Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307-320, 1992)? I'm struggling with the estimation of the asymmetry parameters. -Original Message- From: h.wick...@gmail.com [mailto:h.wick...@gmail.com] On Behalf Of Hadley Wickham Sent: Thursday, September 22, 2011 1:56 PM To: Richard M. Heiberger Cc: R-help; BORIS IGLEWICZ; Goldberg, Ken [JRDUS] Subject: Re: [R] Quelplot Thanks Rich - unfortunately, as far as I can, tell Rand Wilcox only developed relplot code. Hadley On Thu, Sep 22, 2011 at 12:52 PM, Richard M. Heiberger r...@temple.edu wrote: Hadley, I forwarded your request to Boris and Ken. Here is Boris' response. Rich Dear Richard: I looked a bit more and found the second edition of book referenced, Rand R Wilcox, Introduction to Robust Estimation and Hypothesis Testing, Second Edition, Academic Press, 2005. It has over 600 quotes on google scholar. If my memory is correct, Wilcox developed code for relplots and possibly quelplots. Best Wishes, Boris On Wed, Sep 21, 2011 at 3:11 PM, Hadley Wickham had...@rice.edu wrote: Hi all, Does anyone have an R implementation of the queplot (K. M. Goldberg and B. Iglewicz. Bivariate extensions of the boxplot. Technometrics, 34(3):pp. 307-320, 1992)? I'm struggling with the estimation of the asymmetry parameters. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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. -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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,
[R] How make a x,y dataset from a formula based entry
Hello all,
So I am using the (formula entry) method for randomForests:
randomForest(y~x1+x2+...+x39+x40,data=xxx,...) but the issue is that some of
the items in that package dont take a formula entry - you have to explicitly
state the y and x vector:
randomForest(x=xxx[,c('x1','x2',...,'x40')],y=xxx[,'y'],...)
Now my question is whether there is a function/way to tell R to take a
formula and make the two corresponding datasets [x,y] (that way I dont have
to create the x dataset manually with all 40 variables I have).
There must be a more elegant way to do this than
x=xxx[,c('x1','x2',...,'x40')]
Thanks!
George
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Re: [R] How make a x,y dataset from a formula based entry
Hello,
You can check ?model.frame.
I do not know however to extract only the right-hand of left-hand part
of a formula.
JC
2011/9/22 trekvana trekv...@aol.com:
Hello all,
So I am using the (formula entry) method for randomForests:
randomForest(y~x1+x2+...+x39+x40,data=xxx,...) but the issue is that some of
the items in that package dont take a formula entry - you have to explicitly
state the y and x vector:
randomForest(x=xxx[,c('x1','x2',...,'x40')],y=xxx[,'y'],...)
Now my question is whether there is a function/way to tell R to take a
formula and make the two corresponding datasets [x,y] (that way I dont have
to create the x dataset manually with all 40 variables I have).
There must be a more elegant way to do this than
x=xxx[,c('x1','x2',...,'x40')]
Thanks!
George
--
View this message in context:
http://r.789695.n4.nabble.com/How-make-a-x-y-dataset-from-a-formula-based-entry-tp3834477p3834477.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] Limitations of audio processing in R
With all due respect to those of us (including me) who love R, when it comes to audio processing w/ freeware, Audacity FTW. 'nuff said Carl -- - Sent from my Cray XK6 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] create variables through a loop
Hi:
Here's one approach with package reshape2. I copied the same data
frame 10 times to illustrate the idea, but as long as your data frames
have the same structure (same variables, same dimension), this should
work.
library('plyr')
library('reshape2')
# Use your example data as the template:
ds - read.table(textConnection(
probe_name chr_id position y
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10), header = TRUE, stringsAsFactors = FALSE)
closeAllConnections()
# Note how I use y for the response instead of arrayxx.
# Copy the data frame 10 times and put it into a list; these are
# placeholders for the real data frames
L - lapply(seq_len(10), function(i) ds)
# Name the list components array01 - array10, ...
names(L) - c(paste('array0', 1:9, sep = ''), 'array10')
# The advantage of using rbind in conjunction with ldply() is that it outputs
# the list names as an .id variable
u - ldply(L, rbind)
head(u)
# Reshape the data so that the y values in each component are associated
# with the component name:
dcast(u, probe_name + chr_id + position ~ .id, value_var = 'y')
probe_name chr_id position array01 array02 array03 array04 array05 array06
1C-3BFNY 1 854471 10 10 10 10 10 10
2C-4WYLN 1 854278 10 10 10 10 10 10
3C-6HYCN 1 874571 10 10 10 10 10 10
4C-7ONNE 1 874460 10 10 10 10 10 10
5C-7SARK 1 849467 10 10 10 10 10 10
6C-7SCGC 1 874609 10 10 10 10 10 10
array07 array08 array09 array10
1 10 10 10 10
2 10 10 10 10
3 10 10 10 10
4 10 10 10 10
5 10 10 10 10
6 10 10 10 10
HTH,
Dennis
On Thu, Sep 22, 2011 at 10:07 AM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1 C-7SARK 1 849467 10
2 C-4WYLN 1 854278 10
3 C-3BFNY 1 854471 10
4 C-7ONNE 1 874460 10
5 C-6HYCN 1 874571 10
6 C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1 C-7SARK 1 849467 10 10 10
2 C-4WYLN 1 854278 10 10 10
3 C-3BFNY 1 854471 10 10 10
4 C-7ONNE 1 874460 10 10 10
5 C-6HYCN 1 874571 10 10 10
6 C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i -
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
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[R] Bivariate Scatter Plots with Lattice
Data frame has this structure: 'data.frame': 11169 obs. of 4 variables: $ stream : Factor w/ 37 levels Burns,CIL,..: 1 1 1 1 1 1 1 1 1 1 ... $ sampdate: Date, format: 1987-07-23 1987-09-17 ... $ param : Factor w/ 8 levels As,Ca,Cl,..: 1 1 1 1 1 1 1 1 1 1 ... $ quant : num 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0 ... I want to create scatter plots of the concentrations (numeric column 'quant') for two specified chemicals (factor column 'param') for all dates and streams (factor column 'stream') in which there are data. Looking in ?lattice and Deepayan's book did not provide an example. I've tried varies formulae but without success, and would appreciate a pointer to documentation and examples of how to write such an expression. Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bivariate Scatter Plots with Lattice
Hi: Question: Do you want 37 different panels with plots of quant vs. date by param, or two panels (one per chemical) with all 37 streams? If you only want two of the eight chemicals, I'd suggest using subset() to select out the pair you want and then redefine the param factor so that the subset data frame has two factor levels instead of eight. Since there are several ways to interpret 'in which there are data', you might want to expound a little further about your intentions in that regard. HTH, Dennis On Thu, Sep 22, 2011 at 3:03 PM, Rich Shepard rshep...@appl-ecosys.com wrote: Data frame has this structure: 'data.frame': 11169 obs. of 4 variables: $ stream : Factor w/ 37 levels Burns,CIL,..: 1 1 1 1 1 1 1 1 1 1 ... $ sampdate: Date, format: 1987-07-23 1987-09-17 ... $ param : Factor w/ 8 levels As,Ca,Cl,..: 1 1 1 1 1 1 1 1 1 1 ... $ quant : num 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0 ... I want to create scatter plots of the concentrations (numeric column 'quant') for two specified chemicals (factor column 'param') for all dates and streams (factor column 'stream') in which there are data. Looking in ?lattice and Deepayan's book did not provide an example. I've tried varies formulae but without success, and would appreciate a pointer to documentation and examples of how to write such an expression. Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bivariate Scatter Plots with Lattice
On Sep 22, 2011, at 6:03 PM, Rich Shepard wrote: Data frame has this structure: 'data.frame': 11169 obs. of 4 variables: $ stream : Factor w/ 37 levels Burns,CIL,..: 1 1 1 1 1 1 1 1 1 1 ... $ sampdate: Date, format: 1987-07-23 1987-09-17 ... $ param : Factor w/ 8 levels As,Ca,Cl,..: 1 1 1 1 1 1 1 1 1 1 ... $ quant : num 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0 ... I want to create scatter plots of the concentrations (numeric column 'quant') for two specified chemicals (factor column 'param') for all dates and streams (factor column 'stream') in which there are data. Scatterplots are for two variables with continuous valued data. You are asking about one such variable, apparently within some combination of groups of discrete variables. Look at dotplot or bwplot examples. Looking in ?lattice and Deepayan's book did not provide an example. I've tried varies formulae but without success, and would appreciate a pointer to documentation and examples of how to write such an expression. The problem is with the choice of plotting function not fitting the problem, not with the formula. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to do Multiple Comparisons for a Mixed Effects Model
Hello everyone I am currently trying to conduct analysis of my graduate thesis data using a mixed effects model and I have reached an impass. When I try to conduct a multiple comparison, I get an error (See below): fm3- lme(abovegroundbiomass.m.2~medium*amelioration*fertilizer*treatment, random=~1|block/medium/amelioration/fertilizer) tukeytest-glht(fm3, linfct=mcp(treatment=Tukey)) Error in contrMat(table(mf[[nm]]), type = types[pm]) : less than two groups I wonder if anyone could help me interpret this error. Many thanks. Allan Carson [[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] Error: cannot allocate vector of size xxx
Michale and Paul
Thanks for your quick response.
Michael, I am running a 32bit version of R
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
Paul, the dimension of the Data Frame with I am workis is
dim(d)
[1] 7017411
And the size of the file that contains the data is 2946 Kb
The script that I use for manage the data is:
#clean the workspace
rm(list = ls(all = TRUE))
#Increase the memory size
memory.limit(size=4000)
#Set Directory of WorkSpace where whe have the data
setwd('C:/Users/XXX/XXX/R/')
#load data
dat - read.table('dat_fin_age.txt')
#delete empty registry
d-na.omit(dat)
remove(dat) # remove dat (intermedia object) for release resource
#Asigned the name to the variables in the data
names(d)-
c('pesq','year','month','sex','length','weigth','mature','age','soi','temp','k')
#define the ages over the analysis is focuses.
minage-1 # minimum age
maxage-6 # maximum age
# One of the diferent lm I have been tested
l6w-lm(length~as.factor(age)*as.factor(year)*as.factor(sex)*soi*k,data=d[d$age
%in% minage:maxage,])
Today I will prove your recommendation to use the package biglm
Thanks to both for your Help
Regards
2011/9/22 Paul Hiemstra paul.hiems...@knmi.nl
On 09/22/2011 04:00 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Are you running a 32bit or 64bit version of R? Type sessionInfo() to see.
Michael
...in addition, how large is your dataset? Please provide us with a self
contained example which reproduces this problem. You could take a look
at the biglm package.
regards,
Paul
On Sep 21, 2011, at 10:41 PM, Mario Montecinos Carvajal
mariomonteci...@gmail.com wrote:
Hi
I am a new user of the mail list.
Mi problem occurs when I try to test a lineal model (lm), becouse appear
the
messaje Error: cannot allocate vector of size xxx
The data frame whit I am working, Have
dim(d)
[1] 7017411
and the function i am test is:
lm(length~as.factor(age)*as.factor(year)*as.factor(sex)*soi*k,data=d[d$age
%in% minage:maxage,])
I tried with a diferent options for solve this problem, but any one give
me
results.
I tried with:
Change in Function: memory.limit(size=4000)
Change the setting in Windows using BCDEdit /set
Change in the memory availability for R, change the path of the program
(suggested for other user)
My computer have 4GB RAM, Have 20 GB of Virtual Memory, HDD 300 GB with
200
GB of free space and Windows 7 as OS and my R version is 2.11.1
I need solve this problem, any help or suggestion will be very well
received.
I've been thinking in change the OS, but this is may last option.
Regards
I read
--
Mario Montecinos C.
Biologo Marino
Dr (c) en Ciencias
Universidad Austral de Chile
Los acentos han sido omitidos voluntariamente para evitar
incompatibilidades
Evite enviar cartas impresas, cuidemos el medio ambiente y evitemos el
uso innecesario de papel.
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and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide
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--
Paul Hiemstra, Ph.D.
Global Climate Division
Royal Netherlands Meteorological Institute (KNMI)
Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39
P.O. Box 201 | 3730 AE | De Bilt
tel: +31 30 2206 494
http://intamap.geo.uu.nl/~paul
http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770
--
Mario Montecinos C.
Biologo Marino
Dr (c) en Ciencias
Universidad Austral de Chile
Los acentos han sido omitidos voluntariamente para evitar incompatibilidades
Evite enviar cartas impresas, cuidemos el medio ambiente y evitemos el
uso innecesario de papel.
[[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] create variables through a loop
HI, Dennis,
Thanks for the helps! All roads to Rome, appreciated!
On Thu, Sep 22, 2011 at 2:54 PM, Dennis Murphy djmu...@gmail.com wrote:
Hi:
Here's one approach with package reshape2. I copied the same data
frame 10 times to illustrate the idea, but as long as your data frames
have the same structure (same variables, same dimension), this should
work.
library('plyr')
library('reshape2')
# Use your example data as the template:
ds - read.table(textConnection(
probe_name chr_id position y
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10), header = TRUE, stringsAsFactors =
FALSE)
closeAllConnections()
# Note how I use y for the response instead of arrayxx.
# Copy the data frame 10 times and put it into a list; these are
# placeholders for the real data frames
L - lapply(seq_len(10), function(i) ds)
# Name the list components array01 - array10, ...
names(L) - c(paste('array0', 1:9, sep = ''), 'array10')
# The advantage of using rbind in conjunction with ldply() is that it
outputs
# the list names as an .id variable
u - ldply(L, rbind)
head(u)
# Reshape the data so that the y values in each component are associated
# with the component name:
dcast(u, probe_name + chr_id + position ~ .id, value_var = 'y')
probe_name chr_id position array01 array02 array03 array04 array05 array06
1C-3BFNY 1 854471 10 10 10 10 10
10
2C-4WYLN 1 854278 10 10 10 10 10
10
3C-6HYCN 1 874571 10 10 10 10 10
10
4C-7ONNE 1 874460 10 10 10 10 10
10
5C-7SARK 1 849467 10 10 10 10 10
10
6C-7SCGC 1 874609 10 10 10 10 10
10
array07 array08 array09 array10
1 10 10 10 10
2 10 10 10 10
3 10 10 10 10
4 10 10 10 10
5 10 10 10 10
6 10 10 10 10
HTH,
Dennis
On Thu, Sep 22, 2011 at 10:07 AM, Changbin Du changb...@gmail.com wrote:
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1C-7SARK 1 849467 10
2C-4WYLN 1 854278 10
3C-3BFNY 1 854471 10
4C-7ONNE 1 874460 10
5C-6HYCN 1 874571 10
6C-7SCGC 1 874609 10
I have 48 other array data from a list result.fun
array2=result.fun[[1]]
array3=result.fun[[2]]
.
.
I want the following results:
probe_name chr_id position array1 array2 array3
1C-7SARK 1 849467 10 10 10
2C-4WYLN 1 854278 10 10 10
3C-3BFNY 1 854471 10 10 10
4C-7ONNE 1 874460 10 10 10
5C-6HYCN 1 874571 10 10 10
6C-7SCGC 1 874609 10 10 10
I used the following codes:
for (i in 2:3) {
assign(lab=paste(array, i, sep=), value=result.fun[[i-1]])
first -cbind(first, lab)
}
*Error in assign(lab = paste(array, i, sep = ), value = result.fun[[i
-
:
unused argument(s) (lab = paste(array, i, sep = ))*
Can anyone give some hits or helps?
Thanks so much!
--
Sincerely,
Changbin
--
[[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.
--
Sincerely,
Changbin
--
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] (sin asunto)
hello, I want to know as mortality in different families of epiphytes after selective logging in the forest I want to make a survival analysis with left and right censored data. My study begins in 2004 but I have many individuals who enter the study in 2007 I have tried this: surara-survfit(Surv(fecha,estado)~categoria) fecha= time estado= dead categoria= control and experimental but it is working just with right censored data [[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] Error: cannot allocate vector of size xxx
On Sep 22, 2011, at 5:00 PM, Mario Montecinos Carvajal wrote:
Michale and Paul
Thanks for your quick response.
Michael, I am running a 32bit version of R
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
Paul, the dimension of the Data Frame with I am workis is
dim(d)
[1] 7017411
And the size of the file that contains the data is 2946 Kb
Not a very big dataset for a workspace that should be 2GB or more.
The script that I use for manage the data is:
#clean the workspace
rm(list = ls(all = TRUE))
I hate it when people put that code in without a warning and
preferably commented out. Some us boobs have been known to paste in
code without mentally single stepping through it.
#Increase the memory size
memory.limit(size=4000)
#Set Directory of WorkSpace where whe have the data
setwd('C:/Users/XXX/XXX/R/')
#load data
dat - read.table('dat_fin_age.txt')
#delete empty registry
d-na.omit(dat)
remove(dat) # remove dat (intermedia object) for release resource
#Asigned the name to the variables in the data
names(d)-
c
('pesq
','year
','month','sex','length','weigth','mature','age','soi','temp','k')
Bad idea to use length as a variable name. It is a function name.
#define the ages over the analysis is focuses.
minage-1 # minimum age
maxage-6 # maximum age
At this point you should have offered:
str(d)
# One of the diferent lm I have been tested
You are constructing a 5-way interaction that will have way more
interactions than you will know what to do with. Why not start out
with a simple model and move up from there? If these ages and years
are integer valued then you may not have enough data to support such
a model with only 70k records.
What do these models tell you?
l6w.lin - lm(length~as.factor(age) + as.factor(year) + as.factor(sex)
+soi + k,
Or:
l6w.2way - lm(length~ (as.factor(age) + as.factor(year) +
as.factor(sex) +soi + k)^2 ,
data=d[d$age
%in% minage:maxage,])
A much safer way to handle this would be:
data=subset(d, age = minage age = maxage)
%in% is a set operation and you are passing it a vector of integers
rather than a range.
Today I will prove your recommendation to use the package biglm
Should not be necessary. The problem lies elsewhere.
Thanks to both for your Help
Regards
2011/9/22 Paul Hiemstra paul.hiems...@knmi.nl
On 09/22/2011 04:00 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Are you running a 32bit or 64bit version of R? Type sessionInfo()
to see.
Michael
...in addition, how large is your dataset? Please provide us with a
self
contained example which reproduces this problem. You could take a
look
at the biglm package.
regards,
Paul
On Sep 21, 2011, at 10:41 PM, Mario Montecinos Carvajal
mariomonteci...@gmail.com wrote:
Hi
I am a new user of the mail list.
Mi problem occurs when I try to test a lineal model (lm), becouse
appear
the
messaje Error: cannot allocate vector of size xxx
The data frame whit I am working, Have
dim(d)
[1] 7017411
and the function i am test is:
lm
(length~as.factor(age)*as.factor(year)*as.factor(sex)*soi*k,data=d[d
$age
%in% minage:maxage,])
I tried with a diferent options for solve this problem, but any
one give
me
results.
I tried with:
Change in Function: memory.limit(size=4000)
Change the setting in Windows using BCDEdit /set
Change in the memory availability for R, change the path of the
program
(suggested for other user)
My computer have 4GB RAM, Have 20 GB of Virtual Memory, HDD 300
GB with
200
GB of free space and Windows 7 as OS and my R version is 2.11.1
I need solve this problem, any help or suggestion will be very well
received.
I've been thinking in change the OS, but this is may last option.
Regards
I read
David Winsemius, MD
West Hartford, CT
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Re: [R] Bivariate Scatter Plots with Lattice
On Thu, 22 Sep 2011, Dennis Murphy wrote: Question: Do you want 37 different panels with plots of quant vs. date by param, or two panels (one per chemical) with all 37 streams? If you only want two of the eight chemicals, Dennis, I want only 2 chemicals per plot. I'd suggest using subset() to select out the pair you want and then redefine the param factor so that the subset data frame has two factor levels instead of eight. Sure. I keep working with the original data set and haven't yet fully learned to create subsets as needed. Since there are several ways to interpret 'in which there are data', you might want to expound a little further about your intentions in that regard. What I mean that over all locations and chemicals the earliest date for which there is data is 1980-03-01. However, some chemicals might not have been required to be monitored before, say, 1990. If the pair in a given plot have no data prior to 1990 (for example), that's what I want as the xlim. Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bivariate Scatter Plots with Lattice
On Thu, 22 Sep 2011, David Winsemius wrote: Scatterplots are for two variables with continuous valued data. You are asking about one such variable, apparently within some combination of groups of discrete variables. Look at dotplot or bwplot examples. David, Good catch. Point noted. Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Limitations of audio processing in R
Hi, Carl: 1. I've used Audacity and it seemed fine -- though I haven't used it much. 2. What's FTW? (None of the Wikipedia disambiguation entries seemed to fit.) Thanks, Spencer On 9/22/2011 2:41 PM, Carl Witthoft wrote: With all due respect to those of us (including me) who love R, when it comes to audio processing w/ freeware, Audacity FTW. 'nuff said Carl -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.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] Identifying Package for Function
While reading ?subset I'm referred to learn about dropvalues() as a following operation. Yet, when I issue ?dropvalue I see, No documentation for '?dropvalues' in specified packages and libraries:. How do I identify the library/package that contains a specific function such as, in this case, dropvalues()? Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to turn a LaTeX Sweave file (Rnw) into .HTML/.odf/.docx? (under windows)
Hello dear R help members, I have found several references on how to do this, my question is if anyone is actually using them - and if there are some strong points on what to use, and how well it is working out. My goal is to be able to easily create docs from R, but to be able to share it with other researchers (who do not use LaTeX) so they could easily copy/paste the tables and edit them for their needs (pdf is not solving this for me). The only reasonable solution I came by so far is to use HTML markup coupled with R2HTML (or odfWeave or R2wd). But nothing that can work with LaTeX-HTML (easily) I have asked a similar question here: http://stackoverflow.com/questions/7512897/how-to-turn-a-latex-sweave-file-rnw-into-html And also noticed it was asked half a year ago here: http://tex.stackexchange.com/questions/4145/workflow-for-converting-latex-into-open-office-ms-word-format The general issue of TeX to HTML was discussed also in these places: http://tex.stackexchange.com/questions/50/how-can-i-convert-math-less-latex-documents-into-microsoft-word And obviously the following page offers other good resources to consider: http://cran.r-project.org/web/views/ReproducibleResearch.html p.s: I search the R-help for this topic, but sweave html didn't seem to yield good results - my apologies if this has been heavily debated before - links would be welcomed as well. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[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] Limitations of audio processing in R
1) I don't know about automated clipping using Audacity. 2) en.wiktionary.org/wiki/for_the_win --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Spencer Graves spencer.gra...@structuremonitoring.com wrote: Hi, Carl: 1. I've used Audacity and it seemed fine -- though I haven't used it much. 2. What's FTW? (None of the Wikipedia disambiguation entries seemed to fit.) Thanks, Spencer On 9/22/2011 2:41 PM, Carl Witthoft wrote: With all due respect to those of us (including me) who love R, when it comes to audio processing w/ freeware, Audacity FTW. 'nuff said Carl -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.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. [[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] Identifying Package for Function
Do you perhaps mean ?droplevels, as mentioned in See Also of subset help? Otherwise, where exactly do you see 'dropvalues' referred to? Cheers, Mike. On Fri, Sep 23, 2011 at 9:08 AM, Rich Shepard rshep...@appl-ecosys.com wrote: While reading ?subset I'm referred to learn about dropvalues() as a following operation. Yet, when I issue ?dropvalue I see, No documentation for '?dropvalues' in specified packages and libraries:. How do I identify the library/package that contains a specific function such as, in this case, dropvalues()? Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Sumner Institute for Marine and Antarctic Studies, University of Tasmania Hobart, Australia e-mail: mdsum...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Identifying Package for Function
Where is dropvalue(s) mentioned? ?subset subset: logical expression indicating elements or rows to keep: missing values are taken as false. select: expression, indicating columns to select from a data frame. drop: passed on to ‘[’ indexing operator. ...: further arguments to be passed to or from other methods. Details: This is a generic function, with methods supplied for matrices, data frames and vectors (including lists). Packages and users can add further methods. For ordinary vectors, the result is simply ‘x[subset !is.na(subset)]’. For data frames, the ‘subset’ argument works on the rows. Note that ‘subset’ will be evaluated in the data frame, so columns can be referred to (by name) as variables in the expression (see the examples). The ‘select’ argument exists only for the methods for data frames and matrices. It works by first replacing column names in the selection expression with the corresponding column numbers in the data frame and then using the resulting integer vector to index the columns. This allows the use of the standard indexing conventions so that for example ranges of columns can be specified easily, or single columns can be dropped (see the examples). The ‘drop’ argument is passed on to the indexing method for matrices and data frames: note that the default for matrices is different from that for indexing. Value: An object similar to ‘x’ contain just the selected elements (for a vector), rows and columns (for a matrix or data frame), and so on. Author(s): Peter Dalgaard and Brian Ripley See Also: ‘[’, ‘transform’ Examples: subset(airquality, Temp 80, select = c(Ozone, Temp)) subset(airquality, Day == 1, select = -Temp) subset(airquality, select = Ozone:Wind) with(airquality, subset(Ozone, Temp 80)) ## sometimes requiring a logical 'subset' argument is a nuisance nm - rownames(state.x77) start_with_M - nm %in% grep(^M, nm, value=TRUE) subset(state.x77, start_with_M, Illiteracy:Murder) Rich Shepard wrote: While reading ?subset I'm referred to learn about dropvalues() as a following operation. Yet, when I issue ?dropvalue I see, No documentation for '?dropvalues' in specified packages and libraries:. How do I identify the library/package that contains a specific function such as, in this case, dropvalues()? Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://r.789695.n4.nabble.com/Identifying-Package-for-Function-tp3835227p3835252.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] Limitations of audio processing in R
Hi, Michael Ulisses:
ULISSES: If you haven't already, I suggest you look at the hexView
package including the R News article cited below and the readRaw
function in particular. I just used readRaw(filename, offset=4,
nbytes=8) to read bytes 5:12 in filename; in this case, filename was
*.wma created by the Windows 7 Sound Recorder.
MICHAEL: Thanks.
Spencer
On 9/21/2011 4:25 PM, Michael Sumner wrote:
On Thu, Sep 22, 2011 at 8:08 AM, Spencer Graves
spencer.gra...@structuremonitoring.com wrote:
A more general question: What tools are available in R for reading parts of
binary files? 'scan' allows you to 'skip' a certain number of records and
read the next 'nlines'. Unfortunately, scan only seems to work for text
files not binary, and I cannot find a comparable function that would work
for binary files. I tried library(sos); (rb- findFn('read binary')).
This produced 299 matches. Something there might solve the problem, but I
haven't taken the time to study it carefully. I hope someone else will
know.
Spencer
?readBin and ?seek
Also see Viewing Binary Files with the hexView Package in RNews
Volume 7/1, April 2007.
http://www.r-project.org/doc/Rnews/Rnews_2007-1.pdf
Cheers, Mike.
On 9/21/2011 2:15 PM, Ken wrote:
Also with Linux you can add more swap memory(which I'm pretty sure R
spills into if it hasn't reached it's internal limits on 32 bit
installations). Windows pagefile is kind of obnoxious.
Ken Hutchison
On Sep 21, 2554 BE, at 5:05 PM, (Ted Harding)ted.hard...@wlandres.net
wrote:
Hi Ulisses!
Yes, get more creative -- or get more memory!
On the creative side, it may be worth thinking about
using an independent (non-R) audio file editor. I'm
writing from the standpoint of a Linux/Unixoid user
here -- I wouldn;t know how to set ebout this in WIndows.
You could use R to create a shell script which would run
the editor in such a way as to extract your 6 random samples,
and save them, where the script would be fed with the
randomly-chosen 5-minute intervals decided by R. This
could be done under the control of R, so you could set
it up for your 1500 or so sets of samples, which (with
the right editing program) could be done quite quickly.
On Linux (also available for Windows) a flexible audio
editor is 'sox' -- see:
http://en.wikipedia.org/wiki/SoX
To take, say, a 5-minute sample starting at 1 hour,
10 min and 35sec into the audio file infile.wav,
and save this as outfile.wav, you can execute
sox infile.wav outfile.wav trim 01:10:35 00:05:00
and such a command could easily be generated by R and
fed to a shell script (or simply executed from R by
using the system() command). My test just now with
a 5-minute long sample from a .wav file was completed
in about 5 seconds, so it is quite efficient.
There is a huge number of options for 'sox', allowing
you to manipulate almost any aspect of the editing.
Hoping this helps,
Ted.
On 21-Sep-11 19:55:22, R. Michael Weylandt wrote:
If you are running Windows it may be as simple as using
memory.limit() to allow R more memory -- if you are on
another OS, it may be possible to get the needed memory
by deleting various things in your workspace and running
gc()
Of course, if your computer's memory is3GB, you are
probably going to have trouble with R's keeping all objects
in memory and will have to get more creative.
Michael
On Wed, Sep 21, 2011 at 3:43 PM, Ulisses.Camargo
moliterno.cama...@gmail.comwrote:
Hello everybody
I am trying to process audio files in R and had some problems
with files size. I´m using R packages 'audio' and 'sound'.
I´m trying a really simple thing and it is working well with
small sized .wav files. When I try to open huge audio files
I received this error message: cannot allocate vector of
size 2.7 Gb. My job is open in R a 3-hour .wav file, make six
5-minute random audio subsamples, and than save these new files.
I have to do the same process +1500 times. My problems is not
in build the function to do the job, but in oppening the 3-hour
files. Does anybody knows how to handle big audio files in R?
Another package that allows me to do this work? I believe
this is a really simple thing, but I really don´t know what
to do to solve that memory problem.
Thank you very much for your answers,
all the best!
Ulisses
E-Mail: (Ted Harding)ted.hard...@wlandres.net
Fax-to-email: +44 (0)870 094 0861
Date: 21-Sep-11 Time: 22:05:55
-- XFMail --
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Re: [R] Identifying Package for Function
On Fri, 23 Sep 2011, Michael Sumner wrote: Do you perhaps mean ?droplevels, as mentioned in See Also of subset help? Yep. Mis-translation between the help page and the working page. Mea culpa! Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bivariate Scatter Plots with Lattice
I don't see the problem. AFAICT, you want plots of quant vs. sampdate by chemicals for each of the 37 streams. Essentially, you seem to want two superimposed time plots in each panel. A time plot is a scatterplot with a time-ordered (usually horizontal) axis. If you use ggplot2 or lattice to generate the conditioning plots, the default is to use common scales for all panels; this makes eyeball comparisons between plots easier. If you want flexible scales, particularly on the time axis, you'll need to adjust the scales. It's a bit easier to do this in ggplot2, but the lattice approach isn't overly difficult if you have some decent documentation (like the Lattice book) at hand. Dennis On Thu, Sep 22, 2011 at 3:50 PM, Rich Shepard rshep...@appl-ecosys.com wrote: On Thu, 22 Sep 2011, David Winsemius wrote: Scatterplots are for two variables with continuous valued data. You are asking about one such variable, apparently within some combination of groups of discrete variables. Look at dotplot or bwplot examples. David, Good catch. Point noted. Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 turn a LaTeX Sweave file (Rnw) into .HTML/.odf/.docx? (under windows)
So, I was playing around a bit on my Mac LyX can do Sweave (see http://wiki.lyx.org/LyX/LyxWithRThroughSweave), and will actually output HTML or ODT. However, on a cursory pass, I couldn't get the graphics to translate, since the Sweave driver translates the graphics as .ps or .pdf files, and I'm not sure the HTML translator looks for them or can accept them. The math actually translates nicely. So there is probably potential here. Abhijit On Sep 22, 2011, at 7:09 PM, Tal Galili wrote: Hello dear R help members, I have found several references on how to do this, my question is if anyone is actually using them - and if there are some strong points on what to use, and how well it is working out. My goal is to be able to easily create docs from R, but to be able to share it with other researchers (who do not use LaTeX) so they could easily copy/paste the tables and edit them for their needs (pdf is not solving this for me). The only reasonable solution I came by so far is to use HTML markup coupled with R2HTML (or odfWeave or R2wd). But nothing that can work with LaTeX-HTML (easily) I have asked a similar question here: http://stackoverflow.com/questions/7512897/how-to-turn-a-latex-sweave-file-rnw-into-html And also noticed it was asked half a year ago here: http://tex.stackexchange.com/questions/4145/workflow-for-converting-latex-into-open-office-ms-word-format The general issue of TeX to HTML was discussed also in these places: http://tex.stackexchange.com/questions/50/how-can-i-convert-math-less-latex-documents-into-microsoft-word And obviously the following page offers other good resources to consider: http://cran.r-project.org/web/views/ReproducibleResearch.html p.s: I search the R-help for this topic, but sweave html didn't seem to yield good results - my apologies if this has been heavily debated before - links would be welcomed as well. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Correlation of variables with repeated measures.
Hello I have a dataframe that looks like this: Date Min Subj VAR1 VAR2 VAR3 1 8/30/2011 5min1 34.41042 126.08490 55.3548387 2 8/30/2011 10min1 34.53030 133.81343 61.600 3 8/30/2011 15min1 34.66297 118.38193 11.800 4 8/30/2011 20min1 34.82770 110.77767 6.600 5 8/30/2011 5min2 36.36994 116.24861 41.2258065 6 8/30/2011 10min2 36.37420 101.16457 13.600 7 8/30/2011 15min2 36.37453 92.26340 0.400 8 8/30/2011 20min2 36.37697 87.73650 0.000 9 8/30/2011 5min3 35.25667 146.90037 10.0645161 10 8/30/2011 10min3 35.36654 139.49364 6.000 11 8/30/2011 15min3 35.33833 135.75633 0.400 12 8/30/2011 20min3 36.01337 127.83797 0.000 13 8/30/2011 5min4 35.26742 84.78603 0.9677419 14 8/30/2011 10min4 35.17913 91.27093 1.800 15 8/30/2011 15min4 35.09825 92.03692 13.400 16 8/30/2011 20min4 35.36823 88.73337 4.800 and so on for more days. I would like to check the correlation and p of variables VAR1 VAR2 VAR3. if I use cor.test(tel$VAR1, tel$VAR2) the observations are considered independent, and Indeed I got df=14 I have seen that I can obtain a correlation for each block using this script: http://stackoverflow.com/questions/2336056/how-to-do-correlation-with-blocks-or-repeated-measures I was wandering what I should do for obtain a correlation that account for all the blocks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Adding weights to optim
I realize this may be more of a math question. I have the following optim:
optim(c(0.0,1.0),logis.op,x=d1_all$SOA,y=as.numeric(md1[,i]))
which uses the following function:
logis.op - function(p,x,y) {
ypred - 1.0 / (1.0 + exp((p[1] - x) / p[2]));
res - sum((y-ypred)^2)
return(res)
}
I would like to add weights to the optim. Do I have to alter the logis.op
function by adding an additional weights parameter? And if so, how would I
change the ypred formula? Would I just substitute x with x*w?
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: cannot allocate vector of size xxx
David
Thanks for the time that you spent in read and understand my mail, as well
as for your response and recomendations. I apologize if my attempt to put
comment in my code, not was enought.
I appreciate a lot your suggestion and I will take care of change the
variable name length for avoid confusion.
Maybe you have reason about the origin the problem, related to a model with
a lot of interaction and few data for this interaction becouse my variables
age and year are integer.
But, I tested this code in another machine with WinVista and previus version
of R, and with a data frame with 40 k register and I did not have any
problem (at that moment I had not the complete data and only had the half of
years - 1997 to 2008 - that I have now - 1984 - 2008).
I started testing simple model, but I am very interested in test this
complex model, that has been giving me problems.
In relation to the model that I have problem. I used the syntax that I was
believed that allowed test all the factors with all the interaction (for
intruction of my teachers is
lm(length~as.factor(age)*as.factor(year)*as.factor(sex)*soi*k ), but now I
believe maybe this is incorrect, maybe the syntax correct is that suggest
for you (lm(length~ (as.factor(age) + as.factor(year) + as.factor(sex) +soi
+ k)^2), I will tray with this and after tell you.
As data my workspace have 2.5 GB of memory.
Regards David
2011/9/22 David Winsemius dwinsem...@comcast.net
On Sep 22, 2011, at 5:00 PM, Mario Montecinos Carvajal wrote:
Michale and Paul
Thanks for your quick response.
Michael, I am running a 32bit version of R
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
Paul, the dimension of the Data Frame with I am workis is
dim(d)
[1] 7017411
And the size of the file that contains the data is 2946 Kb
Not a very big dataset for a workspace that should be 2GB or more.
The script that I use for manage the data is:
#clean the workspace
rm(list = ls(all = TRUE))
I hate it when people put that code in without a warning and preferably
commented out. Some us boobs have been known to paste in code without
mentally single stepping through it.
#Increase the memory size
memory.limit(size=4000)
#Set Directory of WorkSpace where whe have the data
setwd('C:/Users/XXX/XXX/R/**')
#load data
dat - read.table('dat_fin_age.txt')
#delete empty registry
d-na.omit(dat)
remove(dat) # remove dat (intermedia object) for release resource
#Asigned the name to the variables in the data
names(d)-
c('pesq','year','month','sex',**'length','weigth','mature','**
age','soi','temp','k')
Bad idea to use length as a variable name. It is a function name.
#define the ages over the analysis is focuses.
minage-1 # minimum age
maxage-6 # maximum age
At this point you should have offered:
str(d)
# One of the diferent lm I have been tested
You are constructing a 5-way interaction that will have way more
interactions than you will know what to do with. Why not start out with a
simple model and move up from there? If these ages and years are integer
valued then you may not have enough data to support such a model with only
70k records.
What do these models tell you?
l6w.lin - lm(length~as.factor(age) + as.factor(year) + as.factor(sex) +soi
+ k,
Or:
l6w.2way - lm(length~ (as.factor(age) + as.factor(year) + as.factor(sex)
+soi + k)^2 ,
data=d[d$age
%in% minage:maxage,])
A much safer way to handle this would be:
data=subset(d, age = minage age = maxage)
%in% is a set operation and you are passing it a vector of integers rather
than a range.
Today I will prove your recommendation to use the package biglm
Should not be necessary. The problem lies elsewhere.
Thanks to both for your Help
Regards
2011/9/22 Paul Hiemstra paul.hiems...@knmi.nl
On 09/22/2011 04:00 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Are you running a 32bit or 64bit version of R? Type sessionInfo() to
see.
Michael
...in addition, how large is your dataset? Please provide us with a self
contained example which reproduces this problem. You could take a look
at the biglm package.
regards,
Paul
On Sep 21, 2011, at 10:41 PM, Mario Montecinos Carvajal
mariomonteci...@gmail.com wrote:
Hi
I am a new user of the mail list.
Mi problem occurs when I try to test a lineal model (lm), becouse
appear
the
messaje Error: cannot allocate vector of size xxx
The data frame whit I am working, Have
dim(d)
[1] 7017411
and the function i am test is:
lm(length~as.factor(age)*as.**factor(year)*as.factor(sex)***
soi*k,data=d[d$age
%in% minage:maxage,])
I tried with a diferent options for solve this problem, but any one
give
me
results.
I tried with:
Change in Function: memory.limit(size=4000)
Change the setting in Windows using BCDEdit /set
Change in the memory availability for R, change the path of the program
(suggested
Re: [R] How to turn a LaTeX Sweave file (Rnw) into .HTML/.odf/.docx? (under windows)
On 11-09-22 8:38 PM, Abhijit Dasgupta wrote: So, I was playing around a bit on my Mac LyX can do Sweave (see http://wiki.lyx.org/LyX/LyxWithRThroughSweave), and will actually output HTML or ODT. However, on a cursory pass, I couldn't get the graphics to translate, since the Sweave driver translates the graphics as .ps or .pdf files, Just a note: Sweave is more flexible nowadays, thanks to some big improvements by Brian Ripley. It can produce png or jpeg figures if you need those. Can't help much with the original problem. R doesn't use .tex when it needs to produce HTML: it uses .texi (texinfo) or its own .Rd format. The latter is unlikely to suit general purpose documents, it's just for help pages. The former is a bit of a PITA to use. Duncan Murdoch and I'm not sure the HTML translator looks for them or can accept them. The math actually translates nicely. So there is probably potential here. Abhijit On Sep 22, 2011, at 7:09 PM, Tal Galili wrote: Hello dear R help members, I have found several references on how to do this, my question is if anyone is actually using them - and if there are some strong points on what to use, and how well it is working out. My goal is to be able to easily create docs from R, but to be able to share it with other researchers (who do not use LaTeX) so they could easily copy/paste the tables and edit them for their needs (pdf is not solving this for me). The only reasonable solution I came by so far is to use HTML markup coupled with R2HTML (or odfWeave or R2wd). But nothing that can work with LaTeX-HTML (easily) I have asked a similar question here: http://stackoverflow.com/questions/7512897/how-to-turn-a-latex-sweave-file-rnw-into-html And also noticed it was asked half a year ago here: http://tex.stackexchange.com/questions/4145/workflow-for-converting-latex-into-open-office-ms-word-format The general issue of TeX to HTML was discussed also in these places: http://tex.stackexchange.com/questions/50/how-can-i-convert-math-less-latex-documents-into-microsoft-word And obviously the following page offers other good resources to consider: http://cran.r-project.org/web/views/ReproducibleResearch.html p.s: I search the R-help for this topic, but sweave html didn't seem to yield good results - my apologies if this has been heavily debated before - links would be welcomed as well. Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: cannot allocate vector of size xxx
Paul
I tested your suggestion of use the BIGLM package. With this package, model
run with out any problem.
regards
2011/9/22 David Winsemius dwinsem...@comcast.net
On Sep 22, 2011, at 5:00 PM, Mario Montecinos Carvajal wrote:
Michale and Paul
Thanks for your quick response.
Michael, I am running a 32bit version of R
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
Paul, the dimension of the Data Frame with I am workis is
dim(d)
[1] 7017411
And the size of the file that contains the data is 2946 Kb
Not a very big dataset for a workspace that should be 2GB or more.
The script that I use for manage the data is:
#clean the workspace
rm(list = ls(all = TRUE))
I hate it when people put that code in without a warning and preferably
commented out. Some us boobs have been known to paste in code without
mentally single stepping through it.
#Increase the memory size
memory.limit(size=4000)
#Set Directory of WorkSpace where whe have the data
setwd('C:/Users/XXX/XXX/R/**')
#load data
dat - read.table('dat_fin_age.txt')
#delete empty registry
d-na.omit(dat)
remove(dat) # remove dat (intermedia object) for release resource
#Asigned the name to the variables in the data
names(d)-
c('pesq','year','month','sex',**'length','weigth','mature','**
age','soi','temp','k')
Bad idea to use length as a variable name. It is a function name.
#define the ages over the analysis is focuses.
minage-1 # minimum age
maxage-6 # maximum age
At this point you should have offered:
str(d)
# One of the diferent lm I have been tested
You are constructing a 5-way interaction that will have way more
interactions than you will know what to do with. Why not start out with a
simple model and move up from there? If these ages and years are integer
valued then you may not have enough data to support such a model with only
70k records.
What do these models tell you?
l6w.lin - lm(length~as.factor(age) + as.factor(year) + as.factor(sex) +soi
+ k,
Or:
l6w.2way - lm(length~ (as.factor(age) + as.factor(year) + as.factor(sex)
+soi + k)^2 ,
data=d[d$age
%in% minage:maxage,])
A much safer way to handle this would be:
data=subset(d, age = minage age = maxage)
%in% is a set operation and you are passing it a vector of integers rather
than a range.
Today I will prove your recommendation to use the package biglm
Should not be necessary. The problem lies elsewhere.
Thanks to both for your Help
Regards
2011/9/22 Paul Hiemstra paul.hiems...@knmi.nl
On 09/22/2011 04:00 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Are you running a 32bit or 64bit version of R? Type sessionInfo() to
see.
Michael
...in addition, how large is your dataset? Please provide us with a self
contained example which reproduces this problem. You could take a look
at the biglm package.
regards,
Paul
On Sep 21, 2011, at 10:41 PM, Mario Montecinos Carvajal
mariomonteci...@gmail.com wrote:
Hi
I am a new user of the mail list.
Mi problem occurs when I try to test a lineal model (lm), becouse
appear
the
messaje Error: cannot allocate vector of size xxx
The data frame whit I am working, Have
dim(d)
[1] 7017411
and the function i am test is:
lm(length~as.factor(age)*as.**factor(year)*as.factor(sex)***
soi*k,data=d[d$age
%in% minage:maxage,])
I tried with a diferent options for solve this problem, but any one
give
me
results.
I tried with:
Change in Function: memory.limit(size=4000)
Change the setting in Windows using BCDEdit /set
Change in the memory availability for R, change the path of the program
(suggested for other user)
My computer have 4GB RAM, Have 20 GB of Virtual Memory, HDD 300 GB with
200
GB of free space and Windows 7 as OS and my R version is 2.11.1
I need solve this problem, any help or suggestion will be very well
received.
I've been thinking in change the OS, but this is may last option.
Regards
I read
David Winsemius, MD
West Hartford, CT
--
Mario Montecinos C.
Biologo Marino
Dr (c) en Ciencias
Universidad Austral de Chile
Los acentos han sido omitidos voluntariamente para evitar incompatibilidades
Evite enviar cartas impresas, cuidemos el medio ambiente y evitemos el
uso innecesario de papel.
[[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] How to turn a LaTeX Sweave file (Rnw) into .HTML/.odf/.docx? (under windows)
I have found several references on how to do this, my question is if anyone is actually using them - and if there are some strong points on what to use, and how well it is working out. My goal is to be able to easily create docs from R, but to be able to share it with other researchers (who do not use LaTeX) so they could easily copy/paste the tables and edit them for their needs (pdf is not solving this for me). The only reasonable solution I came by so far is to use HTML markup coupled with R2HTML (or odfWeave or R2wd). But nothing that can work with LaTeX-HTML (easily) [...] Hi, Tal. This isn't an answer to the question you asked, but the Emacs Org-Mode package is pretty good at exporting to various file formats (and the source code, including tables, is purely text anyway). Have a look at: http://orgmode.org/ and, in particular: http://orgmode.org/guide/Exporting.html#Exporting Even if this does, in principle, solve your problem, it may be too big a gulp to swallow if you're not already using Emacs. -- Mike [[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] Plot map by region using kasc and adehabitat
Hi there, I thought it would be useful to answer my own question for anybody else searching Google. An easy way to split a national map into smaller maps at lower levels of aggregation is to use the function mask() in the package raster Alex On 21 September 2011 19:20, Paul Hiemstra paul.hiems...@knmi.nl wrote: On 09/21/2011 01:39 AM, Alex Olssen wrote: Dear R-help, I have a raster map which has a measure of profitability of land by parcel over several regions of geographic aggregation (think of counties). This data is stored in an ASCII file. If I type plot(profit) I get a raster map of profit per parcel for all regions. I want to plot separate maps for each county. I used kasc to combine the profit map with a county map from a separate ASCII file. data.kasc - as.kasc(list(profit, county)) Can anyone help me plot profit maps for each county separately? Kind regards, Alex __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ...to make us more willing to answer the question: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and *provide commented, minimal, self-contained, reproducible code.* Paul -- Paul Hiemstra, Ph.D. Global Climate Division Royal Netherlands Meteorological Institute (KNMI) Wilhelminalaan 10 | 3732 GK | De Bilt | Kamer B 3.39 P.O. Box 201 | 3730 AE | De Bilt tel: +31 30 2206 494 http://intamap.geo.uu.nl/~paul http://nl.linkedin.com/pub/paul-hiemstra/20/30b/770 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] p values in coxph()
Hi, I'm interested in building a Cox PH model for survival modeling, using 2 covariates (x1 and x2). x1 represents a 'baseline' covariate, whereas x2 represents a 'new' covariate, and my goal is to figure out where x2 adds significant predictive information over x1. Ideally, I could get a p-value for doing this. Originally, I thought of doing some kind of likelihood ratio test (LRT), where i measure the (partial) likelihood of the model with just x1, then with x1 and x2, then it becomes a LRT with 1 degree of freedom. But when i use the summary() function for coxph(), i get the following output (shown at the bottom). I have two questions: 1) What exactly are the p-values in the Pr(|z|) representing? I understand that the coefficients have standard errors, etc., but i'm not sure how the p-value there is calculated. 2) At the bottom, where it shows the results of an LRT with 2df, i don't quite understand what model the ratio is being tested against. If the current model has two variables (x1 and x2), and those are the extra degrees of freedom, then the baseline should then have 0 variables, but that's not really a Cox model? thanks for any help. Brian summary(coxph(Surv(myTime,Event)~x1+x2)) Call: coxph(formula = Surv(myTime, Event) ~ x1 + x2) n= 211 coef exp(coef) se(coef) z Pr(|z|) x1 0.03594 1.03660 0.17738 0.203 0.83942 x2 0.53829 1.71308 0.17775 3.028 0.00246 ** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 exp(coef) exp(-coef) lower .95 upper .95 x1 1.037 0.96470.7322 1.468 x2 1.713 0.58371.2091 2.427 Rsquare= 0.111 (max possible= 0.975 ) Likelihood ratio test= 21.95 on 2 df, p=1.714e-05 Wald test= 20.29 on 2 df, p=3.924e-05 Score (logrank) test = 22.46 on 2 df, p=1.328e-05 [[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.
