Re: [R] Finding different hues for a mosaic plot compatible with grayscale printing
Dear Colleagues, Thanks for that JIm, but It strikes me that printing the residual values in the cells might be a simpler way of communicating the direction of each cell. I can get the residuals printed via the labeling_values commands in mosaic, but I cannot seem to *combine* this with labeling_borders commands that I'd like to use to modify the rotation, font size and contents of variable names and labels. The following mosaic command draws the plot with the labeling I'd like. mosaic(~social_class+ctax_agg_scaled, pop=FALSE, shade=TRUE, main=The Liberals Carbon Tax Or Green Shift Would Hurt The Canadian Economy By EGP Class Category, main_gp=gpar(fontsize=16), gp=shading_hcl(CST21$observed, CST21$expected, ASR21, df=12, h=c(260,0), c=c(100,0), l=c(90,50), interpolate=c(1,2,3,4)), labeling_args=list(labels=TRUE, rot_labels=c(25,0,0,25), gp_labels=gpar(fontsize=7), just_labels=center, offset_labels=c(1,0,0,4), offset_varnames=c(2,0,0,4), set_varnames=c(ctax_agg_scaled=The Liberal Green Shift Or Carbon Tax Would Hurt The Canadian Economy, social_class=EGP Class Category))) And when I take out the labeling_borders commands and insert the following, labeling=labeling_values(value_type=c(residuals), suppress=0) then I do get the residuals printed, but the labels are unattractive. How do I combine labeling_borders and labeling_values commands in one command. Yours, Simon Kiss On 12-May-10, at 2:42 PM, Jim Lemon wrote: On 05/12/2010 07:34 PM, Simon Kiss wrote: I'm working with the following code below to generate a how do I set the h,c, and l values such that the significant, positive residuals appear different on a grayscale printer from significant grayscale residuals. The challenge as I see it is that one can only distinguish the positive and negative residuals with the hue/. Varying the chroma and the luminance only affect the distinctions between large and small and significant and non significant. But my positive and negative residuals are both large (absolutely) and significant, meaning that they will have the same chroma and luminosity, but different hues. I guess the key here is to find two separate hue values that appear substantially different *on a grayscale printer* at the same chroma and luminance. I have read through Zeileis et al. (2007, 2008) but can't quite find the answer there. I have also tried the Friendly shading to vary the line type, but I can't find line types that are different enough to communicate the difference between positive and negative residuals clearly. Your assistance is appreciated. mosaic(~educ+trade_off_scaled, shade=TRUE, main=Support For Environmental Protection At The Expense of Creating Jobs By Education, gp=shading_hcl(CST17$observed, CST17$expected, ASR17, df=6, h=c(260,0), c=c(100,0), l=c(90,0)), labeling_args=list(rot_labels=c(25,90,0,0), offset_labels=c(1,0,0,2), offset_varnames=c(2,0,0,4), set_varnames=c(trade_off_scaled=Protecting The Environment Is More Important Than Creating Jobs, educ=Level of Education))) Hi Simon, I thought that the symbolbox function might do something useful, but it required a bit of modification. The attached mod allows the user to fill a rectangle with symbols, which includes things like + and -. Jim symbolbox.R * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ 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] access objects in my environment
Dear group, Here are my objects in my environment: ls() [1] Pos100415 Pos100416 posA pose15pose16pose16t position trade x I need to pass the object Pos100415 to a function. This element is a data.frame, obtained through a function: Pos(x)-myfun(x) with x-100415 in this example. If I do this : posA-paste(c(Pos,100415),collapse=) #I can't use directly Pos100415.I need to access it via paste(c(Pos,x),collapse=) in general. Here is what I got : posA [1] Pos100415 It is certainly not what I want, as I need to have posA as the same data.frame than Pos100415. Any help? TY __ 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] access objects in my environment
Hi,
have a look at function 'get' (and function 'assign' too)
In your example:
x - 1000
assign(paste('Pos',x,sep=''),rnorm(100))
Pos1000
posa - get(paste(c(Pos,x),collapse=))
posa
hope it's help
PF
On Thu, May 13, 2010 at 10:37 AM, arnaud Gaboury
arnaud.gabo...@gmail.com wrote:
Dear group,
Here are my objects in my environment:
ls()
[1] Pos100415 Pos100416 posA pose15 pose16 pose16t
position trade x
I need to pass the object Pos100415 to a function. This element is a
data.frame, obtained through a function: Pos(x)-myfun(x) with x-100415 in
this example.
If I do this :
posA-paste(c(Pos,100415),collapse=) #I can't use directly Pos100415.I
need to access it via paste(c(Pos,x),collapse=) in general.
Here is what I got :
posA
[1] Pos100415
It is certainly not what I want, as I need to have posA as the same
data.frame than Pos100415.
Any help?
TY
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--
+-
| Patrizio Frederic, PhD
| Assistant Professor,
| Department of Economics,
| University of Modena and Reggio Emilia,
| Via Berengario 51,
| 41100 Modena, Italy
|
| tel: +39 059 205 6727
| fax: +39 059 205 6947
| mail: patrizio.frede...@unimore.it
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Re: [R] Vectorized expression to extrapolate matrix columns with columns of another matrix
Thanks Gabor, this looks like it serves my needs. I've extended the code to
work with an example where we have two multicolumn zoo objects, one with the
original data and another that has the growth rates.
# mat1 = zoo object to extend
# mat2 = zoo object whose growth rate is used to extend mat1
mergeGrowth - function(mat1, mat2)
{
ix - is.na(mat1)
mat1.locf - na.locf(mat1, na.rm=F)
mat2.locf - mat2
mat2.locf[ix] - NA
mat2.locf - na.locf(mat2.locf, na.rm=F)
coredata(mat1)[ix] - coredata(mat1.locf * mat2 / mat2.locf)[ix]
mat1
}
Abiel Reinhart
-Original Message-
From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com]
Sent: Wednesday, May 12, 2010 12:00 PM
To: Abiel X Reinhart
Cc: r-help@r-project.org
Subject: Re: [R] Vectorized expression to extrapolate matrix columns with
columns of another matrix
Yes, that is what it does. Note that na.approx interpolates and does
not work precisely as you discussed but its easy, does use m[,2] and
may be good enough. If you really do want something precisely as you
discussed try this. It NAs out the rows of m for which column 1 is NA
and then uses na.locf to move the prior non-NA into it. Then we apply
the formula:
library(zoo)
m - zoo(cbind(c(1, 2, NA, NA, 5, NA, NA), seq(7)^2), as.Date(1:7))
# mm will hold result; m.locf
m.locf - mm - m
ix - is.na(mm[,1])
m.locf[ix,] - NA
m.locf - na.locf(m.locf)
mm[ix, 1] - m.locf[ix, 1] * mm[ix,2] / m.locf[ix,2]
mm
1970-01-02 1.0 1
1970-01-03 2.0 4
1970-01-04 4.5 9
1970-01-05 8.0 16
1970-01-06 5.0 25
1970-01-07 7.2 36
1970-01-08 9.8 49
1970-01-02 1.0 1
1970-01-03 2.0 4
1970-01-04 4.5 9
1970-01-05 8.0 16
1970-01-06 5.0 25
1970-01-07 7.2 36
1970-01-08 9.8 49
Yes, that is what it does. Please read the help file for na.approx and
approx. If you want something different you will have to special case
the end values.
On Wed, May 12, 2010 at 11:11 AM, Abiel X Reinhart
abiel.x.reinh...@jpmchase.com wrote:
Gabor,
Maybe I am doing this wrong, but rule=2 does not look like it is growing the
series out, but rather just carrying the last value forward. It looks like
na.approx() followed by na.locf(). For instance:
m - zoo(cbind(c(1, 2, NA, NA, 5, NA, NA), seq(7)^2), as.Date(1:7))
na.approx(m[, 1], x = m[, 2], rule=2)
1970-01-02 1970-01-03 1970-01-04 1970-01-05 1970-01-06 1970-01-07 1970-01-08
1.0 2.0 2.7 3.7 5.0 5.0 5.0
Abiel Reinhart
-Original Message-
From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com]
Sent: Wednesday, May 12, 2010 10:40 AM
To: Abiel X Reinhart
Cc: r-help@r-project.org
Subject: Re: [R] Vectorized expression to extrapolate matrix columns with
columns of another matrix
Use rule = 2 as in the extrapolation examples in the na.approx help file.
On Wed, May 12, 2010 at 10:10 AM, Abiel X Reinhart
abiel.x.reinh...@jpmchase.com wrote:
Gabor,
This comes close to solving my problem, but I am still left with the problem
of how I can extrapolate, not just interpolate. In our example, if I define
m as,
m - zoo(cbind(c(1, 2, NA, NA, 5, NA, NA), seq(7)^2), as.Date(1:7))
instead of
m - zoo(cbind(c(1, 2, NA, NA, 5, NA, 7), seq(7)^2), as.Date(1:7))
then I will only get five values back, when I really want m[,1] to be fully
extrapolated so that there are seven values. Is there a workaround?
Abiel Reinhart
-Original Message-
From: Gabor Grothendieck [mailto:ggrothendi...@gmail.com]
Sent: Wednesday, May 12, 2010 8:37 AM
To: Abiel X Reinhart
Cc: r-help@r-project.org
Subject: Re: [R] Vectorized expression to extrapolate matrix columns with
columns of another matrix
Try this using the zoo package. See ?na.approx for more and note that
this functionality requires zoo 1.6-3 or later.
. m - zoo(cbind(c(1, 2, NA, NA, 5, NA, 7), seq(7)^2), as.Date(1:7))
na.approx(m[, 1], x = m[, 2])
1970-01-02 1970-01-03 1970-01-04 1970-01-05 1970-01-06 1970-01-07 1970-01-08
1.00 2.00 2.714286 3.714286 5.00 5.916667 7.00
na.approx(m[, 1])
1970-01-02 1970-01-03 1970-01-04 1970-01-05 1970-01-06 1970-01-07 1970-01-08
1 2 3 4 5 6 7
On Tue, May 11, 2010 at 4:48 PM, Abiel X Reinhart
abiel.x.reinh...@jpmchase.com wrote:
I have two identically sized matrices of data that represent time series (I
am storing the data in zoo objects, but the idea should apply to any matrix
of data). The time series in the second matrix extend further than in the
first matrix, and I would like to use the data in matrix 2 to extrapolate
the data in matrix 1. In other words, if mat1[i,j] == NA, then mat1[i,j] -
mat1[i-1, j]*mat2[i,j]/mat2[i-1,j]. Of course, before we can calculate
mat1[i,j] we may need to calculate mat1[i-1,j], and that in turn may
require the computation of mat1[i-2,j], etc. This could all clearly be done
with loops, but I am wondering
Re: [R] Robust SE Heteroskedasticity-consistent estimation
Hi, here my new version:
I submit you my case:
( Pseudo likehood for exponential family with offset )
loglik - function(param) {
b-param
m=as.vector(of+z%*%b)
ll - sum(v*m-exp(m)) }
gradlik - function(param) {
b-param
m=as.vector(of+z%*%b)
gg-(v-exp(m))*z }
hesslik - function(param) {
b-param
m=as.vector(of+z%*%b)
hh - -t(exp(m)*z)%*%z }
resMaxlik -
maxLik(loglik,grad=gradlik,hess=hesslik,start=sc,method=nr,tol=1e-4);
resMaxlik$offset-of
resMaxlik$x-z
resMaxlik$y-v
estfun - function(obj,...)
{
m=as.vector(obj$offset+obj$x%*%obj$estimate)
(obj$y-exp(m))*obj$x
}
M - function(obj, adjust = FALSE, ...)
{
psi - estfun(obj)
k - NCOL(psi)
n - NROW(psi)
rval - crossprod(as.matrix(psi))/n
if(adjust) rval - n/(n - k) * rval
rval
}
B - function(obj, ...)
{ as.matrix(ginv(obj$hessian))
}
So S -B(resMaxlik)*M(resMaxlik)*B(resMaxlik) directly. It's ok.
But I call sandwich function like this : sandwich(resMaxlik,meat.=M,bread.=B)
It returns a error message : Erreur dans UseMethod(estfun) :
pas de méthode pour 'estfun' applicable pour un objet de classe c('maxLik',
'maxim', 'list')
-Message d'origine-
De : Arne Henningsen [mailto:arne.henning...@googlemail.com]
Envoyé : mardi 11 mai 2010 08:25
À : Achim Zeileis; RATIARISON Eric; r-help@r-project.org; Ott-Siim Toomet
Objet : Re: [R] Robust SE Heteroskedasticity-consistent estimation
On 11 May 2010 00:52, Achim Zeileis achim.zeil...@uibk.ac.at wrote:
On Mon, 10 May 2010, RATIARISON Eric wrote:
I'm using maxlik with functions specified (L, his gradient hessian).
Now I would like determine some robust standard errors of my estimators.
So I 'm try to use vcovHC, or hccm or robcov for example
but in use one of them with my result of maxlik, I've a the following
error message :
Erreur dans terms.default(object) : no terms component
Is there some attributes to give to maxlik objet for fitting the call
of vcovHC?
This is discussed in
vignette(sandwich-OOP, package = sandwich)
one of the vignettes accompanying the sandwich package that provides the
vcovHC() function. At the very least, you need an estfun() method which
extracts the gradient contributions per observation. Then you need a bread()
function, typically based on the observed Hessian. Then you can compute the
basic sandwich() estimators.
Is it possible to implement the estfun() method and the bread()
function in the maxLik package so that vcovHC() can be easily used by
all users of the maxLik package? If yes: should we (Eric, Achim, Ott,
Arne) implement this feature together?
/Arne
--
Arne Henningsen
http://www.arne-henningsen.name
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] merge for data.frame and matrix
Hello, how to merge a data.frame and a matrix by one column in the data.frame and rownames of the matrix? df - data.frame(col1=c(kk,yy,kk),col2=c(6,4,3)) df col1 col2 1 kk 6 2 yy 4 3 kk 3 m-matrix(c(3,8,56,9), nrow=2, dimnames = list(c(aa,kk),c(col1,col2))) m col1 col2 aa 3 56 kk 8 9 the result is expected as col1.x col2.x col1.y col2.y kk 6 8 9 kk 3 8 9 Yuan Jian [[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] sem error no variance or error-variance parameter
Hi, I am using the R version 2.11.0 and the version of sem package: sem_0.9-20 under Windows XP. I read the questions: http://r.789695.n4.nabble.com/computationally-singular-and-lack-of-variance-parameters-in-SEM-td891081.html#a891082 and http://r.789695.n4.nabble.com/computationally-singular-and-lack-of-variance-parameters-in-SEM-td891081.html#a891081 but it does not seem to be my problem. I try to replicate the sem model (see the attacheted image) but i got stuck with the problem while computing the estimates of the model: The error message: Error in nlm(if (analytic.gradient) objective.2 else objective.1, start, : probable coding error in analytic gradient In addition: Warning message: In sem.default(ram = ram, S = S, N = N, param.names = pars, var.names = vars, : The following variables have no variance or error-variance parameter (double-headed arrow): Fugural1 The model is almost surely misspecified; check also for missing covariances. Here is my script: cov.matrix - matrix(c(56.21,0,0,0,0,0,0,0,0,31.55,75.55,0,0,0,0,0,0,0,23.27,28.30,44.45,0,0,0,0,0,0,24.48,32.24,22.56,84.64,0,0,0,0,0,22.51,29.54,20.61,57.61,78.93,0,0,0,0,22.65,27.56,15.33,53.57,49.27,73.76,0,0,0,33.24,46.49,31.44,67.81,54.76,54.58,141.77,0,0,32.56,40.37,25.58,55.82,55.33,47.74,98.62,117.33,0,30.32,40.44,27.69,54.78,53.44,59.52,96.95,84.87,106.35),nrow=9,ncol=9,byrow=FALSE) rownames(cov.matrix) - colnames(cov.matrix) - c(IND1,IND2,IND3,FR11,FR12,FR13,FR21,FR22,FR23) # options(nlm=(check.analyticals = TRUE)); I tried to set the nlm on different option, but did not work either m1 - specify.model() Induction - IND1, NA, 1 Induction - IND2, y2, NA Induction - IND3, y3, NA Fugural1 - FR11, NA, 1 Figural1 - FR12, y5, NA Figural1 - FR13, y6, NA Figural2 - FR21, NA, 1 Figural2 - FR22, y8, NA Figural2 - FR23, y9, NA Induction - Figural1, x1, NA Figural1 - Figural2,x2, NA Induction - Figural2, x3, NA IND1 - IND1, e1, NA IND2 - IND2, e2, NA IND3 - IND3, e3, NA FR11 - FR11, e4, NA FR12 - FR12, e5, NA FR13 - FR13, e6, NA FR21 - FR21,e7, NA FR22 - FR22, e8, NA FR23 - FR23, e9, NA Figural1 - Figural1, e10, NA Figural2 - Figural2, e11, NA Induction - Induction, NA, 1 sem1 - sem(m1,cov.matrix,N=220,debug=T) # I added the Induction - Induction, NA, 1 fixed parametr after reading the help from John Fox, that every variable should have an error variance Can anybody please advise me what I am doing wrong? Many thanks! Jan Schubert Institute of Social Science Charles University, Prague -- View this message in context: http://r.789695.n4.nabble.com/sem-error-no-variance-or-error-variance-parameter-tp2196743p2196743.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] Robust SE Heteroskedasticity-consistent estimation
Hi,
the error message tells you that there is no method estfun for maxLik
objects. Which is (unfortunately) true. I try to look at this stuff
during the weekend (given my son sleeps well ;-).
Actually, maxLik can only implement estfun friends given the user
supplies them. AFAIK, you need to supply your likelihood function in
BHHH form, i.e. without 'sum' in the last row in your example below, and
the gradient in the same way. If your function only returns a single
likelihood value, there is now way maxLik can distribute it to
individual observations.
Best,
Ott
Hi, here my new version:
I submit you my case:
( Pseudo likehood for exponential family with offset )
loglik - function(param) {
b-param
m=as.vector(of+z%*%b)
ll - sum(v*m-exp(m)) }
gradlik - function(param) {
b-param
m=as.vector(of+z%*%b)
gg-(v-exp(m))*z }
hesslik - function(param) {
b-param
m=as.vector(of+z%*%b)
hh - -t(exp(m)*z)%*%z }
resMaxlik -
maxLik(loglik,grad=gradlik,hess=hesslik,start=sc,method=nr,tol=1e-4);
resMaxlik$offset-of
resMaxlik$x-z
resMaxlik$y-v
estfun - function(obj,...)
{
m=as.vector(obj$offset+obj$x%*%obj$estimate)
(obj$y-exp(m))*obj$x
}
M - function(obj, adjust = FALSE, ...)
{
psi - estfun(obj)
k - NCOL(psi)
n - NROW(psi)
rval - crossprod(as.matrix(psi))/n
if(adjust) rval - n/(n - k) * rval
rval
}
B - function(obj, ...)
{ as.matrix(ginv(obj$hessian))
}
So S -B(resMaxlik)*M(resMaxlik)*B(resMaxlik) directly. It's ok.
But I call sandwich function like this :
sandwich(resMaxlik,meat.=M,bread.=B)
It returns a error message : Erreur dans UseMethod(estfun) :
pas de méthode pour 'estfun' applicable pour un objet de classe
c('maxLik', 'maxim', 'list')
-Message d'origine-
De : Arne Henningsen [mailto:arne.henning...@googlemail.com]
Envoyé : mardi 11 mai 2010 08:25
À : Achim Zeileis; RATIARISON Eric; r-help@r-project.org; Ott-Siim Toomet
Objet : Re: [R] Robust SE Heteroskedasticity-consistent estimation
On 11 May 2010 00:52, Achim Zeileis achim.zeil...@uibk.ac.at wrote:
On Mon, 10 May 2010, RATIARISON Eric wrote:
I'm using maxlik with functions specified (L, his gradient hessian).
Now I would like determine some robust standard errors of my
estimators.
So I 'm try to use vcovHC, or hccm or robcov for example
but in use one of them with my result of maxlik, I've a the following
error message :
Erreur dans terms.default(object) : no terms component
Is there some attributes to give to maxlik objet for fitting the call
of vcovHC?
This is discussed in
vignette(sandwich-OOP, package = sandwich)
one of the vignettes accompanying the sandwich package that provides
the
vcovHC() function. At the very least, you need an estfun() method which
extracts the gradient contributions per observation. Then you need a
bread()
function, typically based on the observed Hessian. Then you can compute
the
basic sandwich() estimators.
Is it possible to implement the estfun() method and the bread()
function in the maxLik package so that vcovHC() can be easily used by
all users of the maxLik package? If yes: should we (Eric, Achim, Ott,
Arne) implement this feature together?
/Arne
--
Arne Henningsen
http://www.arne-henningsen.name
__
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] read table for Fisher Exact
i have 2 groups i want to compare: group A and group B each group contains let's say 20 patients i want to perform a Fisher Exact test on genotype distribution so, see if there is a sign diff in genotpe frequency/distribution (#AA, #AB, #BB) between group A and B not for 1, but for 1000 different genes my question: how should i build my table so i can do: test - read.table(table1.txt) fisher.test(test) i know a lot is still missing in the syntax, but i do not know what. any help would be soo much appreciated!! -- View this message in context: http://r.789695.n4.nabble.com/read-table-for-Fisher-Exact-tp2196762p2196762.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] summing items within a row
Thank you Dennis. That was a great idea and it worked quite well! -- View this message in context: http://r.789695.n4.nabble.com/summing-items-within-a-row-tp2195458p2196793.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help with interpolation
Hi, I have a two Colum matrix ( I named it holder) as shown bellow. It seems to be three columns, but the first column contains the row names. I am trying to fill all NAs by linear interpolation the known values in the matrix. I tried using the interpNA function, but I get an error message: interpNA(holder, method = linear) Error in approx(idx, x[idx], 1:n, method = method, f = f) : need at least two non-NA values to interpolate In addition: Warning message: In xy.coords(x, y) : NAs introduced by coercion I was wondering if some one could recommend another function to get the interpolated values? Thanks, Jorge 20100319 2010-03-19 1626 20100320 2010-03-20NA 20100321 2010-03-21NA 20100322 2010-03-22NA 20100323 2010-03-23NA 20100324 2010-03-24NA 20100325 2010-03-25NA 20100326 2010-03-26 1638 20100327 2010-03-27NA 20100328 2010-03-28NA 20100329 2010-03-29NA 20100330 2010-03-30NA 20100331 2010-03-31NA 20100401 2010-04-01NA 20100402 2010-04-02 1669 20100403 2010-04-03NA 20100404 2010-04-04NA 20100405 2010-04-05NA 20100406 2010-04-06NA 20100407 2010-04-07NA 20100408 2010-04-08NA 20100409 2010-04-09 1756 20100410 2010-04-10NA 20100411 2010-04-11NA 20100412 2010-04-12NA 20100413 2010-04-13NA 20100414 2010-04-14NA 20100415 2010-04-15NA 20100416 2010-04-16 1829 20100417 2010-04-17NA 20100418 2010-04-18NA 20100419 2010-04-19NA 20100420 2010-04-20NA 20100421 2010-04-21NA 20100422 2010-04-22NA 20100423 2010-04-23 1912 20100424 2010-04-24NA 20100425 2010-04-25NA 20100426 2010-04-26NA 20100427 2010-04-27NA 20100428 2010-04-28NA 20100429 2010-04-29NA 20100430 2010-04-30 1995 [[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] fisher's posthock test or fisher's combination test
(Ted Harding) schrieb: Thank you, for your answer, As to Fisher's combination test, I'm not sure whether this is meant to be something different from the above. It should be the same, only another name. Regards Knut __ 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] ff for 64 bit R for windows gui?
No, it does not work and is on the exclude list for Windows 64-bit building on CRAN - hence no binary available. The maintainer has been contacted and has not yet provided a version that works. So you have to fix it yourself and try to convince the maintainer to do so for you. Uwe Ligges On 12.05.2010 21:59, Hunsicker, Lawrence wrote: Hi, folks: I am running 64-bit R on a 64 bit machine under 64 bit Windows 7. I'd like to try the package ff, but it is not clear to me whether the current version of ff will work in a 64 bit environment. The windows version is compiled, which suggests that there is more than just R p-code. Do any of you know whether the current compiled version of ff will work in my environment? Many thanks in advance for any clarification that you have on this. L. G. Hunsicker, M.D. Professor, Internal Medicine U. Iowa College of Medicine Phone: (319) 356-4763 Fax: (319) 356-7488 lawrence-hunsic...@uiowa.edu [[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] access objects in my environment
Wonderful!!
TY so much for the help.
-Original Message-
From: Patrizio Frederic [mailto:frederic.patri...@gmail.com]
Sent: Thursday, May 13, 2010 10:47 AM
To: arnaud Gaboury
Cc: r-help@r-project.org
Subject: Re: [R] access objects in my environment
Hi,
have a look at function 'get' (and function 'assign' too)
In your example:
x - 1000
assign(paste('Pos',x,sep=''),rnorm(100))
Pos1000
posa - get(paste(c(Pos,x),collapse=))
posa
hope it's help
PF
On Thu, May 13, 2010 at 10:37 AM, arnaud Gaboury
arnaud.gabo...@gmail.com wrote:
Dear group,
Here are my objects in my environment:
ls()
[1] Pos100415 Pos100416 posA pose15 pose16
pose16t
position trade x
I need to pass the object Pos100415 to a function. This element is
a
data.frame, obtained through a function: Pos(x)-myfun(x) with x-
100415 in
this example.
If I do this :
posA-paste(c(Pos,100415),collapse=) #I can't use directly
Pos100415.I
need to access it via paste(c(Pos,x),collapse=) in general.
Here is what I got :
posA
[1] Pos100415
It is certainly not what I want, as I need to have posA as the same
data.frame than Pos100415.
Any help?
TY
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--
+-
| Patrizio Frederic, PhD
| Assistant Professor,
| Department of Economics,
| University of Modena and Reggio Emilia,
| Via Berengario 51,
| 41100 Modena, Italy
|
| tel: +39 059 205 6727
| fax: +39 059 205 6947
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Re: [R] Finding different hues for a mosaic plot compatible with grayscale printing
On Thu, 13 May 2010, Simon Kiss wrote: Dear Colleagues, Thanks for that JIm, but It strikes me that printing the residual values in the cells might be a simpler way of communicating the direction of each cell. I can get the residuals printed via the labeling_values commands in mosaic, but I cannot seem to *combine* this with labeling_borders commands that I'd like to use to modify the rotation, font size and contents of variable names and labels. The following mosaic command draws the plot with the labeling I'd like. mosaic(~social_class+ctax_agg_scaled, pop=FALSE, shade=TRUE, main=The Liberals Carbon Tax Or Green Shift Would Hurt The Canadian Economy By EGP Class Category, main_gp=gpar(fontsize=16), gp=shading_hcl(CST21$observed, CST21$expected, ASR21, df=12, h=c(260,0), c=c(100,0), l=c(90,50), interpolate=c(1,2,3,4)), labeling_args=list(labels=TRUE, rot_labels=c(25,0,0,25), gp_labels=gpar(fontsize=7), just_labels=center, offset_labels=c(1,0,0,4), offset_varnames=c(2,0,0,4), set_varnames=c(ctax_agg_scaled=The Liberal Green Shift Or Carbon Tax Would Hurt The Canadian Economy, social_class=EGP Class Category))) And when I take out the labeling_borders commands and insert the following, labeling=labeling_values(value_type=c(residuals), suppress=0) then I do get the residuals printed, but the labels are unattractive. How do I combine labeling_borders and labeling_values commands in one command. labeling_values() is a combination of labeling_borders() plus labeling_cells(). If you want finer control over what happens, I recommend to use labeling_borderes() in your mosaic() call and then call labeling_cells() manually afterwards. There is an example on how to do this in Section 4.2 of the strucplot vignette: vignette(strucplot, package = vcd) hth, Z Yours, Simon Kiss On 12-May-10, at 2:42 PM, Jim Lemon wrote: On 05/12/2010 07:34 PM, Simon Kiss wrote: I'm working with the following code below to generate a how do I set the h,c, and l values such that the significant, positive residuals appear different on a grayscale printer from significant grayscale residuals. The challenge as I see it is that one can only distinguish the positive and negative residuals with the hue/. Varying the chroma and the luminance only affect the distinctions between large and small and significant and non significant. But my positive and negative residuals are both large (absolutely) and significant, meaning that they will have the same chroma and luminosity, but different hues. I guess the key here is to find two separate hue values that appear substantially different *on a grayscale printer* at the same chroma and luminance. I have read through Zeileis et al. (2007, 2008) but can't quite find the answer there. I have also tried the Friendly shading to vary the line type, but I can't find line types that are different enough to communicate the difference between positive and negative residuals clearly. Your assistance is appreciated. mosaic(~educ+trade_off_scaled, shade=TRUE, main=Support For Environmental Protection At The Expense of Creating Jobs By Education, gp=shading_hcl(CST17$observed, CST17$expected, ASR17, df=6, h=c(260,0), c=c(100,0), l=c(90,0)), labeling_args=list(rot_labels=c(25,90,0,0), offset_labels=c(1,0,0,2), offset_varnames=c(2,0,0,4), set_varnames=c(trade_off_scaled=Protecting The Environment Is More Important Than Creating Jobs, educ=Level of Education))) Hi Simon, I thought that the symbolbox function might do something useful, but it required a bit of modification. The attached mod allows the user to fill a rectangle with symbols, which includes things like + and -. Jim symbolbox.R * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ 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] Finding different hues for a mosaic plot compatible with grayscale printing
On Wed, 12 May 2010, Simon Kiss wrote: I'm working with the following code below to generate a how do I set the h,c, and l values such that the significant, positive residuals appear different on a grayscale printer from significant grayscale residuals. The challenge as I see it is that one can only distinguish the positive and negative residuals with the hue/. Varying the chroma and the luminance only affect the distinctions between large and small and significant and non significant. But my positive and negative residuals are both large (absolutely) and significant, meaning that they will have the same chroma and luminosity, but different hues. I guess the key here is to find two separate hue values that appear substantially different *on a grayscale printer* at the same chroma and luminance. I have read through Zeileis et al. (2007, 2008) but can't quite find the answer there. I have also tried the Friendly shading to vary the line type, but I can't find line types that are different enough to communicate the difference between positive and negative residuals clearly. This is difficult. In grayscale printing you have just one dimension available for color shading, namely the luminance/brightness. This is already used for the size of the residuals and so you need something else to code the sign. In our HCL palettes this is done by the hue but in such a way that the choice of hue does not change the luminance (this is the excellent feature of HCL color space). So, as Jim already pointed out, you can just do something about the type of filling or the borders etc. Another option would be to use a single grayscale with dark colors for large positive residuals and bright colors for large negative residuals (or vice versa). However, none of the approaches will be very intuitive and the color version will be much more powerful. If you are forced to use grayscale, you might consider putting an assocation plot (via function assoc()) next to the mosaic plot. Best, Z Your assistance is appreciated. mosaic(~educ+trade_off_scaled, shade=TRUE, main=Support For Environmental Protection At The Expense of Creating Jobs By Education, gp=shading_hcl(CST17$observed, CST17$expected, ASR17, df=6, h=c(260,0), c=c(100,0), l=c(90,0)), labeling_args=list(rot_labels=c(25,90,0,0), offset_labels=c(1,0,0,2), offset_varnames=c(2,0,0,4), set_varnames=c(trade_off_scaled=Protecting The Environment Is More Important Than Creating Jobs, educ=Level of Education))) * Simon J. Kiss, PhD SSHRC and DAAD Post-Doctoral Fellow John F. Kennedy Institute of North America Studies Free University of Berlin Lansstraße 7-9 14195 Berlin, Germany Cell: +49 (0)1525-300-2812, Web: http://www.jfki.fu-berlin.de/index.html __ 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] merge for data.frame and matrix
Hi: You've got to convert m to a data frame first: m - data.frame(m) m$nms - rownames(m) merge(df, m, by.x = 'col1', by.y = 'row.names') col1 col2.x col1 col2.y 1 kk 68 9 2 kk 38 9 HTH, Dennis On Wed, May 12, 2010 at 5:03 PM, Yuan Jian jayuan2...@yahoo.com wrote: Hello, how to merge a data.frame and a matrix by one column in the data.frame and rownames of the matrix? df - data.frame(col1=c(kk,yy,kk),col2=c(6,4,3)) df col1 col2 1 kk6 2 yy4 3 kk3 m-matrix(c(3,8,56,9), nrow=2, dimnames = list(c(aa,kk),c(col1,col2))) m col1 col2 aa3 56 kk89 the result is expected as col1.x col2.x col1.y col2.y kk 689 kk 389 Yuan Jian [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: qplot won't work
Ralf, inside a function you'll need to print the plot using qplot. Change
it to
P - qplot(1:10, letters[1:10])
print(P)
This is good practice even at the console, as you can then modify your plots
in increments
P2 - P + more commands (text, more points, altered annotations etc)
print(P2)
etc
Bryan
*
Bryan Hanson
Acting Chair
Professor of Chemistry Biochemistry
DePauw University, Greencastle IN USA
On 5/13/10 1:42 AM, Ralf B ralf.bie...@gmail.com wrote:
I have a script running in the StatET Eclipse environment that
executes the ggplot2 command qplot in a function:
# Creates the plot
createPlot - function(){
print(Lets plot!)
qplot(1:10, letters[1:10])
}
When executing the qplot line directly, it works. When executing the
script it does not open a window and it it does not plot. Is there
something important I have forgotten? I know that the function is
called because I always get my 'Lets plot' When using normal
graphics plot functions, its also works seamless.
Of course I am importing the library ggplot2 at the beginning of my
script - here is the import log:
library(gdata) # for trim function
gdata: Unable to locate valid perl interpreter
gdata:
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata:
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: 'gdata'
The following object(s) are masked from package:utils :
object.size
Warning message:
package 'gdata' was built under R version 2.10.1
library(TTR) # for moving averages (SMA,...) smoothing
Loading required package: xts
Loading required package: zoo
Warning messages:
1: package 'TTR' was built under R version 2.10.1
2: package 'xts' was built under R version 2.10.1
3: package 'zoo' was built under R version 2.10.1
library(ggplot2) # for plotting results
Loading required package: proto
Loading required package: grid
Loading required package: reshape
Loading required package: plyr
Loading required package: digest
Attaching package: 'ggplot2'
The following object(s) are masked from package:gdata :
interleave
Warning messages:
1: package 'ggplot2' was built under R version 2.10.1
2: package 'proto' was built under R version 2.10.1
3: package 'reshape' was built under R version 2.10.1
4: package 'plyr' was built under R version 2.10.1
5: package 'digest' was built under R version 2.10.1
What is wrong here?
Ralf
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[R] multinomial regression
I am developing a multinomial regression model with the function multinom. The dependent variable is qualitative with three possible outcomes, the independent variables are all quantitative. I want to check the significance of predictor variables, which function I use to run the correct test? You also have a few examples on the net to be consulted? thanks jj [[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] Compiling R with --enable-R-shlib for rpy2 error
Hi, I am trying to compile R with the command below in order to install rpy2. ./configure --prefix=/usr/local/R/R-2.9.2 --with-gnu-ld --with-cairo --with-x --enable-R-shlib However, error the I have gotten was: /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can not be used when making a shared object; recompile with -fPIC CConverters.o: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libR.so] Error 1 I don't really understand the error message. Is there anything I can change to compile properly so that I can install rpy2? Please help. Thanks in advance! :) Regards, Padma __ 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] Solved: Input encoding problem when using sweave with xetex
With the kind help of Duncan Murdoch, I finally managed to correctly compile LyX-Sweave documents with XeTeX under Windows. In case someone else is struggling with a similar problem in the future, here is a small summary of what worked for me. I assume that you have already set up Lyx to work with Sweave and XeTeX according to the following instructions: http://cran.r-project.org/contrib/extra/lyx/INSTALL http://wiki.lyx.org/LyX/XeTeX My original problem was that accented letters that were read from Excel-files or other external sources from within R during the LyX-Sweave document compilation were not correctly encoded in UTF-8. However, UTF-8 is needed for typsetting the final document with XeTeX. Because R code chunks contained in the Lyx-Sweave document were executed by running R from the command line, it was necessary to start R with UTF-8 encoding from the command line. I managed to do this by editing the Sweave.sh file which can be found in rhome/bin/ directory. Within sweave.sh, I changed the command echo library(\utils\); Sweave(\file.Rnw\) | R --no-restore --slave into echo library(\utils\); options(encoding=\UTF-8\); Sweave(\file.Rnw\) | R --no-restore --slave Because I wanted to run R with UTF-8 encoding only when I compile my documents with XeTeX and not with LaTeX, I saved the Sweave.sh file with the new name UTF8Sweave.sh in the same directory and changed the definition for the conversion of Lyx-Sweave documents to PDF (xelatex). I did this by defining a new file format in LyX under Tools-Preferences-File handling-File formats. The file format that I defined had the same settings as LaTeX (pdflatex), but I saved it with the new name LaTeX (pdflatexUTF8). I then defined a new converter under Tools-Preferences-File handling-File formats with the following settings: From format: Sweave To format: LaTex (pdflatexUTF8) Converter: R CMD /path/to/UTF8Sweave.sh $$i Because the full path to UTF8Sweave.sh file contained blanks, I had to use the 8.3 filename which I determined by using the MSDOS cmd window. See this post for more information: http://article.gmane.org/gmane.comp.lang.r.general/190040 Finally, I changed the converter LaTeX (pdflatex) - PDF(xelatex) which I had already defined for the original LyX-XeTeX installation(see http://wiki.lyx.org/LyX/XeTeX) to LaTeX (pdflatexUTF8) - PDF(xelatex). I hope this helps. Regards, Erich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A primitive OO in R -- where next?
R OO is documented for S3 classes under section 5 (Object-oriented
programming) in the R language definition.
I guess the issue is somewhat philosophial as to how you use it.
R philosophy _mostly_ separates data from operations on data, so the OO
model provides classes for data and essentially separate methods that
apply to those classes. This is the kind of model sometimes called a
'visitor pattern'. An alternative is to include operations on the data
within the data object, which sometimes has advantages if you want to
simplify the look of code for things like display (instead of a display
method for each class, one effectively sends a mesage to any object of
the form display yourself here). In practice, of course, one ends up
writing class-specific operations code; the difference is pretty much
where it's stored.
On balance there seems to me a rationale for a statistician to separate
data from the operations formed on it; one collects and curates data
carefuly, so it as a kind of lifecycle of its own that is unrelated to
mathematical operations performed on it.
But I have allowed _data_ objects to include functions or at least
function names when it is a necessary part of the description of the
data. For example, in some of our interlaboratory studies labs give
uncertainty information in the form of a variance or interval, but may
additionally tell us what the assumed distribution is (eg Normal, t,
lognormal etc). It then makes sense to have the distribution as part of
the data. For these functions, the root name (norm, t, etc)_ suffices in
conjunction with do.call, but to generalise completely, one can consider
allowing a user to specify the distribution as (say) some arbitrary
density function or density/probability family. (It's pretty rare that
we'd need that, but hey - thinking ahead and all that). That would
generate data which in part consisted of a function describing the
(assumed) associated distribution.
Steve Ellison
Ted Harding ted.hard...@manchester.ac.uk 12/05/2010 22:48:17
Greetings All,
Out of curiosity, I've just done a very primitive experiment:
Obj - list(Fun=sum, Dat=c(1,2,3,4))
Obj$Fun(Obj$Dat)
# [1] 10
That sort of thing (much more sophisticated) must be documented
mind-blowingly somewhere. Where?
Where I stand right now: The above (and its immediately obvious
generalisations, like Obj$Fun-cos) is all I know about it so far.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 12-May-10 Time: 22:48:14
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Re: [R] read table for Fisher Exact
On 05/12/2010 03:31 PM, visser wrote: i have 2 groups i want to compare: group A and group B each group contains let's say 20 patients i want to perform a Fisher Exact test on genotype distribution so, see if there is a sign diff in genotpe frequency/distribution (#AA, #AB, #BB) between group A and B not for 1, but for 1000 different genes my question: how should i build my table so i can do: test- read.table(table1.txt) fisher.test(test) i know a lot is still missing in the syntax, but i do not know what. any help would be soo much appreciated!! Note that in this case, Fisher's exact test has a good chance of being less accurate than an approximate Pearson chi-square test. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] long command line cut in 2 parts
Dear group, I have this command line in a function: zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,VALUE= NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F) I want to cut it in 2 lines (just for convenient purpose). Here is what I did : zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL, + VALUE=NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F) But when I source the function, I get an error message: Error in source(C:\\Users\\arno\\Documents\\r\\LSC\\PLwork2.r) : C:\Users\arno\Documents\r\LSC\PLwork2.r:34:10: unexpected '=' 33: zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL, 34: + VALUE= ^ What is wrong? TY for any help __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] long command line cut in 2 parts
Remove the plus sign. On Thu, May 13, 2010 at 9:54 AM, arnaud Gaboury arnaud.gabo...@gmail.comwrote: Dear group, I have this command line in a function: zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,VALUE= NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F) I want to cut it in 2 lines (just for convenient purpose). Here is what I did : zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL, + VALUE=NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F) But when I source the function, I get an error message: Error in source(C:\\Users\\arno\\Documents\\r\\LSC\\PLwork2.r) : C:\Users\arno\Documents\r\LSC\PLwork2.r:34:10: unexpected '=' 33: zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL, 34: + VALUE= ^ What is wrong? TY for any help __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] ff for 64 bit R for windows gui?
Many thanks to Uwe Ligges for his response below. ff for Windows 64 bit? No, it does not work and is on the exclude list for Windows 64-bit building on CRAN - hence no binary available. The maintainer has been contacted and has not yet provided a version that works. So you have to fix it yourself and try to convince the maintainer to do so for you. I will contact the ff maintainer. Larry Hunsicker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A primitive OO in R -- where next?
From: ted.hard...@manchester.ac.uk
On 12-May-10 22:24:21, Erik Iverson wrote:
(Ted Harding) wrote:
Greetings All,
Out of curiosity, I've just done a very primitive experiment:
Obj - list(Fun=sum, Dat=c(1,2,3,4))
Obj$Fun(Obj$Dat)
# [1] 10
That sort of thing (much more sophisticated) must be documented
mind-blowingly somewhere. Where?
Where I stand right now: The above (and its immediately obvious
generalisations, like Obj$Fun-cos) is all I know about it so far.
Well functions are just an object in R, so lists can of
course contain
them. My naive understanding is that you can think of
function calls
as simply lists where the first element is the function
name, and the
rest of the list are the arguments, so:
eval(as.call(Obj))
[1] 10
Well, that's a neat trick! (It seems to depend on my having
put the function name first in the list, though, which wasn't
done with any specific intent).
This has not much to do with OO in the usual sense, just how functions
in R work. See:
http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-lang.html#Function-obj
ects
The styles of OO in S3 and S4 do not encapsulate methods into the class
definitions.
Andy
In fact, the sort of thing I have in mind as possible
applications for the idea in that simple example, is that one
could encapsulate a Study in a list, which would contain as
components the various datasets available (quite possibly of
different structures etc.), and the various functions which
one might use to analyse different datasets, or to combine
analyses, etc.; and possibly also a top-level supervisor
function which could ensure social behaviour in that mob of
entities. Pretty open-ended, really.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 12-May-10 Time: 23:46:34
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Re: [R] long command line cut in 2 parts
Dear Arnaud,
Wrap a pair of curly brackets around the command line and remove the + like
the following;
zz-{merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,
VALUE=NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F )}
Muhammad
arnaud Gaboury wrote:
Dear group,
I have this command line in a function:
zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,VALUE=
NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F)
I want to cut it in 2 lines (just for convenient purpose). Here is what I
did :
zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,
+ VALUE=NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F)
But when I source the function, I get an error message:
Error in source(C:\\Users\\arno\\Documents\\r\\LSC\\PLwork2.r) :
C:\Users\arno\Documents\r\LSC\PLwork2.r:34:10: unexpected '='
33: zz-merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,
34: + VALUE=
^
What is wrong?
TY for any help
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] long command line cut in 2 parts
Removing the + sign resolves the problem.
TY
-Original Message-
From: Muhammad Rahiz [mailto:muhammad.ra...@ouce.ox.ac.uk]
Sent: Thursday, May 13, 2010 3:15 PM
To: arnaud Gaboury
Cc: r-help@r-project.org
Subject: Re: [R] long command line cut in 2 parts
Dear Arnaud,
Wrap a pair of curly brackets around the command line and remove the
+ like the following;
zz-{merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,
VALUE=NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F )}
Muhammad
arnaud Gaboury wrote:
Dear group,
I have this command line in a function:
zz-
merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,VALUE
=
NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F)
I want to cut it in 2 lines (just for convenient purpose). Here is
what I
did :
zz-
merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,
+ VALUE=NULL,PL=-VALUE*pl,quantity=NULL),PosB,all.x=T,sort=F)
But when I source the function, I get an error message:
Error in source(C:\\Users\\arno\\Documents\\r\\LSC\\PLwork2.r) :
C:\Users\arno\Documents\r\LSC\PLwork2.r:34:10: unexpected '='
33: zz-
merge(transform(merge(value,allcon,all.y=T),SHORTDESCRIPTION=NULL,
34: + VALUE=
^
What is wrong?
TY for any help
__
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PLEASE do read the posting guide http://www.R-project.org/posting-
guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] RWinEdt in WinEdt 6
On 12.05.2010 18:16, Gregoire wrote: Yes, I could do that. But the license for WinEdt 6 is not the same as the license for WinEdt 5.x, so I would have to buy WinEdt 5.x to use RWinEdt, which is a bit unfortunate. Maybe I'll do that though. Oh, I do not have such a license for version 6 yet. Will see how I can get things working again. After finally reading the documentation and changes it looks like I'd need to implement RWinEdt from scratch again. :-(( Uwe Gregory __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] merge for data.frame and matrix
On May 13, 2010, at 5:34 AM, Dennis Murphy wrote: Hi: You've got to convert m to a data frame first: Well, that would be one way, but it is not true that it is necessary. The Details section of the help page for merge says that row,names is an acceptable by specification, so without the data.frame coercion, this is another method: merge(df, m, by.x=col1, by.y=row.names) col1 col2.x col1 col2.y 1 kk 68 9 2 kk 38 9 -- David. m - data.frame(m) m$nms - rownames(m) merge(df, m, by.x = 'col1', by.y = 'row.names') col1 col2.x col1 col2.y 1 kk 68 9 2 kk 38 9 HTH, Dennis On Wed, May 12, 2010 at 5:03 PM, Yuan Jian jayuan2...@yahoo.com wrote: Hello, how to merge a data.frame and a matrix by one column in the data.frame and rownames of the matrix? df - data.frame(col1=c(kk,yy,kk),col2=c(6,4,3)) df col1 col2 1 kk6 2 yy4 3 kk3 m-matrix(c(3,8,56,9), nrow=2, dimnames = list(c(aa,kk),c(col1,col2))) m col1 col2 aa3 56 kk89 the result is expected as col1.x col2.x col1.y col2.y kk 689 kk 389 Yuan Jian [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD 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.
[R] select subset based on another variable
Hi, dear R-helpers, I have a simple question regarding selecting subset of a variable based on another variable. Here is the example: xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) Now, all I want is xx's that their id are 6, 1, 8, 2, instead of the position. Any suggestions ? Thank you all your help !! Carrie [[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] select subset based on another variable
On May 13, 2010, at 9:48 AM, Carrie Li wrote: Hi, dear R-helpers, I have a simple question regarding selecting subset of a variable based on another variable. Here is the example: xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) Now, all I want is xx's that their id are 6, 1, 8, 2, instead of the position. Any suggestions ? xx[temp] -- David. Thank you all your help !! Carrie [[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. David Winsemius, MD 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] select subset based on another variable
Try this: subset(xx, id %in% temp) On Thu, May 13, 2010 at 10:48 AM, Carrie Li carrieands...@gmail.com wrote: Hi, dear R-helpers, I have a simple question regarding selecting subset of a variable based on another variable. Here is the example: xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) Now, all I want is xx's that their id are 6, 1, 8, 2, instead of the position. Any suggestions ? Thank you all your help !! Carrie [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] select subset based on another variable
try this: xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) xx[match(temp, id)] [1] 0.4874291 -0.6212406 1.5117812 0.5757814 xx [1] -0.8204684 0.4874291 0.7383247 0.5757814 -0.3053884 1.5117812 0.3898432 -0.6212406 -2.2146999 [10] 1.1249309 id [1] 5 6 4 2 10 8 9 1 7 3 On Thu, May 13, 2010 at 9:48 AM, Carrie Li carrieands...@gmail.com wrote: Hi, dear R-helpers, I have a simple question regarding selecting subset of a variable based on another variable. Here is the example: xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) Now, all I want is xx's that their id are 6, 1, 8, 2, instead of the position. Any suggestions ? Thank you all your help !! Carrie [[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. -- 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.
Re: [R] help! - spectral analysis - spec.pgram
On 12.05.2010 07:48, vikrant wrote: Dear Prof Brian, This is a mailinglist, and I do not know any Prof. Brian so far (or maybe I should expect to be called Prof. Uwe ?). I am new to spectral analysis. I dont know how to obtain period from spectral periodogram. Then you should really start to read textbooks about spectral analysis rather than asking a mailing list (or Prof. Brian unless he is your supervisor). If u could explain me about how to obtain the period from periodogram it will be very helpful. U can explain using the above two examples in the discussiion. Which examples?? Thanks in advance.. Uwe Ligges __ 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] select subset based on another variable
On May 13, 2010, at 9:55 AM, David Winsemius wrote: On May 13, 2010, at 9:48 AM, Carrie Li wrote: Hi, dear R-helpers, I have a simple question regarding selecting subset of a variable based on another variable. Here is the example: xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) Now, all I want is xx's that their id are 6, 1, 8, 2, instead of the position. Any suggestions ? xx[temp] I may have jumped the gun, but on reflection I am not sure that your question was at all clear. Is the first item desired the 6th item of xx or the xx item referenced by the 6th item of id? You gave a specification that would not allow any of us to check, since you did not specify a random seed. We have no way of seeing what either of your xx or id vectors look like since you did not provide either them or the desired output. If it were the second specification then consider this: set.seed(123) xx=rnorm(10) id=sample(1:10, 10) temp=c(6, 1, 8, 2) xx;id [1] -0.56047565 -0.23017749 1.55870831 0.07050839 0.12928774 1.71506499 [7] 0.46091621 -1.26506123 -0.68685285 -0.44566197 [1] 9 7 6 10 4 8 3 2 1 5 xx[id[temp]] [1] -1.2650612 -0.6868529 -0.2301775 0.4609162 -- David. Thank you all your help !! Carrie [[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. David Winsemius, MD 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. David Winsemius, MD 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] fisher's posthock test or fisher's combination test
Knut, With the assumption that you are asking about Fisher's LSD for all pairwise contrasts in ANOVA, then it is available, along with many superior tests, in the multcomp package in R. See ?glht. Since you mention Excel, please look at RExcel, a package which seamlessly merges R and Excel. Any R function can be accessed through Excel and can be placed inside the Excel automatic recalculation model. The Rcmdr menu has been placed on the Excel menu bar. See rcom.univie.ac.at for full information. You can install RExcel on Windows from CRAN with install.packages(RExcelInstaller) For this example, the Tukey comparisons from glht in R are on the Rcmdr menu and hence are available to the Excel user with just a few clicks. Rich [[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] Whiskers on the default boxplot {graphics}
Hi Peter, You're absolutely correct! The description for 'range' in 'boxplot' help file is a little bit confusing by using the words interquartile range. I think it should be changed to the length of the box to be exact and consistent with those in the help file for boxplot.stats. The issue is probably that there are multiple ways (9 to be exact) of defining quantiles in R. See 'type= ' arguement for ?quantile. The quantile function uses type=7 by default which matches the quantile definition used by S-Plus(?), but differs from that used by SPSS. Doesn't fivenum essentially use the equivalent of a different type= arguement (maybe 2 or 5) in constructing the hinges? It seems perfectly reasonable to talk about 'length of box' (or 'box height' depending how you display the boxplot), but aren't the hinges simply Q1 and Q3 defined by one of the possible quartile definitions (as Peter points out the one used by fivenum)? The box height does not necesarily match the distance produced by IQR() which also seems to use the equivalent of quantile(..., type=7), but it is still an IQR, is it not? Quantiles apparantly can be defined in more than one acceptable way (sort of like dealing with ties in rank statistics). The OP seemed to want an exact explanation of the wiskers, and I think Peter has pointed us at the definition of quartiles used by fivenum, as opposed to the default used with quantile(..., type=7). All that said, I'm not convinced that it is wrong to speak of interquartile range in 'boxplot' help. Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a question about latex in Hmisc and .dvi file
HI: If you don't mind me asking this question about latex: Based on Duncan's comment: The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). Where in MikTex can I change to pdflatex? everytime I use latex it displays the dvi file which is a problem because tables that I want to see landscaped don't work. Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA - Original Message From: Duncan Murdoch murdoch.dun...@gmail.com To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org Sent: Wed, May 12, 2010 1:40:50 PM Subject: Re: [R] a question about latex in Hmisc On 12/05/2010 4:33 PM, Shi, Tao wrote: Hi Ista, Thanks for the reply! You actually misunderstood me. I never objected the tmp - latex(x) method (in fact, that's what I'm doing now in my .Rnw file). As I stated in my original post, I'm simply curious about what causes the error window and wanted to get to the bottom of it. latex(x) returns an object of class latex. When you don't assign it, it prints. The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). If you can't run latex, you can't print those objects. That's why you're getting an error. Duncan Murdoch __ ymailto=mailto:R-help@r-project.org; href=mailto:R-help@r-project.org;R-help@r-project.org mailing list href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 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] How ls() only functions or anything else but functions?
Hello, How ls() only functions or only data objects (basically anything other than functions) such as data.frame, numeric ...? John [[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] Source code for gee
Dear all: I am looking for the source code for gee(generalized estimation equations by Liang and Zeger) package. Can you help? Thanks much, Joey [[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] plot error
Hello All: I am having the following error message when I increase the resolution (res=30 to res=350) of my graph: Error in plot.xy(xy, type, ...) : ignoring SIGPIPE signal Calls: plot - plot.default - plot.xy Execution halted Here is the code: ofn - MAY11.png bitmap(ofn, type = png256, width = 21, height = 30, pointsize = 30, bg = white,res=350) If I change res=350 to res=30, everything is fine. par(cex.main=1.2,cex.lab=1.8,cex.axis=1.4) Does anybody have any comment please? Many thanks, Mohsen [[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] 3d surface plot
On 11.05.2010 23:25, kun.z...@wmich.edu wrote: Hi,Sir or Miss: We meet a problem of plotting 3d, which is a part of 5D. In other word, we just fixed the rest of 2 variables and slice 5d into 3d. Consider a function like Y=f(x1, x2, x3, x4). We want to have a 3D surface plot in R for the fitted value Yhat (which is of course a function of x1, x2, x3 and x4) against x1 and x2 say, keeping x3 at its median level and fixing x4 as =1 (note that x4 is binary which can take values of 1 or 0 only). So we plot yhat, x1 and x2 in 3D surface after estimating the whole model (based on all 4 covariates) . See ?persp. Uwe Ligges Awaiting your reply. Thanks for your time, Best Kun [[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] a question about latex in Hmisc and .dvi file
On 13.05.2010 16:32, Felipe Carrillo wrote: HI: If you don't mind me asking this question about latex: Based on Duncan's comment: The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). Where in MikTex can I change to pdflatex? everytime I use latex it displays the dvi file which is a problem because tables that I want to see landscaped don't work. Thanks Run pdflatex rather than latex? Uwe Ligges Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA - Original Message From: Duncan Murdochmurdoch.dun...@gmail.com To: Shi, Taoshida...@yahoo.com Cc: r-help@r-project.org Sent: Wed, May 12, 2010 1:40:50 PM Subject: Re: [R] a question about latex in Hmisc On 12/05/2010 4:33 PM, Shi, Tao wrote: Hi Ista, Thanks for the reply! You actually misunderstood me. I never objected the tmp- latex(x) method (in fact, that's what I'm doing now in my .Rnw file). As I stated in my original post, I'm simply curious about what causes the error window and wanted to get to the bottom of it. latex(x) returns an object of class latex. When you don't assign it, it prints. The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). If you can't run latex, you can't print those objects. That's why you're getting an error. Duncan Murdoch __ ymailto=mailto:R-help@r-project.org; href=mailto:R-help@r-project.org;R-help@r-project.org mailing list href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 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.
Re: [R] a question about latex in Hmisc and .dvi file
On 13/05/2010 10:48 AM, Uwe Ligges wrote: On 13.05.2010 16:32, Felipe Carrillo wrote: HI: If you don't mind me asking this question about latex: Based on Duncan's comment: The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). Where in MikTex can I change to pdflatex? everytime I use latex it displays the dvi file which is a problem because tables that I want to see landscaped don't work. Thanks Run pdflatex rather than latex? Or if using texify, use the --pdf option. Duncan Murdoch Uwe Ligges Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA - Original Message From: Duncan Murdochmurdoch.dun...@gmail.com To: Shi, Taoshida...@yahoo.com Cc: r-help@r-project.org Sent: Wed, May 12, 2010 1:40:50 PM Subject: Re: [R] a question about latex in Hmisc On 12/05/2010 4:33 PM, Shi, Tao wrote: Hi Ista, Thanks for the reply! You actually misunderstood me. I never objected the tmp- latex(x) method (in fact, that's what I'm doing now in my .Rnw file). As I stated in my original post, I'm simply curious about what causes the error window and wanted to get to the bottom of it. latex(x) returns an object of class latex. When you don't assign it, it prints. The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). If you can't run latex, you can't print those objects. That's why you're getting an error. Duncan Murdoch __ ymailto=mailto:R-help@r-project.org; href=mailto:R-help@r-project.org;R-help@r-project.org mailing list href=https://stat.ethz.ch/mailman/listinfo/r-help; target=_blank 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 with Loops
Hi
I have tried many attempts but cant get the loop right, as I am not a strong
programmer. What I am basically trying to do is compare 2 spreadsheets. The
problem is that one of them only contain a portion of the overall data
(TESTSAMP), where the other has a full datasetFULLSAMP. From the complete set I
would like to remove the rows of data which are not in the TESTSAMP. Column 1
contains the sample numbers which can be used to identify samples. Does anyone
have any suggestions?
I have tried various things like double loops and so on, but I am sure there is
an easier way or function to do this.
i tried this method, but Im not sure how to only keep looping until a match is
found. I dont understand how repeat loops work in R.
for (i in 1:length(FULLSAMP[,1])) {
if (FULLSAMP[i,1] != TESTSAMP[i,1]) {
FULLSAMP - FULLSAMP[-i,]
}
Thanks in advance
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Re: [R] How ls() only functions or anything else but functions?
Try this: className - data.frame names(which(eapply(globalenv(), class) == className)) On Thu, May 13, 2010 at 11:02 AM, John Edwards jhnedwards...@gmail.comwrote: Hello, How ls() only functions or only data objects (basically anything other than functions) such as data.frame, numeric ...? John [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] Whiskers on the default boxplot {graphics}
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in
'boxplot' help file is a little bit confusing by using the words
interquartile range. I think it should be changed to the length
of the box to be exact and consistent with those in the help file
for boxplot.stats.
The issue is probably that there are multiple ways (9 to be exact)
of defining quantiles in R. See 'type= ' arguement for ?quantile.
The quantile function uses type=7 by default which matches the
quantile definition used by S-Plus(?), but differs from that used by
SPSS. Doesn't fivenum essentially use the equivalent of a different
type= arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or 'box
height' depending how you display the boxplot), but aren't the
hinges simply Q1 and Q3 defined by one of the possible quartile
definitions (as Peter points out the one used by fivenum)? The box
height does not necesarily match the distance produced by IQR()
which also seems to use the equivalent of quantile(..., type=7), but
it is still an IQR, is it not?
Quantiles apparantly can be defined in more than one acceptable
way (sort of like dealing with ties in rank statistics). The OP
seemed to want an exact explanation of the wiskers, and I think
Peter has pointed us at the definition of quartiles used by fivenum,
as opposed to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4] with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove
that to myself from mathematical arguments. since I do not quite
understand the formalism in the quantile page. If the match is not
exact, this would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
David.
All that said, I'm not convinced that it is wrong to speak of
interquartile range in 'boxplot' help.
Rob
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Re: [R] How ls() only functions or anything else but functions?
On 5/13/2010 10:02 AM, John Edwards wrote: Hello, How ls() only functions or only data objects (basically anything other than functions) such as data.frame, numeric ...? c(ls.str(mode = function)) ls()[!(ls() %in% c(ls.str(mode=function)))] ?ls.str John [[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. -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a question about latex in Hmisc and .dvi file
Felipe Carrillo wrote: HI: If you don't mind me asking this question about latex: Based on Duncan's comment: The print method for latex objects tries to run latex and then display the resulting .dvi file. (Or maybe it runs pdflatex and displays the .pdf file). Where in MikTex can I change to pdflatex? everytime I use latex it displays the dvi file which is a problem because tables that I want to see landscaped don't work. Thanks I don't work in a Windows environment, but I think the process is the same here. You have to know what the print.latex function in Hmisc is doing. It simply calls show.latex. If you look at the source for show.latex, it looks at the latex object passed to it, and inspects the file argument. If the file argument is the empty string ( ), it does not attempt to show the resulting output in a dvi. If the file argument is a file name, show.latex will call dvi.latex on the object, which will wrap the latex code in some basic latex, and call optionsCmds(latex) on the file. This is by default set to optionsCmds(latex) [1] /usr/bin/latex This will of course create a dvi and attempt to display it with show.dvi, which will in turn use optionsCmds(xdvi) [1] xdvi to display the resulting file. I'm guessing MikTex comes with pdflatex, just like it comes with a binary called latex. You'd just have to find it and make sure it's in your path. Then, by setting the relevant options I just described above to pdflatex and a suitable pdf viewer, you might get what you want. But there might be other things I haven't thought of that will prohibit this from working. In fact, it looks like dvi.latex naturally assumes the extension .dvi from its output, and so this may not work. You/I might have to write separate functions to carry this out it appears. Of course, someone else may have already, and I just don't know about it. --Erik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with Loops
You don't need a loop for this, I think. Since you don't provide an
example it's hard to know how your data are set up, but look at this:
FULLSAMP - data.frame(A = 1:10, B=letters[1:10])
TESTSAMP - data.frame(A = c(2,4,5,8), C=1:4)
FULLSAMP
A B
1 1 a
2 2 b
3 3 c
4 4 d
5 5 e
6 6 f
7 7 g
8 8 h
9 9 i
10 10 j
TESTSAMP
A C
1 2 1
2 4 2
3 5 3
4 8 4
FULLSAMP[FULLSAMP$A %in% TESTSAMP$A,]
A B
2 2 b
4 4 d
5 5 e
8 8 h
Sarah
On Thu, May 13, 2010 at 10:49 AM, Amit Patel amitrh...@yahoo.co.uk wrote:
Hi
I have tried many attempts but cant get the loop right, as I am not a strong
programmer. What I am basically trying to do is compare 2 spreadsheets. The
problem is that one of them only contain a portion of the overall data
(TESTSAMP), where the other has a full datasetFULLSAMP. From the complete set
I would like to remove the rows of data which are not in the TESTSAMP. Column
1 contains the sample numbers which can be used to identify samples. Does
anyone have any suggestions?
I have tried various things like double loops and so on, but I am sure there
is an easier way or function to do this.
i tried this method, but Im not sure how to only keep looping until a match
is found. I dont understand how repeat loops work in R.
for (i in 1:length(FULLSAMP[,1])) {
if (FULLSAMP[i,1] != TESTSAMP[i,1]) {
FULLSAMP - FULLSAMP[-i,]
}
Thanks in advance
--
Sarah Goslee
http://www.functionaldiversity.org
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Re: [R] plot error
On 13.05.2010 16:49, Mohsen Jafarikia wrote: Hello All: I am having the following error message when I increase the resolution (res=30 to res=350) of my graph: Error in plot.xy(xy, type, ...) : ignoring SIGPIPE signal Calls: plot - plot.default - plot.xy Execution halted Here is the code: ofn- MAY11.png bitmap(ofn, type = png256, width = 21, height = 30, pointsize = 30, bg = white,res=350) If I change res=350 to res=30, everything is fine. par(cex.main=1.2,cex.lab=1.8,cex.axis=1.4) Does anybody have any comment please? Does not happen for me. This may be a ghostscript issue rather than an R issue, though. Hard to say since we do not know: your R version, OS, ghostscript version etc. Uwe Ligges Many thanks, Mohsen [[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] Help with Loops
Hi,
On Thu, May 13, 2010 at 10:49 AM, Amit Patel amitrh...@yahoo.co.uk wrote:
Hi
I have tried many attempts but cant get the loop right, as I am not a strong
programmer. What I am basically trying to do is compare 2 spreadsheets. The
problem is that one of them only contain a portion of the overall data
(TESTSAMP), where the other has a full datasetFULLSAMP. From the complete set
I would like to remove the rows of data which are not in the TESTSAMP. Column
1 contains the sample numbers which can be used to identify samples. Does
anyone have any suggestions?
I have tried various things like double loops and so on, but I am sure there
is an easier way or function to do this.
i tried this method, but Im not sure how to only keep looping until a match
is found. I dont understand how repeat loops work in R.
for (i in 1:length(FULLSAMP[,1])) {
if (FULLSAMP[i,1] != TESTSAMP[i,1]) {
FULLSAMP - FULLSAMP[-i,]
}
You want to not use for loops as much as possible.
Imagine your samples are identified as letters, so FULLSAMP[,1] will
be letters A..Z, and TESTSAMP[,1] will be some random 15 letters. Now
the job is to match the rows in TESTAMP to the rows in FULLSAMP, and
remove any extra rows in FULLSAMP that don' appear in testamp.
## Making some data
R fullsamp - data.frame(id=LETTERS, something=sample(1:100,
length(letters)), stringsAsFactors=FALSE)
R testsamp - data.frame(id=sample(LETTERS, 15),
something=sample(1:100, 15), stringsAsFactors=FALSE)
## Let's find where the testamp rows appear in fullsamp
R xref - match(testsamp[,1], fullsamp[,1])
## Now reduce fullsamp to have only the data corresponding to testsamp
## (and in the same order
R fullsamp.sub - fullsamp[xref,]
Notice that fullsamp.sub now has only rows with IDs appearing in
testsamp and they are also in the same order as testsamp.
Now go ahead and read the help you'll find in ?match
-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
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Re: [R] How ls() only functions or anything else but functions?
On 5/13/2010 11:04 AM, Chuck Cleland wrote: On 5/13/2010 10:02 AM, John Edwards wrote: Hello, How ls() only functions or only data objects (basically anything other than functions) such as data.frame, numeric ...? c(ls.str(mode = function)) ls()[!(ls() %in% c(ls.str(mode=function)))] ?ls.str Or better ... c(lsf.str()) ls()[!(ls() %in% c(lsf.str()))] John [[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. -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with Loops
On May 13, 2010, at 10:49 AM, Amit Patel wrote:
Hi
I have tried many attempts but cant get the loop right, as I am not
a strong programmer. What I am basically trying to do is compare 2
spreadsheets. The problem is that one of them only contain a portion
of the overall data (TESTSAMP), where the other has a full
datasetFULLSAMP. From the complete set I would like to remove the
rows of data which are not in the TESTSAMP. Column 1 contains the
sample numbers which can be used to identify samples. Does anyone
have any suggestions?
I have tried various things like double loops and so on, but I am
sure there is an easier way or function to do this.
i tried this method, but Im not sure how to only keep looping until
a match is found. I dont understand how repeat loops work in R.
for (i in 1:length(FULLSAMP[,1])) {
if (FULLSAMP[i,1] != TESTSAMP[i,1]) {
FULLSAMP - FULLSAMP[-i,]
}
Abandon the loop. Use merge.
... or the %in% function.
--
David Winsemius, MD
West Hartford, CT
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Re: [R] A primitive OO in R -- where next?
This is not really OO at all, in my opinion. It's an example of the
amazing flexibility of the language.
I'd like to add on to what Erik said, with an example:
sum(1:10)
[1] 55
foo - sum
foo(1:10)
[1] 55
junk - list(a=sum)
junk$a(1:10)
[1] 55
sum is an R object; it happens to be a function.
When I do
foo - sum
I'm creating another R object. It's also a function, so I use it with
the same syntax.
When I do
junk - list(a=sum)
I'm creating another R object. It's a list, and its first element,
named 'a', is a function.
Since the element is a function, I use it just like any other
function, i.e, follow its name with a pair of parentheses with
arguments between them.
Note that in the last example it doesn't matter what the other
elements in the list, if any, are. I could just as well do
junk - list( foo=data.frame(x=1:4), b=c('x','y'), dd=sum)
Then
junk$dd(1:10)
junk$dd( junk$foo$x )
are valid statements. There's no connection between using 'junk' both
inside the parentheses and outside. Since junk$dd is a function, you
can supply it with any R object, and it doesn't matter where that R
object comes from.
I doubt that it's documented in the way you might be expecting. It's
a result of the generality of list elements -- they can be any R
object.
Hope this helps.
-Don
At 10:48 PM +0100 5/12/10, Ted Harding wrote:
Greetings All,
Out of curiosity, I've just done a very primitive experiment:
Obj - list(Fun=sum, Dat=c(1,2,3,4))
Obj$Fun(Obj$Dat)
# [1] 10
That sort of thing (much more sophisticated) must be documented
mind-blowingly somewhere. Where?
Where I stand right now: The above (and its immediately obvious
generalisations, like Obj$Fun-cos) is all I know about it so far.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 12-May-10 Time: 22:48:14
-- XFMail --
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Livermore, CA, USA
925-423-1062
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Re: [R] R version of SAS/IntrNet
Hi, more links in the FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Web-Interfaces On Thursday 13 May 2010 01:46:51 am Scott Czepiel wrote: I recall hearing about -- or was I just dreaming? -- a way to compile R as an apache module so it could stay in memory while the webserver was running. The alternative is to simply use cgi in perl or python or whatever to gather user input, execute R in batch mode, grab the output file and parse it into html. Lots of boiler-plate involved and I would be surprised if nobody has attempted this yet. On Wed, May 12, 2010 at 9:27 AM, Mark Lamias mlam...@yahoo.com wrote: Does an R package exist that is similar to SAS/Intrnet (http://support.sas.com/documentation/onlinedoc/intrnet/index.html) that will allow users to take parameters passed to it by a web request, produce results and return them to the web-browser in HTML format? I tried looking through the package descriptions, but didnt' see anything like this. Any direction or suggestions you could provide would be greatly appreciated. Thanks. Sincerely yours, Mark J. Lamias Statistical Consultant Survey Methodologist [[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. -- Friedrich Schuster Dompfaffenweg 6 69123 Heidelberg __ 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] Source code for gee
On 13.05.2010 16:29, Joey Zhou wrote: Dear all: I am looking for the source code for gee(generalized estimation equations by Liang and Zeger) package. Can you help? download.packages(gee, type=source, destdir=~) Uwe Ligges Thanks much, Joey [[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] Compiling R with --enable-R-shlib for rpy2 error
On 13.05.2010 11:45, Padma TAN wrote: Hi, I am trying to compile R with the command below in order to install rpy2. ./configure --prefix=/usr/local/R/R-2.9.2 --with-gnu-ld --with-cairo --with-x --enable-R-shlib However, error the I have gotten was: /usr/bin/ld: CConverters.o: relocation R_X86_64_32S against `R_FunTab' can not be used when making a shared object; recompile with -fPIC CConverters.o: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libR.so] Error 1 I don't really understand the error message. Is there anything I can change to compile properly so that I can install rpy2? Please help. Thanks in advance! :) Regards, Padma __ 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. Note the last sentence above and try again, i.e. use a recent version of R and report the version number as well as the OS and the compilers in use. Best, Uwe Ligges __ 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] Questions about ggplot2
Hi I have two questions about using ggplot2. First, I have multiple columns of data that I would like to combine into one histogram where each column of data would correspond to one bar in the histogram. Each column has 0 or 1s and I want my bars in the histogram to correspond to the sum of the 1s in each column. Does that make sense? Second, is there a way to completely turn off the legend? Thanks! Chris PS - Please cc me on the email as I'm a digest subscriber. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to make monthly time series out of daily
Reto Baumgartner reto.baumg at gmail.com writes:
I am using the Rmetrics package and would like to convert a daily
price time serie into a monthly one. In SPlus I could use:
aggregateSeries(timeSerie, by=months,FUN=first).
I wrote now my own function. But is there an easier way?
#--
## function to make monthly time series (keep last row of each month)
#
makeMonthly = function(ts){
# ts must be a timeSeries (see: http://www.rmetrics.org/Rmetrics.R;)
ts=sort(ts) #sort
dts=rownames(ts)#get dates
months=substr(dts,6,7) #read out month
len=length(months) #get length of vector
b=months[1:(len-1)]!=months[2:len] #see where month is changing
b=c(b,TRUE) #the last row we always take
mts=ts[b,] #make monthly data and return result
}
#--
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Re: [R] read table for Fisher Exact
How much would that differ? And how should I build my table if I want to do a Pearson Chi Sqaure? - Original Message - From: Frank E Harrell Jr [via R] ml-node+2197479-2091597772-257...@n4.nabble.com Date: Thursday, May 13, 2010 2:36 pm Subject: Re: read table for Fisher Exact To: visser s.m@amc.uva.nl On 05/12/2010 03:31 PM, visser wrote: i have 2 groups i want to compare: group A and group B each group contains let's say 20 patients i want to perform a Fisher Exact test on genotype distribution so, see if there is a sign diff in genotpe frequency/distribution (#AA, #AB, #BB) between group A and B not for 1, but for 1000 different genes my question: how should i build my table so i can do: test- read.table(table1.txt) fisher.test(test) i know a lot is still missing in the syntax, but i do not know what. any help would be soo much appreciated!! Note that in this case, Fisher's exact test has a good chance of being less accurate than an approximate Pearson chi-square test. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ View message @ http://r.789695.n4.nabble.com/read-table-for-Fisher-Exact-tp2196762p2197479.html To unsubscribe from read table for Fisher Exact, click (link removed) = -- View this message in context: http://r.789695.n4.nabble.com/read-table-for-Fisher-Exact-tp2196762p2197720.html Sent from the R help mailing list archive at Nabble.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 with interpolation
Hi, I have a two Colum matrix ( I named it holder) as shown bellow. It seems to be three columns, but the first column contains the row names. I am trying to fill all NAs by linear interpolation the known values in the matrix. I tried using the interpNA function, but I get an error message: interpNA(holder, method = linear) Error in approx(idx, x[idx], 1:n, method = method, f = f) : need at least two non-NA values to interpolate In addition: Warning message: In xy.coords(x, y) : NAs introduced by coercion I was wondering if some one could recommend another function to get the interpolated values? Thanks, Jorge 20100319 2010-03-19 1626 20100320 2010-03-20NA 20100321 2010-03-21NA 20100322 2010-03-22NA 20100323 2010-03-23NA 20100324 2010-03-24NA 20100325 2010-03-25NA 20100326 2010-03-26 1638 20100327 2010-03-27NA 20100328 2010-03-28NA 20100329 2010-03-29NA 20100330 2010-03-30NA 20100331 2010-03-31NA 20100401 2010-04-01NA 20100402 2010-04-02 1669 20100403 2010-04-03NA 20100404 2010-04-04NA 20100405 2010-04-05NA 20100406 2010-04-06NA 20100407 2010-04-07NA 20100408 2010-04-08NA 20100409 2010-04-09 1756 20100410 2010-04-10NA 20100411 2010-04-11NA 20100412 2010-04-12NA 20100413 2010-04-13NA 20100414 2010-04-14NA 20100415 2010-04-15NA 20100416 2010-04-16 1829 20100417 2010-04-17NA 20100418 2010-04-18NA 20100419 2010-04-19NA 20100420 2010-04-20NA 20100421 2010-04-21NA 20100422 2010-04-22NA 20100423 2010-04-23 1912 20100424 2010-04-24NA 20100425 2010-04-25NA 20100426 2010-04-26NA 20100427 2010-04-27NA 20100428 2010-04-28NA 20100429 2010-04-29NA 20100430 2010-04-30 1995 [[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] a question about latex in Hmisc and .dvi file
Here is the full repair for the latex functions in Hmisc to make pdflatex
work in Windows.
This version is still slightly awkward. I hope that Charles and Frank will
smooth it out
and put it in their next release.
I added two new options() and revised show.dvi so it will use them.
Rich
library(Hmisc)
show.dvi -
function (object, width = 5.5, height = 7)
{
viewer - optionsCmds(xdvi)
cmd - if (viewer == yap) {
paste(viewer, object$file)
}
else if (viewer == kdvi) {
paste(viewer, object$file)
}
else if (viewer == xdvi) {
paste(viewer, -paper , width, x, height, in -s 0 ,
object$file, sep = )
}
else if (basename(viewer) == AcroRd32) {
object$file - sub(dvi, pdf, object$file)
paste(viewer, object$file)
}
else {
paste(viewer, object$file)
}
system(cmd, intern = TRUE, wait = TRUE)
invisible(NULL)
}
environment(show.dvi) - environment(print.dvi)
options(latexcmd=pdflatex,
xdvicmd=c:/Progra~1/Adobe/Reader~1.0/Reader/AcroRd32)
x - matrix(1:24, 6,4, dimnames=list(letters[1:6], LETTERS[1:4]))
show.dvi(dvi(x.tex - latex(x)))
paste(getwd(), x.tex$file, sep=/) ## location of the table itself
## The tex file with headers and the pdf file are in the directory
## given in the printed output from dvi().
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] Multiple plots; single x(y) labels
Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) also, how can remove x-tick lables using plot()? Thanks, Xin [[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] Help with interpolation
On Wed, May 12, 2010 at 5:14 PM, Jorge Nieves jorge.nie...@moorecap.com wrote: I have a two Colum matrix ( I named it holder) as shown bellow. It seems to be three columns, but the first column contains the row names. You can't have a matrix whose columns are different classes. I am trying to fill all NAs by linear interpolation the known values in the matrix. I tried using the interpNA function, but I get an error message: interpNA(holder, method = linear) Error in approx(idx, x[idx], 1:n, method = method, f = f) : need at least two non-NA values to interpolate In addition: Warning message: In xy.coords(x, y) : NAs introduced by coercion I was wondering if some one could recommend another function to get the interpolated values? Try this: Lines - 20100319 2010-03-19 1626 20100320 2010-03-20NA 20100321 2010-03-21NA 20100322 2010-03-22NA 20100323 2010-03-23NA 20100324 2010-03-24NA 20100325 2010-03-25NA 20100326 2010-03-26 1638 20100327 2010-03-27NA 20100328 2010-03-28NA 20100329 2010-03-29NA 20100330 2010-03-30NA 20100331 2010-03-31NA 20100401 2010-04-01NA 20100402 2010-04-02 1669 20100403 2010-04-03NA 20100404 2010-04-04NA 20100405 2010-04-05NA 20100406 2010-04-06NA 20100407 2010-04-07NA 20100408 2010-04-08NA 20100409 2010-04-09 1756 20100410 2010-04-10NA 20100411 2010-04-11NA 20100412 2010-04-12NA 20100413 2010-04-13NA 20100414 2010-04-14NA 20100415 2010-04-15NA 20100416 2010-04-16 1829 20100417 2010-04-17NA 20100418 2010-04-18NA 20100419 2010-04-19NA 20100420 2010-04-20NA 20100421 2010-04-21NA 20100422 2010-04-22NA 20100423 2010-04-23 1912 20100424 2010-04-24NA 20100425 2010-04-25NA 20100426 2010-04-26NA 20100427 2010-04-27NA 20100428 2010-04-28NA 20100429 2010-04-29NA 20100430 2010-04-30 1995 library(zoo) z - read.zoo(textConnection(Lines), index = 2)[,2] na.approx(z) Result is: na.approx(z) 2010-03-19 2010-03-20 2010-03-21 2010-03-22 2010-03-23 2010-03-24 2010-03-25 1626.000 1627.714 1629.429 1631.143 1632.857 1634.571 1636.286 2010-03-26 2010-03-27 2010-03-28 2010-03-29 2010-03-30 2010-03-31 2010-04-01 1638.000 1642.429 1646.857 1651.286 1655.714 1660.143 1664.571 2010-04-02 2010-04-03 2010-04-04 2010-04-05 2010-04-06 2010-04-07 2010-04-08 1669.000 1681.429 1693.857 1706.286 1718.714 1731.143 1743.571 2010-04-09 2010-04-10 2010-04-11 2010-04-12 2010-04-13 2010-04-14 2010-04-15 1756.000 1766.429 1776.857 1787.286 1797.714 1808.143 1818.571 2010-04-16 2010-04-17 2010-04-18 2010-04-19 2010-04-20 2010-04-21 2010-04-22 1829.000 1840.857 1852.714 1864.571 1876.429 1888.286 1900.143 2010-04-23 2010-04-24 2010-04-25 2010-04-26 2010-04-27 2010-04-28 2010-04-29 1912.000 1923.857 1935.714 1947.571 1959.429 1971.286 1983.143 2010-04-30 1995.000 __ 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] Whiskers on the default boxplot {graphics}
David,
try this:
fivenum(1:101)
quantile(1:101, c(1,3)/4, type=5)
-Peter
On 2010-05-13 8:55, David Winsemius wrote:
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in 'boxplot'
help file is a little bit confusing by using the words interquartile
range. I think it should be changed to the length of the box to be
exact and consistent with those in the help file for boxplot.stats.
The issue is probably that there are multiple ways (9 to be exact) of
defining quantiles in R. See 'type= ' arguement for ?quantile. The
quantile function uses type=7 by default which matches the quantile
definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different type=
arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or 'box
height' depending how you display the boxplot), but aren't the hinges
simply Q1 and Q3 defined by one of the possible quartile definitions
(as Peter points out the one used by fivenum)? The box height does not
necesarily match the distance produced by IQR() which also seems to
use the equivalent of quantile(..., type=7), but it is still an IQR,
is it not?
Quantiles apparantly can be defined in more than one acceptable way
(sort of like dealing with ties in rank statistics). The OP seemed to
want an exact explanation of the wiskers, and I think Peter has
pointed us at the definition of quartiles used by fivenum, as opposed
to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4] with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove that
to myself from mathematical arguments. since I do not quite understand
the formalism in the quantile page. If the match is not exact, this
would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
Peter Ehlers
University of Calgary
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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] Path to R script
At 13:19 Uhr -0700 12.05.2010, Shi, Tao wrote: Don't quite understand your question, but it looks like a more IT issue to me. I guess you store your R scripts in a central location (e.g. a server) and everybody call them from their own workstation, right? Thank you, but this would be an easy solution. The problem is that the R script and data tables are stored on the individual computers (and therefore on different places depending of the users' preferences and of course the operating system). If it were possible to locate the files relative to the script we could write modular scripts that would run on any machine without modifications. Thanks again, J. W. D. -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Dr. Johannes W. Dietrich, M.D. -- Laboratory XU 44, Endocrine Research -- Medical Hospital I, Bergmannsheil University Hospitals -- Ruhr University of Bochum -- Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, NRW, Germany -- Phone: +49:234:302-6400, Fax: +49:234:302-6403 -- eMail: j.w.dietr...@medical-cybernetics.de -- WWW: http://medical-cybernetics.de -- WWW: http://www.bergmannsheil.de -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with interpolation
... and what package is interpNA in, pray tell? (Such information is requested in the posting guide). Base R does it with a bit of fiddling: ?approx But please read the Help carefully. Here is a simple example of how it is used: x - 1:5 y - c(2,rep(NA,3),7) approx(x,y, xout =1:5)## Note the xout argument $x [1] 1 2 3 4 5 $y [1] 2.00 3.25 4.50 5.75 7.00 So you'll have to convert your dates into a suitable numeric series using whatever date functions you need (e.g. as.Date() ). There are, no doubt, several packages (perhaps zoo) that can do it at one gulp. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jorge Nieves Sent: Thursday, May 13, 2010 8:52 AM To: R-help@r-project.org Subject: [R] Help with interpolation Hi, I have a two Colum matrix ( I named it holder) as shown bellow. It seems to be three columns, but the first column contains the row names. I am trying to fill all NAs by linear interpolation the known values in the matrix. I tried using the interpNA function, but I get an error message: interpNA(holder, method = linear) Error in approx(idx, x[idx], 1:n, method = method, f = f) : need at least two non-NA values to interpolate In addition: Warning message: In xy.coords(x, y) : NAs introduced by coercion I was wondering if some one could recommend another function to get the interpolated values? Thanks, Jorge 20100319 2010-03-19 1626 20100320 2010-03-20NA 20100321 2010-03-21NA 20100322 2010-03-22NA 20100323 2010-03-23NA 20100324 2010-03-24NA 20100325 2010-03-25NA 20100326 2010-03-26 1638 20100327 2010-03-27NA 20100328 2010-03-28NA 20100329 2010-03-29NA 20100330 2010-03-30NA 20100331 2010-03-31NA 20100401 2010-04-01NA 20100402 2010-04-02 1669 20100403 2010-04-03NA 20100404 2010-04-04NA 20100405 2010-04-05NA 20100406 2010-04-06NA 20100407 2010-04-07NA 20100408 2010-04-08NA 20100409 2010-04-09 1756 20100410 2010-04-10NA 20100411 2010-04-11NA 20100412 2010-04-12NA 20100413 2010-04-13NA 20100414 2010-04-14NA 20100415 2010-04-15NA 20100416 2010-04-16 1829 20100417 2010-04-17NA 20100418 2010-04-18NA 20100419 2010-04-19NA 20100420 2010-04-20NA 20100421 2010-04-21NA 20100422 2010-04-22NA 20100423 2010-04-23 1912 20100424 2010-04-24NA 20100425 2010-04-25NA 20100426 2010-04-26NA 20100427 2010-04-27NA 20100428 2010-04-28NA 20100429 2010-04-29NA 20100430 2010-04-30 1995 [[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] Whiskers on the default boxplot {graphics}
And try this (which seems to leave us with type=2) and is listed in
?quantile as Discontinuous sample quantile types 1, 2, and 3
quantile(1:101, c(1,3)/4, type=2)
25% 75%
26 76
David,
try this:
fivenum(1:101)
quantile(1:101, c(1,3)/4, type=5)
-Peter
On 2010-05-13 8:55, David Winsemius wrote:
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in 'boxplot'
help file is a little bit confusing by using the words interquartile
range. I think it should be changed to the length of the box to be
exact and consistent with those in the help file for boxplot.stats.
The issue is probably that there are multiple ways (9 to be exact) of
defining quantiles in R. See 'type= ' arguement for ?quantile. The
quantile function uses type=7 by default which matches the quantile
definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different type=
arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or 'box
height' depending how you display the boxplot), but aren't the hinges
simply Q1 and Q3 defined by one of the possible quartile definitions
(as Peter points out the one used by fivenum)? The box height does not
necesarily match the distance produced by IQR() which also seems to
use the equivalent of quantile(..., type=7), but it is still an IQR,
is it not?
Quantiles apparantly can be defined in more than one acceptable way
(sort of like dealing with ties in rank statistics). The OP seemed to
want an exact explanation of the wiskers, and I think Peter has
pointed us at the definition of quartiles used by fivenum, as opposed
to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4] with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove that
to myself from mathematical arguments. since I do not quite understand
the formalism in the quantile page. If the match is not exact, this
would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
Peter Ehlers
University of Calgary
__
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] Path to R script
At 19:29 Uhr -0400 12.05.2010, Gabor Grothendieck wrote: If you are running the file via source(myfile.R) then just put this in the file: this.dir - dirname(sys.frame(1)$ofile) This is a bit fragile since changes to the internals of source could break it but it does currently work. Great, this is the solution. It works if the script has been saved before running. Thank you, J. W. D. -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Dr. Johannes W. Dietrich, M.D. -- Laboratory XU 44, Endocrine Research -- Medical Hospital I, Bergmannsheil University Hospitals -- Ruhr University of Bochum -- Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, NRW, Germany -- Phone: +49:234:302-6400, Fax: +49:234:302-6403 -- eMail: j.w.dietr...@medical-cybernetics.de -- WWW: http://medical-cybernetics.de -- WWW: http://www.bergmannsheil.de -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple plots; single x(y) labels
?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) opar - par(mfcol=c(2,2)) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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] Whiskers on the default boxplot {graphics}
On May 13, 2010, at 12:18 PM, Robert Baer wrote:
And try this (which seems to leave us with type=2) and is listed in ?
quantile as Discontinuous sample quantile types 1, 2, and 3
quantile(1:101, c(1,3)/4, type=2)
25% 75%
26 76
I think Peter may be right,. If I do it with the rnorm function I
repeatedly get the same result for fivenum[2] and the type 2 first
quartile. I did not test those types because they were designed for
discrete values variables, but I suppose everything is really discrete
on computers, eh?
fivenum(x - rnorm(101) )
[1] -2.6224338 -0.9682586 -0.1897377 0.5999332 2.5409711
quantile(x, c(1,3)/4, type=2)
25%75%
-0.9682586 0.5999332
fivenum(x - rnorm(101) )
[1] -3.8251928 -0.6495966 0.1816233 0.7101774 2.3789054
quantile(x, c(1,3)/4, type=2)
25%75%
-0.6495966 0.7101774
--
David.
David,
try this:
fivenum(1:101)
quantile(1:101, c(1,3)/4, type=5)
-Peter
On 2010-05-13 8:55, David Winsemius wrote:
On May 13, 2010, at 10:25 AM, Robert Baer wrote:
Hi Peter,
You're absolutely correct! The description for 'range' in
'boxplot'
help file is a little bit confusing by using the words
interquartile
range. I think it should be changed to the length of the box
to be
exact and consistent with those in the help file for
boxplot.stats.
The issue is probably that there are multiple ways (9 to be
exact) of
defining quantiles in R. See 'type= ' arguement for ?quantile. The
quantile function uses type=7 by default which matches the quantile
definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different
type=
arguement (maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable to talk about 'length of box' (or
'box
height' depending how you display the boxplot), but aren't the
hinges
simply Q1 and Q3 defined by one of the possible quartile
definitions
(as Peter points out the one used by fivenum)? The box height
does not
necesarily match the distance produced by IQR() which also seems to
use the equivalent of quantile(..., type=7), but it is still an
IQR,
is it not?
Quantiles apparantly can be defined in more than one acceptable
way
(sort of like dealing with ties in rank statistics). The OP
seemed to
want an exact explanation of the wiskers, and I think Peter has
pointed us at the definition of quartiles used by fivenum, as
opposed
to the default used with quantile(..., type=7).
Yes, and experimentation leads me to the conclusion that the only
possible candidate for matching up the results of fivenum[c(2,4]
with
quantile(y, c(1,3)/4, type=i) is for type=5. I'm not able to prove
that
to myself from mathematical arguments. since I do not quite
understand
the formalism in the quantile page. If the match is not exact, this
would be a tenth definition of IQR.
set.seed(123)
y - rexp(300, .02)
fivenum(y)
[1] 0.2183685 15.8740466 42.1147820 74.0362517 360.5503788
for (i in 4:9) {print(quantile(y, c(1,3)/4, type=i) ) }
25% 75%
15.82506 73.93080
25% 75%
15.87405 74.03625
25% 75%
15.84955 74.08898
25% 75%
15.89854 73.98352
25% 75%
15.86588 74.05383
25% 75%
15.86792 74.04943
--
Peter Ehlers
University of Calgary
David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] a question about latex in Hmisc and .dvi file
Looks good. I came up with something on my own which was basically to
re-write print.latex. I call pdflatex a few times because with the
longtable package, sometimes things don't line up right until you run
pdflatex multiple times. I think mine is less flexible though, and I
like your solution better.
The only thing I can see to make your solution more flexible is to note
that there is already options(pdfviewer) in R, so maybe you could just
use whatever that is for options(xdvicmd) and then in show.dvi, you
can test
if(viewer == options(pdfviewer)) {
...
}
--Erik
RICHARD M. HEIBERGER wrote:
Here is the full repair for the latex functions in Hmisc to make
pdflatex work in Windows.
This version is still slightly awkward. I hope that Charles and Frank
will smooth it out
and put it in their next release.
I added two new options() and revised show.dvi so it will use them.
Rich
library(Hmisc)
show.dvi -
function (object, width = 5.5, height = 7)
{
viewer - optionsCmds(xdvi)
cmd - if (viewer == yap) {
paste(viewer, object$file)
}
else if (viewer == kdvi) {
paste(viewer, object$file)
}
else if (viewer == xdvi) {
paste(viewer, -paper , width, x, height, in -s 0 ,
object$file, sep = )
}
else if (basename(viewer) == AcroRd32) {
object$file - sub(dvi, pdf, object$file)
paste(viewer, object$file)
}
else {
paste(viewer, object$file)
}
system(cmd, intern = TRUE, wait = TRUE)
invisible(NULL)
}
environment(show.dvi) - environment(print.dvi)
options(latexcmd=pdflatex,
xdvicmd=c:/Progra~1/Adobe/Reader~1.0/Reader/AcroRd32)
x - matrix(1:24, 6,4, dimnames=list(letters[1:6], LETTERS[1:4]))
show.dvi(dvi(x.tex - latex(x)))
paste(getwd(), x.tex$file, sep=/) ## location of the table itself
## The tex file with headers and the pdf file are in the directory
## given in the printed output from dvi().
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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] Multiple plots; single x(y) labels
On May 13, 2010, at 12:35 PM, David Winsemius wrote: ?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. I'm still not sure what a single x-label might mean for such disparate series. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) A minor refinement: opar - par(mfcol=c(2,2)) lapply(randlist, plot, ylim=c(Reduce(min, randlist), Reduce(max, randlist)), type = s, xaxt=n, main = , ylab=, xlab=) par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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. David Winsemius, MD 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.
[R] Help with reading information of summary-Object
Hi, I am quite new to R - but quite expierience in programming. Nonetheless I have some problemes in accessing information of the summary object. Here is what I do: model - lm ( y ~ myVariable ) summary(model) gives me an object which has a lot of information about the regression. Now I'd like to access programmatically the level of significance which is marked with *** and (**) according to its confidence-interval. As I can access all information of the coefficients via summary(model)$coeff[myVariable] I am now struggling to access the information of the level of significance. Does anyone has an idea how I could achieve that? Or where I could find a similar example? Thanks in advance for any hint, Tino -- Tino Schöllhorn Wittelsbachstr. 7 67061 Ludwigshafen Tel: 0621-4255570 E-Mail: t.schoellh...@gmx.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple plots; single x(y) labels
Hi David, Thanks for your reply. By single x and y-labels I meant something like this: http://zoonek.free.fr/blosxom//R/2006-08-10_lattice_xyplot_quakes.png which lattice gives by default. The code you sent doesn't seem to solve the problem, I'm sorry if I havent' explained it clearly before. Any comments? Thanks, Xin On Thu, May 13, 2010 at 12:51 PM, David Winsemius dwinsem...@comcast.netwrote: On May 13, 2010, at 12:35 PM, David Winsemius wrote: ?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. I'm still not sure what a single x-label might mean for such disparate series. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) A minor refinement: opar - par(mfcol=c(2,2)) lapply(randlist, plot, ylim=c(Reduce(min, randlist), Reduce(max, randlist)), type = s, xaxt=n, main = , ylab=, xlab=) par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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. David Winsemius, MD West Hartford, CT [[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] a question about latex in Hmisc and .dvi file
On Thu, May 13, 2010 at 12:46 PM, Erik Iverson er...@ccbr.umn.edu wrote: Looks good. Thank you. I came up with something on my own which was basically to re-write print.latex. I call pdflatex a few times because with the longtable package, sometimes things don't line up right until you run pdflatex multiple times. I think mine is less flexible though, and I like your solution better. The only thing I can see to make your solution more flexible is to note that there is already options(pdfviewer) in R, so maybe you could just use whatever that is for options(xdvicmd) and then in show.dvi, you can test I set the value of xdvicmd correctly for the pdf viewer on my machine. It would be possible to use options()$pdfviewer instead. That is part of the smoothing that I have implicitly asked Charles and Frank to do. Also, to make things more automatic. Notice that I didn't quite get my function into the Hmisc environment and that is why you need the awkward phrase show.dvi(dvi(x.tex - latex(x))) instead of the smooth phrase latex(x) Rich [[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] pnmath on windows
Hello All, I'd like to enable threaded computing on my system (windows 7 pro x64) if possible. pnmath seems to be the most accepted solution out there for the time being, but it requires compiling. Are there binaries for windows available that don't require manual compiliation? If not, does anyone know what the bottleneck there is? That is, what keeps me from compiling it myself and handing it to a friend with another windows system? Thanks, Allie -- Alexander Shenkin PhD Candidate School of Natural Resources and Environment University of Florida http://snre.ufl.edu/people/students.asp __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with reading information of summary-Object
Hello, Tino Schöllhorn wrote: Hi, I am quite new to R - but quite expierience in programming. Welcome to R! It's easiest if you give reproducible examples so we can help you. You can include code to create objects, or use the ?dput function. Nonetheles I have some problemes in accessing information of the summary object. Here is what I do: model - lm ( y ~ myVariable ) summary(model) gives me an object which has a lot of information about the regression. Now I'd like to access programmatically the level of significance which is marked with *** and (**) according to its confidence-interval. As I can access all information of the coefficients via summary(model)$coeff[myVariable] Use the ?coef function for this. I am now struggling to access the information of the level of significance. Does anyone has an idea how I could achieve that? Or where I could find a similar example? In this case, you need to know one of the most important R functions, str, which tells you the structure of any object. This will let you know what is available in your objects. Assign your summary object to a variable, say summary.model, and then do: str(coef(summary(model))) You can then get at the p.values through the usual indexing techniques, by name or by row, column numbering. From the statistical point of view, we're not sure what you're working on, but there are many considerations to take into account if you're using p-values from regression fits as some sort of screening tool. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple plots; single x(y) labels
On May 13, 2010, at 12:59 PM, Xin Ge wrote: Hi David, Thanks for your reply. By single x and y-labels I meant something like this: http://zoonek.free.fr/blosxom//R/2006-08-10_lattice_xyplot_quakes.png which lattice gives by default. The code you sent doesn't seem to solve the problem, I'm sorry if I havent' explained it clearly before. Any comments? Yes. If you want lattice output, then don't use base graphics functions -- David. Thanks, Xin On Thu, May 13, 2010 at 12:51 PM, David Winsemius dwinsem...@comcast.net wrote: On May 13, 2010, at 12:35 PM, David Winsemius wrote: ?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. I'm still not sure what a single x-label might mean for such disparate series. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) A minor refinement: opar - par(mfcol=c(2,2)) lapply(randlist, plot, ylim=c(Reduce(min, randlist), Reduce(max, randlist)), type = s, xaxt=n, main = , ylab=, xlab=) par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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. David Winsemius, MD West Hartford, CT David Winsemius, MD 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] a question about latex in Hmisc and .dvi file
snip Notice that I didn't quite get my function into the Hmisc environment and that is why you need the awkward phrase show.dvi(dvi(x.tex - latex(x))) instead of the smooth phrase latex(x) Somehow with my own data and not using the awkward bit, it worked on my Linux machine? At least I thought it did, since I believe show.dvi is an exported function, can't you just overwrite it in your global environment and anything that calls it will use your copy? I'll have to look into how I got your code working on my system, because I know I didn't use that trick! --Erik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with reading information of summary-Object
Tino - When you call summary for an lm object, the function that actually gets called is summary.lm. This function has a help page, and, if you type ?summary.lm and look at the Value section, you'll see the following: coefficients: a p x 4 matrix with columns for the estimated coefficient, its standard error, t-statistic and corresponding (two-sided) p-value. Aliased coefficients are omitted. Here's an example of how you could extract the probabilities: set.seed(12) df = data.frame(y=rnorm(100),x1=rnorm(100),x2=rnorm(100)) df.lm = lm(y~x1+x2,df) sdf.lm = summary(df.lm) sdf.lm$coefficients[,4] (Intercept) x1 x2 0.7445605 0.8081874 0.2535098 or sdf.lm$coefficients[,Pr(|t|)] (Intercept) x1 x2 0.7445605 0.8081874 0.2535098 Hope this helps - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Thu, 13 May 2010, Tino Schöllhorn wrote: Hi, I am quite new to R - but quite expierience in programming. Nonetheless I have some problemes in accessing information of the summary object. Here is what I do: model - lm ( y ~ myVariable ) summary(model) gives me an object which has a lot of information about the regression. Now I'd like to access programmatically the level of significance which is marked with *** and (**) according to its confidence-interval. As I can access all information of the coefficients via summary(model)$coeff[myVariable] I am now struggling to access the information of the level of significance. Does anyone has an idea how I could achieve that? Or where I could find a similar example? Thanks in advance for any hint, Tino -- Tino Schöllhorn Wittelsbachstr. 7 67061 Ludwigshafen Tel: 0621-4255570 E-Mail: t.schoellh...@gmx.de __ 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] a question about latex in Hmisc and .dvi file
At least I thought it did, since I believe show.dvi is an exported function, can't you just overwrite it in your global environment and anything that calls it will use your copy? I'll have to look into how I got your code working on my system, because I know I didn't use that trick! I thought so, but it didn't work that way on my machine. Usually when functions inside a namespace call each other, any replacement must also be in the namespace. When I do this type of thing, I usually need to rebuild a local copy of the package to get into the namespace. Rich [[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] Multiple plots; single x(y) labels
Hi David (and Others), I think I messed it up. Lets start afresh, I do not want to use lattice for this. I'm using multiple plot commands and then eventually would like to get a *combine* x-label and y-label for this plot. Like for example, the following plot has a combine x-label (Height) and one y-label (Weight) http://support.sas.com/documentation/cdl/en/grstateditug/61951/HTML/default/images/multi-panel-data.gif Is it possible to get a graph similar to above one using base R only ? # R code (this is just a sample data and not actual data I'm using) par(mfcol=c(2,2)) plot(1:3, 4:6, type = s, main = , ylab=, xlab=) plot(2:5, 5:8, type = s, main = , ylab=, xlab=) plot(3:6, 6:9, type = s, main = , ylab=, xlab=) plot(4:7, 6:9, type = s, main = , ylab=, xlab=) Thanks in advance, Xin On Thu, May 13, 2010 at 1:10 PM, David Winsemius dwinsem...@comcast.netwrote: On May 13, 2010, at 12:59 PM, Xin Ge wrote: Hi David, Thanks for your reply. By single x and y-labels I meant something like this: http://zoonek.free.fr/blosxom//R/2006-08-10_lattice_xyplot_quakes.png which lattice gives by default. The code you sent doesn't seem to solve the problem, I'm sorry if I havent' explained it clearly before. Any comments? Yes. If you want lattice output, then don't use base graphics functions -- David. Thanks, Xin On Thu, May 13, 2010 at 12:51 PM, David Winsemius dwinsem...@comcast.net wrote: On May 13, 2010, at 12:35 PM, David Winsemius wrote: ?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. I'm still not sure what a single x-label might mean for such disparate series. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) A minor refinement: opar - par(mfcol=c(2,2)) lapply(randlist, plot, ylim=c(Reduce(min, randlist), Reduce(max, randlist)), type = s, xaxt=n, main = , ylab=, xlab=) par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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. David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT [[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] Whiskers on the default boxplot {graphics}
On Thu, May 13, 2010 at 7:55 AM, David Winsemius dwinsem...@comcast.net wrote:
Yes, and experimentation leads me to the conclusion that the only possible
candidate for matching up the results of fivenum[c(2,4] with quantile(y,
c(1,3)/4, type=i) is for type=5. I'm not able to prove that to myself from
mathematical arguments. since I do not quite understand the formalism in the
quantile page. If the match is not exact, this would be a tenth definition
of IQR.
David,
Here is some sample data, and the most parsimonious code I could come
up with for how quantile() computes the quartiles when using type=5.
The code for fivenum() seems simple enough, but I am not quite able to
make enough sense of the code for type=5 from quantile() to say
confidently why they are different.
I am open to the possibility that my attempts to extract relevant code
from quantile were flawed, but my tentative conclusion is that
quantile(x, type=5) != fivenum(x).
##
x - c(0.643796386452606, -0.605277531056206, -0.339239367816402,
1.12408365699422, 0.615753476531243, -1.10545696568758,
0.666533406841698, 1.42794492209271, 0.624752921945051,
2.02317205214712, -0.365586657432646, 0.821742701084307,
-0.874753498321076, -0.0298783402061118, 1.18037670706428,
-0.178274986836195, 0.308703365439049, 0.619700844646392,
0.54977981430092, -1.82161514610448, -1.28413556650749,
-0.0443852992196351, 0.704196760556652, -1.88596816676741,
-0.420811351737096)
oldx - x #this is just a backup because x will be transformed
##Start from quantile()
probs - c(0, 0.25, 0.5, 0.75, 1)
type - 5
n - length(x)
switch(type - 3, {
a - 0
b - 1
}, a - b - 0.5, a - b - 0, a - b - 1, a - b - 1/3, a - b - 3/8)
fuzz - 4 * .Machine$double.eps
nppm - a + probs * (n + 1 - a - b)
j - floor(nppm + fuzz)
h - nppm - j
h - ifelse(abs(h) fuzz, 0, h)
x - sort(x, partial = unique(c(1, j[j 0L j = n], (j + 1)[j 0L
j n], n)))
x - c(x[1L], x[1L], x, x[n], x[n])
qs - x[j + 2L]
qs[h == 1] - x[j + 3L][h == 1]
other - (h 0) (h 1)
if (any(other)) qs[other] - ((1 - h) * x[j + 2L] + h * x[j + 3L])[other]
##End from quantile
qs # from the calculations above
quantile(oldx, type=5) #this should match qs
fivenum(oldx) #the 25% does not match
everything else snipped
Josh
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Re: [R] Whiskers on the default boxplot {graphics}
I agree. I was convinced by Ehlers' example that type =2 was a better
match to fivenum's result
--
David..
On May 13, 2010, at 1:36 PM, Joshua Wiley wrote:
On Thu, May 13, 2010 at 7:55 AM, David Winsemius dwinsem...@comcast.net
wrote:
Yes, and experimentation leads me to the conclusion that the only
possible
candidate for matching up the results of fivenum[c(2,4] with
quantile(y,
c(1,3)/4, type=i) is for type=5. I'm not able to prove that to
myself from
mathematical arguments. since I do not quite understand the
formalism in the
quantile page. If the match is not exact, this would be a tenth
definition
of IQR.
David,
Here is some sample data, and the most parsimonious code I could come
up with for how quantile() computes the quartiles when using type=5.
The code for fivenum() seems simple enough, but I am not quite able to
make enough sense of the code for type=5 from quantile() to say
confidently why they are different.
I am open to the possibility that my attempts to extract relevant code
from quantile were flawed, but my tentative conclusion is that
quantile(x, type=5) != fivenum(x).
##
x - c(0.643796386452606, -0.605277531056206, -0.339239367816402,
1.12408365699422, 0.615753476531243, -1.10545696568758,
0.666533406841698, 1.42794492209271, 0.624752921945051,
2.02317205214712, -0.365586657432646, 0.821742701084307,
-0.874753498321076, -0.0298783402061118, 1.18037670706428,
-0.178274986836195, 0.308703365439049, 0.619700844646392,
0.54977981430092, -1.82161514610448, -1.28413556650749,
-0.0443852992196351, 0.704196760556652, -1.88596816676741,
-0.420811351737096)
oldx - x #this is just a backup because x will be transformed
##Start from quantile()
probs - c(0, 0.25, 0.5, 0.75, 1)
type - 5
n - length(x)
switch(type - 3, {
a - 0
b - 1
}, a - b - 0.5, a - b - 0, a - b - 1, a - b - 1/3, a - b -
3/8)
fuzz - 4 * .Machine$double.eps
nppm - a + probs * (n + 1 - a - b)
j - floor(nppm + fuzz)
h - nppm - j
h - ifelse(abs(h) fuzz, 0, h)
x - sort(x, partial = unique(c(1, j[j 0L j = n], (j + 1)[j 0L
j n], n)))
x - c(x[1L], x[1L], x, x[n], x[n])
qs - x[j + 2L]
qs[h == 1] - x[j + 3L][h == 1]
other - (h 0) (h 1)
if (any(other)) qs[other] - ((1 - h) * x[j + 2L] + h * x[j + 3L])
[other]
##End from quantile
qs # from the calculations above
quantile(oldx, type=5) #this should match qs
fivenum(oldx) #the 25% does not match
everything else snipped
Josh
David Winsemius, MD
West Hartford, CT
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Re: [R] Multiple plots; single x(y) labels
Hello Xin, If you need to recreate plots from different systems you need full control over the graphics output. This is not always easy with traditional graphics, better have a look at the plotting functions from lattice (based on grid graphics system in R) or maybe ggplot2. http://www.google.de/search?hl=ensafe=offclient=firefox- ahs=VpIrls=com.ubuntu%3Aen- US%3Aofficialq=R+grid+graphics+aq=faqi=aql=oq=gs_rfai= On Thursday 13 May 2010 07:24:56 pm Xin Ge wrote: Hi David (and Others), I think I messed it up. Lets start afresh, I do not want to use lattice for this. I'm using multiple plot commands and then eventually would like to get a *combine* x-label and y-label for this plot. Like for example, the following plot has a combine x-label (Height) and one y-label (Weight) http://support.sas.com/documentation/cdl/en/grstateditug/61951/HTML/default /images/multi-panel-data.gif Is it possible to get a graph similar to above one using base R only ? # R code (this is just a sample data and not actual data I'm using) par(mfcol=c(2,2)) plot(1:3, 4:6, type = s, main = , ylab=, xlab=) plot(2:5, 5:8, type = s, main = , ylab=, xlab=) plot(3:6, 6:9, type = s, main = , ylab=, xlab=) plot(4:7, 6:9, type = s, main = , ylab=, xlab=) Thanks in advance, Xin On Thu, May 13, 2010 at 1:10 PM, David Winsemius dwinsem...@comcast.netwrote: On May 13, 2010, at 12:59 PM, Xin Ge wrote: Hi David, Thanks for your reply. By single x and y-labels I meant something like this: http://zoonek.free.fr/blosxom//R/2006-08-10_lattice_xyplot_quakes.png which lattice gives by default. The code you sent doesn't seem to solve the problem, I'm sorry if I havent' explained it clearly before. Any comments? Yes. If you want lattice output, then don't use base graphics functions -- David. Thanks, Xin On Thu, May 13, 2010 at 12:51 PM, David Winsemius dwinsem...@comcast.net wrote: On May 13, 2010, at 12:35 PM, David Winsemius wrote: ?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. I'm still not sure what a single x-label might mean for such disparate series. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) A minor refinement: opar - par(mfcol=c(2,2)) lapply(randlist, plot, ylim=c(Reduce(min, randlist), Reduce(max, randlist)), type = s, xaxt=n, main = , ylab=, xlab=) par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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. David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT [[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] Multiple plots; single x(y) labels
On May 13, 2010, at 1:24 PM, Xin Ge wrote: Hi David (and Others), I think I messed it up. Lets start afresh, I do not want to use lattice for this. I'm using multiple plot commands and then eventually would like to get a *combine* x-label and y-label for this plot. Like for example, the following plot has a combine x-label (Height) and one y-label (Weight) http://support.sas.com/documentation/cdl/en/grstateditug/61951/HTML/default/images/multi-panel-data.gif If you want to re-invent the wheel using only hammer and chisel, then I suggest the place to start would be examining the code from pairs.default(). It's not even hidden so just type: pairs.default Is it possible to get a graph similar to above one using base R only ? # R code (this is just a sample data and not actual data I'm using) par(mfcol=c(2,2)) plot(1:3, 4:6, type = s, main = , ylab=, xlab=) plot(2:5, 5:8, type = s, main = , ylab=, xlab=) plot(3:6, 6:9, type = s, main = , ylab=, xlab=) plot(4:7, 6:9, type = s, main = , ylab=, xlab=) Thanks in advance, Xin On Thu, May 13, 2010 at 1:10 PM, David Winsemius dwinsem...@comcast.net wrote: On May 13, 2010, at 12:59 PM, Xin Ge wrote: Hi David, Thanks for your reply. By single x and y-labels I meant something like this: http://zoonek.free.fr/blosxom//R/2006-08-10_lattice_xyplot_quakes.png which lattice gives by default. The code you sent doesn't seem to solve the problem, I'm sorry if I havent' explained it clearly before. Any comments? Yes. If you want lattice output, then don't use base graphics functions -- David. Thanks, Xin On Thu, May 13, 2010 at 12:51 PM, David Winsemius dwinsem...@comcast.net wrote: On May 13, 2010, at 12:35 PM, David Winsemius wrote: ?plot # ylim and you need to have the data in a form (before plotting) where you can determine the shared max and min for the y limits On May 13, 2010, at 12:04 PM, Xin Ge wrote: Hi All, Can anyone please help me with getting a single x and y-axis label while plotting muliple plots. I'm still not sure what a single x-label might mean for such disparate series. Here is the code: par(mfcol=c(2,2)) plot(x - sort(rnorm(7)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(27)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(47)), type = s, main = , ylab=, xlab=) plot(x - sort(rnorm(67)), type = s, main = , ylab=, xlab=) randlist - list(); randlist[[1]] - sort(rnorm(7)) randlist[[2]] - sort(rnorm(27)) randlist[[3]] - sort(rnorm(47)) randlist[[4]] - sort(rnorm(67)) lapply(randlist, plot, ylim=c(min(rapply(randlist, min)), max(rapply(randlist,max))), type = s, xaxt=n, main = , ylab=, xlab=); par(opar) A minor refinement: opar - par(mfcol=c(2,2)) lapply(randlist, plot, ylim=c(Reduce(min, randlist), Reduce(max, randlist)), type = s, xaxt=n, main = , ylab=, xlab=) par(opar) also, how can remove x-tick lables using plot()? ?par # xaxt=n Thanks, Xin [[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. David Winsemius, MD 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. David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT [[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] aggregate.zoo
I have been using aggregate function to determine the annual minimum in
a daily time series. However, I was also hoping to determine the date of
occurrence without having to loop through each year to identify the date
of each minimum returned from aggregate(). Is there a more convenient
way of doing so?
Thanks in advance,
Dave
library(zoo)
n - 1000
dly - zoo( x = rnorm(n), order.by = seq.Date(as.Date('1970-01-01'),
by = 'day', length.out = n) )
year - as.numeric( format(index(dly), '%Y') )
annual.min - aggregate( dly, by = year, FUN = min )
[[alternative HTML version deleted]]
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Re: [R] Whiskers on the default boxplot {graphics}
Hi Robert,
Your points are well taken. However, I reserve mine, b/c I think without this
detailed discussion, an average R user would simply confused the interquartile
range said in boxplot help file with the results of IQR. Changing it to
length of box makes it more exact and consistent, as I stated earlier. With
all these being said, this is up to the R core team to decide.
...Tao
- Original Message
From: Robert Baer rb...@atsu.edu
To: Shi, Tao shida...@yahoo.com; Peter Ehlers ehl...@ucalgary.ca
Cc: R Project Help R-help@r-project.org
Sent: Thu, May 13, 2010 7:25:09 AM
Subject: Re: [R] Whiskers on the default boxplot {graphics}
Hi Peter,
You're absolutely correct! The description
for 'range' in 'boxplot' help file is a little bit confusing by using the
words
interquartile range. I think it should be changed to the length of the
box
to be exact and consistent with those in the help file for
boxplot.stats.
The issue is probably that there are multiple ways (9 to
be exact) of defining quantiles in R. See 'type= ' arguement for
?quantile. The quantile function uses type=7 by default which matches the
quantile definition used by S-Plus(?), but differs from that used by SPSS.
Doesn't fivenum essentially use the equivalent of a different type=
arguement
(maybe 2 or 5) in constructing the hinges?
It seems perfectly reasonable
to talk about 'length of box' (or 'box height' depending how you display the
boxplot), but aren't the hinges simply Q1 and Q3 defined by one of the
possible
quartile definitions (as Peter points out the one used by fivenum)? The
box height does not necesarily match the distance produced by IQR() which
also
seems to use the equivalent of quantile(..., type=7), but it is still an IQR,
is
it not?
Quantiles apparantly can be defined in more than one acceptable
way (sort of like dealing with ties in rank statistics). The OP seemed to
want an exact explanation of the wiskers, and I think Peter has pointed us
at
the definition of quartiles used by fivenum, as opposed to the default
used with quantile(..., type=7).
All that said, I'm not convinced that
it is wrong to speak of interquartile range in 'boxplot'
help.
Rob
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[R] More complex historgram
CID DISTRICTSCHOOL YRofSTUDY DATE.ENTRY SEX AGE EGGS.M EGGS.MIIEGGS.H POBADN0130 PO Badongo 0 18.1.08 2 11 0 -1 73 POBADN0117 PO Badongo 0 18.1.08 1 10 0 -1 59 POBADN0160 PO Badongo 0 18.1.08 1 11 0 -1 56 POBADN0112 PO Badongo 0 18.1.08 2 10 0 -1 47 POBADN0053 PO Badongo 0 18.1.08 1 8 0 -1 42 POBADN0141 PO Badongo 0 18.1.08 2 11 0 -1 36 POBADN0056 PO Badongo 0 18.1.08 1 8 0 -1 26 POBADN0127 PO Badongo 0 18.1.08 1 10 0 -1 26 POBADN0136 PO Badongo 0 18.1.08 2 11 0 -1 24 POBADN0153 PO Badongo 0 18.1.08 1 11 0 -1 22 POBADN0092 PO Badongo 0 18.1.08 1 9 0 -1 21 POBADN0087 PO Badongo 0 18.1.08 1 9 0 -1 17 POBADN0145 PO Badongo 0 18.1.08 1 11 0 -1 16 POBADN0107 PO Badongo 0 18.1.08 2 10 0 -1 15 POBADN0118 PO Badongo 0 18.1.08 1 10 0 -1 14 POBADN0150 PO Badongo 0 18.1.08 1 11 0 -1 14 POBADN0079 PO Badongo 0 18.1.08 2 9 0 -1 12 POBADN0121 PO Badongo 0 18.1.08 1 10 0 -1 11 POBADN0158 PO Badongo 0 18.1.08 1 11 0 -1 10 POBADN0148 PO Badongo 0 18.1.08 1 11 0 -1 7 POBADN0155 PO Badongo 0 18.1.08 1 11 0 -1 6 POBADN0063 PO Badongo 0 18.1.08 1 8 0 -1 4 POBADN0144 PO Badongo 0 18.1.08 2 11 0 -1 2 POBADN0002 PO Badongo 0 18.1.08 2 7 0 -1 0 POBADN0003 PO Badongo 0 18.1.08 2 7 0 -1 0 I need to find out how can I on R, plot the mean egg of EGGS.H according to the district, or sex. Also how to compare the eggs of females on year of study x (in t.test) Thank you! -- View this message in context: http://r.789695.n4.nabble.com/More-complex-historgram-tp2197823p2197823.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Comparing histograms?
Rhelpers: I'm curious what the appropriate analysis to use for testing the hypothesis that two histograms are statistically different from one another? Thanks! --j __ 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] Creating data frames in a loop
Thank yoy. this works. -- View this message in context: http://r.789695.n4.nabble.com/Creating-data-frames-in-a-loop-tp2195527p2197780.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Access to files downloaded
Dear All: I downloaded gee source code and now I am having problem accessing the file. download.packages(gee, type=source, destdir=~) --- Please select a CRAN mirror for use in this session --- trying URL ' http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/gee_4.13-14.tar.gz' Content type 'application/x-gzip' length 55417 bytes (54 Kb) opened URL downloaded 54 Kb [,1] [,2] [1,] gee ~/gee_4.13-14.tar.gz How to access the file and open it? Thanks much, Jeoy [[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] How to display data values for points in a plot?
Hello, I would like to know how to display values for points in a plot funtion. For example, plot( y=dat$a, x=dat$b, main=plot1, ylab=a, xlab=b, ylim=c(-10, 10), xlim=c(-10, 10), type = p, pch=17, col=vector of colors depending on the value of b, cex=1.5 ) How can I add a label to each of points here, if I have a list of values associated with the point. Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/How-to-display-data-values-for-points-in-a-plot-tp2197796p2197796.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] need help in igraph package of R
hi I am struck with a problem in igraph package of R. My problem is as follows I want to plot a power law fit for my data (in .net format --- pajek format) syntax for that in R is g - read.graph(filename.net, pajek) d - degree (g, mode=in) power.law.fit (d+1, 2) it gives me desired out put if my if input a single file but I want to use a variable file name ( such as name1, name2 ) so that I can read all my 100 files at a single stretch if I put this entire code in a loop. names = name1 name2 name3. while (i = 100) g - read.graph(names[i], pajek) d - degree (g, mode=in) power.law.fit (d+1, 2) i - i + 1 } but names[i] does n't seem to work. Is there any alternative ? I want to know how to use a variable file name in this syntax Any help is greately appreciated barabasi -- View this message in context: http://r.789695.n4.nabble.com/need-help-in-igraph-package-of-R-tp2197863p2197863.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] need help in igraph package of R
hi I am struck with a problem in igraph package of R. My problem is as follows I want to plot a power law fit for my data (in .net format --- pajek format) syntax for that in R is g - read.graph(filename.net, pajek) d - degree (g, mode=in) power.law.fit (d+1, 2) it gives me desired out put if my if input a single file but I want to use a variable file name ( such as name1, name2 ) so that I can read all my 100 files at a single stretch if I put this entire code in a loop. names = name1 name2 name3. while (i = 100) g - read.graph(names[i], pajek) d - degree (g, mode=in) power.law.fit (d+1, 2) i - i + 1 } but names[i] does n't seem to work. Is there any alternative ? I want to know how to use a variable file name in this syntax Any help is greately appreciated barabasi -- View this message in context: http://r.789695.n4.nabble.com/need-help-in-igraph-package-of-R-tp2197869p2197869.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] install.packages Error
Hi all! I am trying to install package - GenABEL in a Linux (RedHat) environment using R 2.6.2. The CRAN Mirror starts up, I select the site, but I end up with the following error: ** Warning: unable to access index for repository http://cran.stat.ucla.edu/src/contrib Warning messages: 1: In open.connection(con, r) : unable to resolve 'cran.r-project.org' 2: In install.packages(GenABEL, lib = /home/software) : package âGenABELâ is not available The code in command line: install.packages(GenABEL, lib=/home/software) ** I have tried to use other sites, but it comes back with the same error. I have checked the CRAN files and GenABEL is available for use This problem has just popped up in the last couple of days - I have previously been able to successfully install other packages Where am I going wrong? Any input will be much appreciated! Thanks! (Also, I have searched the forum for other similar posts - I have tried the suggested tips but they do not work) -- View this message in context: http://r.789695.n4.nabble.com/install-packages-Error-tp2201914p2201914.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.
