Hi Fei,
On Fri, Nov 25, 2011 at 7:20 PM, Fei wrote:
>> imp<-mice(mydataframe, seed=1)
> When trying the above command, I got the error term:
>
> iter imp variable
> 1 1 medu
> Error in solve.default(xtx + diag(pen)) :
> system is computationally singular: reciprocal condition number =
> 1.1
Hi,
Has anyone know about how to get the correct plot?
I have use this R script (as below), so I expect the plot is based on x axis,
but the result was opposite. Any suggestion will be great.
library(IRanges)
data <-read.table(file="~/q20snpref/illusmp454merbed",sep="\t",header=F)
colnames(data
> imp<-mice(mydataframe, seed=1)
When trying the above command, I got the error term:
iter imp variable
1 1 medu
Error in solve.default(xtx + diag(pen)) :
system is computationally singular: reciprocal condition number =
1.16487e-025/
What does that mean? How can I address this issue? My
On Nov 25, 2011, at 12:50 PM, Robin Corrià wrote:
Dear all,
I have a
big data frame:
str(data1)
'data.frame': 18272 obs. of 11 variables:
$ tag :
int 11 12 13 15 17
18 19 100011 100012 100014 ...
$ sp :
Factor w/ 18 levels "acassp","acocar",..: 13 5 7
at least put
print(str(Samples))
right after the function call to make sure it is there, and if you
have more code after that, sprinkle that print statement in the
following code. You might at least send the code and indicate where
you have tested to see if the object is still there.
So put som
I am returning a matrix from a function
Samples<-DoMCMC(InitialVactor, CovarianceMatrix, ObservationData,
NumCycles, Burnin, Thin)
When I have one R session open the program works, Samples is a matrix of
samples from the MCMC
When I have two R sessions open, it runs to completion, but when I got
One thing is to define "missing" a little better. For example, as
mentioned previously, are you returning the values from a function
call? If you, print out an indication that they exist at that point.
If there is further processing happening, put some checks as to their
existance as the code con
On Thu, Nov 24, 2011 at 9:23 AM, Joanne Lello wrote:
> Dear all,
>
> I have been using the contrast library
They're packages!
[snip]
For the sake of the good Martin Maechler,
Josh
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
Univers
On 26/11/11 12:19, Duncan Murdoch wrote:
On 11-11-25 1:03 PM, Michael Clawson wrote:
My problem with providing the code, is MCMC is a fairly integrated
process,
so I dont know how I would pare it down to send...
Would it work to send the MCMC code, and the three *.csv files to go
along
with i
Note that you can do what you specified using only the rms package:
require(rms)
f <- Glm(propalive~exptime+infstat*status,
data=dat)
contrast(f,
a = list(status = levels(dat$status), infstat="control", exptime=8230),
b = list(status = levels(dat$status), infstat="infected",exptime=8
On 11-11-25 1:03 PM, Michael Clawson wrote:
My problem with providing the code, is MCMC is a fairly integrated process,
so I dont know how I would pare it down to send...
Would it work to send the MCMC code, and the three *.csv files to go along
with it?
I don't understand. If you can't make y
Hi Ben,
The following is oversimplified but hopefully helpful. Regression
only works with numbers. The trick then becomes how to convert
non-numeric data into meaningful numbers. For so-called continuous
data (the type you get from running: rnorm(100) ), nothing needs to be
done. For others (e
Hello,
Is there an example out there that shows how to treat each of the predictor
variable types when doing logistic regression in R? Something like this:
glm(y~x1+x2+x3+x4, data=mydata, family=binomial(link="logit"),
na.action=na.pass)
I'm drawing mostly from:
http://www.ats.ucla.edu/stat/r/da
Hi Arne,
I believe I figured out why the Stata coefficient estimates differed
from R's: in my case, the outcome response variable is binary, so
the outcome equation is a probit model. From my reading of the
sampleSelection paper, it seems that the Tobit-2 model has a
continuous outcome respons
On Fri, Nov 25, 2011 at 2:47 PM, Jakson Alves de Aquino
wrote:
> On Fri, Nov 25, 2011 at 2:40 PM, Gabor Grothendieck
> wrote:
>>> I think that the following procedure has the result that you want:
>>>
>>> Put in the DESCRIPTION file:
>>>
>>> Imports: RSQLite
>>>
>>> And in the R code write someth
On Nov 25, 2011, at 2:56 PM, magushi wrote:
Hi every one.
I want to analyze my data. The y (density) is very skewed to the
right.
this is my tentative fit<-density~factor(Site)+factor(Species)+ depth.
which model to apply between glm and lm, for sure I can not use
lm( This is
non linear
Hi every one.
I want to analyze my data. The y (density) is very skewed to the right.
this is my tentative fit<-density~factor(Site)+factor(Species)+ depth.
which model to apply between glm and lm, for sure I can not use lm( This is
non linear data)
--
View this message in context:
http://r.78
Michael Clawson gmail.com> writes:
>
> My problem with providing the code, is MCMC is a fairly integrated process,
> so I dont know how I would pare it down to send...
> Would it work to send the MCMC code, and the three *.csv files to go along
> with it?
>
Reproducible is essential, minimal
Inline below. HOWEVER -- my comments are tentative and need
verification by someone more expert because:
1. This is not a reproducible example, so I have no idea what really happening
2. I don't know what your dbQuery command does.Do you?
But see below for my guesses
-- Bert
On Fri, Nov 25, 20
Z[f] would return the fth values in z. That is, if f = c(1,2) z[f] would return
the first and second elements of z. The original intent was to obtain the
indices in z corresponding to the values in f.
Barth
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
jim holtman gmail.com> writes:
> > match(f, names(z))
> [1] 2 3
Jim, thanks so much, that's right on.
Patrick, thanks to you too, but yours is not the same as what I asked:
> z <- c(3,4,5,4)
> names(z)<- c("a","b","c","b")
> z[f]
b c
4 5
Yours returns the actual values in z, not the indexes
On Fri, Nov 25, 2011 at 2:40 PM, Gabor Grothendieck
wrote:
>> I think that the following procedure has the result that you want:
>>
>> Put in the DESCRIPTION file:
>>
>> Imports: RSQLite
>>
>> And in the R code write something like:
>>
>> RSQLite::AnRSQLiteFunction()
>
> I had been thinking of usi
Hi all,
Can any body suggest me the data set which has the length of power of two
and fit for the wavelet smoothing for the regression?
There are alot of datasets like "ethanol" in the package "SemiPar" that can
be used for this smoothing but we have to extend them in the power of two.
I have no id
Did you try:
z[f]
On 25/11/2011 19:23, Jack Tanner wrote:
I have a named vector:
z<- c(1, 2, 3, 2)
names(z)<- c("a","b","c","b")
f<- c("b","c")
I want to know the index in z of the first occurrence of each of the values in
f.
One implementation is
sapply(f, function(x) which(names(z)==x
Try this:
> z <- c(1, 2, 3, 2)
> names(z) <- c("a","b","c","b")
> f <- c("b","c")
> match(f, names(z))
[1] 2 3
> # if you want the names
> x <- match(f, names(z))
> names(x) <- f
> x
b c
2 3
On Fri, Nov 25, 2011 at 2:23 PM, Jack Tanner wrote:
> I have a named vector:
>
>> z <- c(1, 2, 3, 2)
>>
Thank you sire for your help. Thank also for sharing the reference, I'll take
a look at it.
Regards,
Phil
--
View this message in context:
http://r.789695.n4.nabble.com/Legend-tp4103799p4108587.html
Sent from the R help mailing list archive at Nabble.com.
___
I have a named vector:
> z <- c(1, 2, 3, 2)
> names(z) <- c("a","b","c","b")
> f <- c("b","c")
I want to know the index in z of the first occurrence of each of the values in
f.
One implementation is
> sapply(f, function(x) which(names(z)==x)[1])
b c
2 3
Is which() smart enough to stop when i
Dear all,
I have a
big data frame:
str(data1)
'data.frame': 18272 obs. of 11 variables:
$ tag :
int 11 12 13 15 17
18 19 100011 100012 100014 ...
$ sp :
Factor w/ 18 levels "acassp","acocar",..: 13 5 7 14 14 18 3
11 13 10 ...
$ gx :
num 20 10 35 68
On Nov 25, 2011, at 2:10 PM, Ian Strang wrote:
This look really interesting but I don't understand what is happening.
Please can someone explain the last line and what the bit in [] is
doing.
Ian
You just stick the new line on the bottom and return the rows in the
order specified in the
This look really interesting but I don't understand what is happening.
Please can someone explain the last line and what the bit in [] is doing.
Ian
df = data.frame( A=c('a','b','c'), B=c(1,2,3), C=c(10,20,30),
stringsAsFactors=FALSE)
newrow = c('X', 100, 200)
rbind(df,newrow)[c(1,4,2,3),]
___
A) you need to reply-all to keep the discussion on the mailing list.
B) you need to post in plain text.
C) this has the arbitrary smell of homework. This is not a homework help line.
D) You are overwriting your accumulation variable "sumt" after each test. Since
you are not handling this calcul
On Nov 25, 2011, at 11:41 AM, Dhaynes wrote:
Ok let me clarify
I have multidimensional array and I need to convert it to a singular
dimensional array.
The multidimensional array is 359 rows, 2 cols, 3 deep
I need to run a regression model mymatrix[1,1,1:3] and mymatrix
[1,2,1:3]
This is my
My problem with providing the code, is MCMC is a fairly integrated process,
so I dont know how I would pare it down to send...
Would it work to send the MCMC code, and the three *.csv files to go along
with it?
On Fri, Nov 25, 2011 at 9:54 AM, David Winsemius wrote:
>
> On Nov 25, 2011, at 10:08
On Nov 25, 2011, at 10:08 AM, Michael Clawson wrote:
Uwe,
by window I mean instances, by runs I mean, runs the my Markov-Chain
Monte
Carlo simulator
It would probably be better to adopt the terminology that the things
you are calling "windows" are "sessions".
I open two instances of R
Ok let me clarify
I have multidimensional array and I need to convert it to a singular
dimensional array.
The multidimensional array is 359 rows, 2 cols, 3 deep
I need to run a regression model mymatrix[1,1,1:3] and mymatrix [1,2,1:3]
This is my current error, which indicates I have the incorrect
Hi Arne,
Thanks for the reply.
I am using R version 2.14.0 and sampleSelection version 0.6.12.
I estimate the model by the 1-step ML method. However, when I use
the 2-step method, the standard errors are reported as NA.
I use the selection() function, very basic call, something to the
effect
Uwe,
by window I mean instances, by runs I mean, runs the my Markov-Chain Monte
Carlo simulator
I open two instances of R, run a million cycle chain in each instance, and
when they finish, neither window has the object I defined to store the runs.
I tested this morning and when I open two R wind
On Fri, Nov 25, 2011 at 11:52 AM, Jakson Alves de Aquino
wrote:
> On Fri, Nov 25, 2011 at 1:21 PM, Gabor Grothendieck
> wrote:
>
> [...]
>
>> I was framing this in terms of the Matrix example, but perhaps its
>> easier to understand with the actual example which motivated this for
>> me. That is
On Fri, Nov 25, 2011 at 1:21 PM, Gabor Grothendieck
wrote:
[...]
> I was framing this in terms of the Matrix example, but perhaps its
> easier to understand with the actual example which motivated this for
> me. That is, the feature is that whenever sqldf is installed then
> RSQLite is installe
On 24.11.2011 15:59, Johannes Radinger wrote:
Hello,
I'd like to add custom labels to my pair() plot. These
labels include math expression but they aren't correctly
displayed...
Looks fine for me in R-2.14.0 on the windows() device (alpha, text,
beta). (Both version and device you used are
2011/11/25 Uwe Ligges :
>
>
> On 23.11.2011 14:59, Gabor Grothendieck wrote:
>>
>> 2011/11/23 Uwe Ligges:
>>>
>>>
>>> On 23.11.2011 03:18, Gabor Grothendieck wrote:
On Tue, Nov 22, 2011 at 3:16 PM, Gábor Csárdi
wrote:
>
> Dear All,
>
> in some functions of my package
On 23.11.2011 14:59, Gabor Grothendieck wrote:
2011/11/23 Uwe Ligges:
On 23.11.2011 03:18, Gabor Grothendieck wrote:
On Tue, Nov 22, 2011 at 3:16 PM, Gábor Csárdiwrote:
Dear All,
in some functions of my package, I use the Matrix S4 class, as defined
in the Matrix package.
I don't w
You need to read the posting guide. Provide a reproducible code sample,
simplified, with self-contained data.
You might find the "ave" function useful if you are working with vectorized
simulations.
---
Jeff Newmiller
How are you computing the sum? Does FAQ 7.31 apply? Showing at least a
sample of your code would help.
On Friday, November 25, 2011, Sl K wrote:
> Dear R users,
>
> I am running simulations (1000), and in my simulation I am looking at
> specific sums. For example, if the sum is >=4 then count t
On 25.11.2011 16:08, Michael Clawson wrote:
Uwe,
by window I mean instances, by runs I mean, runs the my Markov-Chain Monte
Carlo simulator
I open two instances of R, run a million cycle chain in each instance, and
when they finish, neither window has the object I defined to store the runs.
On 25.11.2011 05:12, Aldo wrote:
Is there a maximum memory allocation for all R windows open? because it is
like 1-3 million runs
So you mean you open a million windows at the same time? In that case we
really need your definition of "window".
so... it may be reaching some sort
On 25.11.2011 05:07, Aldo wrote:
It works when I do not have multiple windows open,
Please read the posting guide! You failed to follow in multiple way,
most important one so far: quote the thread! We do not know your
original question nor the answers you got so far. This is the R mailing
On 24.11.2011 16:49, Filoche wrote:
Thank you for your precious help. It works fine.
However, what about if I have two entries in the legend?
I tryed:
legend('topright', inset = .05, title = 'light ratios', pch = c(21,22),
legend = c(substitute('Green/Red' ~~ R^2 == r2,
list(r2=r2)),su
Hi,
I have experimental response (Y) and many (important or not) actions (X). I
want to create model:
Y = aX1 + bX2 + ... + eX5 (1)
from few most important actions of course.
As I understand I have to use plsr for this task.
I learned read.table and plsr R functions and how to plot some resu
Dear R users,
I am running simulations (1000), and in my simulation I am looking at
specific sums. For example, if the sum is >=4 then count this, if say <3,
then don't count, if the sum=3, then generate a random number from uniform
distribution, if this number is say less than 0.5, then count thi
On 11-11-24 11:22 PM, ivo welch wrote:
Dear R experts---I may have asked this in the past, but I don't think
I figured out how to do this. I would like to execute traceback()
automatically if my R program dies---every R programI ever invoke. I
guessed that I could have wrapped my entire R code
Hello all
I'm running da.norm function in R for climate data
rngseed(1234567)
theta1=da.norm(mydata, thetahat, steps=1000,showits=T)
param1=getparam.norm(mydata,theta1)
As I understand the 1000 steps represent the markov chain values. Is there
a way to plot them? Something like plot(1:1000, para
On Fri, 25 Nov 2011, juliastone wrote:
Hi everybody,
i'm trying to draw rarefaction curves to estimate a population size from
genotyped faeces.
I used the Gimlet software which gave me a script and a "rarefaction.txt"
file. I've copied both files in the work directory of R.
I changed library(nls
I don't know why my last email didn't go through properly, but library
copula is still active.
Here is a toy example with reference.
## Toy example for gumbel copula with log-normal distribution
## (Taken from the documentation of copula::fitMvdc)
## Specify the copula
gumbel.cop <- gumbelCopu
library(copula) could be helpful as well.
## Toy example for gumbel copula with log-normal distribution
## (Taken from the documentation of copula::fitMvdc)
## Specify the copula
gumbel.cop <- gumbelCopula(3, dim=2)
myMvd <- mvdc(gumbel.cop, c("lnorm","lnorm"), list(list(meanlog = 1.17),
Hi everybody,
i'm trying to draw rarefaction curves to estimate a population size from
genotyped faeces.
I used the Gimlet software which gave me a script and a "rarefaction.txt"
file. I've copied both files in the work directory of R.
I changed library(nls) by library(stats) in the script.
But now
Hi All,
I have a parameter that is bimodal, and I want to get some sort of linear model
done with it
results = some.linear.function(bimodal.param ~ factor1 + some other stuff,
mydata)
I want to see if factor 1 matters (it has 3 levels, of of which can be taken as
baseline), i.e:
summary(resu
?"::"
-- Bert
On Fri, Nov 25, 2011 at 12:49 AM, Alaios wrote:
> Dear all,
> I have two questions regarding packaging.
>
> a. What is the inverse action of require(). I want to "detach" one of the two
> libraries I loaded as there are two functions with the same name and come
> from two differe
Inline below.
-- Bert
On Fri, Nov 25, 2011 at 2:31 AM, Milan Bouchet-Valat wrote:
> Le vendredi 25 novembre 2011 à 00:02 -0800, Dhaynes a écrit :
>> Hello,
>>
>> I am new to R.
>> I have multidimensional array (379,2,3) and I need to create a series of
>> linear regressions (379 to be exact)
>>
Hello list,
I need to analyse some data but before that I would like to use plots like
as follows
to visualise the variance in the data:
Page 38, Fig 2.9: http://lme4.r-forge.r-project.org/book/Ch2.pdf
Page 42, Fig 2.11: http://lme4.r-forge.r-project.org/book/Ch2.pdf
and
Page 4, Fig 1: http:
Two comments on the ability of the 'sos' package to identify this kind
of thing:
1. The object returned by "findFn" can be passed to two other
useful functions (as documented in a vignette, previously published in
the R Journal):
1.1. "installPackages", which attempts t
Le vendredi 25 novembre 2011 à 00:02 -0800, Dhaynes a écrit :
> Hello,
>
> I am new to R.
> I have multidimensional array (379,2,3) and I need to create a series of
> linear regressions (379 to be exact)
> I have the array stored properly I believe, but I can not use the
> lm(myarray[1,1,1:3]~myar
On 25 November 2011 04:37, Yuan Yuan wrote:
> Hello,
>
> I am working on reproducing someone's analysis which was done in
> Stata. The analysis is estimation of a standard Heckman sample
> selection model (Tobit-2), for which I am using the sampleSelection
> package and the selection() function. I
Hello Denis & Fayyad,
in principal the advice given is appropriate, but QRMlib has been removed from
CRAN lately, due to a glitch with its dependencies and the current version of
R. Hence, to get the package installed and does not want to wait until it shows
up on CRAN, one should to the follow
On Thu, 24-Nov-2011 at 09:17PM +, Prof Brian Ripley wrote:
|> On Fri, 25 Nov 2011, Patrick Connolly wrote:
|>
|> [... about a completely different topic]
|>
|> >With the one using multicore, I get a strange error that didn't occur
|> >with R-2.13.1. A function which runs on 7 cores produces
Dear all,
I have two questions regarding packaging.
a. What is the inverse action of require(). I want to "detach" one of the two
libraries I loaded as there are two functions with the same name and come from
two different libraries
b. If I do not "detach" the one library how I can refer to the
Please ask about RDBMSs on R-sig-db.
On 25/11/2011 06:34, Jeff Zhang wrote:
Hi all,
I try to use RODBC on my mac machine. I google a lot but could not find a
very comprehensive tutorial. Finally, I install iODBC, but there's no
Hmm, iODBC is part of Mac OS X.
driver in iODBC. And I found so
On Thu, 24-Nov-2011 at 08:59PM +, Prof Brian Ripley wrote:
|> On Fri, 25 Nov 2011, Patrick Connolly wrote:
|>
|> >On Mon, 21-Nov-2011 at 09:46PM +1300, Rolf Turner wrote:
|> >
|> >[]
|>
|> Please don't excise content, nor mix up topics. I am going to
I was indicating two reasons why I
Hi:
This is the type of question for which the sos package can come to the rescue:
library('sos')
findFn('Gumbel Clayton copula')
It appears that the QRMlib package would be a reasonable place to start.
Dennis
On Thu, Nov 24, 2011 at 7:29 PM, cahaya iman wrote:
> Hi,
>
> Is anybody using Copu
Hello,
I am new to R.
I have multidimensional array (379,2,3) and I need to create a series of
linear regressions (379 to be exact)
I have the array stored properly I believe, but I can not use the
lm(myarray[1,1,1:3]~myarray[1,2,1:3])
I have checked to make sure they are exactly the same length.
Hello everyone. I've got some acoustic data I want to display for a project
in my linguistics class.
The vowels pkg supposedly does precisely what I need, but even the samples
given in the documentation won't run on my system.
Package and example is here:
http://ncslaap.lib.ncsu.edu/tools/no
Hi all,
I try to use RODBC on my mac machine. I google a lot but could not find a
very comprehensive tutorial. Finally, I install iODBC, but there's no
driver in iODBC. And I found some commercial ODBC driver. Actaully I just
want to learn it ,so free driver will be suitable for me.
Does anyone h
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