[R] Issues with fa() function in psych
Hi Team, I was using your psych package for factor analysis and was also comparing the results with SAS results. I have some suggestions and/or confusions regarding the fa() function in the package: - The fa() function *doesn't account for Heywood cases* (communality greater than 1) and never ever throws out any error related to that which other softwares do. This is a serious and common issue in iterative factor analysis and hence should have been accounted for. - The fa() function doesn't provide equamax rotation in its rotation list and still if you specify *rotation=equamax*, it will run without throwing out any error and even mentioning in the result that equamax has been applied. But I have thoroughly compared results from *rotation=none* and *rotation=equamax* options and they are exactly same. *That means fa() is not doing the rotation at all and yet telling that it is doing that!!* I have even mentioned *rotation=crap* option just to check and surprisingly it ran(without any error) with the result showing: *Factor Analysis using method = gls* * Call: fa(r = cor_mat, nfactors = 4, n.obs = 69576, rotate = crap, fm = gls)* I hope you understand the severity of this bug and hence request you to correct this. - To my sense, there might be some problem with fm=ml and fm=pa options since the convergence issue should be with MLE method and not PA method but while running factor analysis with PA, I am getting the following warning: *maximum iteration exceeded* *The estimated weights for the factor scores are probably incorrect. Try a different factor extraction method.* If I compare the results of R and SAS,* I am getting convergence error for MLE in SAS whereas I am getting the same error for PA in R *!! I am not being able to understand this mismatch. - If I call the *loading matrix like efa_pa$loadings, the matrix shown has many blank cells whereas the final result showing the loadings doesn't have so* !! *Loadings:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 0.123 0.170 * - Could you please explain* what the com column means* in the output:? * PA1 PA3 PA2 PA4 h2 u2 com* *Var1 0.44 0.14 -0.03 -0.10 0.22665 0.773 1.3* *Var2 0.08 0.11 0.02 0.78 0.62951 0.370 1.1* *Var3 0.62 0.12 0.15 0.14 0.43578 0.564 1.3* - Request you to add option for *equamax rotation* also if possible. I have come across the above issues until now. Please do correct me if I am wrong. Awaiting your revert which would clear out my confusions, Thanks for your valuable time, Sagnik -- Regards, *SAGNIK CHAKRAVARTY* *Mob:* +919972865435 *Email:* sagnik.st...@gmail.com sagnik@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] Issues with fa() function in psych
Hello, And what about submitting your suggestions directly to the package author/maintainer? And please don't post in HTML. Regards, Pascal On Tue, Apr 8, 2014 at 3:13 PM, sagnik chakravarty sagnik.st...@gmail.com wrote: Hi Team, I was using your psych package for factor analysis and was also comparing the results with SAS results. I have some suggestions and/or confusions regarding the fa() function in the package: - The fa() function *doesn't account for Heywood cases* (communality greater than 1) and never ever throws out any error related to that which other softwares do. This is a serious and common issue in iterative factor analysis and hence should have been accounted for. - The fa() function doesn't provide equamax rotation in its rotation list and still if you specify *rotation=equamax*, it will run without throwing out any error and even mentioning in the result that equamax has been applied. But I have thoroughly compared results from *rotation=none* and *rotation=equamax* options and they are exactly same. *That means fa() is not doing the rotation at all and yet telling that it is doing that!!* I have even mentioned *rotation=crap* option just to check and surprisingly it ran(without any error) with the result showing: *Factor Analysis using method = gls* * Call: fa(r = cor_mat, nfactors = 4, n.obs = 69576, rotate = crap, fm = gls)* I hope you understand the severity of this bug and hence request you to correct this. - To my sense, there might be some problem with fm=ml and fm=pa options since the convergence issue should be with MLE method and not PA method but while running factor analysis with PA, I am getting the following warning: *maximum iteration exceeded* *The estimated weights for the factor scores are probably incorrect. Try a different factor extraction method.* If I compare the results of R and SAS,* I am getting convergence error for MLE in SAS whereas I am getting the same error for PA in R *!! I am not being able to understand this mismatch. - If I call the *loading matrix like efa_pa$loadings, the matrix shown has many blank cells whereas the final result showing the loadings doesn't have so* !! *Loadings:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 0.123 0.170 * - Could you please explain* what the com column means* in the output:? * PA1 PA3 PA2 PA4 h2 u2 com* *Var1 0.44 0.14 -0.03 -0.10 0.22665 0.773 1.3* *Var2 0.08 0.11 0.02 0.78 0.62951 0.370 1.1* *Var3 0.62 0.12 0.15 0.14 0.43578 0.564 1.3* - Request you to add option for *equamax rotation* also if possible. I have come across the above issues until now. Please do correct me if I am wrong. Awaiting your revert which would clear out my confusions, Thanks for your valuable time, Sagnik -- Regards, *SAGNIK CHAKRAVARTY* *Mob:* +919972865435 *Email:* sagnik.st...@gmail.com sagnik@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. -- Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] {metafor} variance explaination for paired pre-test/posttest
The standardized mean change using 'change score standardization' is described
in this article:
Gibbons, R. D., Hedeker, D. R., Davis, J. M. (1993). Estimation of effect
size from a series of experiments involving paired comparisons. Journal of
Educational Statistics, 18(3), 271-279.
For a comparison of the standardized mean change using change versus raw score
standardization, see:
Morris, S. B., DeShon, R. P. (2002). Combining effect size estimates in
meta-analysis with repeated measures and independent-groups designs.
Psychological Methods, 7(1), 105-125.
Viechtbauer, W. (2007). Approximate confidence intervals for standardized
effect sizes in the two-independent and two-dependent samples design. Journal
of Educational and Behavioral Statistics, 32(1), 39-60.
These articles also provide equations for the sampling variance of the
standardized mean change. The equation 1/ni + yi^2/(2*ni) is the estimate based
on the asymptotic variance of the standardized mean change using change score
standardization.
Best,
Wolfgang
--
Wolfgang Viechtbauer, Ph.D., Statistician
Department of Psychiatry and Psychology
School for Mental Health and Neuroscience
Faculty of Health, Medicine, and Life Sciences
Maastricht University, P.O. Box 616 (VIJV1)
6200 MD Maastricht, The Netherlands
+31 (43) 388-4170 | http://www.wvbauer.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of John Williams
Sent: Tuesday, April 08, 2014 02:30
To: r-help@r-project.org
Subject: [R] {metafor} variance explaination for paired pre-test/posttest
In a previous post
https://stat.ethz.ch/pipermail/r-help/2012-April/308946.html
https://stat.ethz.ch/pipermail/r-help/2012-April/308946.html , the
following calculation was given for imputing the variance of change
scores
for paired studies:
// begin quote
2) Often, the dependent variable is not the same in each study. Then you
will have to resort to a standardized outcome measure. There are two
options:
a) standardization based on the change score standard deviation
Then yi = (m1i - m2i) / sdi with sampling variance vi = 1/ni + yi^2 /
(2*ni).
// end quote
I used the sampling variance equation above in a paper that is being
reviewed by a coauthor, who is a biostatistician.
He commented that he has never seen this equation for variance before,
and
it looks strange to him. To put my knowledge into perspective, I am an
undergraduate taking my first statistics course. I imputed the t-
statistic
from two-sided p-values reported in the paper, and used that to get the
sdi
(as in the previous post).
I consulted the Cochrane Handbook and The Handbook of Research Syntheses
and
Meta-analysis 2nd Ed (Cooper, Hedges, Valentine 2009) and couldn't find
that
equation anywhere.
Would Prof. Viechtbauer, or anyone else knowledgeable, mind explaining
the
sample variance above? I need to be able to defend my choice of equation.
Since it's the only method that I found that doesn't rely on a
correlation
coefficient (which are not included in the papers), I'd like to be able
to
justify it and not redo calculations for 23 studies if possible.
Thank you very much,
John
John Williams
ALB Candidate, Harvard University (Expected May 2014)
johnwilli...@fas.harvard.edu
jawilliam...@gmail.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] {metafor} variance explaination for paired pre-test/posttest
Prof. Viechtbauer, thanks for the articles. I appreciate your help. Yours, John John Williams ALB Candidate, Harvard University (Expected May 2014) johnwilli...@fas.harvard.edu jawilliam...@gmail.com -- View this message in context: http://r.789695.n4.nabble.com/metafor-variance-explaination-for-paired-pre-test-posttest-tp4688365p4688382.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] rpart and randomforest results
The function rpart may well overfit if the value of the CP statistic is left at its default. Use the functions printcp() and plotcP() to check how the cross-validation estimate of relative error (xerror) changes with the number of splits (NB that the CP that leads to a further split changes monotonically with the number of splits). The rel error column from printcp() can be hopelessly optimistic. John Maindonald email: john.maindon...@anu.edu.aumailto: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. On 8/04/2014, at 8:00 pm, r-help-requ...@r-project.orgmailto:r-help-requ...@r-project.org wrote: From: r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Schillo, Sonja Sent: Thursday, April 03, 2014 3:58 PM To: Mitchell Maltenfort Cc: r-help@r-project.orgmailto:r-help@r-project.org Subject: Re: [R] rpart and randomforest results Hi, the random forest should do that, you're totally right. As far as I know it does so by randomly selecting the variables considered for a split (but here we set the option for how many variables to consider at each split to the number of variables available so that I thought that the random forest does not have the chance to randomly select the variables). The next thing that randomforest does is bootstrapping. But here again we set the option to the number of cases we have in the data set so that no bootstrapping should be done. We tried to take all the randomness from the randomforest away. Is that plausible and does anyone have another idea? Thanks Sonja [[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] Time interactions for coxph object
The very first step is to understand the possible nature of proportional hazards. This is parallel to the usual advice in linear models to graph the data before you start fitting complicated non-linear models. zp - cox.zph(CSHR.shore.fly, transform=identity) plot(zp)# or plot(zp[3]) for the third variable of a model, but you have only 1 print(zp) This looks at the working model hazard = exp( beta(t) * x); a time dependent coefficient. Propoprtional hazards corresponds to a horizontal line, i.e., beta(t) = constant. The steps are 1. Visualize 2. THINK 3. Act appropriately The tt addition to coxph allows complex time-dependent coefficients and is explained in a vignette. (See ?vignette). I've seen scores of data sets with non-proportional hazards, and used the tt functionality perhaps 3 times. Don't jump too quickly into complexity. Terry Therneau - begin included message - Hi All, I am working in the 'survival' library and need to know how to code a variable time interaction for left truncated data (not all subjects followed from the start of the study). I therefor add in the entry time and exit time variables into the formula. Here is my basic formula CSHR.shore.fly - coxph(Surv(entry, exit, to == 1) ~ shore.cat, data glba.mod) My variable shore.cat is violating the proportional hazards assumption so I am trying to add in an interaction with time. Do I interact exit? entry? or the range of the two? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] What Directs R to Executable Directory? [RESOLVED]
On Mon, 7 Apr 2014, Rich Shepard wrote: However, when I try to start R as either a user or as root it aborts because it cannot find /usr/local/bin/R. When I stepped back from the problem, but shutting down the laptop for the evening, it occurred to me that the system needed to be rebooted to see the new installation and forget about the older one. Sure enough, when I booted the laptop this morning, R worked as expected. Thanks very much, Bill, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] locating a data value in 3-dimensional data set
I have a 3-dimentional data set with dimensions longitude, latitude, and time. Unfortunately, when I look at the range of values in the data set, I noticed some very extremely large(positive and negative) values which are unexpected to be there. So I wanted to point-out the location (lon, lat and time) which these extreme values correspond to in order to see what is happening there. But I could not point-out these grid points and time. I tried: which(3ddata==x) # 3ddata is name of data set, x is the observed extreme value But this couldn't help me. Any suggestion please? Thanks B __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] locating a data value in 3-dimensional data set
I tried:
which(3ddata==x) # 3ddata is name of data set, x is the observed extreme
value But this couldn't help me.
You'll need which(3ddata$long==x) if 3ddata is a data frame* with columns long,
lat, time, or something like 3ddata[ ,'long'] if it's a matrix with dimnames or
[,1] if just a matrix.
But you'll be better off with =x if the values are floating point; see R FAQ
7.31
*clearly, '3ddata' cannot be a data frame name - it's not legal R. I assume you
have some legal name for it.
***
This email and any attachments are confidential. Any use...{{dropped:8}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] locating a data value in 3-dimensional data set
Dear Mamuash Bukana, is this a data frame with variable names you indicated? you will need something like which(dataframename$variablename == x) but if you have more you might use HTH kd Feladó: r-help-boun...@r-project.org [r-help-boun...@r-project.org] ; meghatalmaz#243;: mamuash bukana [mamushbuk...@gmail.com] Küldve: 2014. április 8. 15:50 To: r-help@r-project.org Tárgy: [R] locating a data value in 3-dimensional data set I have a 3-dimentional data set with dimensions longitude, latitude, and time. Unfortunately, when I look at the range of values in the data set, I noticed some very extremely large(positive and negative) values which are unexpected to be there. So I wanted to point-out the location (lon, lat and time) which these extreme values correspond to in order to see what is happening there. But I could not point-out these grid points and time. I tried: which(3ddata==x) # 3ddata is name of data set, x is the observed extreme value But this couldn't help me. Any suggestion please? Thanks B __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] locating a data value in 3-dimensional data set
Hi I know there is a arr.index (or something like that, I'm not near my R right now) argument to which (). I have used it for 2-dim arrays and never for higher dimensions. But try it out by setting the argument to TRUE. Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: mamuash bukana Dato:08/04/2014 15.51 (GMT+01:00) Til: r-help@r-project.org Emne: [R] locating a data value in 3-dimensional data set I have a 3-dimentional data set with dimensions longitude, latitude, and time. Unfortunately, when I look at the range of values in the data set, I noticed some very extremely large(positive and negative) values which are unexpected to be there. So I wanted to point-out the location (lon, lat and time) which these extreme values correspond to in order to see what is happening there. But I could not point-out these grid points and time. I tried: which(3ddata==x) # 3ddata is name of data set, x is the observed extreme value But this couldn't help me. Any suggestion please? Thanks B __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] locating a data value in 3-dimensional data set
Sorry forgot to mention that you probably are better of using = and = instead of == Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: mamuash bukana Dato:08/04/2014 15.51 (GMT+01:00) Til: r-help@r-project.org Emne: [R] locating a data value in 3-dimensional data set I have a 3-dimentional data set with dimensions longitude, latitude, and time. Unfortunately, when I look at the range of values in the data set, I noticed some very extremely large(positive and negative) values which are unexpected to be there. So I wanted to point-out the location (lon, lat and time) which these extreme values correspond to in order to see what is happening there. But I could not point-out these grid points and time. I tried: which(3ddata==x) # 3ddata is name of data set, x is the observed extreme value But this couldn't help me. Any suggestion please? Thanks B __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Ignore escape characters in a string...
R-helpers: One of the minor irritations I have is copying paths from Windows explorer, which look like: C:\Program Files\R\R-3.0.3 and using them in a setwd() statement, since the \ is, of course, interpreted as an escape character. I have to, at present, manually add in the double slashes or reverse them. So, I'd like to write a quick function that takes this path: winpath - C:\Program Files\R\R-3.0.3 and converts it to a ready-to-go R path -- is there a way to have R IGNORE escape characters in a character vector? Alternatively, is there some trick to using a copy/paste from Windows explorer I'm not aware of? --j -- Jonathan A. Greenberg, PhD Assistant Professor Global Environmental Analysis and Remote Sensing (GEARS) Laboratory Department of Geography and Geographic Information Science University of Illinois at Urbana-Champaign 259 Computing Applications Building, MC-150 605 East Springfield Avenue Champaign, IL 61820-6371 Phone: 217-300-1924 http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype: jgrn3007 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Ignore escape characters in a string...
On Tue, Apr 8, 2014 at 4:00 PM, Jonathan Greenberg j...@illinois.eduwrote: C:\Program Files\R\R-3.0.3 Does R on windows have clipboard support? I can do this on Linux: readLines(file(clipboard)) [1] C:\\Program Files\\R\\R-3.0.3 - that's from a copy of a path with only single slashes in. But help(connections) on my linux system doesn't mention the Windows clipboard Some ppl on SO have assorted solutions involving Windows scripting tools that tweak the clipboard so you can Ctrl-V a modified value: http://stackoverflow.com/questions/1407238/relief-from-backslash-irritation-in-r-for-windows Barry [[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] Ignore escape characters in a string...
Yes R on Windows have something like that you mentioned. I have only tried it in conjunction with read.table. I'm a bit surprised about the \\ on a linux OS. I'm also surprised that in a file manager on Windows you can paste e.g. C:/users/frtog/Desktop and it can find its way to the folder. Weird. Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: Barry Rowlingson Dato:08/04/2014 17.20 (GMT+01:00) Til: Jonathan Greenberg Cc: r-help Emne: Re: [R] Ignore escape characters in a string... On Tue, Apr 8, 2014 at 4:00 PM, Jonathan Greenberg j...@illinois.eduwrote: C:\Program Files\R\R-3.0.3 Does R on windows have clipboard support? I can do this on Linux: readLines(file(clipboard)) [1] C:\\Program Files\\R\\R-3.0.3 - that's from a copy of a path with only single slashes in. But help(connections) on my linux system doesn't mention the Windows clipboard Some ppl on SO have assorted solutions involving Windows scripting tools that tweak the clipboard so you can Ctrl-V a modified value: http://stackoverflow.com/questions/1407238/relief-from-backslash-irritation-in-r-for-windows Barry [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ignore escape characters in a string...
Hello, There is support for the clipboard on Windows 7. Also, note that on Windows your solution leaves a connection open so maybe the following is better. # copy the next line C:\Program Files\R\R-3.0.3 clipb - file(clipboard) winpath - readLines(clipb) close(clipb) And, just to avoid backslashes altogether, fun - function(x) gsub(, /, x) fun(winpath) Hope this helps, Rui Barradas Em 08-04-2014 16:17, Barry Rowlingson escreveu: On Tue, Apr 8, 2014 at 4:00 PM, Jonathan Greenberg j...@illinois.eduwrote: C:\Program Files\R\R-3.0.3 Does R on windows have clipboard support? I can do this on Linux: readLines(file(clipboard)) [1] C:\\Program Files\\R\\R-3.0.3 - that's from a copy of a path with only single slashes in. But help(connections) on my linux system doesn't mention the Windows clipboard Some ppl on SO have assorted solutions involving Windows scripting tools that tweak the clipboard so you can Ctrl-V a modified value: http://stackoverflow.com/questions/1407238/relief-from-backslash-irritation-in-r-for-windows Barry [[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] Ignore escape characters in a string...
On Tue, Apr 8, 2014 at 4:30 PM, Frede Aakmann Tøgersen fr...@vestas.comwrote: I'm a bit surprised about the \\ on a linux OS. I'm also surprised that in a file manager on Windows you can paste e.g. C:/users/frtog/Desktop and it can find its way to the folder. Weird. Well, the clipboard contained a path separated by single backslashes. R read that (via the file(clipboard)) and correctly read single backslashes. Its only when printed out that R 'escapes' them as double-backslashes - there's really only one character there. What R seems to lack is 'raw string' functionality. In python you do this with a string quote prefix, for example 'r': len(\t) 1 In that case the \t is interpreted as a single character, \t, or tab. Add the r modifier: len(r\t) 2 and now you get two characters, backslash and t. You'll often see regular expressions in Python using raw strings since they tend to contain slashes and backslashes which you really want in there. Barry [[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] Label axis tick marks with a simple function of axis value
Don suggested something like this: h=c(1,2,3,4,5,6,7,8,9) v=c(9,8,7,6,5,4,3,2,1) plot(h,v,xaxt='n') xat=pretty(h) axis(1,at=xat,labels=1/xat) But it puts the tick marks at the data-x-locations. If the tick locations are not automatic or automatically separate from the data locations, then I want to tell it where to put them using a separate indicator. I am not familiar enough with R to find the answer. But if it would work, it would be valuable. -- View this message in context: http://r.789695.n4.nabble.com/Label-axis-tick-marks-with-a-simple-function-of-axis-value-tp4687917p4688399.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] Ignore escape characters in a string...
Thank you Barry, this explains some of the things going on on the different platforms. One of my colleague told me some time ago that in C#/.NET they have this raw string functionality as you call it. However there they use @ and not r. That could be a nice thing to have in R. Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance Modeling Technology Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.commailto:fr...@vestas.com http://www.vestas.comhttp://www.vestas.com/ Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/noticehttp://www.vestas.com/legal/notice If you have received this e-mail in error please contact the sender. From: b.rowling...@gmail.com [mailto:b.rowling...@gmail.com] On Behalf Of Barry Rowlingson Sent: 8. april 2014 17:40 To: Frede Aakmann Tøgersen Cc: Jonathan Greenberg; r-help Subject: Re: [R] Ignore escape characters in a string... On Tue, Apr 8, 2014 at 4:30 PM, Frede Aakmann Tøgersen fr...@vestas.commailto:fr...@vestas.com wrote: I'm a bit surprised about the \\ on a linux OS. I'm also surprised that in a file manager on Windows you can paste e.g. C:/users/frtog/Desktop and it can find its way to the folder. Weird. Well, the clipboard contained a path separated by single backslashes. R read that (via the file(clipboard)) and correctly read single backslashes. Its only when printed out that R 'escapes' them as double-backslashes - there's really only one character there. What R seems to lack is 'raw string' functionality. In python you do this with a string quote prefix, for example 'r': len(\t) 1 In that case the \t is interpreted as a single character, \t, or tab. Add the r modifier: len(r\t) 2 and now you get two characters, backslash and t. You'll often see regular expressions in Python using raw strings since they tend to contain slashes and backslashes which you really want in there. Barry [[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] Plotting does odd line thing
THANK you for the help!! One more question. Being I need to compare 4 different wells, I like to have them all at the same scale which I can do with the ylim=c(min,max). But so the low concentrations don't get washed out, I like to plot the y axis in log format. ie 0.001, 0.010, 0.100. Below is the code I have so far. Thanks in advance. setwd(c:/R) mydata -read.csv(http://doylesdartden.com/R/2014_02_data.csv;, sep=,) attach(mydata) plot(Arsenic~Year,data=mydata, subset = Well.ID %in% c(MW-1, D_Arsenic), col=ifelse(D_Arsenic, black, red), ylab = mg/L,xlab = , pch=ifelse(D_Arsenic, 19, 17), cex = 1.5, ylim=c(0, 0.1)) subset-Well.ID %in% c(MW-1, D_Arsenic) lines(Arsenic[subset]~Year[subset]) #Add title title(main=MW-1) On Tue, Apr 8, 2014 at 12:52 AM, Frede Aakmann Tøgersen fr...@vestas.comwrote: Well the lines() function has a subset argument as does plot() so why not do this? lines(EMD ~ Year, data = mydata, subset = Well.ID %in% c(MW-1, D_EMD)) And yes lines() also have a data argument so why do you not use that (as you do with plot()) instead of attaching. Attaching dataframes may be a potential danger when some time in the future you have forgot that you attached the dataframe and you have forgot the warnings you get when attaching (making debugging difficult). Try this: ## Define an object named Year ## in which case call to lines do not what you think it will do Year - 1:nrow(mydata) ## or Year - 'foo' in which case one gets an error later ## attach the dataframe attach(mydata) The following object is masked _by_ .GlobalEnv: Year Now what will happen if you do lines(EMD ~ Year)? Here is the search path in my session: search() [1] .GlobalEnvmydatapackage:lattice [4] package:RODBC package:stats package:graphics [7] package:grDevices ESSR package:utils [10] package:datasets package:methods Autoloads [13] package:base Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance Modeling Technology Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.com http://www.vestas.com Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/notice If you have received this e-mail in error please contact the sender. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jim Lemon Sent: 8. april 2014 04:53 To: David Doyle Cc: r-help@r-project.org Subject: Re: [R] Plotting does odd line thing On 04/08/2014 12:20 PM, David Doyle wrote: Hello folks, When I use the lines function below it connects all my points but then draws a line back to the start point. Any suggestions on what is going on?? mydata-read.csv(http://doylesdartden.com/R/test_data.csv;, sep=,) attach(mydata) plot(EMD~Year,data=mydata, subset = Well.ID %in% c(MW-1, D_EMD), col=ifelse(D_EMD, black, red), pch=ifelse(D_EDM, 19, 17), cex = 1.5) lines(EMD~Year) Hi David, While you will get what you expect with: lines(EMD[1:39]~Year[1:39]) I would be unnecessarily obscure in suggesting it. Try this: subset-Well.ID %in% c(MW-1, D_EMD) lines(EMD[subset]~Year[subset]) You haven't selected the same points for the lines function as you have for the plot function. 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. [[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] locating a data value in 3-dimensional data set
Many thanks to you all; specially to Frede. which(3ddata$variablename=x,arr.ind=TRUE) answers my question perfectly. Cheers! Bukana On Tue, Apr 8, 2014 at 11:33 AM, Frede Aakmann Tøgersen fr...@vestas.com wrote: Hi I know there is a arr.index (or something like that, I'm not near my R right now) argument to which (). I have used it for 2-dim arrays and never for higher dimensions. But try it out by setting the argument to TRUE. Br. Frede Sendt fra Samsung mobil Oprindelig meddelelse Fra: mamuash bukana Dato:08/04/2014 15.51 (GMT+01:00) Til: r-help@r-project.org Emne: [R] locating a data value in 3-dimensional data set I have a 3-dimentional data set with dimensions longitude, latitude, and time. Unfortunately, when I look at the range of values in the data set, I noticed some very extremely large(positive and negative) values which are unexpected to be there. So I wanted to point-out the location (lon, lat and time) which these extreme values correspond to in order to see what is happening there. But I could not point-out these grid points and time. I tried: which(3ddata==x) # 3ddata is name of data set, x is the observed extreme value But this couldn't help me. Any suggestion please? Thanks B __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Meta-analysis of prevalence at the country level with mgcv/gamm4
Dear R community, I'm working on a meta-analysis of prevalence data. The aim is to get estimates of prevalence at the country level. The main issue is that the disease is highly correlated with age, and the sample ages of included studies are highly heterogeneous. Only median age is available for most studies, so I can't use SMR-like tricks. I figured I could use meta-regression to solve this, including age as a fixed-effect and introducing study-level and country-level random-effects. The idea (that I took from Fowkes et alhttp://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2813%2961249-0/abstract) was to use this model to make country-specific predictions of prevalence for each 5-year age group from 15 to 60 (using the median age of the group), and to apply these predictions to the actual population size of each of those groups in the selected country, in order to obtain total infected population and to calculate age-adjusted prevalence in the 15-60 population from that. I tried several ways to do this using R with packages meta and mgcv. I got some satisfying results, but I'm not that confident with my results and would appreciate some feedback. First is some simulated data, then the description of my different approaches: data-data.frame(id_study=c(UK1,UK2,UK3,FRA1,FRA2,BEL1,GER1,GER2,GER3), country=c(UK,UK,UK,FRANCE,FRANCE,BELGIUM,GERMANY,GERMANY,GERMANY), n_events=c(91,49,18,10,50,6,9,10,22), n_total=c(3041,580,252,480,887,256,400,206,300), study_median_age=c(25,50,58,30,42,26,27,28,36)) *Standard random-effect meta-analysis* with package meta. I used metaprop() to get a first estimate of the prevalence in each country without taking age into account, and to obtain weights. As expected, heterogeneity was very high, so I used weights from the random-effects model. meta - metaprop(event=n_events,n=n_total,byvar=country,sm=PLOGIT,method.tau=REML,data=data) summary(meta) data$weight-meta$w.random I used meta to get a first estimate of the prevalence without taking age into account, and to obtain weights. As expected, heterogeneity was very high, so I used weights from the random-effects model. *Generalized additive model* to include age with package mgcv. The gam() model parameters (k and sp) were chosen using BIC and GCV number (not shown here). model - gam( cbind(n_events,n_total-n_events) ~ s(study_median_age,bs=cr,k=4,sp=2) + s(country,bs=re), weights=weight, data=data, family=binomial(link=logit), method=REML) plot(model,pages=1,residuals=T, all.terms=T, shade=T) Predictions for each age group were obtained from this model as explained earlier. CI were obtained directly using predict.gam(), that uses the Bayesian posterior covariance matrix of the parameters. For exemple considering UK: newdat-data.frame(country=UK,study_median_age=seq(17,57,5)) link-predict(model,newdat,type=link,se.fit=T)$fit linkse-predict(model,newdat,type=link,se.fit=T)$se newdat$prev-model$family$linkinv(link) newdat$CIinf-model$family$linkinv(link-1.96*linkse) newdat$CIsup-model$family$linkinv(link+1.96*linkse) plot(newdat$prev~newdat$study_median_age, type=l,ylim=c(0,.12)) lines(newdat$CIinf~newdat$study_median_age, lty=2) lines(newdat$CIsup~newdat$study_median_age, lty=2) The results were satisfying, representing the augmentation of the prevalence with advanced age, with coherent confidence intervals. I obtained a total prevalence for the country using the country population structure (not shown, I hope it is clear enough). However, I figured I needed to include study-level random-effects since there was a high heterogeneity (even though I did not calculate heterogeneity after the meta-regression). *Introducing study-level random-effect* with package gamm4. Since mgcv models can't handle that much random-effect parameters, I had to switch to gamm4. model2 - gamm4(cbind(n_events,n_total-n_events) ~ s(study_median_age,bs=cr,k=4) + s(country,bs=re), random=~(1|id_study), data=data, weights=weight, family=binomial(link=logit)) plot(model2$gam,pages=1,residuals=T, all.terms=T, shade=T) link-predict(model2$gam,newdat,type=link,se.fit=T)$fit linkse-predict(model2$gam,newdat,type=link,se.fit=T)$se newdat$prev2-model$family$linkinv(link) newdat$CIinf2-model$family$linkinv(link-1.96*linkse) newdat$CIsup2-model$family$linkinv(link+1.96*linkse) plot(newdat$prev2~newdat$study_median_age, type=l,col=red,ylim=c(0,0.11)) lines(newdat$CIinf2~newdat$study_median_age, lty=2,col=red) lines(newdat$CIsup2~newdat$study_median_age, lty=2,col=red) lines(newdat$prev~newdat$study_median_age, type=l,ylim=c(0,.12)) lines(newdat$CIinf~newdat$study_median_age, lty=2) lines(newdat$CIsup~newdat$study_median_age, lty=2) Since the study-level random effect was in the mer part of the fit, I didn't have to handle it. As you can see, I obtain rather different results, with a much smoother relation between age and prevalence, and quite different
Re: [R] Splitting columns and forming new data files in R
Hi,
Try:
#Tmin,Tmax,Tmean,Precip
#Tmean -999.9 in all files
#working directory is sample
#created folder final
list.files()
#[1] coordinates.csv final Precip Tmax
#[5] Tmin
Coord - read.csv(list.files(pattern=.csv),header=TRUE,stringsAsFactors=FALSE)
lfile - list.files()[!grepl(.csv|final,list.files())]
files - paste(paste(getwd(),lfile,sep=/), list.files(lfile),sep=/)
lst1 - split(files,gsub(.*\\/(.*)\\.csv,\\1,files))
names1 - gsub(.*\\/(.*)\\/.*\\.csv,\\1,lst1[[1]])
lst1New - lapply(lst1,function(x) {lst2 - setNames(lapply(x,function(y)
{dat - read.table(y,sep= ,header=TRUE, stringsAsFactors=FALSE); dat[,1:104]}
), names1); dat2 - do.call(cbind,lst2); indx - grepl(Sim,names(dat2)); dat3
- dat2[indx];dat4 - dat2[!indx][,1:4]; names(dat4) -
gsub(.*\\.,,names(dat4));
lapply(split(names(dat3),gsub(.*\\.,,names(dat3))),function(x) {dat5 -
cbind(dat4,dat3[,x]); dat5$Tmean - -999.9; dat6 -
dat5[,c(1:4,7:6,8,5)];colnames(dat6)[2:3] - Coord[match(unique(dat6$Site),
Coord$Site),3:2];dat7 - dat6[,-4]; dat7; colnames(dat7)[-(2:3)] - NA; dat7})})
sapply(lst1New,length)
#G100 G101 G102 G103
# 100 100 100 100
lapply(names(lst1New),function(x) {nm1 - paste(x,
names(lst1New[[x]]),sep=_); nm2 -
paste0(paste(paste0(getwd(),/final),nm1,sep=/),.csv);lapply(seq_along(lst1New[[x]]),function(i)
{x1 - lst1New[[x]][i]; write.table(x1, nm2[i],quote=FALSE,row.names=FALSE)})})
length(list.files(paste0(getwd(),/final)))
#[1] 400
A.K.
On Tuesday, April 8, 2014 1:17 AM, Zilefac Elvis zilefacel...@yahoo.com wrote:
Hi AK,
Please I need your help. I finally solved the previous task I sent to you.
I have Precip,Tmin and Tmax in three different folders (attached).
Each folder has 4 files with identical names in all folders (we can match case).
Within each file are [,YYY MM DD sim001...sim100] (some files may have more
than 100 simulations. Use only the first 100).
Q1) Open all three folders, go to file 1 (e.g G100), copy column 1 (sim001, do
not copy date) and paste it in a new folder called final. Do so for column 2
(sim002),...,column 100 (sim100). So from file 1 alone with 100 sims, you will
have 100 files in final. The files in final should be labelled for example
as G100_sim001, G100_sim002,...,G100_sim100; G101_sim001,G101_sim002 etc.
The format of all files in final is similar to:
50-110.7
196111-999.9-999.9-999.90
196112-999.9-999.9-999.92.38
196113-999.9-999.9-999.90
196114-999.9-999.9-999.90
196115-999.9-999.9-999.90
196116-999.9-999.9-999.90
196117-999.9-999.9-999.90
196118-999.9-999.9-999.90
196119-999.9-999.9-999.95.19
1961110-999.9-999.9-999.90
196-999.9-999.9-999.90
1961112-999.9-999.9-999.90
1961113-999.9-999.9-999.90
1961114-999.9-999.9-999.90
1961115-999.9-999.9-999.90
The columns after the date should be [Tmin,Tmax,Tmean,Precip]. Please do not
include column names in output. Output files are .csv.
*Fill column Tmean with -999.9 in all files.
Therefore, using the sample I have provided, you will have 4sites*100 sims =
400 files in folder final.
Q2) From the attached coordinates file, please copy Lat andLong corresponding
to the Site and past it in the first row of every file starting with that site
code.
For example, all files beginning with G100_sim... will have their first row
similar to:
49.53-96.7
196111-999.9-999.9-999.90
This looks very cumbersome for me to handle.
Thanks very much.
Atem.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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 logistic analysis
I'm trying to conduct a single level logistic analysis (as a beginning step for a more advanced Multi-level analysis). However, when I try to run it, I get following error: Warning messages: 1: In model.response(mf, numeric) : using type = numeric with a factor response will be ignored 2: In Ops.factor(y, z$residuals) : - not meaningful for factors I haven't got a clue why I'm getting this because I used the exact same syntax (same data preparation etc...) for a similar analysis (same datastructure, different country). Syntax: Single_model1 - lm(openhrs1 ~ genhealt1 + age + sexpat1 + hhincome1 + edupat1 + etniciteit1, data=Slovakije) My Missing data are coded as such, I already tried to run the analysis in a data frame without the missing cases, but that didn't work either. -- View this message in context: http://r.789695.n4.nabble.com/Error-logistic-analysis-tp4688385.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] Error logistic analysis
On Apr 8, 2014, at 7:20 AM, lghansse lise.hanss...@ugent.be wrote: I'm trying to conduct a single level logistic analysis (as a beginning step for a more advanced Multi-level analysis). However, when I try to run it, I get following error: Warning messages: 1: In model.response(mf, numeric) : using type = numeric with a factor response will be ignored 2: In Ops.factor(y, z$residuals) : - not meaningful for factors I haven't got a clue why I'm getting this because I used the exact same syntax (same data preparation etc...) for a similar analysis (same datastructure, different country). Syntax: Single_model1 - lm(openhrs1 ~ genhealt1 + age + sexpat1 + hhincome1 + edupat1 + etniciteit1, data=Slovakije) My Missing data are coded as such, I already tried to run the analysis in a data frame without the missing cases, but that didn't work either. You are using the lm() function above, which is a regular least squares linear regression for a continuous response variable. If you want to run a logistic regression, you need to use glm() with 'family = binomial': Single_model1 - glm(openhrs1 ~ genhealt1 + age + sexpat1 + hhincome1 + edupat1 + etniciteit1, family = binomial, data = Slovakije) Regards, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] moses extreme reaction test
Is there a package that contains moses extreme reaction test? Thank's __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] moses extreme reaction test
On Apr 8, 2014, at 12:37 PM, José Trujillo Carmona truji...@unex.es wrote: Is there a package that contains moses extreme reaction test? Thank's A search using rseek.org indicates that the DescTools package on CRAN contains a function called MosesTest() that appears to implement it. http://cran.r-project.org/web/packages/DescTools/ Regards, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] moses extreme reaction test
On Apr 8, 2014, at 10:37 AM, José Trujillo Carmona wrote: Is there a package that contains moses extreme reaction test? Learn to search. install.packages(sos) library(sos) findFn(moses extreme) found 5 matches; retrieving 1 page Downloaded 3 links in 1 packages -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Ignore escape characters in a string...
What is wrong with winpath - readLines(clipboard ) ? If you want to show that as a literal in your code, then don't bother assigning it to a variable, but let it echo to output and copy THAT and put it in your source code. There is also file.choose()... --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On April 8, 2014 8:00:03 AM PDT, Jonathan Greenberg j...@illinois.edu wrote: R-helpers: One of the minor irritations I have is copying paths from Windows explorer, which look like: C:\Program Files\R\R-3.0.3 and using them in a setwd() statement, since the \ is, of course, interpreted as an escape character. I have to, at present, manually add in the double slashes or reverse them. So, I'd like to write a quick function that takes this path: winpath - C:\Program Files\R\R-3.0.3 and converts it to a ready-to-go R path -- is there a way to have R IGNORE escape characters in a character vector? Alternatively, is there some trick to using a copy/paste from Windows explorer I'm not aware of? --j __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Pull Stock Symbol Out of String
Dear R Helpers, My regex skills are beginner to intermediate and banging around the web has not resulted in a solution to the problem below so I hope that one of you who has mad skills can help me out. I want to extract the stock ticker--AMT-- out of the string American Tower Corporation (REIT) (AMT) The presence of the other parenthetical text (REIT) makes this difficult. Please note that the string may or may not have a interfering set of characters such as the (REIT) so the solution needs to be generalizable to the last set of characters that are contained in parentheses in the larger string. So an example of a string without the interfering (REIT) would be Aetna Inc. (AET) Your assistance would be very much appreciated. --John Sparks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ggplot2 and geom_tile
Dear community, I have been using ggplot2 for visualisation and I am really impressed by this. I do however have a problem that returns when plotting various types of spatial datasets as raster images. This is probably due to me not fully understanding the package. When I am plotting images using geom_tile, I sometimes only have small dots in the image and at other times I have apparently blank images. On other occasions it works nicely without me being able to spot the differences between these plot requests nor the underlying data. I am usually plotting geophysical information either on a geographical grid (latitude/longitude) or on a map projection (normally using proj4 for the projection of data). I have tried to play with the position attribute, but without success so far, but believe that I suffer from some form of effect from this. I have tried to google for information and I have read the manual pages but so far without success. Do you have some suggested reading for problems like this? Is the problem likely to be related to position? I apologise for the vague description of the problem. All the best Øystein -- Dr. Oystein Godoy Norwegian Meteorological Institute P.O.BOX 43, Blindern, N-0313 OSLO, Norway Ph: (+47) 2296 3000 (switchb) 2296 3334 (direct line) Fax:(+47) 2296 3050 Institute home page: http://met.no/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Pull Stock Symbol Out of String
The following gets the last parenthesized sequence of non-parentheses sub(.*(\\([^()]+\\))([^()]*)$, \\1, c(Aetna(AET), American Tower Corp(REIT)(ATC), No Parens, Qwerty Corp (ASD)(ZXC)(123) extra stuff)) [1] (AET) (ATC) No Parens (123) Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sparks, John James Sent: Tuesday, April 08, 2014 11:29 AM To: r-help@r-project.org Subject: [R] Pull Stock Symbol Out of String Dear R Helpers, My regex skills are beginner to intermediate and banging around the web has not resulted in a solution to the problem below so I hope that one of you who has mad skills can help me out. I want to extract the stock ticker--AMT-- out of the string American Tower Corporation (REIT) (AMT) The presence of the other parenthetical text (REIT) makes this difficult. Please note that the string may or may not have a interfering set of characters such as the (REIT) so the solution needs to be generalizable to the last set of characters that are contained in parentheses in the larger string. So an example of a string without the interfering (REIT) would be Aetna Inc. (AET) Your assistance would be very much appreciated. --John Sparks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] moses extreme reaction test
Very useful. Very Thanks. El 08/04/14 19:43, David Winsemius escribió: On Apr 8, 2014, at 10:37 AM, José Trujillo Carmona wrote: Is there a package that contains moses extreme reaction test? Learn to search. install.packages(sos) library(sos) findFn(moses extreme) found 5 matches; retrieving 1 page Downloaded 3 links in 1 packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] moses extreme reaction test
What's the problem with this:? package ‘DscTools’ is not available (for R version 3.1.0 beta) El 08/04/14 19:42, Marc Schwartz escribió: On Apr 8, 2014, at 12:37 PM, José Trujillo Carmona truji...@unex.es wrote: Is there a package that contains moses extreme reaction test? Thank's A search using rseek.org indicates that the DescTools package on CRAN contains a function called MosesTest() that appears to implement it. http://cran.r-project.org/web/packages/DescTools/ Regards, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] xts Annual series
Hello! If I have the following: x - as.yearqtr(2000 + seq(0,7)/4) x [1] 2000 Q1 2000 Q2 ... which is as it should be. Then if I set up time as time - xts(1:8,x) time 2000 Q1 1 2000 Q2 2 2000 Q3 3 . . Also fine Now suppose I want to have an annual xts object. How do I go about setting that up, please? Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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] moses extreme reaction test
Typo: DescTools ? On 2014-04-08, at 3:13 PM, José Trujillo wrote: What's the problem with this:? package ‘DscTools’ is not available (for R version 3.1.0 beta) El 08/04/14 19:42, Marc Schwartz escribió: On Apr 8, 2014, at 12:37 PM, José Trujillo Carmona truji...@unex.es wrote: Is there a package that contains moses extreme reaction test? Thank's A search using rseek.org indicates that the DescTools package on CRAN contains a function called MosesTest() that appears to implement it. http://cran.r-project.org/web/packages/DescTools/ Regards, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need to download this data... can someone help?
Hi again, I am looking some way to download this data: http://www.cmegroup.com/trading/interest-rates/stir/eurodollar_quotes_openOutcry.html So far I have tried following code: library(XML) data - xmlParse( http://www.cmegroup.com/trading/interest-rates/stir/eurodollar_quotes_openOutcry.html ) However not be able to get in right way. Really appreciate if someone point me on right approach. Thanks for your time. [[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] browser always enters debug mode
This is something peculiar about the environment on one particular linux
box, because it doesn't happen on other computers. Whenever I invoke
browser() inside a function, it automatically enters debugging mode,
with line-by-line execution of code:
dum - function() { browser(); x - rnorm(10); print(x) }
dum()
Called from: dum()
Browse[1]
debug at #1: x - rnorm(10)
Browse[2]
debug at #1: print(x)
Browse[2]
[1] -0.41466890 0.02276493 1.01332894 -2.72784447 0.73471652 0.41360718
[7] 1.67942142 -1.47384724 1.12129541 -1.13447881
isdebugged(dum)
[1] FALSE
Thanks in advance for any tips on how to revert to the normal browser()
behavior.
-Paul
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need to download this data... can someone help?
Hello, Try the following. library(XML) URL - http://www.cmegroup.com/trading/interest-rates/stir/eurodollar_quotes_openOutcry.html; dat - readHTMLTable(readLines(URL), which=1, header=TRUE, na.strings = -) str(dat) dat[4:10] - lapply(dat[4:10], function(x) as.numeric(as.character(x))) head(dat) Hope this helps, Rui Barradas Em 08-04-2014 20:40, Christofer Bogaso escreveu: Hi again, I am looking some way to download this data: http://www.cmegroup.com/trading/interest-rates/stir/eurodollar_quotes_openOutcry.html So far I have tried following code: library(XML) data - xmlParse( http://www.cmegroup.com/trading/interest-rates/stir/eurodollar_quotes_openOutcry.html ) However not be able to get in right way. Really appreciate if someone point me on right approach. Thanks for your time. [[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] browser always enters debug mode
On 08/04/2014 3:34 PM, Paul Murtaugh wrote:
This is something peculiar about the environment on one particular linux
box, because it doesn't happen on other computers. Whenever I invoke
browser() inside a function, it automatically enters debugging mode,
with line-by-line execution of code:
dum - function() { browser(); x - rnorm(10); print(x) }
dum()
Called from: dum()
Browse[1]
debug at #1: x - rnorm(10)
Browse[2]
debug at #1: print(x)
Browse[2]
[1] -0.41466890 0.02276493 1.01332894 -2.72784447 0.73471652 0.41360718
[7] 1.67942142 -1.47384724 1.12129541 -1.13447881
isdebugged(dum)
[1] FALSE
Thanks in advance for any tips on how to revert to the normal browser()
behavior.
-Paul
That looks like the normal browser() behaviour to me. What do you see
elsewhere?
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] xts Annual series
On Apr 8, 2014, at 15:15, Erin Hodgess erinm.hodg...@gmail.com wrote: Hello! If I have the following: x - as.yearqtr(2000 + seq(0,7)/4) x [1] 2000 Q1 2000 Q2 ... which is as it should be. Then if I set up time as time - xts(1:8,x) time 2000 Q1 1 2000 Q2 2 2000 Q3 3 . . Also fine Now suppose I want to have an annual xts object. How do I go about setting that up, please? Not quite as transparently. R does not (to my knowledge) have a commonly used 'year' class. You can of course use yearqtr objects and skip 3/4 per year. Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] xts Annual series
At first pass it would seem that 'integer' would make a perfectly fine year class. But for some reason it's disallowed: xts(rnorm(8), 2000L:2007) Error in xts(rnorm(8), 2000L:2007) : order.by requires an appropriate time-based object Which is a bit unexpected, since xts descends from zoo and this works fine: zoo(rnorm(8), 2000L:2007) 2000 2001 2002 2003 2004 2005 2006 2007 0.2963980 -1.7928750 1.9253476 -0.6851739 0.3223047 0.7776734 -0.3255266 -1.0980489 That doesn't feel very eXtensible to me. -John On Tue, Apr 8, 2014 at 4:27 PM, Michael Weylandt michael.weyla...@gmail.com wrote: On Apr 8, 2014, at 15:15, Erin Hodgess erinm.hodg...@gmail.com wrote: Hello! If I have the following: x - as.yearqtr(2000 + seq(0,7)/4) x [1] 2000 Q1 2000 Q2 ... which is as it should be. Then if I set up time as time - xts(1:8,x) time 2000 Q1 1 2000 Q2 2 2000 Q3 3 . . Also fine Now suppose I want to have an annual xts object. How do I go about setting that up, please? Not quite as transparently. R does not (to my knowledge) have a commonly used 'year' class. You can of course use yearqtr objects and skip 3/4 per year. Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] moses extreme reaction test
Just for the fun of it, I searched for R package moses extreme reaction test on google. The 8th hit was the package DescTools, but that included the 3 earlier hits and responses from r-help. So I guess the point is that Learn to Search may even be a bit over the top -- is there anyone on the internet who does not use standard search engines like google, bing, and yahoo? Best, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. H. Gilbert Welch On Tue, Apr 8, 2014 at 10:43 AM, David Winsemius dwinsem...@comcast.net wrote: On Apr 8, 2014, at 10:37 AM, José Trujillo Carmona wrote: Is there a package that contains moses extreme reaction test? Learn to search. install.packages(sos) library(sos) findFn(moses extreme) found 5 matches; retrieving 1 page Downloaded 3 links in 1 packages -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Pull Stock Symbol Out of String
You could try:
# Use ?regexec and ?regmatches to return a list of grouped matches.
# Use \\( and \\) to match literal parentheses.
# Use ... to match three characters.
# Use $ to match at end of string.
s1 - American Tower Corporation (REIT)Â (AMT)
s2 - Aetna Inc. (AET)
getSym - function(s) {regmatches(s, regexec(\\((...)\\)$, s))[[1]][2]}
getSym(s1) # [1] AMT
getSym(s2) # [1] AET
Cheers,
B.
On 2014-04-08, at 2:29 PM, Sparks, John James wrote:
Dear R Helpers,
My regex skills are beginner to intermediate and banging around the web
has not resulted in a solution to the problem below so I hope that one of
you who has mad skills can help me out.
I want to extract the stock ticker--AMT-- out of the string
American Tower Corporation (REIT)Â (AMT)
The presence of the other parenthetical text (REIT) makes this difficult.
Please note that the string may or may not have a interfering set of
characters such as the (REIT) so the solution needs to be generalizable to
the last set of characters that are contained in parentheses in the larger
string. So an example of a string without the interfering (REIT) would be
Aetna Inc. (AET)
Your assistance would be very much appreciated.
--John Sparks
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] xts Annual series
On Apr 8, 2014, at 17:32, John Laing john.la...@gmail.com wrote: That doesn't feel very eXtensible to me. xts is quite obviously past tense. ;-) The list of allowable index classes is found in is.timeBased IIRC and the exclusion of integers is because there's no obvious way to have them play nice with other index classes. M __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Label axis tick marks with a simple function of axis value
On 04/09/2014 02:06 AM, Hurr wrote: Don suggested something like this: h=c(1,2,3,4,5,6,7,8,9) v=c(9,8,7,6,5,4,3,2,1) plot(h,v,xaxt='n') xat=pretty(h) axis(1,at=xat,labels=1/xat) But it puts the tick marks at the data-x-locations. If the tick locations are not automatic or automatically separate from the data locations, then I want to tell it where to put them using a separate indicator. I am not familiar enough with R to find the answer. But if it would work, it would be valuable. Hi Hurr, If you want to use pretty: pretty(1:9) [1] 0 2 4 6 8 10 you don't necessarily get axis ticks at the same locations as the data points. Maybe you want to specify your own axis ticks and use those: axis_ticks-c(1,4,7,10) axis(1,at=axis_ticks,labels=1/axis_ticks) but that seems too obvious. Could you supply an example of what you want to do? Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] rJava not loading on Windows
I also have this problem, did you find a solution? [[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] browser always enters debug mode
It appears to be a difference between versions 2.* and 3.* in the way
that a newline ('enter') is handled at the browser prompt. Formerly, it
would continue execution of the function; now it kicks you into
debugging mode. To get the old behavior, you need to enter 'c' at the
browser prompt.
On 04/08/2014 12:34 PM, I wrote:
This is something peculiar about the environment on one particular linux
box, because it doesn't happen on other computers. Whenever I invoke
browser() inside a function, it automatically enters debugging mode,
with line-by-line execution of code:
dum - function() { browser(); x - rnorm(10); print(x) }
dum()
Called from: dum()
Browse[1]
debug at #1: x - rnorm(10)
Browse[2]
debug at #1: print(x)
Browse[2]
[1] -0.41466890 0.02276493 1.01332894 -2.72784447 0.73471652 0.41360718
[7] 1.67942142 -1.47384724 1.12129541 -1.13447881
isdebugged(dum)
[1] FALSE
Thanks in advance for any tips on how to revert to the normal browser()
behavior.
-Paul
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] moses extreme reaction test
On Apr 8, 2014, at 2:41 PM, Bert Gunter wrote: Just for the fun of it, I searched for R package moses extreme reaction test on google. The 8th hit was the package DescTools, but that included the 3 earlier hits and responses from r-help. So I guess the point is that Learn to Search may even be a bit over the top -- is there anyone on the internet who does not use standard search engines like google, bing, and yahoo? I don't think I'm the only one. Using Spencer Graves' excellent package is very convenient and has delivered many answers to questions posed on R help. It pops up a browser window directly from an R console command. I like the fact that I get an R help page with `findFn`. I suspect it has prevented many more questions that we never see. The other search tool I have used in preference to Google is Markmail. I find Google to be sometimes non-specific and possesses an very annoying tendency to give priority to Nabble citations. None of the first page Google citations actually answered the question when I tried. Rseek was much better, but I have found it to be less focused than sos::findFn. De gustibus non disputandem, I suppose. I suppose I should crack open Spencer's code and learn how to call Markmail and Rseek from my console session, that is unless he accepts this feature request and beats me to it. -- David. Best, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. H. Gilbert Welch On Tue, Apr 8, 2014 at 10:43 AM, David Winsemius dwinsem...@comcast.net wrote: On Apr 8, 2014, at 10:37 AM, José Trujillo Carmona wrote: Is there a package that contains moses extreme reaction test? Learn to search. install.packages(sos) library(sos) findFn(moses extreme) found 5 matches; retrieving 1 page Downloaded 3 links in 1 packages -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] browser always enters debug mode
On 08/04/2014, 6:05 PM, Paul Murtaugh wrote:
It appears to be a difference between versions 2.* and 3.* in the way
that a newline ('enter') is handled at the browser prompt. Formerly, it
would continue execution of the function; now it kicks you into
debugging mode. To get the old behavior, you need to enter 'c' at the
browser prompt.
Right, I didn't realize you were using old versions on those other
machines. Things are more consistent now (though I imagine there are
still inconsistencies, depending on how you enter the debugging system).
Duncan Murdoch
On 04/08/2014 12:34 PM, I wrote:
This is something peculiar about the environment on one particular linux
box, because it doesn't happen on other computers. Whenever I invoke
browser() inside a function, it automatically enters debugging mode,
with line-by-line execution of code:
dum - function() { browser(); x - rnorm(10); print(x) }
dum()
Called from: dum()
Browse[1]
debug at #1: x - rnorm(10)
Browse[2]
debug at #1: print(x)
Browse[2]
[1] -0.41466890 0.02276493 1.01332894 -2.72784447 0.73471652 0.41360718
[7] 1.67942142 -1.47384724 1.12129541 -1.13447881
isdebugged(dum)
[1] FALSE
Thanks in advance for any tips on how to revert to the normal browser()
behavior.
-Paul
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] getting arg names in function calls?
Hi, Bill: Thanks for the reply. Unfortunately, I don't see how that solves the example I gave of extracting plot(x=0, y=1) from tstFn - function()plot(0, 1). As I noted, body(tstFn) returns plot(0, 1) as an language object of class call. My challenge is to convert that into something similar, with explicit names for the arguments. Any thoughts? Spencer On 4/7/2014 3:18 PM, William Dunlap wrote: Look at match.call(). E.g., f - function(x, y = log2(x), ...) match.call() f() f() f(1, x=2, anotherArg=3, 4) f(x = 2, y = 1, anotherArg = 3, 4) or, using its 'definition' and 'call' arguments directly match.call(function(x, y, ...)NULL, quote(foo(1, x=2, extraArg=3, 4))) foo(x = 2, y = 1, extraArg = 3, 4) match.call(function(x, y, ...)NULL, quote(foo(1, x=2, extraArg=3, 4)), expand.dots=FALSE) foo(x = 2, y = 1, ... = list(extraArg = 3, 4)) Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Spencer Graves Sent: Monday, April 07, 2014 3:05 PM To: R list Subject: [R] getting arg names in function calls? How can I convert plot(0, 1) into plot(x=0, y=1)? More generally, how can I get argument names assigned to function calls in language objects? Example: tstFn - function()plot(0, 1) bo - body(tstFn) tstFnxy - function()plot(x=0, y=1) boxy - body(tstFnxy) Is there a function that will modify bo to match boxy? My current solution requires me to know the names of the arguments for plot (in this example). I'd prefer a more general solution. Thanks, Spencer p.s. I'm trying to create an animation by repeatedly calling a function that contains something like text(0, 1, abc). By computing on the language object 'text(0, 1, abc)', I can call text(0, 1, 'a') the first time, text(0, 1, 'ab') the second, and text(0, 1, 'abc') the third. The function will be more general if I can get the names of the arguments as just described. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] moses extreme reaction test
On 4/8/2014 3:56 PM, David Winsemius wrote:
On Apr 8, 2014, at 2:41 PM, Bert Gunter wrote:
Just for the fun of it, I searched for R package moses extreme
reaction test on google. The 8th hit was the package DescTools, but
that included the 3 earlier hits and responses from r-help.
So I guess the point is that Learn to Search may even be a bit over
the top -- is there anyone on the internet who does not use standard
search engines like google, bing, and yahoo?
I don't think I'm the only one. Using Spencer Graves' excellent package is very
convenient and has delivered many answers to questions posed on R help. It pops
up a browser window directly from an R console command. I like the fact that I
get an R help page with `findFn`. I suspect it has prevented many more
questions that we never see.
The other search tool I have used in preference to Google is Markmail. I find
Google to be sometimes non-specific and possesses an very annoying tendency to
give priority to Nabble citations. None of the first page Google citations
actually answered the question when I tried. Rseek was much better, but I have
found it to be less focused than sos::findFn. De gustibus non disputandem, I
suppose.
I suppose I should crack open Spencer's code and learn how to call Markmail and
Rseek from my console session, that is unless he accepts this feature request
and beats me to it.
1. I would happily accept code to generalize findFn{sos} to use
another search capability like Google, Markmail, Nabble or Rseek.
However, that might not be feasible, because the current code rests on a
database of R packages (CRAN, Bioconductor, plus a few others)
maintained by Jonathan Baron. When Jonathan stops maintaining that
database, that will be the end of findFn, unless someone else takes over
that maintenance.
2. Do you also use writeFindFn2xls{sos}? That produces an Excel
file with 3 sheets, the first of which is a summary by package. In
addition to the sort by count, maxScore and totalScore, I get the date
of the latest update, whether the package has a vignette, and the names
of author(s) and maintainer. That tells me whether the package is being
maintained and how easy it might be to learn. It is by far the fastest
literature search I know for anything statistical. In seconds, I can
have the outline for a talk on R capabilities for __ (as
mentioned in the sos vignette ;-)
3. Thanks for the kind words about findFn.
Spencer
--
Spencer Graves, PE, PhD
President and Chief Technology Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
web: www.structuremonitoring.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting arg names in function calls?
You might find it helpful to read http://adv-r.had.co.nz/Expressions.html, and look at pryr:: standardise_call(). Hadley On Tue, Apr 8, 2014 at 6:52 PM, Spencer Graves spencer.gra...@structuremonitoring.com wrote: Hi, Bill: Thanks for the reply. Unfortunately, I don't see how that solves the example I gave of extracting plot(x=0, y=1) from tstFn - function()plot(0, 1). As I noted, body(tstFn) returns plot(0, 1) as an language object of class call. My challenge is to convert that into something similar, with explicit names for the arguments. Any thoughts? Spencer On 4/7/2014 3:18 PM, William Dunlap wrote: Look at match.call(). E.g., f - function(x, y = log2(x), ...) match.call() f() f() f(1, x=2, anotherArg=3, 4) f(x = 2, y = 1, anotherArg = 3, 4) or, using its 'definition' and 'call' arguments directly match.call(function(x, y, ...)NULL, quote(foo(1, x=2, extraArg=3, 4))) foo(x = 2, y = 1, extraArg = 3, 4) match.call(function(x, y, ...)NULL, quote(foo(1, x=2, extraArg=3, 4)), expand.dots=FALSE) foo(x = 2, y = 1, ... = list(extraArg = 3, 4)) Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Spencer Graves Sent: Monday, April 07, 2014 3:05 PM To: R list Subject: [R] getting arg names in function calls? How can I convert plot(0, 1) into plot(x=0, y=1)? More generally, how can I get argument names assigned to function calls in language objects? Example: tstFn - function()plot(0, 1) bo - body(tstFn) tstFnxy - function()plot(x=0, y=1) boxy - body(tstFnxy) Is there a function that will modify bo to match boxy? My current solution requires me to know the names of the arguments for plot (in this example). I'd prefer a more general solution. Thanks, Spencer p.s. I'm trying to create an animation by repeatedly calling a function that contains something like text(0, 1, abc). By computing on the language object 'text(0, 1, abc)', I can call text(0, 1, 'a') the first time, text(0, 1, 'ab') the second, and text(0, 1, 'abc') the third. The function will be more general if I can get the names of the arguments as just described. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting arg names in function calls?
I don't see how that solves the example I gave of extracting plot(x=0, y=1) from tstFn - function()plot(0, 1). Try match.call(definition=plot, call=body(tstFn)) plot(x = 0, y = 1) plot() is not a great example, since some of its methods do not have an argument called 'y' (e.g., plot.stepfun) and it has a lot of ... arguments which you need to go to the help file for. Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: Spencer Graves [mailto:spencer.gra...@structuremonitoring.com] Sent: Tuesday, April 08, 2014 4:53 PM To: William Dunlap; R list Subject: Re: [R] getting arg names in function calls? Hi, Bill: Thanks for the reply. Unfortunately, I don't see how that solves the example I gave of extracting plot(x=0, y=1) from tstFn - function()plot(0, 1). As I noted, body(tstFn) returns plot(0, 1) as an language object of class call. My challenge is to convert that into something similar, with explicit names for the arguments. Any thoughts? Spencer On 4/7/2014 3:18 PM, William Dunlap wrote: Look at match.call(). E.g., f - function(x, y = log2(x), ...) match.call() f() f() f(1, x=2, anotherArg=3, 4) f(x = 2, y = 1, anotherArg = 3, 4) or, using its 'definition' and 'call' arguments directly match.call(function(x, y, ...)NULL, quote(foo(1, x=2, extraArg=3, 4))) foo(x = 2, y = 1, extraArg = 3, 4) match.call(function(x, y, ...)NULL, quote(foo(1, x=2, extraArg=3, 4)), expand.dots=FALSE) foo(x = 2, y = 1, ... = list(extraArg = 3, 4)) Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Spencer Graves Sent: Monday, April 07, 2014 3:05 PM To: R list Subject: [R] getting arg names in function calls? How can I convert plot(0, 1) into plot(x=0, y=1)? More generally, how can I get argument names assigned to function calls in language objects? Example: tstFn - function()plot(0, 1) bo - body(tstFn) tstFnxy - function()plot(x=0, y=1) boxy - body(tstFnxy) Is there a function that will modify bo to match boxy? My current solution requires me to know the names of the arguments for plot (in this example). I'd prefer a more general solution. Thanks, Spencer p.s. I'm trying to create an animation by repeatedly calling a function that contains something like text(0, 1, abc). By computing on the language object 'text(0, 1, abc)', I can call text(0, 1, 'a') the first time, text(0, 1, 'ab') the second, and text(0, 1, 'abc') the third. The function will be more general if I can get the names of the arguments as just described. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Spencer Graves, PE, PhD President and Chief Technology Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 web: www.structuremonitoring.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Label axis tick marks with a simple function of axis value
This still puts tick marks at data points: h=c(1,2,3,4,5,6,7,8,9) v=c(9,8,7,6,5,4,3,2,1) plot(h,v,xaxt='n') x-c(1.6,2.6,6.6,9.6,12.9) axis_labels-1/pretty(x) axis(1,at=pretty(x),labels=axis_labels) How do I get the axis to approx 13 ? -- View this message in context: http://r.789695.n4.nabble.com/Label-axis-tick-marks-with-a-simple-function-of-axis-value-tp4687917p4688443.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] Pull Stock Symbol Out of String
Hi, You may try: library(qdap) str1 - c(American Tower Corporation (REIT) (AMT), Aetna Inc. (AET)) unlist(lapply(bracketXtract(str1,round),tail,1),use.names=F) #[1] AMT AET A.K. On Tuesday, April 8, 2014 7:48 PM, Sparks, John James jspa...@uic.edu wrote: Dear R Helpers, My regex skills are beginner to intermediate and banging around the web has not resulted in a solution to the problem below so I hope that one of you who has mad skills can help me out. I want to extract the stock ticker--AMT-- out of the string American Tower Corporation (REIT) (AMT) The presence of the other parenthetical text (REIT) makes this difficult. Please note that the string may or may not have a interfering set of characters such as the (REIT) so the solution needs to be generalizable to the last set of characters that are contained in parentheses in the larger string. So an example of a string without the interfering (REIT) would be Aetna Inc. (AET) Your assistance would be very much appreciated. --John Sparks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Plotting does odd line thing
See ? plot.default. Add the log = y to your call. Remember to set ylim to positive values since log only takes positive values, e.g. ylim = c(1e-6, 0.1). Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance Modeling Technology Service Solutions T +45 9730 5135 M +45 2547 6050 fr...@vestas.commailto:fr...@vestas.com http://www.vestas.comhttp://www.vestas.com/ Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/noticehttp://www.vestas.com/legal/notice If you have received this e-mail in error please contact the sender. From: David Doyle [mailto:kydaviddo...@gmail.com] Sent: 8. april 2014 18:52 To: Frede Aakmann Tøgersen Cc: Jim Lemon; r-help@r-project.org Subject: Re: [R] Plotting does odd line thing THANK you for the help!! One more question. Being I need to compare 4 different wells, I like to have them all at the same scale which I can do with the ylim=c(min,max). But so the low concentrations don't get washed out, I like to plot the y axis in log format. ie 0.001, 0.010, 0.100. Below is the code I have so far. Thanks in advance. setwd(c:/R) mydata -read.csv(http://doylesdartden.com/R/2014_02_data.csv;, sep=,) attach(mydata) plot(Arsenic~Year,data=mydata, subset = Well.ID %in% c(MW-1, D_Arsenic), col=ifelse(D_Arsenic, black, red), ylab = mg/L,xlab = , pch=ifelse(D_Arsenic, 19, 17), cex = 1.5, ylim=c(0, 0.1)) subset-Well.ID %in% c(MW-1, D_Arsenic) lines(Arsenic[subset]~Year[subset]) #Add title title(main=MW-1) On Tue, Apr 8, 2014 at 12:52 AM, Frede Aakmann Tøgersen fr...@vestas.commailto:fr...@vestas.com wrote: Well the lines() function has a subset argument as does plot() so why not do this? lines(EMD ~ Year, data = mydata, subset = Well.ID %in% c(MW-1, D_EMD)) And yes lines() also have a data argument so why do you not use that (as you do with plot()) instead of attaching. Attaching dataframes may be a potential danger when some time in the future you have forgot that you attached the dataframe and you have forgot the warnings you get when attaching (making debugging difficult). Try this: ## Define an object named Year ## in which case call to lines do not what you think it will do Year - 1:nrow(mydata) ## or Year - 'foo' in which case one gets an error later ## attach the dataframe attach(mydata) The following object is masked _by_ .GlobalEnv: Year Now what will happen if you do lines(EMD ~ Year)? Here is the search path in my session: search() [1] .GlobalEnvmydatapackage:lattice [4] package:RODBC package:stats package:graphics [7] package:grDevices ESSR package:utils [10] package:datasets package:methods Autoloads [13] package:base Yours sincerely / Med venlig hilsen Frede Aakmann Tøgersen Specialist, M.Sc., Ph.D. Plant Performance Modeling Technology Service Solutions T +45 9730 5135tel:%2B45%209730%205135 M +45 2547 6050tel:%2B45%202547%206050 fr...@vestas.commailto:fr...@vestas.com http://www.vestas.com Company reg. name: Vestas Wind Systems A/S This e-mail is subject to our e-mail disclaimer statement. Please refer to www.vestas.com/legal/noticehttp://www.vestas.com/legal/notice If you have received this e-mail in error please contact the sender. -Original Message- From: r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org] On Behalf Of Jim Lemon Sent: 8. april 2014 04:53 To: David Doyle Cc: r-help@r-project.orgmailto:r-help@r-project.org Subject: Re: [R] Plotting does odd line thing On 04/08/2014 12:20 PM, David Doyle wrote: Hello folks, When I use the lines function below it connects all my points but then draws a line back to the start point. Any suggestions on what is going on?? mydata-read.csv(http://doylesdartden.com/R/test_data.csv;, sep=,) attach(mydata) plot(EMD~Year,data=mydata, subset = Well.ID %in% c(MW-1, D_EMD), col=ifelse(D_EMD, black, red), pch=ifelse(D_EDM, 19, 17), cex = 1.5) lines(EMD~Year) Hi David, While you will get what you expect with: lines(EMD[1:39]~Year[1:39]) I would be unnecessarily obscure in suggesting it. Try this: subset-Well.ID %in% c(MW-1, D_EMD) lines(EMD[subset]~Year[subset]) You haven't selected the same points for the lines function as you have for the plot function. Jim __ R-help@r-project.orgmailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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
