Re: [R] Export to .txt
Oh, Im sorry. My file isnt a function but script 'script.R' which looks
something like that:
cat('Instruction no 1', '\n')
browser() # place for fulfilling it
cat('Instruction no 2', '\n')
browser() # place for fulfilling it
etc.
I am running it by
sink(file='output.txt')
source('script.R')
sink(NULL)
but it doesnt work as I would like. I cant see the output also via saving
workaspace into .Rhistory file. The goal I would like to achieve is the same
file as via File - Save to file... option - but I work in command line.
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[R] where to get chr_rpts file for dbSNP human 36.3 assembly
Dear list, In terms of dbSNP database in NCBI, I can get the chr_rpts files for the most recent 37.3 assembly from the following FTP site, ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/ My question is how/where I can get these chr_rpts files based on the 36.3 assembly Thanks, Shirley __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Removing or ignoring package version for generic function in locked environment
Interesting. I have a few (untested) thoughts. Before I get into those though, this seem to me like a case where contacting either the maintainer of epicalc or of the functions not under your control that give warnings. I think either would be appropriate because if the default method works correctly with no error, I really do not think aggregate.numeric should give a warning. The onus seems somewhat on the writer of methods for classes as common as numeric to write something that works. That said, without any idea what it is being used on there are endless possibilities for why a warning is being generated. But supposing neither of those are options, here are some ideas. 1) if you happen to be using this in your own package, try just importing aggregate numeric, rather than fully loading the epicalc package. 2) create a method that mimics aggregate but is for numeric, and make sure it is in an environment between the out of control functions and epicalc so it is called rather than epicalcs version. 3) use epicalc and then unload it rather than just removing that function (may not fly) 4) copy the epicalc aggregate numeric and just use that code and never load the package 5) you may be able to unlock() the name space so you can remove the methods (I think the function is unlock but there may be caps somewhere in there) 6) if the offending functions have a class that is not numeric but inherits from numeric, you could write a method for their particular class that would then supersede the inherited numeric method All of these are highly unsatisfactory in one way another. I am not in a position to test anything out at the moment (iPhone, well that's not true, I could ssh to my cluster, start r there and try via the terminal but that is truly painful on a phones keyboard) Good luck, Josh On Nov 1, 2011, at 17:31, Oliver Mannion (COMPASS) o.mann...@auckland.ac.nz wrote: Hi, I use the epicalc package which provides the function aggregate.numeric. Unfortunately aggregate.numeric produces warnings when aggregate is used by functions not under my control on a numeric value. If I don't load epicalc, aggregate.default is used instead by these functions and does not produce any warning. However I need epicalc. So to get around this, what I would do is firstly remove aggregate.numeric: rm(aggregate.numeric, pos=which(search() == package:epicalc)) This worked fine in R 2.13.1. However in R 2.14.0 I am getting the following: Error in rm(aggregate.numeric, pos = which(search() == package:epicalc)) : cannot remove bindings from a locked environment Is there some way I can remove aggregate.numeric, or otherwise prevent it from being used? Thanks in advance, Oliver __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 'tcltk' does not have a name space
It also have this problem when I install qvalue package ... -- View this message in context: http://r.789695.n4.nabble.com/tcltk-does-not-have-a-name-space-tp3020504p3971898.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] 'tcltk' does not have a name space
Please quote the original message you are replying to and read the posting guide! Please update your version of R to R-2.14.0. Looks like the package assumes a more recent version of R without declaring the dependency. You may want to inform the package maintainer. Uwe Ligges On 02.11.2011 06:43, christear wrote: It also have this problem when I install qvalue package ... -- View this message in context: http://r.789695.n4.nabble.com/tcltk-does-not-have-a-name-space-tp3020504p3971898.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I really need help to merge two data frames
On 02.11.2011 01:32, Tony wrote: Hello, I need help getting two data sets to merge. The structure of my two data sets are: str(bcusip) 'data.frame': 1391 obs. of 3 variables: $ bond_id : Factor w/ 1391 levels AAGH,AAGI,..: 1 2 3 4 5 6 $ Freq: num 41361 4126 5206 10125 45536 ... $ CUSIP_ID: Factor w/ 1391 levels 00184AAC9,00184AAF2,..: str(bdescr) 'data.frame': 3674 obs. of 7 variables: $ bond_id: Factor w/ 3674 levels AAGH ,AAGI ,..: $ Issuer.Name: Factor w/ 635 levels 3M CO ,ABBOTT LABORAT $ Coupon : num 6 6.75 6.5 5.95 5.55 5.9 5.72 5.87 6 6.75 ... $ Maturity : Factor w/ 1076 levels 1/1/2015,1/1/2016,..: $ Callable : Factor w/ 2 levels No ,Yes : 2 2 2 2 2 $ Moody.s: Factor w/ 20 levels A1 ,A2 ,A3 ,..: 16 16 16 $ S.P: Factor w/ 22 levels - ,A- ,A ,..: 15 15 15 15 1 Look at the levels above, in bcusip ist is AAGH, on bdescr it is AAGH (note the blanks! etc. Uwe Ligges I am trying to attach the descriptive variables in the first data set to the sample variables in the second data set. My code worked in an example that I re-created from a tutorial, but it will not work on my data Here is my data code: ### bond description bdescr-read.table(file=index3705.R.csv,header=TRUE,sep=,) bdescr- bdescr[!duplicated(bdescr$bond_id),] ### bond cusip number bcusip = read.table(file=selected1526.R.csv,header=TRUE,sep=,) bcusip- bcusip[!duplicated(bcusip$bond_id),] bcusip$Freq = as.numeric(bcusip$Freq) And here is my attempt to merge: (I tried a few) merge (bdescr,bcusip,by=bond_id,all=TRUE) merge (bdescr,bcusip,by=bond_id) merge (bdescr,bcusip) superfile- merge(bdescr,bcusip,by=bond_id,all=TRUE) Thank you for any help. I am new and going crazy at the moment. Sincerely, Tony __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RC33 8th Int Conf on Social Science Methodology -- The R System ...
I wish to draw attention to an R-related session that is planned for the RC33 Eighth International Conference on Social Science Methodology, to be held over July 9 - July 13 2012, at the University of Sydney. The focus of the conference is on innovations and current best practice in all aspects of social science research methodology. It provides an opportunity to reflect on contemporary methods, as applied in a range of settings and disciplinary contexts, to hear about emerging methods, tools, techniques and technologies, and to discover what resources are available to social science researchers and users of research. The title for the planned session is: The R System as a Platform for Analysis and Development of Analysis Methodology http://conference.acspri.org.au/index.php/rc33/2012/schedConf/trackPolicies John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. http://www.maths.anu.edu.au/~johnm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Size of windows graphics device
R for Windows 2.14.0 Is there a function reporting the size of the current windows device after it has been resized manually? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 interpret Spearman Correlation
Hi David, This is not private tutoring, just someone trying to help, and I'm sorry for my distraction. On Tue, Nov 1, 2011 at 10:34 PM, David Winsemius dwinsem...@comcast.netwrote: Shahab; You would be well advised not to seek private tutoring from someone on the Internet who tells you that a p-value of 0.008736 is not significant. On Nov 1, 2011, at 8:09 PM, Raphael Saldanha saldanha.plan...@gmail.com wrote: Hi Shahab, This test shows that there is some positive statistical correlation, BUT the p-value of the test - this is, the level of significance - shows that the correlation is not statistically significant at 95% confidence level. So, the correlation may be equal to zero. To understand this concepts in a good way, you need to be secure about variance and hypothesis test. I can help you more if you need. Send me a direct mail (this list is for doubts about R, not conceptual statistics). I will be happy to help you with Statistics. My e-mail: saldanha.plan...@gmail.com On Tue, Nov 1, 2011 at 8:58 PM, shahab shahab.mok...@gmail.com wrote: Hi, I am not really familiar with Correlation foundations, although I read a lot. So maybe if someone kindly help me to interpret the following results. I had the following R commands: correlation -cor( vector_CitationProximity , vector_Impact, method = spearman, use=na.or.complete) cor_test-cor.test(vector_CitationProximity, vector_Impact, method=spearman) and the results are: correlation Correlation = 0.04715686 cor_test Spearman's rank correlation rho data: vector_CitationProximity and vector_Impact S = 5581032104, p-value = 0.008736 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.04582115 So apparently, there is positive correlation between two given variables since Correlation = 0.04715686 0 However I couldn't interpret the significance ?' what does rho say? Is there any simple sample that I can read and try to understand? I am do confused in understanding how significance can be interpreted. Thanks, /Shahab __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Atenciosamente, Raphael Saldanha saldanha.plan...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Atenciosamente, Raphael Saldanha saldanha.plan...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] triangles point left, filled?
On 11/01/2011 08:05 PM, Martin Ivanov wrote: Dear R users, I want to plot not only triangles point up and triangles point down, which is easy using the pch argument to points. I want to plot left and right pointing triangles as well. They must be fillable with colour. I browsed a little in the documentation, tried rotating the up and down pointing triangles, but of no avail. Any suggestions will be appreciated. Hi Martin, Have a look at the my.symbols function in the TeachingDemos package. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] why the a[-indx] does not work?
-Original Message-
From:Alaios
Sent: 30 October 2011 21:09
To: William Dunlap; andrija djurovic
Cc: R-help@r-project.org
Subject: Re: [R] why the a[-indx] does not work?
What is the difference between though
!numericVector==0 and
-numericVector==0
Er... you need to be (a lot) more careful with operator precendence. See
?Syntax for operator precedence.
-numericVector==0
will usually* give the same answer as
numericVector==0
because unary minus has higher precedence than ==, so this is read implicitly
as (-numericvector)==0. -1 and 1 are still both nozero, while -0 and 0 are both
still zero. ( *'usually' because you may be comparing a double precision
nearly-zero with another double precision nearly-zero, and that is _always_
asking for trouble.)
!numericVector==0
behaves quite differently because unary negation (!, or NOT) has _lower_
precedence than ==, so this one is read as
!(numericVector==0)
Operatopr preference rules for programmers:
Rule 1: If in doubt about operator precedence, use parentheses
Rule 2: Always have doubts about operator precedence unless you have looked it
up for _that_ version of _that_ language _that day_.
Rule 3: Check the operator precedence of parentheses.
S Ellison
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Re: [R] Size of windows graphics device
par(fin) : The figure region dimensions, |(width,height)|, in inches. par(din) : the device dimensions, |(width,height)|, in inches. On 2011-11-2 18:50, Erich Neuwirth wrote: R for Windows 2.14.0 Is there a function reporting the size of the current windows device after it has been resized manually? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Size of windows graphics device
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Dejian Zhao
Sent: 02 November 2011 12:01
To: r-help@r-project.org
Subject: Re: [R] Size of windows graphics device
par(fin) : The figure region dimensions, |(width,height)|,
in inches.
par(din) : the device dimensions, |(width,height)|, in inches.
... except between windows() and plot.new(). But reports accurately after
plot.new(), plot() and the like.
S Ellison
***
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to interpret Spearman Correlation
What David was getting at is that you interpreted the P-value as one minus the P-value, not a safe practice. There is also some question about whether it would have been better to recommend a good book or course. Frank Raphael Saldanha wrote: Hi David, This is not private tutoring, just someone trying to help, and I'm sorry for my distraction. On Tue, Nov 1, 2011 at 10:34 PM, David Winsemius lt;dwinsemius@gt;wrote: Shahab; You would be well advised not to seek private tutoring from someone on the Internet who tells you that a p-value of 0.008736 is not significant. On Nov 1, 2011, at 8:09 PM, Raphael Saldanha lt;saldanha.plangeo@gt; wrote: Hi Shahab, This test shows that there is some positive statistical correlation, BUT the p-value of the test - this is, the level of significance - shows that the correlation is not statistically significant at 95% confidence level. So, the correlation may be equal to zero. To understand this concepts in a good way, you need to be secure about variance and hypothesis test. I can help you more if you need. Send me a direct mail (this list is for doubts about R, not conceptual statistics). I will be happy to help you with Statistics. My e-mail: saldanha.plangeo@ On Tue, Nov 1, 2011 at 8:58 PM, shahab lt;shahab.mokari@gt; wrote: Hi, I am not really familiar with Correlation foundations, although I read a lot. So maybe if someone kindly help me to interpret the following results. I had the following R commands: correlation -cor( vector_CitationProximity , vector_Impact, method = spearman, use=na.or.complete) cor_test-cor.test(vector_CitationProximity, vector_Impact, method=spearman) and the results are: correlation Correlation = 0.04715686 cor_test Spearman's rank correlation rho data: vector_CitationProximity and vector_Impact S = 5581032104, p-value = 0.008736 alternative hypothesis: true rho is not equal to 0 sample estimates: rho 0.04582115 So apparently, there is positive correlation between two given variables since Correlation = 0.04715686 0 However I couldn't interpret the significance ?' what does rho say? Is there any simple sample that I can read and try to understand? I am do confused in understanding how significance can be interpreted. Thanks, /Shahab __ R-help@ mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Atenciosamente, Raphael Saldanha saldanha.plangeo@ [[alternative HTML version deleted]] __ R-help@ mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Atenciosamente, Raphael Saldanha saldanha.plangeo@ [[alternative HTML version deleted]] __ R-help@ mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/How-to-interpret-Spearman-Correlation-tp3965809p3972797.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] Generate a sequence of vectors of different length
Hi everyone
After the following setup
sector=2 # Define Number of Sectors
sectors=LETTERS[seq( from = 1, to = sector )] # Name sectors
No_ent=round(3/runif(sector)) # Number of entities per sector
#Tot_No_ent=sum(No_ent)
Goal is to get a List like
(A1, A2, A3, B1, B2, B3, B4) where A is denoting an industrial sector and
then a numbered sequence of companies within the sector.
The step I am missing is how to generate a sequence of vectors (one for each
sector) with individual length being determined by No_ent.
The goal is to generate a set of entities from different sectors. One simple
way out of it would be to set the number of entities equal per sector and
have a matrix, but I am quite sure it should also be possible for having a
different number of entities in each sector.
Once this is done, I can bind them together as vector with
as.vector(rbind(?)) (both as an (A,A,A,B,B,B,B) and (1,2,3,1,2,3,4) and
then concatenate)
Thanks, Christian
Trials included the following bits
A=for (i in 1:sector){
rep(i,No_ent[i])
}
paste(LETTERS[i], seq(from =1, to =No_ent[i]), sep = )
but I don't get the correct object definition right.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Generate a sequence of vectors of different length
One approach is:
sectors - 2
namSec - LETTERS[seq_len(sectors)]
nSec - round(3 / runif(sectors))
mapply(paste, namSec, sapply(nSec, seq_len),
MoreArgs = list(sep = ))
I hope it helps.
Best,
Dimitris
On 11/2/2011 2:56 PM, Christian Langkamp wrote:
Hi everyone
After the following setup
sector=2 # Define Number of Sectors
sectors=LETTERS[seq( from = 1, to = sector )] # Name sectors
No_ent=round(3/runif(sector)) # Number of entities per sector
#Tot_No_ent=sum(No_ent)
Goal is to get a List like
(A1, A2, A3, B1, B2, B3, B4) where A is denoting an industrial sector and
then a numbered sequence of companies within the sector.
The step I am missing is how to generate a sequence of vectors (one for each
sector) with individual length being determined by No_ent.
The goal is to generate a set of entities from different sectors. One simple
way out of it would be to set the number of entities equal per sector and
have a matrix, but I am quite sure it should also be possible for having a
different number of entities in each sector.
Once this is done, I can bind them together as vector with
as.vector(rbind(?)) (both as an (A,A,A,B,B,B,B) and (1,2,3,1,2,3,4) and
then concatenate)
Thanks, Christian
Trials included the following bits
A=for (i in 1:sector){
rep(i,No_ent[i])
}
paste(LETTERS[i], seq(from =1, to =No_ent[i]), sep = )
but I don't get the correct object definition right.
[[alternative HTML version deleted]]
__
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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/
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Re: [R] Imputing Missing Data: A Good Starting Point?
You might look at Allison's short book for a quick introduction to the issues: Paul D. Allison. 2002. Missing Data. Sage Quantitative Applications in the Social Sciences No. 136. Online there is http://www.multiple-imputation.com/ which provides a bibliography (with links to articles that are available online). Chapter 25 on Missing Data Imputation (Andrew Gelman and Jennifer Hill. 2006. Data Analysis Using Regression and Multilevel/Hierarchical Models. Cambridge University Press) which is available at http://lane.compbio.cmu.edu/courses/gelmanmissing.pdf provides examples of several approaches and provides R code for them. -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ken Sent: Tuesday, November 01, 2011 4:48 PM To: Sascha Vieweg Cc: r-help@r-project.org Subject: Re: [R] Imputing Missing Data: A Good Starting Point? Hope this helps: http://rss.acs.unt.edu/Rdoc/library/randomForest/html/rfImpute.html Ken Hutchison On Nov 1, 2554 BE, at 5:29 PM, Sascha Vieweg saschav...@gmail.com wrote: Hello I am working on my first attempt to impute missing data of a data set with systematically incomplete answers (school performance tests). I was googling around for some information and found Amelia (Honaker et al., 2010) and the mi package (Yu-Sung et al., n.d.). However, since I am new to this field, I was wondering whether some experts could give a good recommendation of a starting point for me, that is a point that combines theory as well as practical examples. Of course, My primary interest is to complete the task in time (1 week), however, I want to acquire skills for a program that provides some future, and of course I want some background on what I am doing (and what not). Could you help with some hints, experiences, and recommendations? Thank you. Regards *S* -- Sascha Vieweg, saschav...@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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Export to .txt
So playing around with it quickly, it seems that print() works with
sink but cat() doesn't unless you put the sink call in the script at
which point it does as you would expect.
Does that help?
Michael
On Wed, Nov 2, 2011 at 2:14 AM, stat.kk stat...@gmail.com wrote:
Oh, Im sorry. My file isnt a function but script 'script.R' which looks
something like that:
cat('Instruction no 1', '\n')
browser() # place for fulfilling it
cat('Instruction no 2', '\n')
browser() # place for fulfilling it
etc.
I am running it by
sink(file='output.txt')
source('script.R')
sink(NULL)
but it doesnt work as I would like. I cant see the output also via saving
workaspace into .Rhistory file. The goal I would like to achieve is the same
file as via File - Save to file... option - but I work in command line.
--
View this message in context:
http://r.789695.n4.nabble.com/Export-to-txt-tp3965699p3971924.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Proper Syntax for Logical Subset in Subset()
I have measured values for 47 chemicals in a stream. After processing
the original data frame through reshape2, the recast data frame has this
structure:
'data.frame': 256 obs. of 47 variables:
$ site : Factor w/ 143 levels BC-0.5,BC-1,..: 1 1 1 2 2 2 2 2 2 2
...
$ sampdate : Date, format: 1996-04-19 1996-05-21 ...
$ Acid : num NA NA NA NA NA NA NA NA NA NA ...
$ Ag : num NA NA NA NA NA NA NA NA NA NA ...
$ Al : num 0.07 NA NA NA NA NA NA NA NA NA ...
$ Alk-HO : num NA NA NA NA NA NA NA NA NA NA ...
$ Alk-Tot : num 162 152 212 NA NA NA NA NA NA NA ...
$ As : num 0.01 NA NA 0 0 0 0 0.01 0 0.01 ...
$ Ba : num 0.18 NA NA NA NA NA NA NA NA NA ...
$ Be : num NA NA NA NA NA NA NA NA NA NA ...
$ Bo : num NA NA NA NA NA NA NA NA NA NA ...
$ CO3 : num NA NA NA NA NA NA NA NA NA NA ...
$ Ca : num 76.6 NA NA NA NA ...
$ Cd : num NA NA NA NA NA NA NA NA NA NA ...
$ Cl : num 12 NA NA NA NA NA NA NA NA NA ...
$ Cn : num NA NA NA NA NA NA NA NA NA NA ...
$ Co : num NA NA NA NA NA NA NA NA NA NA ...
$ Cond : num 712 403 731 NA NA NA NA NA NA NA ...
$ Cr : num NA NA NA NA NA NA NA NA NA NA ...
$ DO : num NA NA NA NA NA NA NA NA NA NA ...
$ F: num NA NA NA NA NA NA NA NA NA NA ...
$ Fe : num 0.06 NA NA NA NA NA NA NA NA NA ...
$ Flow : num NA NA NA NA NA NA NA NA NA NA ...
$ HCO3 : num 162 152 212 NA NA NA NA NA NA NA ...
$ Hg : num 0 NA NA NA NA NA NA NA NA NA ...
$ K: num 1.7 NA NA NA NA NA NA NA NA NA ...
$ Mg : num 43.2 NA NA NA NA ...
$ Mn : num NA NA NA NA NA NA NA NA NA NA ...
$ NO2-N: num NA NA NA NA NA NA NA NA NA NA ...
$ NO3-N: num NA 0.47 0.09 NA NA NA NA NA NA NA ...
$ NO3-NO2-N: num 1.97 NA NA NA NA NA NA NA NA NA ...
$ Na : num NA NA NA NA NA NA NA NA NA NA ...
$ Ni : num NA NA NA NA NA NA NA NA NA NA ...
$ OH : num NA NA NA NA NA NA NA NA NA NA ...
$ P: num 0.03 NA NA NA NA NA NA NA NA NA ...
$ Pb : num NA NA NA NA NA NA NA NA NA NA ...
$ SO4 : num 175 57 194 NA NA NA NA NA NA NA ...
$ Sb : num 0 NA NA NA NA NA NA NA NA NA ...
$ Se : num 0.01 NA NA NA NA NA NA NA NA NA ...
$ Si : num NA NA NA NA NA NA NA NA NA NA ...
$ TDS : num 460 212 530 NA NA NA NA NA NA NA ...
$ TSS : num NA 26 NA NA NA NA NA NA NA NA ...
$ Temp : num NA NA NA NA NA NA NA NA NA NA ...
$ Tl : num NA NA NA NA NA NA NA NA NA NA ...
$ Turb : num 2.2 NA NA NA NA NA NA NA NA NA ...
$ Zn : num 0.02 NA NA NA NA NA NA NA NA NA ...
$ pH : num 8.12 8.19 8.46 NA NA NA NA NA NA NA ...
I want a subset of this with only 7 chemicals: Ca, Cl, Cond, Mg, Na, SO4,
and TDS. The subset help page tells me that I can use a logical subset to
extract these 7 rows while keeping all columns, but I do not know how to
write that logical subset. I tried emulating the example on the help page of
avoiding the subset but R didn't like the '%in%' as I wrote it; putting the
desired row names in a subset vector fails:
burns.tds - subset(burns.cast, subset(c('Ca', 'Cl', 'Cond', 'Mg', 'Na',
'SO4', 'TDS')))
Error in subset.default(c(Ca, Cl, Cond, Mg, Na, SO4, TDS)) :
argument subset is missing, with no default
What is the proper syntax to extract only these rows into a new data
frame? And, is the recast data frame the appropriate format as the source?
Rich
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Re: [R] Proper Syntax for Logical Subset in Subset()
On Wed, 2 Nov 2011, Rich Shepard wrote: I want a subset of this with only 7 chemicals: Ca, Cl, Cond, Mg, Na, SO4, and TDS. I should have also written that what I ultimately want is to create a box-and-whisker plot for these 7 chemicals in a single panel. If that can be done directly from the source data frame without creating another subset, I want to learn the syntax for that. 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] Proper Syntax for Logical Subset in Subset()
I have measured values for 47 chemicals in a stream. After processing
the original data frame through reshape2, the recast data frame has this
structure:
'data.frame': 256 obs. of 47 variables:
$ site : Factor w/ 143 levels BC-0.5,BC-1,..: 1 1 1 2 2 2 2 2
2 2...
$ sampdate : Date, format: 1996-04-19 1996-05-21 ...
$ Acid : num NA NA NA NA NA NA NA NA NA NA ...
...
I want a subset of this with only 7 chemicals: Ca, Cl, Cond, Mg, Na,
SO4,
and TDS. The subset help page tells me that I can use a logical subset
to
extract these 7 rows while keeping all columns, but I do not know how to
write that logical subset.
Wow, I don't see how you wound up with the code you tried based on the
instructions. I guess for some of us the best instruction is a bloody
nose, myself often included.
It sounds like you want to get rid of some columns in the reshaped
dataframe, not rows.
new - old[c('site', 'Ca', 'Cl', 'Cond', 'Mg', 'Na', 'SO4', 'TDS')]
will work, as will the following if you insist on using the subset
function.
new - subset(old, c(site, Ca, Cl, Cond, Mg, Na, SO4, TDS))
If you actually want to get rid of rows that aren't the minerals of
interest, then work with your unreshaped dataframe:
new - subset(reallyOld, parameter in c('Ca', 'Cl', 'Cond', 'Mg', 'Na',
'SO4', 'TDS'))
--
Curt Seeliger, Data Ranger
Raytheon Information Services - Contractor to ORD
seeliger.c...@epa.gov
541/754-4638
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Re: [R] Proper Syntax for Logical Subset in Subset()
To make such a plot, I would have thought your want your data structure to be: yourdat: Column A: Date Column B; Chemical Column C: Result After subsetting this to the chemicals you want or doing the subsetting in your plot command, something like (base R) boxplot(Result ~ Chemical, subset=yourdat$Chemical %in% c(Ca,Cl, Cond,Mg,Na,SO2,TDS)) You probably can get what you want one way or the other with your current data structure -- though you may have to use ggplot or trellis -- but it does appear to be inconvenient. Whether I'm correct or not in my understanding of your situation, an important message is: you should choose your data structure to facilitate the analysis that you have in mind. IMHO, this is one of R's great strengths: it provides rich facilities for manipulating data tightly integrated with plotting and analytical capabilities. Cheers, Bert On Wed, Nov 2, 2011 at 9:46 AM, Rich Shepard rshep...@appl-ecosys.comwrote: On Wed, 2 Nov 2011, Rich Shepard wrote: I want a subset of this with only 7 chemicals: Ca, Cl, Cond, Mg, Na, SO4, and TDS. I should have also written that what I ultimately want is to create a box-and-whisker plot for these 7 chemicals in a single panel. If that can be done directly from the source data frame without creating another subset, I want to learn the syntax for that. Rich __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Proper Syntax for Logical Subset in Subset()
Of course I left out the data argument: boxplot(Result ~ Chemical, data= yourdat,subset=yourdat$Chemical %in% c(Ca,Cl, Cond,Mg,Na,SO2,TDS)) -- Bert On Wed, Nov 2, 2011 at 10:08 AM, Bert Gunter bgun...@gene.com wrote: To make such a plot, I would have thought your want your data structure to be: yourdat: Column A: Date Column B; Chemical Column C: Result After subsetting this to the chemicals you want or doing the subsetting in your plot command, something like (base R) boxplot(Result ~ Chemical, subset=yourdat$Chemical %in% c(Ca,Cl, Cond,Mg,Na,SO2,TDS)) You probably can get what you want one way or the other with your current data structure -- though you may have to use ggplot or trellis -- but it does appear to be inconvenient. Whether I'm correct or not in my understanding of your situation, an important message is: you should choose your data structure to facilitate the analysis that you have in mind. IMHO, this is one of R's great strengths: it provides rich facilities for manipulating data tightly integrated with plotting and analytical capabilities. Cheers, Bert On Wed, Nov 2, 2011 at 9:46 AM, Rich Shepard rshep...@appl-ecosys.comwrote: On Wed, 2 Nov 2011, Rich Shepard wrote: I want a subset of this with only 7 chemicals: Ca, Cl, Cond, Mg, Na, SO4, and TDS. I should have also written that what I ultimately want is to create a box-and-whisker plot for these 7 chemicals in a single panel. If that can be done directly from the source data frame without creating another subset, I want to learn the syntax for that. Rich __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to count number of occurrences
Dear R users, I have this data frame, y samp 8 0.03060419X 18 0.06120838Y 10 0.23588374X 3 0.32809965X 1 0.36007100X 7 0.36730571X 20 0.47176748Y 13 0.65619929Y 11 0.72014201Y 17 0.73461142Y 6 0.76221313X 2 0.77005691X 4 0.92477243X 9 0.93837591X 5 0.98883581X 16 1.52442626Y 12 1.54011381Y 14 1.84954487Y 19 1.87675183Y 15 1.97767162Y and I am trying to find the number of X's that occur before ith Y occurs. For example, there is 1 X before the first Y, so I get 1. There are 4 X's before the second Y, so I get 4, there is no X between second and third Y, so I get 0 and so on. Any hint to at least help me to start this will be appreciated. Thanks a lot! [[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] 2nd parameter Power Curves/ANCOVAs
Hi, I am trying to compare the slopes and y-intercepts of the power curves between two plant species to see if they follow similar trends (photosynthesis y-axis, stomatal conductance x-axis). I can fit linear regression lines to the data and run the stats using an ANCOVA, but the specific parameters require I fit a 2 Parameter Power Curve to the data. Is running an ANCOVA with the abline function the best bet here, or does R have a specific function to fit and compare power curves? Here is my code thus far, and I was able to compare the linear regressions lines with this code, but the data requires a power curve fit. Any thoughts? Any help is much appreciated, Steve ###compares slope mod1-aov(photosynthesis~conductance*species,data=data) summary(mod1) ###compares y-intercept mod2-aov(photosynthesis ~ conductance +species,data=data) summary(mod2) anova(mod1,mod2) BA-subset(data,species==B.attenuata) BM-subset(data,species==B.menziesii) reg1-lm(photosynthesis ~ conductance,data=BA) summary(reg1) reg2-lm(photosynthesis ~ conductance,data=BM) summary(reg2) plot(photosynthesis ~ conductance, data=data, type='n') points(BA$conductance,BA$photosynthesis, pch=20) points(BM$conductance,BM$photosynthesis, pch=10) abline(reg1, lty=1) abline(reg2, lty=2) reg.todo-lm(photosynthesis~species/conductance-1, data=data) summary(reg.todo) [[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] does there any function like sumif in excel?
I have a similar problem I have a dataframe : CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 I wouldlike to sum the AreaProtected if it is the same CELLCD in another column : CELLCD AreaProtectedSumAreaProtected 8928 52.39389 94.309 8928 41.91511 8929 21.21975 84,879 8929 63.65925 8930 26.08547 8930 14.04602 I am just started with R and I don't know how I can do that. Do you have any ideas ? -- View this message in context: http://r.789695.n4.nabble.com/does-there-any-function-like-sumif-in-excel-tp858444p3972963.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] mapping bathymetries and species abundances
Dear all,
I am new to R and even newer to mapping with R. I have installed
PBSMapping, maptools and maps, and I am struggling to produce a map of
fish abundance in the Grand Banks. I have tried several approaches to
plot the bathymetry in my study area:
1) download the data from http://topex.ucsd.edu/cgi-bin/get_data.cgi
(42N46N313W307W)
To start with, the map I get is blank between lon -52W -53W.
Besides, it seems that the shallower isobath is 500 m. Or maybe I am
wrong here?
2) import a shapefile with the bathymetry, but I get the following error:
test - read.shapefile(C:/data)
Error in seq.default(1, (num.points * 2), by = 2) :
wrong sign in 'by' argument
3) use a Rdata version of the above mentioned shapefile. This is the map
I like the most, but when I try to plot the study area (which is 200 nm
from the nearest shore), I get the error
map('worldHires',xlim=c(-53,-47),ylim=c(42,46))
Error in map.poly(database, regions, exact, xlim, ylim,
boundary, interior, : nothing to draw: all regions out of bounds
The next problem will be plotting fish abundance. I was thinking of
contours or scaled bubbles, but I am not sure I can do any of those with
PBSMapping. Am I right? Any advice?
Thanks for your help,
Elena
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[R] Creating deciles on data using one variable
I need to deciles data containing more than one variables using any one variable. I am using script below : id -c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20) tot -c(1230, 1230, 2345, 3456, 456, 4356, 123, 124, 987, 785, 5646, 345, 2345, 3456, 456, 4356, 123, 124, 987, 785) data - data.frame ( cbind(id , tot)) data$decile-cut(data$tot,quantile(data$tot,(0:10)/10),include.lowest=TRUE,lable=TRUE) data$decile New variable decile taking values as below where as I need it should take values from 1,2..10, Where I am going wrong? data$decile [1] (987,1.23e+03] (987,1.23e+03] (1.23e+03,2.34e+03] [4] (2.34e+03,3.46e+03] (301,456] (3.46e+03,4.36e+03] [7] [123,124] (124,301] (785,987] [10] (456,785] (4.36e+03,5.65e+03] (301,456] [13] (1.23e+03,2.34e+03] (2.34e+03,3.46e+03] (301,456] [16] (3.46e+03,4.36e+03] [123,124] (124,301] [19] (785,987] (456,785] -Ajit -- View this message in context: http://r.789695.n4.nabble.com/Creating-deciles-on-data-using-one-variable-tp3973086p3973086.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] nproc parameter in efpFunctional
Hello all, could anyone explain the exact meaning of parameter nproc? Why different values of nproc give so different critical values, i.e. meanL2BB$computeCritval(0.05,nproc=3) [1] 0.9984853 meanL2BB$computeCritval(0.05,nproc=1) [1] 0.4594827 The strucchange-package description gives integer specifying for which number of processes Brownian motions should be simulated - do I need nproc-dimensional Brownian bridge? Thank you in advance! Julia -- View this message in context: http://r.789695.n4.nabble.com/nproc-parameter-in-efpFunctional-tp3972419p3972419.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] Sum with condition
I guess my problem is simple for most of you but I am new with R and I need some help, I have a dataframe : CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 I wouldlike to sum the AreaProtected if it is the same CELLCD in another column : CELLCD AreaProtectedSumAreaProtected 8928 52.39389 94.309 8928 41.91511 8929 21.21975 84,879 8929 63.65925 8930 26.08547 8930 14.04602 I am just started with R and I don't know how I can do that. Do you have any ideas ? Thanks a lot for your help, -- View this message in context: http://r.789695.n4.nabble.com/Sum-with-condition-tp3972839p3972839.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] overloading + operator for chars
Hello, I would like to overload the + operator so that it can be used to concatenate two strings, e.g John + Doe = JohnDoe. How can I 'unseal' the + method? setMethod(+, signature(e1=character, e2=character), function(e1, e2) paste(e1, e2, sep=) ) Error in setMethod(+, signature(e1 = character, e2 = character), : the method for function + and signature e1=character, e2=character is sealed and cannot be re-defined Cheers!! Albert-Jan ~~ All right, but apart from the sanitation, the medicine, education, wine, public order, irrigation, roads, a fresh water system, and public health, what have the Romans ever done for us? ~~ [[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] Creating deciles on data using one variable
I need to deciles data containing more than one variables using any one variable. I am using script below : id -c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20) tot -c(1230, 1230, 2345, 3456, 456, 4356, 123, 124, 987, 785, 5646, 345, 2345, 3456, 456, 4356, 123, 124, 987, 785) data - data.frame ( cbind(id , tot)) data$decile-cut(data$tot,quantile(data$tot,(0:10)/10),include.lowest=TRUE,lable=TRUE) data$decile New variable decile taking values as below where as I need it should take values from 1,2..10, Where I am going wrong? - You have a factor with labels, but if you use as.numeric(data$decile) you will get what you were aiming for. -- david -- View this message in context: http://r.789695.n4.nabble.com/Creating-deciles-on-data-using-one-variable-tp3973086p3973412.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Multiple comparison test about whole population, not about mean
Multiple comparison tests are usually used to compare groups based on the confidence region about the mean. Some great packages, like agricolae, proposes grouping information based on statistical tests. I am looking for a way to perform such a test, but based on the confidence region about the whole population. I tried to hack LSD.test and HSD.test functions (agricolae), without much success. (1) Is this valid to use multiple comparisons across population? (2) If it is, anyone knows how I could do that? Kind Regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] difference between foo$a[2] - 1 and foo[2,a] - 1
Hallo Can anyone tell me the difference between foo$a[2] - 1 and foo[2,a] - 1 ? I thought that both expressions are equivalent, but when I run the following example, there is obviously a difference. foo - data.frame(a=NA,b=NA) foo a b 1 NA NA foo$a[1] - 1 foo$b[1] - 2 foo$a[2] - 1 Error in `$-.data.frame`(`*tmp*`, a, value = c(1, 1)) : replacement has 2 rows, data has 1 foo[2,a] - 1 foo a b 1 1 2 2 1 NA Thanks, Rebecca Hiller -- ETH Zürich Rebecca Hiller Institute of Agricultural Sciences LFW A2 Universitätsstrasse 2 8092 Zürich SWITZERLAND rebecca.hil...@ipw.agrl.ethz.ch http://www.gl.ethz.ch/ +41 44 632 31 90 Telefon +41 44 632 11 53 Fax __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sum with condition
Hi, On Wed, Nov 2, 2011 at 8:44 AM, Celine bellard.cel...@gmail.com wrote: CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 You'll need to figure out how you want it to be combined with the original data frame, since there can't be empty cells, but: dput(testdata) structure(list(CELLCD = c(8928L, 8928L, 8929L, 8929L, 8930L, 8930L), AreaProtected = c(52.39389, 41.91511, 21.21975, 63.65925, 26.08547, 14.04602)), .Names = c(CELLCD, AreaProtected), class = data.frame, row.names = c(NA, -6L)) aggregate(testdata$AreaProtected, by=list(CELLCD=testdata$CELLCD), FUN=sum) CELLCDx 1 8928 94.30900 2 8929 84.87900 3 8930 40.13149 -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] array manipulation
Hello,
I'm at the very beginning of the learning process of this language.
Sorry in advance for the (possible but plausible) stupidity of my question.
I would like to find a way to permute the DIMENSIONS of an array.
Something that sounds like the function permute() in matlab.
Given an array C of dimensions c x d x T , for instance, the command
permute(C, [2 1 3])
would provide (in Matlab) an array very similar to C, but this time each
one of the T matrices c x d has changed into its transposed.
Any alternatives to the following (and primitive) 'for' cycle?
*# (previously defined) phi=array with dimensions c(c,d,T)*
*
*
*temp=array(0,dim=c(c,d,T))*
* for(i in 1:T)*
* {*
* temp[,,i]=t(phi[,,i])*
* }*
* phi=temp*
*
*
Thank you very much!
S
--
---
Simone Salvadei
Faculty of Economics
Department of Financial and Economic Studies and Quantitative Methods
University of Rome Tor Vergata
e-mail: simone.salva...@uniroma2.it federico.belo...@uniroma2.it
url: http://www.economia.uniroma2.it/phd/econometricsempiricaleconomics/
http://www.econometrics.it/
---
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Re: [R] how to count number of occurrences
Is the following what you want? It should give the number of Xs immediately preceding each Y. samp - c(X, Y, X, X, X, X, Y, Y, Y, Y, X, X, X, X, X, Y, Y, Y, Y, Y) diff((seq_along(samp) - cumsum(samp==Y))[samp==Y]) [1] 4 0 0 0 5 0 0 0 0 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 Sl K Sent: Wednesday, November 02, 2011 9:55 AM To: r-help@r-project.org Subject: [R] how to count number of occurrences Dear R users, I have this data frame, y samp 8 0.03060419X 18 0.06120838Y 10 0.23588374X 3 0.32809965X 1 0.36007100X 7 0.36730571X 20 0.47176748Y 13 0.65619929Y 11 0.72014201Y 17 0.73461142Y 6 0.76221313X 2 0.77005691X 4 0.92477243X 9 0.93837591X 5 0.98883581X 16 1.52442626Y 12 1.54011381Y 14 1.84954487Y 19 1.87675183Y 15 1.97767162Y and I am trying to find the number of X's that occur before ith Y occurs. For example, there is 1 X before the first Y, so I get 1. There are 4 X's before the second Y, so I get 4, there is no X between second and third Y, so I get 0 and so on. Any hint to at least help me to start this will be appreciated. Thanks a lot! [[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] Time Series w/ daily or stochastic observation prediction
Hi, I've got two different types of behaviors for which I have to predict the future development. One is a set of historical data with daily observations and which are following some kind of a seasonal pattern, the second one a set of historical data (measure points), with two observation occurring each week, consisting of ten unique (within one single observation) values in parallel, and which doesn't appear to follow any seasonal pattern. The former one I've aggregated on a monthly level and calculated a prediction model based on Holt Winters, which appears to be pretty nicely fitting when comparing the predicted history with the actual one, and now I have to accomplish the very same on a daily basis (including February 29th in case of a leap year). The latter one I have not clue at all as how to prepare the data and run it with any potetially qualifying model. Cheers, Martin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 count number of occurrences
On Nov 2, 2011, at 12:54 PM, Sl K wrote: Dear R users, I have this data frame, y samp 8 0.03060419X 18 0.06120838Y 10 0.23588374X 3 0.32809965X 1 0.36007100X 7 0.36730571X 20 0.47176748Y 13 0.65619929Y 11 0.72014201Y 17 0.73461142Y 6 0.76221313X 2 0.77005691X 4 0.92477243X 9 0.93837591X 5 0.98883581X 16 1.52442626Y 12 1.54011381Y 14 1.84954487Y 19 1.87675183Y 15 1.97767162Y dat$nXs - cumsum(dat$samp==X) dat$nYs - cumsum(dat$samp==Y) dat # y samp nXs nYs 8 0.03060419X 1 0 18 0.06120838Y 1 1 10 0.23588374X 2 1 3 0.32809965X 3 1 1 0.36007100X 4 1 7 0.36730571X 5 1 20 0.47176748Y 5 2 13 0.65619929Y 5 3 11 0.72014201Y 5 4 17 0.73461142Y 5 5 6 0.76221313X 6 5 2 0.77005691X 7 5 4 0.92477243X 8 5 9 0.93837591X 9 5 5 0.98883581X 10 5 16 1.52442626Y 10 6 12 1.54011381Y 10 7 14 1.84954487Y 10 8 19 1.87675183Y 10 9 15 1.97767162Y 10 10 I find that there are 5 X's before the second Y. nXbefore_mthY - function(m) dat[which(dat$nYs==m), nXs] nXbefore_mthY(2) [1] 5 and I am trying to find the number of X's that occur before ith Y occurs. For example, there is 1 X before the first Y, so I get 1. There are 4 X's before the second Y, so I get 4, there is no X between second and third Y, so I get 0 and so on. Any hint to at least help me to start this will be appreciated. Thanks a lot! [[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 Heritage Laboratories 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] how to count number of occurrences
Hi, On Wed, Nov 2, 2011 at 12:54 PM, Sl K s.ka...@gmail.com wrote: Dear R users, I have this data frame, y samp 8 0.03060419 X 18 0.06120838 Y 10 0.23588374 X 3 0.32809965 X 1 0.36007100 X 7 0.36730571 X 20 0.47176748 Y 13 0.65619929 Y 11 0.72014201 Y 17 0.73461142 Y 6 0.76221313 X 2 0.77005691 X 4 0.92477243 X 9 0.93837591 X 5 0.98883581 X 16 1.52442626 Y 12 1.54011381 Y 14 1.84954487 Y 19 1.87675183 Y 15 1.97767162 Y and I am trying to find the number of X's that occur before ith Y occurs. For example, there is 1 X before the first Y, so I get 1. There are 4 X's before the second Y, so I get 4, there is no X between second and third Y, so I get 0 and so on. Any hint to at least help me to start this will be appreciated. Thanks a lot! Using dput() to provide reproducible data would be nice, but failing that here's a simple example with sample data: testdata - c(x, y, x, x, x, y, x, x, x, x, x, y, y) rle(testdata) Run Length Encoding lengths: int [1:6] 1 1 3 1 5 2 values : chr [1:6] x y x y x y You can use the values component of the list returned by rle to subset the lengths component of the list to get only the x values if that's what you need to end up with. rle(testdata)$lengths[rle(testdata)$values == x] [1] 1 3 5 -- 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] Proper Syntax for Logical Subset in Subset()
On Wed, 2 Nov 2011, Bert Gunter wrote: To make such a plot, I would have thought your want your data structure to be: Column A: Date Column B; Chemical Column C: Result Thanks, Bert. I have a data frame in that format. After subsetting this to the chemicals you want or doing the subsetting in your plot command, something like (base R) boxplot(Result ~ Chemical, subset=yourdat$Chemical %in% c(Ca,Cl, Cond,Mg,Na,SO2,TDS)) Great! I'll work with this. I tend to use lattice so I can learn its capabilities better. Whether I'm correct or not in my understanding of your situation, an important message is: you should choose your data structure to facilitate the analysis that you have in mind. IMHO, this is one of R's great strengths: it provides rich facilities for manipulating data tightly integrated with plotting and analytical capabilities. I recognize this and continue to learn how best to represent the same data for different analyses and plots. Much appreciated, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nproc parameter in efpFunctional
On Wed, 2 Nov 2011, bonda wrote: Hello all, could anyone explain the exact meaning of parameter nproc? Why different values of nproc give so different critical values, i.e. meanL2BB$computeCritval(0.05,nproc=3) [1] 0.9984853 meanL2BB$computeCritval(0.05,nproc=1) [1] 0.4594827 The strucchange-package description gives integer specifying for which number of processes Brownian motions should be simulated - do I need nproc-dimensional Brownian bridge? Yes, see the 2006 CSDA paper, especially pages 2998/9. Thank you in advance! Julia -- View this message in context: http://r.789695.n4.nabble.com/nproc-parameter-in-efpFunctional-tp3972419p3972419.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple comparison test about whole population, not about mean
1. I found the post incoherent. 2. This appears to have nothing to do with R -- post elsewhere, e.g. http://stats.stackexchange.com/ -- Bert On Wed, Nov 2, 2011 at 10:47 AM, Serge-Étienne Parent separ...@yahoo.comwrote: Multiple comparison tests are usually used to compare groups based on the confidence region about the mean. Some great packages, like agricolae, proposes grouping information based on statistical tests. I am looking for a way to perform such a test, but based on the confidence region about the whole population. I tried to hack LSD.test and HSD.test functions (agricolae), without much success. (1) Is this valid to use multiple comparisons across population? (2) If it is, anyone knows how I could do that? Kind Regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] does there any function like sumif in excel?
On Nov 2, 2011, at 9:06 AM, Celine wrote: I have a similar problem I have a dataframe : CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 I wouldlike to sum the AreaProtected if it is the same CELLCD in another column : CELLCD AreaProtectedSumAreaProtected 8928 52.39389 94.309 8928 41.91511 8929 21.21975 84,879 8929 63.65925 8930 26.08547 8930 14.04602 I am just started with R and I don't know how I can do that. Do you have any ideas ? You could get sums within groups using the ave() function. It would put values on all rows. Was there a reason you only wanted values on the first? Then if you wanted to make the non-first elements NA that could also be done. -- View this message in context: http://r.789695.n4.nabble.com/does-there-any-function-like-sumif-in-excel-tp858444p3972963.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. David Winsemius, MD Heritage Laboratories 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] Sum with condition
On Nov 2, 2011, at 2:11 PM, Sarah Goslee wrote: Hi, On Wed, Nov 2, 2011 at 8:44 AM, Celine bellard.cel...@gmail.com wrote: Celine. Please stop posting duplicates. CELLCD AreaProtected 8928 52.39389 8928 41.91511 8929 21.21975 8929 63.65925 8930 26.08547 8930 14.04602 You'll need to figure out how you want it to be combined with the original data frame, since there can't be empty cells, but: dput(testdata) structure(list(CELLCD = c(8928L, 8928L, 8929L, 8929L, 8930L, 8930L), AreaProtected = c(52.39389, 41.91511, 21.21975, 63.65925, 26.08547, 14.04602)), .Names = c(CELLCD, AreaProtected), class = data.frame, row.names = c(NA, -6L)) aggregate(testdata$AreaProtected, by=list(CELLCD=testdata$CELLCD), FUN=sum) CELLCDx 1 8928 94.30900 2 8929 84.87900 3 8930 40.13149 Or: testdata$SumArea - with(testdata, ave(AreaProtected, CELLCD, FUN=sum)) testdata CELLCD AreaProtected SumArea 1 8928 52.39389 94.30900 2 8928 41.91511 94.30900 3 8929 21.21975 84.87900 4 8929 63.65925 84.87900 5 8930 26.08547 40.13149 6 8930 14.04602 40.13149 -- David Winsemius, MD Heritage Laboratories 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] array manipulation
On Nov 2, 2011, at 12:16 PM, Simone Salvadei wrote:
Hello,
I'm at the very beginning of the learning process of this language.
Sorry in advance for the (possible but plausible) stupidity of my
question.
I would like to find a way to permute the DIMENSIONS of an array.
Something that sounds like the function permute() in matlab.
Given an array C of dimensions c x d x T , for instance, the command
permute(C, [2 1 3])
?aperm
would provide (in Matlab) an array very similar to C, but this time
each
one of the T matrices c x d has changed into its transposed.
Any alternatives to the following (and primitive) 'for' cycle?
*# (previously defined) phi=array with dimensions c(c,d,T)*
*
*
*temp=array(0,dim=c(c,d,T))*
* for(i in 1:T)*
* {*
* temp[,,i]=t(phi[,,i])*
* }*
* phi=temp*
*
*
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Re: [R] Sum with condition
If you used aggregate() on the data frame you would have a new data frame
containing the sum of all AreaProtected for each CELLCD. For your mini-example,
using d as your data frame,
d2-aggregate(d[,2], by=list(CELLCD=d$CELLCD),sum)
d2
# CELLCDx
# 1 8928 94.30900
# 2 8929 84.87900
# 3 8930 40.13149
If you then use merge() you get
merge(d,d2)
# CELLCD AreaProtectedx
#1 8928 52.39389 94.30900
#2 8928 41.91511 94.30900
#3 8929 21.21975 84.87900
#4 8929 63.65925 84.87900
#5 8930 26.08547 40.13149
#6 8930 14.04602 40.13149
Maybe one of those is what you want?
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Celine
Sent: 02 November 2011 12:44
To: r-help@r-project.org
Subject: [R] Sum with condition
I guess my problem is simple for most of you but I am new
with R and I need some help, I have a dataframe :
CELLCD AreaProtected
8928 52.39389
8928 41.91511
8929 21.21975
8929 63.65925
8930 26.08547
8930 14.04602
I wouldlike to sum the AreaProtected if it is the same CELLCD
in another column :
CELLCD AreaProtectedSumAreaProtected
8928 52.39389 94.309
8928 41.91511
8929 21.21975 84,879
8929 63.65925
8930 26.08547
8930 14.04602
I am just started with R and I don't know how I can do that.
Do you have any ideas ?
Thanks a lot for your help,
--
View this message in context:
http://r.789695.n4.nabble.com/Sum-with-condition-tp3972839p397
2839.html
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[R] heteroscedastic bivariate distribution with linear regression - prediction interval
Dear forum, which is the most suitable method to get the prediction interval of a bivariate normal distribution which is consistent with a linear model y = ax + b? I assume it is gls + predict. Am I correct? I'm rather new to R. Is there some reliable sample code for that problem? Thank you best regards -- View this message in context: http://r.789695.n4.nabble.com/heteroscedastic-bivariate-distribution-with-linear-regression-prediction-interval-tp3981793p3981793.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] HOW TO REMOVE MTEXT FROM PLOT, plotting changing populations with titles in loop
is there a way to hide/undraw mtext (or lines etc.) in a loop like
plot(runif(10))
iterCol - rainbowPalette(10)
for(i in 1:10){
mtext(paste(this is iteration , i, sep=))
points(runif(10),col=iterCol[i])
Sys.sleep(1)
## UNDRAW/HIDE the text so that it does not mess up the plot in the next
iteration
}
--
View this message in context:
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Re: [R] HOW TO REMOVE MTEXT FROM PLOT, plotting changing populations with titles in loop
It's not perfect, but you could use:
mtext(paste(this is iteration , i, sep=), col=white)
to overwrite it, or polygon() to draw a white rectangle over the text each time.
Sarah
On Wed, Nov 2, 2011 at 3:15 PM, prinzOfNorway torgrim...@gmail.com wrote:
is there a way to hide/undraw mtext (or lines etc.) in a loop like
plot(runif(10))
iterCol - rainbowPalette(10)
for(i in 1:10){
mtext(paste(this is iteration , i, sep=))
points(runif(10),col=iterCol[i])
Sys.sleep(1)
## UNDRAW/HIDE the text so that it does not mess up the plot in the next
iteration
}
--
Sarah Goslee
http://www.functionaldiversity.org
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Re: [R] overloading + operator for chars
On 11/02/2011 06:52 AM, Albert-Jan Roskam wrote:
Hello,
I would like to overload the + operator so that it can be used to concatenate two strings, e.g
John + Doe = JohnDoe.
How can I 'unseal' the + method?
setMethod(+, signature(e1=character, e2=character), function(e1, e2) paste(e1, e2,
sep=) )
Error in setMethod(+, signature(e1 = character, e2 = character), :
the method for function + and signature e1=character, e2=character is
sealed and cannot be re-defined
Hi -- I think the two issues are that + is part of the Arith group
generic (?Methods, ?Arith) and that `+` (actually, members of the Ops
group) for primitive types dispatches directly without doing method
look-up. Personally I might
setClass(Character, contains=character)
Character - function(...) new(Character, ...)
setMethod(Arith, c(Character, Character), function(e1, e2) {
switch(.Generic,
+=Character(paste(e1, e2, sep=)),
stop(unhandled 'Arith' operator ', .Generic, '))
})
and then
Character(c(foo, bar)) + Character(baz)
[1] foobaz barbaz
Some might point to
`%+%` - function(e1, e2) paste(e1, e2, sep=)
foo %+% bar
[1] foobar
Martin
Cheers!!
Albert-Jan
~~
All right, but apart from the sanitation, the medicine, education, wine, public
order, irrigation, roads, a fresh water system, and public health, what have
the Romans ever done for us?
~~
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Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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[R] Help with curr directory in R
Hello All Thanks for all responses in advance, I am invoking R from command line from C:\TEMP as C:\Program Files\R\R-2.9.1\bin\R.exe --vanilla -f C:\temp\test.R On two different machines The test.R looks like: --SNIP- print(c(CurrDir=, getwd())) proc.time() warnings() --SNIP- On one machine I get the currDir Correctly printed as C:/TEMP But on another it gets printed as C:/ Does anyone know why this can be.. Is there some env variable that R is giving priority over current dir? Thanks Shank [[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] palettes for the color-blind
Everyone, I'm working with scatter plots with different colored symbols (via lattice). I'm currently using these colors for points and lines: col1 - c(rgb(1, 0, 0), rgb(0, 0, 1), rgb(0, 1, 0), rgb(0.55482458, 0.40350876, 0.0416), rgb(0, 0, 0)) plot(seq(along = col1), pch = 16, col = col1, cex = 1.5) I'm also using these with transparency (alpha between .5-.8 depending on the number of points). I'd like to make sure that these colors are interpretable by the color bind. Doing a little looking around, this might be a good palette: col2 - c(rgb(0, 0.4470588, 0.6980392), rgb(0.8352941, 0.3686275, 0, ), rgb(0.800, 0.4745098, 0.6549020), rgb(0.1686275, 0.6235294, 0.4705882), rgb(0.9019608, 0.6235294, 0.000)) plot(seq(along = col2), pch = 16, col = col2, cex = 1.5) but to be honest, I'd like to use something a little more vibrant. First, can anyone verify that these the colors in col2 are differentiable to someone who is color blind? Second, are there any other specific palettes that can be recommended? How do the RColorBrewer palettes rate in this respect? Thanks, Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] palettes for the color-blind
Hi, Try the dichromat package (also dichromat_pal in the scales package). HTH, baptiste On 3 November 2011 10:26, Max Kuhn mxk...@gmail.com wrote: Everyone, I'm working with scatter plots with different colored symbols (via lattice). I'm currently using these colors for points and lines: col1 - c(rgb(1, 0, 0), rgb(0, 0, 1), rgb(0, 1, 0), rgb(0.55482458, 0.40350876, 0.0416), rgb(0, 0, 0)) plot(seq(along = col1), pch = 16, col = col1, cex = 1.5) I'm also using these with transparency (alpha between .5-.8 depending on the number of points). I'd like to make sure that these colors are interpretable by the color bind. Doing a little looking around, this might be a good palette: col2 - c(rgb(0, 0.4470588, 0.6980392), rgb(0.8352941, 0.3686275, 0, ), rgb(0.800, 0.4745098, 0.6549020), rgb(0.1686275, 0.6235294, 0.4705882), rgb(0.9019608, 0.6235294, 0.000)) plot(seq(along = col2), pch = 16, col = col2, cex = 1.5) but to be honest, I'd like to use something a little more vibrant. First, can anyone verify that these the colors in col2 are differentiable to someone who is color blind? Second, are there any other specific palettes that can be recommended? How do the RColorBrewer palettes rate in this respect? Thanks, Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] palettes for the color-blind
On Thu, Nov 3, 2011 at 10:26 AM, Max Kuhn mxk...@gmail.com wrote: First, can anyone verify that these the colors in col2 are differentiable to someone who is color blind? Second, are there any other specific palettes that can be recommended? How do the RColorBrewer palettes rate in this respect? If you go to www.colorbrewer.org, the ColorBrewer site, it has ratings of the palettes for visibility under a variety of conditions, including red-green color blindness. Some of them are good, but not all of them. The dichromat package attempts to show the impact of both sorts of red:green anomalous vision on color visibility. It isn't quite right because of gamma correction, but people have told me that it is a fairly good representation, and it does have the right impact on clustering of pixels in some of the Ishihara color vision tests. It suggests that your colors 1 and 3 will be too similar and 2 and 4 will also be too similar for someone with protanopia. You aren't going to be able to get five colors that are equal luminance, equal chroma, and distinguishable to dichromats: you're putting three constraints on a three-dimensional space and you will end up with just two points. For three colors I would suggest orange, blue, gray. More than three will be hard. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] difference between foo$a[2] - 1 and foo[2,a] - 1
Columns in data frames must all have the same number of elements. Your first example attempts to violate that, because it works with a single column. The second example works on the entire data frame, so it is able to lengthen the other column to match. --- 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. Rebecca Hiller hille...@gmail.com wrote: Hallo Can anyone tell me the difference between foo$a[2] - 1 and foo[2,a] - 1 ? I thought that both expressions are equivalent, but when I run the following example, there is obviously a difference. foo - data.frame(a=NA,b=NA) foo a b 1 NA NA foo$a[1] - 1 foo$b[1] - 2 foo$a[2] - 1 Error in `$-.data.frame`(`*tmp*`, a, value = c(1, 1)) : replacement has 2 rows, data has 1 foo[2,a] - 1 foo a b 1 1 2 2 1 NA Thanks, Rebecca Hiller -- ETH Zürich Rebecca Hiller Institute of Agricultural Sciences LFW A2 Universitätsstrasse 2 8092 Zürich SWITZERLAND rebecca.hil...@ipw.agrl.ethz.ch http://www.gl.ethz.ch/ +41 44 632 31 90 Telefon +41 44 632 11 53 Fax _ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] palettes for the color-blind
Before you pick out a palette: you are aware that their are several different types of color-blindness, aren't you? http://en.wikipedia.org/wiki/Color_blind -- Sent from my Cray XK6 Pendeo-navem mei anguillae plena est. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with curr directory in R
I think I have solved this problem The issue was: some user had changed the registry entry for HKEY_CURRENT_USER\Software\Microsoft\Command Processor (added Autorun and set it to C:\) So the current dir was always pointing to C:\ I deleted that and everything works. Thanks Shank -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Khanvilkar, Shashank Sent: Wednesday, November 02, 2011 2:15 PM To: R Mailing List Subject: [R] Help with curr directory in R Hello All Thanks for all responses in advance, I am invoking R from command line from C:\TEMP as C:\Program Files\R\R-2.9.1\bin\R.exe --vanilla -f C:\temp\test.R On two different machines The test.R looks like: --SNIP- print(c(CurrDir=, getwd())) proc.time() warnings() --SNIP- On one machine I get the currDir Correctly printed as C:/TEMP But on another it gets printed as C:/ Does anyone know why this can be.. Is there some env variable that R is giving priority over current dir? Thanks Shank [[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] Error: serialization is too large to store in a raw vector
Dear all, I have quite large code (with lapply and mclapply) and I am getting the following error. Error: serialization is too large to store in a raw vector Is it possible to ask from R to extend the Error messages with more details? I would like to see where this problem exists. B.R Alex [[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] palettes for the color-blind
On Thu, Nov 3, 2011 at 11:04 AM, Carl Witthoft c...@witthoft.com wrote: Before you pick out a palette: you are aware that their are several different types of color-blindness, aren't you? Yes, but to first approximation there are only two, and they have broadly similar, though not identical impact on choice of color palettes. The dichromat package knows about them, and so does Professor Brewer. More people will be unable to read your graphs due to some kind of gross visual impairment (cataracts, uncorrected focusing problems, macular degeneration, etc) than will have tritanopia or monochromacy. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: serialization is too large to store in a raw vector
?traceback ?options ## especially _recover_ for the error option. -- Bert On Wed, Nov 2, 2011 at 3:37 PM, Alaios ala...@yahoo.com wrote: Dear all, I have quite large code (with lapply and mclapply) and I am getting the following error. Error: serialization is too large to store in a raw vector Is it possible to ask from R to extend the Error messages with more details? I would like to see where this problem exists. B.R Alex [[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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] mysterious warning message regarding bytecode...
While running a long script which source()s other scripts I get the following warning: Warning message: In t(object$S[[1]]) : bytecode version mismatch; using eval I cannot replicate it if I run the sourced files line by line though... What is that error? And do I care about it? It doesn't seem to affect my output as far as I can tell. Thanks! Justin sessionInfo() R version 2.13.2 (2011-09-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-9stringr_0.5 RPostgreSQL_0.2-0 biglm_0.8 DBI_0.2-5 doMC_1.2.3multicore_0.1-7 [8] foreach_1.3.2 codetools_0.2-8 iterators_1.0.5 cairoDevice_2.19 pixmap_0.4-11 gridExtra_0.8.5 splancs_2.01-29 [15] sp_0.9-91 ellipse_0.3-5 ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6 MASS_7.3-14 loaded via a namespace (and not attached): [1] compiler_2.13.2 digest_0.5.1lattice_0.19-33 Matrix_1.0-1nlme_3.1-102 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] StatET: Commands are not submitted to the console
Hello! I am working for quite a while now with the Eclipse/StatET approach and it always worked very well until I updated to the 2.0 version of StatET. After the official release the RJ console did not start. After they released another update a couple of days later it worked fine again. I did not do any programming for a week now and today I realised that when I execute the selected lines in an R file they are not submitted to the console. I also tried RTerm instead of RJ but it's the same problem. Commands are not submitted to the console. Did anyone come across the same problem and knows how to fix that. Googling does not result in any useful pages I am running Mac OS X Lion + Newest version of Eclipse and StatET. Everything is up to date. Cheers, syrvn -- View this message in context: http://r.789695.n4.nabble.com/StatET-Commands-are-not-submitted-to-the-console-tp3983662p3983662.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] Lattice plots and missing x-axis labels on second page
Hello, I'm trying to make a lattice plot (using xyplot()). I have included a layout=c(3,4) statement, giving me 12 plots per page and an as.table=TRUE statement, directing the way the plots are laid out. I have 18 plots altogether and so 6 of them end up on the second page. Everything looks fine for the first page, but the x-axis labels (e.g. 1993, 1994...) are all missing on the second page. The x-axis variable name (Year) is there at the bottom, however. Any help is appreciated. Thanks. David G. Evans Biometrician Division of Sport Fish Alaska Dept . of Fish and Game Anchorage, Ak 99518 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 2.14.0 installation problem (?)
Hi all, I downloaded R-2.14.0.tar.gz, unpacked, ran configure with --with-blas=-lgoto2, built, then issued make install rhome=/usr/local/lib/R-2.14.0-goto This produced the following error: [lots of output deleted] make[3]: Entering directory `/home/plangfelder/Download/R-2.14.0/src/modules/lapack' cp: cannot create regular file `/usr/local/lib/R-2.14.0-goto/lib/libRlapack.so': No such file or directory make[3]: *** [install] Error 1 make[3]: Leaving directory `/home/plangfelder/Download/R-2.14.0/src/modules/lapack' make[2]: *** [install] Error 1 make[2]: Leaving directory `/home/plangfelder/Download/R-2.14.0/src/modules' make[1]: *** [install] Error 1 make[1]: Leaving directory `/home/plangfelder/Download/R-2.14.0/src' make: *** [install] Error 1 Apparently the error was caused by the fact that the script neglected to create the directory /usr/local/lib/R-2.14.0-goto/lib/ before attempting to copy the libRlapack.so file into it. Creating the directory manually and re-running make install rhome=/usr/local/lib/R-2.14.0-goto solved the problem. The installed R seems to work fine. Is it a bug in the appropriate Makefile, or did I do something wrong? I'm on Fedora 9 (i686, i386, kernel 2.6.27.25-78.2.56.fc9.i686 if that makes any difference)... Thanks, Peter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Kolmogorov-Smirnov-Test on binned data, I guess gumbel-distributed data
Hi R-Users, I read some texts related to KS-tests. Most of those authors stated, that KS-Tests are not suitable for binned data, but some of them refer to 'other' authors who are claiming that KS-Tests are okay for binned data. I searched for sources and can't find examples which approve that it is okay to use KS-Tests for binned data - do you have any links to articles or tutorials? Anyway, I look for a test which backens me up that my data is gumbel-distributed. I estimated the gumbel-parameters mue and beta and after having a look on resulting plots, in my opinion: that looks quite good! You can the plot, related data, and the rscript here: www.jochen-bauer.net/downloads/kstest/Rplots-1000.pdf http://www.jochen-bauer.net/downloads/kstest/rm2700-1000.txt http://www.jochen-bauer.net/downloads/kstest/rcalc.R The story about the data: I am wondering what test I should choose if KS-Test is not appropriate? I get real high p-Values for data-row-1-histogram-heights and fitted-gumbel-distribution-function-to-bin-midth-vals. Most of the time, KS-test results in distances of 0.01 and p-Values of 0.99 or 1. This sounds strange to me, too high. Otherwise my plots are looking good and as you can see, in my first experiment I sampled 1000 values. In a second experiment I created only 50 random-values for the gumbel-parameter-estimation. I try to reduce permutations, so I will be able to create results faster, but I have to find out, when data fails for gumbel-distribution. The results surprised me, I expected that my tests and plots get worse, but I got still high p-values for the KS-Test and still a nice looking plot. www.jochen-bauer.net/downloads/kstest/Rplots-0050.pdf http://www.jochen-bauer.net/downloads/kstest/rm2700-0050.txt Moreover besides the shuffled data of my randomisation-test there are real-data-values. I calculated the p-value that my real data point occurs under estimated gumbel distribution. Those p-values between 1000permutation-experiment and 50-permutation-experiment are correlating enormously ... around 0.98. Pearson and Spearman-correlation-coefficients told me this. I guess that backens up the fact, that my plots are not getting worse nor the KS-Tests do. I hope I was able to state my current situation and you are able to give me some hints, for some literature or other tests or backen me up in my guess that my data is gumbel-distributed. Thanks in advance. Jochen I hope I was able to tell -- View this message in context: http://r.789695.n4.nabble.com/Kolmogorov-Smirnov-Test-on-binned-data-I-guess-gumbel-distributed-data-tp3983781p3983781.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] Lattice plots and missing x-axis labels on second page
I should say I'm using Windows-7, R version 2.13.0 and lattice version 0.19-33. I've pared down my code to this : pdat = read.table(RGRAPHSDGE.csv,header=T,sep=,,fill=T) print(xyplot(pdat$NITRATE~pdat$DATEYR|pdat$WELL, as.table=TRUE, layout=c(3,4), xlab=Year, ylab=Nitrate mg / litre, strip=FALSE )) First 3 lines of pdat looks like this: WELL DATEYR NITRATE 1 ALASKA CHILDRENS SERVICES 1993.8360.81 2 ALASKA CHILDRENS SERVICES 1994.8500.91 3 ALASKA CHILDRENS SERVICES 1995.8030.94 Thanks again. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Evans, David G (DFG) Sent: Wednesday, November 02, 2011 3:24 PM To: r-help@r-project.org Subject: [R] Lattice plots and missing x-axis labels on second page Hello, I'm trying to make a lattice plot (using xyplot()). I have included a layout=c(3,4) statement, giving me 12 plots per page and an as.table=TRUE statement, directing the way the plots are laid out. I have 18 plots altogether and so 6 of them end up on the second page. Everything looks fine for the first page, but the x-axis labels (e.g. 1993, 1994...) are all missing on the second page. The x-axis variable name (Year) is there at the bottom, however. Any help is appreciated. Thanks. David G. Evans Biometrician Division of Sport Fish Alaska Dept . of Fish and Game Anchorage, Ak 99518 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] anova or liklihood ratio test from biglm output
(Sorry if this is a repost, I got a bounce reply from the r-help server) Hi, Im using the biglm() function to create some linear models for a very large data set than lm() cant fit due to memory issues (the problem is with the number of interactions, I can fit the main effects model) I need to determine if the 2-way interactions are necessary or not. Ideally Id like to use anova() to get an anova table and a p-value for the interactions, however it appears that anova is not supported for biglm objects. So my next idea was to compare the main effects model with the 2-way interaction model using a likelihood ratio test. I seem to be able to get the deviance and residual DF from a biglm object, so I think I should be able to calculate the LRT and get my p-value if I assume a chi-squared distribution. I was wondering if anyone sees any problems with this approach (or would be kind enough to confirm it)? Or has any better suggestions, ideas or comments? Thankyou Chris Howden B.Sc. (Hons) GStat. Founding Partner Evidence Based Strategic Development, IP Commercialisation and Innovation, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 ch...@trickysolutions.com.au [[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: serialization is too large to store in a raw vector
On Nov 2, 2011, at 6:37 PM, Alaios ala...@yahoo.com wrote: Dear all, I have quite large code (with lapply and mclapply) and I am getting the following error. Error: serialization is too large to store in a raw vector Is it possible to ask from R to extend the Error messages with more details? I would like to see where this problem exists. ?traceback B.R Alex [[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] palettes for the color-blind
Yes, I was aware of the different type and their respective prevalences. The dichromat package helped me find what I needed. Thanks, Max On Wed, Nov 2, 2011 at 6:38 PM, Thomas Lumley tlum...@uw.edu wrote: On Thu, Nov 3, 2011 at 11:04 AM, Carl Witthoft c...@witthoft.com wrote: Before you pick out a palette: you are aware that their are several different types of color-blindness, aren't you? Yes, but to first approximation there are only two, and they have broadly similar, though not identical impact on choice of color palettes. The dichromat package knows about them, and so does Professor Brewer. More people will be unable to read your graphs due to some kind of gross visual impairment (cataracts, uncorrected focusing problems, macular degeneration, etc) than will have tritanopia or monochromacy. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
