[R] error with RNetLogo on a mac
gist with code and respective errors: http://goo.gl/r6VrHl would appreciate any input on how to get around the java vm problem. btw, the very idea of connecting R and netlogo is superb copying Jan in case he might have some input many thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tm::stemDocument function not work
thanks Pascal. actually, right after I sent the post I realized that I didn't send my sessionInfo (at the bottom of this message now). Just to make sure, everything in my script works except for the line with stemDocument, which was commented in my gist. Below is the specific warning I am getting: corpus - tm_map(corpus, stemDocument, language = english) Warning message: In parallel::mclapply(x, FUN, ...) : all scheduled cores encountered errors in user code sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base On Wed, Sep 4, 2013 at 12:54 AM, Pascal Oettli kri...@ymail.com wrote: Hello, Your example worked for me. R sessionInfo() R version 3.0.1 Patched (2013-09-02 r63805) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] scatterplot3d_0.3-33 lsa_0.63-3 RWeka_0.4-19 [4] Snowball_0.0-10 ggplot2_0.9.3.1 tm_0.5-9.1 loaded via a namespace (and not attached): [1] colorspace_1.2-2 dichromat_2.0-0digest_0.6.3 grid_3.0.1 [5] gtable_0.1.2 labeling_0.2 MASS_7.3-29munsell_0.4.2 [9] parallel_3.0.1 plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 [13] reshape2_1.2.2 rJava_0.9-4RWekajars_3.7.10-1 scales_0.2.3 [17] slam_0.1-28stringr_0.6.2 Regards, Pascal 2013/9/4 Ricardo Pietrobon pietr...@gmail.com https://gist.github.com/rpietro/6430771 stemDocument function doesn't seem to be working. Tried to look up and a few people have reported the problem, but no solution that I could find. would appreciate any help __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] tm::stemDocument function not work
https://gist.github.com/rpietro/6430771 stemDocument function doesn't seem to be working. Tried to look up and a few people have reported the problem, but no solution that I could find. would appreciate any help __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting Where People Live on a U.S. Map
Dan, google refine http://goo.gl/AeKml can actually transform zip codes into longitude/latitude - http://goo.gl/1HDWb will show you how to do this from street adresses, but it should also work from city names -- i think it will allocate a default long/lat for a city, but not sure of the exact mechanism On Fri, Aug 3, 2012 at 1:10 PM, Lopez, Dan lopez...@llnl.gov wrote: Thank you! Dan From: Sarah Goslee [mailto:sarah.gos...@gmail.com] Sent: Thursday, August 02, 2012 5:51 PM To: Lopez, Dan Cc: R help (r-help@r-project.org) Subject: Re: [R] Plotting Where People Live on a U.S. Map Hi Dan, For question 1, yes you'll need geographic coordinates. I thinknit's possible to get a shapefile of zip codes, but maybe someone else will know the details. For #2, you probably want maps instead of map, and you need to load a package before you can use it: install.packages(maps) library(maps) and then your code. Sarah On Thursday, August 2, 2012, Lopez, Dan wrote: Hi, QUESTION TOPIC #1 I have some data I want to plot on a map. But what I have are home addresses: street, City, State, complete postal code--i.e 95377-1234. Is there a way to plot this data or do I need latitudinal and longitude coordinates? If so how do I convert them? Is there a package that will do the conversion in R? QUESTION TOPIC #2 I was trying to experiment with this code that I found at the site below but got a message that indicated that the map function is not found. So I tried installing the maps package but got the below message. Is there an alternative way of doing this (please refer to URL below)? # The message I got: install.packages(map) Warning message: package 'map' is not available (for R version 2.15.0) # The code I tried to run: states - data.frame(map(state, plot=FALSE)[c(x,y)]) colnames(states) - c(Lon,Lat) ggplot(states, aes(x=Lon, y=Lat)) + geom_path() + geom_point(alpha=0.6,size=0.3,data=subway) # Where I got the code from and also an image of what I am attempting to do (please enter this in your URL) http://www.google.com/imgres?um=1hl=enbiw=1790bih=845tbm=ischtbnid=4rMjXYA_w1qDiM:imgrefurl=http://www.informaniac.net/docid=SJqcsPghztrj0Mimgurl=http://lh5.ggpht.com/_yBbodrC25kU/Ta6Ifqr0ZLI/AAABRCg/98rIF-kMMns/map%25255B7%25255D.pngw=512h=319ei=mgsbUIzqJuKbiAL5v4DQDgzoom=1iact=hcvpx=176vpy=477dur=5741hovh=177hovw=285tx=110ty=113sig=117496213270544868088page=2tbnh=125tbnw=200start=32ndsp=40ved=1t:429,r:0,s:32,i:175 Dan [[alternative HTML version deleted]] __ R-help@r-project.orgjavascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[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] rrdf package for mac not working
Uwe, sorry for the HTML. In answer to your post: I did try to contact
the developer, no response. but a colleague pointed me to a way out
yesterday through the RCurl and XML packages:
library(RCurl)
library(XML)
endpoint - http://qcrumb.com/sparql;
query - PREFIX sdmx-measure:
http://purl.org/linked-data/sdmx/2009/measure# SELECT * FROM
http://estatwrap.ontologycentral.com/data/lfst_r_lfp3pop WHERE {?s
sdmx-measure:obsValue ?o.} LIMIT 3
accept=application/sparql-results+xml
results - getForm(endpoint, .params = c(query=query,accept=accept))
results - xmlParse(results)
results - xmlRoot(results)[[results]]
frame - xmlToDataFrame(colClasses=c(character,double), nodes =
xmlChildren(results))
max(frame[2],na.rm=TRUE)
On Tue, Jun 26, 2012 at 9:52 AM, Uwe Ligges
lig...@statistik.tu-dortmund.de wrote:
Please contact the package maintainer.
Best,
Uwe Ligges
On 26.06.2012 00:41, Ricardo Pietrobon wrote:
rrdf is incredibly helpful, but I've notice that the rrdf package for mac
hasn't been working for some time: http://goo.gl/5Ukpn . wondering if there
is still a plan to maintain that in the long run, or if there is some other
alternative to read RDF files.
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[R] rrdf package for mac not working
rrdf is incredibly helpful, but I've notice that the rrdf package for mac hasn't been working for some time: http://goo.gl/5Ukpn . wondering if there is still a plan to maintain that in the long run, or if there is some other alternative to read RDF files. [[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] Decision Trees or Markov Models for Cost Effectiveness
not quite an R package, but one way of taking advantage of R would be to use something like treeplan http://goo.gl/wHsb6 along with RExcel http://goo.gl/ToD77 On Thu, Jun 14, 2012 at 11:34 AM, stefan.d...@gmail.com stefan.d...@gmail.com wrote: Hi Noah, I did ask basically the same question about a year ago and there wasn't anything around (http://tolstoy.newcastle.edu.au/R/e14/help/11/06/3651.html) Although I agree that R would be very suitable for this kind of calculations exist. I guess one reason is that a decision tree is not really a branch of statistics. The advanced user of a decision tree will more likely program something in Excel. If you find something, please let us know. Best, Stefan On Tue, Jun 12, 2012 at 12:28 AM, Noah Silverman noahsilver...@ucla.edu wrote: Hello, I was just assigned to perform a cost effectiveness study in healthcare. We are studying the cost effectiveness of a proposed diagnostic vs. current screening procedures. One of the team members suggest a commercial software package called TreeAge Pro. Looking at the description, it appears to be a nice GUI to some very simple models that could be easily constructed in R. Are there any packages in R for this type of analysis? Additionally, does anyone have any suggestions in general regarding doing this type of analysis in R? Thank You, -- Noah Silverman UCLA Department of Statistics 8117 Math Sciences Building Los Angeles, CA 90095 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding title to colorkey
Stephen, for ggplot2 you might want to check http://goo.gl/0Wx0B
On Sat, Jun 16, 2012 at 4:40 AM, Stephen Eglen s.j.eg...@damtp.cam.ac.ukwrote:
A recent paper on visualisation (in Neuron, a leading neuroscience
journal) surveyed how well previous articles in this journal labelled their
graphs (e.g. axis labelling and describing their error bars). Of
particular interest is that (only) 40% of plots labelled what their
colorkey was showing (variable and units).
The paper is at http://dx.doi.org/10.1016/j.neuron.2012.05.001
R is not yet that prominent (compared to matlab) in Neuroscience, so I
doubt many of the graphs were generated by levelplot() and friends.
However, how can the colorkey be labelled? I notice that this topic has
been raised before, e.g.
http://tolstoy.newcastle.edu.au/R/e16/help/11/11/2281.html
For now, I've done:
library(lattice)
library(grid)
levelplot(matrix(1:9,3,3),
par.settings = list(layout.widths = list(axis.key.padding = 4)))
grid.text('title here', y=unit(0.5, npc),
rot=90, x=unit(0.88, npc))
i.e. adding some space between levelplot and colorkey. The
x,y positions of the grid.text call need fine-tuning once the plot is
close to finalised.
Does anyone have a better solution for vertical colorkeys? e.g. can the
plot objected be interrogated to work out what the central x,y value is?
Thanks, Stephen
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Re: [R] Decision Trees or Markov Models for Cost Effectiveness
hi Noah, you might want to look at http://goo.gl/KqXpJ -- haven't played with it, and was actually surprised because whenever i think about decision trees -- which as you know are completely different from CART type of models -- i tend to think of excel add-ons or treeage. interested in learning what you think about the package On Mon, Jun 11, 2012 at 6:28 PM, Noah Silverman noahsilver...@ucla.eduwrote: Hello, I was just assigned to perform a cost effectiveness study in healthcare. We are studying the cost effectiveness of a proposed diagnostic vs. current screening procedures. One of the team members suggest a commercial software package called TreeAge Pro. Looking at the description, it appears to be a nice GUI to some very simple models that could be easily constructed in R. Are there any packages in R for this type of analysis? Additionally, does anyone have any suggestions in general regarding doing this type of analysis in R? Thank You, -- Noah Silverman UCLA Department of Statistics 8117 Math Sciences Building Los Angeles, CA 90095 [[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] R and Ruby integration using RSruby gem
you might want to look at http://goo.gl/g6hGK On Mon, Jun 11, 2012 at 12:53 PM, Ashy43 ashy4...@gmail.com wrote: Hi All, Could anyone please tell the installation steps of RSruby gem on Windows XP. I have latest version of ruby R installed on Windows. Thanks -- View this message in context: http://r.789695.n4.nabble.com/R-and-Ruby-integration-using-RSruby-gem-tp4633020.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] where to find a host server with R
EC2 is an option http://goo.gl/uw0Ze On Tue, Jun 12, 2012 at 4:03 PM, Xiaokuan Wei weixiaok...@yahoo.com wrote: Hi, I am building a website with using R and bioconductor packages. I am wondering where I can find a good quality hosting service which provides servers running R and allows me to install various bioconductor packages. Does anyone have such experience? Thank you. -Xiaokuan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re-post data format question (apologies)
Drew, would look at the reshape package On Sat, Feb 7, 2009 at 2:47 PM, Drew Garey coryda...@gmail.com wrote: Hello all, I have a *.csv file that looks like this (actual file is orders of magnitude larger): Site taxa no.ind forestLMA1 forestLCY1 forestSCO1 meadow LMA2 meadow LCY1 meadow PNT 3 I am interested in, but have failed to create, code that efficiently converts it to a site-by-taxa matrix or data frame that looks like this: LMALCYSCOPNT Forest 1 1 1 0 Meadow 2 1 0 3 With no repeating taxa names and zeros where a taxon is not listed for a site. Any help would be greatly appreciated. Regards, Drew Garey Aquatic Ecoloy Lab Manager Virginia Commonwealth University [[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] converting a data set to a format for time series analysis
Jim, it worked perfectly. thanks a lot On Mon, Jun 9, 2008 at 8:58 PM, jim holtman [EMAIL PROTECTED] wrote: This should do it: x - read.table(textConnection(subject hospitaldate_enrollment hospital_beds + 1 hospitalA 1/3/2002300 + 2 hospitalA 1/6/2002300 + 3 hospitalB 2/4/2002150 + 4 hospitalC 3/2/2002200), header=TRUE) closeAllConnections() y - as.Date(x$date_enrollment, %m/%d/%Y) z - cbind(x, year=format(y, %Y), month=format(y, %m)) # partition the data z.s - split(z, list(z$year, z$month, z$hospital), drop=TRUE) # now aggregate do.call(rbind, lapply(z.s, function(a) data.frame(hospital=a$hospital[1], cases=nrow(a), + year=a$year[1], month=a$month[1], beds=a$hospital[1]))) hospital cases year month beds 2002.01.hospitalA hospitalA 2 200201 hospitalA 2002.02.hospitalB hospitalB 1 200202 hospitalB 2002.03.hospitalC hospitalC 1 200203 hospitalC On Mon, Jun 9, 2008 at 1:51 PM, Ricardo Pietrobon [EMAIL PROTECTED] wrote: Jim, thanks a lot. This does the trick for dates, but what I have been struggling the most with is actually the conversion from having one subject per row to having one month per row. I didn't explain that well at all in my previous email and so let me try again. The idea is that the current data set is displayed with one subject per row. I would like to have it displayed having one hospital per month per row. For example, the new data set would look like this: month yearsite number_enrolled_subjects hospital_beds 1 2002 hospitalA 22 300 meaning that hospital A enrolled 22 subjects in 01/2002, and hospital A has 300 beds -- the beds variable is one variable in a vector that would display all the covariates for my ARIMA model your suggestion solved the problem for the dates, but the command I am looking for now is something that would count the number of subjects per site per month of a year and then displayed it in the format above. any thoughts? I really appreciate your help On Mon, Jun 9, 2008 at 1:04 PM, jim holtman [EMAIL PROTECTED] wrote: Will something like this work for you: x - read.table(textConnection(subject hospitaldate_enrollment hospital_beds + 1 hospitalA 1/3/2002300 + 2 hospitalA 1/6/2002300 + 3 hospitalB 2/4/2002150 + 4 hospitalC 3/2/2002200), header=TRUE) closeAllConnections() y - as.Date(x$date_enrollment, %m/%d/%Y) cbind(x, year=format(y, %Y), month=format(y, %m)) subject hospital date_enrollment hospital_beds year month 1 1 hospitalA1/3/2002 300 200201 2 2 hospitalA1/6/2002 300 200201 3 3 hospitalB2/4/2002 150 200202 4 4 hospitalC3/2/2002 200 200203 On Mon, Jun 9, 2008 at 12:45 PM, Ricardo Pietrobon [EMAIL PROTECTED] wrote: I currently have a data set describing human subjects enrolled into an international clinical trial, the name of the hospital enrolling this human subject, the date when the subject was enrolled, and a vector with variables representing characteristics of the site (e.g., number of beds in a hospital). my data sets looks like this: subject hospitaldate_enrollment hospital_beds 1 hospitalA 1/3/2002300 2 hospitalA 1/6/2002300 3 hospitalB 2/4/2002150 4 hospitalC 3/2/2002200 to perform a time series analysis I am now trying to get to a format that would give me the following variables: month yearsitenumber_enrolled_subjectshospital_beds the data would be displayed on one-month intervals, and number of subjects clustered around sites. any help would be greatly appreciate thanks Ricardo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] converting a data set to a format for time series analysis
I currently have a data set describing human subjects enrolled into an international clinical trial, the name of the hospital enrolling this human subject, the date when the subject was enrolled, and a vector with variables representing characteristics of the site (e.g., number of beds in a hospital). my data sets looks like this: subject hospitaldate_enrollment hospital_beds 1 hospitalA 1/3/2002300 2 hospitalA 1/6/2002300 3 hospitalB 2/4/2002150 4 hospitalC 3/2/2002200 to perform a time series analysis I am now trying to get to a format that would give me the following variables: month yearsitenumber_enrolled_subjectshospital_beds the data would be displayed on one-month intervals, and number of subjects clustered around sites. any help would be greatly appreciate thanks Ricardo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] diagnostic meta-analyses
List members, has anybody developed functions or formal R packages to conduct meta-analysis of diagnostic tests? What I have in mind is something along the lines of Meta-DiSc (http://www.biomedcentral.com/1471-2288/6/31) thanks Ricardo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] computational ontology to research questions, and statistical methods
our group at Duke is currently attempting to connect two data sets fed through a web-based system, one containing research questions (i.e., variables positioned with certain roles) and a database of statistical methods. this connection is done informally in a number of R packages and related software such as Rcmdr, R4calc, and Rkward where a variable of a certain type is matched to a certain test. For example, a logistic regression model requires a dichotomous variable as its dependent variable. our goal is to formalize this link through a computational ontology, which would standardize and hopefully facilitate package and library development for R. we have started some parallel efforts regarding both our requirements for this ontology as well a search for existing ontologies. So far we couldn't find any existing ontology, which seems odd given the widespread application such an ontology has Question for the list members: Is anybody aware of any existing ontologies computational focusing on this topic? thanks Ricardo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Input appreciated: R teaching idea + a way to improve R-
I agree with Frank - decentralization is key in a wiki environment since it allows the system to dynamically correct itself. That said, there are some ongoing experiments trying to change this -- check, for example, http://scholarpedia.org/ , which seems to be somewhat along the lines Ted described. You will notice that the content is of very high quality, but apparently the site doesn't seem to expand its content as fast as other environments that are completely decentralized. There is probably not a single answer to this issue, as different degrees of centralization will serve different purposes to different audiences in different environments and at different times ... such as in ecological and evolutionary models On 10/23/07, Frank E Harrell Jr [EMAIL PROTECTED] wrote: (Ted Harding) wrote: On 23-Oct-07 16:11:12, Tony Plate wrote: [...] Is there any way on the R-Wiki for people to quickly and easily add an annotation indicating that they believe some particular advice is poor practice? Ideally, these annotations would be easily searchable so that other users could find and fix or respond to them. -- Tony Plate I think the ideal medium for this kind of thing (and in my opinion it can -- and in the future will -- expand to the general domain of on-line publication) is on the following lines. A. Someone puts up a document. This is owned by its author and cannot be changed by anyone else. (There is also an argument for stipulating that on such a medium the author cannot change it either--the back-trace could be meaningful and important). B. There is one exception to (A). Anyone can mark a place in the document with a link to another contribution (which might be a further contribution, a comment, a correction, a link to something else altogether, ... ). All such links can also be followed in the reverse direction. C. Rules (A) and (B) appliy to all documents in the hierarchy. D. At some stage, the original author or anyone else can wrap up what has happened so far by creating a new root document. The previous version can be archived. E. There is a case for plain-text file format where the content can be expressed in words. More generally, though (and, of course, especially for content which includes graphics or mathematics), a generally-readable file format with the necessary capacilities should be used. This seems to me to imply PDF (and exclude such proprietary formats as Word or Excel, and unfortunately even PS which is not universally readable). Where data need to be included, this whould be possible using CSV files. Having said all that, I'm wondering what web format and software can conveniently implement such a structure. I have very little experience with Wikis (apart from reading them from time to time), so I don't really know how well a Wiki would lend itself to this. There are some other considerations which would be at least desirable. F. Searchability. G. A user should be able to bring up a tree representation, using edges to link nodes which, when clicked/hovered on, would pop up a box giving a brief descrption of what the link is about; and the user should be able to drop (prune) branches which are not of interest in order to simplify the task. I'd be very interested to see commments on these thoughts! Best wishes to all, Ted. Ted, The experience we're having with wikis has to my satisfaction shown that such levels of control, and keeping an initial draft intact, are not necessary and can be counter-productive. Refactoring and sparing readers from out-of-date thoughts is a key to productivity and knowledge transfer. Cheers Frank E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 23-Oct-07 Time: 18:11:17 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ricardo Pietrobon, MD, PhD, MBA Associate Vice Chair and Assistant Professor, Department of Surgery Director of Biomedical Informatics, Duke Translational Medicine Institute http://www.dtmi.duke.edu/ my calendar is available at http
Re: [R] Input appreciated: R teaching idea + a way to improve R-wiki
Bill, very interesting comment. However, do you believe that by posting these tutorials on a wiki they could, even if initially faulty, be improved by the community over time? Ricardo On 10/22/07, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I think you need to see how things work before making any decision on this. While the principle seems OK, in a optimistic sort of way, you may be a little disappointed by the outcome. Some will likely be superb, useful, well written and accessible. Others, I suspect, will fall short of this ideal, with some falling a fair way short. That's the way students learn, after all. They should use these exercises to straighten things out in their own minds, and some of them seem to have rather twisted ideas, at least initially, even at graduate-level. Some people argue it's useful to see the learning process in action, and some books I could mention seem to be written this way - but they don't get very good reviews. I just think there is a real danger here of giving misleading and inefficient teaching materials a spurious cloak of legitimacy, even if there are disclaimers all over it. I see a need to be very cautious about this, in other words. Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Matthew Keller Sent: Monday, 22 October 2007 9:45 AM To: R list Subject: [R] Input appreciated: R teaching idea + a way to improve R-wiki Hi all, I will be teaching a graduate-level course on R at CU Boulder next semester. I have a teaching idea that might also help improve the R wiki page... I wanted to know what you all thought of it and wanted to solicit some advice about doing it. During the latter part of the course, students will choose a topic of interest (e.g., hierarchical linear modeling), and show how to achieve it in R. They would present their findings to the class, and would also be responsible for writing a concise but well-written How To manual on the topic. These would be ~ 5-10 pages and would include basic background of the statistical procedure and a commented example with code in R. The goal would be for these to read like Baron Li's Notes on the use of R for psychology experiments and questionnaires. Originally I was going to post these as PDFs on my own web-page and let them grow into a compendium of how-to manuals as I teach this course over the years. However, perhaps a better idea, and one that probably benefits more people, is to have my students post their short manuals (not as PDFs but rather typed in) on the R-wiki page. Does this seem like a good idea to folks? Another question has to do with how barren the current R wiki page is... is it still being actively developed or has the community given up on it? Finally, any thoughts on where on the R-wiki site we should post our How To manuals? The tips and tricks section seems to barely be more than snippets of conversations from this list-serve (often sans the context). My guess is that the Guides section is where these should go. Your input would be most appreciated. Best, Matt -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.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. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R and FDA trials
Yesterday I just noticed the new document on R and regulatory aspects for biomedical research posted at http://www.r-project.org/doc/R-FDA.pdf Coming from an institution that performs a large number of clinical trials for FDA and being an advocate of R myself, I have found that the following issues usually come up when discussing the use of R for FDA trials: 1. Most FDA submissions come down to a series of r x k tables, and it is hard to claim that one system is better than another for that. 2. Data is to be submitted to the FDA in SAS (considered by many as the industry standard) or CDISC XML formats (http://www.cdisc.org/); there are pretty good SAS tools for that; does R have comparable? 3. Some packages in R provide acknowledgedly better functionality than their SAS-equivalent, but an entire FDA validation would have to occur each time an enhancement is made to the R package because often an enhancement breaks something else or the syntax would change from one release to another. would be interested in opinions on how to respond to these comments Ricardo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Updating packages for R 2.6.0
I must be making some really basic mistake, since I keep getting an error message when using update.packages(checkBuilt=TRUE, ask=FALSE) - an example for MASS is below. I am running ubuntu 7.04, with a clean install done today of version 2.6.0 straight from the R repository. here is the message: * Installing *source* package 'MASS' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c lqs.c -o lqs.o In file included from lqs.c:31: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7, from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11, from /usr/share/R/include/R.h:30, from lqs.c:31: /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error: limits.h: No such file or directory In file included from lqs.c:31: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory lqs.c: In function 'lqs_fitlots': lqs.c:222: warning: implicit declaration of function 'fabs' lqs.c:222: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'do_one': lqs.c:319: warning: implicit declaration of function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'mve_fitlots': lqs.c:376: warning: incompatible implicit declaration of built-in function 'log' make: *** [lqs.o] Error 1 ERROR: compilation failed for package 'MASS' ** Removing '/usr/local/lib/R/site-library/MASS' ** Removing '/usr/local/lib/R/site-library/class' ** Removing '/usr/local/lib/R/site-library/nnet' ** Removing '/usr/local/lib/R/site-library/spatial' The downloaded packages are in /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Since this has come up already: It is a good idea to re-install all packages for a minor-version increment of R, e.g. 2.5.1 - 2.6.0 (it is major.minor.patchlevel). This is most easily done by update.packages(checkBuilt=TRUE, ask=FALSE) However, if you don't want to do that yet, be aware that - Certain S4-using packages must be reinstalled, and using old versions can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and kappalab. - Any S4 package that makes an existing function S4-generic will grab that function as it existed in the version of R under which they were installed. If it has changed, there is potential trouble. - Packages that create or change character strings at C level will have needed to be updated for R 2.6.0 (and some have not yet been). Using such a package can in principle result in other character data being changed (since most character strings now share storage). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Updating packages for R 2.6.0
you got it. works perfectly now. thanks On 10/4/07, Gabor Csardi [EMAIL PROTECTED] wrote: You need to install the libc6-dev ubuntu package to be able to compile programs. sudo apt-get install libc6-dev Gabor On Thu, Oct 04, 2007 at 09:54:26AM -0400, Ricardo Pietrobon wrote: I must be making some really basic mistake, since I keep getting an error message when using update.packages(checkBuilt=TRUE, ask=FALSE) - an example for MASS is below. I am running ubuntu 7.04, with a clean install done today of version 2.6.0 straight from the R repository. here is the message: * Installing *source* package 'MASS' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c lqs.c -o lqs.o In file included from lqs.c:31: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7, from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11, from /usr/share/R/include/R.h:30, from lqs.c:31: /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error: limits.h: No such file or directory In file included from lqs.c:31: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory lqs.c: In function 'lqs_fitlots': lqs.c:222: warning: implicit declaration of function 'fabs' lqs.c:222: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'do_one': lqs.c:319: warning: implicit declaration of function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'mve_fitlots': lqs.c:376: warning: incompatible implicit declaration of built-in function 'log' make: *** [lqs.o] Error 1 ERROR: compilation failed for package 'MASS' ** Removing '/usr/local/lib/R/site-library/MASS' ** Removing '/usr/local/lib/R/site-library/class' ** Removing '/usr/local/lib/R/site-library/nnet' ** Removing '/usr/local/lib/R/site-library/spatial' The downloaded packages are in /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Since this has come up already: It is a good idea to re-install all packages for a minor-version increment of R, e.g. 2.5.1 - 2.6.0 (it is major.minor.patchlevel). This is most easily done by update.packages(checkBuilt=TRUE, ask=FALSE) However, if you don't want to do that yet, be aware that - Certain S4-using packages must be reinstalled, and using old versions can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and kappalab. - Any S4 package that makes an existing function S4-generic will grab that function as it existed in the version of R under which they were installed. If it has changed, there is potential trouble. - Packages that create or change character strings at C level will have needed to be updated for R 2.6.0 (and some have not yet been). Using such a package can in principle result in other character data being changed (since most character strings now share storage). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK -- Ricardo Pietrobon, MD, PhD, MBA
