Thank you very much, Marc! That was exactly the solution I was looking for!
Regards,
Lauri
2007/1/26, Marc Schwartz [EMAIL PROTECTED]:
On Thu, 2007-01-25 at 22:23 +0200, Lauri Nikkinen wrote:
Hi R-users,
I'm new to R and I'm trying to make a barplot combined with two lines
(refering
I wanted to compare odds ratio across studies and tried to replicate the
results from a study but have not been able to determine how to do this in R.
The study reported a sample of 961 men, of whom 41 had a disorder. The
reported raw odds ratio was 6.52 (4.70-9.00)
I did a search of the
Hi everyone,
I've been having difficulty writing wrapper functions for some
functions where those same functions include other functions with
eval()
calls where the environment is specified. A very simple example using
function lmer from lme4:
lmerWrapper - function(formula, data, family =
Jose == Jose Quesada [EMAIL PROTECTED]
on Fri, 26 Jan 2007 05:24:12 +0100 writes:
Jose Dear R users,
Jose I need to normalize a bunch of row vectors. At a certain point I need
to divide a matrix by a vector of norms. I find that the behavior of Matrix
objects differs from normal
Check out this post and the entire thread to which it belongs:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/67474.html
On 1/26/07, Colin Beale [EMAIL PROTECTED] wrote:
Hi everyone,
I've been having difficulty writing wrapper functions for some
functions where those same functions include
Hello!
I try to fit a non linear model. It is a quite complex (4 parameters)
biological model and therefore the optimization surface is probably very
rough, i.e. there are several optima. The optimum being found by the
algorithm depends thus on the starting values I feed in. I have seen the
SANN
I don't think your subject line is relevant. You do not have 'functions
within functions': lmerFrames is not within lmer. (You seem to be
confusing functions within and calls from.)
Your example does not work (did you test it?). When the erroneous runif
call is corrected (it gives a result
At 09:04 26/01/2007, Bob Green wrote:
I wanted to compare odds ratio across studies and tried to replicate
the results from a study but have not been able to determine how to
do this in R.
The study reported a sample of 961 men, of whom 41 had a disorder.
The reported raw odds ratio was 6.52
If I define my function that includes others internal functions, how can I
define the parameter's functions?
That is:
myfunc-function(y){...
func.int1- function(x){ sum(x}}
func.int2-function(z){funct.int1(z)^2} .
}
Is it possible to use func.int1 into
Hello,
for a frequency modelling problem I want to combine expert knowledge with
incoming real-life data (which is not available up to now). The frequency
has to be modelled with a poisson distribution. The parameter lambda has to
be normal distributed (for certain reasons we did not NOT choose
Michael Dewey wrote:
At 09:04 26/01/2007, Bob Green wrote:
I wanted to compare odds ratio across studies and tried to replicate
the results from a study but have not been able to determine how to
do this in R.
The study reported a sample of 961 men, of whom 41 had a disorder.
The
andrea evangelista wrote:
Dear all, my aim is to estimate the efficacy over time of a treatment for
headache prevention. Data consist of long sequences of repeated binary
outcomes (1 if the subject has at least 1 episode of headache , 0
otherwise) on subjects randomized to placebo or
Le Vendredi 26 Janvier 2007 08:56, Carsten Steinhoff a écrit :
Hello,
for a frequency modelling problem I want to combine expert knowledge with
incoming real-life data (which is not available up to now). The frequency
has to be modelled with a poisson distribution. The parameter lambda has to
Hi
The pruned dataset has 8 unique genomes in it while
the dataset before pruning has 65 unique genomes in
it.
However calling unique on the pruned dataset seems to
return 65 no matter what.
Any assistance in this matter would be appreciated.
Thanks
Lalitha
--- Weiwei Shi [EMAIL PROTECTED]
Greetings guRus --
If a variable, e.g., 'varname', is a character string, e.g. varname -
datavector, and I want to apply a function, such as table(), to
datavector, what syntax or method will do so using only the variable
varname? This seems similar to indirect addressing, but I have not seen
On Fri, 2007-01-26 at 09:48 -0600, Ben Fairbank wrote:
Greetings guRus --
If a variable, e.g., 'varname', is a character string, e.g. varname -
datavector, and I want to apply a function, such as table(), to
datavector, what syntax or method will do so using only the variable
varname? This
Dear All,
Monthly and Quarterly ts obj. is easy to understand. But I couldn't
find an example in R manual how to create daily or weekly ts object.
Could you please shed some light on it?
I really appreciate it.
__
R-help@stat.math.ethz.ch mailing list
does expand.grid do what you want?
expand.grid(c(0, 1), c(0, 1), c(0, 1))
Var1 Var2 Var3
1000
2100
3010
4110
5001
6101
7011
8111
Hi all R users,
I want to create a matrix having n columns and
hello,
today while trying to extract data from a list for subsequent analysis, i
stumbled upon this funny behavior on my system:
x-c(0.1,0.9)
1-x[2]
[1] 0.1
x[1]
[1] 0.1
x[1]==1-x[2]
[1] FALSE
x[1]1-x[2]
[1] TRUE
x-c(0.3,0.7)
x[1]
[1] 0.3
x[2]
[1] 0.7
1-x[2]
[1]
Without knowing more about your data, it is hard to say for certain,
but might you be confusing unique _values_ with _factor levels_?
mydata - as.factor(sort(rep(1:5, 2)))
# mydata has 10 values, 5 unique values, and 5 factor levels
mydata
[1] 1 1 2 2 3 3 4 4 5 5
Levels: 1 2 3 4 5
Hi all R users,
I want to create a matrix having n columns and 2^n rows, and all its entries
are only 0 or 1. In each row, column i is 0 means dimension i is chosen, 0
means not. The matrix will contains all the possible combination of those n
dimensions.
Here is an example, if n = 3, the matrix
Can I ask why you aren't just passing in the object to your function,
but instead a text name for that object?
Ben Fairbank wrote:
Greetings guRus --
If a variable, e.g., 'varname', is a character string, e.g. varname -
datavector, and I want to apply a function, such as table(), to
If you want the dates to show up as such you are better off using
a zooreg object with times of class Date from the zoo package.
You can always use as.ts on it if you require a ts object.
library(zoo)
zd - zooreg(1:10, start = Sys.Date())
zd
as.ts(zd)
plot(zd)
zw - zooreg(1:10, start =
martin sikora [EMAIL PROTECTED] wrote:
today while trying to extract data from a list for subsequent analysis, i
stumbled upon this funny behavior on my system:
x-c(0.1,0.9)
1-x[2]
[1] 0.1
x[1]
[1] 0.1
x[1]==1-x[2]
[1] FALSE
x[1]1-x[2]
[1] TRUE
Not at all
Hi, there
I'm trying to plot what is returned from a call to tapply, and can't figure
out how to do it. My guess is that it has something to do with the
inclusion of row names when you ask for the values you're interested in,
but if anyone has any ideas on how to get it to work, that would be
Thanks a lot! That's exactly what I need.
On 1/26/07, ken knoblauch [EMAIL PROTECTED] wrote:
does expand.grid do what you want?
expand.grid(c(0, 1), c(0, 1), c(0, 1))
Var1 Var2 Var3
1000
2100
3010
4110
5001
6101
a little improvement on ken knoblauch's method by adding the variable n
so,
n - 3
expand.grid(lapply(1:n, function(i) (c(0,1
HTH,
weiwei
On 1/26/07, Zhiliang Ma [EMAIL PROTECTED] wrote:
Hi all R users,
I want to create a matrix having n columns and 2^n rows, and all its entries
are
Then you need to provide more details about the calls you made and your dataset.
For example, you can tell us by
str(prunedrelatives, 1)
how did you call unique on prunedrelative and so on? I made a test
data it gave me what you wanted (omitted here).
On 1/26/07, lalitha viswanath [EMAIL
Steffen,
When the new biomaRt tries to load it errors out because I do not have
RMySQL installed. There is not a Windows binary for RMySQL and it does
contain C code that I do not know how to build.
I do not use the MySQL option in biomaRt. Does RMySQL need to be a
required dependency? Below is
In addition to Mike's comment:
x-c(0.1,0.9)
1-x[2]
[1] 0.1
x[1]==1-x[2]
[1] FALSE
all.equal(x[1], 1-x[2])
[1] TRUE
b
On Jan 26, 2007, at 11:40 AM, Mike Prager wrote:
Not at all strange, an expected property of floating-point
arithmetic and one of the most frequently asked questions
I am using spss.get to import an SPSS database
Data.sav, created with SPSS 14 :
df1 - spss.get(C:/temp/Data.sav , lowernames=TRUE,
datevars = c(dateinte))
I am getting this warning. I get the same warning with
read.spss.
Warning message:
C:/temp/Data.sav: Unrecognized record type
Hi all,
I've now got a problem with some modified lmer code (function lmer1
pasted at end) - I've made only three changes to the lmer code (marked),
and I'm not really looking for comments on this function, but would like
to know why execution of the following commands that use it almost
FAQ on R 7.31. ?all.equal ?identical
Have you read these?
Bert Gunter
Genentech Nonclinical Statistics
South San Francisco, CA 94404
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mike Prager
Sent: Friday, January 26, 2007 8:41 AM
To:
On Fri, 2007-01-26 at 11:50 -0500, Michael Rennie wrote:
Hi, there
I'm trying to plot what is returned from a call to tapply, and can't figure
out how to do it. My guess is that it has something to do with the
inclusion of row names when you ask for the values you're interested in,
but
All,
I'm sure that this is covered somewhere, but I can't seem to find a good
explanation. I have an existing table that contains information grouped by
date. This is as so:
Day NumberOfCustomers NumberOfComplaints
2006051210040 40
On Fri, 2007-01-26 at 12:39 -0500, Kalish, Josh wrote:
All,
I'm sure that this is covered somewhere, but I can't seem to find a
good explanation. I have an existing table that contains information
grouped by date. This is as so:
Day NumberOfCustomers
Marc,
Thanks for pointing out the merge function. That gets me part of the way
there. The only thing is that I can't get the tapply() results into a format
that merge() will take. For example:
merge( set1 , tapply( set2$f1 , set2$commonField, mean ) , by=commonField )
Gives me Error in
Josh,
As per the Value section of ?tapply, it returns a single atomic value
for each cell. This is easily viewed by using:
tapply(set2$f1, set2$commonField, mean)
in a stand alone fashion or:
str(tapply(set2$f1, set2$commonField, mean))
which will display the internal structure of the
Hi.
This is a real basic question about results from rlm. I want to compute the
properly scaled residual variance.
Suppose M is my rlm result object; my example regression is against two
variables, and based on 225 observations.
summary(M) tells me that
Residual standard error: 0.0009401 on
Dear Rlist!
I´ve got two lists which contain sets of DNA-sequences. They look
something like this:
List of 33
$ Cunonia_atrorubens : chr [1:247] t t n t ...
$ Cunonia_balansae : chr [1:254] t c c c ...
$
On Fri, 2007-01-26 at 20:23 +0100, Christoph Heibl wrote:
Dear Rlist!
Ruh-Ro
;-)
I´ve got two lists which contain sets of DNA-sequences. They look
something like this:
List of 33
$ Cunonia_atrorubens : chr [1:247] t t n t ...
$
Sometimes one might like to obtain pointwise bootstrap bias-corrected,
accelerated (BCA) confidence intervals for a large number of statistics
computed from a single dataset. For instance, one might like to get
(so as to plot graphically) bootstrap confidence bands for the fitted
values in a
?invisible
if you return in this function with invisible, then you need to assign like this
x0 - lapply(1:3, function(i) (c(0,1)))
names(x0) - c(a, b, c)
x0
$a
[1] 0 1
$b
[1] 0 1
$c
[1] 0 1
x1 - lapply(1:3, function(i) (c(2,3)))
names(x1) - c(a, b, c)
x2 - interleave(x0, x1)
x2
$a
[1]
Dear Marc, dear Weiwei,
Thanks a lot!
As I now see me question was quite silly, but we´re always much
smarter with hindsight...
: )
Best,
Christoph
On 26.01.2007, at 21:16, Marc Schwartz wrote:
On Fri, 2007-01-26 at 20:23 +0100, Christoph Heibl wrote:
Dear Rlist!
Hi
I read in my dataset using
dt read.table(filename)
calling unique(levels(dt$genome1)) yields the
following
aero aful aquae atum_D
bbur bhal bmel bsub
[9] buch cace ccre cglu
cjej cper cpneuAcpneuC
[17] cpneuJ
Ok, Thanks. I wasn't sure what the actual output of a tapply was.
-Original Message-
From: Marc Schwartz [mailto:[EMAIL PROTECTED]
Sent: Friday, January 26, 2007 1:47 PM
To: Kalish, Josh
Cc: 'r-help@stat.math.ethz.ch'
Subject: Re: [R] Using tapply to create a new table
Josh,
As per
check
?read.table
and add as.is=T in the option. So you read string as character now
and avoid the factor things.
Then repeat your work.
For example
x0 - read.table(~/Documents/tox/noodles/four_sheets_orig/reg_r2.txt,
sep=\t, nrows=10)
str(x0,1)
`data.frame': 10 obs. of 7 variables:
$
oh, i forgot, you can also convert factor into string like
dataset$genome1 - as.character(dataset$genome1)
so you don't have to use
as.numeric(dataset$score) if you use as.is=T when you read.table
HTH,
weiwei
On 1/26/07, Weiwei Shi [EMAIL PROTECTED] wrote:
check
?read.table
and add as.is=T
Hi everyone,
My background is not math and I am trying to figure out exactly what equation
to use to map a response variable in GIS based on the coefficients obtained
from the GLM and the values of the independent variables in each grid cell of
my study area. Most specifically, I want to know
Peetr Michael,
I now see my description may have confused the issue. I do want to compare
odds ratios across studies - in the sense that I want to create a table
with the respective odds ratio for each study. I do not need to
statistically test two sets of odds ratios.
What I want to do is
Hi
I am looking for a package that
1. reads in a phylogenetic tree in NEXUS format
2. given two members/nodes on the tree, can return the
distance between the two using the tree.
I came across the following packages on CRAN
ouch, ape, apTreeShape, phylgr all of which seem to
provide extensive
Peter Michael,
I just came across the following on another mailing list and realized that
my use (and the authors of the article use of the term 'odds ratio' ) is
probably incorrect. I believe my interest is in the 'odds' of schizophrenia
among the population of homicide, rather than a
Bob Green wrote:
Peetr Michael,
I now see my description may have confused the issue. I do want to compare
odds ratios across studies - in the sense that I want to create a table
with the respective odds ratio for each study. I do not need to
statistically test two sets of odds ratios.
library(R2HTML, verbose = FALSE)
Leo Gürtler wrote:
Dear alltogether,
I want to use CGIwithR in conjunction with R2HTML.
A small example called 'test.R':
#
#! /usr/bin/R
invisible(capture.output(library(R2HTML)))
HTML(summary(as.numeric(scanText(formData$numbers))), file=stdout())
Hello R-users,
Does anyone know how to customize a corStruct object to be used in gls?
I would either like to create the covariance matrix from scratch, or
alter the diagonal elements of an existing corStruct object and pass
that to gls.
Any ideas would be appreciated!
First question: Yes
Second question: z in func.int2 is z in myfunc (z=y^3).
You can easily test:
f0-function(){
z-1
f1-function()print(f1)
f2-function(z){f1();print(z)}
f2(z)
}
z-0
f0()
R language definition may be helpful
Hi,
I wrote a simple derivative program
(ftest=deriv(y~x^2, c(x), function(x){} ))
I put (ftest=deriv(y~x^2, c(x), function(x){} ))(1) which return 2 which
is correct.
however, if I want the output to be 0 and hopefully a new inverse function
can take in
output (2) and return x=1. Can this be
Have you looked at the references on ?glm ? They will all explain this to
you (the first and last are simpler than the other two).
The short answer is that predictions from the linear part of your model
are for the natural log of the mean response. That is the default option
for predict() on
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