Hi,
I have 2 questions, both pertaining to additive mixed models using mgcv(). I
have fit several additive mixed models using the mgcv package (v 1.4) in R
(v 2.8) modeling log chlorophyll as follows:
mod-try(gamm(log(Chl) ~ s(Year,bs=cs) + s(Latitude,Longitude,bs=tp) +
Thanks for the reply, that was a typo only in the post. as i was trying to
remove some 'sensitive names'. In my real work, i made sure that
1) this command runs without problem
qdata.glm = glm(X258 ~ ., family = binomial, data = qdata[
sample(dim(qdata)[1], 1000), ] )
2) these two gave a
Hello,
I have a univariate data set, and the unconditional variance is 1. I would
like to fit a GARCH(1,1) model to the data set with a constraint: \omega
(the constant parameter in GARCH(1,1)) is equal to 1-\alpha-\beta. So the
unconditional variance can be controled to be \omega
Hi,
How do I extract the standard errors of the coefficients in a glm.nb model?
Thanks.
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Roger wrote:
Thanks for the reply, that was a typo only in the post. as i was trying to
remove some 'sensitive names'. In my real work, i made sure that
1) this command runs without problem
qdata.glm = glm(X258 ~ ., family = binomial, data = qdata[
sample(dim(qdata)[1], 1000), ] )
2)
Dear John - thank you for your detailed answer and help.
Your answer encourages me to ask further: by choosing different contrasts,
what are the different hypothesis which are being tested? (or put
differently - should I prefer contr.sum over contr.poly or contr.helmert,
or does this makes no
jpl s-jlubben1 at math.unl.edu writes:
How do I extract the standard errors of the coefficients in a glm.nb model?
library(MASS)
quine.nb1 - glm.nb(Days ~ Sex/(Age + Eth*Lrn), data = quine)
sumnb1 = summary(quine.nb1)
sumnb1
str(sumnb1) # tells you about the anatomy. Check for $coefficients
Provide some example data code and someone may be able to help.
On Sat, Feb 14, 2009 at 2:46 PM, Joe King j...@joepking.com wrote:
Hi all, I am trying to run a two factor anova, but one of the factors is a
random factor, now I am also running in SPSS and it seems its dividing by
the wrong
I have searched this forum with keywords contour and percent, it only
give one irrelevent result.
My problems is how to plot contour in percent.
In my figure, I have use kde2d to generate density of an array with
two dimension point.
Using image and contour could plot it.
But the line contour
Dear all ,
I want to do PRESS (prediction error sums of squares)
or the residual mean square error of prediction (RMSEP) which will give me
value that is valid for 'future predictions of independent data'. I am
using different methods for example, Multiple Linear Regression,
Hello R-Users
Is there a package in R, that handles Markov (Regime) Switching (ARMA) Models
for time series modelling and prediction?
Thank you very much.
Regards,
Andreas.
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On Feb 14, 2009, at 6:48 PM, Jason Rupert wrote:
Many thanks to Greg L. Snow and David Winsemius for their responses.
First off I can safely say I don't know enough statistics to be
dangerous, but hopefully I will get to that point:)
Regarding the goal - ultimately I would like to use
On Feb 15, 2009, at 7:55 AM, yk wrote:
I have searched this forum with keywords contour and percent, it only
give one irrelevent result.
My problems is how to plot contour in percent.
In my figure, I have use kde2d to generate density of an array with
two dimension point.
Using image and
Dear Tal,
A complete explanation of this issue is too long for an email; I do address
it in my Applied Regression Analysis and Generalized Linear Models text. The
question seems to come up so frequently that Georges Monette and I are
writing a paper on it (and related issues) for the upcoming
Hi Dieter,
I don't see anything in the str(model) output that matches the standard
errors of the coefficients given in summary(model). Any other suggestion?
Thanks.
jpl
Dieter Menne wrote:
jpl s-jlubben1 at math.unl.edu writes:
How do I extract the standard errors of the
Dear all,
I am currently trying to use the dlm package for Kalman filtering.
My model is very simple:
Y_t = F'_t Theta_t + v_t
Theta_t = G_t Theta_t-1 + w_t
v_t ~ N(0,V_t) = N(0,V)
w_t ~ N(0,W_t) = N(0,W)
Y_ t is a univariate time series (1x1)
F_t is a vector of factor
Look more thoroughly?
You should see this about 2/3 the way down the output:
$ coefficients : num [1:14, 1:4] 3.019 -0.475 -0.709 -0.724 -0.615 ...
..- attr(*, dimnames)=List of 2
.. ..$ : chr [1:14] (Intercept) SexM SexF:AgeF1
SexM:AgeF1 ...
.. ..$ : chr [1:4] Estimate Std. Error z
Dear List,
Catching up with my backlog, I stumbled upon this :
On Wed, 11 Feb 2009 10:33:13 +1300, Rolf Turner wrote :
I am appealing to the general collective wisdom of this list in respect
of a statistics (rather than R) question. This question comes to me
from a friend who is a
Hi ,When I try to load the 'mgcv package, often, but not always, get this
error message. What am I doing wrong? I even tried reinstalling a few times.
__
This is mgcv 1.4-1.1
Error in runif(1) :
.Random.seed is not an integer vector but of type 'list'
Error : .onAttach failed in
Hi,
This is probably really obvious, by I can't seem to find anything on it.
Is there a fast version of ave for when the data is already sorted in
terms of the factor, or if the breaks are already known?
Basically, I have:
X = 0.1, 0.2, 0.32, 0.32, 0.4, 0.56, 0.56, 0.7...
Y = 223, 434, 343,
Hi Joe,
you might want to have a look at the nlme package with the lme command.
Another option is the more advanced lmer package.
Lastly, you could have a look at the ?aov command, and notice the option of
using the +Error() term (but that would only work for balanced design cases,
so I've heard,
Dear Sirs and madams :-)
I am trying to teach myself multidimensional scaling. To that effect I have
collected a survey asking people to rank 10 philosophers and politicians
according to their preference. I have collected 61 answers. The data is
organized in ten columns and 61 rows. the columns
I was trying to fit a linear mixed model with a user specified correlation
structure with lme (package nlme). In the book of Pinheiro and Bates
(2000), it was mentioned that new corStruct classes can be added, and the
corAR1 constructor and methods can serve as templates. But I am just too
dumb
On 13/02/2009, at 5:42 PM, Edna Bell wrote:
Dear R Gurus:
I'm building a package and am wondering whether to use S3 or S4
methods.
Any advice, please?
Thanks,
See fortune(121)!
cheers,
Rolf Turner
Dear Fellows: Thanks you all for your great help. Without your
guidance I'd not have been able to get this far. So this is the
current problem: I have a series (dataframe with 1 column and 283
rows, all with numbers (no NA's) that go from 0 to 3 or 4 with up to
14 decimals. They indicate a
Hi R user,
I came across a question when I played around with mnormt package (mvtnorm as
well), could any of you let me know where I made the mistake? Thanks!
For instance, with a multivariate normal distribution with known mean and
variance (to be simple, I tried the i.i.d case first)
u1 -
On Sun, 15 Feb 2009, Zhou Fang wrote:
Hi,
This is probably really obvious, by I can't seem to find anything on it.
Is there a fast version of ave for when the data is already sorted in terms
of the factor, or if the breaks are already known?
If all you want are means, you can use rle()
On Sun, 15 Feb 2009, achristoffersen wrote:
Dear Sirs and madams :-)
I am trying to teach myself multidimensional scaling. To that effect I have
collected a survey asking people to rank 10 philosophers and politicians
according to their preference. I have collected 61 answers. The data is
Thanks! That does exactly what I want. (Heck, maybe this should be
included as a default sorted alternative to ave.)
I was thinking of doing it another way using cumsums, but maybe this
method is faster.
Zhou
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Hey
I'm a relative newbie to R my question is:
is it possible to plot the MaximumLiklihood function of the parameter
estimation of a garch(arch,arma...) model??
Best regards
Rainer
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R-help@r-project.org mailing list
Ok well heres my data, with the second variable (B variable) being the
random variable and the other fixed. Although the F values are about half of
what SPSS puts out.
My code is anova(lm(dependentrandom~typemusic+typemusic*musicselection))
This is just dummy data for a class but I am
Hi Shrikanth --
SHRIKANTH SHANKAR shrikanth.shan...@gmail.com writes:
I have been trying to write a new class that reimplements the vector
class. As a test of my overloading I decided to try and and call
t.test on two vectors which were objects of my class rather than the
default class.
This is supposed to be an easy operation, but R 2.8.1 on Mac OS X gives me a
lot trouble. the t() function simply does not work properly. What I mean is
it works sometimes but does not work at the most of the time, even with the
same matrix.
this is an example taken from R help
a -
On 16/02/2009, at 8:36 AM, Roger wrote:
This is supposed to be an easy operation, but R 2.8.1 on Mac OS X
gives me a
lot trouble. the t() function simply does not work properly. What
I mean is
it works sometimes but does not work at the most of the time, even
with the
same matrix.
this
You probably did not forget to attach the data the first time, either.
You, instead, probably did not remember to read the posting guide
thoroughly regarding what constitutes an acceptable attachment type.
Suggest that you change your mail client settings to transmit plain
text and follow
This is a trivial example I set up to see if I could pass an environment and
use the variables in it
(this is for a function that will be called many times and might need to use
a lot of variables that
won't be changing, so it seemed more sensible to use an environment).
Here's the code:
John Tillinghast wrote:
This is a trivial example I set up to see if I could pass an environment and
use the variables in it
(this is for a function that will be called many times and might need to use
a lot of variables that
won't be changing, so it seemed more sensible to use an environment).
Dear all,I had just started to learn R. So my question may sound a bit
stupid for you.
Is that possible to match and merge two tables in R? I mean I have two
tables, in the first I have two columns: RING NUMBER, WEIGHT and CAPTURE
DATE, in the second RING NUMBER, SEX and CAPTURE DATE.
1) First I
Roger wrote:
This is supposed to be an easy operation, but R 2.8.1 on Mac OS X gives me a
lot trouble. the t() function simply does not work properly. What I mean is
it works sometimes but does not work at the most of the time, even with the
same matrix.
this is an example taken from R help
Here's one way that seems to work:
a - matrix(1:30,5,6)
# Create a target for the transpose
b - matrix(1:(nrow(a)*ncol(a)),ncol(a),nrow(a))
# populate b with the transpose of a
for (i in 1:ncol(a)) { b[i,1:(nrow(a))] - a[1:(nrow(a)),i]}
# Check: Did it work?
all.equal(b,t(a))
I'm sure there's a
Rolf Turner wrote:
On 16/02/2009, at 8:36 AM, Roger wrote:
This is supposed to be an easy operation, but R 2.8.1 on Mac OS X
gives me a
lot trouble. the t() function simply does not work properly. What I
mean is
it works sometimes but does not work at the most of the time, even
with the
Vincze Orsolya wrote:
Dear all,I had just started to learn R. So my question may sound a bit
stupid for you.
Is that possible to match and merge two tables in R? I mean I have two
tables, in the first I have two columns: RING NUMBER, WEIGHT and CAPTURE
Err, ... for large values of two? Or is
Note that you can do things like this too:
env$x
with(env, x^2)
Also its possible you are really getting into object oriented
programming without realizing it with the your environments
being the objects your functions being the methods. In that
case check out the proto package which
Dear R community,
I have two questions regarding fitting GLMM using maximum likelihood method.
The first one arises from trying repeat an analysis in the Breslow and
Clayton 1993 JASA paper. Model 3 of the epileptic dataset has two random
effects, one subject specific, and one observation
Charles C. Berry wrote:
Something like
dat - t( apply( your.data, 1 , order ) )
colnames(dat) - paste( 'philosopher', 1:10, sep='_' )
HTH,
Hi Chuck - thx - but I have trouble geting further. I think I need rank
not sort - but this still doesnet solve my conundrum.
I have data like
Also see the sqldf package which lets you do this using SQL within R.
http://sqldf.googlecode.com
On Sun, Feb 15, 2009 at 3:43 PM, Peter Dalgaard
p.dalga...@biostat.ku.dk wrote:
Vincze Orsolya wrote:
Dear all,I had just started to learn R. So my question may sound a bit
stupid for you.
Is
Youyi Fong yfong at u.washington.edu writes:
Dear R community,
I have two questions regarding fitting GLMM using maximum likelihood method.
The first one arises from trying repeat an analysis in the Breslow and
Clayton 1993 JASA paper. Model 3 of the epileptic dataset has two random
Hi,
This is a practical question and I am sure there are many statisticians can
give me a hand.
I have 500 time series data (500 rows), each row contains 100 intervals,
i.e., on each row, I have X1, X2, . X100. I am trying to reduce the
dimension of this input because the data at the end of
To all,
Apologies if this question has already been asked but I can't find anything. I
can't seem to think of more specific search terms. I want to display/create a
file of a pure plot with a specific height and width. I want to utilise every
single pixel inside the axes. I do not want to
Are the standard errors of the covariance matrix elements for the random
effects in lme4 (lmer) available. That is,
R using lme4 function lmer gives me
Random effects:
Groups NameVariance Std.Dev. Corr
id (Intercept) 0.6360.797
time0.155
Hi everyone,
I have a question to solve linear equations with argument is a matrix.
For example, X is a q by p matrix satisfies
F(X)=A and t(B)%*%X+t(X)%*%B=0,
where A and B are known q by p matrices and 0 is p by p matrix with
all elements are 0s. And F(.) is a known function of matrix, X.
Mea culpa. Thanks!
jpl
David Winsemius wrote:
Look more thoroughly?
You should see this about 2/3 the way down the output:
$ coefficients : num [1:14, 1:4] 3.019 -0.475 -0.709 -0.724 -0.615 ...
..- attr(*, dimnames)=List of 2
.. ..$ : chr [1:14] (Intercept) SexM SexF:AgeF1
Hello!
I'm using Mac OS X 10.4.11 on a G4.
I use the R command, straight from a terminal, because the GUI is
slower, and I've never liked GUIs anyway.
I tried to set up my environment to use the vi editor, but it always
tries to save it in wierd things like this:
/private/tmp/RtmpWIhhuo/41a7
Hi,
This looks like a Lyapanov equation. It is used in control theory I
think. There might be something if you search in those packages that
deal with this.
HTH,
On Feb 16, 9:25 am, �|珊�x koaihs...@gmail.com wrote:
Hi everyone,
I have a question to solve linear equations with argument is a
On Sun, 15 Feb 2009, greggal...@gmail.com wrote:
Hello!
I'm using Mac OS X 10.4.11 on a G4.
I use the R command, straight from a terminal, because the GUI is
slower, and I've never liked GUIs anyway.
I tried to set up my environment to use the vi editor, but it always
tries to save it in
I was thinking of a more focused search including the terms contour
and either r-help or r-project, but not one restricted to
GoogleGroups, ,,, more along the lines of:
http://www.google.com/search?hl=enrlz=1B3GGGL_enUS278US278q=r-help+quantile+contourstart=20sa=N
or...
Depending on F, there may already be software to solve your system. If
not, have you considered recasting the problem as minimizing the sum of
squares of deviations from solutions? Then you could use 'optim' or
'nlminb' or ... .
Spencer Graves
andrew wrote:
Hi,
This looks like a Lyapanov
Dear listers,
I would like to compare the levels of a factor with 8 age categories
(0,10] (10,20] (20,30] (30,40] (40,50] (50,60] (60,70] (70,90] (however,
the factor has not been ordered yet). The default in glm is
cont.treatment (for unordered factors) and that leads to compare each
level
Hi
I'm calculating McFaddens pseudo R2 (1- (Lmodel/L0)) for some models, and i
ran into a model where the model of interest has a positive likelihood,
while the null has a negative. This of course results in odd values. I
searched the list, but find no help. Can anyone provide insight?
Thanks
On Fri, Feb 13, 2009 at 3:14 PM, Marc Schwartz
marc_schwa...@comcast.net wrote:
on 02/13/2009 02:19 PM Paul Johnson wrote:
On Fri, Feb 13, 2009 at 1:51 PM, Marc Schwartz
OK, so given all of the above, something like the following should work:
set.seed(1233240)
x - rnorm(100)
z - gl(2,50)
Hello everyone.
I am trying to plot data from a time series in R and have run across some
problems. I was wondering if someone could help.
I have data taken every 15 minutes of a list of rankings of 25 titles. I
want to plot one of the article's titles's ranks as a time series.
I've been trying
I have a data frame in R where all the variables are character in nature.
kindly let know how I can transform these character variable into say
numeric,Categorical,continuous etc.Please provide me with the proper
syntax. Thank you in advance.
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