Re: [R] Plotting numeric values against non numeric items
On 01/09/2010 12:38 PM, lse1986 wrote: Hi i want do a line graph. My y axis contains numeric values. My x axis contains non numeric statements. This is what i want the graph to look like. When i try to plot this graph on R it comes up with the following error message: Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion 2: In min(x) : no non-missing arguments to min; returning Inf 3: In max(x) : no non-missing arguments to max; returning -Inf Hi Sam, While I don't know what you want the graph to look like, I would suggest the following: xf-factor(x) plot(as.numeric(xf),rnorm(10),type=l,xaxt=n) axis(1,at=1:10,labels=xf) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Arguments of a function
You could define a list and then just access the
appropriate elements of that list:
my.f - function(a, b)
{
x1 = equation 1
x2 = equation 2
x3 = equation 3
L - list(x1, x2, x3)
y - L[[a]] + L[[b]]
}
my.f(1,2)
my.f(2,3)
-Peter Ehlers
Lisa wrote:
Dear all,
I have a question about how to set arguments in my own function. For
example, I have a function that looks like this:
my.f - function(a = x1, b = x2)
{
x1 = equation 1
x2 = equation 2
x3 = equation 3
y = a + b
}
x1, x2, and x3 are temporary variables (intermediate results) calculated
from other variables within the funciton. I want to use two of these three
variables to calculate y, and write R script as below:
my.f(a = x1, b = x2)
or
my.f(a = x2, b = x3)
The error information shows that: “objects 'x1', 'x2', or 'x3' not found”.
Can anybody help me solve this problem? Thanks in advance.
Lisa
--
Peter Ehlers
University of Calgary
403.202.3921
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[R] Is there any function in R like ezplot in matlab?
Hi, Is there any function in R like ezplot in matlab? How to draw the relationship between x y like this x^y+y^(sinx)=log(x+y) Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there any function in R like ezplot in matlab?
On 09/01/2010 5:22 AM, 军 吕 wrote: Hi, Is there any function in R like ezplot in matlab? How to draw the relationship between x y like this x^y+y^(sinx)=log(x+y) It's not pre-packaged, but drawing a contour plot of the function f - function(x,y) x^y+y^sin(x) - log(x+y) should do it: xvals - yvals - seq(0, 30, len=1000) zvals - outer(xvals, yvals, f) contour(xvals, yvals, zvals, levels=0) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] aov function syntax
Hello, I have a simple question about using the aov function syntax (ie. * + or :) for the interaction of 2 factors. I have read the help files, and researched other sites, and have included my source files. My goal is to measure the signifigance of the interaction between population and condition (aka. population:condition). I can't seem to figure it out. 1. In the first example the significance of population:condition works with the allData but not with the studentData. Can you please explain why it fails and how I can fix it? 2. In the second example I can get the measure the significance of population:condition with 2 different methods, but I get 2 different results (using the allData source). Can you please explain why these Pr(F) values are different? Thank you so much for your help!! Sincerely, Dave Deriso UCSD Psychiatry #Example 1 ---COPY PASTE THE FOLLOWING #import the data allDataSource=http://files.davidderiso.com/r/allData.data; allData.import=read.table(allDataSource,header=T) studentDataSource=http://files.davidderiso.com/r/allData.data; studentData.import=read.table(studentDataSource,header=T) #aov for allData WORKS allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #aov for studentData DOES NOT GIVE Pr(F) of population:condition studentData.integral.aov = aov(integral~population*condition, data=studentData.import) summary(studentData.integral.aov) #Example 2 ---COPY PASTE THE FOLLOWING #population:condition has a Pr(F) of 0.96372 allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #population:condition has a Pr(F) of 1.070e-06 *** allData.integral.aov = aov(integral~population:condition, data=allData.import) summary(allData.integral.aov) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] aov function syntax
Oops small error Use this to import the data #import the data allData.import=read.table(http://files.davidderiso.com/r/allData.data ,header=T) studentData.import=read.table( http://files.davidderiso.com/r/studentData.data,header=T) everything else is good On Sat, Jan 9, 2010 at 3:33 AM, Dave Deriso dder...@ucsd.edu wrote: Hello, I have a simple question about using the aov function syntax (ie. * + or :) for the interaction of 2 factors. I have read the help files, and researched other sites, and have included my source files. My goal is to measure the signifigance of the interaction between population and condition (aka. population:condition). I can't seem to figure it out. 1. In the first example the significance of population:condition works with the allData but not with the studentData. Can you please explain why it fails and how I can fix it? 2. In the second example I can get the measure the significance of population:condition with 2 different methods, but I get 2 different results (using the allData source). Can you please explain why these Pr(F) values are different? Thank you so much for your help!! Sincerely, Dave Deriso UCSD Psychiatry #Example 1 ---COPY PASTE THE FOLLOWING #import the data allDataSource=http://files.davidderiso.com/r/allData.data; allData.import=read.table(allDataSource,header=T) studentDataSource=http://files.davidderiso.com/r/allData.data; studentData.import=read.table(studentDataSource,header=T) #aov for allData WORKS allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #aov for studentData DOES NOT GIVE Pr(F) of population:condition studentData.integral.aov = aov(integral~population*condition, data=studentData.import) summary(studentData.integral.aov) #Example 2 ---COPY PASTE THE FOLLOWING #population:condition has a Pr(F) of 0.96372 allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #population:condition has a Pr(F) of 1.070e-06 *** allData.integral.aov = aov(integral~population:condition, data=allData.import) summary(allData.integral.aov) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strange behavior of R
On Fri, Jan 8, 2010 at 10:57 PM, Fahim fahim...@gmail.com wrote: arr [1] y1 y2 At this moment 'arr' no longer has two dimensions, but only one. So you can access it only as a vector. Problem: I want to access the first row now using: arr[1, ] Error in arr[1, 1] : incorrect number of dimensions Correct. It has only one dim. Though it is showing the value as under: arr[1] [1] y1 arr[2] [1] y2 This is how you would access individual elements in vectors. Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] aov function syntax
What are you trying to do? Your example is not what is commonly called ANOVA (some call it ANCOVA) and more often lm() is used. I suspect that you intended 'population' to be a factor, and it is not. So population:condition is not an interaction but different slopes for population by levels of condition. population*condition expands to population + condition + population:condition and this is a larger model with different intercepts by levels of condition. I suggest you need study the primary reference (Chambers Hastie 1992) or at least Bill Venables' exposition in MASS (the book, any edition). And note that you cannot test interactions in a two-way layout without replication, so perhaps you also need to talk to a statistician about ANOVA. BTW: I think you have messed up your first example: perhaps you meant studentDataSource=http://files.davidderiso.com/r/studentData.data; There are no P values in that example because there is no residual variation: the model fits exactly. On Sat, 9 Jan 2010, Dave Deriso wrote: Hello, I have a simple question about using the aov function syntax (ie. * + or :) for the interaction of 2 factors. I have read the help files, and researched other sites, and have included my source files. My goal is to measure the signifigance of the interaction between population and condition (aka. population:condition). I can't seem to figure it out. 1. In the first example the significance of population:condition works with the allData but not with the studentData. Can you please explain why it fails and how I can fix it? 2. In the second example I can get the measure the significance of population:condition with 2 different methods, but I get 2 different results (using the allData source). Can you please explain why these Pr(F) values are different? Thank you so much for your help!! Sincerely, Dave Deriso UCSD Psychiatry #Example 1 ---COPY PASTE THE FOLLOWING #import the data allDataSource=http://files.davidderiso.com/r/allData.data; allData.import=read.table(allDataSource,header=T) studentDataSource=http://files.davidderiso.com/r/allData.data; studentData.import=read.table(studentDataSource,header=T) #aov for allData WORKS allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #aov for studentData DOES NOT GIVE Pr(F) of population:condition studentData.integral.aov = aov(integral~population*condition, data=studentData.import) summary(studentData.integral.aov) #Example 2 ---COPY PASTE THE FOLLOWING #population:condition has a Pr(F) of 0.96372 allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #population:condition has a Pr(F) of 1.070e-06 *** allData.integral.aov = aov(integral~population:condition, data=allData.import) summary(allData.integral.aov) [[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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] aov function syntax
Thank you for your help professor Ripley! I suppose my problem is more theoretical related than syntax. I will review your suggested literature. and yes, I did error on the data source, thank you for catching my mistake!! Best, Dave On Sat, Jan 9, 2010 at 3:56 AM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: What are you trying to do? Your example is not what is commonly called ANOVA (some call it ANCOVA) and more often lm() is used. I suspect that you intended 'population' to be a factor, and it is not. So population:condition is not an interaction but different slopes for population by levels of condition. population*condition expands to population + condition + population:condition and this is a larger model with different intercepts by levels of condition. I suggest you need study the primary reference (Chambers Hastie 1992) or at least Bill Venables' exposition in MASS (the book, any edition). And note that you cannot test interactions in a two-way layout without replication, so perhaps you also need to talk to a statistician about ANOVA. BTW: I think you have messed up your first example: perhaps you meant studentDataSource=http://files.davidderiso.com/r/studentData.data; There are no P values in that example because there is no residual variation: the model fits exactly. On Sat, 9 Jan 2010, Dave Deriso wrote: Hello, I have a simple question about using the aov function syntax (ie. * + or :) for the interaction of 2 factors. I have read the help files, and researched other sites, and have included my source files. My goal is to measure the signifigance of the interaction between population and condition (aka. population:condition). I can't seem to figure it out. 1. In the first example the significance of population:condition works with the allData but not with the studentData. Can you please explain why it fails and how I can fix it? 2. In the second example I can get the measure the significance of population:condition with 2 different methods, but I get 2 different results (using the allData source). Can you please explain why these Pr(F) values are different? Thank you so much for your help!! Sincerely, Dave Deriso UCSD Psychiatry #Example 1 ---COPY PASTE THE FOLLOWING #import the data allDataSource=http://files.davidderiso.com/r/allData.data; allData.import=read.table(allDataSource,header=T) studentDataSource=http://files.davidderiso.com/r/allData.data; studentData.import=read.table(studentDataSource,header=T) #aov for allData WORKS allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #aov for studentData DOES NOT GIVE Pr(F) of population:condition studentData.integral.aov = aov(integral~population*condition, data=studentData.import) summary(studentData.integral.aov) #Example 2 ---COPY PASTE THE FOLLOWING #population:condition has a Pr(F) of 0.96372 allData.integral.aov = aov(integral~population*condition, data=allData.import) summary(allData.integral.aov) #population:condition has a Pr(F) of 1.070e-06 *** allData.integral.aov = aov(integral~population:condition, data=allData.import) summary(allData.integral.aov) [[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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] time series analysis for a time series without a regular frequency
On Fri, 8 Jan 2010, Erin Hestir wrote: I am trying to conduct a time series analysis on historic hydrologic data, but I cannot coerce it into class ts because it does not have regular sampling intervals (some years have 20 samples, other have 8). Specifically I am trying to perform a CUSUM or or other step change detection, but the packages all seem to require data as ts. As Gabor already pointed out: the zoo package can be used to store such data. If you want to use the strucchange package for detecting changes then you can do two things: - use a plain data.frame (without ts or some other time series class) which can be easily produced via as.data.frame(zoo_obj). Then the axis annotation in graphics won't be the time axis but the standard unit interval (= proportion of data). This is not so pretty but all statistical interpretations are still correct. - If zoo_obj is just a univariate series and you want to conduct a CUSUM test for a change in the mean you can do cus - gefp(zoo_obj ~ 1) plot(cus) plot(cus, functional = meanL2BB) and so on. gefp() is the only function in strucchange that automatically supports zoo. hth, Z Is there a way to coerce my data into ts while maintaining all of my samples? Or alternatively, can someone recommend a package that does not require data as ts? Thanks! -- Erin Hestir Center for Spatial Technology and Remote Sensing University of California Davis [[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] Arguments of a function
Normally one designs their function to input a formula in such a case
rather than design it to take the names directly. Thus:
f - function(formula = ~ x1 + x2) {
xs - c(x1 = 1, x2 = exp(1), x3 = 2*pi)
v - all.vars(formula)
stopifnot(length(v) == 2, all(v %in% names(xs)))
sum(xs[v])
}
# test
f()
f(~ x1 + x2) # same
f(~ x2+x3)
On Fri, Jan 8, 2010 at 1:15 PM, Lisa lisa...@gmail.com wrote:
Dear all,
I have a question about how to set arguments in my own function. For
example, I have a function that looks like this:
my.f - function(a = x1, b = x2)
{
x1 = equation 1
x2 = equation 2
x3 = equation 3
y = a + b
}
x1, x2, and x3 are temporary variables (intermediate results) calculated
from other variables within the funciton. I want to use two of these three
variables to calculate y, and write R script as below:
my.f(a = x1, b = x2)
or
my.f(a = x2, b = x3)
The error information shows that: “objects 'x1', 'x2', or 'x3' not found”.
Can anybody help me solve this problem? Thanks in advance.
Lisa
--
View this message in context:
http://n4.nabble.com/Arguments-of-a-function-tp1009883p1009883.html
Sent from the R help mailing list archive at Nabble.com.
__
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and provide commented, minimal, self-contained, reproducible code.
__
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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] how to flatten a list to the same level?
Henrique,
thanks for the code!! It works out fine for vectors. I forgot to
mention I also have dataframes as list elements.
Thus I want the structure of the list element to be kept intact.
I tried an recursive approach (which unfortunately resulted in some
more code) which works.
.getNonListElements - function(x, env){
if(class(x)==list) {
for(i in seq(along=x)) .getNonListElements(x[[i]], env) # call
recursively
} else {
res - get(res, envir = env) # get res from other
env
res - c(res, list(x)) # add one
list element
assign(res, res, envir=env) # assign back to env
}
}
flattenList - function(l){
res - list()# make
list object
env - environment() # get current env
.getNonListElements(l, env) # search for non list elements
recursively
return(res)
}
l - list(DF=data.frame(A=c(1,2)), vec=c(a, b))
l - list(l,l)
flattenList(l)
[[1]]
A
1 1
2 2
[[2]]
[1] a b
[[3]]
A
1 1
2 2
[[4]]
[1] a b
I am not sure if one can avoid the wrapper function or still use
rapply to simplify the code. I do not know how.
One more thing I would like to add are the objects names to the
generated list. But I did not succeed in that.
Mark
Am 08.01.2010 um 18:29 schrieb Henrique Dallazuanna:
Try something about like this:
split(unlist(l), rep(1:length(idx - rapply(l, length)), idx))
On Fri, Jan 8, 2010 at 1:35 PM, Mark Heckmann mark.heckm...@gmx.de
wrote:
I have a nested list l like:
l - list(A=c(1,2,3), B=c(a, b))
l - list(l,l, list(l,l))
I want the list to be unlisted, but not on the lowest level of each
branch.
I want the lowest level of each list branch to remain as it is.
So unlist or unlist(rec=F) do not work here as the level of nesting
may
differ on the elements.
The result should look like:
$A
[1] 1 2 3
$B
[1] a b
$A
[1] 1 2 3
$B
[1] a b
$A
[1] 1 2 3
$B
[1] a b
$A
[1] 1 2 3
$B
[1] a b
Any ideas?
TIA!
Mark
–––
Mark Heckmann
Dipl. Wirt.-Ing. cand. Psych.
Vorstraße 93 B01
28359 Bremen
Blog: www.markheckmann.de
R-Blog: http://ryouready.wordpress.com
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and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
–––
Mark Heckmann
Dipl. Wirt.-Ing. cand. Psych.
Vorstraße 93 B01
28359 Bremen
Blog: www.markheckmann.de
R-Blog: http://ryouready.wordpress.com
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Re: [R] postscript, greek lellters
Hi, Something like this maybe, plot.new() lab = expression(bar(T)*(*-x* ; *alpha*)-G*(*x* ; *alpha* , *J*)) text(0.5,0.5,lab) ?plotmath HTH, baptiste 2010/1/8 bernardo lagos alvarez blacert...@gmail.com: Dear useRs, How can I, writting the correct greek letter using postscrip or pdf function. In my figures appears only the first letter (a of alpha, n of nu) when include the graphs in my .tex doxument. I am using title( expression(bar(T)(paste(-x,;,alpha))-G(paste(x,;,alpha,,,J title( expression(bar(T)(paste(-x,;~alpha))-G(paste(x,;~alpha,,,J title( expression(bar(T)(paste(-x,;*alpha))-G(paste(x,;*alpha,,,J, not work. sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks for your help, Bernardo. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] errors when installing packages (ubuntu)
Hi List, I'm having problems installing certain packages. When I try to install fields, I get the output below. I have highlighted the what I perceive as the first error (spam seems to be a dependency of fields). Can I assume this is causing dependency problems for fields, which fails to install at the end, or is there a deeper problem? I run Ubuntu Karmic Koala on R 2.9.2. 2 install.packages(fields) Warning in install.packages(fields) : argument 'lib' is missing: using '/home/romunov/R/i486-pc-linux-gnu-library/2.9' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done also installing the dependency spam trying URL 'http://cran.at.r-project.org/src/contrib/spam_0.20-2.tar.gz' Content type 'application/x-gzip' length 470013 bytes (458 Kb) opened URL == downloaded 458 Kb trying URL 'http://cran.at.r-project.org/src/contrib/fields_6.01.tar.gz' Content type 'application/x-gzip' length 3670039 bytes (3.5 Mb) opened URL == downloaded 3.5 Mb * Installing *source* package spam ... ** libs gfortran -fpic -g -O2 -c bckslvmodified.f -o bckslvmodified.o gfortran -fpic -g -O2 -c cholmodified.f -o cholmodified.o gfortran -fpic -g -O2 -c dist.f -o dist.o gfortran -fpic -g -O2 -c fromsparsekit.f -o fromsparsekit.o gfortran -fpic -g -O2 -c kronecker.f -o kronecker.o gfortran -fpic -g -O2 -c spamown.f -o spamown.o gfortran -fpic -g -O2 -c xybind.f -o xybind.o gcc -std=gnu99 -shared -o spam.so bckslvmodified.o cholmodified.o dist.o fromsparsekit.o kronecker.o spamown.o xybind.o -lgfortran -lm -L/usr/lib/R/lib -lR ** R ** data ** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading Creating a new generic function for print in spam Creating a new generic function for summary in spam Creating a new generic function for diag in spam Creating a new generic function for diag- in spam Creating a new generic function for t in spam Error in setOldClass(c(dist, numeric)) : inconsistent old-style class information for numeric; the class is defined but does not extend oldClass Error : unable to load R code in package 'spam' ERROR: lazy loading failed for package spam * Removing /home/romunov/R/i486-pc-linux-gnu-library/2.9/spam * Installing *source* package fields ... ** libs gfortran -fpic -g -O2 -c css.f -o css.o gfortran -fpic -g -O2 -c csstr.f -o csstr.o gfortran -fpic -g -O2 -c cvrf.f -o cvrf.o gfortran -fpic -g -O2 -c dchold.f -o dchold.o gfortran -fpic -g -O2 -c dcopy.f -o dcopy.o gfortran -fpic -g -O2 -c ddfind.f -o ddfind.o gfortran -fpic -g -O2 -c ddot.f -o ddot.o gfortran -fpic -g -O2 -c derrb.f -o derrb.o gfortran -fpic -g -O2 -c dlv.f -o dlv.o gfortran -fpic -g -O2 -c dmaket.f -o dmaket.o gfortran -fpic -g -O2 -c drdfun.f -o drdfun.o gfortran -fpic -g -O2 -c dsetup.f -o dsetup.o gfortran -fpic -g -O2 -c evlpoly.f -o evlpoly.o gfortran -fpic -g -O2 -c evlpoly2.f -o evlpoly2.o gfortran -fpic -g -O2 -c expbs.f -o expbs.o gfortran -fpic -g -O2 -c expfn.f -o expfn.o gfortran -fpic -g -O2 -c gaspbs.f -o gaspbs.o gfortran -fpic -g -O2 -c gaspfn.f -o gaspfn.o gfortran -fpic -g -O2 -c gcvcss.f -o gcvcss.o gfortran -fpic -g -O2 -c gcvfc.f -o gcvfc.o gfortran -fpic -g -O2 -c hsort.f -o hsort.o gfortran -fpic -g -O2 -c ifind.f -o ifind.o gfortran -fpic -g -O2 -c igpoly.f -o igpoly.o gfortran -fpic -g -O2 -c inpoly.f -o inpoly.o gfortran -fpic -g -O2 -c lscv.f -o lscv.o gfortran -fpic -g -O2 -c m2deb.f -o m2deb.o gfortran -fpic -g -O2 -c mkpoly.f -o mkpoly.o gfortran -fpic -g -O2 -c mltdrb.f -o mltdrb.o gfortran -fpic -g -O2 -c mltdtd.f -o mltdtd.o gfortran -fpic -g -O2 -c msort.f -o msort.o gfortran -fpic -g -O2 -c multeb.f -o multeb.o gfortran -fpic -g -O2 -c multgb.f -o multgb.o gfortran -fpic -g -O2 -c multrb.f -o multrb.o gfortran -fpic -g -O2 -c radbas.f -o radbas.o gfortran -fpic -g -O2 -c radfn2.f -o radfn2.o gfortran -fpic -g -O2 -c radfun.f -o radfun.o gfortran -fpic -g -O2 -c rcss.f -o rcss.o gfortran -fpic -g -O2 -c rcssr.f -o rcssr.o gfortran -fpic -g -O2 -c rcsswt.f -o rcsswt.o gfortran -fpic -g -O2 -c sortm.f -o sortm.o gcc -std=gnu99 -shared -o fields.so css.o csstr.o cvrf.o dchold.o dcopy.o ddfind.o ddot.o derrb.o dlv.o dmaket.o drdfun.o dsetup.o evlpoly.o evlpoly2.o expbs.o expfn.o gaspbs.o gaspfn.o gcvcss.o gcvfc.o hsort.o ifind.o igpoly.o inpoly.o lscv.o m2deb.o mkpoly.o mltdrb.o mltdtd.o msort.o multeb.o multgb.o multrb.o radbas.o radfn2.o radfun.o rcss.o rcssr.o rcsswt.o sortm.o -lgfortran -lm -L/usr/lib/R/lib -lR ** R ** data ** preparing package for lazy loading Warning in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'spam' Error : package 'spam' could not be loaded ERROR: lazy loading failed for package fields * Removing
Re: [R] parsing pdf files
On Sat, Jan 9, 2010 at 1:11 PM, David Kane d...@kanecap.com wrote: 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? What could it do that saving as text from Acrobat couldn't do? Here's the problem - PDF is a page description format, it's not designed to be read back. There's no guarantee that the letters on the page appear in the PDF in the same order as they seem on the page. The page could have all the letter 'a's, then the 'b's and so on, positioned in their right places to make up words. To reconstruct the words you'd have to spot where the letters were being placed, and then figure out the breaks and make up the words. Good luck making the sentences. Most PDFs aren't that perverse, and you can often get sensible text out of them. But then you run into font encodings and graphics and column layouts and stuff. Any effort put into writing a readPDF() would have to be redone every time someone tried to read a PDF :) On Linux/Unix there's a bunch of command line tools for trying to do this kind of thing with PDF files - see pdftotext for example. You could run that from R with system() and then read the text with readLines. But there's absolutely no guarantees this will work. Windows/Mac versions (did you say what your platform was?) of the command line tools may be available. The real answer is to get the original data in a format with some kind of semantics that R could read, for example a CSV or some nice XML format. Barry -- blog: http://geospaced.blogspot.com/ web: http://www.maths.lancs.ac.uk/~rowlings web: http://www.rowlingson.com/ twitter: http://twitter.com/geospacedman pics: http://www.flickr.com/photos/spacedman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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
Hi, I used pdftk (pdf toolkit) before. A quick glance at the features seems to tell that it does *not* support what you are looking for, but it may nonetheless be a useful starting point: http://www.accesspdf.com/pdftk/ . The nice thing is that it's a command-line tool. Cheers!! Albert-Jan ~~ In the face of ambiguity, refuse the temptation to guess. ~~ --- On Sat, 1/9/10, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: From: Barry Rowlingson b.rowling...@lancaster.ac.uk Subject: Re: [R] parsing pdf files To: David Kane d...@kanecap.com Cc: r-help@r-project.org Date: Saturday, January 9, 2010, 2:47 PM On Sat, Jan 9, 2010 at 1:11 PM, David Kane d...@kanecap.com wrote: 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? What could it do that saving as text from Acrobat couldn't do? Here's the problem - PDF is a page description format, it's not designed to be read back. There's no guarantee that the letters on the page appear in the PDF in the same order as they seem on the page. The page could have all the letter 'a's, then the 'b's and so on, positioned in their right places to make up words. To reconstruct the words you'd have to spot where the letters were being placed, and then figure out the breaks and make up the words. Good luck making the sentences. Most PDFs aren't that perverse, and you can often get sensible text out of them. But then you run into font encodings and graphics and column layouts and stuff. Any effort put into writing a readPDF() would have to be redone every time someone tried to read a PDF :) On Linux/Unix there's a bunch of command line tools for trying to do this kind of thing with PDF files - see pdftotext for example. You could run that from R with system() and then read the text with readLines. But there's absolutely no guarantees this will work. Windows/Mac versions (did you say what your platform was?) of the command line tools may be available. The real answer is to get the original data in a format with some kind of semantics that R could read, for example a CSV or some nice XML format. Barry -- blog: http://geospaced.blogspot.com/ web: http://www.maths.lancs.ac.uk/~rowlings web: http://www.rowlingson.com/ twitter: http://twitter.com/geospacedman pics: http://www.flickr.com/photos/spacedman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] parsing pdf files
David Kane a écrit : 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. Did you know this site ? http://www.accesspdf.com/pdftk/ There could be a command line to transform the pdf file in XML format and then read the XML file with R. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] importing home range polygon
Hi everyone, I am using adehabitat package for habitat selection analysis, I know R also do home range analysis, but I want to import home range polygon to R and run K-select analysis on this home range polygon. Do you know any material to help me? Thanks, Mustafa [[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] Boxplots
I have a data set with four columns and need to make boxplots from them. Data is as follows: tank TanksTotal cons_hat 1aa4 5.651017 5.59 2aa5 5.017499 5.29 3aa6 4.894238 4.69 4cc4 3.986347 3.40 5cc5 4.099442 3.58 6cc6 4.150522 3.64 7hh4 5.187792 6.32 8hh5 6.713422 6.44 9hh6 5.168555 5.62 This is simply consumption data with Total being the actual measured consumption and cons_hat being the predicted. I need a boxplot of tank a (consisting of a4,a5,a6) Total vs. cons_hat. boxplot(Total~tank) of course creates a boxplot with only Total by tank, but how do I put the other column in this boxplot? Thanks ahead of time. keith -- M. Keith Cox, Ph.D. Alaska NOAA Fisheries, National Marine Fisheries Service Auke Bay Laboratories 17109 Pt. Lena Loop Rd. Juneau, AK 99801 keith@noaa.gov marlink...@gmail.com U.S. (907) 789-6603 [[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] Reducing the size of a large script top speed onset of execution
Colleagues,
(R 2.10 on all platforms)
I have a lengthy script (18000 lines) that runs within a graphical
interface. The script consists of 100's of function followed by a
single command that calls these functions (execution depends on a
number of environment variables passed to the script). As a result,
nothing is executed until the final line of code is read. It takes
15-20 seconds to load the code - I would like to speed that process.
Two questions:
1. The code contains numerous large blocks that are executed under
only one set of conditions (which are known when the code is called).
For example, there might be code such as:
if (CONDITION)
{
... (hundreds of lines of code, including embedded curly
brackets)
} else invisible()
if (!CONDITION)
{
... (hundreds of lines of code, including embedded curly
brackets)
}
I assume that I could speed loading appreciably if I set up two
scripts, each of which excluded irrelevant code depending on the
CONDITION. For example, if I knew that CONDITION was false, I would
exclude the first block of code above; conversely, if I know that
CONDITION was true, I would exclude the second block.
I would like to write code in R (or in sed [UNIX stream editor]) to
create these two new scripts. However, the regular expressions that
would be needed are beyond me and I would appreciate help from this
forum. Specifically, I would like to search for:
if (CONDITION
or
if (!CONDITION
as the start of the block and
} - the matching curly bracket
at the end of the block, then remove those lines from the code. These
text entries are always on a line by themselves. Finding the if
(CONDITION line should be relatively easy. The difficulty for me is
identifying the matching curly bracket - there are often paired
brackets within the block of code:
if (CONDITION)
{
...
if (SOMETHINGELSE) { }
if (YETANOTHER)
{
}
} - this is the bracket that I
need to match
There are also instances in which the entire block occurs on one line:
if (CONDITION) { ...} else invisible()
or
if (CONDITION ... else invisible()
Of note, I can remove the else invisible() statements if they are
problematic to a solution.
2. A related issue regards loading in the graphical interface vs.
loading at the command line (OS X). The graphical interface loads in
15-20 seconds - the graphical interface is sending code as rapidly as
it can. In contrast, at the command line, the course is source()'d
and it takes 30-40 seconds. I would have expected the latter approach
to be as fast or faster because R would accept code as fast as it could.
Does anyone have an explanation for this behavior; also, any ideas as
to how to speed the process at the command line would be appreciated.
Thanks for any suggestions.
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting numeric values against non numeric items
Hey Jim, Thanks for your reply! I tried what you said, i still kept getting errors. here's what i want my graph to look like: http://i.imagehost.org/0474/Untitled_5.jpg i have x-c(not stir, stir) i can't plot it though :( Jim Lemon wrote: On 01/09/2010 12:38 PM, lse1986 wrote: Hi i want do a line graph. My y axis contains numeric values. My x axis contains non numeric statements. This is what i want the graph to look like. When i try to plot this graph on R it comes up with the following error message: Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion 2: In min(x) : no non-missing arguments to min; returning Inf 3: In max(x) : no non-missing arguments to max; returning -Inf Hi Sam, While I don't know what you want the graph to look like, I would suggest the following: xf-factor(x) plot(as.numeric(xf),rnorm(10),type=l,xaxt=n) axis(1,at=1:10,labels=xf) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://n4.nabble.com/Plotting-numeric-values-against-non-numeric-items-tp1010129p1010311.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building static HTML help pages in R 2.10.x on Windows
Michal Kulich wrote: This works. Not entirely invisible but not a big deal about that. The R code run within Rterm is options(help_type=html,help.ports=6800) help.start() library(audio) wait(-1) I tried to run your code with System.sleep(10) instead of wait(-1) inside Winserv, which is an open-source replacement for srvany (MS). Winserv has a very clean interface and is much more flexible than srvany. http://sw4me.com/wiki/Winserv?v=qw0 The service installs (install) and runs (start), status is RUNNING, but I could not connect to the port. Dieter -- View this message in context: http://n4.nabble.com/Building-static-HTML-help-pages-in-R-2-10-x-on-Windows-tp977326p1010340.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting numeric values against non numeric items
Try this: # create data x - rbind(Not Stir=c(400, 700), Stir=c(50, 180)) matplot(x, type='o', pch=16, cex=2, xaxt='n') axis(1, at=1:2, labels=rownames(x)) On Sat, Jan 9, 2010 at 9:29 AM, lse1986 sam_eden1...@yahoo.co.uk wrote: Hey Jim, Thanks for your reply! I tried what you said, i still kept getting errors. here's what i want my graph to look like: http://i.imagehost.org/0474/Untitled_5.jpg i have x-c(not stir, stir) i can't plot it though :( Jim Lemon wrote: On 01/09/2010 12:38 PM, lse1986 wrote: Hi i want do a line graph. My y axis contains numeric values. My x axis contains non numeric statements. This is what i want the graph to look like. When i try to plot this graph on R it comes up with the following error message: Error in plot.window(...) : need finite 'xlim' values In addition: Warning messages: 1: In xy.coords(x, y, xlabel, ylabel, log) : NAs introduced by coercion 2: In min(x) : no non-missing arguments to min; returning Inf 3: In max(x) : no non-missing arguments to max; returning -Inf Hi Sam, While I don't know what you want the graph to look like, I would suggest the following: xf-factor(x) plot(as.numeric(xf),rnorm(10),type=l,xaxt=n) axis(1,at=1:10,labels=xf) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://n4.nabble.com/Plotting-numeric-values-against-non-numeric-items-tp1010129p1010311.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.htmlhttp://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? [[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] aov vs lme for split plot analysis
Dear R community, I am trying to do a split-plot analysis as follows. I have a data set (“morf”) with plant data from 6 “blocks” at different latitudes, each divided in 3 plots. The full-plot “treatment” is “soil type” and has three levels. Within each plot I have two levels of radiation, coded as “SUN” and “SHADE”. I have data for several response traits for 30 plants within each subplot, that is 1080 plants in total (6 Blocks x 3Plots x 2Radiation levels x 30 Plants). I want to measure a) if there are differences between latitudes (“blocks”) and b) how these differences interact with radiation levels. I am not so interested in the effect of soil type, which I already know, but radiation effects depend on soil type. The model I’m looking for should look something like: Response ~ Block*Radiation | Soil type I have tried to use lme. The basic formulation I have tried is: lme(Resp~Block*Radiation, random=~ 1 | Plot/Radiation, data=morf) but I keep on getting the error message: “Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups” I don’t know why this is happening, could it be because “Radiation” has only two levels? I don't have missing values or any other obvious source of noise Since neither lme nor lmer weren’t working, I tried “aov”. I played around a bit with the Oats data set and saw that: aov( yield ~ ordered(nitro) * Variety + Error(Block/Variety), data = Oats) gives the same results as the standard lme( yield ~ ordered(nitro) * Variety, data = Oats, random = ~ 1 | Block/Variety ) So I used the following formulation aov(Resp~Block*Radiation+Error(Plot/Radiation), data=morf) This seems to work fine, but I am not that confident I am using the correct syntax. Any advice and/or guidance would be much appreciated. Thank you in advance. RAFA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Reducing the size of a large script top speed onset of execution
Please just use make a package; then all the effort of parsing the
code is done at install time, you can use lazy-loading Or if you
are for some reason averse to that, source the code into an
environment, save that and simply attach() its save file next time.
Packages of that size load in a few milliseconds (as you see each time
you start R: stats is 27000 lines).
source() is doing more work to allow it to guess encodings, keeping
references to the original sources, back out code if the whole script
does not parse
On Sat, 9 Jan 2010, Dennis Fisher wrote:
Colleagues,
(R 2.10 on all platforms)
I have a lengthy script (18000 lines) that runs within a graphical interface.
The script consists of 100's of function followed by a single command that
calls these functions (execution depends on a number of environment variables
passed to the script). As a result, nothing is executed until the final line
of code is read. It takes 15-20 seconds to load the code - I would like to
speed that process. Two questions:
1. The code contains numerous large blocks that are executed under only one
set of conditions (which are known when the code is called). For example,
there might be code such as:
if (CONDITION)
{
... (hundreds of lines of code, including embedded curly
brackets)
} else invisible()
if (!CONDITION)
{
... (hundreds of lines of code, including embedded curly
brackets)
}
I assume that I could speed loading appreciably if I set up two scripts, each
of which excluded irrelevant code depending on the CONDITION. For example,
if I knew that CONDITION was false, I would exclude the first block of code
above; conversely, if I know that CONDITION was true, I would exclude the
second block.
I would like to write code in R (or in sed [UNIX stream editor]) to create
these two new scripts. However, the regular expressions that would be needed
are beyond me and I would appreciate help from this forum. Specifically, I
would like to search for:
if (CONDITION
or
if (!CONDITION
as the start of the block and
} - the matching curly bracket
at the end of the block, then remove those lines from the code. These text
entries are always on a line by themselves. Finding the if (CONDITION line
should be relatively easy. The difficulty for me is identifying the matching
curly bracket - there are often paired brackets within the block of code:
if (CONDITION)
{
...
if (SOMETHINGELSE) { }
if (YETANOTHER)
{
}
}- this is the bracket that
I need to match
There are also instances in which the entire block occurs on one line:
if (CONDITION) { ...} else invisible()
or
if (CONDITION ... else invisible()
Of note, I can remove the else invisible() statements if they are
problematic to a solution.
2. A related issue regards loading in the graphical interface vs. loading at
the command line (OS X). The graphical interface loads in 15-20 seconds -
the graphical interface is sending code as rapidly as it can. In contrast,
at the command line, the course is source()'d and it takes 30-40 seconds. I
would have expected the latter approach to be as fast or faster because R
would accept code as fast as it could.
Does anyone have an explanation for this behavior; also, any ideas as to how
to speed the process at the command line would be appreciated. Thanks for
any suggestions.
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com
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University of Oxford, Tel: +44 1865 272861 (self)
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Re: [R] postscript, greek lellters
Thank you, Dennis and Baptisite By including the. eps in my . tex and the compilation of the .tex, this does not generate the symbol of the greek letter. Bernardo. 2010/1/9 baptiste auguie baptiste.aug...@googlemail.com: Hi, Something like this maybe, plot.new() lab = expression(bar(T)*(*-x* ; *alpha*)-G*(*x* ; *alpha* , *J*)) text(0.5,0.5,lab) ?plotmath HTH, baptiste 2010/1/8 bernardo lagos alvarez blacert...@gmail.com: Dear useRs, How can I, writting the correct greek letter using postscrip or pdf function. In my figures appears only the first letter (a of alpha, n of nu) when include the graphs in my .tex doxument. I am using title( expression(bar(T)(paste(-x,;,alpha))-G(paste(x,;,alpha,,,J title( expression(bar(T)(paste(-x,;~alpha))-G(paste(x,;~alpha,,,J title( expression(bar(T)(paste(-x,;*alpha))-G(paste(x,;*alpha,,,J, not work. sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks for your help, Bernardo. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] postscript, greek lellters
The problem is of the .dvi. It was arranged,using the solution of Baptiste. Bernardo. 2010/1/9 bernardo lagos alvarez blacert...@gmail.com: Thank you, Dennis and Baptisite By including the. eps in my . tex and the compilation of the .tex, this does not generate the symbol of the greek letter. Bernardo. 2010/1/9 baptiste auguie baptiste.aug...@googlemail.com: Hi, Something like this maybe, plot.new() lab = expression(bar(T)*(*-x* ; *alpha*)-G*(*x* ; *alpha* , *J*)) text(0.5,0.5,lab) ?plotmath HTH, baptiste 2010/1/8 bernardo lagos alvarez blacert...@gmail.com: Dear useRs, How can I, writting the correct greek letter using postscrip or pdf function. In my figures appears only the first letter (a of alpha, n of nu) when include the graphs in my .tex doxument. I am using title( expression(bar(T)(paste(-x,;,alpha))-G(paste(x,;,alpha,,,J title( expression(bar(T)(paste(-x,;~alpha))-G(paste(x,;~alpha,,,J title( expression(bar(T)(paste(-x,;*alpha))-G(paste(x,;*alpha,,,J, not work. sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Thanks for your help, Bernardo. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] [Lattice] panel.levelplot - shrink argument to highlight absolute z-values
Hi -
I have a levelplot with positive and negative z-values. I'd like
to scale the levelplot rectangles proportional to the *absolute*
z-values to highlight the z-value extremes (while retaining the color
difference to track the positive/negative attribute). I've likely
missed something in the documentation, but have been at it a couple
days without finding a solution (other than patching the
panel.levelplot routine). Is there a way to do this? If not, can we
add the functionality?
By way of a very simple example, I'd like to make the deep-colors
bigger in the following example (please note the I am using the
`expression` version of the leveplot() function with a data frame
instead of the `matrix` version in my particular application).
levelplot(matrix(runif(21),nrow=7,ncol=3)-0.5,panel=function(x,y,z,subscript,
...) { panel.levelplot(x,y,z,shrink=c(0,2),...)})
Thanks!
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[R] bootstrapping a matrix using boot package
Dear All,
I am trying to bootstrap a large data matrix 'exp' of dimension
9275x898 using package 'boot'. I am trying to calculate correlation of
the obtained samples. I have done following so far:
library(boot)
load(ratio_exp.RData) #loading the data matrix
dim(ratio_exp)
[1] 9275 898
sample.cor=function(ratio_exp,d){return(cor(t(ratio_exp[d,])))} #function for
obtaing correlation
boot.exp=boot(ratio_exp,sample.cor,R=50)
Error in matrix(NA, sum(R), lt0) : too many elements specified
But when I reduced the no of replication that is 10 then I got following
boot.exp=boot(ratio_exp,sample.cor,R=10)
str(boot.exp$t)
num [1:5, 1:86025625] 1 1 1 1 1 ...
In both the cases its not correct. So I am doing something wrong in
writing the function sample.cor. Please help!
regards
Amit
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Re: [R] errors when installing packages (ubuntu)
Looks like spam depends on R-2.10.x which the package maintainer (CCing) has not declared in the DESCRIPTION file. So either install R-2.10.1 and try again or use an older spam version from the CRAN archives for your old version of R. To Reinhard Furrer: can you please upload a new version with increased version number to CRAN that declares the dependency. Thank you. Best wishes, Uwe Ligges On 09.01.2010 14:27, romunov wrote: Hi List, I'm having problems installing certain packages. When I try to install fields, I get the output below. I have highlighted the what I perceive as the first error (spam seems to be a dependency of fields). Can I assume this is causing dependency problems for fields, which fails to install at the end, or is there a deeper problem? I run Ubuntu Karmic Koala on R 2.9.2. 2 install.packages(fields) Warning in install.packages(fields) : argument 'lib' is missing: using '/home/romunov/R/i486-pc-linux-gnu-library/2.9' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done also installing the dependency ‘spam’ trying URL 'http://cran.at.r-project.org/src/contrib/spam_0.20-2.tar.gz' Content type 'application/x-gzip' length 470013 bytes (458 Kb) opened URL == downloaded 458 Kb trying URL 'http://cran.at.r-project.org/src/contrib/fields_6.01.tar.gz' Content type 'application/x-gzip' length 3670039 bytes (3.5 Mb) opened URL == downloaded 3.5 Mb * Installing *source* package ‘spam’ ... ** libs gfortran -fpic -g -O2 -c bckslvmodified.f -o bckslvmodified.o gfortran -fpic -g -O2 -c cholmodified.f -o cholmodified.o gfortran -fpic -g -O2 -c dist.f -o dist.o gfortran -fpic -g -O2 -c fromsparsekit.f -o fromsparsekit.o gfortran -fpic -g -O2 -c kronecker.f -o kronecker.o gfortran -fpic -g -O2 -c spamown.f -o spamown.o gfortran -fpic -g -O2 -c xybind.f -o xybind.o gcc -std=gnu99 -shared -o spam.so bckslvmodified.o cholmodified.o dist.o fromsparsekit.o kronecker.o spamown.o xybind.o -lgfortran -lm -L/usr/lib/R/lib -lR ** R ** data ** moving datasets to lazyload DB ** demo ** inst ** preparing package for lazy loading Creating a new generic function for print in spam Creating a new generic function for summary in spam Creating a new generic function for diag in spam Creating a new generic function for diag- in spam Creating a new generic function for t in spam Error in setOldClass(c(dist, numeric)) : inconsistent old-style class information for numeric; the class is defined but does not extend oldClass Error : unable to load R code in package 'spam' ERROR: lazy loading failed for package ‘spam’ * Removing ‘/home/romunov/R/i486-pc-linux-gnu-library/2.9/spam’ * Installing *source* package ‘fields’ ... ** libs gfortran -fpic -g -O2 -c css.f -o css.o gfortran -fpic -g -O2 -c csstr.f -o csstr.o gfortran -fpic -g -O2 -c cvrf.f -o cvrf.o gfortran -fpic -g -O2 -c dchold.f -o dchold.o gfortran -fpic -g -O2 -c dcopy.f -o dcopy.o gfortran -fpic -g -O2 -c ddfind.f -o ddfind.o gfortran -fpic -g -O2 -c ddot.f -o ddot.o gfortran -fpic -g -O2 -c derrb.f -o derrb.o gfortran -fpic -g -O2 -c dlv.f -o dlv.o gfortran -fpic -g -O2 -c dmaket.f -o dmaket.o gfortran -fpic -g -O2 -c drdfun.f -o drdfun.o gfortran -fpic -g -O2 -c dsetup.f -o dsetup.o gfortran -fpic -g -O2 -c evlpoly.f -o evlpoly.o gfortran -fpic -g -O2 -c evlpoly2.f -o evlpoly2.o gfortran -fpic -g -O2 -c expbs.f -o expbs.o gfortran -fpic -g -O2 -c expfn.f -o expfn.o gfortran -fpic -g -O2 -c gaspbs.f -o gaspbs.o gfortran -fpic -g -O2 -c gaspfn.f -o gaspfn.o gfortran -fpic -g -O2 -c gcvcss.f -o gcvcss.o gfortran -fpic -g -O2 -c gcvfc.f -o gcvfc.o gfortran -fpic -g -O2 -c hsort.f -o hsort.o gfortran -fpic -g -O2 -c ifind.f -o ifind.o gfortran -fpic -g -O2 -c igpoly.f -o igpoly.o gfortran -fpic -g -O2 -c inpoly.f -o inpoly.o gfortran -fpic -g -O2 -c lscv.f -o lscv.o gfortran -fpic -g -O2 -c m2deb.f -o m2deb.o gfortran -fpic -g -O2 -c mkpoly.f -o mkpoly.o gfortran -fpic -g -O2 -c mltdrb.f -o mltdrb.o gfortran -fpic -g -O2 -c mltdtd.f -o mltdtd.o gfortran -fpic -g -O2 -c msort.f -o msort.o gfortran -fpic -g -O2 -c multeb.f -o multeb.o gfortran -fpic -g -O2 -c multgb.f -o multgb.o gfortran -fpic -g -O2 -c multrb.f -o multrb.o gfortran -fpic -g -O2 -c radbas.f -o radbas.o gfortran -fpic -g -O2 -c radfn2.f -o radfn2.o gfortran -fpic -g -O2 -c radfun.f -o radfun.o gfortran -fpic -g -O2 -c rcss.f -o rcss.o gfortran -fpic -g -O2 -c rcssr.f -o rcssr.o gfortran -fpic -g -O2 -c rcsswt.f -o rcsswt.o gfortran -fpic -g -O2 -c sortm.f -o sortm.o gcc -std=gnu99 -shared -o fields.so css.o csstr.o cvrf.o dchold.o dcopy.o ddfind.o ddot.o derrb.o dlv.o dmaket.o drdfun.o dsetup.o evlpoly.o evlpoly2.o expbs.o expfn.o gaspbs.o gaspfn.o gcvcss.o gcvfc.o hsort.o ifind.o igpoly.o inpoly.o lscv.o
Re: [R] Online R documentation
Karl Ove Hufthammer wrote: In case anybody is looking for ideas in how to improve the above site, inclusion of rendered example graphs, similar to the ones at http://www.metaresearch.de/exlib/;, would be nice. If the format you use on your site were accepted as the standard in R, this would be a great step forward in improving the dinosaur. I prefer to have help locally, though, because I would like to have the first search restricted to the packages I have installed, to avoid being drowned by 2000 packages I never need. Dieter -- View this message in context: http://n4.nabble.com/Online-R-documentation-tp1009656p1010376.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Online R documentation
On 09/01/2010 12:48 PM, Dieter Menne wrote: Karl Ove Hufthammer wrote: In case anybody is looking for ideas in how to improve the above site, inclusion of rendered example graphs, similar to the ones at http://www.metaresearch.de/exlib/;, would be nice. If the format you use on your site were accepted as the standard in R, this would be a great step forward in improving the dinosaur. I prefer to have help locally, though, because I would like to have the first search restricted to the packages I have installed, to avoid being drowned by 2000 packages I never need. Including graphical output in the man pages is one of the eventual goals of the new help system. I doubt it will make it into 2.11.x, but it will probably be there in 2.12.x. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Directory operations
Hi Jim,
Thanks for your suggestion. I tried scripting but gives me an
error. Can you tell me what am I doing wrong here ?
* list.files()-org_xml_dirs
for (i in org_xml_dirs){
+ setwd(/home/anupam/Research/Anupam_data/ORG_XML_FILES/i)}
Error in setwd(/home/anupam/Research/Anupam_data/ORG_XML_FILES/i) :
cannot change working directory
*
On Fri, Jan 8, 2010 at 11:37 PM, jim holtman jholt...@gmail.com wrote:
?list.files
?file.info
?setwd
You can get a list of all the files in a directory (list.files) and then do
a file.info to determine which ones are the directories you want to
search. A list.files on that directory will give you the list of file names
that you can then process.
On Fri, Jan 8, 2010 at 12:41 PM, anupam sinha anupam.cont...@gmail.comwrote:
Dear all,
I have this directory structure :
Dir1 Dir2 Dir3 Dir4 .
A.xml D.xmlG.xml
B.xml E.xml H.xml
C.xml F.xml I.xml
Within each of these directories (Dir1, Dir2 etc) there are a num of xml
files (A.xml, B.xml etc).
What I want to do is to enter into the first directory read all the xml
files do certain operations come out of the directory and do the same
thing
for another directory. Can anyone help me out ? Thanks in advance for any
suggestions.
Regards,
Anupam Sinha
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--
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+1 513 646 9390
What is the problem that you are trying to solve?
--
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Re: [R] Panel order in lattice with xyplot
Carol wrote: I am a new user of R and I am going very slow…. Never mind, R has s a steep (or, more accurately, shallow) learning curve. Carol wrote: I am using lattice and am trying to draw a multipanel figure. The problems are that I am not able to find out how to: 1. Set the order of the panels. 2. Set the order of the x axes. For an easy, but restricted, way to change the order of the panels, see as.table in the documentation of xyplot. To change the order panels with categorical variable, it is easiest to change the order of the categories; see, for example, reorder. Carol wrote: Benthic- read.table(file=WWTP 1 WICK 5.txt,header = TRUE) .. Code removed Your example is fine, with the exception that other people cannot reproduce it because they do not have the data file. So always include dummy data for a detailed reply -- View this message in context: http://n4.nabble.com/Panel-order-in-lattice-with-xyplot-tp1009866p1010379.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Online R documentation
Duncan Murdoch wrote: Including graphical output in the man pages is one of the eventual goals of the new help system. I doubt it will make it into 2.11.x, but it will probably be there in 2.12.x. This is good news; while I did not love Hadley Wickham's decision to put documentation of ggplot2 on an external server, I can understand his rationale that documenting a graphics package in ASCII/Unicode is not a good idea. Maybe we should have a small-footprint portable help server that could be run as a service/daemon without the overhead of calling rterm for 2.10. Dieter -- View this message in context: http://n4.nabble.com/Online-R-documentation-tp1009656p1010385.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Boxplots
I'm guessing that you want side-by-side boxplots. If that's correct, then try the following. It stacks the y-values, makes an appropriate grouping factor and plots with reasonable spacing. dat - read.table(textConnection( tank TanksTotal cons_hat 1aa4 5.651017 5.59 2aa5 5.017499 5.29 3aa6 4.894238 4.69 4cc4 3.986347 3.40 5cc5 4.099442 3.58 6cc6 4.150522 3.64 7hh4 5.187792 6.32 8hh5 6.713422 6.44 9hh6 5.168555 5.62),header=T) closeAllConnections() library(reshape) #or you can use stats::reshape() with suitable # modifications tmp - melt(dat, id.vars=tank, measure.vars=c(Total, cons_hat), variable_name=Group) tmp tmp$grp - with(tmp, factor(paste(tank, as.numeric(Group), sep=:))) tmp boxplot(value ~ grp, data=tmp, boxwex=0.5, col=c(red, blue), at=c(1.2,1.8,3.2,3.8,5.2,5.8)) -Peter Ehlers Marlin Keith Cox wrote: I have a data set with four columns and need to make boxplots from them. Data is as follows: tank TanksTotal cons_hat 1aa4 5.651017 5.59 2aa5 5.017499 5.29 3aa6 4.894238 4.69 4cc4 3.986347 3.40 5cc5 4.099442 3.58 6cc6 4.150522 3.64 7hh4 5.187792 6.32 8hh5 6.713422 6.44 9hh6 5.168555 5.62 This is simply consumption data with Total being the actual measured consumption and cons_hat being the predicted. I need a boxplot of tank a (consisting of a4,a5,a6) Total vs. cons_hat. boxplot(Total~tank) of course creates a boxplot with only Total by tank, but how do I put the other column in this boxplot? Thanks ahead of time. keith -- Peter Ehlers University of Calgary 403.202.3921 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R in English Version
Dear Sir/Madam I am living in germany but do not know German Language. so could you please help me to download R in English working Language, because automatically it gives German version of R when I download it from UK or US or Germany. Thanking you and Best regards Pooja [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Directory operations
On 09.01.2010 19:04, anupam sinha wrote:
Hi Jim,
Thanks for your suggestion. I tried scripting but gives me an
error. Can you tell me what am I doing wrong here ?
* list.files()-org_xml_dirs
Please do turn that arrow around
for (i in org_xml_dirs){
+ setwd(/home/anupam/Research/Anupam_data/ORG_XML_FILES/i)}
There is no directory .../i
Your probably want:
setwd(file.path(/home/anupam/Research/Anupam_data/ORG_XML_FILES/, i))
Uwe Ligges
Error in setwd(/home/anupam/Research/Anupam_data/ORG_XML_FILES/i) :
cannot change working directory
*
On Fri, Jan 8, 2010 at 11:37 PM, jim holtmanjholt...@gmail.com wrote:
?list.files
?file.info
?setwd
You can get a list of all the files in a directory (list.files) and then do
a file.info to determine which ones are the directories you want to
search. A list.files on that directory will give you the list of file names
that you can then process.
On Fri, Jan 8, 2010 at 12:41 PM, anupam sinhaanupam.cont...@gmail.comwrote:
Dear all,
I have this directory structure :
Dir1 Dir2 Dir3 Dir4 .
A.xml D.xmlG.xml
B.xml E.xml H.xml
C.xml F.xml I.xml
Within each of these directories (Dir1, Dir2 etc) there are a num of xml
files (A.xml, B.xml etc).
What I want to do is to enter into the first directory read all the xml
files do certain operations come out of the directory and do the same
thing
for another directory. Can anyone help me out ? Thanks in advance for any
suggestions.
Regards,
Anupam Sinha
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://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
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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] R in English Version
On 09.01.2010 18:45, pooja pandey wrote: Dear Sir/Madam I am living in germany but do not know German Language. So time to learn it... ;-) so could you please help me to download R in English working Language, because automatically it gives German version of R when I download it from UK or US or Germany. Well, R uses the language reported by the OS (and you have not said which one it is). For details how to change and understand what happens see the manual R Installation and Administration, particularly section 7.2 (for R-2.10.1): Localization of messages. Best wishes, Uwe Ligges Thanking you and Best regards Pooja [[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] R in English Version
On Jan 9, 2010, at 12:45 PM, pooja pandey wrote: Dear Sir/Madam I am living in germany but do not know German Language. so could you please help me to download R in English working Language, because automatically it gives German version of R when I download it from UK or US or Germany. http://cran.r-project.org/doc/manuals/R-admin.html#Localization-of-messages -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] svm
Hi,
On Fri, Jan 8, 2010 at 11:57 AM, Amy Hessen amy_4_5...@hotmail.com wrote:
Hi Steve,
Thank you very much for your reply. Your code is more readable and obvious
than mine…
No Problem.
Could you please help me in these questions?:
1) “Formula” is an alternative to “y” parameter in SVM. is it correct?
No, that's not correct.
There are two svm functions, one that takes a formula object
(svm.formula), and one that takes an x matrix, and a y vector
(svm.default). The svm.formula function is called when the first
argument in your svm(..) call is a formula object. This function
simply parses the formula and manipulates your data object into an x
matrix and y vector, then calls the svm.default function with those
params ... I usually prefer to just skip the formula and provide the x
and y objects directly.
Load the e1071 library and look at the source code:
R library(e1071)
R e1071:::svm.formula
You'll see what I mean.
2) I forgot to remove the “class label” from the dataset besides I gave the
program the class label in formula parameter but the program works! Could
you please clarify this point to me?
The author of the e1071 package did you a favor. The predict.svm
function checks to see if your svm object was built using the formula
interface .. if so, it looks for you label column in the data you are
trying to predict on and ignores it.
Look at the function's source code (eg, type e1071:::predict.svm at
the R prompt), and look for the call to the delete.response function
... you can also look at the help in ?delete.response.
-steve
Date: Wed, 6 Jan 2010 18:44:13 -0500
Subject: Re: [R] svm
From: mailinglist.honey...@gmail.com
To: amy_4_5...@hotmail.com
CC: r-help@r-project.org
Hi Amy,
On Wed, Jan 6, 2010 at 4:33 PM, Amy Hessen amy_4_5...@hotmail.com wrote:
Hi Steve,
Thank you very much for your reply.
I’m trying to do something systematic/general in the program so that I
can
try different datasets without changing much in the program (without
knowing
the name of the class label that has different name from dataset to
another…)
Could you please tell me your opinion about this code:-
library(e1071)
mydata-read.delim(the_whole_dataset.txt)
class_label - names(mydata)[1] # I’ll always put
the
class label in the first column.
myformula - formula(paste(class_label,~ .))
x - subset(mydata, select = - mydata[, 1])
mymodel-(svm(myformula, x, cross=3))
summary(model)
Since you're not doing anything funky with the formula, a preference
of mine is to just skip this way of calling SVM and go straight to
the svm(x,y,...) method:
R mydata - as.matrix(read.delim(the_whole_dataset.txt))
R train.x - mydata[,-1]
R train.y - mydata[,1]
R mymodel - svm(train.x, train.y, cross=3, type=C-classification)
## or
R mymodel - svm(train.x, train.y, cross=3, type=eps-regression)
As an aside, I also like to be explicit about the type= parameter to
tell what I want my SVM to do (regression or classification). If it's
not specified, the SVM picks which one to do based on whether or not
your y vector is a vector of factors (does classification), or not
(does regression)
Do I have to the same steps with testingset? i.e. the testing set must
not
contain the label too? But contains the same structure as the training
set?
Is it correct?
I guess you'll want to report your accuracy/MSE/something on your
model for your testing set? Just load the data in the same way then
use `predict` to calculate the metric your after. You'll have to have
the labels for your data to do that, though, eg:
testdata - as.matrix(read.delim('testdata.txt'))
test.x - testdata[,-1]
test.y - testdata[,1]
preds - predict(mymodel, test.x)
Let's assume you're doing classification, so let's report the accuracy:
acc - sum(preds == test.y) / length(test.y)
Does that help?
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
Sell your old one fast! Time for a new car?
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Calling FING.EXE under RGui.EXE for windows.
On 07/01/2010 1:25 PM, Uwe Ligges wrote: Argh. I see it as well. Will dig a lit tomorrow. I don't know exactly what's going on, but it looks as though it is something specific to the find.exe utility, e.g. maybe it is assuming that it's being run inside a console and reading CONIN$ or writing to CONOUT$ without checking whether they can be opened. When you run it from Rterm, Rterm is in a console, which appears to be good enough. So it may be anyone who wants to use it will have to contact Microsoft to find out how... Duncan Murdoch Uwe On 07.01.2010 12:25, Gabor Grothendieck wrote: I get a problem with shell too: Under Rgui: R.version.string [1] R version 2.10.1 Patched (2010-01-01 r50884) system(C:\\windows\\system32\\find /?, intern = TRUE) character(0) system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE) character(0) shell(C:\\windows\\system32\\find /?) Warning message: In shell(C:\\windows\\system32\\find /?) : 'C:\windows\system32\find /?' execution failed with error code 1 They all work, i.e. they give the required help message, under Rterm and when I issue this from the Windows console it works: C:\windows\system32\find /? 2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de: On 07.01.2010 02:04, Gabor Grothendieck wrote: If you have C:\Rtools\bin on your PATH note that it contains a UNIX-like find utility that conflicts with the find utility in Windows. If that is the problem then remove that from your PATH and then run the batch file. The batchfiles distribution at http://batchfiles.googlecode.com has utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically add C:\Rtools\bin to your path temporarily or only while R is running so that you can leave it off your PATH. I guess it's the use of system() rather than shell() that causes the problem. Under Windows, you have to use shell in order to start a command interpreter. Uwe Ligges On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com wrote: This is sort of a strange bug. Not show stopping, but annoying. I was wondering if anyone else has noticed this and reported it before I submit a bug report. I noticed while running the RGui and attempting to debug one of my scripts that I encountered a Windows error informing me that Find String [grep] Utility has encountered a problem and needs to close. It is being generated by a call to a DOS batch file which contains a call to Find.exe. It can be reproduced by simply typing System(find) in RGui. What I found strange is that I have been running this script daily without this problem for months. I now realize I never ran that portion of the script while in RGui.exe. It has always run in batch mode which is done by Rterm.exe. I have tried this on three separate machines now all running Windows XP SP3, with versions of R 2.8.1 and R 2.10.1 If executing System(find) under RGui, an error window for the Find String Utility is generated and the command is not exectuted. If the same command is issued in Rterm the expected FIND: Parameter format not correct message is properly returned. It doesn't seem an important bug, but it could be the canary in the mine for a larger problem somewhere down the road. Re, John Schexnayder IBM Tape Manufacturing - Information Technology San Jose, CA 95138 jsc...@us.ibm.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Linear regression - R^2
Hello, I was doing a linear regression with the following formula: *lm(y~x+0)*, so it passes through the origin. But when I called the summary of the regression i saw that R squared is abnormally high (it's a lot lower in other programs such as SigmaPlot and MS Excel).The manual explained the cause of the difference (because of the different computing method), but what should I do to get the same R^2 in excel and R? WITHOUT PASSING THROUGH THE ORIGIN: R^2: Multiple R-squared: 0.9711, Adjusted R-squared: 0.9654 In MS Excel: 0,9711 *So it's OK.* WITH PASSING THROUGH THE ORIGIN: Multiple R-squared: 0.9848, Adjusted R-squared: 0.9822 In MS Excel: 0,8907 *So almost 10% difference.* Thank you for your help. Csanad Bertok, Hungary [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R^2 in linear regression
Hello, I was doing a linear regression with the following formula: lm(y~x+0), so it passes through the origin. But when I called the summary of the regression i saw that R squared is abnormally high (it's a lot lower in other programs such as SigmaPlot and MS Excel).The manual explained the cause of the difference (because of the different computing method), but what should I do to get the same R^2 in excel and R? WITHOUT PASSING THROUGH THE ORIGIN: R^2: Multiple R-squared: 0.9711, Adjusted R-squared: 0.9654 In MS Excel: 0,9711 So it's OK. WITH PASSING THROUGH THE ORIGIN: Multiple R-squared: 0.9848, Adjusted R-squared: 0.9822 In MS Excel: 0,8907 So almost 10% difference. Thank you for your help. Csanad Bertok, Hungary -- View this message in context: http://n4.nabble.com/R-2-in-linear-regression-tp1010473p1010473.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R^2 in linear regression
Terias wrote: Hello, I was doing a linear regression with the following formula: lm(y~x+0), so it passes through the origin. But when I called the summary of the regression i saw that R squared is abnormally high (it's a lot lower in other programs such as SigmaPlot and MS Excel).The manual explained the cause of the difference (because of the different computing method), but what should I do to get the same R^2 in excel and R? If you insist, I think you can get what Excel does like this: x - 1:10 y - rnorm(10) ## Residual sums of squares ss1 - anova(lm(y~1))[1,2] ss2 - anova(lm(y~x+0))[2,2] ## Relative reduction in sum of squares (ss1-ss2)/ss1 [1] -0.08576713 Now if you dislike the fact that R^2 can come out negative, that's your problem WITHOUT PASSING THROUGH THE ORIGIN: R^2: Multiple R-squared: 0.9711, Adjusted R-squared: 0.9654 In MS Excel: 0,9711 So it's OK. WITH PASSING THROUGH THE ORIGIN: Multiple R-squared: 0.9848, Adjusted R-squared: 0.9822 In MS Excel: 0,8907 So almost 10% difference. Thank you for your help. Csanad Bertok, Hungary -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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^2 in linear regression
Thank you, it worked :) Csanad Bertok Biology BSc University of Debrecen Debrecen, Hungary -- View this message in context: http://n4.nabble.com/Re-R-2-in-linear-regression-tp1010477p1010484.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling FING.EXE under RGui.EXE for windows.
That doesn't explain why this returns character(o) even though we have launched a console for it: system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE) On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 07/01/2010 1:25 PM, Uwe Ligges wrote: Argh. I see it as well. Will dig a lit tomorrow. I don't know exactly what's going on, but it looks as though it is something specific to the find.exe utility, e.g. maybe it is assuming that it's being run inside a console and reading CONIN$ or writing to CONOUT$ without checking whether they can be opened. When you run it from Rterm, Rterm is in a console, which appears to be good enough. So it may be anyone who wants to use it will have to contact Microsoft to find out how... Duncan Murdoch Uwe On 07.01.2010 12:25, Gabor Grothendieck wrote: I get a problem with shell too: Under Rgui: R.version.string [1] R version 2.10.1 Patched (2010-01-01 r50884) system(C:\\windows\\system32\\find /?, intern = TRUE) character(0) system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE) character(0) shell(C:\\windows\\system32\\find /?) Warning message: In shell(C:\\windows\\system32\\find /?) : 'C:\windows\system32\find /?' execution failed with error code 1 They all work, i.e. they give the required help message, under Rterm and when I issue this from the Windows console it works: C:\windows\system32\find /? 2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de: On 07.01.2010 02:04, Gabor Grothendieck wrote: If you have C:\Rtools\bin on your PATH note that it contains a UNIX-like find utility that conflicts with the find utility in Windows. If that is the problem then remove that from your PATH and then run the batch file. The batchfiles distribution at http://batchfiles.googlecode.com has utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically add C:\Rtools\bin to your path temporarily or only while R is running so that you can leave it off your PATH. I guess it's the use of system() rather than shell() that causes the problem. Under Windows, you have to use shell in order to start a command interpreter. Uwe Ligges On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com wrote: This is sort of a strange bug. Not show stopping, but annoying. I was wondering if anyone else has noticed this and reported it before I submit a bug report. I noticed while running the RGui and attempting to debug one of my scripts that I encountered a Windows error informing me that Find String [grep] Utility has encountered a problem and needs to close. It is being generated by a call to a DOS batch file which contains a call to Find.exe. It can be reproduced by simply typing System(find) in RGui. What I found strange is that I have been running this script daily without this problem for months. I now realize I never ran that portion of the script while in RGui.exe. It has always run in batch mode which is done by Rterm.exe. I have tried this on three separate machines now all running Windows XP SP3, with versions of R 2.8.1 and R 2.10.1 If executing System(find) under RGui, an error window for the Find String Utility is generated and the command is not exectuted. If the same command is issued in Rterm the expected FIND: Parameter format not correct message is properly returned. It doesn't seem an important bug, but it could be the canary in the mine for a larger problem somewhere down the road. Re, John Schexnayder IBM Tape Manufacturing - Information Technology San Jose, CA 95138 jsc...@us.ibm.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] string functions
Hi! Does anybody know a string function that would calculate how many characters two strings share? I.e. (Hello World,Hello Peter) would be 7. Thanks. Laetitia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] commandArgs return value
Hello,
I plan to use a script with R CMD BATCH on different platforms Linux,
Windows and Mac OSX. I use the commandArgs(trailing = FALSE) function
to retrieve the name of the script and the arguments (example below
with output.) The online docs for Introduction to R (sections B.1
Invoking R from the command line and B.4 Scripting with R) and
help(commandArgs) leave my head spinning regarding the contents of
the arguments when trailing = FALSE.
(1) What should I expect from commandArgs() when used with R CMD BATCH?
The docs for commandArgs() states, These arguments are captured
before the standard R command line processing takes place. This means
that they are the unmodified values. However, if I call a script
like this ...
R CMD BATCH --slave --vanilla '--args dogs cats verbose=TRUE' /Users/
Shared/code/R/hbb/pam/script.r my.out
... the actual arguments are as shown in the example output below.
You can see that --restore --save --no-readline were picked up which
seems to contradict the documentation. In the online docs (http://cran.r-project.org/doc/manuals/R-intro.html#Invoking-R
) the --vanilla argument is described as a combination of --no-save, --
no-environ, --no-site-file, --no-init-file and --no-restore. So now I
am wondering if I am confounding the arguments to invoke R with the
arguments to invoke R via CMD BATCH.
(2) Does the name of the script being called always fall in the third
element of the commandArgs() value? If so, does it always include the
full path?
(3) Are --arg and the supplied arguments always last in the
commandArgs() value? The docs for commandArgs() states, This is
especially useful with the --args command-line flag to R, as all of
the command line after that flag is skipped, so I feel pretty
confident that they will be last. But given my confusion in (1)
above
Thanks,
Ben
## script begin
args = commandArgs()
cat(All the arguments...\n\n)
cat(args, sep = \n)
cat( \n)
cat(paste(nargs=, length(args)), \n)
cat( \n)
cat(paste(source is, basename(args[3]), sep = ), sep = \n)
ix = grep(--arg, args, fixed = TRUE)
if (ix length(args)){
for (i in (ix+1):length(args)) {
cat(paste(argument #,i-ix,--,args[i], sep= ), sep = \n)
}
}
ecode = 0
q(runLast = FALSE, save = no, status = ecode)
## script end
## output file begin
All the arguments...
/Library/Frameworks/R.framework/Resources/bin/exec/i386/R
-f
/Users/Shared/code/R/hbb/pam/script.r
--restore
--save
--no-readline
--slave
--vanilla
--args
dogs
cats
verbose=TRUE
nargs= 12
source is script.r
argument # 1 -- dogs
argument # 2 -- cats
argument # 3 -- verbose=TRUE
output file end
# session info
sessionInfo()
R version 2.10.1 (2009-12-14)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.10.1
###
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Re: [R] string functions
On 1/9/10, Laetitia Schmid laetitia.sch...@gmx.ch wrote: Does anybody know a string function that would calculate how many characters two strings share? I.e. (Hello World,Hello Peter) would be 7. Perhaps package ‘stringr’ has something related? Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling FING.EXE under RGui.EXE for windows.
On 09/01/2010 6:31 PM, Gabor Grothendieck wrote:
That doesn't explain why this returns character(o) even though we have
launched a console for it:
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
I don't see any console launched. R redirects stdin and stdout (and
stderr, I think), and it appears that Windows doesn't open a console. I
do see a console flash by if I do
system('cmd /c c:/WINDOWS/system32/find.exe /?', wait=FALSE,
invisible=FALSE)
but of course then we don't capture the output, so it's not very useful.
Looking at the source, the only case where we ask to create a console
is the combination wait=FALSE, invisible=FALSE, but there might be
combinations of other options that make this a default. The MS
documentation says that a console will be created automatically for any
console application, but that doesn't appear to be happening.
So I guess you could get find.exe to work by calling it from a batch
file with a pause at the end and using the wait=FALSE,invisible=FALSE
options.
The above observations are in Win XP SP3, not anything newer.
Duncan Murdoch
On Sat, Jan 9, 2010 at 5:24 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 07/01/2010 1:25 PM, Uwe Ligges wrote:
Argh. I see it as well. Will dig a lit tomorrow.
I don't know exactly what's going on, but it looks as though it is something
specific to the find.exe utility, e.g. maybe it is assuming that it's being
run inside a console and reading CONIN$ or writing to CONOUT$ without
checking whether they can be opened. When you run it from Rterm, Rterm is
in a console, which appears to be good enough.
So it may be anyone who wants to use it will have to contact Microsoft to
find out how...
Duncan Murdoch
Uwe
On 07.01.2010 12:25, Gabor Grothendieck wrote:
I get a problem with shell too:
Under Rgui:
R.version.string
[1] R version 2.10.1 Patched (2010-01-01 r50884)
system(C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
system(cmd /c C:\\windows\\system32\\find /?, intern = TRUE)
character(0)
shell(C:\\windows\\system32\\find /?)
Warning message:
In shell(C:\\windows\\system32\\find /?) :
'C:\windows\system32\find /?' execution failed with error code 1
They all work, i.e. they give the required help message, under Rterm
and when I issue this from the Windows console it works:
C:\windows\system32\find /?
2010/1/7 Uwe Liggeslig...@statistik.tu-dortmund.de:
On 07.01.2010 02:04, Gabor Grothendieck wrote:
If you have C:\Rtools\bin on your PATH note that it contains a
UNIX-like find utility that conflicts with the find utility in
Windows. If that is the problem then remove that from your PATH and
then run the batch file.
The batchfiles distribution at http://batchfiles.googlecode.com has
utilities (Rgui.bat, R.bat, Rtools.bat, etc.) that will automatically
add C:\Rtools\bin to your path temporarily or only while R is running
so that you can leave it off your PATH.
I guess it's the use of system() rather than shell() that causes the
problem. Under Windows, you have to use shell in order to start a
command
interpreter.
Uwe Ligges
On Wed, Jan 6, 2010 at 6:51 PM, John Schexnayderjsc...@us.ibm.com
wrote:
This is sort of a strange bug. Not show stopping, but annoying. I
was
wondering if anyone else has noticed this and reported it before I
submit
a bug report.
I noticed while running the RGui and attempting to debug one of my
scripts
that I encountered a Windows error informing me that Find String
[grep]
Utility has encountered a problem and needs to close. It is being
generated by a call to a DOS batch file which contains a call to
Find.exe.
It can be reproduced by simply typing System(find) in RGui.
What I
found strange is that I have been running this script daily without
this
problem for months. I now realize I never ran that portion of the
script
while in RGui.exe. It has always run in batch mode which is done by
Rterm.exe.
I have tried this on three separate machines now all running Windows
XP
SP3, with versions of R 2.8.1 and R 2.10.1 If executing
System(find)
under RGui, an error window for the Find String Utility is generated
and
the command is not exectuted. If the same command is issued in Rterm
the
expected FIND: Parameter format not correct message is properly
returned.
It doesn't seem an important bug, but it could be the canary in the
mine
for a larger problem somewhere down the road.
Re,
John Schexnayder
IBM Tape Manufacturing - Information Technology
San Jose, CA 95138
jsc...@us.ibm.com
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Re: [R] string functions
Laetitia,
One approach:
lettermatch - function(stringA, stringB) {
sum(unique(unlist(strsplit(stringA, ))) %in%
unique(unlist(strsplit(stringB,
}
lettermatch(Hello World,Hello Peter)
yields 6, as the l is only singly counted.
This treats uppercase and lowercase as different letters and counts how
many of the unique letters in stringA show up in stringB.
In another approach, letters are set to lowercase first. This I think
gives you what you want:
lettermatch2 - function(stringA, stringB) {
tb - merge(as.data.frame(table(strsplit(tolower(stringA), ))),
as.data.frame(table(strsplit(tolower(stringB), ))), by=Var1)
sum(apply(tb[-1], 1, min))
}
lettermatch(Hello World,Hello Peter)
yields 7.
Greg
On 1/9/10 1:51 PM, Laetitia Schmid wrote:
Hi!
Does anybody know a string function that would calculate how many
characters two strings share? I.e. (Hello World,Hello Peter) would
be 7.
Thanks.
Laetitia
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Greg Hirson
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Graduate Student
Agricultural and Environmental Chemistry
1106 Robert Mondavi Institute North
One Shields Avenue
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Re: [R] Linear regression - R^2
Dear Csanad, PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html Reproducible code/problem are welcome. By the way, who you believe is right? bests milton On Sat, Jan 9, 2010 at 5:40 PM, Csanád Bertók bertok.csa...@gmail.comwrote: Hello, I was doing a linear regression with the following formula: *lm(y~x+0)*, so it passes through the origin. But when I called the summary of the regression i saw that R squared is abnormally high (it's a lot lower in other programs such as SigmaPlot and MS Excel).The manual explained the cause of the difference (because of the different computing method), but what should I do to get the same R^2 in excel and R? WITHOUT PASSING THROUGH THE ORIGIN: R^2: Multiple R-squared: 0.9711, Adjusted R-squared: 0.9654 In MS Excel: 0,9711 *So it's OK.* WITH PASSING THROUGH THE ORIGIN: Multiple R-squared: 0.9848, Adjusted R-squared: 0.9822 In MS Excel: 0,8907 *So almost 10% difference.* Thank you for your help. Csanad Bertok, Hungary [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] string functions
Maybe I don't understand the question. I can think of four ways to count, none of which give me 7: a - Hello World b - Hello Peter #counting duplicates and the space: sa - strsplit(a, split=)[[1]] sb - strsplit(b, split=)[[1]] length(which(sb %in% sa == TRUE)) #counting the space but not the duplicates: sa - unique(strsplit(a, split=)[[1]]) sb - unique(strsplit(b, split=)[[1]]) length(which(sb %in% sa == TRUE)) #counting the duplicates but not the space: sa - strsplit(a, split=)[[1]] sa - sa[-which(sa == )] sb - strsplit(b, split=)[[1]] sb - sb[-which(sb == )] length(which(sb %in% sa == TRUE)) #not counting duplicates or the space: sa - unique(sa) sb - unique(sb) length(which(sb %in% sa == TRUE)) What am I missing? On Sat, Jan 9, 2010 at 4:51 PM, Laetitia Schmid laetitia.sch...@gmx.ch wrote: Hi! Does anybody know a string function that would calculate how many characters two strings share? I.e. (Hello World,Hello Peter) would be 7. Thanks. Laetitia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] scatterplot matrix with ggplot2
#I would like to use the below data to make a scatter plot matrix with #code similar to that below the data #conceptually this is the right approach I think #thanks in advance melt.gg - structure(list(stream = c(Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper), agg_site = c(Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham,
Re: [R] how to organize a lot of R source files
Hi Henrik, Thanks for your suggestion. I created a directory with 10 R files and tried the following and measured its time system.time(sourceDirectory(~/fun, modifiedOnly = F)) system.time(sourceDirectory(~/fun, modifiedOnly = T)) But the second line seems to spend as much time as the first line, I thought the second line would be faster since no modification is made. Also the first line reports a warning as follows In readLines(con = fh) : incomplete final line found on ~/fun/util1.R I don't see such a warning when I use source. Maybe the two issues are related. Please advise. thanks Jeff On Fri, January 8, 2010 7:56 pm, Henrik Bengtsson wrote: library(R.utils); sourceDirectory(myRFiles/, modifiedOnly=TRUE); See ?sourceDirectory (regardless what the Rd help say, any '...' argument is passed to sourceTo()). /Henrik On Fri, Jan 8, 2010 at 7:38 AM, Hao Cen h...@andrew.cmu.edu wrote: Hi, I wonder what is a better way to organize a lot of R source files. I have a lot of utility functions written and store them in several source files (e.g util1.R, util2.R,..utilN.R). I also have a master file in which the source command is used to load all the util.R files. When I need to use the utility functions in a new project, I create a new R file (e.g main.R) in which I source the master file. The problem with this approach is that anytime a single utility function is modified, I need to rerun the source command in main.R to load the master file, which loads all the utility R files via a loop over each file. Sometimes I have to wait for 10 seconds to get them all loaded. Sometimes I forget to run the source command. Is there a way in R to 1) only reload the file changed (like a make utility) when I run source on all utility files and/or even better 2) reload the changed utility files, when I run a command that use one of those utility functions, without the need for me to source those files. Not sure if packaging solves this issue because the library command has be used every time a utility function is modified and in addition the package has to be rebuilt. I don't worry about sharing the source files at this moment as I am the only user of those utility files. This may be a common issue many R users face. I wonder how other R users solve this issue. thanks Jeff __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] scatterplot matrix with ggplot2
I don't think this approach will work. In your call to facet_grid you call variable twice. Another way to do this is create another variable, call it variable2 and set it equal to variable. Now look at the dataframe. You have values for variable = x1, variable2 = x1, but no values for variable = x1, variable2 = x2 etc. In other words, I think it's more complicated than you were hoping. There is plotmatrix, but I've never been able to get it to work correctly when I try to map additional variables to color or shape scales etc. -Ista On Sat, Jan 9, 2010 at 8:02 PM, stephen sefick ssef...@gmail.com wrote: #I would like to use the below data to make a scatter plot matrix with #code similar to that below the data #conceptually this is the right approach I think #thanks in advance melt.gg - structure(list(stream = c(Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Lower, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, Bonham Upper, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Lower, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper, Sally Upper), agg_site = c(Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, Bonham, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, D13, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, sally, Bonham, Bonham, Bonham, Bonham, Bonham,
Re: [R] how to organize a lot of R source files
Hi. On Sat, Jan 9, 2010 at 6:16 PM, Hao Cen h...@andrew.cmu.edu wrote: Hi Henrik, Thanks for your suggestion. I created a directory with 10 R files and tried the following and measured its time system.time(sourceDirectory(~/fun, modifiedOnly = F)) system.time(sourceDirectory(~/fun, modifiedOnly = T)) But the second line seems to spend as much time as the first line, I thought the second line would be faster since no modification is made. Use modifiedOnly=TRUE the first time too, and you'll see it'll work the 2nd time. When you call it the first time, R consider it as modified (since last time), because it has never seen the code before (in that R session). If you add some verbose output in your scripts, you'll definitely see when the scripts get sourced. I guess you could say it should the way you did it, but the way it is currently designed/implemented is that it does not record the last source time unless you use modifiedOnly=TRUE. Next release will also support what you did. Also the first line reports a warning as follows In readLines(con = fh) : incomplete final line found on ~/fun/util1.R I don't see such a warning when I use source. Unrelated. Nothing to worry about. I've added readLines(con=fh, warn=FALSE) for the next release to get rid of such warnings. /Henrik Maybe the two issues are related. Please advise. thanks Jeff On Fri, January 8, 2010 7:56 pm, Henrik Bengtsson wrote: library(R.utils); sourceDirectory(myRFiles/, modifiedOnly=TRUE); See ?sourceDirectory (regardless what the Rd help say, any '...' argument is passed to sourceTo()). /Henrik On Fri, Jan 8, 2010 at 7:38 AM, Hao Cen h...@andrew.cmu.edu wrote: Hi, I wonder what is a better way to organize a lot of R source files. I have a lot of utility functions written and store them in several source files (e.g util1.R, util2.R,..utilN.R). I also have a master file in which the source command is used to load all the util.R files. When I need to use the utility functions in a new project, I create a new R file (e.g main.R) in which I source the master file. The problem with this approach is that anytime a single utility function is modified, I need to rerun the source command in main.R to load the master file, which loads all the utility R files via a loop over each file. Sometimes I have to wait for 10 seconds to get them all loaded. Sometimes I forget to run the source command. Is there a way in R to 1) only reload the file changed (like a make utility) when I run source on all utility files and/or even better 2) reload the changed utility files, when I run a command that use one of those utility functions, without the need for me to source those files. Not sure if packaging solves this issue because the library command has be used every time a utility function is modified and in addition the package has to be rebuilt. I don't worry about sharing the source files at this moment as I am the only user of those utility files. This may be a common issue many R users face. I wonder how other R users solve this issue. thanks Jeff __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Mixtures of Discrete Uniforms
I want to create the mixture formulation of a discrete uniform ie, say f(x) = 1/10, for i = 1,2,3,4,5,6,7,8,9 and 10 and another discrete distribution which has the same values of x, but he probabilities can vary. Can this be done on any package in R? an if so, can the package estimate the 'probabilities' of each of the x value as well as the mixing proportion if I have the data? Thanks, Jim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data frame names in sequence. please help!!!
Zoho wrote:
I've been stuck with this problem for a whole afternoon. It's silly but
totally pissed me off. I have a set of data frames with names in a
sequence: df_1, df_2, df_3, ..., df_20. Now I want to access each data
frame (read or write) in a for loop, in a way something like this:
for (i in 1:20) {
df_i - ##
length(which(df_i[,7]==1))
##
}
I tried paste or cat (df_, i, sep=). But neither way works. Your help
is highly appreciated!! Thanks in advance!
df_1 - data.frame(x1=3,x2=5)
df_2 - data.frame(x1=2,x2=7)
df_3 - data.frame(x1=-1,x2=1)
for(k in 1:3){v - paste(df_,k,sep=); print(get(v))}
for(k in 1:3){v - paste(df,k,sep=_); print(get(v)[,2])}
Have a look at get:
?get
Berend
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