I guess I was wrong there. However it does seem that it will come down
to fontsize 9 without clipping (or if it does I find it hard to see).
-Original Message-
From: Mulholland, Tom
Sent: Friday, 11 July 2003 1:38 PM
To: David Forrest; [EMAIL PROTECTED]
Subject: RE: [R] postscript/eps
When compiling a package, is there any way of making the help files
(html or chtml) have separate sections for functions and data sets? When
looking at the help file for a package with a large number of help
pages, it would be nice to have the functions appear first and the data
sets appear second
HI
I'm a student in chemical engineering, and i have to implement an algoritm about FIVE
PARAMETERS INTERPOLATION for a calibration curve (dose, optical density)
y = a + (c - a) /(1+ e[-b(x-m])
where
x = ln(analyte dose + 1)
y = the optical absorbance data
a = the curves top asymptote
b = the
On 07/11/03 09:58, C.E.Marshall wrote:
I am running simulations calculating correlation coefficients from bivariate
data and I was wondering whether there is a way of exporting 1000 simulation
results from R to a text file or to another file for further manipulation. I
am having difficulty I
I assume you mean the following:
chemYield -
function(a, x)(a[1]+(a[3]-a[2])/(1+exp(-a[2]*(x-a[4]))
If you want to estimate parameters a[1:4] from data on pairs of (x,
y=chemYield), create a data.frame(x, y), and estimate the parameter
vector a using nls.
If you have trouble getting nls
I am having problems getting the unz() function to work as a connection to
start reading a file...
z - unz(c:/temp/stoxx.zip, close_tmi_components.txt, r)
readLines(z,2)
yields the following problems:
z - unz(c:/temp/stoxx.zip, close_tmi_components.txt, r)
Error in unz(c:/temp/stoxx.zip,
Dear R users,
I am interested in uni- bi- multimodality tests, for analysing reaction
times data. I was lead to Hartigan's dip test (Ann. Statistics, 13, 1985,
pp. 70-84, Applied Statistics, 34, 1985, 320-325). Not being a programmer
I am unable to translate the Fortran code given in ref. 2 into
Dear R users,
can someone help with these short puzzles?
1) Is there a function like outer() that evaluates a three-argument function
on a threedimensional grid - or else how to define such a function, say,
outer.3()? E.g., calculate (x/y)^z on (x,y,z) element of {1,2,3}x{3,4}x{4,5} and
return
On Thu, 10 Jul 2003 19:09:16 -0700 (PDT), Nicholas Konidaris
[EMAIL PROTECTED] wrote :
Dear R users,
I have searched the web and CRAN fairly carefully. Does a FITS
format file reader for R currently exist that I can download?
www.wotsit.org has a 13 year old document describing FITS,
Marc Vandemeulebroecke wrote:
Dear R users,
can someone help with these short puzzles?
1) Is there a function like outer() that evaluates a three-argument function
on a threedimensional grid - or else how to define such a function, say,
outer.3()? E.g., calculate (x/y)^z on (x,y,z) element of
Duncan Murdoch wrote:
If you do locate code to read it, or you end up writing some yourself,
you should consider contributing it to the foreign package.
There's a C (and fortran)-level library for reading FITS files here:
http://heasarc.gsfc.nasa.gov/docs/software/fitsio/fitsio.html
- together
On Fri, 11 Jul 2003 18:56:58 +0900
Yukihiro Ishii [EMAIL PROTECTED] wrote:
Hi,
I am an old hand at chemistry but a complete beginner at statistics
including R computations.
My question is whether you can carry out nonlinear
multivariate regression analysis in R using neural networks,
The most commonly used dose-response functions for nonlinear calibration
curves are the four- and five-parameter logistic functions. The four-
parameter logistic is specified as
F(z) = delta + (alpha - delta)/(1 + (z/gamma)^beta)
so I'm not sure where you are getting your dose-response
Dear R help community,
I want to calculate correlations between environment parameters and species
abundance data. When I use the cor() for my table (121 columns 91 rows) R
generates a dataset with the correlations between all columns;
1) How can I limit the calculations to the correlations of
Jerome == Jerome Sackur [EMAIL PROTECTED]
on Fri, 11 Jul 2003 12:17:33 +0200 (MET DST) writes:
Jerome Dear R users, I am interested in uni- bi-
Jerome multimodality tests, for analysing reaction times
Jerome data. I was lead to Hartigan's dip test
Jerome (Ann. Statistics,
Dear list,
is there a function available which provides an estimate of the hazard
function
based on a cox proportional hazard model? I only found the cumulative
hazard and the survival function as survfit options.
Thanks for your help
Peter
__
[EMAIL
This really depends on what your output is. As previously suggested
save() and write() are excellent suggestions.
for(ii in 1:1000){
out - cor( x[ii, ], y[ii, ] ) # or whatever
cat(ii, \t, out, \n, append=TRUE, file=output.txt)
}
This method is really not worth it for small
I've got a colleague who's using a GLMM to analyse her data, and I've
told her that she needs to include an offset. However, glmmPQL doesn't
seem to allow one to be included. Is there anyway of doing this?
Bob
--
Bob O'Hara
Rolf Nevanlinna Institute
P.O. Box 4 (Yliopistonkatu 5)
FIN-00014
Calandra's dose-response function is very close to what you wrote:
She has x = ln(z+1), while x = ln(z) and m = ln(gamma) would give what
you wrote. I would guess that your comments and references should help
her.
Spencer Graves
Paul, David A wrote:
The most commonly used dose-response
The hazard function is the derivative of the cumulate hazard. There
was a discussion only a few days ago on smoothing the hazard rate, which
as I recall may have dealt with smoothing the cumulative hazard and then
differentiating that.
Have you checked http://www.r-project.org/ - search
Did you look at ?cor?
The documentation observes that cor accepts an optional second argument.
The following works:
df1 - data.frame(a=1:8, b=rep(c(-1, 1), 4),
+ c=rep(c(-1, 1), each=4))
cor(df1[,1], df1[, -1])
b c
[1,] 0.2182179 0.8728716
hope this helps. spencer
1) Calculating a 121 x 121 correlation matrix and then extracting the relevant
correlating is extremely inefficient and slow. Instead try this :
data - as.matrix( data ) # data is your 91 x 121 matrix or
dataframe
colInterest - data[ ,1]
apply( data, 2, function(x)
library(survival)
?basehaz
gives
For `basehaz', a dataframe with the baseline hazard, times, and
strata.
Ruud
*** REPLY SEPARATOR ***
On 7/11/2003 at 4:01 Dr. Peter Schlattmann wrote:
Dear list,
is there a function available which provides an estimate of the
Thanks to Andy Liaw, Patrick Burns, Sundar Dorai-Raj and Matthiew Wiener for
the answers to my puzzles. Here is a summary:
** The original question: **
Dear R users,
can someone help with these short puzzles?
1) Is there a function like outer() that
I've solve my own problem! apologies.
For the record:
the filename argument should include the full path of the file within the
directory structure of the zip file.
but there seeks to be an issue with readLines:
readLines(z,2)
Error in readLines(z, 2) : seek not enabled for this connection
Hi,
I read the 2000 thread on a MetaPost device in R. If I understand
correctly, the main problem with the concept is that R wants the device
driver to give back information on the size of strings/labels.
To the bet of my knowledge, MetaPost _does_ make it possible to
measure the bounding box of
Hey, R-listers
I am going to plot a scatter-plot matrix using R.
For example, give a matrix X=[x1, x2, ..., xn]
where each xi is a column vector, how to plot
all the pair scatter-plots between two different
xi and xj?
Is PAIRS able to achieve this function?
Thanks for your help.
Fred
I would like a 3d plot of a matrix such that individual trapezoids
that make up the surface are colored according to the z-value of that
point (or preferably the midpoint of its four corners, or something
similar). MS Excel has something like that.
I know that persp can have an nx by ny matrix
Andrea Calandra [EMAIL PROTECTED] writes:
I'm a student in chemical engineering, and i have to implement an algoritm about
FIVE PARAMETERS INTERPOLATION for a calibration curve (dose, optical density)
y = a + (c - a) /(1+ e[-b(x-m])
where
x = ln(analyte dose + 1)
y = the optical
On Fri, 11 Jul 2003, Ruud H. Koning wrote:
library(survival)
?basehaz
gives
For `basehaz', a dataframe with the baseline hazard, times, and
strata.
Yes, but that's the cumulative hazard, not the hazard rate.
-thomas
Thomas Lumley Assoc. Professor,
Dear R-users,
I have one question about using SVD to get an inverse
matrix of covariance matrix
Sometimes I met many singular values d are close to 0:
look this example
$d
[1] 4.178853e+00 2.722005e+00 2.139863e+00
1.867628e+00 1.588967e+00
[6] 1.401554e+00 1.256964e+00 1.185750e+00
Fred,
[from help on pairs() ]:
...
Arguments:
x: the coordinates of points given as columns of a matrix.
So yes, pairs will do what you ask. See ?pairs for more info.
Also you might consider the alternative function from the lattice package:
library(lattice) #load lattice graphics
Anon. [EMAIL PROTECTED] writes:
I've got a colleague who's using a GLMM to analyse her data, and I've
told her that she needs to include an offset. However, glmmPQL
doesn't seem to allow one to be included. Is there anyway of doing
this?
We just discovered and fixed a similar problem in
If some of the eigenvalues of a square matrix are (close to) zero, then
it's inverse does not exist. However, you can always calculate it's
generalized inverse ginv().
library(MASS)
help(ginv)
It'll allow you to specify a tol argument:
tol: A relative tolerance to detect zero singular
Hi all,
Is there a simple way to constrain the Asym argument in the SSasymp
function so that it does not exceed some maximum value?
Thanks!
Martin
--
Martin Biuw
Sea Mammal Research Unit
Gatty Marine Laboratory, University of St Andrews
St Andrews, Fife KY16 8PA
Scotland
Ph: +44-(0)1334-462637
Hi Folks,
Example:
t-c(1,2,3,4,5,6,7,8,9)
u-c(1,NA,3,NA,5,NA,7,NA,9)
t[u==5]
-- NA NA 5 NA NA
Now, if I could somehow set things so that NA was FALSE for
indexing, then
t[u==5]
-- 5
I know I can do it with
t[(u==5)(!is.na(u))]
but in the situation I am dealing with this leads to massively
[EMAIL PROTECTED] wrote:
I know I can do it with
t[(u==5)(!is.na(u))]
but in the situation I am dealing with this leads to massively
cumbersome, typo-prone and hard-to-read code.
You could redefine '[' or '==', but that would lead to massively
dangerous code. Anything could happen. Anyone who
On Fri, 11 Jul 2003 [EMAIL PROTECTED] wrote:
Hi Folks,
Example:
t-c(1,2,3,4,5,6,7,8,9)
u-c(1,NA,3,NA,5,NA,7,NA,9)
t[u==5]
-- NA NA 5 NA NA
Now, if I could somehow set things so that NA was FALSE for
indexing, then
t[u==5]
-- 5
t[u %in% 5]
I know I can do it with
Hi all;
This is my first message to the list, and I've got three basic questions:
How could I insert comments in a file with commands to be used as source in R?
Is it possible to quickly display a window with all the colors available in
colors()? How?
I'm displaying points, but they overlap,
I'm using the new irts class from package tseries which I find quite useful.
However, I have data of different type being sample at irregular times (i.e.
my data is more of a data frame than a matrix).
Function irts that is used to create irts objects demands that the value
component is either a
This is my first message to the list, and I've got three basic questions:
How could I insert comments in a file with commands to be used as source in R?
use the pound sign #
Is it possible to quickly display a window with all the colors available in
colors()? How?
I've got such a
I want to be able to write a program in R that does the following:
- it allows the user to enter the dimensions of the matrix from the
console
- it allows the user then to enter each element of the matrix from the
console.
I am looking for an equivalent for the C++ command read, or read.ln.
Put your code in a function. See below.
Cheers,
Jerome
mat - function()
{
cat('Number of populations:', '\n')
m-scan(,n=1, quiet=TRUE)
cat('Number of categories:', '\n')
k-scan(,n=1, quiet=TRUE)
N-matrix(0,m,k)
for(i in 1:m) for(j in 1:k) {
N[i,j]-scan(,n=1, quiet=TRUE)
}
N
}
mat()
Number
On Fri, 2003-07-11 at 12:27, J.R. Lockwood wrote:
This is my first message to the list, and I've got three basic questions:
How could I insert comments in a file with commands to be used as source in R?
use the pound sign #
Is it possible to quickly display a window with all
More presicely, if M is singular, then M%*%x = b will have multiple
solutions only if b is in the subspace spanned by columns of M.
Example:
M - array(1:2, dim=c(2,2))
(svdM - svd(M))
$d
[1] 3.162278 0.00
$u
[,1] [,2]
[1,] -0.4472136 -0.8944272
[2,] -0.8944272
On Fri, 11 Jul 2003, Mulholland, Tom wrote:
I guess I was wrong there. However it does seem that it will come down
to fontsize 9 without clipping (or if it does I find it hard to see).
Thanks. It seemed like that is the way it was working, but it also seems
counterintuitive: reduced
I would have expected the function getAnywhere to have behaved
differently in the following:
search()
[1] .GlobalEnv file:C:/R/Rdata/miya/.Rdata
[3] package:bootpackage:methods
[5] package:ctest package:mva
[7] package:modreg
Hi everyone,
The Spatial Dependence (spdep) library, has a function called 'dnearneigh', which
identifies neighbours of region points by Euclidean distance between lower (greater
than) and upper (less than or equal to) bounds. The function returns a list of
integer vectors giving the region
Hi,
Consider this example which I have modified from the persp() help file.
It uses topo.colors() to create a series of colors.
Cheers,
Jerome
x - seq(-10, 10, length= 30)
y - x
f - function(x,y) { r - sqrt(x^2+y^2); 10 * sin(r)/r }
z - outer(x, y, f)
z[is.na(z)] - 1
Dear R community:
I want to simulate a regression matrix which is generated from an orthonormal matrix X
of dimension 30*10 with different between-column pairwise correlation coefficients
generated from uniform distribution U(-1,1).
Thanks in advance!
Rui
[[alternative HTML version
What problem are you really trying to solve? The problem statement
as I read it contains two logical contradictions that I see:
1. Orthonormal means X'X = Identity matrix (10 x 10). That means
the pairwise correlation coefficients can NOT be different from 0.
2. Not all symmetric
Hi,
I have been trying to work with error terms given back from aov to
make confidence intervals. However, the numbers seem to be incorrect.
If there is more than one term in the ANOVA then the error terms can be
inflated by the number of factors in the extra terms. The F's are
correct so
Dear R community:
I am trying to do a simulation study mentioned by Fu (1998), Journal of Computational
and Graphical Statistics, Volume7, Number 3, Page 397-416. In order to give a clear
statement of quesion I copy the following paragraph from the article: We compare the
bridge model with the
On 11 Jul 03, at 21:20, John Christie wrote:
Hi,
I have been trying to work with error terms given back from aov to
make confidence intervals. However, the numbers seem to be incorrect.
If there is more than one term in the ANOVA then the error terms can be
inflated by the number
Dear Rui:
If noone else responds, I suggest you forward my earlier comments to
Fu and ask him.
Spencer Graves
rui wrote:
Dear R community:
I am trying to do a simulation study mentioned by Fu (1998),
Journal of Computational and Graphical Statistics, Volume7,
Number 3, Page 397-416. In
On Friday, July 11, 2003, at 09:38 PM, JRG wrote:
On 11 Jul 03, at 21:20, John Christie wrote:
In what sense are the SSs incorrect, exactly? And what do you think
the correct values should be?
Well, if I take the residuals for one of the main effects I should be
able to calculate a
On 11 Jul 2003 at 18:56, Yukihiro Ishii wrote:
Hi,
I am an old hand at chemistry but a complete beginner at statistics
including R computations.
My question is whether you can carry out nonlinear
multivariate regression analysis in R using neural networks, where the
output variable can
Dear John Christie:
People tend to get the quickest and most helpful responses when they
provide a toy problem that produces what they think are anamolous
results. This increases the chances that someone will be able to
provide a sensible answer in the few seconds they have available for
Dear R users:
I have a dataset with two variables (2 observations, two samples from same
subject) and I used kernSur from library(Genkern) to
get a estimated bivariate density and corresponding plots as follows:
new.data.normal-data.normal[!is.na(data.normal[,2]),]
x-new.data.normal[,2]
OK, I do see that there is a problem in my first email. I have noticed
this with repeated measures designs. Otherwise, of course, there is
only one error term for all factors. But, with repeated measures
designs this is not the case.
On Friday, July 11, 2003, at 10:00 PM, Spencer Graves
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