Many thanks Dr. Ripley. I was made aware that the problem for me was that I
was sending HTML in my email message. Transgression noted.
On Wed, Jun 29, 2011 at 10:17 PM, Prof Brian Ripley
wrote:
> On Wed, 29 Jun 2011, Sam Albers wrote:
>
> I know that this has been asked before in other variation
On Fri, Jul 1, 2011 at 9:45 PM, Joshua Wiley wrote:
> Hi Peter,
>
> There are lots and lots of ways. Here are examples of a few that came
> to mind. If you have never used the ggplot2 package, you will first
> need to install it, which you can do by typing:
>
> [snip]
Incredible! This gives
Hi Peter,
There are lots and lots of ways. Here are examples of a few that came
to mind. If you have never used the ggplot2 package, you will first
need to install it, which you can do by typing:
install.packages("ggplot2")
The code below should run "as is". You may see various trends over
ti
Dear David,
it is showing this error-
data.frame(A = unlist(lapply( lapply( sapply(mydf[,5], strsplit,
+ split="a|A"), length) , "-", 1)),C = unlist(lapply( lapply( sapply((mydf[,5],
strsplit, split="c|C"),
Error: unexpected ',' in:
"data.frame(A = unlist(lapply( lapply( sapply(mydf[,5], st
Dear David,
Thanks for your reply.I tried your code it is running but as I mentioned in my
mail,I am working on pileup file.So I used a command-
mydf=read.table("Case2.pileup",fill=T,sep="\t")
to read pileup file to have data frame i:e mydf.Now the problem is it has 10
columns and have to count
On Jul 1, 2011, at 9:18 PM, Bansal, Vikas wrote:
Dear David,
it is showing this error-
Looks like a syntax error rather than a semantic error.
data.frame(A = unlist(lapply( lapply( sapply(mydf[,5], strsplit,
+ split="a|A"), length) , "-", 1)),C =
unlist(lapply( lapply( sapply((mydf[,5],
On Jul 1, 2011, at 8:15 PM, David Winsemius wrote:
>
> On Jul 1, 2011, at 7:44 PM, Marc Schwartz wrote:
>
>> On Jul 1, 2011, at 4:50 PM, David Winsemius wrote:
>>
>>>
>>> I would like to do some operations inside a function using only one value
>>> for the last dimension of a table/matrix:
>>
On Jul 1, 2011, at 7:44 PM, Marc Schwartz wrote:
On Jul 1, 2011, at 4:50 PM, David Winsemius wrote:
I would like to do some operations inside a function using only one
value for the last dimension of a table/matrix:
tabfn <- function (dfrm, facvec, YN ="event"){
return( Etbl <
Hi - beginning R user question here - each day, over the course of several
months, I've tracked the time I go to bed, the time I wake up, and my hours
spent sleeping. What would be a good way to display this information? I
think it would be ideal to show something resembling a bar and whisker gra
Thanks, Dennis!
Do you or anyone know how do I create a dataset like total.data of the
example in [1]??
My dataset is a matrix, not a list structure.
Is there a way to convert it?
Thanks!
[1] - http://www.cls.zju.edu.cn/binfo/BNArray/
Em 01-07-2011 20:15, Dennis Murphy escreveu:
Hi:
See i
On Jul 1, 2011, at 6:46 PM, Tom Porteus wrote:
> Hi list,
>
>
>
> I've thus far not found a solution to my problem and hope someone can help.
> I have a data matrix and wish to plot a stacked bar plot using barplot().
> This is simple enough, but I have a problem with the legend labels being in
Hi list,
I've thus far not found a solution to my problem and hope someone can help.
I have a data matrix and wish to plot a stacked bar plot using barplot().
This is simple enough, but I have a problem with the legend labels being in
the reverse order from what I want. The default appears to
On Jul 1, 2011, at 4:50 PM, David Winsemius wrote:
>
> I would like to do some operations inside a function using only one value for
> the last dimension of a table/matrix:
>
> tabfn <- function (dfrm, facvec, YN ="event"){
> return( Etbl <- do.call(table, dfrm[ , c(facvec, "event")
On Jul 1, 2011, at 5:50 PM, David Winsemius wrote:
I would like to do some operations inside a function using only one
value for the last dimension of a table/matrix:
Sorry, I had meant to poste a test dataset:
testdf <- data.frame(x=sample(letters[1:5], 25, replace=TRUE),
On Fri, Jul 1, 2011 at 12:47 PM, Bansal, Vikas wrote:
> Dear all,
>
> I am doing a project on variant calling using R.I am working on pileup
> file.There are 10 columns in my data frame and I want to count the number of
> A,C,G and T in each row for column 9.example of column 9 is given below-
>
On Jul 1, 2011, at 12:47 PM, Bansal, Vikas wrote:
Dear all,
I am doing a project on variant calling using R.I am working on
pileup file.There are 10 columns in my data frame and I want to
count the number of A,C,G and T in each row for column 9.example of
column 9 is given below-
On Jul 1, 2011, at 12:14 PM, Trying To learn again wrote:
Hi all,
I want to create a new matrix based on a previous matrix.
You see, If my "data" matrix accomplises this:
if(rowSums(data[i,])>16|rowSums(data[i,])<28)
data[i,]= data[i,]
'if' is not the right command.
# if sum of rows is m
Sorry:
[1] - http://www.cls.zju.edu.cn/binfo/BNArray/
Em 01-07-2011 18:10, Sergio Mira escreveu:
> Hi,
>
> I'm trying to understand some details about an example maintened in [1].
> According that link, I have total.data as a data set (am I right?).
>
> But I don't understand how is built that ta
Hi,
I'm trying to understand some details about an example maintened in [1].
According that link, I have total.data as a data set (am I right?).
But I don't understand how is built that table.
I saved the dataset in a file, with dput(), and had something like this:
structure(list(df.all = struct
Hi,
Does anybody use girafe to analyze .sam file extracting from bowtie.
Some example is better.
thanks so much,
Jiang
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLE
Hi I know that putting write(f,file="bar.txt") it should work but the txt
cannot be openned well I don ´t know exactly why.
My mai doubt is how to make this
I want to create a new matrix based on a previous matrix.
You see, If my "data" matrix accomplises this:
if(rowSums(data[i,])>16|rowSums(
On Jul 1, 2011, at 1:31 PM, Marc Jekel wrote:
Dear R-Fans,
The more I work with matrices (e.g., data.frames) the more I think
it would be helpful to have functions to apply (several!)
mathematical and/or logical operators column- or row-wise in a matrix.
I know the function apply() and a
Dear all,
I am doing a project on variant calling using R.I am working on pileup
file.There are 10 columns in my data frame and I want to count the number of
A,C,G and T in each row for column 9.example of column 9 is given below-
.a,g,,
.t,t,,
.,c,c,
Hi all,
I want to create a new matrix based on a previous matrix.
You see, If my "data" matrix accomplises this:
if(rowSums(data[i,])>16|rowSums(data[i,])<28)
data[i,]= data[i,]
# if sum of rows is more than 16 and less 28 I conservate the row
#but How I say if else "remove" the line (I tried
Hello R users,
I am reading data into R from RMySQL or SQLite databases which are in
Spanish language. I am using RMySQL library and function dbReadTable but I
could not get characters with ñ and tilde, instead R does put ?.
In the past I could manage it modifying the R options as (using windows)
Dear R-Fans,
The more I work with matrices (e.g., data.frames) the more I think it
would be helpful to have functions to apply (several!) mathematical
and/or logical operators column- or row-wise in a matrix.
I know the function apply() and all its derivates (e.g., lapply) but I
think this
I would like to do some operations inside a function using only one
value for the last dimension of a table/matrix:
tabfn <- function (dfrm, facvec, YN ="event"){
return( Etbl <- do.call(table, dfrm[ , c(facvec,
"event") ]) )
# just want Etbl[,,,"TRUE"] or Etbl[,
Dear R-helpers,
I'm using a GLM with poisson errors to model integer count data as a
function of one non-integer covariate.
The model formula is: log(DV) ~ glm(log(IV,10),family=poisson).
I'm getting a warning because the logged DV is no longer an integer.
I have three questions:
1) Can I igno
On 01.07.2011 19:47, Cody Hamilton wrote:
Hello Marc,
I think I am quite a dunce!
I have diff.exe in the folder C:\Program Files\R\R-2.13.0\bin, which is where
the R.exe file is located.
I ran the following from the command line:
diff C:/Program Files/R/R-2.13.0/tests/eval-etc.Rout C:/Progr
Hello Marc,
I think I am quite a dunce!
I have diff.exe in the folder C:\Program Files\R\R-2.13.0\bin, which is where
the R.exe file is located.
I ran the following from the command line:
> diff C:/Program Files/R/R-2.13.0/tests/eval-etc.Rout C:/Program
> Files/R/R-2.13.0/tests/eval-etc.Rout.
Cody,
The 'diff' program should be installed with Duncan's RTools package on Windows
and if in your path, should be usable via the CLI.
>From a Windows console command line, in the folder where the output files in
>question are located, use:
diff eval-etc.Rout eval-etc.Rout.save > diff.txt
OK, I missed that he did state the OS, my apologies to Steven.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Thursday, June 30, 2011
Hello Uwe,
Please forgive my ignorance - how can I get my diffs?
Regards,
-Cody
--- On Fri, 7/1/11, Uwe Ligges wrote:
> From: Uwe Ligges
> Subject: Re: [R] testInstalledBasic
> To: "Cody Hamilton"
> Cc: r-help@r-project.org
> Date: Friday, July 1, 2011, 9:13 AM
>
>
> On 01.07.2011 18:07
That concern has nothing to do with centering variables before including them
in a model.
Your multiple significance testing strategy is not based on statistical
principles and will distort all inferences you obtain from the "final"
model.
Frank
stamkiral wrote:
>
> variables were centered (exce
On 01.07.2011 18:07, Cody Hamilton wrote:
Hi Uwe,
Thank you for taking the time to look into this!
I created the function my.test by modifying testInstalledBasic with the line
change you list below and then ran:
Sys.setenv(LC_COLLATE="C")
my.test('basic')
I get the same error message as be
Hi Uwe,
Thank you for taking the time to look into this!
I created the function my.test by modifying testInstalledBasic with the line
change you list below and then ran:
Sys.setenv(LC_COLLATE="C")
my.test('basic')
I get the same error message as before:
> my.test('basic')
running strict speci
> From: bbol...@gmail.com
> Date: Fri, 1 Jul 2011 13:16:45 +
> Subject: Re: [R] How to fit ARMA model
>
> UnitRoot gmail.com> writes:
>
> >
> > Hello,
> > I am having some problems with fitting an ARMA model to my time series data
> > (randomly generated numbers). The thing is I have tr
In addition to Uwe's suggestion of creating a pdf and then plotting
to it, it is useful to set the gap size to 0 (gap=0)
You might also look at pairs.panels in the psych package which
implements one of the examples in pairs (i.e., it gives histograms on
the diagonal and reports the correlation
Is there any right censoring?
If not, then plain old lme, lmer, gam (in mgcv), ... etc. would seem
to me do just fine for time to waking = ORIENTATION as a response --
or are you thinking of this as interval-censored data, which it would
appear to be since you've binned the response? I strongly s
We have posted a major new version 2.0 of the samr package for large
scale significance testing, especially
for gene expression data. This new version handles RNA-seq data, using
the new method described in
http://www-stat.stanford.edu/~tibs/ftp/Li_Tibs.pdf
We have also added simple interface fu
On Jul 1, 2011, at 11:02 AM, Rainer M Krug wrote:
Hi
I have a question concerning regexp - I want to select with grep all
character strings which contain the numbers 11:20 (code below).
At the moment I am using [], but that obviously does not work, as it
matches
each element in the []. Is t
On Fri, Jul 1, 2011 at 5:08 PM, Gabor Grothendieck
wrote:
> On Fri, Jul 1, 2011 at 11:02 AM, Rainer M Krug wrote:
> > Hi
> >
> > I have a question concerning regexp - I want to select with grep all
> > character strings which contain the numbers 11:20 (code below).
> >
> > At the moment I am usin
On Fri, Jul 1, 2011 at 11:02 AM, Rainer M Krug wrote:
> Hi
>
> I have a question concerning regexp - I want to select with grep all
> character strings which contain the numbers 11:20 (code below).
>
> At the moment I am using [], but that obviously does not work, as it matches
> each element in t
Hi
I have a question concerning regexp - I want to select with grep all
character strings which contain the numbers 11:20 (code below).
At the moment I am using [], but that obviously does not work, as it matches
each element in the []. Is there a way to specify that the regexp should
match 11, b
variables were centered (except DV), because in social sciences zero is
rarely a meaningful point on a scale (Cohen, Cohen, West, Aiken, 2006). for
example in percieved social support questionnaire there is no value as zero.
It is a Likert Type questionnaire and on questionnaire 1= strongly
yes
I am trying to create a set of wavelets in frequency space--namely Cauchy
wavelets for an intensity analysis (von Tscharner, 2000). The wavelets are
defined by the following formula:
[(f/cf)^(cf*scale)]*[e^((-f/cf)+1)^(cf*scale)]
where *f *is frequency of length *n*, *cf* is center frequency (de
On Jul 1, 2011, at 10:22 AM, David Winsemius wrote:
On Jul 1, 2011, at 10:10 AM, dunner wrote:
Hello all, thanks for your time and patience.
I'm looking for a method in R to analyse the following data:
Time to waking after anaesthetic for medical procedures repeated on
the same
individu
On Jul 1, 2011, at 15:22 , Petr PIKAL wrote:
> Hi
>
> r-help-boun...@r-project.org napsal dne 01.07.2011 14:32:31:
>
>> B Marktplaats
>>
>>
>> I'm new to R and I'm trying to define new quite simple variable but I'm
>> struggling with R syntax (when coming to dates) for a while and still
>>
On Jul 1, 2011, at 10:10 AM, dunner wrote:
Hello all, thanks for your time and patience.
I'm looking for a method in R to analyse the following data:
Time to waking after anaesthetic for medical procedures repeated on
the same
individual.
str(mysurv)
labelled [1:740, 1:2] 20 20 15 20
See ?clusterEvalQ
Uwe Ligges
On 01.07.2011 16:11, Lui ## wrote:
Dear group,
does anybody know how to export libraries/functions to all nodes when
launching snow? I want to use a function from fBasics (dstable) for a
rGenoud optimization routine, but I fail "making the function
accessible" to t
Dear group,
does anybody know how to export libraries/functions to all nodes when
launching snow? I want to use a function from fBasics (dstable) for a
rGenoud optimization routine, but I fail "making the function
accessible" to the nodes created. I know how it works for variables, I
know how it w
Hello all, thanks for your time and patience.
I'm looking for a method in R to analyse the following data:
Time to waking after anaesthetic for medical procedures repeated on the same
individual.
> str(mysurv)
labelled [1:740, 1:2] 20 20 15 20 30+ 40+ 50 30 15 10 ...
- attr(*, "dimname
Hi
r-help-boun...@r-project.org napsal dne 01.07.2011 14:32:31:
> B Marktplaats
> Odeslal: r-help-boun...@r-project.org
>
> 01.07.2011 14:32
>
> Komu
>
> r-help@r-project.org
>
> Kopie
>
> Předmět
>
> [R] defining new variable
>
> Hello,
>
> I'm new to R and I'm trying to define new qui
How does it help to center the variables? What statistical principles are
you using to fit your model and how are you ensuring statistical validity of
inferential estimates? Why do it in multiple steps? Why use a mixture of
software tools? What is the utility of standardized regression
coeffici
UnitRoot gmail.com> writes:
>
> Hello,
> I am having some problems with fitting an ARMA model to my time series data
> (randomly generated numbers). The thing is I have tried many packages
> [tseries, fseries, FitARMA etc.] and all of them giving very different
> results. I would appreciate if s
# stringr
Strings are not glamorous, high-profile components of R, but they do
play a big role in many data cleaning and preparations tasks. R
provides a solid set of string operations, but because they have grown
organically over time, they can be inconsistent and a little hard to
learn. Addition
On 01.07.2011 01:17, Cody Hamilton wrote:
Hello,
I installed R 2.13.0 on a Windows 2003 server. I downloaded the Rtools213.exe
from http://www.murdoch-sutherland.com/Rtools/ and placed it in the path
(C:\Program Files\R\R-2.13.0\bin).
I submitted the following code:
library(tools)
Sys.set
Dear R users,
subject: How to filter XY pairs of inacurate gps position along track, taking
into account the time index to not mix track from different days in one average
track
or subject as: How to filter XY pairs of inacurate gps position: (latitude,
longtitude)
to get estimated correct
Ok, thanks a lot for ?Rscript
Best regards
Vincent
Dr Vincent Chouraki
Assistant hospitalier universitaire
Service d'épidémiologie régional
CHRU de Lille, France
De : peter dalgaard
Cc : r-help@r-project.org
Envoyé le : V
Hello,
I'm new to R and I'm trying to define new quite simple variable but I'm
struggling with R syntax (when coming to dates) for a while and still
getting on it.
I would be very grateful if someone could help me with this, to be able to
move on.
I have the following variables:
- Transplant
thanks for the Italian!
I apologize for my previuos explanation which was not clear
actually there are two "k" parameters, so I change one them; let's put it
this way
/# these are the 3 parameters
a<- 414.566
b<- 345.5445
g<- -0.9695679
xstar<- 1397.923
*m<-100*
#I create a vector
pars <-
You need to read the help page for optimize. Again, if you already have ;-)
The error message
>Error in optimize(llik, init.params = F) : element 1 is empty;
>the part of the args list of 'min' being evaluated was:
>(interval)
is telling you that the parameter (interval) required by o
Please
a) read the posting guide
b) really submit reproducible code. Yours is not.
c) read ?optimize and learn to specify the interval
d) you specified an argument init.params, but that is not used in
optimize() nor can it be usefully passed to llik.
Uwe Ligges
On 01.07.2011 02:46, Edward B
hi,
ım studying moderated effects of percieved social support and justice world
belief on relationship between stress coping strategies and depression
level. ı haver never run this analysis before soi ı want to check my steps
whether correct or not.
first ı run regression
in step 1
centered in
Hi
I need help figure out how to fix my code.
When I call into R
>optimize(llik,init.params=F)
I get this error message
Error in optimize(llik, init.params = F) : element 1 is empty;
the part of the args list of 'min' being evaluated was:
(interval)
My data and my code looks like b
On Jul 1, 2011, at 12:52 , vincent chouraki wrote:
> Dear all,
>
> As the object of this mail suggests, the methods package is not loaded by
> default in R2.13 when using Rscript whereas it is loaded when using an
> interactive session.
>
> An example with the metafor package :
>
> library(m
Vincent Chouraki wrote:
>
> Dear all,
>
> As the object of this mail suggests, the methods package is not loaded by
> default in R2.13 when using Rscript whereas it is loaded when using an
> interactive session.
>
?Rscript
will tell you why and what you could do to change the default.
Be
Dear all,
As the object of this mail suggests, the methods package is not loaded by
default in R2.13 when using Rscript whereas it is loaded when using an
interactive session.
An example with the metafor package :
library(metafor)
example(addpoly.rma)
this works in an interaction R shell, but
Thanks to the advice from Brian, the next version of Rattle (2.6.7) will
have the two bugs fixed. Then your launcher will simply need to be:
sh -c 'R_DEFAULT_PACKAGES="rattle" R "$@"'
Regards,
Graham
On 16 April 2011 20:57, Iurie Malai wrote:
> Thank you!
> Your code worked!
>
> I tested all
On Jul 1, 2011, at 06:48 , Jeff Newmiller wrote:
> You haven't provided a reproducible example.
>
> I do notice you are using T and F which are variables that can be redefined
> (which is why TRUE and FALSE are preferred.
Also, if x and y really are "vectors" (I bet they're not, though), you'l
Thanks very much,
I got, it runs perfect.
-
Mario Garrido Escudero
PhD student
Dpto. de Biología Animal, Ecología, Parasitología, Edafología y Qca. Agrícola
Universidad de Salamanca
--
View this message in context:
http://r.789695.n4.nabble.com/Looking-for-Filliben-correlation-test-tp3636069
Hi
I need help figure out how to fix my code.
When I call into R
>optimize(llik,init.params=F)
I get this error message
Error in optimize(llik, init.params = F) : element 1 is empty;
the part of the args list of 'min' being evaluated was:
(interval)
My data and my code looks like
thank you very much for your suggestion!
I tried to do that with the psf I need to use: the 3 parameters Lognormal. I
did that with a single xstar and a single triplet of parameters to check it
works.[I put some numbers to make it woks , but actually they comes from
statistical analysis]
/# the
Hello,
I am having some problems with fitting an ARMA model to my time series data
(randomly generated numbers). The thing is I have tried many packages
[tseries, fseries, FitARMA etc.] and all of them giving very different
results. I would appreciate if someone could post here what the best packag
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