David Crow david.crow at cide.edu writes:
Hi, R users-
I'm estimating random effects models with cross-level interactions; I want
to interact each of a vector of level-1 variables with each of a vector of
level-2 variables. Here's the code:
#create data frame
peter dalgaard pdalgd at gmail.com writes:
On 28 Mar 2015, at 00:32 , RiGui raluca.gui at business.uzh.ch wrote:
Hello everybody,
I have encountered the following problem with lm():
When running lm() with a regressor close to zero -
of the order e-10, the
value of the
Amelia Marsh amelia_marsh08 at yahoo.com writes:
Dear R forum
I have following data
amounts = c(928906.144,156091.0576,433798.3404,993425.7224,
1323976.364,649106.9339, 369967.2612,2528872.35,1226093.655,
1145446.149,1809624.453,599329.0394,2200955.213,2583318.064,
,] - exp(piYc_ir[i,])
follow-ups should probably go to r-sig-mixed-mod...@r-project.org
instead ...
Ben Bolker
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Fatemeh a f.alimadadi at gmail.com writes:
Hi all,
I am running a software which is shinybased within R : it gives me this
error:
Warning: running command 'octave -qf octave/muxMultisliceCommunity.m'
had status 1
I was wondering if anyone could help me where the problem is and what
CHIRIBOGA Xavier xavier.chiriboga at unine.ch writes:
Dear all,
I attempted to transform my data using asin but a WARNING message appears:
dat1$Abu.tr-asin(sqrt(dat1$Abundance/100))
Warning message:
In asin(sqrt(dat1$Abundance/100)) : NaNs produced
What does it mean? Is it a
C W tmrsg11 at gmail.com writes:
Hi list,
I am running the following R code, the answer should be zero. But R gives
a very small negative number, what should I do?
##R code
library(numDeriv)
h_x - function(x){
a = x[1]
b = x[2]
c = x[3]
d = x[4]
(a^2 + c^2 + d^2) *
David Barron dnbarron at gmail.com writes:
It's in the magrittr package.
David
It also exists in dplyr.
(I would guess that it's imported/exported from magrittr.)
Although I think the documentation in magrittr is a little better.
__
michael.eisenring at agroscope.admin.ch writes:
2.50% 97.50%
intercept 29787966
glands13143611
damage169 6144
treatment L1 778 6703
treatment L4 -3899 5125
Length-1817 1828
plotrix::plotCI(..., err=x)
??
Marco Barbàra jabbba at gmail.com writes:
DeaR userRs,
I recently read this Liang-Zeger article:
http://sankhya.isical.ac.in/search/62b1/fpaper7.html
in which (among other things) they adopt a random intercept model for
pre-post designed trials, using a conditional likelihood
anord andreas.nord at biol.lu.se writes:
[snip snip]
We are working on a data set in which we have measured repeatedly a
physiological response variable (y)
every 20 min for 12 h (time variable; 'x') in subjects ('id') beloning to
one of five groups ('group'; 'A' to 'E'). Data are
Torbjørn Håkan Ergon t.h.ergon at ibv.uio.no writes:
Dear list,
I'm trying to supply a summary function to confint.merMod(method=boot)
{lme4} but get persistent
errors. The following example generates the errors:
fm1 - lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
test =
obscured data points.
David
Not sure, but setting the background to NA (bg=NA) might? help.
-Original Message- From: R-help
[mailto:r-help-boun...@r-project.org] On Behalf Of Ben Bolker
Sent: Monday, February 9, 2015 5:43 PM To: r-h...@stat.math.ethz.ch
Subject: Re: [R] Coordinate
David L Carlson dcarlson at tamu.edu writes:
This is more complicated, but it could be rolled up into a function.
Replace your mtext() call with the following:
# Set character expansion size
cx - 2.5
# Get the plot coordinates and the character size
ur - par(usr)[c(1, 4)]
chr - par(cxy)
Ravi Varadhan ravi.varadhan at jhu.edu writes:
I would like to run lme() on a number of response variables
in a dataframe in an automatic manner. Bu, when I
use eval(parse(text=yname)) to denote the LHS of the formula in lme(),
I get the following error message:
require(nlme)
mod2
maggy yan kiotoqq at gmail.com writes:
I read something on http://glmm.wikidot.com/faq, under How can I deal with
overdispersion in GLMMs?:
library(lme4) ## 1.0-4set.seed(101)
d - data.frame(y=rpois(1000,lambda=3),x=runif(1000),
f=factor(sample(1:10,size=1000,replace=TRUE)))
Mike Miller mbmiller+l at gmail.com writes:
I've got to remember to use more spaces. Here's the basic problem:
These are the same:
v 1
v1
But these are extremely different:
v -1
v-1
This is indeed documented, in passing, in one of the pages you listed:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
For what it's worth, you can use either nlminb (directly) or optimx
within the mle2 wrapper by specifying the 'optimizer' parameter ...
this gives you flexibility in optimization along with the convenience
of mle2 (likelihood ratio tests via
Mosab Alqurashi malqurashi at KSU.EDU.SA writes:
?Hello,
I want to get the Maximum Likelihood Estimate (MLE) for an Extended
weibull with three parameters. I have two problems. First, some
times if I change the starting point for one of the parameters I got
an error message. Second,
(although
occasionally you need to use s(IV,k=something_bigger) to adjust the
default *maximum* complexity chosen by the code)
On Sun, Jan 11, 2015 at 5:23 PM, Marc Schwartz marc_schwa...@me.com wrote:
On Jan 11, 2015, at 4:00 PM, Ben Bolker bbol...@gmail.com wrote:
Stanislav Aggerwal
Stanislav Aggerwal stan.aggerwal at gmail.com writes:
I have the following problem.
DV is binomial p
IV is quantitative variable that goes from negative to positive values.
The data look like this (need nonproportional font to view):
[snip to make gmane happy]
If these data were
...@gmail.com wrote:
On 5 January 2015 at 21:08, Ben Bolker bbol...@gmail.com wrote:
Roger Coppock rcoppock at cox.net writes:
When will R implement the se.fit option to the
predict.nls() function? Is there some schedule?
I think this is unlikely to happen, ever (sorry). The exact method
Jinsong Zhao jszhao at yeah.net writes:
In the following code snippet,
#
a - strptime(121114 0510, %m%d%y %H%M)
b - data.frame(date = a, res = 1:5)
class(a)
class(b[1,1])
#
I am wondering why the class of a and b[1,1] are not the same.
How to make the class of a and b[1,1] to be same?
Roger Coppock rcoppock at cox.net writes:
When will R implement the se.fit option to the
predict.nls() function? Is there some schedule?
I think this is unlikely to happen, ever (sorry). The exact method
for finding confidence intervals on nonlinear fits would be
to compute
increase your odds
of getting an answer, if you can post a minimum workable example,
that is a _small_ piece of data/code that people can use to replicate
your problem: see http://tinyurl.com/reproducible-000 ...
Ben Bolker
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Ben Bolker bbolker at gmail.com writes:
Paul Hudson paulhudson028 at gmail.com writes:
[snip]
library(tweedie)
set.seed(1001)
r - rtweedie(1000,1.5,mu=2,phi=2)
library(bbmle)
dtweedie2 - function(x,power,mu,phi,log=FALSE,debug=FALSE) {
if (debug) cat(power,mu,phi,\n)
res
Paul Hudson paulhudson028 at gmail.com writes:
Hello all,
I want to fit a tweedie distribution to the data I have.
The R packages I have been able to find assume that I want to use it as
part as of a generalized linear model.
This is not the case, I want to directly fit the
Therneau, Terry M., Ph.D. therneau at mayo.edu writes:
On 12/26/2014 05:00 AM, r-help-request at r-project.org wrote:
i want to analyse survival data using typeI HALF LOGISTIC
DISTRIBUTION.how can i go about it?it installed one on R in the
survival package didn't include the
more appropriate
follow-up venues.
Ben Bolker
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and provide
Rolf Turner r.turner at auckland.ac.nz writes:
I know nothing about the bbmle package and its mle2() function, but it
is a general truth that if you need to constrain a parameter to be
positive in an optimisation procedure a simple and effective approach is
to reparameterize using
catalin roibu catalinroibu at gmail.com writes:
Dear all!
Is there a R package to compute neighborhood competition index (Shutz,
Hegyi, and many index).
Thank you very much!
library(sos)
findFn(Hegyi)
leads to
http://finzi.psych.upenn.edu/R/library/siplab/html/pairwise.html
Glenn Schultz glennmschultz at me.com writes:
Hello All,
I need some help with optimx, mostly due to my apparent lack of
imagination than optimx itself. Below is the pertinent code for
which I have a question. I am fitting to the term structure of swap
rates per Cox, Ingersoll, and
Doran, Harold HDoran at air.org writes:
Daniel
Lmer has never returned p-values from a model summary;
this is a well-known and discussed issue. You must
have post-processed the data in some way to get the p-values.
But it's worth noting that lmerTest does, and the way it works
makes
, then you're going to have to provide more
information.
Follow-ups to r-sig-mixed-mod...@r-project.org , please .
Ben Bolker
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David Kikuchi dwkikuchi at gmail.com writes:
Hi all,
I'm modeling the probability that a subject attacks or rejects a prey
item based on its proportion of yellow coloration and size. There are
two populations of prey, one defended and the other undefended, so
subjects should reject
Wim Kreinen wkreinen at gmail.com writes:
[snip]
Actually, I started with rgamma to generate some random vectors because I
wanted to play around with various conditions (and become familiar with
gamma shape). But before you can start with gamma shape you need to have a
glm object.
eliza botto eliza_botto at hotmail.com writes:
Dear useRs,
Is there a direct command in R to calculate standard deviation of BURR
distribution in R? I know the direct
function in VBA and worksheet. but is there a similar function in R?
VBA
=BurrStdev(k,alpha,beta,[gamma])
Worksheet:
Bob O'Hara rni.boh at gmail.com writes:
This isn't an R question at all, so I don't know why it's on this list. But
the best answer I've got is a truncated t-distribution with an infinite
number of degrees of freedom.
Bob
Or, perhaps more productively: since your question is a
Nia Gupta nia_gupta at yahoo.com writes:
Hello,
I have a column with a bunch of letters. I would like to keep some
of these letters (A,C,D,L) and turn the rest into 'X'.
I have tried using ifelse with '|' in between the argument but it
didn't work nor did 4 separate ifelse statements.
Yuan Jian jayuan2008 at yahoo.com writes:
Hello,
I found the residuals of glm is not the same as calculated manually.
y=c(12,14,33,50,67,74,123,141,165,204,253,246,240)
t=1:13
m1=glm(y~t+I(t^2),family=poisson(link=log))
coefficients(m1)[1]+coefficients(m1)[2]*log(t)+
Arnab Dutta arnab.killy at gmail.com writes:
Hi,
In order to have robust standard errors in R, what would be the command
that can generate results similar to the robust option in STATA? I tried
using the lmrob command from the package robustbase. With that, the
Adjusted R squared is
Padmanand Madhavan Nambiar padmanandm at gmail.com writes:
Hi Sir,
How to use the optim for maximization. I don't understand the
control$fnscale option that is given on help page. It says if the
control$fnscale is negative, the function will be maximized.
Thanks a lot
Padmanand
Chad Danyluck c.danyluck at gmail.com writes:
About a year ago I ran some analyses using lmer. The general syntax was:
mlm - lmer(var1 ~ (1|dyad) +
var2 + var3*var4*var5, na.action=na.exclude);
summary(mlm)
The model ran fine and I saved the output. I've recently turned back to
those
package, or the equivalent from the nloptr package -- neither
computes the hessian, but the numDeriv package makes that pretty
easy ...
Ben Bolker
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do some benchmarking of your problems on an existing
machine that would probably be a good idea.
Ben Bolker
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Dan Dillon dgdillon at gmail.com writes:
Colleagues:
[snip]
My data are from a behavioral experiment in which two groups of subjects
complete 200+ trials of a task with two conditions. Each subject is tested
in one of four separate locations. I record accuracy (0 or 1) and response
Ravi Varadhan ravi.varadhan at jhu.edu writes:
Dear All,
I am fitting a model for a binary response variable measured
repeatedly at multiple visits. I am using the binomial GLMM using
the glmer() function in lme4 package. How can I evaluate the model
assumptions (e.g., residual
Juan Andres Hernandez jhernandezcabrera at gmail.com writes:
Does anyone know how to extract the convergence code of an lmer object. I
am working in a monte carlo simulation with mixed model and I need to know
if a model has or not convergence. With unclass(mymodel) the following
Ferra Xu ferra.xu at yahoo.com writes:
Hello All
I intend to plot a 3-D marked point process.
Could you please help me to find a code or a related package?
How about scatterplot3d or rgl::plot3d ?
Googling r 3d point plot gets you a lot of good starting points.
(The easiest way to
Roxane Foulser-Piggott rf371 at cam.ac.uk writes:
R version 3.1.0 (2014-04-10) -- Spring Dance. Platform:
x86_64-apple-darwin13.1.0 (64-bit).
I would like to convert the following function from nlme to nlmer.
I am finding it difficult to apply the documentation I can find on
this
Heather Baldwin heather.baldwin at uni-ulm.de writes:
I have four sets of glmms (binomial, logit-linked) which I have run in
various incarnations with no problems over the last weeks. All converged,
data assumptions checked, reasonable goodness-of-fit (0.75-85). They are
based on three
significantly across conditions.
This is a stats question, not an R question per se ... I would
recommend posting to CrossValidated (http://stats.stackexchange.com)
good luck,
Ben Bolker
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https://stat.ethz.ch/mailman
(http://tinyurl.com/reproducible-000); this will
greatly increase your chances of getting an answer.
Ben Bolker
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.
Alternatively you could ignore the distribution and use a randomization
(permutation or bootstrap) approach to get reasonable p-values/confidence
intervals, although you'll have to be careful to do the randomization
respecting the grouping by individual.
Ben Bolker
where you substitute the expression
for mu(b) into the expression for L. In either case you'll have to
solve your link expression for mu.
Wolfram Alpha might help too.
good luck
Ben Bolker
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https
Ashis Deb ashisdeb83 at gmail.com writes:
Hi all I had made a package in R-3.0.3 , and its running well ,
my issue is it is not running in other versions or R like
R-3.0.2/3.0.1 it is showing error like ---
Error: This is R 3.0.2, package âxxxâ needs = 3.0.3
Brian Willis b.h.willis at bham.ac.uk writes:
Hi All,
I need to be able to manipulate the names of the coefficients from
*ranef()*.
If there is any missing data when fitting a mixed model using lmer, no
estimate is returned for the associated level for that random effect. Thus
if the
John Kane jrkrideau at inbox.com writes:
Can you resend the information in plain text?
It looks like you sent it in html format and it is very close to
completely unreadable.
John Kane
Kingston ON Canada
You've also posted this question at CrossValidated:
Karina Charest Castro jlonkc at gmail.com writes:
Hi!
This question is more appropriate for r-sig-mixed-mod...@r-project.org.
Please repost there (I will add a few questions/comments below that
you should probably address when you repost)
I am trying to do a glmer.nb but get this error:
...@r-project.org , but it would be a good idea to
invest in a copy of Pinheiro and Bates 2000 and find out as much
as you can for yourself first.
Ben Bolker
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PLEASE do
a log-likelihood model for the
truncated/censored case and using bbmle. It would be much less efficient
and stable than pscl, but it should work ...
Ben Bolker
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PLEASE
CASTELLI christel christel.CASTELLI at chu-nimes.fr writes:
Dear All,
I have updated my OS - Windows 7, and I found a
situation where R stops working
with reported error R for Windows GUI front-end has
stopped working. My script worked before (on windows XP).
The error occured when
Pascal Oettli kridox at ymail.com writes:
Hello,
There is no package opVar in the available CRAN packages list.
Regards,
Pascal
On Sat, Mar 8, 2014 at 6:06 PM, Charles Thuo tcmuigai at
gmail.com wrote:
[snip]
Warning message:
package 'opVar' is not available (for R version
Daniel Patón Domínguez d.paton.d at gmail.com writes:
The library of packages that installs with R includes the stats
package, in the stats package is the glm function for fitting
generalized linear models. Using glm with a binomial family will fit
a logistic regression which can be
to have to do a lot of re-engineering
from scratch. Maybe as a shortcut you could figure out a way to
get robust (Huber-White/sandwich) estimates of the standard errors?
Ben Bolker
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, MARSS, ... figuring out which is best
in your case isn't trivial ...
Ben Bolker
On 14-01-25 01:52 PM, Daniel Patón Domínguez wrote:
Dear all:
In the book Logistic Regression: An Overview Lawrence M. Healy
Eastern Michigan University, College of Technology I read this
paragraph:
Logistic
this problem via aov() with
an Error stratum
Ben Bolker
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained
? Are there big outliers, or zero-inflation,
or ... ?
If you are using glmmADMB for mixed model fitting, I would suggest
follow-ups go to r-sig-mixed-mod...@r-project.org ...
Ben Bolker
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that the confidence intervals are very wide ...) (4) I'm guessing
lrtest() is from the lmtest package, but you didn't tell us that ...
Ben Bolker
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PLEASE do read
Santiago Guallar sguallar at yahoo.com writes:
Hi,
I'd like to incorporate a random intercept in a
zero-inflated negative binomial model. Package pscl is
great but does not allow random effects, and package
MCMCglmm doesn't support the negative binomial. I'm
aware that package glmmADMB
--vanilla).
Ben Bolker
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
categorical data like a or b in the the following figure. Could
anybody let me know what command line I should go with?
These are called beeswarm plots. Try googling beeswarm plot R for
a variety of options ...
Ben Bolker
__
R-help@r-project.org
, and about your problem, to know
whether the answers are correct within sensible error bounds.
Il Mercoledì 25 Dicembre 2013 17:49, Ben Bolker bbol...@gmail.com ha
scritto:
Tia Borrelli tiaborrelli at yahoo.it writes:
Thanks for answering, in ret i've the returns of FTSE MIB (the
benchmark stock
Tia Borrelli tiaborrelli at yahoo.it writes:
Thanks for answering, in ret i've the returns of FTSE MIB (the
benchmark stock market index in Italy) and i'm estimating the
parametres of the distribution of the returns of the index using
different methods.
OK, but this still isn't a
Tia Borrelli tiaborrelli at yahoo.it writes:
Hello, i'm using R for the exploration of a time series and i'm stuck in a
problem with the fitting of the distribution.
What's the difference between fitdistr and mle?
Hard to say without a reproducible example. In the example below
the
with just the
focal parameter?
Ben Bolker
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and provide commented, minimal, self-contained
Shane Carey careyshan at gmail.com writes:
it just keeps crashing on me,
It seems to crash on this line
rgl.surface(akima.li$x,akima.li$y,akima.li$z,color=green,alpha=c(0.5))
When I run the code you gave us along with the data you gave us,
I get
Error in rgl.surface(akima.li$X,
surface without any trouble ...)
Ben Bolker
On Wed, Dec 11, 2013 at 3:24 PM, Ben Bolker bbol...@gmail.com wrote:
Shane Carey careyshan at gmail.com writes:
it just keeps crashing on me,
It seems to crash on this line
rgl.surface(akima.li$x,akima.li$y,akima.li$z,color=green,alpha=c
laurie bayet lauriebayet at gmail.com writes:
Hi,
I want to set up a mixed model ANCOVA but cannot find a way to do it.
There is:
* 1 subject factor (random, between subjects) called Subject
* 3 categorical within subjects factors called Emotion, Sex, Race
* 1 continuous covariate
Robert Lynch robert.b.lynch at gmail.com writes:
I am modeling grade as a function of membership in
various cohorts. There
are four cohorts. (NONE, ISE07,ISE08,ISE09) and two times of cohorts
coded as ISE = TRUE (ISE0#) or FALSE (NONE). There is clear co-linearity
but that is to be
running? an anova analysis is too vague.
Ben Bolker
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are probably more appropriate for
r-sig-mixed-mod...@r-project.org ...
Ben Bolker
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and provide
Cynthia Tedore Cynthia.Tedore at biol.lu.se writes:
males is a factor. If I don't specify that, then it
treats it as a numeric.
any other suggestions?
transform(spiders,focal.chel=as.numeric(focal.chel),
opponent.chel=as.numeric(opponent.chel),fmales=factor(males))
eliza botto eliza_botto at hotmail.com writes:
Dear Users of R,
I have a data frame with three column, the first column contains years,
the second one months and third one,
the days (cbind( mm dd)). I want to combine them so that i have one
column with the date format as (dd.mm.).
Erika Barthelmess barthelmess at stlawu.edu writes:
Hi everyone,
I'm new to this list and have searched R help prior for an answer
to this question, without luck. If I'm
posting in error, please forgive.
I'm thinking about using package MuMIn to do multimodel inference
with logistic
Jonas Josefsson jonas.josefsson at slu.se writes:
Hi!
(I was initially going to say that this question would probably be
better on r-sig-mixed-mod...@r-project.org, but now that I've been
through it I've changed my mind -- there aren't really any issues here
that are specific to mixed
Tomer Czaczkes Tomer.Czaczkes at biologie.uni-regensburg.de writes:
Dear Forumites,
Hi, I'm a long time eavesdropper, first time poster, but I simply couldn't
find any answer to this perhaps rather naive question:
I am trying to see if my data is significantly different from a null
Neal Fultz nfultz at gmail.com writes:
Noah,
If N is # of rows, k is # of unique IDs
Using which() is O(N), using which() in a loop is going to be O(Nk);
sorting the entire data is O(N ln N) and then you can process it in
contiguous blocks, no which required.
-Neal
You might
megan herting mherting at chla.usc.edu writes:
Hello,
I installed the newest version of R (3.0.2) as well as the
newest version of
nlme (3.1-113) in order to use summary.lmList and other
nlme functions. Once
loading the new library, lmList and summary.lm can be found,
but a number
David Winsemius dwinsemius at comcast.net writes:
On Nov 19, 2013, at 10:59 AM, Calum wrote:
Hi there,
I hope someone can help me.
I have a dataset of Concentration against Mortality, and I am trying to
compare the use of Logit and Probit models using this data.
[snip snip
Floor Biemans floor_biemans at hotmail.com writes:
[snip]
The stata code I have is:
glm c IndA fia, family(binomial s) link(cloglog) offset(offset)
The R code is:
glmt - glm(data=dataset, c ~ IndA + fia, offset = offset, family =
binomial(link = cloglog))
Which yields different
categorical, which may
be helpful terminology in searching for solutions.)
Ben Bolker
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aline.frank at wsl.ch writes:
Hello
I'm working with mixed effects models using lmer() and have some
problems to get all variance components of the model's random
effects. I can get the variance of the random effect out of the
summary and use it for further calculations, but not the
...
Ben Bolker
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a_lampei anna.lampei-bucharova at uni-tuebingen.de writes:
Dear all,
I have a problem with interactions in lmer. I have 2 factors (garden and
gebiet) which interact, plus one other variable (home),
dataframe arr. When
I put:
/
lmer (biomass ~ home + garden:gebiet + ( 1|Block), data =
Ken Knoblauch ken.knoblauch at inserm.fr writes:
Roland Deutsch roland.deutsch at tuwien.ac.at writes:
in my research I frequently work with binomial
response models, which
are of course part of the generalized linear
models. While I do use
common link functions such as the logit,
Martin Turcotte mart.turcotte at gmail.com writes:
Dear list,
I am trying to use MuMIn to compare all possible mixed models
using the dredge function on binomial data but I
am getting an error message that I cannot decode. This error
only occurs when I use glmer. When I use an lmer
to the cross-post).
Ben Bolker
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kmmoon100 k.moon at student.unimelb.edu.au writes:
Hello,
How can I do a test of two weibull distributions?
I have two weibull distribution sets from two wind datasets in order to
check whether they are same.
I thought 2 sample t-test would be applicable but I couldn't find any ways
to
, but I would
have to look a lot more carefully to know for sure.
Ben Bolker
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