[R] Writing Unicode Text into Text File from R (in Windows)
Dear R Helpers, See the Code: a - intToUtf8(1777) show(a) zz - file(description=test.txt,open=w,encoding=UTF-8) cat(a, file = zz) close(zz) in a Unicode aware environment (such as RGui console or RStudio Console) you will see this as output: [1] Û± but the character is not written correctly in the file test.txt (which is encoded in UTF-8 without BOM) : U+06F1 The problem seems to be this: R changes text to the locale of system (for me this is Arabic Windows (Codepage 1256) that does not have a relevant code for U+06F1, then changes it back to UTF-8 and writes it into file. What do I miss here? How can I write a Unicode string into a text file correctly? Majid Einian, Economics Researcher, Monetary and Banking Research Institute, Central Bank of Islamic Republic of Iran, Tehran, IRAN and PhD Candidate in Economics, Graduate School of Management and Economics, Sharif University of Technology, Tehran, IRAN [[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] Selecting elements in lists with a row condition
Dear Contributors I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- [[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] Selecting elements in lists with a row condition
Dear Contributors sorry but the message was sent involuntary. I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 Each of these matrixes changes for the column name bank_name and for the suffix _CIB which reports the name as in bank_name. Moreover each matrix as a different number of rows, so that I cannot transform it into a large matrix. I need to create a matrix made of the rows of each element of the list that respect the criterium that the column p_made is = to 406. I need to pick each of the elements of each matrix that is contained in the list elements, that satisfy this condition. It seems difficult to me but perhaps is super easy. Thanks for any help you can provide. Francesca On 4 February 2014 12:42, Francesca francesca.panco...@gmail.com wrote: Dear Contributors I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- [[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] Running the Loop
Dear R forum, I have following data.frames dat = data.frame(id = c(1:3), root = c(0.10, 0.20, 0.74), maturity_period = c(20, 155, 428), mtm = c(1000, 1, 10), curve = c(USD, USD, USD)) dat id root maturity_period mtm curve 1 1 0.10 20 1e+03 USD 2 2 0.20 155 1e+04 USD 3 3 0.74 428 1e+05 USD standard_tenors = data.frame(T = c(1m, 3m, 6m, 12m, 5yr), D = c(30, 91, 182, 365, 1825)) standard_tenors T D 1 1m 30 2 3m 91 3 6m 182 4 12m 365 5 5yr 1825 # . library(plyr) T = standard_tenors$T D = standard_tenors$D n = length(standard_tenors$T) mtm_split_function = function(maturity_period, curve, root, mtm) { for(i in 1:(n-1)) { if (maturity_period D[i]) { N1 = paste(curve, T[i], sep =_) N2 = paste(curve, T[i], sep =_) PV1 = mtm PV2 = 0 }else if (maturity_period D[i] maturity_period D[i+1]) { N1 = paste(curve, T[i], sep =_) N2 = paste(curve, T[1+1], sep =_) PV1 = (mtm)*root PV2 = (mtm)*(1-root) }else if (maturity_period D[i+1]) { N1 = paste(curve, T[i], sep =_) N2 = paste(curve, T[i], sep =_) PV1 = 0 PV2 = mtm } } return(data.frame(Risk_factor1 = N1, Risk_factor2 = N2, Risk_factor1_mtm = PV1, Risk_factor2_mtm = PV2)) } # . splitted_mtm - ddply(.data = dat, .variables = id, .fun=function(x) mtm_split_function(maturity_period = x$maturity_period, curve = x$curve, root = x$root, mtm = x$mtm)) # OUTPUT I am getting id Risk_factor1 Risk_factor2 Risk_factor1_mtm Risk_factor2_mtm 1 1 USD_12m USD_12m 1000 0 2 2 USD_12m USD_12m 1 0 3 3 USD_12m USD_3m 74000 26000 # My PROBLEM However, My OUTPUT should be id Risk_factor1 Risk_factor2 Risk_factor1_mtm Risk_factor2_mtm 1 1 USD_1m USD_1m 1000 0 2 2 USD_3m USD_6m 2000 8000 3 3 USD_12m USD_5yr 74000 26000 Kindly guide With warm regards Katherine [[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] Capturing output of a C executable
On 14-02-03 5:44 PM, Phil Spector wrote: Dennis - The return value from .C will almost never be useful. Are you limiting this to the specific situation Dennis described, or making a more general claim? The more general claim is clearly false. Lots of packages return useful results using .C calls. The idea is that all arguments to the C function are passed by reference and may be modified in place, so you just pass a vector to receive the result. That's equivalent to what you describe below, but I think it seems simpler, since passing an address from R sounds like an exotic operation, not the norm. Duncan Murdoch If you want to bring results from the C environment into R, you need to do it by passing an address to .C which will receive the result. You may find this document helpful when interfacing R to C: http://www.stat.berkeley.edu/classes/s243/calling.pdf - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Sun, 2 Feb 2014, Dennis Fisher wrote: R 3.0.1 OS X Colleagues, I am experimenting with incorporating C code into R. After compiling the C code with: R CMD SHLIB -o FILE.so FILE.c and executing: dyn.load(“FILE.so”) (without any errors), I execute the following R functions in a terminal window: READSAS - function(sourcefile) .C(readsas, sourcefile) OUTPUT - READSAS(../SASFILES/sdrug.sas7bdat) R / C then reads a sas7bdat file and sends the contents to the terminal window. I expected OUTPUT to contain the text that appear in the terminal window (i.e., the contents of the file). But, that is not the case; OUTPUT contains: [[1]] [1] ../SASFILES/sdrug.sas7bdat It is not clear to my how to capture that appears in the terminal window. Ultimately, I may need to modify the C code so that the output goes to a file, which I then read into R. However, it would be better if I did not need to modify the C code. Does anyone have any ideas of how I can capture this output within R? Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-866-PLessThan (1-866-753-7784) www.PLessThan.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fit Negbin glm model with autoregressive correlation structure
Dear Cristiano, Thank you for your suggestion. It looks like an interesting option for what we are trying to do. We'll look at your paper and package in more details. Regards, Flavie -- View this message in context: http://r.789695.n4.nabble.com/Fit-Negbin-glm-model-with-autoregressive-correlation-structure-tp4684489p4684694.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] Writing Unicode Text into Text File from R (in Windows)
On 14-02-04 5:49 AM, Majid Einian wrote: Dear R Helpers, See the Code: a - intToUtf8(1777) show(a) zz - file(description=test.txt,open=w,encoding=UTF-8) cat(a, file = zz) close(zz) in a Unicode aware environment (such as RGui console or RStudio Console) you will see this as output: [1] Û± but the character is not written correctly in the file test.txt (which is encoded in UTF-8 without BOM) : U+06F1 The problem seems to be this: R changes text to the locale of system (for me this is Arabic Windows (Codepage 1256) that does not have a relevant code for U+06F1, then changes it back to UTF-8 and writes it into file. What do I miss here? How can I write a Unicode string into a text file correctly? There are a lot of places in R where it converts strings to the local encoding, perhaps too many. On the other hand, maybe Windows should be offering UTF-8 locales by now. I haven't tested in your locale, but I believe writeLines() to a connection declared to be in a UTF-8 encoding will maintain the encoding. You can declare a file to be in encoding UTF-8-BOM if you want to ignore a BOM on input; I forget whether it will write one on output. If it doesn't, you can always write one explicitly. I was hoping to make some progress on this before R 3.1.0 so that more cases of writing strings to UTF-8 files would work, but time is running out. Duncan Murdoch Majid Einian, Economics Researcher, Monetary and Banking Research Institute, Central Bank of Islamic Republic of Iran, Tehran, IRAN and PhD Candidate in Economics, Graduate School of Management and Economics, Sharif University of Technology, Tehran, IRAN [[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] creating an equivalent of r-help on r.stackexchange.com ?
On Feb 3, 2014, at 8:54 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Feb 3, 2014 at 8:41 PM, Marc Schwartz marc_schwa...@me.com wrote: Hi All, As I have noted in a prior reply in this thread, which began last November, I don't post in SO, but I do keep track of the traffic there via RSS feeds. However, the RSS feeds are primarily for new posts and do not seem to update with follow ups to the initial post. I do wish that they would provide an e-mail interface, which would help to address some of the issues raised here today. They do provide notifications on comments to posts, as do many other online fora. However, there is no routine mailing of new posts with a given tag (eg. 'R'), at least as far as I can see, as I had searched there previously for that functionality. That would be a nice push based approach, as opposed to having to go to the web site. You can set up email subscriptions for specific tags. See the preferences section of your account. I get regular emails of the r_filter. Here are the first few lines of an email I juist received (I have pasted it into this text plain email but they are received as HTML and there are links to the specific questions). snip Thanks for the pointer Gabor. I did not have an account on SE/SO and had only searched the various help resources there attempting to find out what kind of e-mail push functionality was available. A number of posts had suggested a non real time e-mail ability, which indeed seems to be the case. I went ahead and created an account to get a sense of what was available. As you note, you can sign up for e-mail subscriptions based upon various tag criteria. However, it would seem that you need to specify time intervals for the frequency of the e-mails. These can be daily, every 3 hours or every 15 minutes. So there seems to be a polling/digest based process going on. I created an e-mail subscription last evening and selected every 15 minutes. What appears to be happening is that the frequency of the e-mails actually varies. Overnight and this morning, I have e-mails coming in every 20 to 30 minutes or more apart. It is not entirely clear what the trigger is, given the inconsistency in frequency. Perhaps the infrastructure is not robust enough to support a more consistent polling/digest e-mail capability yet. The e-mails contain snippets of new questions only and not responses (paralleling the RSS feed content). I need to actually go to the web site to see the full content of the question and to see if the question has been answered. In most cases, by the time that I get to the site, even right away after getting the e-mail, there are numerous replies already present. There is, of course, no way to respond via e-mail. I would say that if one is looking for an efficient e-mail based interface to SE/SO, it does not exist at present. It is really designed as a web site only interaction, where you are likely going to need to have a browser continuously open to the respective site or sites in order to be able to interact effectively, if it is your intent to monitor and to respond in a timely fashion to queries. Alternatively, perhaps a real-time or near real-time updating RSS feed reader might make more sense for the timeliness of knowing about new questions. It is not clear to me how those who respond quickly (eg. within minutes) are interacting otherwise. There appear to be some browser extensions to support notifications (eg. for Chrome), but again, you need to have your browser open. There also appear to be some desktop apps in alpha/beta stages that might be helpful. However, they seem to track new comments to questions that are specifically being followed (eg. questions that you have posted), rather than all new questions, thus paralleling the SE/SO Inbox content. That being said, obviously, a lot of people are moving in that direction given the traffic decline here and the commensurate increase there. Regards, Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Selecting elements in lists with a row condition
Hi, Try: If `lst1` is the list: do.call(rbind,lapply(lst1,function(x) x[x[,p_made]==406,])) A.K. On Tuesday, February 4, 2014 8:53 AM, Francesca francesca.panco...@gmail.com wrote: Dear Contributors sorry but the message was sent involuntary. I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Y p_made p_for 1 CIB 10/02/06 1.33 p406-q406 406 406 2 CIB 10/23/06 1.28 p406-q406 406 406 3 CIB 11/22/06 1.28 p406-q406 406 406 4 CIB 10/02/06 1.35 p406-q107 406 107 5 CIB 10/23/06 1.32 p406-q107 406 107 6 CIB 11/22/06 1.32 p406-q107 406 107 Each of these matrixes changes for the column name bank_name and for the suffix _CIB which reports the name as in bank_name. Moreover each matrix as a different number of rows, so that I cannot transform it into a large matrix. I need to create a matrix made of the rows of each element of the list that respect the criterium that the column p_made is = to 406. I need to pick each of the elements of each matrix that is contained in the list elements, that satisfy this condition. It seems difficult to me but perhaps is super easy. Thanks for any help you can provide. Francesca On 4 February 2014 12:42, Francesca francesca.panco...@gmail.com wrote: Dear Contributors I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Y p_made p_for 1 CIB 10/02/06 1.33 p406-q406 406 406 2 CIB 10/23/06 1.28 p406-q406 406 406 3 CIB 11/22/06 1.28 p406-q406 406 406 4 CIB 10/02/06 1.35 p406-q107 406 107 5 CIB 10/23/06 1.32 p406-q107 406 107 6 CIB 11/22/06 1.32 p406-q107 406 107 -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Handling special characters in reading and writing to CSV
Hi All, I have some data with different special characters, newline character, and different language characters in a CSV file like `~!@#$%^*| ()-_+={[}]|\:;',.?/ in data, while I am trying to read this CSV and trying to do calculations I am not able to get this data as there in single cell. I found something like RFC 4180 format can help to solve this problem. If anyone can give suggestion related to handling these special characters it will be help full for me Thanks in advance, D V Kiran Kumar [[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] correlog function in pgirmess package
Dear R-help, I used the correlog function of pgirmess package to create a spatial correlogram for Moran's I. The function gives Moran's coefficient with a p value for each distance class. My question is what is the unit for the distance classes? Here is the outcome of the function: Moran I statistic dist.class coefp.valuen [1,] 1.283804 -0.0127393244 0.62182018 3288 [2,] 3.851412 -0.0070005170 0.53767024 5642 [3,] 6.419020 -0.0020360457 0.41371395 6546 [4,] 8.986627 0.0173943620 0.07212314 5814 [5,] 11.554235 -0.0225794695 0.84271228 4918 [6,] 14.121842 -0.0050324772 0.49452160 3372 [7,] 16.689450 -0.0007194256 0.42712852 2232 [8,] 19.257058 -0.0162570231 0.60272799 1242 [9,] 21.824665 -0.0330641732 0.74239660 1208 [10,] 24.392273 0.0602675483 0.09440368 508 [11,] 26.959881 -0.0007420201 0.43708138 270 [12,] 29.527488 0.0765320993 0.10876925 190 [13,] 32.095096 -0.0046161786 0.44659399 142 [14,] 34.662703 -0.0797066199 0.61910376 58 [15,] 37.230311 -0.7840212074 0.99986700 28 [16,] 39.797919 -0.7770962373 0.99839965 18 I first thought the distance unit was kilometers but the dist.class are only going until 40 and my data are taken from all around the Mediterranean sea (about 3700km long) so it cannot be right. In the correlog help it is said that Distances are in the same unit as the spatial coordinates but I don't get what that means. I gave spatial coordinates in decimal degree. It must be very simple but I was not able to find the answer anywhere. Thanks for your help, Cheers, Alicia -- View this message in context: http://r.789695.n4.nabble.com/correlog-function-in-pgirmess-package-tp4684706.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] GCV=0
Dear List I am trying to use gam function in mgcv 17.26. I have a big data set of about 40,000 data points. Every time that I run it ,it results in GCV score of 0 Family: gaussian Link function: identity Formula: D ~ s(Ghazl_res) + s(Depth) Estimated degrees of freedom: 3.77 2.91 total = 7.68 GCV score: 0 Plotting the curves of the predictor variables also gives a straight horizontal line along the zero value of the y axis. I really couldn't interpret whats going wrong. Appreciate it if anyone can comment Husam El Alqamy, B.Sc, M.Phil. Sr. Biodiversity GIS Analyst, Enivronmental Information Sector Environment Agency - Abu Dhabi [[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] Categorizing and displaying excel data in tabular format
R_format.csv http://r.789695.n4.nabble.com/file/n4684711/R_format.csv Hi, I am new to R Programming and need help on categorizing and plotting the data in the attached excel file into tabular format. Please help. -- View this message in context: http://r.789695.n4.nabble.com/Categorizing-and-displaying-excel-data-in-tabular-format-tp4684711.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] Categorizing and displaying excel data in tabular format
First, .csv files are not Excel files (and I was unable to open the one you link to). Second, while the word Help is used many ways, this list is intended to assist, i.e. you show that you have done some work and tell us where you are stuck and we are happy to give hints and pointers to help you get unstuck. This list is not a we do everything for you list. You should read the posting guide (link at the bottom of this and every post) and An Introduction to R. Then show us what you have tried, what is not working for you, and what you would like to see. As it is, your question does not even have enough information to let us know what question(s) you are trying to answer. There are many different plots to explore data in many different ways to answer different questions, your question does not narrow things down enough to give us a direction to point you. See `fortune(122)`. On Tue, Feb 4, 2014 at 9:27 AM, ashrafali ashraf...@techie.com wrote: R_format.csv http://r.789695.n4.nabble.com/file/n4684711/R_format.csv Hi, I am new to R Programming and need help on categorizing and plotting the data in the attached excel file into tabular format. Please help. -- View this message in context: http://r.789695.n4.nabble.com/Categorizing-and-displaying-excel-data-in-tabular-format-tp4684711.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. -- Gregory (Greg) L. Snow Ph.D. 538...@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] update.formula() to add interaction terms
Many thanks, that is exactly what I was looking for. I did not know about bquote, interesting! MP On Mon, Feb 3, 2014 at 6:29 PM, William Dunlap wdun...@tibco.com wrote: Is this the sort of thing you are looking for? fm - y ~ x1 + x2 + x3 + log(x4) # Use terms() instead of just all.vars() to keep log(x4) as log(x4) xVars - with(attributes(terms(fm)), as.list(variables)[-c(1,response+1)]) str(xVars) List of 4 $ : symbol x1 $ : symbol x2 $ : symbol x3 $ : language log(x4) # use bquote to make the addition to the formula update(fm, bquote( ~ . + .(xVars[[1]]) * .(xVars[[length(xVars)]]))) y ~ x1 + x2 + x3 + log(x4) + x1:log(x4) As a function it would be addInteraction - function(formula){ xVars - with(attributes(terms(formula)), as.list(variables)[-c(1,response+1)]) update(formula, bquote( ~ . + .(xVars[[1]]) * .(xVars[[length(xVars)]]))) } used as addInteraction(y~x1+x2+sqrt(x3)) y ~ x1 + x2 + sqrt(x3) + x1:sqrt(x3) If the last 'term' in the formula is a compound like x4:x5 and you want x1:x4:x5 added you will need to do more work (look at the 'factors' attribute of terms()'s output) - currently it adds x1:x5. 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 Marie-Pierre Sylvestre Sent: Monday, February 03, 2014 12:54 PM To: r-help@r-project.org Subject: [R] update.formula() to add interaction terms Hi, I have a list of formulae that I need to modify. For each formula, I need to add an interaction term between the first independent variable and the last one. I want to write a function to achieve that because the list of formulae to modify is long. For example, if the formula is y ~ x1 + x2 + x3 + x4, then I need to turn it either into y ~ x1*x4 + x2 + x3 or y ~ x1 + x2 + x3 + x4 + x4:x1 (I know they are the same, but one may be easier to work with than the other). Suppose I have the formula a which is defined as a - formula(y ~ x1+x2+x3+x4) I know how to access to the first and last independent variables of my formula: firstvar - all.vars(a[[3]])[1] lastvar - all.vars(a[[3]])[length( all.vars(a[[3]]))] What I can't figure out is how to use update.formula() to include my interaction term in order to get y ~ x1+x2+x3+x4 + x1:x4. Specifically, update.formula(a, ~ . + paste(all.vars(a[[3]])[1],firstvar, lastvar, sep = ':')) is not producing y ~ x1+x2+x3+x4 + x1:x4. Any idea? Thanks in advance, MP [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] mgcv: distribution of dev with Poisson data
mgcv: distribution of dev hi I can't tell if this is a simple error. I'm puzzled by the distribution of dev when fitting a gam to Poisson generated data. I expected dev to be approximately chi-squared on residual d.f., i.e. about 1000 in each case below. In particular, the low values in the 3rd and 4th versions would suggest scale 1, yet the data is Poisson generated. The problem isn't caused by insufficient k values in the smoother. Does this mean that with sparse data the distribution of dev is no longer approx chi-sq on residual df? Does it mean the scale estimate when fitting quasipoisson should be the Pearson version? thanks greg library(mgcv) set.seed(1) x1-runif(1000) linp-2+exp(-2*x1)*sin(8*x1) sum(exp(linp)) dev1-dev2-sums-rep(0,20) for (j in 1:20) { y-rpois(1000,exp(linp)) sums[j]-sum(y) m1-gam(y~s(x1),family=poisson) m2-gam(y~s(x1,k=20),family=poisson) dev1[j]=m1$dev dev2[j]=m2$dev } mean(sums) sd(sums) mean(dev1) sd(dev1) mean(dev2) sd(dev2) #dev slighly higher than expected linpa--1+exp(-2*x1)*sin(8*x1) sum(exp(linpa)) dev1a-dev2a-sumsa-rep(0,20) for (j in 1:20) { y-rpois(1000,exp(linpa)) sumsa[j]-sum(y) m1-gam(y~s(x1),family=poisson) m2-gam(y~s(x1,k=20),family=poisson) dev1a[j]=m1$dev dev2a[j]=m2$dev } mean(sumsa) sd(sumsa) mean(dev1a) sd(dev1a) mean(dev2a) sd(dev2a) #dev a bit lower than expected linpb--1.5+exp(-2*x1)*sin(8*x1) sum(exp(linpb)) dev1b-dev2b-sumsb-rep(0,20) for (j in 1:20) { y-rpois(1000,exp(linpb)) sumsb[j]-sum(y) m1-gam(y~s(x1),family=poisson) m2-gam(y~s(x1,k=20),family=poisson) dev1b[j]=m1$dev dev2b[j]=m2$dev } mean(sumsb) sd(sumsb) mean(dev1b) sd(dev1b) mean(dev2b) sd(dev2b) #dev much lower than expected m1q-gam(y~s(x1),family=quasipoisson,scale=-1) m1q$scale m1q$dev/(1000-sum(m1q$edf)) #scale estimate 1 sum((y-fitted(m1q))^2/fitted(m1q))/(1000-sum(m1q$edf)) #Pearson estimate of scale closer, but also 1 linpc--2+exp(-2*x1)*sin(8*x1) sum(exp(linpc)) dev1c-dev2c-sumsc-rep(0,20) for (j in 1:20) { y-rpois(1000,exp(linpc)) sumsc[j]-sum(y) m1-gam(y~s(x1),family=poisson) m2-gam(y~s(x1,k=20),family=poisson) dev1c[j]=m1$dev dev2c[j]=m2$dev } mean(sumsc) sd(sumsc) mean(dev1c) sd(dev1c) mean(dev2c) sd(dev2c) #dev much lower than expected m1q-gam(y~s(x1),family=quasipoisson,scale=-1) m1q$scale m1q$sig2 m1q$dev/(1000-sum(m1q$edf)) #scale estimate 1 sum((y-fitted(m1q))^2/fitted(m1q))/(1000-sum(m1q$edf)) #Pearson estimate of scale ok __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to describe gls post-hoc test in manuscript
Hello, I used the gls function from the nlme package to run a generalized least squares model. One of the predictor variables is a factor with 3 levels. Here is a reproducible example: library(nlme) response - c(rnorm(5,1,3), rnorm(5,6,1), rnorm(5,10,5)) foo - data.frame(response = response, X=rep(letters[1:3], each=5), Y=rep(LETTERS[1:3], each=5)) m1 - gls(response ~ X, weights = varIdent(form= ~1|Y), data=foo) The anova command indicates that the factor X is significant: anova(m1) The summary command compares the mean of each level of X to the reference level, which is 'a' in this case: summary(m1) Based on the summary command, I will report that levels 'b' and 'c' are greater than 'a' at the p 0.05 level. My question is, what test should I cite for these post hoc comparisons? Are these contrasts a version of Tukeys, Scheffe, Fisher LSD, or something similar. This reproducible example can also be viewed at: http://rpubs.com/jbeaulie/12839 == Jake J. Beaulieu, PhD US Environmental Protection Agency National Risk Management Research Lab 26 W. Martin Luther King Drive Cincinnati, OH 45268 USA 513-569-7842 (desk) 513-487-2511 (fax) beaulieu.j...@epa.gov [[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] Not able to find files in working directory
Hello. I am new to R here and I am coming across a small error in my code I am trying to run. I am trying to make a table of some value from a folder on my computer. I was able to pull a txt file from the folder and make bar graphs etc... however now I cannot do anything from this file and R is throwing errors at me from every direction. I will paste what I am trying to do. table(Squid$YEAR) Error in table(Squid$YEAR) : object 'Squid' not found table(Squid$MONTH,Squid$YEAR) Error in table(Squid$MONTH, Squid$YEAR) : object 'Squid' not found setwd(/Users/SamSchratz/Desktop/Spring 2014/Taking/Bio Stats/Lab/Lab 2 - Descriptive Statistics) Error in setwd(/Users/SamSchratz/Desktop/Spring 2014/Taking/Bio Stats/Lab/Lab 2 - Descriptive Statistics) : cannot change working directory It is confusing because I was able to run this earlier: barplot(table(Squid$MONTH,Squid$YEAR),main=Sampling by Year and Month,xlab=Year and Month, ylab=Sampling Size) and got: http://r.789695.n4.nabble.com/file/n4684710/SquidYearMonth.png Thoughts? I appreciate whatever you can tell me... -- View this message in context: http://r.789695.n4.nabble.com/Not-able-to-find-files-in-working-directory-tp4684710.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] Change file name
Hi, Try: from1 - list.files() ##folder where files are stored from1 #[1] p126r62_5t19880613_nn1.tif.gz p126r62_5t19880613_nn2.tif.gz #[3] p200r65_5t19880613_nn1.tif.gz to1 - gsub(^p(\\d+)r(\\d+)\\_.{2}(\\d{8})\\_nn(.*),LT5\\10\\2\\3_B\\4,from1) file.rename(from1,to1) #[1] TRUE TRUE TRUE list.files() #[1] LT512606219880613_B1.tif.gz LT512606219880613_B2.tif.gz #[3] LT520006519880613_B1.tif.gz A.K. Hi guys, Thank you for reply Actually I have thousands of files and I would like to change file name, then I can use it in my software e.g The original file p126r62_5t19880613_nn1.tif.gz The expected change LT512606219880613_B1.tif.gz The every single character in original files has some meaning p126r62_5t19880613_nn1.tif.gz p(path)126(path number) r (raw)62(rownumber)_5t(name of instrument)19880613(date)_nn1(band number).tif.gz So I would like to replace some part p = LT5 r = 0 _5t =remove _nn =B =add after date I have tried file.rename() function but I was unable to apply this change to all files. is it possible to use file.rename function to apply for all file? On Monday, February 3, 2014 10:48 AM, arun smartpink...@yahoo.com wrote: Hi, Check ?file.rename() http://stackoverflow.com/questions/10758965/how-do-i-rename-files-using-r A.K. I have list of files in folder e.g p126r62_5t19880613_nn1.tif.gz p126r62_5t19880613_nn2.tif.gz p200r65_5t19880613_nn1.tif.gz and I would like to change file name to LT512606219880613XX_B1.tif.gz LT512606219880613XX_B2.tif.gz LT520006519880613XX_B1.tif.gz Does any body knows how It can be changed? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R Books from Chapman Hall/CRC
Take advantage of a 20% discount on the most recent R books from Chapman Hall/CRC! We are pleased to offer our latest R books at a 20% discount through our website. To take advantage of this offer, simply visit www.crcpress.com, choose your titles, and insert code EZL20 in the Promotion Code field at checkout. Standard Shipping is always FREE on all orders from CRCPress.com! *** Analyzing Spatial Models of Choice and Judgment with R David A. Armstrong, II, Ryan Bakker, Royce Carroll, Christopher Hare, Keith T. Poole, and Howard Rosenthal ISBN: 978-1-4665-1715-8 Publication Date: Jan 2014 Number of Pages: 352 With recent advances in computing power and the widespread availability of political choice data, such as legislative roll call and public opinion survey data, the empirical estimation of spatial models has never been easier or more popular. This book demonstrates how to estimate and interpret spatial models using a variety of methods with the popular, open-source programming language R. List Price: $69.95 / £44.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466517158 Also available as an eBook *** Nonlinear Time Series: Theory, Methods and Applications with R Examples Randal Douc, Eric Moulines, and David Stoffer ISBN: 978-1-4665-0225-3 Publication Date: Jan 2014 Number of Pages: 551 This text emphasizes nonlinear models for a course in time series analysis. After introducing stochastic processes, Markov chains, Poisson processes, and ARMA models, the authors cover functional autoregressive, ARCH, threshold AR, and discrete time series models as well as several complementary approaches. They discuss the main limit theorems for Markov chains, useful inequalities, statistical techniques to infer model parameters, and GLMs. Moving on to HMM models, the book examines filtering and smoothing, parametric and nonparametric inference, advanced particle filtering, and numerical methods for inference. List Price: $99.95 / £63.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466502253 *** Analyzing Baseball Data with R Max Marchi and Jim Albert ISBN: 978-1-4665-7022-1 Publication Date: Oct 2013 Number of Pages: 334 This book provides an introduction to R for sabermetricians, baseball enthusiasts, and students interested in exploring the rich sources of baseball data. It equips readers with the necessary skills and software tools to perform all of the analysis steps, from gathering the datasets and entering them in a convenient format to visualizing the data via graphs to performing a statistical analysis. List Price: $39.95 / £25.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466570221 Visit the authors' blog for advice on using R in sabermetrics research and for keeping up to date with new developments: http://baseballwithr.wordpress.com/. *** Reproducible Research with R and RStudio Christopher Gandrud ISBN: 978-1-4665-7284-3 Publication Date: Jul 2013 Number of Pages: 294 Bringing together computational research tools in one accessible source, this book guides you in creating dynamic and highly reproducible research. Suitable for researchers in any quantitative empirical discipline, it presents practical tools for data collection, data analysis, and the presentation of results. Whether you're an advanced user or just getting started with tools such as R and LaTeX, this book saves you time searching for information and helps you successfully carry out computational research. It provides a practical reproducible research workflow that you can use to gather and analyze data as well as dynamically present results in print and on the web. List Price: $69.95 / £44.99 For more details and to order: http://www.crcpress.com/product/isbn/9781466572843 Also available as an eBook *** Dynamic Documents with R and knitr Yihui Xie ISBN: 978-1-4822-0353-0 Publication Date: Jul 2013 Number of Pages: 216 Suitable for both beginners and advanced users, this book shows you how to write reports in simple languages such as Markdown. The reports range from homework, projects, exams, books, blogs, and web pages to any documents related to statistical graphics, computing, and data analysis. While familiarity with LaTeX and HTML is helpful, the book requires no prior experience with advanced programs or languages. For beginners, the text provides enough features to get started on basic applications. For power users, the last several chapters enable an understanding of the extensibility of the knitr package. List Price: $59.95 / £38.99 For more details and to order: http://www.crcpress.com/product/isbn/9781482203530 Also available as an eBook *** Foundations of Statistical Algorithms: With References to R Packages Claus Weihs, Olaf Mersmann, and Uwe Ligges ISBN: 978-1-4398-7885-9 Publication Date: Dec 2013 Number of Pages: 474 A new and refreshingly different approach
Re: [R] Not able to find files in working directory
You need to read the file in first. More generally, you need to spend some time with an introductory R tutorial. There are many, including the Introduction to R shipped with every copy of R, as well as the ones listed on the R website at http://cran.r-project.org/other-docs.html. Best, Ista On Tue, Feb 4, 2014 at 11:27 AM, Sschratz87 samuel.schr...@smail.astate.edu wrote: Hello. I am new to R here and I am coming across a small error in my code I am trying to run. I am trying to make a table of some value from a folder on my computer. I was able to pull a txt file from the folder and make bar graphs etc... however now I cannot do anything from this file and R is throwing errors at me from every direction. I will paste what I am trying to do. table(Squid$YEAR) Error in table(Squid$YEAR) : object 'Squid' not found table(Squid$MONTH,Squid$YEAR) Error in table(Squid$MONTH, Squid$YEAR) : object 'Squid' not found setwd(/Users/SamSchratz/Desktop/Spring 2014/Taking/Bio Stats/Lab/Lab 2 - Descriptive Statistics) Error in setwd(/Users/SamSchratz/Desktop/Spring 2014/Taking/Bio Stats/Lab/Lab 2 - Descriptive Statistics) : cannot change working directory It is confusing because I was able to run this earlier: barplot(table(Squid$MONTH,Squid$YEAR),main=Sampling by Year and Month,xlab=Year and Month, ylab=Sampling Size) and got: http://r.789695.n4.nabble.com/file/n4684710/SquidYearMonth.png Thoughts? I appreciate whatever you can tell me... -- View this message in context: http://r.789695.n4.nabble.com/Not-able-to-find-files-in-working-directory-tp4684710.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] two active RGL device / linked devices
Dear list! My question is, if there is an option in RGL, that two devices can be active. It means, when eg. points in first device is rotated also points in second devies is rotated. For example: library(rgl) x - rnorm(1000) y - rnorm(1000) z - rnorm(1000) open3d() points3d(x,y,z) open3d() points3d(x,y,z) rgl.set(c(1,2), silent=TRUE) #does not work Thanks for suggestions. OV __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] creating an equivalent of r-help on r.stackexchange.com ?
My sentiments exactly! Thanks to all for taking the time to flesh out the potential flaws of the stackexchange solution. KW Date: Tue, 04 Feb 2014 10:36:21 +1300 From: Rolf Turner r.tur...@auckland.ac.nz To: Bert Gunter gunter.ber...@gene.com Cc: r-help@r-project.org r-help@r-project.org Subject: Re: [R] creating an equivalent of r-help on r.stackexchange.com ? Message-ID: 52f00bd5@auckland.ac.nz Content-Type: text/plain; charset=ISO-8859-1; format=flowed For what it's worth, I would like to say that I concur completely with Don and Bert. (Also I would like second Bert's vote of thanks to Don for expressing the position so clearly.) cheers, Rolf Turner -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] two active RGL device / linked devices
On 04/02/2014 12:08 PM, Omphalodes Verna wrote: Dear list! My question is, if there is an option in RGL, that two devices can be active. It means, when eg. points in first device is rotated also points in second devies is rotated. For example: library(rgl) x - rnorm(1000) y - rnorm(1000) z - rnorm(1000) open3d() points3d(x,y,z) open3d() points3d(x,y,z) rgl.set(c(1,2), silent=TRUE) #does not work The demo(stereo) code does something like this. There are plans for some changes that might make this all easier, but they are likely several months away from completion. (The idea will be to allow multiple scenes to be displayed in the same window; there should be a lot of flexibility in how the mouse affects them. The demo(stereo) method will still be needed to control multiple devices.) 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] creating an equivalent of r-help on r.stackexchange.com ? (was: Re: Should there be an R-beginners list?)
Clint and Liviu, Stackoverflow also has rss feeds available, if you prefer being pushed the information that way. For the R tagged questions it's here: http://stackoverflow.com/feeds/tag/r. Since some e-mail clients double as feed readers, you may be able to read the feed from your e-mail client. Otherwise, it does mean another application. Regards, Jason -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Liviu Andronic Sent: Monday, February 03, 2014 11:24 PM To: Clint Bowman Cc: r-help@r-project.org; Bert Gunter Subject: Re: [R] creating an equivalent of r-help on r.stackexchange.com ? (was: Re: Should there be an R-beginners list?) Dear Clint, On Tue, Feb 4, 2014 at 1:27 AM, Clint Bowman cl...@ecy.wa.gov wrote: Liviu, Thanks for the excellent description of the advantages of SE. However, there is a significant fraction of the population that prefers that information be pushed out to them rather than having to pull it to them. The best system is one that accommodates both equally well. It's not exactly the same as in a mail client, but you also have a push-like interface on SE, sort of: http://stackoverflow.com/questions/tagged/r - The 'Newest' tab displays all recent questions, sorted in chronological order with latest on top; it gets refreshed automatically, as in a mail client (hence, push-like) - The 'Active' tab displays all questions with recent activity (question asked, answered or commented upon) - You also have the very useful 'Unanswered' tab, which allows to identify questions that haven't yet received useful advice Another push-like element in SE is that once you ask a question or answer, any subsequent comments on your post will be notified to you either in the web interface or by email. This helps keep discussions alive. Regards, Liviu Clint Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Tue, 4 Feb 2014, Liviu Andronic wrote: Dear Don and Bert, Allow me to address some of your concerns below. On Mon, Feb 3, 2014 at 9:56 PM, Bert Gunter gunter.ber...@gene.com wrote: I find SO's voting for posting business especially irritating. I wish merely to post or to read the posts of others without being subjected to some kind of online pseudo game and ratings competition. That alone keeps me away. But Don said it better. On SO voting is irrelevant for either posting a question or an answer. *Anyone* (with an account) can ask a question, and *anyone* can answer a question. Their system of privileges is explained here: http://askubuntu.com/help/privileges . But to summarize: - if you're interested only in giving help, then the only really relevant threshold is 10 and 50 votes (removing some new user restrictions and allowing you to comment on posts, respectively) - if you're interested only in seeking help, then all thresholds are irrelevant really All other thresholds are relevant only if you're interested in contributing to the organization of information, or in moderating this whole forum-slash-wiki thingy. And as a note, given the quality of your answers on r-help, Bert, I have no doubt that you will clock upwards 50 upvotes in a couple of hours or so. I realize that I may be out of step with the masses here, and the masses should certainly decide. Hopefully I won't be around if/when they decide that R-help should go. The proposal is not necessarily to close down r-help. From the myriad lists it currently has, R Core could keep only r-help and r-devel, and encourage new users to seek help on r.stackexchange.com. The scope of r-help could be redefined. On Mon, Feb 3, 2014 at 12:42 PM, MacQueen, Don macque...@llnl.gov wrote: - They waste copious amounts of screen space on irrelevant things such as votes, the number of views, the elapsed time since something or other happened, fancy web-page headers, and so on. Oh, and advertisements. The Mathematica stackexchange example given in a link in one of the emails below (http://mathematica.stackexchange.com/) illustrates these shortcomings -- and it's not the worst such example. Well, I've seen my fair share of advertisements on Gmail, Yahoo Mail or what have you. I know some use dedicated clients, but not all do. (And sofar I haven't noticed one single intrusive or distracting ad on SE.) As for the number of votes, this is actually the most useful bit of this QA interface: it allows for the best questions (or most often asked) to stand out from all the noise. And it allows for the best answers (or those most authoritative) to stand
Re: [R] Selecting elements in lists with a row condition
Hello A. k. thanks for the suggestion. I tried this but it does not work. I probably use it in the wrong way. This is what it tells me, do.call(rbind,lapply(bank.list,function(x) x[x[,p_made]==406,])) Errore in match.names(clabs, names(xi)) : names do not match previous names What am I doing wrong? f. -- Francesca Pancotto Università degli Studi di Modena e Reggio Emilia Palazzo Dossetti - Viale Allegri, 9 - 42121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- Il giorno 04/feb/2014, alle ore 16:42, arun smartpink...@yahoo.com ha scritto: Hi, Try: If `lst1` is the list: do.call(rbind,lapply(lst1,function(x) x[x[,p_made]==406,])) A.K. On Tuesday, February 4, 2014 8:53 AM, Francesca francesca.panco...@gmail.com wrote: Dear Contributors sorry but the message was sent involuntary. I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 Each of these matrixes changes for the column name bank_name and for the suffix _CIB which reports the name as in bank_name. Moreover each matrix as a different number of rows, so that I cannot transform it into a large matrix. I need to create a matrix made of the rows of each element of the list that respect the criterium that the column p_made is = to 406. I need to pick each of the elements of each matrix that is contained in the list elements, that satisfy this condition. It seems difficult to me but perhaps is super easy. Thanks for any help you can provide. Francesca On 4 February 2014 12:42, Francesca francesca.panco...@gmail.com wrote: Dear Contributors I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- [[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] Categorizing and displaying excel data in tabular format
Hello, With me the following worked: URL - http://r.789695.n4.nabble.com/file/n4684711/R_format.csv; dat - read.csv(URL) str(dat) 'data.frame': 34 obs. of 2 variables: $ Tasks : Factor w/ 10 levels Code upgrade BE/FE,..: 4 4 4 4 8 6 6 6 6 6 ... $ Client.Mnemonic: Factor w/ 18 levels AHSW_CA,ANMC_AK,..: 2 2 18 18 2 9 9 8 8 8 ... I also find fortune(122) appropriate. Rui Barradas Em 04-02-2014 16:49, Greg Snow escreveu: First, .csv files are not Excel files (and I was unable to open the one you link to). Second, while the word Help is used many ways, this list is intended to assist, i.e. you show that you have done some work and tell us where you are stuck and we are happy to give hints and pointers to help you get unstuck. This list is not a we do everything for you list. You should read the posting guide (link at the bottom of this and every post) and An Introduction to R. Then show us what you have tried, what is not working for you, and what you would like to see. As it is, your question does not even have enough information to let us know what question(s) you are trying to answer. There are many different plots to explore data in many different ways to answer different questions, your question does not narrow things down enough to give us a direction to point you. See `fortune(122)`. On Tue, Feb 4, 2014 at 9:27 AM, ashrafali ashraf...@techie.com wrote: R_format.csv http://r.789695.n4.nabble.com/file/n4684711/R_format.csv Hi, I am new to R Programming and need help on categorizing and plotting the data in the attached excel file into tabular format. Please help. -- View this message in context: http://r.789695.n4.nabble.com/Categorizing-and-displaying-excel-data-in-tabular-format-tp4684711.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MCPMod method
I can't answer your question, but I did notice the CRAN page for the MCPMod package states, The MCPMod package will not be further developed, all future development of the MCP-Mod methodology will be done in the DoseFinding R-package. http://cran.r-project.org/web/packages/MCPMod/index.html Jean On Mon, Feb 3, 2014 at 2:32 PM, Mahboobe Akhlaghi mahboobe.akhla...@ymail.com wrote: hi, I have a question about MCPMod package for finding optimal dose. does MCPMod method better than fuzzy method for finding dose?and why? many thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] Which analysis for a set of dummy variables alone ?
This sounds more like a statistics question than an R question. You may have better luck posting to a different forum, e.g., Cross Validated, http://stats.stackexchange.com/. Jean On Tue, Feb 4, 2014 at 3:19 AM, sylvain willart sylvain.will...@gmail.comwrote: Dear R-users, I have a dataset I would like to analyze and plot It consists of 100 dummy variables (0/1) for about 2,000,000 observations There is absolutely no quantitative variable, nor anything I could use as an explained variable for a regression analysis. Actually, the dataset represents the patronage of 2 billion customers for 100 stores. It equals 1 if the consumer go to the store, 0 if he doesn't. With no further information. As the variable look like factors (0/1), I thought I could go for a Mutliple Correspondence Analysis (MCA). However, the resulting plot consists of 2 points for each variable (one for 1 and one for 0) which is not easily interpretable. (or is there a method for not plotting certain points in MCA?) I also tried to consider my dataset as a bipartite network (consumer-store). However, the plot is not really insightful, as I am especially looking for links between stores. (kind of if a consumer go to that store, he probably also goes to this one...) So, I have a simple question: which method you would choose for computing and plotting the links between a set of dummy variable? Thanks in advance Sylvain PhD Marketing Associate Professor University of Lille - FR [[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] GLM weights for the Poisson family
On Feb 3, 2014, at 11:12 PM, IamRandom wrote: I am running a simple example of GLM. If I include weights when family=poisson then the weights are calculated iteratively and $weights and $prior.weights return different values. The $prior.weights are what I supplied and $weights are the posterior weights of the IWLS. If I include weights with family=gaussian then the weights are static and $weights and $prior.weights return the same values; it seems to ignore IWLS algorithm procedure. I don't think so. I think it's just starting where you specify and proceeding normally from there. I really want the family=poisson to behave like the family=gaussian and use the static weights. Thoughts? I was under the impression there is no need to iterate for family=gaussian. If my understanding is correct only one iteration gets done. Maybe you should say what you are trying to accomplish. -- 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] GLM weights for the Poisson family
On 04/02/14 20:12, IamRandom wrote: I am running a simple example of GLM. If I include weights when family=poisson then the weights are calculated iteratively and $weights and $prior.weights return different values. The $prior.weights are what I supplied and $weights are the posterior weights of the IWLS. If I include weights with family=gaussian then the weights are static and $weights and $prior.weights return the same values; it seems to ignore IWLS algorithm procedure. I really want the family=poisson to behave like the family=gaussian and use the static weights. Thoughts? As far as I understand things, your desideratum makes no sense. The prior weights and the just-plain-weights are very different creatures. The reason they wind up being the same for the gaussian family is that for the gaussian family the likelihood is maximized by least squares; there is no need for iteration or for re-weighting. The poisson family cannot behave like the gaussian family because for the poisson family (or any family *other* than gaussian) iteration is necessary in order to maximize the likelihood. You might get some insight into what's going on if you were to read Annette Dobson's book An Introduction to Generalized Linear Models (Chapman and Hall, 1990). cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] creating an equivalent of r-help on r.stackexchange.com ? (was: Re: Should there be an R-beginners list?)
Jason, Thanks--I've found an RSS feed from EPA very useful and will check Stackoverflow's. Clint Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Tue, 4 Feb 2014, Law, Jason wrote: Clint and Liviu, Stackoverflow also has rss feeds available, if you prefer being pushed the information that way. For the R tagged questions it's here: http://stackoverflow.com/feeds/tag/r. Since some e-mail clients double as feed readers, you may be able to read the feed from your e-mail client. Otherwise, it does mean another application. Regards, Jason -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Liviu Andronic Sent: Monday, February 03, 2014 11:24 PM To: Clint Bowman Cc: r-help@r-project.org; Bert Gunter Subject: Re: [R] creating an equivalent of r-help on r.stackexchange.com ? (was: Re: Should there be an R-beginners list?) Dear Clint, On Tue, Feb 4, 2014 at 1:27 AM, Clint Bowman cl...@ecy.wa.gov wrote: Liviu, Thanks for the excellent description of the advantages of SE. However, there is a significant fraction of the population that prefers that information be pushed out to them rather than having to pull it to them. The best system is one that accommodates both equally well. It's not exactly the same as in a mail client, but you also have a push-like interface on SE, sort of: http://stackoverflow.com/questions/tagged/r - The 'Newest' tab displays all recent questions, sorted in chronological order with latest on top; it gets refreshed automatically, as in a mail client (hence, push-like) - The 'Active' tab displays all questions with recent activity (question asked, answered or commented upon) - You also have the very useful 'Unanswered' tab, which allows to identify questions that haven't yet received useful advice Another push-like element in SE is that once you ask a question or answer, any subsequent comments on your post will be notified to you either in the web interface or by email. This helps keep discussions alive. Regards, Liviu Clint Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Tue, 4 Feb 2014, Liviu Andronic wrote: Dear Don and Bert, Allow me to address some of your concerns below. On Mon, Feb 3, 2014 at 9:56 PM, Bert Gunter gunter.ber...@gene.com wrote: I find SO's voting for posting business especially irritating. I wish merely to post or to read the posts of others without being subjected to some kind of online pseudo game and ratings competition. That alone keeps me away. But Don said it better. On SO voting is irrelevant for either posting a question or an answer. *Anyone* (with an account) can ask a question, and *anyone* can answer a question. Their system of privileges is explained here: http://askubuntu.com/help/privileges . But to summarize: - if you're interested only in giving help, then the only really relevant threshold is 10 and 50 votes (removing some new user restrictions and allowing you to comment on posts, respectively) - if you're interested only in seeking help, then all thresholds are irrelevant really All other thresholds are relevant only if you're interested in contributing to the organization of information, or in moderating this whole forum-slash-wiki thingy. And as a note, given the quality of your answers on r-help, Bert, I have no doubt that you will clock upwards 50 upvotes in a couple of hours or so. I realize that I may be out of step with the masses here, and the masses should certainly decide. Hopefully I won't be around if/when they decide that R-help should go. The proposal is not necessarily to close down r-help. From the myriad lists it currently has, R Core could keep only r-help and r-devel, and encourage new users to seek help on r.stackexchange.com. The scope of r-help could be redefined. On Mon, Feb 3, 2014 at 12:42 PM, MacQueen, Don macque...@llnl.gov wrote: - They waste copious amounts of screen space on irrelevant things such as votes, the number of views, the elapsed time since something or other happened, fancy web-page headers, and so on. Oh, and advertisements. The Mathematica stackexchange example given in a link in one of the emails below (http://mathematica.stackexchange.com/) illustrates these shortcomings --
Re: [R] Selecting elements in lists with a row condition
Hi, Looks like the colnames of list elements are not the same. For e.g. lst1 - list(structure(list(bankname = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = CIB, class = factor), date = structure(c(1L, 2L, 3L, 1L, 2L, 3L), .Label = c(10/02/06, 10/23/06, 11/22/06 ), class = factor), px_last_CIB = c(1.33, 1.28, 1.28, 1.35, 1.32, 1.32), Q.Y = structure(c(2L, 2L, 2L, 1L, 1L, 1L), .Label = c(p406-q107, p406-q406), class = factor), p_made = c(406L, 406L, 406L, 406L, 406L, 406L), p_for = c(406L, 406L, 406L, 107L, 107L, 107L )), .Names = c(bankname, date, px_last_CIB, Q.Y, p_made, p_for), class = data.frame, row.names = c(1, 2, 3, 4, 5, 6)), structure(list(bank_name = structure(c(1L, 1L, 1L, 1L), .Label = CBA, class = factor), date = structure(c(1L, 2L, 3L, 1L), .Label = c(10/02/06, 10/23/06, 11/22/06), class = factor), px_last_CIB = c(1.33, 1.28, 1.28, 1.35), Q.Y = structure(c(2L, 2L, 2L, 1L), .Label = c(p406-q107, p406-q406), class = factor), p_made = c(406L, 406L, 402L, 402L), p_for = c(406L, 406L, 402L, 107L)), .Names = c(bank_name, date, px_last_CIB, Q.Y, p_made, p_for), class = data.frame, row.names = c(1, 2, 3, 4)), structure(list(bank_name = structure(c(1L, 1L, 1L, 1L), .Label = CAA, class = factor), date = structure(c(1L, 2L, 3L, 1L), .Label = c(10/02/06, 10/23/06, 11/22/06), class = factor), px_last_CIB = c(1.33, 1.28, 1.28, 1.35), Q.Y = structure(c(2L, 2L, 2L, 1L), .Label = c(p406-q107, p406-q406), class = factor), p_made = c(401L, 401L, 406L, 402L), p_for = c(401L, 401L, 406L, 107L)), .Names = c(bank_name, date, px_last_CIB, Q.Y, p_made, p_for), class = data.frame, row.names = c(1, 2, 3, 4))) names(lst1[[2]])[1] #[1] bank_name names(lst1[[2]])[1] #[1] bank_name do.call(rbind,lapply(lst1,function(x) x[x[,p_made]==406,])) Error in match.names(clabs, names(xi)) : names do not match previous names lst2 - lapply(lst1,function(x) {names(x) -names(lst1[[2]]);x}) do.call(rbind,lapply(lst2,function(x) x[x[,p_made]==406,])) bank_name date px_last_CIB Q.Y p_made p_for 1 CIB 10/02/06 1.33 p406-q406 406 406 2 CIB 10/23/06 1.28 p406-q406 406 406 3 CIB 11/22/06 1.28 p406-q406 406 406 4 CIB 10/02/06 1.35 p406-q107 406 107 5 CIB 10/23/06 1.32 p406-q107 406 107 6 CIB 11/22/06 1.32 p406-q107 406 107 11 CBA 10/02/06 1.33 p406-q406 406 406 21 CBA 10/23/06 1.28 p406-q406 406 406 31 CAA 11/22/06 1.28 p406-q406 406 406 A.K. On Tuesday, February 4, 2014 3:01 PM, Francesca Pancotto francesca.panco...@gmail.com wrote: Hello A. k. thanks for the suggestion. I tried this but it does not work. I probably use it in the wrong way. This is what it tells me, do.call(rbind,lapply(bank.list,function(x) x[x[,p_made]==406,])) Errore in match.names(clabs, names(xi)) : names do not match previous names What am I doing wrong? f. -- Francesca Pancotto Università degli Studi di Modena e Reggio Emilia Palazzo Dossetti - Viale Allegri, 9 - 42121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- Il giorno 04/feb/2014, alle ore 16:42, arun smartpink...@yahoo.com ha scritto: Hi, Try: If `lst1` is the list: do.call(rbind,lapply(lst1,function(x) x[x[,p_made]==406,])) A.K. On Tuesday, February 4, 2014 8:53 AM, Francesca francesca.panco...@gmail.com wrote: Dear Contributors sorry but the message was sent involuntary. I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Y p_made p_for 1 CIB 10/02/06 1.33 p406-q406 406 406 2 CIB 10/23/06 1.28 p406-q406 406 406 3 CIB 11/22/06 1.28 p406-q406 406 406 4 CIB 10/02/06 1.35 p406-q107 406 107 5 CIB 10/23/06 1.32 p406-q107 406 107 6 CIB 11/22/06 1.32 p406-q107 406 107 Each of these matrixes changes for the column name bank_name and for the suffix _CIB which reports the name as in bank_name. Moreover each matrix as a different number of rows, so that I cannot transform it into a large matrix. I need to create a matrix made of the rows of each element of the list that respect the criterium that the column p_made is = to 406. I need to pick each of the elements of each matrix that is contained in the list elements, that satisfy this condition. It seems difficult to me but perhaps is super easy. Thanks for any help you can provide. Francesca On 4 February 2014 12:42, Francesca francesca.panco...@gmail.com wrote: Dear Contributors I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a
Re: [R] Handling special characters in reading and writing to CSV
On Feb 4, 2014, at 7:58 AM, Venkata Kirankumar wrote: Hi All, I have some data with different special characters, newline character, and different language characters in a CSV file like `~!@#$%^*| ()-_+={[}]|\:;',.?/ in data, while I am trying to read this CSV and trying to do calculations I am not able to get this data as there in single cell. I found something like RFC 4180 format can help to solve this problem. If anyone can give suggestion related to handling these special characters it will be help full for me I'm having a difficult time understanding your expectations and thedata situation. If it's a csv file, then how can all three of comma, single-quote, and double-quote be properly distinguished when they are also part of the data? You might consider using readLines (from base) or read.fwf (from the utils package) Thanks in advance, D V Kiran Kumar [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius 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] Selecting elements in lists with a row condition
On 02/05/2014 06:54 AM, Francesca Pancotto wrote: Hello A. k. thanks for the suggestion. I tried this but it does not work. I probably use it in the wrong way. This is what it tells me, do.call(rbind,lapply(bank.list,function(x) x[x[,p_made]==406,])) Errore in match.names(clabs, names(xi)) : names do not match previous names What am I doing wrong? Hi Francesca, This is not as elegant as Arun's solution, but it seems to work: bank.list-list() bank.list[[1]]-read.table( text=bank_name date px_last_CIB Q.Yp_made p_for CIB 10/02/061.33 p406-q406406 406 CIB 10/23/061.28 p406-q406406 406 CIB 11/22/061.28 p406-q406406 406 CIB 10/02/061.35 p406-q107406 107 CIB 10/23/061.32 p406-q107406 107 CIB 11/22/061.32 p406-q107406 107,header=TRUE) bank.list[[2]]-read.table( text=bank_name date px_last_CIB Q.Yp_made p_for DIB 10/02/061.33 p406-q406406 406 DIB 10/23/061.28 p406-q406406 406 DIB 11/22/061.28 p406-q406406 406 DIB 10/02/061.35 p406-q107406 107 DIB 10/23/061.32 p406-q107406 107 DIB 11/22/061.32 p406-q107406 107,header=TRUE) bank.list[[3]]-read.table( text=bank_name date px_last_CIB Q.Yp_made p_for EIB 10/02/061.33 p406-q406406 406 EIB 10/23/061.28 p406-q406406 406 EIB 11/22/061.28 p406-q406406 406 EIB 10/02/061.35 p406-q107406 107 EIB 10/23/061.32 p406-q107406 107 EIB 11/22/061.32 p406-q107406 107,header=TRUE) get_rows-function(x,field_name,field_value) { return(x[x[,field_name]==field_value,]) } collapse_df_list-function(x,collapse_field) { listlen-length(x) newdf-x[[1]] for(listel in 2:listlen) newdf-rbind(newdf,x[[listel]]) return(newdf) } select_list-lapply(bank.list,get_rows,p_for,406) merged_list-collapse_df_list(select_list,p_for) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Selecting elements in lists with a row condition
On Feb 4, 2014, at 11:54 AM, Francesca Pancotto wrote: Hello A. k. thanks for the suggestion. I tried this but it does not work. I probably use it in the wrong way. This is what it tells me, do.call(rbind,lapply(bank.list,function(x) x[x[,p_made]==406,])) Errore in match.names(clabs, names(xi)) : names do not match previous names As teh message says, you are either working with a set of list which have different names or you are creating data.frames with that problem. What does this show sapply(bank.list, names) If they are all the same, then the output should be very , very regular. -- david. What am I doing wrong? f. -- Francesca Pancotto Università degli Studi di Modena e Reggio Emilia Palazzo Dossetti - Viale Allegri, 9 - 42121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- Il giorno 04/feb/2014, alle ore 16:42, arun smartpink...@yahoo.com ha scritto: Hi, Try: If `lst1` is the list: do.call(rbind,lapply(lst1,function(x) x[x[,p_made]==406,])) A.K. On Tuesday, February 4, 2014 8:53 AM, Francesca francesca.panco...@gmail.com wrote: Dear Contributors sorry but the message was sent involuntary. I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 Each of these matrixes changes for the column name bank_name and for the suffix _CIB which reports the name as in bank_name. Moreover each matrix as a different number of rows, so that I cannot transform it into a large matrix. I need to create a matrix made of the rows of each element of the list that respect the criterium that the column p_made is = to 406. I need to pick each of the elements of each matrix that is contained in the list elements, that satisfy this condition. It seems difficult to me but perhaps is super easy. Thanks for any help you can provide. Francesca On 4 February 2014 12:42, Francesca francesca.panco...@gmail.com wrote: Dear Contributors I am asking some advice on how to solve the following problem. I have a list composed of 78 elements, each of which is a matrix of factors and numbers, similar to the following bank_name date px_last_CIB Q.Yp_made p_for 1 CIB 10/02/061.33 p406-q406406 406 2 CIB 10/23/061.28 p406-q406406 406 3 CIB 11/22/061.28 p406-q406406 406 4 CIB 10/02/061.35 p406-q107406 107 5 CIB 10/23/061.32 p406-q107406 107 6 CIB 11/22/061.32 p406-q107406 107 -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- -- Francesca -- Francesca Pancotto, PhD Università di Modena e Reggio Emilia Viale A. Allegri, 9 40121 Reggio Emilia Office: +39 0522 523264 Web: https://sites.google.com/site/francescapancotto/ -- [[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. 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] Categorizing and displaying excel data in tabular format
On Feb 4, 2014, at 8:49 AM, Greg Snow wrote: First, .csv files are not Excel files (and I was unable to open the one you link to). This is what was in the linked file: Tasks,Client Mnemonic Ibus ,ANMC_AK Ibus ,ANMC_AK Ibus ,YAVA_AZ Ibus ,YAVA_AZ Release upgrade(BE),ANMC_AK OS upgrades ,LACJ_CA OS upgrades ,LACJ_CA OS upgrades ,HMH_CA OS upgrades ,HMH_CA OS upgrades ,HMH_CA P2 ,CITY_CA P2 ,CITY_CA Code upgrade BE/FE,PALO_CA Xenapp builds ,CDC_CA Code upgrade BE/FE,WYOM_WY Code upgrade BE/FE,WYOM_WY Ibus ,AHSW_CA Ibus ,DEAC_MT Ibus ,DEAC_MT Ibus ,SVCH_AZ Ibus ,TORR_C Ibus ,TORR_C Ibus ,SVCH_AZ Release upgrade(FE),ANMC_AK CPDI,CHOC_CA CPDI,CHOC_CA CPDI,STVN_NM CPDI,STVN_NM Go-live support ,UNIV_UT New Foot Print,HMH_CA Xenapp builds ,NAH_AZ,HMH_CA Xenapp builds ,CERN_RWX Release upgrade(BE),PACF_CA Release upgrade(BE),PACF_CA Second, while the word Help is used many ways, this list is intended to assist, i.e. you show that you have done some work and tell us where you are stuck and we are happy to give hints and pointers to help you get unstuck. This list is not a we do everything for you list. You should read the posting guide (link at the bottom of this and every post) and An Introduction to R. Then show us what you have tried, what is not working for you, and what you would like to see. As it is, your question does not even have enough information to let us know what question(s) you are trying to answer. There are many different plots to explore data in many different ways to answer different questions, your question does not narrow things down enough to give us a direction to point you. See `fortune(122)`. I would add that many people get the incorrect notion that Nabble is actually Rhelp. It's not, and many postings to Nabble are blocked by the ETHZ mailing list server. -- David. On Tue, Feb 4, 2014 at 9:27 AM, ashrafali ashraf...@techie.com wrote: R_format.csv http://r.789695.n4.nabble.com/file/n4684711/R_format.csv Hi, I am new to R Programming and need help on categorizing and plotting the data in the attached excel file into tabular format. Please help. -- View this message in context: http://r.789695.n4.nabble.com/Categorizing-and-displaying-excel-data-in-tabular-format-tp4684711.html Sent from the R help mailing list archive at Nabble.com. __ -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com 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] Renumber series
Hi, Try: set.seed(89) dat1 - within(data.frame(column1=LETTERS[1:5],column2=rnorm(5)),order1 - order(order(column2))+32) within(dat1,order2 - order(order(dat1$order1))) column1 column2 order1 order2 1 A -1.4516020 33 1 2 B 0.7081001 35 3 3 C 1.5930974 36 4 4 D -0.8375955 34 2 5 E 1.9294701 37 5 #or (dat1$order1-33)+1 #[1] 1 3 4 2 5 A.K. Hi, I have data with a column that is the order of my data, it starts with 33 and goes on but not one by one, for example like this: column1 column2 order … …. 33 .. … 36 … … 45 … … .. I want to make 33 equals to 1, and then it calculates for other numbers, like 36 be 4 and so on. Is there a way to do thins in R? Thank you so much __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Renumber series
??? What's wrong with simply order - 32 ?? -- 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, Feb 4, 2014 at 2:37 PM, arun smartpink...@yahoo.com wrote: Hi, Try: set.seed(89) dat1 - within(data.frame(column1=LETTERS[1:5],column2=rnorm(5)),order1 - order(order(column2))+32) within(dat1,order2 - order(order(dat1$order1))) column1column2 order1 order2 1 A -1.4516020 33 1 2 B 0.7081001 35 3 3 C 1.5930974 36 4 4 D -0.8375955 34 2 5 E 1.9294701 37 5 #or (dat1$order1-33)+1 #[1] 1 3 4 2 5 A.K. Hi, I have data with a column that is the order of my data, it starts with 33 and goes on but not one by one, for example like this: column1 column2 order … …. 33 .. …36 … …45 … … .. I want to make 33 equals to 1, and then it calculates for other numbers, like 36 be 4 and so on. Is there a way to do thins in R? Thank you so much __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Revolution blog: January 2014 roundup
[Apologies if you already saw this on r-devel, email error on my behalf -- DMS] Revolution Analytics staff write about R every weekday at the Revolutions blog: http://blog.revolutionanalytics.com and every month I post a summary of articles from the previous month of particular interest to readers of r-help. In case you missed them, here are some articles related to R from the month of January: Princeton's Germán Rodríguez has published a useful Introduction to R guide, with a focus on linear and logistic regression: http://bit.ly/1c1bero The rxDForest function in the RevoScaleR package fits random forests of histogram-binning trees: http://bit.ly/1b08qAq A tutorial on using the xts package to analyze http://bit.ly/1c1bc30 and plot time series data http://bit.ly/1c1bc31 In a video interview with Trevor Hastie, John Chambers recounts the history of S and R: http://bit.ly/1c1bern A review of Doing Data Science, a new book by Rachel Schutt and Cathy O'Neil http://bit.ly/1c1berp Hadley Wickham introduces the dplyr package, with its grammar of data manipulation http://bit.ly/1c1bcje The new choroplethr package makes it easier to create data maps in R: http://bit.ly/1c1bcjf A developer preview of SparkR, an interface between R and Apache Spark, is now available: http://bit.ly/1c1berq Joseph Rickert reviews the capabilities of R for topological data analysis: http://bit.ly/1c1berr In a recent survey of data scientists, R is the most-used software tool other than SQL: http://bit.ly/1c1bers A new JSS article on computing with massive data, and a change in policy for acceptable JSS software licenses: http://bit.ly/1b08srV Large scale optimization with the optim and rxDataStep functions: http://bit.ly/1c1bert Large enterprise software vendors with connections to R: http://bit.ly/1c1bcji A preview of a forthcoming update to Max Kuhn's caret package, and an interactive chart showing similarities amongst the 143 statistical and machine learning models it supports: http://bit.ly/1c1beru Simulation-based forecasts by combining expert opinion: http://bit.ly/1c1bcjj Tips on getting R help: http://bit.ly/1c1bcjk The top 10 posts on the Revolutions blog from 2013: http://bit.ly/1b08qAt Some non-R stories in the past month included: levitation with sound waves (http://bit.ly/1c1bcjl), the NYT's 4th Down Bot (http://bit.ly/1c1berv), bird flight patterns (http://bit.ly/1c1bcjm), camera magic on Vine (http://bit.ly/1c1berw), visualizing whisky flavor profiles (http://bit.ly/1c1bcjn), the Cornsweet illusion (http://bit.ly/1b08srW), and a one-sentence explanation of the Fourier Transform (http://bit.ly/1c1berz). Meeting times for local R user groups (http://bit.ly/eC5YQe) can be found on the updated R Community Calendar at: http://bit.ly/bb3naW If you're looking for more articles about R, you can find summaries from previous months at http://blog.revolutionanalytics.com/roundups/. You can receive daily blog posts via email using services like blogtrottr.com, or join the Revolution Analytics mailing list at http://revolutionanalytics.com/newsletter to be alerted to new articles on a monthly basis. As always, thanks for the comments and please keep sending suggestions to me at da...@revolutionanalytics.com . Don't forget you can also follow the blog using an RSS reader, or by following me on Twitter (I'm @revodavid). Cheers, # David -- David M Smith da...@revolutionanalytics.com VP of Marketing, Revolution Analytics http://blog.revolutionanalytics.com Tel: +1 (650) 646-9523 (Seattle WA, USA) Twitter: @revodavid __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Categorizing and displaying excel data in tabular format
I have converted the excel file to csv and imported the data using R Studio. This is the file R_format.xlsx http://r.789695.n4.nabble.com/file/n4684737/R_format.xlsx I have coded the following: list(R_format$Tasks) list(R_format$Client.Mnemonic) task.freq=table(R_format$Tasks) task.freq cbind(task.freq) I am not sure how to categorize the things. In the excel sheet I have the same tasks done for different client mnemonics. I want to categorize them accordingly and display them in tabular format one after the other. The works are: * Categorize according to Tasks * Syntax for plotting the table with two columns Tasks and ClientMnemonics. thanks!! Ashraf -- View this message in context: http://r.789695.n4.nabble.com/Categorizing-and-displaying-excel-data-in-tabular-format-tp4684711p4684737.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] Not able to find files in working directory
I have already done that. It was working and now it isn't. The program was not closed or restarted. It just stopped working. Squid-read.table(Squid.txt,header=T) Error in file(file, rt) : cannot open the connection In addition: Warning message: In file(file, rt) : cannot open file 'Squid.txt': No such file or directory' but the file is still in the same folder and has not moved. I am in a class that is based off R. Still learning the basics. -- View this message in context: http://r.789695.n4.nabble.com/Not-able-to-find-files-in-working-directory-tp4684710p4684736.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Adjusting the x axis range in effects plots
G'day All, I am having some difficulties with effects plots from the effects package. I am doing partial regression analyses of normal linear models and obtain lovely effect plots with a linear effect line and 95%CL. No problem so far. The problem is that I want to overlay the actual datapoints on the plot and, when I do so, I find that several of them are falling off the edge of the plot. In other words the x-axis range is too narrow to show all the data points. When I try to adjust the plot using xlim, then nothing happens. I can adjust the plots with ylim, color etc but the range of the x axis seems to be set somewhere in the package, and xlim disabled, and as far as I can see that is a problem because the axis range doesn't always fit the actual data range. It doesn't seem anyone else has posted about this problem. Am I wasting my time trying to adjust the x range in plots from the effects package? If so, is there a way to output the partial regression + confidence limit lines so that I can just plot them up myself not using effects? Thanks for any pointers. Mark A/Prof. Mark Hovenden Locked Bag 55 School of Biological Sciences Hobart Tas. 7001 University of Tasmania Australia phone: +61 3 6226 7874 fax: +61 3 6226 2698 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Merging xts List created using panel data
Hi, I have done the following: library(foreign) RNOM - read.dta(Return Panel without missing.dta) library(PerformanceAnalytics) RNOM_list-split(RNOM,RNOM$gvkey) xtsList - lapply(RNOM_list, function(x) { attrCol - c(conm) numCol - c(gvkey,prccm,trfm, trt1m) y - xts(x[,numCol], as.Date(x$datadate,format=%d/%m/%Y)) xtsAttributes(y) - as.list(x[1,attrCol]) y }) logreturns - lapply(xtsList, function(x) { Return.calculate(x$prccm, method = log) } ) Now I get, xts List of logreturns and xtsList of my data. Can anyone please tell me, how can I merge logreturns with my original dataframe or xtsList; and export it as a csv/excel file for further regression analysis (after merging the file needs to look like panel data)? The description of variables is as follows: datadatelong %d Data Date - Security Monthly gvkey str6 %6sGlobal Company Key - Security Monthly Descriptor conmstr58 %58s Company Name prccm double %20.0g Price - Close - Monthly trfmdouble %8.0g Monthly Total Return Factor trt1m double %8.0g Monthly Total Return gvkeynumlong %8.0g gvkeynum Global Company Key - Security Monthly Descriptor The data can be downloaded from here: https://drive.google.com/file/d/0B8usDJAPeV85ZG1MSHNDeFQtM28/edit?usp=sharing Thanks Regards, Jairaj Gupta PhD Finance Candidate Hull University Business School Student No. 201201551 Mobile: 00-44-(0)7795904913 SSRN Author: http://ssrn.com/author=1936478 Linkedin Profile: http://www.linkedin.com/pub/jairaj-gupta/54/13a/b61** To view the terms under which this email is distributed, please go to http://www2.hull.ac.uk/legal/disclaimer.aspx **__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Merging xts List created using panel data
This is related to: http://stackoverflow.com/q/21393866/271616 http://stackoverflow.com/q/21484267/271616 -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com On Tue, Feb 4, 2014 at 6:07 PM, Jairaj Gupta j.gu...@2012.hull.ac.uk wrote: Hi, I have done the following: library(foreign) RNOM - read.dta(Return Panel without missing.dta) library(PerformanceAnalytics) RNOM_list-split(RNOM,RNOM$gvkey) xtsList - lapply(RNOM_list, function(x) { attrCol - c(conm) numCol - c(gvkey,prccm,trfm, trt1m) y - xts(x[,numCol], as.Date(x$datadate,format=%d/%m/%Y)) xtsAttributes(y) - as.list(x[1,attrCol]) y }) logreturns - lapply(xtsList, function(x) { Return.calculate(x$prccm, method = log) } ) Now I get, xts List of logreturns and xtsList of my data. Can anyone please tell me, how can I merge logreturns with my original dataframe or xtsList; and export it as a csv/excel file for further regression analysis (after merging the file needs to look like panel data)? The description of variables is as follows: datadatelong %d Data Date - Security Monthly gvkey str6 %6sGlobal Company Key - Security Monthly Descriptor conmstr58 %58s Company Name prccm double %20.0g Price - Close - Monthly trfmdouble %8.0g Monthly Total Return Factor trt1m double %8.0g Monthly Total Return gvkeynumlong %8.0g gvkeynum Global Company Key - Security Monthly Descriptor The data can be downloaded from here: https://drive.google.com/file/d/0B8usDJAPeV85ZG1MSHNDeFQtM28/edit?usp=sharing Thanks Regards, Jairaj Gupta PhD Finance Candidate Hull University Business School Student No. 201201551 Mobile: 00-44-(0)7795904913 SSRN Author: http://ssrn.com/author=1936478 Linkedin Profile: http://www.linkedin.com/pub/jairaj-gupta/54/13a/b61 ** To view the terms under which this email is distributed, please go to http://www2.hull.ac.uk/legal/disclaimer.aspx ** __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Running the Loop
Hi Katherine,Not sure if this helps. I was able to the result after making up some additional conditions into your function. fun1 - function(x){ lst1 - lapply(seq(n-1),function(i){ with(x,if(maturity_period D[i] maturity_period D[i+1]){ data.frame(N1=paste(curve,T[i],sep=_),N2=paste(curve,T[i+1],sep=_),PV1=mtm*root,PV2=(mtm)*(1-root)) } else if(maturity_period D[i]) { data.frame(N1=paste(curve,T[i],sep=_),N2=paste(curve,T[i],sep=_),PV1=mtm,PV2=0) } else if(maturity_period D[i+1]) { data.frame(N1=paste(curve,T[i],sep=_),N2=paste(curve,T[i],sep=_),PV1=0,PV2=mtm) } ) } ) dat2 - cbind(id=x$id,do.call(rbind,lst1)) indx - with(dat2,PV1!=0 PV2!=0) dat2New- if(!any(indx)){ dat2[1,] } else dat2[indx,] colnames(dat2New)[-1] -paste0(paste0(Risk_factor,rep(1:2,2)),rep(c(,_mtm),each=2)) dat2New } ddply(dat,.(id),fun1) # id Risk_factor1 Risk_factor2 Risk_factor1_mtm Risk_factor2_mtm #1 1 USD_1m USD_1m 1000 0 #2 2 USD_3m USD_6m 2000 8000 #3 3 USD_12m USD_5yr 74000 26000 A.K. On Tuesday, February 4, 2014 7:22 AM, Katherine Gobin katherine_go...@yahoo.com wrote: Dear R forum, I have following data.frames dat = data.frame(id = c(1:3), root = c(0.10, 0.20, 0.74), maturity_period = c(20, 155, 428), mtm = c(1000, 1, 10), curve = c(USD, USD, USD)) dat id root maturity_period mtm curve 1 1 0.10 20 1e+03 USD 2 2 0.20 155 1e+04 USD 3 3 0.74 428 1e+05 USD standard_tenors = data.frame(T = c(1m, 3m, 6m, 12m, 5yr), D = c(30, 91, 182, 365, 1825)) standard_tenors T D 1 1m 30 2 3m 91 3 6m 182 4 12m 365 5 5yr 1825 # . library(plyr) T = standard_tenors$T D = standard_tenors$D n = length(standard_tenors$T) mtm_split_function = function(maturity_period, curve, root, mtm) { for(i in 1:(n-1)) { if (maturity_period D[i]) { N1 = paste(curve, T[i], sep =_) N2 = paste(curve, T[i], sep =_) PV1 = mtm PV2 = 0 }else if (maturity_period D[i] maturity_period D[i+1]) { N1 = paste(curve, T[i], sep =_) N2 = paste(curve, T[1+1], sep =_) PV1 = (mtm)*root PV2 = (mtm)*(1-root) }else if (maturity_period D[i+1]) { N1 = paste(curve, T[i], sep =_) N2 = paste(curve, T[i], sep =_) PV1 = 0 PV2 = mtm } } return(data.frame(Risk_factor1 = N1, Risk_factor2 = N2, Risk_factor1_mtm = PV1, Risk_factor2_mtm = PV2)) } # . splitted_mtm - ddply(.data = dat, .variables = id, .fun=function(x) mtm_split_function(maturity_period = x$maturity_period, curve = x$curve, root = x$root, mtm = x$mtm)) # OUTPUT I am getting id Risk_factor1 Risk_factor2 Risk_factor1_mtm Risk_factor2_mtm 1 1 USD_12m USD_12m 1000 0 2 2 USD_12m USD_12m 1 0 3 3 USD_12m USD_3m 74000 26000 # My PROBLEM However, My OUTPUT should be id Risk_factor1 Risk_factor2 Risk_factor1_mtm Risk_factor2_mtm 1 1 USD_1m USD_1m 1000 0 2 2 USD_3m USD_6m 2000 8000 3 3 USD_12m USD_5yr 74000 26000 Kindly guide With warm regards Katherine [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Pubmed (XML) data to data.frame
Dear all, I would like to obtain a data.frame with some data selected from pubmed information. For example, I would like to do an specific search and obtain a data.frame with the title of each article and the publication type. Example of syntax: library(reutils) library(XML) pmid - esearch('Epidemiology [Journal]', pubmed, mindate=2013/01/01, maxdate=paste(2013/12/31, sep=), retmax=1000) Mensajes de aviso perdidos NCBI requests that you provide an email address with each query to their API. Set the global option 'reutils.email' to your address to make this message go away. articles - efetch(pmid, db=pubmed, retmax=1000) Mensajes de aviso perdidos NCBI requests that you provide an email address with each query to their API. Set the global option 'reutils.email' to your address to make this message go away. journal - articles$xmlValue(//Title) BUT HERE I HAVE THE PROBLEM Each article (PMID) can have more than one type of publication. ptype - articles$xmlValue(//PublicationType) With this syntax I can select the first type of publication ptype1 - articles$xmlValue(//PublicationTypeList//PublicationType[1]) length(ptype1) [1] 181 With this syntax I can select the second type of publication. ptype2 - articles$xmlValue(//PublicationTypeList//PublicationType[2]) length(ptype2) [1] 152 But I would like to obtain a vector of length 181 (as ptype1) with NA's when there is no information of publication list Therefore I cannot obtain a data.frame because I don't obtain a NA when there is no data in ptype2 df1 - data.frame(journal=journal, ptype1=ptype1, ptype2=ptype2 ) Error en data.frame(journal = journal, ptype1 = ptype1, ptype2 = ptype2) : arguments imply differing number of rows: 181, 152 How can I do this data.frame??? Best Regards, Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Categorizing and displaying excel data in tabular format
On Feb 4, 2014, at 1:40 PM, ashrafali wrote: I have converted the excel file to csv and imported the data using R Studio. This is the file R_format.xlsx http://r.789695.n4.nabble.com/file/n4684737/R_format.xlsx I have coded the following: list(R_format$Tasks) list(R_format$Client.Mnemonic) task.freq=table(R_format$Tasks) task.freq cbind(task.freq) I would have instead used the table function. table(R_format$Tasks) table(R_format$Client.Mnemonic) with(R_format, table(Tasks,Client.Mnemonic ) You could, of course, assign them to object names. task.freq cbind(task.freq) cbind is used to put two columns side by side. It doesn't make much sense to supply it with only one argument. I am not sure how to categorize the things. In the excel sheet I have the same tasks done for different client mnemonics. I want to categorize them accordingly and display them in tabular format one after the other. The works are: * Categorize according to Tasks * Syntax for plotting the table with two columns Tasks and ClientMnemonics. Using table with two arguments may give you wnat you requested. thanks!! Ashraf -- View this message in context: http://r.789695.n4.nabble.com/Categorizing-and-displaying-excel-data-in-tabular-format-tp4684711p4684737.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius 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] Obtain the hex code for a given character.
If I have a character such as £ stored in a object called xxx, how can I obtain the hex code representation of this character? In this case I know that the hex code is \u00A3, but if I didn't, how would I find out? I would like a function foo() such that foo(xxx) would return, say, the string 00A3. I have googled and otherwise searched around and have come up with nothing that seemed at all helpful to me. If I am missing something obvious, please point me at it. (I have found a table on the web, which contains the information that I need, but it is only accessible by eye as far as I can discern.) Supplementary question: Suppose I have the string 00A3 stored in an object called yyy. How do I put that string together with \u so as to obtain £? I thought I could do xxx - paste(\u,yyy,sep=) but R won't let me use \u without hex digits. How can I get around this? Thanks. cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Adjusting the x axis range in effects plots
Dear Mark, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Mark Hovenden Sent: Tuesday, February 04, 2014 6:52 PM To: r-help@r-project.org Subject: [R] Adjusting the x axis range in effects plots G'day All, I am having some difficulties with effects plots from the effects package. I am doing partial regression analyses of normal linear models and obtain lovely effect plots with a linear effect line and 95%CL. No problem so far. The problem is that I want to overlay the actual datapoints on the plot and, when I do so, I find that several of them are falling off the edge of the plot. In other words the x-axis range is too narrow to show all the data points. When I try to adjust the plot using xlim, then nothing happens. I can adjust the plots with ylim, color etc but the range of the x axis seems to be set somewhere in the package, and xlim disabled, and as far as I can see that is a problem because the axis range doesn't always fit the actual data range. See the xlevels argument to Effect() in ?Effect; you can set any values you want for which the effect is evaluated. It doesn't seem anyone else has posted about this problem. Am I wasting my time trying to adjust the x range in plots from the effects package? If so, is there a way to output the partial regression + confidence limit lines so that I can just plot them up myself not using effects? Yes, the object returned by Effect() includes components fit, upper, and lower. See the description in ?Effect. Additional comment: If there is more than one predictor in the model, it's not obvious what points to plot, particularly if there is an interaction between continuous predictors. The development version of the effects package on R-Forge includes the ability to compute and plot partial residuals for effects. Their definition isn't entirely straightforward, and the implementation is preliminary, but if you want to try it, you can install the package from R-Forge and see the partial.residuals argument in ?Effect. I hope this helps, John Thanks for any pointers. Mark A/Prof. Mark Hovenden Locked Bag 55 School of Biological Sciences Hobart Tas. 7001 University of TasmaniaAustralia phone: +61 3 6226 7874 fax: +61 3 6226 2698 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] GLM weights for the Poisson family
You should direct your inquiry to R-help, not to me personally. I am taking the liberty of cc-ing my reply back to the list. I really haven't the time at the moment to think the issue through thoroughly, but off the top of my head: If you are going to use weighted log likelihoods then any comparison of models that you engage in should involve the *same* weights, otherwise you doing the good old apples-with-oranges thing. So yes, the weights will change the log-likelihood and the AIC. And so they should. And if you use AIC to compare models which are meaningfully comparable (id est, have the same weights) this is not a problem. As I say, this is off the top of my head. Others older (???) and wiser than I may correct me. cheers, Rolf Turner On 05/02/14 11:56, IamRandom wrote: I am trying to do weighted Poisson regression. I have count data. Simple example: set.seed(50) x=seq(0,1,length=100) y=numeric(100) y[seq(1,100,by=2)]=round(exp(1.5*x[seq(1,100,by=2)]+rnorm(50,0,.1)),0) y[seq(2,100,by=2)]=round(exp(1.5*x[seq(1,100,by=2)]+rnorm(50,0,1)),0) weigh1=numeric(100) weigh1[seq(1,100,by=2)]=rep(5,50) weigh1[seq(2,100,by=2)]=rep(1,50) The -2*loglikelihood of both of these regressions is the same with lm, which makes sense. The scaling of the weights does not affect the log-likelihood. -2*logLik( lm(y~x, weights=weigh1))[1] -2*logLik( lm(y~x, weights=weigh1/3))[1] The -2*loglikelihood of these two regressions are different with glm: -2*logLik(glm(y~x, family=poisson, weights=weigh1))[1] -2*logLik(glm(y~x, family=poisson, weights=weigh1/3))[1] This means that the AIC and other model comparison techniques with this weighted Poisson regression are dependent on the scaling of the weights. So I assume I misunderstand what the weights are doing in the glm function. -Tracy On 2/4/2014 12:56 PM, Rolf Turner wrote: On 04/02/14 20:12, IamRandom wrote: I am running a simple example of GLM. If I include weights when family=poisson then the weights are calculated iteratively and $weights and $prior.weights return different values. The $prior.weights are what I supplied and $weights are the posterior weights of the IWLS. If I include weights with family=gaussian then the weights are static and $weights and $prior.weights return the same values; it seems to ignore IWLS algorithm procedure. I really want the family=poisson to behave like the family=gaussian and use the static weights. Thoughts? As far as I understand things, your desideratum makes no sense. The prior weights and the just-plain-weights are very different creatures. The reason they wind up being the same for the gaussian family is that for the gaussian family the likelihood is maximized by least squares; there is no need for iteration or for re-weighting. The poisson family cannot behave like the gaussian family because for the poisson family (or any family *other* than gaussian) iteration is necessary in order to maximize the likelihood. You might get some insight into what's going on if you were to read Annette Dobson's book An Introduction to Generalized Linear Models (Chapman and Hall, 1990). cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Obtain the hex code for a given character.
On 14-02-04 7:57 PM, Rolf Turner wrote: If I have a character such as £ stored in a object called xxx, how can I obtain the hex code representation of this character? In this case I know that the hex code is \u00A3, but if I didn't, how would I find out? charToRaw will give you the bytes used to store it: charToRaw(£) [1] c2 a3 That was on MacOS, which uses UTF-8 encoding. On Windows, using Latin1, charToRaw(£) [1] a3 You won't see 00A3, because that's not an encoding that R uses, that's the Unicode code point. It's not too hard to get to that from the UTF-8 encoding, but I don't know any R function that does it. I would like a function foo() such that foo(xxx) would return, say, the string 00A3. I don't know how to get that string, but as.character(charToRaw(x)) will put the bytes for x in strings, e.g. as.character(charToRaw(£)) gives [1] c2 a3 on a Mac. I have googled and otherwise searched around and have come up with nothing that seemed at all helpful to me. If I am missing something obvious, please point me at it. (I have found a table on the web, which contains the information that I need, but it is only accessible by eye as far as I can discern.) Supplementary question: Suppose I have the string 00A3 stored in an object called yyy. How do I put that string together with \u so as to obtain £? I thought I could do xxx - paste(\u,yyy,sep=) but R won't let me use \u without hex digits. How can I get around this? The \u notation with a code point is handled by the R parser, so you need to parse that string, which means putting it in quotes first, e.g. xxx - eval(parse(text = paste0('\\u, yyy, '))) That seems pretty excessive. You'd probably be better off doing all of this in C instead... Duncan Murdoch Thanks. cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Justify axis labels in mosaic plot
Hello All, I'm trying to right-justify the y-axis labels in a mosaic plot from base R. I've tried too many commands (adj specifically) to list here and nothing works so far. I'm sure this could be done in the vcd or ggplot2 packages, but I would prefer to do it with mosaicplot in base R if at all possible and I suspect it is possible. Illustration code is below- I'm trying to make q, qwe, and qwertyqwerty right-justified instead of left. The prop.table and order bits are unnecessary for the sample but I need them for my actual analyses so I included them here in case that somehow affects the code needed. I would be incredibly appreciative of any help! #demo a-c(qwertyqwerty, qwertyqwerty, qwertyqwerty, qwe, qwe, qwe, q, q, q) b-c(1, 2, 3, 1, 1, 3, 2, 2, 3) demo-data.frame(a, b) y-table(demo) y-as.table(y[order(rowSums(y)),]) y-prop.table(y) plot(y, dir=c(h, v), las=1) Ryan Derickson VHA NCOD 513-247-4294 [[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] Obtain the hex code for a given character.
On 02/05/2014 01:01 PM, Duncan Murdoch wrote: On 14-02-04 7:57 PM, Rolf Turner wrote: If I have a character such as £ stored in a object called xxx, how can I obtain the hex code representation of this character? In this case I know that the hex code is \u00A3, but if I didn't, how would I find out? charToRaw will give you the bytes used to store it: charToRaw(£) [1] c2 a3 That was on MacOS, which uses UTF-8 encoding. On Windows, using Latin1, charToRaw(£) [1] a3 You won't see 00A3, because that's not an encoding that R uses, that's the Unicode code point. It's not too hard to get to that from the UTF-8 encoding, but I don't know any R function that does it. I would like a function foo() such that foo(xxx) would return, say, the string 00A3. I don't know how to get that string, but as.character(charToRaw(x)) will put the bytes for x in strings, e.g. as.character(charToRaw(£)) gives [1] c2 a3 on a Mac. I have googled and otherwise searched around and have come up with nothing that seemed at all helpful to me. If I am missing something obvious, please point me at it. (I have found a table on the web, which contains the information that I need, but it is only accessible by eye as far as I can discern.) Supplementary question: Suppose I have the string 00A3 stored in an object called yyy. How do I put that string together with \u so as to obtain £? I thought I could do xxx - paste(\u,yyy,sep=) but R won't let me use \u without hex digits. How can I get around this? The \u notation with a code point is handled by the R parser, so you need to parse that string, which means putting it in quotes first, e.g. xxx - eval(parse(text = paste0('\\u, yyy, '))) That seems pretty excessive. You'd probably be better off doing all of this in C instead... Hi Rolf, I almost got it in Linux with: x-\u00A3 paste(\\u, toupper(paste(as.character(charToRaw(x)),sep=,collapse=)), sep=,collapse=) [1] \\uC2A3 But I couldn't get rid of the double backslash, so I must agree with Duncan. Also, I don't know how the C2 gets in there. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Obtain the hex code for a given character.
On Feb 4, 2014, at 4:57 PM, Rolf Turner wrote: If I have a character such as £ stored in a object called xxx, how can I obtain the hex code representation of this character? In this case I know that the hex code is \u00A3, but if I didn't, how would I find out? I would like a function foo() such that foo(xxx) would return, say, the string 00A3. Close: as.hexmode(utf8ToInt(£)) [1] a3 I have googled and otherwise searched around and have come up with nothing that seemed at all helpful to me. If I am missing something obvious, please point me at it. (I have found a table on the web, which contains the information that I need, but it is only accessible by eye as far as I can discern.) Supplementary question: Suppose I have the string 00A3 stored in an object called yyy. intToUtf8(as.hexmode('00A3')) [1] £ How do I put that string together with \u so as to obtain £? I thought I could do xxx - paste(\u,yyy,sep=) but R won't let me use \u without hex digits. How can I get around this? Thanks. cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Obtain the hex code for a given character.
On Feb 4, 2014, at 8:56 PM, David Winsemius wrote: On Feb 4, 2014, at 4:57 PM, Rolf Turner wrote: If I have a character such as £ stored in a object called xxx, how can I obtain the hex code representation of this character? In this case I know that the hex code is \u00A3, but if I didn't, how would I find out? I would like a function foo() such that foo(xxx) would return, say, the string 00A3. Close: as.hexmode(utf8ToInt(£)) [1] a3 Looking at the help page again I realized that there was a `format.hexmode` to deliver as requested: format(as.hexmode(utf8ToInt(£)), width=4, upper=TRUE) [1] 00A3 -- David. I have googled and otherwise searched around and have come up with nothing that seemed at all helpful to me. If I am missing something obvious, please point me at it. (I have found a table on the web, which contains the information that I need, but it is only accessible by eye as far as I can discern.) Supplementary question: Suppose I have the string 00A3 stored in an object called yyy. intToUtf8(as.hexmode('00A3')) [1] £ How do I put that string together with \u so as to obtain £? I thought I could do xxx - paste(\u,yyy,sep=) but R won't let me use \u without hex digits. How can I get around this? Thanks. cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. 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] creating an equivalent of r-help on r.stackexchange.com ? (was: Re: Should there be an R-beginners list?)
Dear all, On Sun, Feb 2, 2014 at 10:49 PM, Liviu Andronic landronim...@gmail.com wrote: It seems that StackOverflow is officially proposing user-generated content for download/mirroring: http://blog.stackoverflow.com/2014/01/stack-exchange-cc-data-now-hosted-by-the-internet-archive/?cb=1 All community-contributed content on Stack Exchange is licensed under the Creative Commons BY-SA 3.0 license. And it is currently being mirrored at least at the Internet Archive: https://archive.org/details/stackexchange So, in principle, it would be possible/desirable to: - spin the 'r' tag from StackOverflow and propose an r.stackexchange.com at http://area51.stackexchange.com/categories/8/technology . Such a SE site would be similar to http://mathematica.stackexchange.com/ As Duncan suggested earlier, tying R Core to StackExchange may or may not be a good idea as it would make it somewhat dependent on external corporate interests. (Personally I see both advantages and disadvantages.) So in the end my proposal is not necessarily for r-help to go to SE, but more for R to have its own QA forum/wiki for helping R users. This could perfectly take the form of setting up its own open-source https://github.com/ialbert/biostar-central QA interface (a SE-like web interface) on R Core's servers. In this case the website would look like the following: http://www.biostars.org/ . Regards, Liviu - involve R Core to give blessing for using the R logo, if necessary. This would be similar to what Ubuntu does with AskUbuntu: http://meta.askubuntu.com/questions/5444/is-ask-ubuntu-official-ubuntu - set a mirror on r-project.org for all the user content that is produced by r.stackexchange.com , and thus allow R Core to keep the info publicly available at all times. The mirroring on Internet Archive would still hold. 2. I think an interface like StackOverflow is better than the mailing list interface, and will eventually win out. R-help needs to do nothing, once someone puts together something like StackOverflow that attracts most of the people who give good answers, R-help will just fade away. The advantages for such a move are countless (especially wrt to efficiently organizing R-related knowledge and directing users to appropriate sources of info), so I won't go into that. I would only note that most 'r-sig-*' MLs would become obsolete in such a setup, and would be replaced by the much more efficient tagging system of the SE QA web interface (for example, all posts appropriate for r-sig-gui would simply be tagged with 'gui'; no need for duplicated efforts of monitoring multiple mailing lists). Opinions? Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error in building R-2.15.3: configure: error: linking to Fortran libraries from C fails
Hi, I am trying to build R-2.15.3 and get the following error in /configure --with-readline --enable-R-shlib snip checking for dummy main to link with Fortran 77 libraries... unknown configure: error: in `/home/dinesh/R-build/R-2.15.3': configure: error: linking to Fortran libraries from C fails packages installed: zypper in texinfo readline-devel xorg-x11-devel Compilers: GNU Fortran (SUSE Linux) 4.3.4 [gcc-4_3-branch revision 152973] gcc (SUSE Linux) 4.3.4 [gcc-4_3-branch revision 152973] g++ (SUSE Linux) 4.3.4 [gcc-4_3-branch revision 152973] Linux: Linux hanaserver 2.6.32.27-0.2-default #1 SMP 2010-12-29 15:03:02 +0100 x86_64 x86_64 x86_64 GNU/Linux FROM config.log configure:23444: checking for dummy main to link with Fortran 77 libraries configure:23478: gcc -std=gnu99 -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib64 conftest.c -ldl -lm -lgfortran -lm 5 /usr/lib64/gcc/x86_64-suse-linux/4.3/libgfortran.so: undefined reference to `__gttf2@GCC_4.3.0' /usr/lib64/gcc/x86_64-suse-linux/4.3/libgfortran.so: undefined reference to `__netf2@GCC_4.3.0' /usr/lib64/gcc/x86_64-suse-linux/4.3/libgfortran.so: undefined reference to `__lttf2@GCC_4.3.0' collect2: ld returned 1 exit status configure:23478: $? = 1 Will greatly appreciate your help in working this out. Regards Dinesh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Justify axis labels in mosaic plot
On 02/05/2014 12:41 PM, Derickson, Ryan, VHACIN wrote: Hello All, I'm trying to right-justify the y-axis labels in a mosaic plot from base R. I've tried too many commands (adj specifically) to list here and nothing works so far. I'm sure this could be done in the vcd or ggplot2 packages, but I would prefer to do it with mosaicplot in base R if at all possible and I suspect it is possible. Illustration code is below- I'm trying to make q, qwe, and qwertyqwerty right-justified instead of left. The prop.table and order bits are unnecessary for the sample but I need them for my actual analyses so I included them here in case that somehow affects the code needed. I would be incredibly appreciative of any help! #demo a-c(qwertyqwerty, qwertyqwerty, qwertyqwerty, qwe, qwe, qwe, q, q, q) b-c(1, 2, 3, 1, 1, 3, 2, 2, 3) demo-data.frame(a, b) y-table(demo) y-as.table(y[order(rowSums(y)),]) y-prop.table(y) plot(y, dir=c(h, v), las=1) Hi Ryan, The only thing I can offer, and it is an awful kludge, is to overwrite the labels on the left: plot(y,dir=c(h,v),las=1) library(plotrix) boxed.labels(rep(0.1,3),c(0.83,0.48,0.13), c( q, qwerty,qwertyqwerty), adj=1,border=NA,cex=0.8,ypad=1.5) 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.