Re: [R] side-effects in functions that replace object values andattributes
Hi Bill, thanks for your response. There are many cases in which I find direct
use of `names-`, `mode-`, `body-`, `[-`, `[[-`, `$-`, etc. to be
helpful... so wrapping each function individually seems a bit verbose. Thanks
for pointing out the compatibility with S-Plus - that was originally not a
concern of mine but I suppose one should keep this in mind. So I propose two
solutions, in addition to yours, and wonder if you or others have additional
thoughts regarding this issue. Starting with the original problem:
x - 1:3
`names-`(x,letters[1:3])
a b c
1 2 3
x
a b c
1 2 3
(the modification of the original variable, x, is undesirable - how to prevent
it?)
--- solution 1) force evaluation within the function environment using force().
(perhaps still not S-Plus friendly)
x - 1:3
`names-`(force(x),letters[1:3])
a b c
1 2 3
x
[1] 1 2 3
--- solution 2) wrap it in a general function, Funcall(), which will evaluate
all arguments into a list before function application. (S-Plus friendly?)
Funcall - function(f,...)
+ do.call(f,list(...))
x - 1:3
Funcall(`names-`,x,letters[1:3])
a b c
1 2 3
x
[1] 1 2 3
- Original Message
From: William Dunlap wdun...@tibco.com
To: Stephen Tucker brown_...@yahoo.com; r-help@r-project.org
Sent: Tue, February 16, 2010 5:50:38 PM
Subject: RE: [R] side-effects in functions that replace object values
andattributes
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Stephen Tucker
Sent: Tuesday, February 16, 2010 5:32 PM
To: r-help@r-project.org
Subject: [R] side-effects in functions that replace object
values andattributes
Hello list,
I encountered some surprising behavior in R and wanted to
check to see if I was imagining things. Previously, I thought
that replacement/setter operators in prefix notation (e.g.,
`[-`(x,1,y) rather than x[1] - y) did not produce side
effects (i.e., left 'x' unchanged), but just realized that
this is not the case anymore (or has it always been this way?
- I don't have access to old R distributions at the moment,
but using R 2.10.1 on Ubuntu and OS X)? I went through the
NEWS file but did not see a change documented if there was
one, but just going by my recollection...
In any case, my understanding was that when modifying a value
or attribute of an object, R reassigned the modified object
to the original symbol. For instance, the help file for
`name-`() says that
names(z)[3] - c2
is evaluated as
z - names-(z, [-(names(z), 3, c2))
But the final (re)assignment (`-`) seems redundant as
invisible(names-(z, [-(names(z), 3, c2)))
does the same thing.
In this case, I wonder if there is a preferred way to use the
replacement/setter operators in prefix notation without
producing such side effects
I would never recommend using replacement operators
this way. In part this is because S+ doesn't like it:
S+ x-1:10
S+ `[-`(x, 1, value=66.6)
[1] 66.6 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0
Warning messages:
looks like the internal reference count was not updated in: x[1] -
66.6
S+ x
[1] 1 2 3 4 5 6 7 8 9 10
in part because it is ugly, but mostly it is because
forcing the program to accept such usage closes off,
or at least restricts, an avenue for saving memory when
doing replacement operations.
If you have a replacement function that you are tempted
to use in this way, I recommend that you write a wrapper
function for it. E.g., instead of using
namedX - `names-`(x, value=as.character(x))
write
setNames - function(x, names) {
names(x) - names
x
}
and use it as
namesX - setNames(x, as.character(x))
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
(replace() exists for `[-`() and
`[[-`(), but perhaps something more general). For instance,
if I did not desire the following modification in x:
x - c(1,2)
y - `names-`(x,c(a,b))
y
a b
1 2
x
a b
1 2
I might take advantage of R's lazy evaluation and use create
a copy in the local function environment and allow that copy
to be modified:
x - c(1,2)
y - `names-`(`-`(x,x),c(a,b))
y
a b
1 2
x
[1] 1 2
The interesting thing is that `mode-`(), while also a
setter function in that it sets an object attribute, does
not behave as `names-`():
x - c(1,2)
y - `mode-`(x,integer)
y
[1] 1 2
x
[1] 1 2
mode(x)
[1] character
So another question that naturally arises is whether there a
general rule by which we can predict the behavior of these
types of operators (whether they produce side effects or not)?
Thanks,
Stephen
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[R] side-effects in functions that replace object values and attributes
Hello list, I encountered some surprising behavior in R and wanted to check to see if I was imagining things. Previously, I thought that replacement/setter operators in prefix notation (e.g., `[-`(x,1,y) rather than x[1] - y) did not produce side effects (i.e., left 'x' unchanged), but just realized that this is not the case anymore (or has it always been this way? - I don't have access to old R distributions at the moment, but using R 2.10.1 on Ubuntu and OS X)? I went through the NEWS file but did not see a change documented if there was one, but just going by my recollection... In any case, my understanding was that when modifying a value or attribute of an object, R reassigned the modified object to the original symbol. For instance, the help file for `name-`() says that names(z)[3] - c2 is evaluated as z - names-(z, [-(names(z), 3, c2)) But the final (re)assignment (`-`) seems redundant as invisible(names-(z, [-(names(z), 3, c2))) does the same thing. In this case, I wonder if there is a preferred way to use the replacement/setter operators in prefix notation without producing such side effects (replace() exists for `[-`() and `[[-`(), but perhaps something more general). For instance, if I did not desire the following modification in x: x - c(1,2) y - `names-`(x,c(a,b)) y a b 1 2 x a b 1 2 I might take advantage of R's lazy evaluation and use create a copy in the local function environment and allow that copy to be modified: x - c(1,2) y - `names-`(`-`(x,x),c(a,b)) y a b 1 2 x [1] 1 2 The interesting thing is that `mode-`(), while also a setter function in that it sets an object attribute, does not behave as `names-`(): x - c(1,2) y - `mode-`(x,integer) y [1] 1 2 x [1] 1 2 mode(x) [1] character So another question that naturally arises is whether there a general rule by which we can predict the behavior of these types of operators (whether they produce side effects or not)? Thanks, Stephen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Compose in roxygen - order of function application?
Hello,
I wonder if anyone has used the Compose() function in the 'roxygen' package. I
find its behavior a bit surprising:
f - function(x) x + 1
g - function(x) x * 2
f(g(2))
[1] 5
Compose(f,g)(2)
[1] 6
g(f(2))
[1] 6
Compose(g,f)(2)
[1] 5
I would have expected Compose(f,g)(x) == f(g(x)) but it appears the order of
application is reversed. It would be easy for me to modify with rev():
Compose - function (...) {
fs - rev(list(...))
function(...) Reduce(function(x, f) f(x), fs, ...)
}
But does the current implementation follow another convention I am unaware of?
Thanks -
Stephen
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Re: [R] Merge data frames but with a twist.
You may want to use the reshape package for this task:
library(reshape)
recast(DF3,Show ~ Datetime, id.var=names(DF3),value=Measure)
Show 08/26/2009 11:30 AM 08/26/2009 9:30 AM
1 Firefly 3 1
2 Red Dwarf 4 2
If you want to plot time series, you can do something like the following
mydf - .Last.value ## save the output from above to mydf
library(zoo)
zobj - zoo(`mode-`(t(mydf),numeric),
as.chron(strptime(names(mydf)[-1],%m/%d/%Y %I:%M %p)))
plot(zobj)
(zobj is a time series object of the zoo class)
- Original Message
From: Tony Breyal tony.bre...@googlemail.com
To: r-help@r-project.org
Sent: Thursday, August 27, 2009 4:04:30 AM
Subject: [R] Merge data frames but with a twist.
Dear all,
Question: How to merge two data frames such that new column are added
in a particular way?
I'm not actually sure how to best articulate my question to be honest,
so i hope showing you what I want to achieve will communicate my
question better.
Lets say I have two data frames:
DF1 - data.frame(cbind(Show=c('Firefly', 'Red Dwarf'), Measure=1:2,
Datetime=c('08/26/2009 9:30 AM', '08/26/2009 9:30 AM')))
DF2 - data.frame(cbind(Show=c('Firefly', 'Red Dwarf'), Measure=3:4,
Datetime=c('08/26/2009 11:30 AM', '08/26/2009 11:30 AM')))
And then let us merge these:
DF3 - merge(DF1, DF2, all=TRUE)
Show MeasureDatetime
1 Firefly 1 08/26/2009 9:30 AM
2 Firefly 3 08/26/2009 11:30 AM
3 Red Dwarf 2 08/26/2009 9:30 AM
4 Red Dwarf 4 08/26/2009 11:30 AM
What i would like to do is merge the data frames such that i end up
with the following:
Show 08/26/2009 9:30 AM08/26/2009 11:30 AM
Firefly 13
Red Dwarf24
my reason for doing this is so that i can plot a time series somehow.
I hope the formating stays when i post this message and that what i'm
trying to do is easy to understand. Thank you kindly for any help in
advance.
Tony
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Re: [R] Merge data frames but with a twist.
Ah, thanks always - I originally thought as.chron() was required to have all fields (m/d/y hh:mm:ss) as for chron() but I see that the former passes its 'format' argument to as.POSIXct() Good deal! Stephen - Original Message From: Gabor Grothendieck ggrothendi...@gmail.com To: Stephen Tucker brown_...@yahoo.com Cc: Tony Breyal tony.bre...@googlemail.com; r-help@r-project.org Sent: Thursday, August 27, 2009 7:27:26 AM Subject: Re: [R] Merge data frames but with a twist. On Thu, Aug 27, 2009 at 9:55 AM, Stephen Tuckerbrown_...@yahoo.com wrote: You may want to use the reshape package for this task: library(reshape) recast(DF3,Show ~ Datetime, id.var=names(DF3),value=Measure) Show 08/26/2009 11:30 AM 08/26/2009 9:30 AM 1 Firefly 3 1 2 Red Dwarf 4 2 If you want to plot time series, you can do something like the following mydf - .Last.value ## save the output from above to mydf library(zoo) zobj - zoo(`mode-`(t(mydf),numeric), as.chron(strptime(names(mydf)[-1],%m/%d/%Y %I:%M %p))) plot(zobj) (zobj is a time series object of the zoo class) Note that as.chron can take % codes directly so the as.chron portion can be shortened to: as.chron(names(mydf)[-1],%m/%d/%Y %I:%M %p) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] concatenating multiple columns from files
You can do something like
mat - do.call(cbind, lapply(list.files(.data),read.table))
## explanation:
lapply(list.files(.data),read.table)
will store all tables in a list
do.call(cbind,...)
will bind all the columns stored in the list created above.
- Original Message
From: ferreirafm ferreir...@lim12.fm.usp.br
To: r-help@r-project.org
Sent: Thursday, July 30, 2009 5:29:46 PM
Subject: [R] concatenating multiple columns from files
R-users,
I want to concatenate columns from different files in a single object.
I'm doing bad. My peace of code is as follow:
rawdata - list.files(./data)
for (i in rawdata) {
mat[ ] - read.table(paste(i ,sep=))
}
At the end of the loop I have just one column. What I'm doing wrong?
Thanks,
Fred
--
View this message in context:
http://www.nabble.com/concatenating-multiple-columns-from-files-tp24748542p24748542.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] PDF Compression
There was a previous post about this also:
http://tolstoy.newcastle.edu.au/R/e2/help/07/05/17475.html
I was able to use bitmap(,type=pdfwrite) on Ubuntu Linux but had trouble
getting it to work on Windows.
For now, it's kind of kludgey but I have in my .Rprofle (or .Rprofile.site on
Windows):
compressPDF - function(x) {
system(paste(pdftk,x,output,sub(\\.pdf,c.pdf,x),
compress dont_ask))
unlink(x)
}
so after I plot something I would call compressPDF() on the same pdf file
pdf(plot.pdf); plot(1:10); dev.off()
compressPDF(plot.pdf)
which renames it from 'plot.pdf' to 'plotc.pdf' to remind myself that I already
compressed it...
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[R] R_LIBS in Windows Vista
Hello, I am trying to install R and have it running through ESS on a Vista machine that is not mine (I am only familiar with Windows XP and Ubuntu Linux) so please pardon my unfamiliarity... The Rgui.exe installation works fine and package installation also appears to work fine. The base packages are installed in C:/Program Files/R/R-2.8.0/library/ and user-installed packages are installed in C:/Users/Name/Documents/R/win-library/2.8/ When I run R with Rgui.exe, everything appears to run fine, and I can load the libraries. When I try to run R through ESS, I get library(chron) ...library not found error and library(chron,lib.loc=C:/Users/Name/Documents/R/win-library/2.8/) still same problem, though chron/ is indeed located in C:/Users/Name/Documents/R/win-library/2.8/ I looked at the R Windows FAQ and decided to check Sys.getenv(R_LIBS_USER) and it's not C:/Users/Name/Documents/R/win-library/2.8/ but instead C:/Users/Name/AppData/R/win-library/2.8/ (I think, trying to recall from memory as it is not my machine) So as instructed in the FAQ I did dir.create(Sys.getenv(R_LIBS_USER), recursive = TRUE) and tried reinstalling chron with install.packages() but was denied permission. I also: 1) created Renviron.site (and also .Renviron) and set R_LIBS=C:/Users/Name/Documents/R/win-library/2.8/ as suggested in the R FAQ, but I could neither load from or write to this directory. 2) I tried Sys.setenv(R_LIBS_USER=C:/Users/Name/Documents/R/win-library/2.8/) but also no luck... I wonder if anyone has further suggestions? Thanks very much, Stephen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] behavior of squishplot in TeachingDemos
Hi list,
I wonder if anyone has had this experience with squishplot() in the
TeachingDemos package.
Taking the example from the ?image help page,
library(TeachingDemos)
x - 10*(1:nrow(volcano))
y - 10*(1:ncol(volcano))
layout(matrix(c(1,2,3,4),ncol=2,byrow=TRUE),height=c(2,1))
## 1st plot
op - squishplot(range(x),range(y),1)
image(x, y, volcano, col = terrain.colors(100))
par(op)
## 2nd plot
op - squishplot(range(x),range(y),1)
image(x, y, volcano, col = terrain.colors(100))
par(op)
The second plot comes out looking as expected, but the first plot is not
squished in the desired proportions. I tried tracking the modifications to
par('pin') and par('plt') in the function but gave up midway through in desire
for haste - not sure what is going on but I did find that taking advantage of
the behavior above, calling
plot.new(); par(new=TRUE)
before the first plot makes things work as expected. So the full code would be
layout(matrix(c(1,2,3,4),ncol=2,byrow=TRUE),height=c(2,1))
## 1st plot
op - squishplot(range(x),range(y),1)
plot.new()
par(new=TRUE)
image(x, y, volcano, col = terrain.colors(100))
par(op)
## 2nd plot
op - squishplot(range(x),range(y),1)
image(x, y, volcano, col = terrain.colors(100))
par(op)
+++
I wonder if this behavior is not surprising? It is a great function overall
though - thanks for the contribution.
Stephen
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[R] importing data to SQLite database with sqldf
Hi all,
I am attempting to learn SQL through sqldf...
One task I am particularly interested in is merging separate
(presumably large) files into a single table without loading these
files into R as an intermediate step (by loading them into SQLite and
merging them there).
Taking a step back, I've considered these alternatives:
1) I know if I use straight SQLite commands I might use the 'IMPORT'
or 'INSERT INTO' command, which is not terribly flexible... (I can
read large files line-by-line in Python and use the 'INSERT INTO'
command, which is reasonably fast; I could do this in R as well but my
experience with R's input/output is that it's much slower...? and
sometimes setting up the table column definitions can be tedious if
there are many variables).
2) dbWriteTable() with append=TRUE is very convenient except that it
requires I load the data into R first...
3) sqldf's capability to put data directly into a database is
something I'd like to work out.
So in this case I have a series of tab-delimited text file with the
first line being a header.
For some reason I cannot seem to get it working. Combining examples 6
and 9 from the Google Code page (and R-help archives), I tried
source(http://sqldf.googlecode.com/svn/trunk/R/sqldf.R;)
(do I need it for SQLite?)
##
sqldf(attach 'mydb.db' as new)
f - file(myexample.txt)
attr(f,file.format) - list(header=TRUE,sep=\t)
sqldf(create table myexample as select * from f,
stringsAsFactors=FALSE,
dbname=mydb.db)
## or
f - file(fi)
sqldf(create table myexample as select * from f,
stringsAsFactors=FALSE,file.format=list(header=TRUE,sep=\t),
dbname=mydb.db)
##
sqldf(select * from myexample,dbname=mydb.db)
gives me tables with 0 rows and 0 columns...
So in any case I have a few questions:
=== 1
Would this be scalable to files with few GBs of data in them (I guess
I am uncertain of the underlying mechanism for transporting data from
the .txt file to the .db file... I see there is a call the
dbWriteTable() internally in sqldf but through the connection)? And
is there anything obviously doing wrong above?
=== 2 ===
Since I cannot 'append' rows to existing tables in SQLite (or any SQL
database), I think what I would have to do is to load each of the
files into the database and then 'rbind' them into a new table using
'union all'? The following code is what I have (the part where I read
in each file before dumping into the database file would hopefully be
replaced by the method above, if it can be made to work).
## (1) create a database file
sqldf(attach 'alltables.db' as new)
## (2) convenience function
sql - function(...) sqldf(...,dbname=alltables.db)
## (3) load data as separate tables
for( fi in list.files(.,txt$) ) {
mydata - read.delim(fi)
sql(sprintf(create table %s as select * from mydata,sub(\\.txt,,fi)))
}
rm(fi,mydata)
## (4) merge tables
tablenames - as.character(sql(select * from sqlite_master)$name)
sql(paste(create table myfulltable as,
paste(sprintf(select * from %s,tablenames),
collapse= union all )))
## (5) delete separate tables since we have a merged one
for( nm in tablenames ) sql(sprintf(drop table %s,nm))
=== 3 ===
The following command
sqldf(attach 'mydb.db' as new)
DF - read.delim(fi)
sqldf(create table myexample as select * from DF,dbname=mydb.db)
will usually create a .db file twice the size of the .txt file (for
now I am playing with a files ~500KB so the .db files are around
~1MB). When I create a .db file using SQLite's 'import' command,
RSQLite's dbWriteTable(), or inserting values from the same .txt file
from Python's SQLite interface, I get .db files that are approximately
the same size as the .txt file (~500KB). Is the larger file size for
sqldf's method expected?
Many thanks in advance!
Stephen Tucker
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[R] plot order in multi-panel figure
Hi, Does anyone know if there is a way to 'reset the plot number' on a traditional graphics device? For instance, I want to have two plots on stacked top of each other (mfrow=c(2,1)) but with underlying grid lines spanning both figures vertically. I can put the grid lines on top if I add them last: par(mfrow=c(2,1)) plot.new() plot.window(c(0,1),c(0,1)) for( i in 1:2) axis(i) box(bty=L) rect(0.2,0.2,0.5,0.5,col=8) plot.new() plot.window(c(0,1),c(0,1)) for( i in 1:2) axis(i) box(bty=L) par(mfrow=c(1,1)) plot.window(c(0,1),c(0,1)) abline(v=seq(0,1,by=0.2),lty=3) But ideally I would like to draw the grid lines before drawing other objects on top of it, but something like par(mfrow=c(1,1)) plot.new() plot.window(c(0,1),c(0,1)) abline(v=seq(0,1,by=0.2),lty=3) par(mfrow=c(2,1)) plot.window(c(0,1),c(0,1)) for( i in 1:2) axis(i) box(bty=L) rect(0.2,0.2,0.5,0.5,col=8) plot.new() plot.window(c(0,1),c(0,1)) for( i in 1:2) axis(i) box(bty=L) does not work because the first of the two plots appears in the bottom of the figure and not the top (as it is interpreted as the second of the mfrow=c(2,1) plots). I've also played around with layout() but I also get the same behavior. I suspect I can do this eventually with grid graphics but was wondering if it is also possible in traditional graphics. I would appreciate any help - thanks very much! Stephen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Pdf file size for very scatter plots
I thought running it through latex will compress the pdf - but this post nicely summarizes some options: http://tolstoy.newcastle.edu.au/R/e2/help/07/05/17475.html I personally prefer the pdftk approach* over the ghostscript option** as the latter seems to give me a number of problems on Windows XP. *if you install pdftk (and put it in your search path), after you create filename.pdf with pdf(), do pdftk filename.pdf cat output newfilename.pdf compress or pdftk filename.pdf cat output newfilename.pdf compress dont_ask **if you have ghostview installed (and in your search path), bitmap(filename.pdf,type=pdfwrite) plot(...) dev.off() - Original Message From: Nazareno Andrade [EMAIL PROTECTED] To: r-help r-help@r-project.org Sent: Friday, August 15, 2008 12:46:52 PM Subject: Re: [R] Pdf file size for very scatter plots Jim, Thanks for the answer. Using pch=. reduces the file to ~3MB... Still large. I'll look into hexbins, but if I understand it right, it would 'round' points which are nearby into a same hexagon, right? Couldn't that result in an inaccurate view of a scatter plot? Here's the code I'm using: pdf(); plot(rnorm(1e5), rnorm(1e5), pch = .); dev.off() thanks again, Nazareno On Fri, Aug 15, 2008 at 12:27 PM, jim holtman [EMAIL PROTECTED] wrote: Have you tried using pch='.'? Also you might consider using 'hexbin' for creating the scatter plot. On Fri, Aug 15, 2008 at 12:24 PM, Nazareno Andrade [EMAIL PROTECTED] wrote: Dear all, I am plotting a scatter plot for a large sample (1e+05 ordered pairs). This produces a large (~5MB) file in a pdf or postscript terminal, and I am wondering whether there are methods for reducing the size of the resulting file so that it is easier to include it in a document. I'd rather stick with pdf or ps as I am using latex. thanks, Nazareno __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 that 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] tryCatch question
Hi Kevin, I learned to use tryCatch() from this page: http://www1.maths.lth.se/help/R/ExceptionHandlingInR/ Hope this helps, ST - Original Message From: Luke Tierney [EMAIL PROTECTED] To: [EMAIL PROTECTED] Cc: r-help@r-project.org Sent: Thursday, August 14, 2008 8:59:35 AM Subject: Re: [R] tryCatch question Read the argment descriptions and Look at the examples in ?tryCatch. The `expr' argument (i.e. the code to try) and the `finally' argument are expressions that are evaluated (via standard lazy evaluation of arguments). The error condition handlers, provided as the `...' argument in errorClass = handler form(s), are functions of one argument, the error condition. As in the examples I usualy use fuctions writen in-line. There is no non-standard evaluation involved, so standard scoping rules apply. luke On Thu, 14 Aug 2008, [EMAIL PROTECTED] wrote: I would like to use the 'tryCatch' function but am having a hard time getting my head around it. In 'C' like languages try/catch/finally means try a block of statements and if any throw an error then do the statements in the catch block and then error or not always do the staements in the finally block. In 'R' as best as I can tell the block of staements in the try block is a single function. Does this mean I need to construct a temporary function that contains what I would have put in the try blck? Also in 'R' it seems the 'finally' function (of 'tryCatch' most closely mimics the catch block of 'C'. Right? A similar comment on the finally function. Do I need to create a temporary function that contains the staements that I normally would put in a 'C' like catch clause? If I do need to create functions for the try and error conditions what is the scope or enviironment that the functions are called under? The 'try' function is relatively straightforward but when an error occurs what variable will I have access to? Thank you. Kevin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] levels values of cut()
Not sure what you're looking for, but does this help? Extending your code, library(gsubfn) t(strapply(levels(my.cuts),([0-9.]+),([0-9.]+), + function(...) as.numeric(c(...)),backref=-2,simplify=TRUE)) [,1] [,2] [1,] 15.9 38.3 [2,] 38.3 60.7 [3,] 60.7 83.1 - Original Message From: baptiste auguie [EMAIL PROTECTED] To: r-help@r-project.org Sent: Saturday, August 9, 2008 1:51:01 AM Subject: [R] levels values of cut() Dear list, I have the following example, from which I am hoping to retrieve numeric values of the factor levels (that is, without the brackets): x - seq(1, 15, length=100) y - sin(x) my.cuts - cut(which(abs(y) 1e-1), 3) levels(my.cuts) hist() does not suit me for this, as it does not necessarily respect the number of breaks. getAnywhere hasn't got me very far: I cannot seem to find a readable code for the built-in cut function in the base library. I think getMethod should do it but I don't understand the arguments to pass. Any pointers appreciated, Thanks, baptiste _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK Phone: +44 1392 264187 http://newton.ex.ac.uk/research/emag __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Extract Element of String with R's Regex
In the example below, a straight application of strsplit() is probably the simplest solution. In a more general case where it may be desirable to match patterns, a combination of sub() or gsub() with strsplit() might do the trick: x - Best-K Gene 11340 211952_at RANBP5 Noc= 3 - 2 LL= -963.669 -965.35 patt - Best-K Gene \\d+ (\\w+) (\\w+) Noc= \\d - (\\d) LL= (.*) unlist(strsplit(gsub(patt,\\1,\\2,\\3,x,perl=TRUE),,)) [1] 211952_at RANBP52 Alternatively, you may want to take a look at the gsubfn package - it is quite useful. Still learning to use it myself... library(gsubfn) unlist(strapply(x,patt,function(x1,x2,x3) c(x1,x2,x3),backref=-3,perl=TRUE)) [1] 211952_at RANBP52 - Original Message From: Simon Blomberg [EMAIL PROTECTED] To: Edward Wijaya [EMAIL PROTECTED] Cc: r-help@r-project.org Sent: Thursday, July 31, 2008 11:48:23 PM Subject: Re: [R] Extract Element of String with R's Regex How about: unlist(strsplit(x, split= ))[c(4:5,10)] That perl script looks like a good reason to avoid perl. Simon. On Fri, 2008-08-01 at 15:13 +0900, Edward Wijaya wrote: Hi, I have this string, in which I want to extract some of it's element: x - Best-K Gene 11340 211952_at RANBP5 Noc= 3 - 2 LL= -963.669 -965.35 yielding this array [1] 211952_at RANBP5 2 In Perl we would do it this way: __BEGIN__ my @needed =(); my $str = Best-K Gene 11340 211952_at RANBP5 Noc= 3 - 2 LL= -963.669 -965.35; $str =~ /Best-K Gene \d+ (\w+) (\w+) Noc= \d - (\d) LL= (.*)/; push @needed, ($1,$2,$3); __END___ How can we achieve this with R? - E.W. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] chron objects: input/output
Hi list, I have some questions regarding 1) conversion of date + time characters to chron 2) formatting chron object printing Regarding (1), Gabor's Rnews 2004 4/1 article has been indispensible, but I often work with files where dates and times are contained in a single field. In this case, I would like to control input/output of chron objects when each observation of date and time is stored as a single string. So here are some procedures that I've tried: ## define character vector x - c(07/01/2001 12:00:00,07/17/2001 15:00:00) ## method 1 library(chron) chron(substring(x,1,10),substring(x,12)) [1] (07/01/01 12:00:00) (07/17/01 15:00:00) ## method 2 (recently inspired by Gabor's post) do.call(c,strapply(x,(.*) (.*),chron,backref=-2)) [1] (07/01/01 12:00:00) (07/17/01 15:00:00) ## method 3 (chronObj - as.chron(strptime(x,%m/%d/%Y %T))) [1] (07/01/01 12:00:00) (07/17/01 15:00:00) Could there be any gotchas with the third method (as.chron(strptime(...)))? The 'tz' attribute for POSIXlt objects are ignored, but I am not sure if there are any implications of the '$isdst' field are for conversions. I do like this alternative for the conciseness-flexibility tradeoff; in my experience, I have not had any problems - but wanted to inquire if at some point the '$isdst' field (or possibly something else) could give me trouble. Regarding the printing of chron objects, this behavior is peculiar to me: format(chronObj,format=c(m/d,h:m)) [1] (0701 1200) (0717 1500) The special characters (/,:) are not printed - I've tried changing the attribute of the chron object, looked at the format.chron() method (getS3method(format,chron)), etc. and am still confused; the chron() documentation says its specification should be similar the input format. Could I have missed something? Thanks! ST __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Colors in Sweave
From: Duncan Murdoch murdoch_at_stats.uwo.ca
Date: Tue, 29 Jul 2008 19:45:28 -0400
On 27/07/2008 3:10 PM, Stephen Tucker wrote:
Hi list,
I was using Sweave and was
wondering if anyone has had any luck changing the font colors of the
code chunks. For instance, in my .Rnw preample I tried including:
===
\usepackage[usenames]{colors}
\definecolor{darkred}{rgb}{0.545,0,0}
\definecolor{midnightblue}{rgb}{0.098,0.098,0.439}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl,formatcom={\color{midnightblue}}}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{formatcom={\color{darkred}}}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl,formatcom={\color{blue}}}
===
which works in the sense that
colors do show up in the processed pdf document, but extra spaces in
between the input and output code chunks appear (which is not the case
when colors are not specified), resulting in a long document with many
blank lines.
Alternatively, in the resulting tex
document I replaced all instances of \begin{Sinput}... \end{Sinput}
with {\color{midnightblue}\begin{Sinput} ... \end{Sinput}} and darkred
for Soutput and so on. When I do this, I get the following error
message:
=== LaTeX excerpt ===
\begin{Schunk}
{\color{midnightblue}\begin{Sinput}
ISOdatetime(1970, 1, 1, 0, 0, 0, ) - ISOdatetime(1970, 1, 1,
+ 0, 0, 0, GMT)
\end{Sinput}}
{\color{darkred}\begin{Soutput}
Time difference of 8 hours
\end{Soutput}}
\end{Schunk}
===
=== error message ===
)
! FancyVerb Error:
Extraneous input `}\end{}' between \end{Sinput} and line end
.
\FV_at_Error ... {FancyVerb Error:
\space \space #1
}
l.13 \end{Sinput}}
===
I guess I don't know enough of the
Schunk/Sinput/Soutput definitions to toy with it and was wondering if
anyone had tried something similar.
The definitions are very simple: see Sweave.sty, they're just
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
I would use
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl,formatcom=\color{midnightblue}}
(i.e. no extra braces), but whether or not I do that, I don't notice
extra spacing beyond what Sweave always puts in. To get rid of the
usual Sweave extra spacing, try
\fvset{listparameters={\setlength{\topsep}{0pt}}}
\renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}}
Duncan Murdoch
=
Hi Duncan,
For some reason I never saw your response until now but this is great! Thanks -
incidentally, I realized it was something to do with either the color or
fancyvrb package so I posted a question to the latex help list and got a
helpful response. Essentially, the idea would be to combine both S input and
output into a single Verbatim environment and change the colors within it
(requires fancyvrb package which Sweave uses):
\renewcommand{\FancyVerbFormatLine}[1]{%
\ifnum\value{FancyVerbLine}5\color{red}#1%
\else\color{blue}#1\fi}
\begin{Verbatim}
line 1
line 2
line 3
line 4
line 5
line 6
line 7
\end{Verbatim}
However, in the context of the Sweave application, your solution is elegant and
simpler than processing the entire document and replacing all
\begin{Sinput}...\end{Sinput}, \begin{Soutput}...\end{Soutput} instances with
the \renewcommand and Verbatim environement calls.
Thanks very much,
Stephen
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Re: [R] Storing Matrices into Hash
Hm didn't know about the abind package. That is pretty sweet.
I do often opt for the 'list of matrices' myself though because I'm more
familiar with the methods for lists...
To answer one of Gundala's questions directly (assuming list of matrices is
acceptable):
Since you can do this,
x - list()
x[[a]] - 1
x[[b]] - 2
x
$a
[1] 1
$b
[1] 2
You should be able to do this as well:
all_mat - list()
for (matno in 1:10) {
all_mat[[paste(mat,matno,sep=)]] -
process_to_create_matrix(da[matno])
}
and refer to
mat$mat_no
etc.
- Original Message
From: Bert Gunter [EMAIL PROTECTED]
To: Erik Iverson [EMAIL PROTECTED]; Gundala Viswanath [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Sent: Thursday, July 31, 2008 7:56:49 PM
Subject: Re: [R] Storing Matrices into Hash
R also has arrays (?array). If all the matrices are the **same dimension**
and **same mode** (i.e. all numeric or all character), this is perhaps
easier, especially if you want to access various pieces of your matrices.
Given existing matrices, mat1, mat2,..., the slightly tricky way to combine
them into an array is:
your_array - array(c(mat1,mat2,..),dim=c(dim(mat1,n))
## where n is the number of matrices.
This is slightly tricky because you have to understand that matrices are
actually vectors in column major order with a dim attribute.
An easier way to do it is to install the abind package from CRAN and just do
your_array - abind(mat1,mat2, ..., along =3)
Accessing the matrices is then easy using array indexing. Again, this is
only possible if they're all the same dimension. Otherwise Erik's approach
must be used.
I recommend that you spend some time learning about R's data structures. R's
internal documentation, especially An Intro to R, is a good starting point,
but there are now many books, both in English and other major European
languages, out there to help you. The CRAN website lists many of them.
Cheers,
Bert Gunter
Genentech, Inc.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Erik Iverson
Sent: Thursday, July 31, 2008 7:01 PM
To: Gundala Viswanath
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Storing Matrices into Hash
I think a named list is probably the easiest way to start off, something
like:
all_mat - list(mat1 = mat1, mat2 = mat2)
all_mat$mat2
Gundala Viswanath wrote:
Hi,
Suppose I have these two matrices (could be more).
What I need to do is to store these matrices into a hash.
So that I can call back any of the matrix back later.
Is there a way to do it?
mat_1
[,1][,2]
[1,] 9.327924e-01 0.067207616
[2,] 9.869321e-01 0.013067929
[3,] 9.892814e-01 0.010718579
[4,] 9.931603e-01 0.006839735
[5,] 9.149056e-01 0.08509
mat_2
[,1][,2]
[1,] 9.328202e-01 0.067179769
[2,] 9.869402e-01 0.013059827
[3,] 9.892886e-01 0.010711437
[4,] 9.931660e-01 0.006833979
[5,] 9.149391e-01 0.085060890
This method I have is not favorable
because it just stack the matrices together as another matrix.
Makes it hard to get individual matrix later.
all_mat - NULL
all_mat - c(all_mat, mat1,mat2)
- Gundala Viswanath
Jakarta - Indonesia
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Colors in Sweave
Hi list,
I was using Sweave and was wondering if anyone has had any luck changing the
font colors of the code chunks. For instance, in my .Rnw preample I tried
including:
===
\usepackage[usenames]{colors}
\definecolor{darkred}{rgb}{0.545,0,0}
\definecolor{midnightblue}{rgb}{0.098,0.098,0.439}
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl,formatcom={\color{midnightblue}}}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{formatcom={\color{darkred}}}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl,formatcom={\color{blue}}}
===
which works in the sense that colors do show up in the processed pdf document,
but extra spaces in between the input and output code chunks appear (which is
not the case when colors are not specified), resulting in a long document with
many blank lines.
Alternatively, in the resulting tex document I replaced all instances of
\begin{Sinput}... \end{Sinput} with {\color{midnightblue}\begin{Sinput} ...
\end{Sinput}} and darkred for Soutput and so on. When I do this, I get the
following error message:
=== LaTeX excerpt ===
\begin{Schunk}
{\color{midnightblue}\begin{Sinput}
ISOdatetime(1970, 1, 1, 0, 0, 0, ) - ISOdatetime(1970, 1, 1,
+ 0, 0, 0, GMT)
\end{Sinput}}
{\color{darkred}\begin{Soutput}
Time difference of 8 hours
\end{Soutput}}
\end{Schunk}
===
=== error message ===
)
! FancyVerb Error:
Extraneous input `}\end{}' between \end{Sinput} and line end
.
[EMAIL PROTECTED] ... {FancyVerb Error:
\space \space #1
}
l.13 \end{Sinput}}
===
I guess I don't know enough of the Schunk/Sinput/Soutput definitions to toy
with it and was wondering if anyone had tried something similar.
Thanks!
Stephen
__
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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 for Java programmers?
I've never used it myself but I recall reading about this R.oo package a while ago - might be worth considering? http://www1.maths.lth.se/help/R/R.oo/ - Original Message From: Werner Wernersen [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Sunday, July 27, 2008 4:55:26 AM Subject: [R] Object-oriented programming in R for Java programmers? Hi, I was wondering if anybody might have a reference for me: My R code is growing and getting more and more confusing. Thus, I figure it's time to switch to object-oriented again. I have done oo programming in C++ and Java before but the first few tutorial on R oo were a bit confusing for me. Is there any brief tutorial on oo programming in R especially for people who have done oo in Java or C++ before? That would be really helpful. Many thanks and have a great Sunday, Werner __ Dem pfiffigeren Posteingang. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Object-oriented programming in R for Java programmers?
This page is also a brief introduction to the S3 classes: http://www.ibm.com/developerworks/linux/library/l-r3.html (see section on 'Object-oriented R') and for S4, in addition to How S4 methods work: http://developer.r-project.org/methodDefinition.html - Original Message From: Johannes Huesing [EMAIL PROTECTED] To: r-help@r-project.org Sent: Sunday, July 27, 2008 12:21:37 PM Subject: Re: [R] Object-oriented programming in R for Java programmers? Werner Wernersen [EMAIL PROTECTED] [Sun, Jul 27, 2008 at 01:55:26PM CEST]: [...] Is there any brief tutorial on oo programming in R especially for people who have done oo in Java or C++ before? That would be really helpful. How S4 methods work highlights the differences between R's function-centric approach to OO and the class-centric approach highlighted by languages such as C++. This 10-page article is written by John Chambers. -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:[EMAIL PROTECTED] from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] help with data layout
Hi, hope this will help: txt - Col1,Col2 A,3 , 2 ,3 B,4 , 5 , 4 C,1 , 4 , 3 ## read data dat - read.csv(textConnection(txt),na.string=) ## fill in empty cells with correct category dat$Col1[] - Reduce(function(x,y) c(x,ifelse(is.na(y),tail(x,1),y)),dat$Col1) ## calculate mean and standard deviation mat - t(sapply(split(dat$Col2,f=dat$Col1),function(X) c(mean=mean(X),sd=sd(X ## look at results (stored in a matrix) print(mat) meansd A 2.67 0.5773503 B 4.33 0.5773503 C 2.67 1.5275252 - Original Message From: Iain Gallagher [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Thursday, July 17, 2008 8:50:42 AM Subject: [R] help with data layout Hello list I have been given some Excel sheets with data laid like this: Col1Col2 A 3 2 3 B 4 5 4 C 1 4 3 I was hoping to import this into R as a csv and then get the mean and SD for each letter in column 1. Could someone give me some guidance on best to approach this? Thanks Iain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot Mixtures of Synthetically Generated Gamma Distributions
Are you trying to look at the difference in the gamma distributions due to
variations in the shape and scale parameters? In this case, the following
approach might be more straightforward:
## assign parameter values
params - list(curve1=c(1,1),curve2=c(1,2),curve3=c(1,3))
## define function
gammafun - function(shape,scale) {
p - seq(0.001,0.999,length=1000)
x - qgamma(p,shape,scale)
y - dgamma(x,shape,scale)
list(x=x,y=y)
}
## apply function to parameters
dat - lapply(params,function(p) gammafun(p[1],p[2]))
## plot lines
xlim - range(sapply(dat,`[[`,x))
ylim - range(sapply(dat,`[[`,y))
plot.new()
plot.window(xlim,ylim)
for( i in 1:3 ) lines(dat[[i]],col=i)
lapply(1:2,axis)
box()
legend(topright,lty=1,col=1:3,legend=names(dat))
- Original Message
From: Gundala Viswanath [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Sunday, July 6, 2008 8:24:06 PM
Subject: [R] Plot Mixtures of Synthetically Generated Gamma Distributions
Hi,
I have the following vector
which is created from 3 distinct distribution (three components) of gamma:
x=c(rgamma(30,shape=.2,scale=14),rgamma(30,shape=12,scale=10),rgamma(30,shape=5,scale=6))
I want to plot the density curve of X, in a way that it shows
a distinct 3 curves that represent each component.
How can I do that?
I tried this but doesn't work:
lines(density(x))
Please advise.
- Gundala Viswanath
Jakarta - Indonesia
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Re: [R] Method for checking automatically which distribtions fits a data
I don't know that there is a single function, but you can perhaps apply a sequence of available functions - For instance, you can use fitdistr() in library(MASS) to estimate optimal parameters for a candidate set of distributions; then look at each fit and also compare the deviance among the fits (possibly penalizing distributions which require more parameters - for instance, using the Akaike Information Criterion(?)). - Original Message From: Gundala Viswanath [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Sunday, July 6, 2008 4:50:20 PM Subject: [R] Method for checking automatically which distribtions fits a data Hi, Suppose I have a vector of data. Is there a method in R to help us automatically suggest which distributions fits to that data (e.g. normal, gamma, multinomial etc) ? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] operations on all pairs of columns from two matrices
how about this? m1 - matrix(rep(1:3,each=5),ncol=3) m2 - matrix(1:15,ncol=3) array(apply(m1,2,function(x,m) m-x,m2),dim=c(dim(m2),ncol(m1))) - Original Message From: Daren Tan [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Wednesday, June 18, 2008 7:36:45 AM Subject: [R] operations on all pairs of columns from two matrices m1 - matrix(rnorm(40), ncol=4) m2 - matrix(rnorm(40), ncol=4) I would like to subtract first column of m1 from all columns of m2, subtract 2nd of m1 from all columns of m2, and so on. Obviously, I am not using the appropriate function outer(m1, m1, -), since the first column isn't all 0s. _ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] try catch block
This is a useful reference on the tryCatch() function: http://www1.maths.lth.se/help/R/ExceptionHandlingInR/ I think something like this should work: xml - tryCatch(xmlTreeParse(xmlTxt, useInternal=TRUE), error=function(err) xmlMalFormed()) - Original Message From: ppatel3026 [EMAIL PROTECTED] To: r-help@r-project.org Sent: Tuesday, June 17, 2008 2:15:43 PM Subject: [R] try catch block How can I use the try catch block such that if this statement fails xml - xmlTreeParse(xmlTxt, useInternal=TRUE) then this statement is executed xml - xmlMalFormed() ? This code does not work but assuming its somewhere along these lines: tryCatch(xml - xmlTreeParse(xmlTxt, useInternal=TRUE), xml - xmlMalFormed(f1)) -- View this message in context: http://www.nabble.com/try-catch-block-tp17938467p17938467.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] adding custom axis to image.plot() and strange clipping behavior
Hi list,
I wanted to plot an image with a colorbar to the right of the plot, but set my
own axis labels (text rather than numbers) to the image. I have previously
accomplished this with two calls to image(), but the package 'fields' has a
wrapper function, image.plot(), which does this task conveniently.
However, I could not add axes to the original image after a call to
image.plot(); I have found that I needed to set par(xpd=TRUE) within the
function to allow this to happen:
###=== begin code
library(fields)
## make data matrix
m - matrix(1:15,ncol=3)
## plot
image.plot(m,axes=FALSE)
axis(1) # doesn't work
par(xpd=TRUE)
axis(1) # still doesn't work
## replace the 28th element of the body of image.plot()
## and assign to new function called 'imp'
## here I just use the second condition of 'if' statement
## and set 'xpd = TRUE'
imp - `body-`(image.plot,value=`[[-`(body(image.plot),28,
quote({par(big.par)
par(plt = big.par$plt, xpd = TRUE)
par(mfg = mfg.save, new = FALSE)
invisible()})))
imp(m,axes=FALSE)
box()
axis(1,axTicks(1),lab=letters[1:length(axTicks(1))])
## clip to plotting region for additional
## graphical elements to be added:
par(xpd=FALSE)
abline(v=0.5)
###=== end code
I wonder if anyone has any insights into this behavior? Since in the axis()
documentation, it says:
Note that xpd is not accepted as clipping is always to the device region
I am surprised to find (1) that the par(xpd=TRUE) works in the case above, and
(2) that it must be called before the function call is terminated.
I wonder if anyone has any insights into this behavior. I have reproduced this
on both my Linux box (Ubuntu Gutsy Gibbon 64-bit, R 2.7.0, fields package
version 4.1) and Windows machine (32-bit XP Pro, R 2.7.0, fields package
version 4.1).
Thanks very much,
Stephen
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Re: [R] Data manipulation
Hi Klaus,
I am not exactly sure what you are asking for, but something like this? This
would be option (2) from your list - I don't know that it would be too
difficult in R that you would want to use another tool.
filt - function(x)
with(x,which(Hole 1))
normalize - function(x,y)
{
x$Feature - x$Feature - with(y,Nominel[match(x$Hole,Hole)])
return(x)
}
# from CSV import
mydata - read.csv(...)
# answer
normalizedData - normalize(filt(mydata))
--- Klaus Friis Østergaard [EMAIL PROTECTED] wrote:
Hi,
I have a data set which is like this I write as the CSV I import:
Sample;Hole;Feature;Value
1;5;x;4,2334
1;5;y;3,3434
1;5;r;0,1080
1;10;x;5,2526
1;10;y;4,3434
1;10;r;0,1080
with 98 sample and 10 different holes. These are measured values.
Now I also have a list of nominel values:
Hole;Feature;Nominel;LSL;USL
5;x;4,25,4,20;4,30
5;y;3,35;3,30;3,40
5;r;0,10;0,07;0,13
10;x;5,25;5,20;5,30
...
If I want to normalize the measured values. The results are to be used in
a Sweave file that I plan to reuse for several similar data sets in the
furture.
I have been looking at different approache:
1. do it in a script out side R
2. do it the long and hard way by filtering out all the single holes and
Feature, the on this list subtract the nominel values, and then combine it
back.
3. ?
Any help and guidence apriciated
--
Klaus F. Østergaard, farremosen(at)gmail dot com
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Re: [R] vector name
Hi, Either of the following should work (I assume there are 28 elements in your list): fdata - cbind(as.matrix(as.data.frame(filtered)), myregime) fdata - cbind(colnames-(matrix(unlist(filtered),ncol=28), names(filtered)), myregime) --- livia [EMAIL PROTECTED] wrote: I have got a list named filtered, I would like to construct alist named fdata as following: fdata - cbind(matrix(unlist(filtered),ncol=28), myregime) If I try names(filtered), it gives all the correct name for each vector, but if I try names(fdata), it appears filtered[[1]] filtered[[2]] ..., How can I keep the name in fdata? Could anyone give me some advice? -- View this message in context: http://www.nabble.com/vector-name-tf4466025.html#a12733890 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. Luggage? GPS? Comic books? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
