Hi,
I am trying to use CART to find an ideal cut-off value for a simple
diagnostic test (ie when the test score is above x, diagnose the condition).
When I put in the model
fit=rpart(outcome ~ predictor1(TB144), method=class, data=data8)
sometimes it gives me a tree with multiple nodes for
Hi,
You need an additional id column in your data frame, which represents the
replication number within each subject (the 1, 2 in the column headings
after reshaping in what you showed).
test - data.frame(subject=c(1,1,2,2,3,3), coder=c(1,2,3,2,2,1),
score=c(20,30,10,5,15,NA),
Hi
you have got some response about how to avoid an error but I am curious
what you really want to achieve.
lll-as.list(rnorm(15))
cbind(unlist(lll),order(unlist(lll)))
[,1] [,2]
[1,] 0.93344282 13
[2,] 0.63501664 14
[3,] 0.059764468
[4,] -0.491819449
[5,]
Dear list,
I have been trying to apply a simple lasso regression on a 10-element
vector, just to see how this method works so as to later implement it on
larger datasets. I thus create an input vector x:
* x=rnorm(10)*
I add some noise
*noise=runif(n=10, min=-0.1, max=0.1)*
and I
On Wed, 16 Dec 2009, Romain Francois wrote:
On 12/16/2009 08:32 AM, Achim Zeileis wrote:
On Tue, 15 Dec 2009, Michael Friendly wrote:
Achim and others:
Achim's solution could be directly usable if it also added a BibTeX key,
perhaps just the name of the package to the '@Manual{,' initial
On 12/16/2009 08:32 AM, Achim Zeileis wrote:
On Tue, 15 Dec 2009, Michael Friendly wrote:
Achim and others:
Achim's solution could be directly usable if it also added a BibTeX key,
perhaps just the name of the package to the '@Manual{,' initial line
of each. I wrapped the previous
On Wed, 16 Dec 2009, S Devriese wrote:
On 12/16/2009 08:32 AM, Achim Zeileis wrote:
On Tue, 15 Dec 2009, Michael Friendly wrote:
Achim and others:
Achim's solution could be directly usable if it also added a BibTeX key,
perhaps just the name of the package to the '@Manual{,' initial line
of
Is there a function in R that could find the significant digit of a specific
number? Such as for 3.1415, return '5'?
Thanks in advance.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
On Wed, Dec 16, 2009 at 10:26 AM, Xiang Wu xiang@gmail.com wrote:
Is there a function in R that could find the significant digit of a
specific
number? Such as for 3.1415, return '5'?
Thanks in advance.
[[alternative HTML version deleted]]
On 12/16/2009 10:26 AM, Xiang Wu wrote:
Is there a function in R that could find the significant digit of a specific
number? Such as for 3.1415, return '5'?
Thanks in advance.
Not sure to understand what you mean, but you can have a look at ?signif
Something like this perhaps:
foo -
On 12/16/2009 10:12 AM, Achim Zeileis wrote:
On Wed, 16 Dec 2009, S Devriese wrote:
On 12/16/2009 08:32 AM, Achim Zeileis wrote:
On Tue, 15 Dec 2009, Michael Friendly wrote:
Achim and others:
Achim's solution could be directly usable if it also added a BibTeX
key,
perhaps just the name
Try this:
f - function(x) length(gregexpr([[:digit:]], as.character(x))[[1]])
f(3.14)
[1] 3
f(3.1415)
[1] 5
f(3.14159265)
[1] 9
On Wed, Dec 16, 2009 at 1:39 PM, Xiang Wu xiang@gmail.com wrote:
Is there a function in R that could find the significant digit of a specific
number? Such as
I have a client who uses Stata 11.
Can anyone advise me on ways of transferring data from this version of
Stata to R?
Reading the documentation for read.dta in package foreign it seems it
only allows for versions up to Stata 10. I don't know Stata at all but a
bit of poking around on their
Hello
After performing NLS estimates for some sigmoid model(like logistic growth
model and Gompertz growth models), how can we get the RMSE(root mean square
error) and MAPE(mean absolute percentage error) in R statistical tool for
comparison between two models
Thanks
Ruchita
Have you tried read.dta?
The URL on the help page for read.dta now says 'Stata 11 help for
dta', but it seems to document the same format (114) as Stata 10 (see
the value section). So in so far as Stata is telling us, it looks
like Stata 10 and 11 use the same format (as Stata 8 and 9 did).
Hi all,
I tried many things to read any dataset but I receive different error messages
every time.
One new message is: vector size specified is too large
Can any one please send any part from any dataset just for testing a regression
system and to know where is the problem??
Many thanks,
Many thanks for both replying and fixing the typo!
jc
On Tue, Dec 15, 2009 at 21:20, Charles C. Berry cbe...@tajo.ucsd.eduwrote:
On Tue, 15 Dec 2009, Jean-Christophe Domenge wrote:
Dear R gurus,
I'm looking for a way to expand a matrix to a data frame as detailed
below:
given a Matrix M
Try this also:
reshape(test, direction = 'wide', idvar = 'subject', timevar = 'coder')
On Sun, Dec 13, 2009 at 6:04 PM, dadrivr dadr...@gmail.com wrote:
I am trying to reshape a data set. Could someone please help me with the
reshape, cast, and melt functions? I am new to R and I have tried
Hi,
I very recently started using R (as in: last week) and I was wondering if
anyone could point me to website(s) with sample code to deal with large
datasets (length- and/or breadthwise). I understood that R was never designed
to work with datasets larger than, say, a couple of hundred Mb.
On 12/16/2009 11:59 AM, Albert-Jan Roskam wrote:
Hi,
I very recently started using R (as in: last week) and I was wondering if
anyone could point me to website(s) with sample code to deal with large
datasets (length- and/or breadthwise). I understood that R was never designed
to work
The sqldf package may be of help to you.
Regards
Søren
-Oprindelig meddelelse-
Fra: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] På
vegne af Albert-Jan Roskam
Sendt: 16. december 2009 11:59
Til: r-help@r-project.org
Emne: [R] R very large files
Hi,
I very
Albert-Jan Roskam wrote:
Hi,
I very recently started using R (as in: last week) and I was wondering if anyone could point me to website(s) with sample code to deal with large datasets (length- and/or breadthwise). I understood that R was never designed to work with datasets larger than, say, a
Hello.
This is to get you started with data.frames, next time please
- read the posting guide
- see the documentation, especially the builtin R data import/export
manual form the help menu
## begin R examples, paste into console ##
data(mtcars) # builtin database
class(mtcars) # what it is
Hi
r-help-boun...@r-project.org napsal dne 16.12.2009 11:26:03:
Hi all,
I tried many things to read any dataset but I receive different error
messages
every time.
One new message is: vector size specified is too large
Can any one please send any part from any dataset just for testing
On 16/12/2009 12:39 AM, Xiang Wu wrote:
Is there a function in R that could find the significant digit of a specific
number? Such as for 3.1415, return '5'?
The question may not have an unambiguous answer: I would say 1.00 and
1.0 have a different number of significant digits, but once
On 16 Dec 2009 at 10:24, Prof Brian Ripley wrote:
Have you tried read.dta?
The URL on the help page for read.dta now says 'Stata 11 help for
dta', but it seems to document the same format (114) as Stata 10 (see
the value section). So in so far as Stata is telling us, it looks
like
Thank you all! I got very useful advice and I saw some nice solutions that even
made me drool! ;-)
Cheers!!
Albert-Jan
~~
In the face of ambiguity, refuse the temptation to guess.
--- begin included message ---
Hi,
I am trying to write my own split function for rpart. The aim is to do,
instead of anova, a linear regression to determine the split (minimize
some criterion like sum of rss left and right of the split). The
regression (lm) should simply use the dependent and
Katie N wrote:
Hi,
I am trying to use CART to find an ideal cut-off value for a simple
diagnostic test (ie when the test score is above x, diagnose the condition).
When I put in the model
fit=rpart(outcome ~ predictor1(TB144), method=class, data=data8)
sometimes it gives me a tree with
I am not sure why you are reading and writing from disk so many times?
It will degrade performance.
Also avoid loops when you can.
just use
ONS$labels - paste(ONS$Var1[i], ONS$Var2[i], ONS$Var3[i], ONS
$Var4[i], ONS$Var5[i], ONS$Var6[i], ONS$Var7[i], ONS$Var8[i],ONS
$Var9[i],
On 16/12/2009 8:48 AM, Xiang Wu wrote:
Yes, that's true. But what I need is the original precision of a
numeric. So to me, 1.00 and 1. are different.
In that case, they are not numbers, but strings: and you can probably
use nchar() to count characters, after stripping off any leading or
Is there a way to tell it to make a tree with only one node?
- see the maxdepth parameter in ?rpart.control
Is it safe to assume that the cut-off value on the primary node is the
ideal cut-off?
- trees are built sequentially; the first split will be the same for a
tree with only one split or
Dear Jarrett et al.,
I apologize for missing Ralf Finne's original posting -- I was out of town
at the time.
A few comments on this code:
(1) You should be able to get standard errors from the GLS solution (though
there's a missing factor 0.5 in the definition of objective.2 that should
deflate
I don't know of any prepackaged functions to do this, but I have done
this with some success,
using compositional methods: forecasting the total, and then
forecasting the compositions.,, with compositional
data analysis.
The package compositions or robCompositions
might be usefull. Or not.
Kjetil
Hi,
I am trying to create a set of dummy variables to use within a multiple linear
regression and am unable to find the codes within the manuals.
For example i have:
Price Weight Clarity
IF VVS1VVS2
5008 1 0 0
For example, subtracting 1:2 from the rows of a two-column matrix:
t(apply(matrix(1:6,ncol=2),MARGIN=1,function(y) y - 1:2))
[,1] [,2]
[1,]02
[2,]13
[3,]24
sweep(matrix(1:6,ncol=2),MARGIN=2,1:2,FUN=-)
[,1] [,2]
[1,]02
[2,]13
[3,]24
Is
Hi
r-help-boun...@r-project.org napsal dne 16.12.2009 15:58:56:
Hi,
I am trying to create a set of dummy variables to use within a multiple
linear
regression and am unable to find the codes within the manuals.
For example i have:
Price Weight Clarity
On 12/16/2009 03:58 PM, whitaker m. (mw1006) wrote:
Hi,
I am trying to create a set of dummy variables to use within a multiple
linear regression and am unable to find the codes within the manuals.
For example i have:
Price Weight Clarity
IF VVS1
On Wed, 16 Dec 2009, whitaker m. (mw1006) wrote:
Hi,
I am trying to create a set of dummy variables to use within a multiple linear
regression and am unable to find the codes within the manuals.
For example i have:
Price Weight Clarity
IF VVS1VVS2
I don't think R will complain, if you use the approach below. However,
IF, VVS1 and VVS2 are linearly dependent.
Better use the factor approach and define which factor should be the
contrast
Nikhil
On 16 Dec 2009, at 10:12AM, Petr PIKAL wrote:
what commands did you use for regression
I
Is your variable Clarity a categorical with 4 levels? Thus, the need for
k-1 (3) dummies? Your error may be the result of creating k instead of
k-1 dummies, but can't be sure from the example.
In R, you don't have to (unless you really want to) explicitly create
separate variables. You can use
Hello All,
I am interested in estimating a duration model (also known as survival
analysis or event-history analysis). I use an economic dataset. In
economics terms, the model is duration model with sample selection (or
selectivity). The time spell variable is only observed for a sample
that
Hi,
I wanted to install Rgraphviz. From the R GUI, I downloaded the package but
when I tried to load it I got the following error message:
This application has failed to start because libcdt-4.dll was not
found. Re-installing the application may fix this problem.
The R commands and errors are:
Hi Paul
Rgraphviz is a bioconductor package, so ask on the Bioconductor mailing
list.
http://bioconductor.org/docs/mailList.html
Install Bioconductor packages following the instructions here
http://bioconductor.org/docs/install/
Rgraphviz on Windows installed from binary (as you're doing
Dear R-help,
I am trying to obtain the baseline survival estimate of a fitted Cox model
(S_0 (t)). I know that previous posts have said use 'basehaz' but this
gives the baseline hazard function and not the baseline survival estimate.
Is there a way to obtain the baseline survival estimate or do
survival = exp(-hazard)
-thomas
On Wed, 16 Dec 2009, Laura Bonnett wrote:
Dear R-help,
I am trying to obtain the baseline survival estimate of a fitted Cox model
(S_0 (t)). I know that previous posts have said use 'basehaz' but this
gives the baseline hazard function and not the
I might just extend Thomas' succinct reply with a pointer to ?
survfit.coxph in the 'survival' package, which will provide the
baseline survival estimates at the mean values of the covariates from
the Cox model. It also has nice summary and plot methods and allows
for estimating predicted
On Wed, 16 Dec 2009, Levi Waldron wrote:
For example, subtracting 1:2 from the rows of a two-column matrix:
t(apply(matrix(1:6,ncol=2),MARGIN=1,function(y) y - 1:2))
[,1] [,2]
[1,]02
[2,]13
[3,]24
sweep(matrix(1:6,ncol=2),MARGIN=2,1:2,FUN=-)
[,1] [,2]
[1,]
Hi,
i have a script how i launch lattice to make a densityplot.
in the script:
jpeg(file=XXX.jpg)
densityplot(~f_diametro+m_diametro+n_diametro, plot.points=rug,
auto.key=T)
dev.off()
does'nt work and in R i dont have any output
but if i launch by R row by row, runs correctly.
any idea?
FAQ:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f
you need to print()
HTH,
baptiste
2009/12/16 c...@autistici.org c...@autistici.org:
Hi,
i have a script how i launch lattice to make a densityplot.
in the script:
jpeg(file=XXX.jpg)
instead of densityplot(...) use
print(densityplot(...))
b
On Dec 16, 2009, at 3:19 PM, c...@autistici.org wrote:
Hi,
i have a script how i launch lattice to make a densityplot.
in the script:
jpeg(file=XXX.jpg)
densityplot(~f_diametro+m_diametro+n_diametro, plot.points=rug,
auto.key=T)
Dear list,
I'm not so familiar with the internals of the fortunes package, but I
really like the interface. I was wondering if someone had implemented
a similar functionality to parse the entries of the R FAQ
http://cran.r-project.org/doc/FAQ/R-FAQ.html . Say, if I was to
answer a question Why
Dear R gurus,
to compute the correlation matrix of n variables with n_obs observations
each,
possibly including NA, I use cor(M, use=pairwise.obs)
where m is a n x nobs matrix.
Now I want to know the number of observations actually used in this
computation,
namely for each pair of columns in M,
On Tue, 15-Dec-2009 at 01:55PM +0100, Gustaf Rydevik wrote:
| Hi,
|
| ?write.table and the argument append should be of help.
| example:
|
| sink(test.csv)
| cat(-)
| cat(\n)
| cat(This is \n a test of header)
| cat(\n)
| cat(-)
|
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of
Jean-Christophe Domenge
Sent: Wednesday, December 16, 2009 11:48 AM
To: r-help
Subject: [R] number of observations used in cor when
use=pairwise.obs
Dear R gurus,
to
great, thanks!
jc
On Wed, Dec 16, 2009 at 20:55, William Dunlap wdun...@tibco.com wrote:
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of
Jean-Christophe Domenge
Sent: Wednesday, December 16, 2009 11:48 AM
To: r-help
I have a small request regarding this append feature. As it is now if the
data is appended to the file so is the header. I would like to have the header
only entered once and appends just append the data.
Doable?
Kevin
Patrick Connolly p_conno...@slingshot.co.nz wrote:
On Tue,
I have a small request regarding this append feature. As it is now if the
data is appended to the file so is the header. I would like to have the header
only entered once and appends just append the data.
Doable?
Kevin
Patrick Connolly p_conno...@slingshot.co.nz wrote:
On Tue,
Dear all and dear Marc, it seems you hit the target.
I checked as you suggested, and... it is a 32 bit version!
Now I'm fixing it. Thank you very much.
Alessandro
From: Marc Schwartz [marc_schwa...@me.com]
Sent: 11 December 2009 17:02
To: Ambrosi
Hi,
I installed R.10.1 and Graphviz 2.26 - which doesnt contain the
libcdt-4.dll, so I get the same error message 'This application has failed
to start because libcdt-4.dll was not found' when loading in R
library (Rgraphviz)
I cannot find an installation file for Graphviz 2.20 to use under
Appologies for cross-posting
Dear R users,
I am using R2WinBUGS to call WinBUGS from R. After loading data, model, and
initial values I call this command
res - bugs(data = dfile, inits = list(ifile), parameters.to.save = c(beta),
model.file = mfile, working.directory = tdir, n.thin =
Dear:
I am trying to work out the regularised incomplete beta function in R. I
searched google
on this and found UCS library. But I can not find this in R packages. Does
anyone have use
this before or how to insert UCS in R?
Many Thanks!
Xin
Xin
---
Dr.Xin Shi
Senior Lecturer in
?pbeta
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email:
Hi, I would plot a Henon map:
plot(henon(start=rnorm(2), a=1.4, b=0.3, n.sample=2000,
n.transient=10),pch=.,cex=0.1)
but give me some errors:
Error in henon(start = rnorm(2), a = 1.4, b = 0.3, n.sample = 2000, n.transient
= 10) :
could not find function checkVectorType
Error in
Currently, I load the RData file then ls() and str(). But loading the file
takes too long if the file is big. Most of the time, I only interested what
the variables are in the the file and the attributes of the variables (like
if it is a data.frame, matrix, what are the colnames/rownames, etc.)
I have a much larger dataset than in my original email (attached - price
dependent upon weight, Clarity (different levels IF-SI2), colour(levels D-L)
and Cut (ideal-fair), and tried the regression command:
On 16 Dec 2009, at 21:40, Ravi Varadhan wrote:
?pbeta
And the zipfR package wraps these in terms of the usual terminology
for incomplete/regularised upper/lower Beta functions (see ?Rbeta
there), for people like me who can't get their head around the
equivalence between the Beta
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of whitaker m. (mw1006)
Sent: Wednesday, December 16, 2009 2:14 PM
To: Nikhil Kaza; Petr PIKAL
Cc: r-help@r-project.org
Subject: Re: [R] Odp: Creating Dummy Variables in R
I have
Just write the headers once and append as many times as needed?
You can append as many datasets as you want.
--- On Wed, 12/16/09, rkevinbur...@charter.net rkevinbur...@charter.net wrote:
From: rkevinbur...@charter.net rkevinbur...@charter.net
Subject: Re: [R] write.csv and header
To:
Nordlund, Dan (DSHS/RDA) wrote:
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of whitaker m. (mw1006)
Sent: Wednesday, December 16, 2009 2:14 PM
To: Nikhil Kaza; Petr PIKAL
Cc: r-help@r-project.org
Subject: Re: [R] Odp: Creating
On 17/12/2009, at 11:14 AM, whitaker m. (mw1006) wrote:
I have a much larger dataset than in my original email (attached -
price dependent upon weight, Clarity (different levels IF-SI2),
colour(levels D-L) and Cut (ideal-fair), and tried the regression
command:
Thank you both (JRG and BDR) for the advice. Just to clarify Brian, I
don't actually have any example .dta files yet to test. I wanted to be
prepared and be able to advise the client what to do.
I don't see anything about 'Stata 11 help for dta' Brian: must have a
different URL. But I did
Hi,
I have installed the necessary tools for making a R package under windows
and am sure these tool have been correctly configured. I am very new to try
writing a package, so the error may be very obvious for you. Forgive me if
it is too easy.
My package name is *stam*, and i put it under the
Hi,
I would like to change a scale of the grid lines in a plot. I can see the
default is 0.2, so how do I change to 0.1?
Thank you so much for any help given.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing
Hi all.
So I have a data frame with multiple columns/variables. The first variable
is a major sample name for which there are some sub-samples. Currently I
have used the following command to remove the duplicates:
Samps_working-Samps[-c(which(duplicated(Samps$ESR_Ref_edit))),]
This removes
Hi,
Try:
subset(Samps, !duplicated(Samps$ESR_ref_edit) | Samps$Loaded == Y)
I'd need specific code to be sure that this is exactly what you want
(ie you specify input and desired output), but indexing with a logical
vector is probably going to be the solution.
Best,
Gray
On Wed, Dec 16, 2009
Hi, Thanks in advance for any advice you can give me, I am very stumped on this
problem...
I use R every day and consider myself a confident user, but this seems to be an
elementary problem..
Outline of problem: I am analysing the results of a study on protein expression
in cancer tissues. I
On 12/17/2009 02:22 PM, Roslina Zakaria wrote:
Hi,
I would like to change a scale of the grid lines in a plot. I can see the default is 0.2, so how do I change to 0.1?
Hi Roslina,
This depends very much on the plot you are using. grid, which will add
grid lines to a base graphics
Dear R helpers
I am having following data
Name Numbers
A 25
B 3
C 13
A 5
B 7
C 0
A 2
B 10
C 9
CONDITIONS
If Name is
Dear R helpers, please ignore my earlier mail. Here is the corrected mail.
Please forgive me for the lapses on my part. Extremely sorry.
Here is the corrected mail.
Dear R helpers
I am having following data
Name Numbers
A11 12
A12 17
A13
On Thu, 17-Dec-2009 at 03:17PM +1000, Zoe van Havre wrote:
[...]
| The problem is that I have been tracking one factor in particular
| ('branch', values 2 or 3) and once the final merge occurs, the
| second level of this factor seems to disappear in the last dataset,
| even though it was present
Hi, does this do what you want to do? I take the first six lines of the data
you provided. Note that letters corresponds to your Name, and number
corresponds to your Numbers variable.
letters=rep(c(A,B,C),2)
letters
number=c(25,3,13,5,7,0)
number
letters2=rep(letters,number)
letters2
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