Re: [R] parsing pdf files
If you can use a R - java interface, you could use itext to do this as long as the PDF is fairly sane. see http://itextpdf.com/ It is what pdftk uses. b/w Mark 2010/1/9 David Kane d...@kanecap.com: I have a pdf file that I would like to parse into R: http://www.williams.edu/Registrar/geninfo/faculty.pdf For now, I open the file in Acrobat by hand, then save it as text and then use readLines(). That works fine but a) I am concerned that some information may be lost and b) I may be doing this a lot, so I would rather have R grab the information from the pdf file directly. So: is there something like readPDF() for R? Thanks, Dave Kane PS. If you're curious, here is the sort of work that I want to do with this data: http://www.ephblog.com/2010/01/08/class-update-and-faculty-ages/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] parsing pdf files
[copied to list for posterity...] Sorry. I am completely wrong. I've been using itext to split, fill in forms and recombine PDF so assumed (wrongly) that text extraction was possible. In fact, reading the mailing lists is quite informative - clearly PDF is not designed for this. Try this http://pdfbox.apache.org/commandlineutilities/ExtractText can be run from command line so potentially could be automated. Mark 2010/1/10 Mark Wardle m...@wardle.org: If you can use a R - java interface, you could use itext to do this as long as the PDF is fairly sane. see http://itextpdf.com/ It is what pdftk uses. b/w Mark 2010/1/9 David Kane d...@kanecap.com: I have a pdf file that I would like to parse into R: http://www.williams.edu/Registrar/geninfo/faculty.pdf For now, I open the file in Acrobat by hand, then save it as text and then use readLines(). That works fine but a) I am concerned that some information may be lost and b) I may be doing this a lot, so I would rather have R grab the information from the pdf file directly. So: is there something like readPDF() for R? Thanks, Dave Kane PS. If you're curious, here is the sort of work that I want to do with this data: http://www.ephblog.com/2010/01/08/class-update-and-faculty-ages/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice in a loop does not produce output
Try printing the plot created.
print(xyplot(...))
--
Dr. Mark Wardle
Specialist registrar, Neurology
(Sent from my mobile)
On 18 Aug 2009, at 13:13, Alex van der Spek am...@xs4all.nl wrote:
I cannot understand why xyplot does not work within a simple for loop.
This works up to the for loop; inside the for loop the png files are
opened and closed, but nothing is plotted. No error messages are
written
to the console either. This is the case on both Windows and Linux.
By the way, running the script below on Linux using source() does not
even produce the first xyplot. This is less of an issue for me though.
#! usr/bin/env R
# Test lattice loop
rm(list=ls())
x-1:16
y-2*x-1
z-rep(c('A','B','C','D'),4)
xyz-data.frame(x=x,y=y,z=z)
require(lattice)
png('Test.png')
xyplot(y~x|z)
dev.off()
for (i in 1:5) {
f-paste('Test',i,'.png',sep='')
png(f)
xyplot(y~x|z)
dev.off()
}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] read.csv from a remote machine
I would use sshfs or an alternatively remote file system access. Ssh to your Linux box and then mount the mac os x filesystem via sshfs, or afs for example. Alternatively, can't you copy the data to the Linux box using sftp first? -- Dr. Mark Wardle Specialist registrar, Neurology (Sent from my mobile) On 4 Aug 2009, at 18:50, Olga Lyashevska o...@herenstraat.nl wrote: Thanks Barry and Steve, I am trying to import data with read.csv and my file is on remote machine. I believe that I need to open a connection, not sure about syntax though. Probably works with ftp: too. How remote is it? In fact it is a bit more complicated. I am working on a Mac machine, from this machine I establish ssh with a Linux machine. I run R on Linux, while all my data files are stored on Mac. So in this case although physically I am using Mac, it is in fact remote. I hope it answers your question. Thanks again, Olga __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Dump plots to powerpoint?
I generate PDF images and then rasterise using imagemagick to large, high quality JPG files. Then manually insert into powerpoint. Former two can definitely be automated, I'm sure the latter insertion could be automated with judicious use of scripting if really necessary. 2009/7/7 Thomas aikto...@yahoo.com: Hi, Is it possible to dump a series of plots directly into a powerpoint presentation (as is possible in Splus)? Thank you, Thomas [[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. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] OK - I got the data - now what? :-)
Hi. As I said in my first email, converting your data into a long format makes a lot of sense. I'm sorry that you find it hard ... to understand why this would make plotting easier. Wide format: Subject ID, Experiment ID, humidity, light, whatever, T1, T2,T3,T4. is much better rotated to be Subject ID, Experiment ID, humidity, light, whatever, time, result So you end up with multiple rows per patient/individual/experiment. It is much easier to analyse and plot data like this, particularly if the original data is ragged. ie. you have a different number of measurements per patient/individual/experiment. Many plotting functions will support connecting related data (e.g. by virtue of a particular identifier) and support much of what you are likely to want (different plotting symbols, panelled plots depending on experimental conditions etc) without you having to manually work through data as you are suggesting. Best wishes, Mark 2009/7/6 Mark Knecht markkne...@gmail.com: On Sun, Jul 5, 2009 at 1:44 PM, hadley wickhamh.wick...@gmail.com wrote: I think the root cause of a number of my coding problems in R right now is my lack of skills in reading and grabbing portions of the data out of arrays. I'm new at this. (And not a programmer) I need to find some good examples to read and test on that subject. If I could locate which column was called C1, then read row 3 from C1 up to the last value before a 0, I'd have proper data to plot for one line. Repeat as necessary through the array and I get all the lines. Doing the lines one at a time should allow me the opportunity to apply color or not plot based on values in the first few columns. Thanks, Mark test - data.frame(A=1:10, B=100, C1=runif(10), C2=runif(10), C3=runif(10), C4=runif(10), C5=runif(10), C6=runif(10)) test-round(test,2) #Make array ragged test$C3[2]-0;test$C4[2]-0;test$C5[2]-0;test$C6[2]-0 test$C4[3]-0;test$C5[3]-0;test$C6[3]-0 test$C6[7]-0 test$C4[8]-0;test$C5[8]-0;test$C6[8]-0 #Print array test Are the zeros always going to be arranged like this? i.e. for experiment there is a point at which all later values are zero? If so, the following is a much simpler way of getting to the core of your data, without fussing with overly complicated matrix indexing: library(reshape) testm - melt(test, id = c(A, B)) subset(testm, value 0) I suspect you will also find this form easier to plot and analyse. Hadley -- http://had.co.nz/ Hi Hadley, I wanted to look at reshape. Yes, there exists a point in each row (unless I get to the end with all numbers) where I get to a zero and everything to the right is zero. I'm looking at ReShape. It's interesting but I clearly don't understand it yet so I'm reading your ReShaping data with the reshap package form 11/07. Interesting. I know so little about R that I'm sort of drowning at this point that it's hard for me to understand why this would make plotting easier. Analysis possibly. Just the way it goes when you get started with something new. In ReShape lingo I think I have ID's. They cover things like time, date, success/failure and a few other things of interest. Once the data starts on a row it is all data from there on to the end of the row. My initial goal is to make a line plot of the data on a single row. All the data points should connect together. There is no real interaction planned with data on other rows, at least at this time. Thanks for the pointers and the code stub. I'll be looking at this. Cheers, Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] OK - I got the data - now what? :-)
Hi. Essentially your data is currently in wide format, with repeated measures in different columns. For most analysis and in particular for graphing, it is frequently helpful to reshape your data into a long format, with one row per data value and additional variables to list experiment or subject identifier, experimental conditions etc. see ?reshape and Dr. Wickham's reshape package (http://had.co.nz/reshape/) Good luck, Mark 2009/7/5 Mark Knecht markkne...@gmail.com: OK, I guess I'm getting better at the data part of R. I wrote a program outside of R this morning to dump a bunch of experimental data. It's a sort of ragged array - about 700 rows and 400 columns, but the amount of data in each column varies based on the length of the experiment. The real data ends with a 0 following some non-zero value. It might be as short as 5 to 10 columns or as many as 390. The first 9 columns contain some data about when the experiment was run and a few other things I thought I might be interested in later. All the data starts in column 10 and has headers saying C1, C2, C3, C4, etc., up to C390 The first value for every experiment is some value I will normalize and then the values following are above and below the original tracing out the path that the experiment took, ending somewhere to the right but not a fixed number of readings. R reads it in fine and it looks good so far. Now, what I thought I might do with R is plot all 700 rows as individual lines, giving them some color based on info in columns 1-9, but suddenly I'm lost again in plots which I think should be fairly easy. How would I go about creating a plot for even one line, much less all of them? I don't have a row with 1,2,3,4 to us as the X axis values. I could go back and put one in the data but then I don't think that should really be required, or I could go back and make the headers for the whole array 1:400 and then plot from 10:400 but I thought I read that headers cannot start with numbers. Maybe the X axis values for a plot can actually be non-numeric C1, C2, C3, C4, etc and I could use line (C1,0) to (C2,5) and so on? Or maybe I should strip the C from C1 and be left with 1? Maybe the best thing is to copy the data for one line to another data.frame or array and then plot that? Just sort of lost looking at help files. Thanks for any ideas you can send along. Ask questions if I didn't explain my problem well enough. Not looking for anyone to do my work, just trying to get the concepts right Cheers, Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to use current value of variable in function definition?
2009/7/2 Peter Dalgaard p.dalga...@biostat.ku.dk: Mark Wardle wrote: [...] Otherwise, it sounds like a recipe for obfuscation! What are you trying to do really? Not really obfuscation, there are legitimate reasons to want this sort of behaviour. See demo(scoping) for a related example [...] I would have implemented this using either a OO approach or (if there was not going to be future code re-use) by defining a hidden variable with a lazy initialisation helper function that returns a cached value of the data or acquires data for the first time. Not as elegant as the solution given by Dr. Dalgaard. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to use current value of variable in function definition?
Hi.
I've stared at your code for a number of minutes and can't understand
what you're trying to achieve here. It looks as if you're fighting
scope - it may be worth refactoring your approach to simplify matters.
Otherwise, it sounds like a recipe for obfuscation! What are you
trying to do really?
b/w
Mark
2009/7/2 Allan Engelhardt all...@cybaea.com:
Must be the heat or something but I can't get my brain into gear and figure
out how to get something like
if (1) { c - 1; foo - function () print(c); }
c - 2
foo()
to print 1, not 2. (The real life example is a little more complex, but you
get the idea. I don't want the variable c in the function definition, I
want its value at that time.)
The only thing I have been able to come up with is something like
if (1) foo - (function () { c - 1; return(function () print(c)) })()
c - 2
foo()
# [1] 1
but that just hurts. Please make the pain go away.
Can someone wake up my brain?
Allan.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Drawing schematics
Hi. Have you looked at graphviz? I have previously used R to generate graphviz diagrams. I create a template graphviz diagram and then use R to parse this template, substitute appropriate values and then outputto a temporary file. I then use a system() call to run graphviz on thisoutputted intermediary file to generate a PDF which is then incorporated into a report using Sweave. There is an Rgraphviz package, but I simply used a system() call instead. I use RODBC to extract data directly from my research databases. I've used it to generate pretty publication-quality graphs showing patient recruitment, drop-outs etc., with patient numbers updated every time it is run! Hope this helps, Best wishes, Mark 2009/5/29 George Chen glc...@stanford.edu: Hi, I would like to represent the treatment course of a subject with an arrow representing passage through time and various ticks, arrows, or bars representing treatments done to the patient along the arrow. I would like to generate this sort of schematic for each patient in a database taking information from the database such as time of treatment and type of treatment. Does anybody know how I can do this? Is there a premade R package for this sort of thing or should I try to make a new graphics function? If a new graphics function, where could I start? Thanks in advance. George __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] question about using a remote system
I've not ever tried something like this. You didn't quite answer the question though. Do you need interactive sessions, or are users choosing from a number of batch jobs? If the latter, then perhaps you would be better forsaking Rcmdr (which I have not used) and instead consider a shell-based, or web-based interface (have you seen Rweb?). I presume by job you mean batch jobs that are pre-written? If you need an interactive session, then I can't see any easy way of doing as you describe. I was waiting for someone else to suggest something. My only suggestion would be to look at the unix program screen. You could then have a simple click-on application (shell script or something) that connects to your remote system, runs screen, gives them a prompt, and allows them to run arbitrary R interactive sessions. For long-running tasks, they can then detach the screen and leave it running on the remote system. I'm only guessing at your specific requirements here as I don't have enough information about exactly you want to do! Best wishes, Mark 2009/5/28 Erin Hodgess erinm.hodg...@gmail.com: My goal is for a user to sit down at a Linux laptop, get to an Rcmdr type screen, submit jobs on a remote system and then get the results back in R. We will assume that the user is naive, and the only thing he/she can do is get to the Rcmdr screen. The Rcmdr plugin will have a submit jobs menu. The user presses that option, and gets results, without having to know the underside. thanks, Erin On Thu, May 28, 2009 at 1:54 AM, Mark Wardle m...@wardle.org wrote: Hi. Do you need an interactive session at the remote machine, or are you simply wanting to run a pre-written script? If the latter, then you can ask ssh to execute a remote command, which conceivably could be R CMD x If you explain exactly why and what you are trying to do, then perhaps there's a better solution bw Mark 2009/5/28 Erin Hodgess erinm.hodg...@gmail.com: Dear R People: I would like to set up a plug-in for Rcmdr to do the following: I would start on a Linux laptop. Then I would log into another outside system and run a some commands. Now, when I tried to do system(ssh e...@xxx.edu) password xx It goes to the remote system. how do I continue to issue commands from the Linux laptop please? (hope this makes sense) thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] question about using a remote system
Hi. Do you need an interactive session at the remote machine, or are you simply wanting to run a pre-written script? If the latter, then you can ask ssh to execute a remote command, which conceivably could be R CMD x If you explain exactly why and what you are trying to do, then perhaps there's a better solution bw Mark 2009/5/28 Erin Hodgess erinm.hodg...@gmail.com: Dear R People: I would like to set up a plug-in for Rcmdr to do the following: I would start on a Linux laptop. Then I would log into another outside system and run a some commands. Now, when I tried to do system(ssh e...@xxx.edu) password xx It goes to the remote system. how do I continue to issue commands from the Linux laptop please? (hope this makes sense) thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Object-oriented programming in R
Hi. I remember considering these options myself but concluded that for most analyses a strictly procedural approach was satisfactory. Although I may re-run multiple analyses, the data manipulation (and subsequent analysis - the former always more complex than the latter IMHO) is fairly project- and data-specific. As such, quick and specific code always seemed more appropriate than slow (to write) and generic. Obviously that doesn't apply to package creators and maintainers, creating something that is going to re-used in many different projects and can be made generic. That's the heuristic I now use - is this good enough for other people's consumption - if so, create a package and adopt some of the OO approaches seen in the base R packages. Otherwise, stick to bespoke and specific (procedural) functions. I've a small library of helper functions, but these don't use OO usually. They sometimes make assumptions about data passed in, don't have particularly robust error checking, but in general, work well. I suppose it depends on what you're trying to achieve and how much time you've got! Interested in other's thoughts too as clearly there's no right answer here. bw Mark 2009/5/27 Luc Villandre villa...@dms.umontreal.ca: Dear R-users, I have very recently started learning about object-oriented programming in R. I am far from being an expert in programming, although I do have an elementary C++ background. Please take a look at these lines of code. some.data = data.frame(V1 = 1:5, V2 = 6:10) ; p.plot = ggplot(data=some.data,aes(x=V1, y=V2)) ; class(p.plot) ; [1] ggplot My understanding is that the object p.plot belongs to the ggplot class. However, a new class definition like setClass(AClass, representation(mFirst = numeric, mSecond = ggplot)) ; yields the warning Warning message: In .completeClassSlots(ClassDef, where) : undefined slot classes in definition of AClass: mSecond(class ggplot) The ggplot object is also a list : is.list(p.plot) [1] TRUE So, I guess I could identify mSecond as being a list. However, I don't understand why ggplot is not considered a valid slot type. I thought setClass() was analogous to the class declaration in C++, but I guess I might be wrong. Would anyone care to provide additional explanations about this? I decided to explore object-oriented programming in R so that I could organize the output from my analysis in a more rigorous fashion and then define custom methods that would yield relevant output. However, I'm starting to wonder if this aspect is not better suited for package builders. R lists are already very powerful and convenient templates. Although it wouldn't be as elegant, I could define functions that would take lists outputted by the different steps of my analysis and do what I want with them. I'm wondering what the merits of both approaches in the context of R would be. If anyone has any thoughts about this, I'd be most glad to read them. Cheers, -- *Luc Villandré* /Biostatistician McGill University Health Center - Montreal Children's Hospital Research Institute/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Problem accessing row number from subset on a dataframe
Hi. I may be missing what you're trying to achieve, but... what about subset(airquality, airquality$Month!=6) instead? You can do arbitrarily complex queries if you wish, combining terms logically. You don't have to use the subset function. You may find it helpful to see what the following result in: airquality$Month==6 airquality[airquality$Month==6, ] airquality[airquality$Month==6, ] There are ways of getting the row numbers, but I suspect you don't actually need to do that, do you? Best wishes, Mark 2009/5/26 Jason Rupert jasonkrup...@yahoo.com: I would like to use the row number information returned from performing a subset command on a dataframe. For example, I would like to automatically delete some rows from a dataframe if they match a criteria. Here is my example below. data(airquality) names(airquality) subset(airquality, airquality$Month == 6) Now how do I delete the row numbers returned automatically? I know I can type airquality_mod-airquality[-c(32:60)] However, I would like to check the row information and then use it to delete the stuff out of the dataframe. Thank again for any feedback and insights. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Problem accessing row number from subset on a dataframe
Ok, if you insist [although it's still unclear why you need this level of indirection!] Try ?which e.g. which(airquality$Month==5) [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 which(airquality$Month==6) [1] 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 gives the vector indices. These can be used as row indices for the dataframe. bw Mark 2009/5/26 Jason Rupert jasonkrup...@yahoo.com: Mark, I really apprecaite your response and continue to be amazed by the responsiveness and support on the R forums. And, well actually, I would like to get the row number(s) and then delete or not via the row number. Again, I really appreciate the response... --- On Tue, 5/26/09, Mark Wardle m...@wardle.org wrote: From: Mark Wardle m...@wardle.org Subject: Re: [R] Problem accessing row number from subset on a dataframe To: Jason Rupert jasonkrup...@yahoo.com Cc: R-help@r-project.org Date: Tuesday, May 26, 2009, 3:18 PM Hi. I may be missing what you're trying to achieve, but... what about subset(airquality, airquality$Month!=6) instead? You can do arbitrarily complex queries if you wish, combining terms logically. You don't have to use the subset function. You may find it helpful to see what the following result in: airquality$Month==6 airquality[airquality$Month==6, ] airquality[airquality$Month==6, ] There are ways of getting the row numbers, but I suspect you don't actually need to do that, do you? Best wishes, Mark 2009/5/26 Jason Rupert jasonkrup...@yahoo.com: I would like to use the row number information returned from performing a subset command on a dataframe. For example, I would like to automatically delete some rows from a dataframe if they match a criteria. Here is my example below. data(airquality) names(airquality) subset(airquality, airquality$Month == 6) Now how do I delete the row numbers returned automatically? I know I can type airquality_mod-airquality[-c(32:60)] However, I would like to check the row information and then use it to delete the stuff out of the dataframe. Thank again for any feedback and insights. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] create string of comma-separated content of vector
see ?paste e.g. x - seq(0,10,1) paste(x, collapse=, ) 2009/5/19 Katharina May may.kathar...@googlemail.com: Hi, how do I create a string of the comma-separated content of a vector? I've got the vector i with several numeric values as content: str(i) num 99 and want to create a SQL statement to look like the following where the part '(2, 4, 6, 7)' should be the content of the vector i: select * from [biomass_data$] where site_no in (2, 4, 6, 7) Here my approach (which doesn't work): site_all_data = sqlQuery(channel, select * from [biomass_data$] where site_no in (,paste(i,sep=,),) ) sorry for spaming so much today to the mailing list... -Katharina -- Time flies like an arrow, fruit flies like bananas. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] SQL Queries from Multiple Servers
Hi. Depending on your requirements, one option would be to do the join in R using merge() If you wish to run SQL joins across multiple databases, then it is not an R problem but a database problem. For a quick solution, I would write scripts that bring all your data together into one database (could be written in any scripting language, and of course R) and then process from there. Bw Mark 2009/5/13 Tom Schenk Jr tomschen...@gmail.com: I use RODBC as my conduit from R to SQL. It works well when the tables are stored on one channel, e.g., channel - odbcConnect(data_base_01, uid=, dsn=) However, I often need to match tables across multiple databases, e.g., data_base_01 and data_base_02. However, odbcConnect() appears limited insofar as you may only query from tables within a single channel, e.g., database. I do not have access to write and create new tables on the SQL servers, which is a possible solution (e.g., copy all tables into a single database). Is there any way, in RODBC or another R-friendly SQL package, to perform SQL operations across multiple databases? Warm regards. -- Tom Schenk Jr. tomschen...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 graph into MS Word: which format to use?
They may stipulate word files for the manuscript, but during submission, journals usually request EPS or PDF formats. In fact, all I've dealt with stipulate NEVER include graphcis into a Word document. May be worth checking again! Mark 2009/4/20 jjh21 jjhar...@gmail.com: Hello, The journal I am publishing in requires MS Word files. What is my best option for getting a high quality image of a graph done in R into Word? JPEG? Postscript? Thanks. -- View this message in context: http://www.nabble.com/R-graph-into-MS-Word%3A-which-format-to-use--tp23133745p23133745.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. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Faced Problems with RODBC package 1.2-5 and 1.2-4 for windows
You need to include much more information. Try creating a reproducible example - you may find the answer in the process of doing this. You may find the posting guide for the mailing list to be helpful - you've had no replies because you haven't explained your problem well enough. Mark 2009/1/28 Nikhil Bhide nikhil.bh...@tcs.com: Hi, I am facing problems with RODBC package 1.2-5 and 1.2-4 built for windows. I am using R 2.8.1 version. I faced some problems when I was trying to execute sql procedure from R with exec/execute statement . Stored procedure contains code/statements : 1) Call to another procedure (R calls one procedure which itself calls another procedure) 2) Iteration (while loop) I created stored procedure in which I used while loop and while loop contains two insert statements.I executed procedure from R. I found that expected results are not matching with the results I got. Also results are not consistent. 3) SET QUOTED_IDENTIFIER OFF statement Please give me a solution regards, Nikhil Ashok Bhide Cell:- +919604848030 Mailto: nikhil.bh...@tcs.com Website: http://www.tcs.com Experience certainty. IT Services Business Solutions Outsourcing ForwardSourceID:NT1B0E =-=-= Notice: The information contained in this e-mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and/or attachments to it are strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately and permanently delete the message and any attachments. Thank you [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] OT: Adding verbatim R code text into LaTeX documents: texttt; verb or url?
2009/1/28 Peter Dunn pdu...@usc.edu.au:
Hi all
I use Sweave extensively to mix R and LaTeX, and often have R code appearing
in my LaTeX document.
Just a quick question then: What is the best way to add example of R commands
into LaTeX in-line? (That is, not using Sweave.) For example, suppose I
wish to place in my document this instruction:
[...] *snip*
Try this:
\usepackage{listings}
\lstset{%
basicstyle=\scriptsize,
breaklines=true,
frame=single,
literate=
{-}{$\leftarrow$}{2}
}
\renewcommand\lstlistlistingname{List of listings}
Have a look at the listings package... You can see I'm making the font
size smaller, giving all code a frame, and converting - into a proper
left arrow (just for R!)
listings is very capable.
http://www.ctan.org/tex-archive/macros/latex/contrib/listings/
http://www.ctan.org/get/macros/latex/contrib/listings/listings.pdf
bw
Mark
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] using Sweave with a master file that has several iputted .tex files
The benefit of Makefiles is that one is essentially breaking up one
project into many smaller projects. My thesis has seven or so real
chapters. To build it all takes a few minutes on this laptop - not
intolerable but frustrating if one has to do it repeatedly. Using make
means a build for a single chapter is cached unless the source file
changes and so one can see the results of changes to one source file
almost immediately.
bw
Mark
2009/1/28 Christopher W. Ryan cr...@binghamton.edu:
That's pretty slick! Thanks.
It did not like absolute paths (unless I had spelled them out
improperly.) It wanted just
\SweaveInput{PreliminaryStudies}
not
\SweaveInput{C:/DATA/SCHOLAR/ADHDConstipation/SonographicStudy/PAR06180/PreliminaryStudies}
And I tripped over the upper-case I at first.
--Chris
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
40 Arch Street, Johnson City, NY 13790
cryanatbinghamtondotedu
PGP public keys available at http://home.stny.rr.com/ryancw/
If you want to build a ship, don't drum up the men to gather wood,
divide the work and give orders. Instead, teach them to yearn for the
vast and endless sea. [Antoine de St. Exupery]
Renaud Lancelot wrote:
What about \Sweaveinput ?
\begin{document}
This command allows the inclusion of Sweave files:
\SweaveInput{file1.Rnw}
\SweaveInput{file2.Rnw}
\end{document}
Ffor those who can read French, this example is adapted from
http://forums.cirad.fr/logiciel-R/viewtopic.php?t=1554 .
Renaud
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email
__
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Avoiding multiple outputs using RODBC package
Hi. You don't need to download the whole of the output database table to look for an already generated answer. You can write a SQL query to do that instead. ie. give me any rows with these parameters... Get the database to do the work - it is what they are designed to do. So the procedure is: 1. Get input parameters 2. Query the output database to see whether analysis has already been done (select * from output_table where...) 3. If not already done, do the calculation and insert result into output table Note: you don't have to use sqlSave to save data. One can add single rows by running arbitrary SQL. Mark 2008/12/12 Brigid Mooney bkmoo...@gmail.com: I am using R as a data manipulation tool for a SQL database. So in some of my R scripts I use the RODBC package to retreive data, then run analysis, and use the sqlSave function in the RODBC package to store the results in a database. There are two problems I want to avoid, and they are highly related: (1) having R rerun analysis which has already been done and saved into output database table, and (2) ending up with more than one identical row in my output database table. - The analysis I am running allows the user to input a large number of variables, for example: date, version, a, b, c, d, e, f, g, ... After R completes its analysis, I write the results to a database table in the format: Value, date, version, a, b, c, d, e, f, g, ... where Value is the result of the R analysis, and the rest of the columns are the criteria that was used to get that value. -- Can anyone think of a way to address these problems? The only thing I can think of so far is to run an sqlQuery to get a table of all the variable combinations that are saved at the start, and then simply avoid computing and re-outputing those results. However, my results database table currently has over 200K rows (and will grow very quickly as I keep going with this project), so I think that would not be the most expeditious answer as I think just the SQL query to download 200K rows x 10+ columns is going to be time consuming in and of itself. I know this is kindof a weird problem, and am open to all sorts of ideas... 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. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] merge two data sets
Please see ?merge In particular, see all.x parameter. Mark 2008/6/4 kayj [EMAIL PROTECTED]: I would like to merge data1 that contains 100 unique ID's with another data set data 2 with 150 ID's and the age of those individuals ( the ID in data1 is a subset of the ID in data 2) I would like to merge these data1 with data2 and have the result of the merge to have the ID ordered as in data1. Can this be done in R? -- View this message in context: http://www.nabble.com/merge-two-data-sets-tp17636278p17636278.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. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Sweave / Latex per-chapter output
for proper display; also I would loose the latex-y beauty of my PDF As I'm a novice in Latex and Makefiles usage, I'd be glad if you could tell me if what I want to do is feasible (I'm sure it is), and which would be the best, fussless method to do it (i.e. generate both types of output without changing the R/Sweave code). I know you'll probably tell me to break my long Sweave code into smaller parts, but as I briefly said above, I do some variable setting and table querying at the start - things I will repeatedly need in later chapters (e.g. I query a population table for computing incidence rates several times in later chapters). If there is a better way to split the code without having to requery the database at each chapter, I'll be glad to know about that too! BTW, I'm working on Ubuntu Linux. Thanks a lot for your insight, Anne-Marie __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Lattice book
Dear all, I haven't seen this mentioned and presumably Dr. Deepayan Sarkar is too polite to advertise! I just received a flyer from Springer: A new book on Lattice released today!! http://www.springer.com/statistics/computational/book/978-0-387-75968-5?cm_mmc=NBA-_-Apr-08_UK_1753460-_-product-_-978-0-387-75968-5 http://www.amazon.co.uk/exec/obidos/ASIN/0387759689/ref=ord_cart_shr?%5Fencoding=UTF8m=A3P5ROKL5A1OLE Well done and many congratulations. My order is being processed as we speak! Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to write a table to pdf
I would look at Sweave, particularly outputting to LaTeX. Then have a look at the xtable or Hmisc's latex() functions. I believe one can write to OpenOffice file formats too which may be an alternative solution. Best wishes, Mark On 14/04/2008, Ng Stanley [EMAIL PROTECTED] wrote: Hi, Is there a way to write a table to pdf ? I have checked write.table, it only writes to text file. [[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. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to include files in .R?
?source bw Mark On 04/04/2008, Jonas Stein [EMAIL PROTECTED] wrote: Hi, may be its a very simple question, but i did not find any documentation about a 'include' command or something like this. I have to set many constants in my R-files and want to move all these to one file, so that i can reuse it in all other R-files. Something like include(~/R/myconstants.R) kind regards, -- Jonas Stein [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple plots question
1. Work out what you want on the x and y scales from your data. 2. In your first call (to plot) set the xlim and ylim parameters to the required range. Good luck, Mark On 20/03/2008, Andre Nathan [EMAIL PROTECTED] wrote: Hello (Sorry if this appears twice, had some mail problems...) I have a number of different data sets, each loaded as a matrix. I'd like to plot them in a way that the data in the first column of each matrix is plotted on the same pair of axes. What I'm doing now is to call plot() for the data on the first matrix, then call points() for the other ones. However, the axes are set by R according to the data passed to plot(), and sometimes the data passed to points() has larger values on the x axis, and the plot ends up being cut (the y axis is not a problem since they're all probabilities). Is there a way to dynamically adapt the axes so that all data can be seen? I know I could build a new matrix with the columns I want to plot but each matrix has 1 million rows, so I figure this would be inefficient. Do I have to check beforehand which column has the largest value and call plot() on it, and then points() on the others, or is there an automatic way to do this? Thanks in advance, Andre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] factanal and plotting?
Dear Martin, The plot you refer to is a scree plot. One option (there are many) is to have a look at the nFactors package. Despite its package description, it includes the function plotnScree. You will find it helpful to search google for scree plot R and/or use rseek.org as there are many possibilities. Good luck. Best wishes, Mark On 13/03/2008, Martin Kaffanke [EMAIL PROTECTED] wrote: Hi there! To make a good choice for the estimation of the number of usefull factors. And I'd like to plot a graph like: http://de.wikipedia.org/wiki/Bild:Parallelanalyse.jpg where I don't need the green line (random values). But with str(factanal(data, factors=10)) I cannot figure out where I can find the values for plotting. Can you please help me in this question? Thanks, Martin -- Ihr Partner für Webdesign, Webapplikationen und Webspace. http://www.roomandspace.com/ Martin Kaffanke +43 650 4514224 __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help
I don't really understand your question, but try this: http://www.econ.uiuc.edu/~roger/research/links/Rnews.pdf http://cran.r-project.org/web/packages/VGAM/NEWS Try typing cauchit into rseek.org In addition, follow the references in the help page in VGAM cauchit help page. Best wishes, Mark On 09/03/2008, kike díaz peñaloza [EMAIL PROTECTED] wrote: Hello, nowadays I am employed at my thesis with the link cauchit, nevertheless I have not found theory it brings over of this one, if someone could help one would be grateful for it very much. You forgive for my English, I am from Chile. Regards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] data frame question
On 10/02/2008, joseph [EMAIL PROTECTED] wrote:
Hello
I have 2 data frames df1 and df2. I would like to create a
new data frame new_df which will contain only the common rows based on the
first 2
columns (chrN and start). The column score in the new data frame
should
be replaced with a column containing the average score (average_score) from
df1
and df2.
Try this: (avoiding underscores)
new.df - merge(df1, df2, by=c('chrN','start'))
new.df$average.score - apply(df3[,c('score.x','score.y')], 1, mean, na.rm=T)
As always, interested to see whether it can be done in one line...
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] is it safe to replace every - by = in R code?
Thank you (all) for the helpful explanations! My own R code tends to simpler constructs, but now perhaps we can start having obfuscated code competitions: something common in Perl, but I have not seen in R (yet). Anyone up for the challenge? Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] is it safe to replace every - by = in R code?
On 14/01/2008, Gabor Grothendieck [EMAIL PROTECTED] wrote: Its not related to scoping. f(b = 10) passes 10 as argument b but f(b - 10) assigns to variable b (which has nothing to do with argument b) and then passes the result of the b-10 expression (which is 10) to f. Since no argument was specified it uses positional matching and the first position is argument a. Thus its the same as f(10). Note that f(b-10) isthe same as f( (b - 10) ) which may make it clearer. Of course! Straightforward! Many thanks, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] run setwd at the launch of R
It may be disgusting, but I'm not how you expect R to know where to startup. On my Mac, I keep all my scripts in a per-project working directory. I therefore type cd ~/Documents/ataxia If you have multiple nested directories then why not create a directory alias (soft-link) so it is easy to cd to? Or move the relevant folders to a better place? Alternatively, use the Mac OS X GUI, which has an option in preferences about initial working directory. Mark On 06/01/2008, bunny , lautloscrew.com [EMAIL PROTECTED] wrote: Dear all, my R files (and the .csv files as well) are saved somewhere pretty deep down my hard disk. i have to chage to working directory therefore everytime i run R (i run it on powerPC mac), which is disgusting. using the setwd command at the beginning of an R script doesnt really help because i have to find this file first by hand. I am looking for possibility to run setwd during the launch process of R are straight after it ... any suggestions ? i would be very glad about good ideas or help ! thanks in advance matthias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] modify a data.frame within a function
You need to read about scope.
Try using return() from within your function to return the modified
data frame to the caller.
Best wishes,
Mark
On 15/12/2007, Yuval Sapir [EMAIL PROTECTED] wrote:
Hello all,
I'm trying to modify a single column of a data frame to remove randomly half
of the values. I want to do it within a function, but can not assign the
modified column back into the data frame. It was easy and successful without
a function, so I suspect the problem is the call of the single column within
the function.
removedata-function(datafull,var.removed)
{
attach(datafull)
NArandom-rnorm(n=length(var.removed), mean=0, sd=1)
for (i in 1:length(var.removed))
if(NArandom[i]0)
var.removed[i]-NA
datamiss-datafull
detach(datafull)
}
-- Yuval Sapir, PhDResearcherInstitute of Evolution, Haifa UniversityHaifa,
Israel 3190
[[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.
__
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email
__
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting estimates from survfit.coxph
Can't ask for more than that! Many many thanks for making all these tools available. I wince when I see my colleagues struggling with SPSS or SAS! R and the bundled and third-party libraries have saved me an inordinate amount of time and effort! Best wishes, Mark On 10/12/2007, Terry Therneau [EMAIL PROTECTED] wrote: The problem will be fixed in the next resease of the survival code. (That is, it is fixed on our local version of R). The summary.survfit result now includes an element 'table' containing the matrix that is shown by print.survfit. Terry __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Getting estimates from survfit.coxph
Dear all,
I'm having difficulty getting access to data generated by survfit and
print.survfit when they are using with a Cox model (survfit.coxph).
I would like to programmatically access the median survival time for
each strata together with the 95% confidence interval. I can get it on
screen, but can't get to it algorithmically. I found myself examining
the source of print.survfit to try to work out how it is done
internally, but is there a better way?
An example (and I realise that estimating survival curses from an
average status and time is incorrect in this instance, but it keeps
this example simple):
test1 - list(time= c(4, 3,1,1,2,2,3),
status=c(1,NA,1,0,1,1,0),
x= c(0, 2,1,1,1,0,0),
sex= c(0, 0,0,0,1,1,1))
c1 - coxph( Surv(time, status) ~ x + strata(sex), test1) #stratified model
f1 - survfit(c1)
sf1 - summary(f1)
str(f1)
print(f1)
print(sf1)
str(sf1)
I'm sure I am missing something obvious. Apologies - but any help
greatfully received!
Best wishes,
Mark
P.S. I can get to diferrent estimates for median survival for
different groups using simpler mechanisms, but they yield different
estimates: From my data, so no reproducible (and ataxSurv() is a
wrapper function that calls plain Surv() after manipulating the data
simply):
# For an average patient: (doesn't make any sense biologically)
survfit(surv.results$cox)
Call: survfit.coxph(object = surv.results$cox)
n events median 0.95LCL 0.95UCL
136 96 6 6 8
#
# predict a curve for a patient: (these are the answers I really want
to extract)
#
survfit(surv.results$cox, newdata=data.frame(onset=50, ic.duration=10,
simple.msa=c('MSA','Not MSA'), autoimmune=F, carcinoma=F))
Call: survfit.coxph(object = surv.results$cox, newdata = data.frame(onset = 50,
ic.duration = 10, simple.msa = c(MSA, Not MSA), autoimmune = F,
carcinoma = F))
n events median 0.95LCL 0.95UCL
[1,] 136 96 8 7 11
[2,] 136 96 3 2 6
#
# without using Cox regression:
#
survfit(ataxSurv(surv.support, surv.follow.up, surv.results$data) ~
simple.msa, data=surv.results$data)
Call: survfit(formula = ataxSurv(surv.support, surv.follow.up,
surv.results$data) ~
simple.msa, data = surv.results$data)
1 observation deleted due to missingness
n events median 0.95LCL 0.95UCL
simple.msa=Not MSA 120 80 8 6 11
simple.msa=MSA 19 17 2 1 4
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting estimates from survfit.coxph
On 09/12/2007, Frank E Harrell Jr [EMAIL PROTECTED] wrote: Dieter Menne wrote: Thank you both! Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Export in pdf, png, jpg, eps, etc...
I don't have any problems with this: I generate PDFs directly. All other formats I post-process using command line tools to automatically batch convert (using ImageMagick). Best wishes, Mark On 27/11/2007, Sébastien [EMAIL PROTECTED] wrote: Dear R-users, I have created a bunch of R scripts that automatically create multiple plots, all saved in a pdf device. I initially chose pdf output in order to easily access to multiple plots in a single file. Now, I am trying to play with different devices, like png or eps and I realize that the settings I used to have nice plots in a pdf device are giving awful outputs with the other devices... Playing with the resolution, for instance, impacts directly on the width of lines and sympbols, making them almost invisible at high resolution. Optimizing all these settings for every devices might be very tidious for me, given the number and the length of my scripts. Is there any easy way to keep the aspect of my plots the same way using different devices ? Thanks you in advance for your feedback. Sebastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] question about multiple comparison in ANOVA
Hello. I'm replying because you haven't had a reply. You haven't said which system you are running or which version of different packages you have installed. On my system (see below for the results from running sessionInfo()) that code runs fine with no errors at all. library(multcomp) # Loading required package: mvtnorm amod - aov(minutes ~ blanket, data=recovery) rht - glht(amod, linfct = mcp(blanket = Dunnett), alternative = less) rht produces: General Linear Hypotheses Multiple Comparisons of Means: Dunnett Contrasts Linear Hypotheses: Estimate b1 - b0 = 0 -2.133 b2 - b0 = 0 -7.467 b3 - b0 = 0 -1.667 On 21/11/2007, Qiu Anqi [EMAIL PROTECTED] wrote: I am not sure whether there is a bug. When I tested the example given for glht in the help, I entered the following error: Running commands: amod - aov(minutes ~ blanket, data = recovery) rht - glht(amod, linfct = mcp(blanket = Dunnett), alternative = less) Errors are: Error in try(coef.(model)) : could not find function coef. Error in modelparm.default(model, ...) : no 'coef' method for 'model' found! This all sounds a bit odd, and (although I am not an R expert by any means) therefore wonder whether you have an installation problem of some form? my sessionInfo(): R version 2.6.0 (2007-10-03) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] multcomp_0.992-6 mvtnorm_0.8-1lattice_0.16-5 RODBC_1.2-2 loaded via a namespace (and not attached): [1] grid_2.6.0 -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Query an Access database based on a date attribute
On 12/11/2007, Tudor Bodea [EMAIL PROTECTED] wrote: Dear useRs, I would like to query an Access database through R based on a date attribute but, unfortunately, I fail to do so. For example, the table test_table of the test.mdb looks like: ID cd market competitor dd price 1 1 2007-11-20 atl-bos delta 2007-11-20 210 2 2 2007-11-20 atl-bos delta 2007-11-21 190 3 3 2007-11-20 atl-bos delta 2007-11-22 180 4 4 2007-11-20 atl-bos united 2007-11-20 205 5 5 2007-11-20 atl-bos united 2007-11-21 195 6 6 2007-11-20 atl-bos united 2007-11-22 175 7 7 2007-11-20 atl-sfa delta 2007-11-20 350 8 8 2007-11-20 atl-sfa delta 2007-11-21 320 9 9 2007-11-20 atl-sfa delta 2007-11-22 300 10 10 2007-11-20 atl-sfa aa 2007-11-20 340 11 11 2007-11-20 atl-sfa aa 2007-11-21 320 12 12 2007-11-20 atl-sfa aa 2007-11-22 300 In this context, I try to get all the records for which market is atl-bos, competitor is delta and dd is 2007-11-20 (first record above). To do this I used # channel - odbcConnectAccess(test.mdb) res - sqlQuery(channel, select * from test_table where market = 'atl-bos' and competitor = 'delta' and dd = 2007-11-20) but the result seems to be incorrect. Dear Tudor, Try running your query in Microsoft Access/Query first. Once it works, then move to R/RODBC... I don't use MS Access routinely in this way, but presumably there is a problem with your SQL. Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fwd: Produce a multiple formats graphic
-- Forwarded message -- From: Mark Wardle [EMAIL PROTECTED] Date: 6 Nov 2007 16:01 Subject: Re: [R] Produce a multiple formats graphic To: Cuvelier Etienne [EMAIL PROTECTED] You have several options: 1. Write a function that creates your plot, and call that function repeatedly manually. 2. Write a wrapper function that takes the name of a function, and an output filename, and calls that function repeatedly after creating different graphics devices. 3. Create as PDF, and use something else (like ImageMagick) to convert to different formats. I tend to do option 3 as it is the most flexible. Best wishes, Mark On 06/11/2007, Cuvelier Etienne [EMAIL PROTECTED] wrote: Is it possible to produce the same graphic in different formats in one shot? Now if I want to produce the same graphic in pdf, ps and jpeg I run the producing code, but I change the graphic device, and I choose successively : pdf(...) ps(...) jpeg(...) So in this case I run the same code 3 times, or I have to choose a format and use converters... Is it possible to produce the 3 graphics in once ? Thank you very much -- === Cuvelier Etienne Assistant FUNDP - Institut d'Informatique rue Grandgagnage, 21 B-5000 Namur (Belgique) tel: 32.81.72.49.93fax: 32.81.72.49.67 === Top 10 reasons to become a Statistician 1. Deviation is considered normal 2. We feel complete and sufficient 3. We are 'mean' lovers 4. Statisticians do it discretely and continuously 5. We are right 95% of the time 6. We can legally comment on someone's posterior distribution 7. We may not be normal, but we are transformable 8. We never have to say we are certain 9. We are honestly significantly different 10. No one wants our jobs __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Package Installer Fails in OSX 10.5 Leopard
least=list. it is late (here)! On 28/10/2007, Mark Wardle [EMAIL PROTECTED] wrote: Hi. Sorry to hear you are having problems. I'm not installing Leopard just yet, as I cannot live without a working system running R, PostgreSQL, Filemaker, and Adobe applications. At least two on that least are said to have problems with Leopard! If no-one else replies, try the Mac R help list. I can't see any mention in the archives on a brief search of September's and October's archives. See https://stat.ethz.ch/mailman/listinfo/r-sig-mac Best wishes, Mark On 27/10/2007, Don Kalar [EMAIL PROTECTED] wrote: Hello all, I apologize in advance if this is not the correct list to post these sorts of issues. When attempting to install the latest stable build of R (2.6) or the most recent nightly build from R.research.att.com, the installer disables the ability to actually install R or any of the other bundled frameworks (i.e. the list is unchecked and grayed out). Before I start trying to either coerce the package definitions or build from source, I was wondering if there's any recommended way to get R running on Leopard. I've searched the lists and online, but as of yet have found no posted solution. cheers, -d == Donald Kalar, M.A. Graduate Student, Cognitive Neuroscience UCLA Department of Psychology 1285 Franz Hall, Box 951563 Los Angeles, CA 90095-1563 == [[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. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Package Installer Fails in OSX 10.5 Leopard
Hi. Sorry to hear you are having problems. I'm not installing Leopard just yet, as I cannot live without a working system running R, PostgreSQL, Filemaker, and Adobe applications. At least two on that least are said to have problems with Leopard! If no-one else replies, try the Mac R help list. I can't see any mention in the archives on a brief search of September's and October's archives. See https://stat.ethz.ch/mailman/listinfo/r-sig-mac Best wishes, Mark On 27/10/2007, Don Kalar [EMAIL PROTECTED] wrote: Hello all, I apologize in advance if this is not the correct list to post these sorts of issues. When attempting to install the latest stable build of R (2.6) or the most recent nightly build from R.research.att.com, the installer disables the ability to actually install R or any of the other bundled frameworks (i.e. the list is unchecked and grayed out). Before I start trying to either coerce the package definitions or build from source, I was wondering if there's any recommended way to get R running on Leopard. I've searched the lists and online, but as of yet have found no posted solution. cheers, -d == Donald Kalar, M.A. Graduate Student, Cognitive Neuroscience UCLA Department of Psychology 1285 Franz Hall, Box 951563 Los Angeles, CA 90095-1563 == [[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. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in if loop
On 21/10/2007, stat stat [EMAIL PROTECTED] wrote:
I have created a if loop as follows:
name = e
if (name == v)
{
u = 0
}
else u = 1
however i am getting error : Error: unexpected 'else' in else
There are 3 issues here:
1. Do you appreciate the difference between ifelse and if ? What are
you actually trying to do - in this context, ifelse would usually be
more sensible but as you've not said what you want to do, it is
difficult to guess.
2. I don't get the same error as you. Which version of R are you using?
if (name==v)
+ {
+ u=0
+ }
else u=1
Error: syntax error
This error message makes it clear that there is a syntax problem. In
fact, look at the lefthand column of characters and you should see
what the problem is
3. R is interpreting your code as two separate expressions because you
are using an interactive shell. Try this instead:
if (name=='v') {
u=1
} else {
u=0
}
Hope this helps.
Best wishes,
Mark
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in if loop
No.
Think of if only as a means to control program flow.
Use ifelse to use conditional logic on each item of a vector
Best wishes,
Mark
On 21/10/2007, stat stat [EMAIL PROTECTED] wrote:
Dear Mark,
Thanks for this. Can you please explain me what is the difference between
ifelse and if?
generally if there is more than one syntax within the 'if' I use 'if' loop
otherwise I use 'ifelse' loop. Is it the only difference between them?
Mark Wardle [EMAIL PROTECTED] wrote:
On 21/10/2007, stat stat wrote:
I have created a if loop as follows:
name = e
if (name == v)
{
u = 0
}
else u = 1
however i am getting error : Error: unexpected 'else' in else
There are 3 issues here:
1. Do you appreciate the difference between ifelse and if ? What are
you actually trying to do - in this context, ifelse would usually be
more sensible but as you've not said what you want to do, it is
difficult to guess.
2. I don't get the same error as you. Which version of R are you using?
if (name==v)
+ {
+ u=0
+ }
else u=1
Error: syntax error
This error message makes it clear that there is a syntax problem. In
fact, look at the lefthand column of characters and you should see
what the problem is
3. R is interpreting your code as two separate expressions because you
are using an interactive shell. Try this instead:
if (name=='v') {
u=1
} else {
u=0
}
Hope this helps.
Best wishes,
Mark
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
thanks in advance
Forgot the famous last words? Access your message archive online. Click
here.
__
This email has been scanned by the MessageLabs Email Security System.
For more information please visit
http://www.messagelabs.com/email
__
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] A read.table mystery (data for Filemaker Mac)
On 12/10/2007, Emmanuel Charpentier [EMAIL PROTECTED] wrote: Mark Wardle a écrit : 1. Which version of Filemaker? NB: Framemaker is a different program (desktop publishing), so do be a little precise! Dunno. The file is named export.fm7 ; one might be tempted to infer Filemaker 7. Probably: Filemaker 7 or later, as newer versions share the same file format. Framemaker is a typo 2. If it is an ancient version, then I suggest exporting a block of columns at a time, and then using merge() in R to join it all back up Not an option : I do not make the export myself, and I do not have Filemaker on any machine I can lay my hands on... So you can't ask the person doing the export to do this? I have to say I have no problem exporting data from Filemaker 7 and above - with no size limitations. Mind you, you may not believe me, but one very good way of doing export is to export as HTML, and then import into Excel. 3. I store all my clinical data in Filemaker 8.5 on the Mac. It is great. There have been no significant data export or import issues. Except for date formats (DD/MM/ in lieu of -MM-DD), numeric values (comma as decimal mark) and character set (something looking like Latin-1 in lieu of utf8). Sigh ... Weird. My numeric values aren't exported like that! I can get dates converted easily? One problem (with this version - may be fixed in 9.0) is that Filemaker ODBC drivers are pretty dreadful and so I do not use ODBC to access the data held in a Filemaker database. However, Filemaker's client ODBC access works fine, and, in conjunction with some commercial ODBC drivers for PostgreSQL, export my data into postgresql, and then from there import data into R. It is fast and works very well, albeit in a rather convoluted fashion! That would be a (good !) option if both the data producer and me had access to a common database server. It turns out not to be the case (alas...). As a general comment, I fpound the combination of a DBMS (Postgres in my case), an ODBC-able front end (OOo base, MS-Access, Filemaker : pîck ypouir poison...) and R a very good working setup. I use it every time I can. However, in this case, that's pipedream... If you wish, I would be happy to look at your FP7 file and see what the problem is. Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] confusion with R syntax
On 11/10/2007, Leeds, Mark (IED) [EMAIL PROTECTED] wrote: I just noticed something by accident with R syntax that I'm sure is correct but I don't understand it. If I have a simple numeric vector x and I subscript it, it seems that I can then subscript a second time with TRUE or FALSE, sort of like a 2 dimensional array in C. Does someone know if this is documented somewhere Because it's neat but I never knew it existed. To me it seems like a 1 dimensional vector should have only one dimensional indexing ? x - seq(1,10) x [1] 1 2 3 4 5 6 7 8 9 10 x[2:4][c(TRUE,FALSE,TRUE)] [1] 2 4 But, it only works for TRUE or FALSE and not numbers so I think it's not really 2 dimensional indexing. x[1][2] [1] NA If someone could explain this mechanism or tell me what I should look for in the archives, it would be appreciated. Thanks. I may be being naive, but it is much simply than you are trying to make it. Aren't the two indexing operations run in sequence? Therefore x[2:4][c(TRUE,FALSE,TRUE)] actually is interpreted in two steps. Try this: x - seq(1,10) y - x[2:4] z - y[c(TRUE, FALSE, TRUE)] Indeed, while your code: x[1][2] doesn't work, if you try x[2:4][3] then you get the third index of the vector created by 2:4 ie y - x[2:4] z - y[3] Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] A read.table mystery (data for Framemaker Mac)
1. Which version of Filemaker? NB: Framemaker is a different program (desktop publishing), so do be a little precise! 2. If it is an ancient version, then I suggest exporting a block of columns at a time, and then using merge() in R to join it all back up 3. I store all my clinical data in Filemaker 8.5 on the Mac. It is great. There have been no significant data export or import issues. One problem (with this version - may be fixed in 9.0) is that Filemaker ODBC drivers are pretty dreadful and so I do not use ODBC to access the data held in a Filemaker database. However, Filemaker's client ODBC access works fine, and, in conjunction with some commercial ODBC drivers for PostgreSQL, export my data into postgresql, and then from there import data into R. It is fast and works very well, albeit in a rather convoluted fashion! Best wishes, Mark On 12/10/2007, Emmanuel Charpentier [EMAIL PROTECTED] wrote: Gabor Grothendieck a écrit : On 10/11/07, Emmanuel Charpentier [EMAIL PROTECTED] wrote: I have to read some clinical data a file coming from Filemaker on Macintosh (Ugh ! But it could be worse and come from Excel...). Exporting via Excel is out of question since the file has 467 columns and 121 lines (+ headers), which is out of reach of Excel. So I received an mer files, which is what Filemaker exports as a text file. The limits for Excel are 1 million rows and 16,000 columns (based on Excel 2007 which is what I have). I don't. More important, the version of Framemaker used by my correspondent still uses old Excel limits (,o more than 256 columns). Read the last line on every message to r-help, I do ... Emmanuel Charpentier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with functions (iterations)
Dear Letticia,
Are you using R-help for your homework?
See your previous postings:
1. 15th September:
With a single R command complete the following:
create a vector calles seqvec that repeats the sequence 1, 3,6,
10,15,21.( I was trying to use c() but this does not work)
create a 5-row, 6-column matirx from seqvec wuth each row containg the
sequence from before
and complete the two task above in a single step.
2. 16th September
iven the following data for a data set called airquality. To identify
the nature of the objects from the data set airquality example Ozone
would it be best to use the command is. like
is.character(airquality$Ozone) ... I tried
attributes(airquality$Ozone) but it came up null. Would there be a
better way to identify these objects.
3. 27th September
Using a 3-level input factor alternative so that a function(below) can
compute both a two-sided and one-sided p-values. Making the two-sided
test the default. And produce output information about which
alternative was tested.
4. Today
Need to create a for loop that saves the estimate of pi from each 0f
100 separate iterations and store it in a numeric vector (of length
100). The for loop should be placed in a function that allows the user
to vary the sample size, the simulation size, the integration limits
and the input function. In addition construct a histogram of the
estimates and include a red vertical line at pi.
Mark
On 29/09/2007, Letticia Ramlal [EMAIL PROTECTED] wrote:
Hello:
I am a bit confused by this problem. Can anyone give me some advice on this I
would greatly appreciate it. Thank you for all your help.
Need to create a for loop that saves the estimate of pi from each 0f 100
separate iterations and store it in a numeric vector (of length 100). The for
loop should be placed in a function that allows the user to vary the sample
size, the simulation size, the integration limits and the input function. In
addition construct a histogram of the estimates and include a red vertical
line at pi.
ex1.fcn-function(x){
h-4/(1+x^2)
return(h)
}
n=1000
a=0
b=1
my.rand.x=runif(n,min=a,max=b)
pi.MC = ((b-a)/n)*sum(ex1.fcn(my.rand.x))
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email
__
--
Dr. Mark Wardle
Specialist registrar, Neurology
Cardiff, UK
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to read stored functions
Jared: I agree with your advice - I use source() too! I think I work in a different way to many, and don't ever save current workspace but use the interactive R environment cutting and pasting code from documents held under version control. As long as one is careful, I don't think there is any problem! Best wishes, Mark On 25/09/2007, Jared O'Connell [EMAIL PROTECTED] wrote: ...and my R education (and embarassment) continues ;) On 9/25/07, Vladimir Eremeev [EMAIL PROTECTED] wrote: source'ing is a bad practice because this saves additional copies of functions and data in the local workspace. Wasting disk space is not a problem now since HDDs are cheap and function bodies are generally small. But, when you change any function body, you have to repeat that source() call in local workspace of every project using the functions. Jared O'Connell wrote: Having your functions in a text file, say functions.r and then calling: source(functions.r) is also an option. This assumes you are in the same directory as functions.r. Perhaps take a look at ?setwd and ?getwd as well. On 9/25/07, Vladimir Eremeev [EMAIL PROTECTED] wrote: You can save your functions to a file with save(names,file=/path/to/func_lib.RData) and then attach(/path/to/func_lib.RData). Or, you can create a package and load it with library() or require() Mauricio Malfert wrote: Hi I'm simulating missing data patterns and I've started to get a lot of functions in the same .R file is it possible to store al these functions in a library like one does in C++ (i.e the .h file) and read the functions from the main .R file /Mauricio -- View this message in context: http://www.nabble.com/How-to-read-stored-functions-tf4513863.html#a12875031 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. __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
