make sure that you
have converted 'year' to a factor rather than a numeric variable ...)
but if you re-post this to the r-sig-mixed mod...@r-project.org list I will
answer more fully ...
Ben Bolker
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arunkumar akpbond007 at gmail.com writes:
Please any one help in finding the predicted value for lmer function
model- lmer(formula =formula,data=data,verbose=TRUE,family = gaussian)
I need to get predicted value for this model.
Please see the code at http://glmm.wikidot.com/faq ,
xfei xiaoyifei at gmail.com writes:
I have a dataset with the following properties:
Y_i ~ N(mu_i, theta * (mu_i)^2)
ln(mu_i) = B'Xi
theta and beta's are the parameters here.
I want to come up with a model to fit the data with the above property and
test that model on the built in R
plocq less.is.mo_ at hotmail.com writes:
Hi,
I try to use the function profile() of the SpatialExtremes' package to
obtain the profile likelihood of parameters for an extreme values fit based
on Poisson process :
fit-fpot(data, threshold, model=pp, npp=365).
But when I call
into an error because I hadn't specified the
times variable. Presumably you have defined a times variable?
Ben Bolker
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Richard J. Buning rbuning at ufl.edu writes:
Hi,
I am attempting to impute my data for missing values using the mice
function. However every time I run the function it freezes or lags.
I have tried running it over night, and it still does not finish. I am
working with 17000
R. Michael Weylandt michael.weylandt at gmail.com writes:
Fit y-b without an intercept? (which you do by adding + 0 or - 1
to the model formula) Not sure if this is the optimal result, but it
will give you a pretty reasonable answer.
This seems backward. The OP has the slope and wants the
stat999 yumik091186 at gmail.com writes:
Hi, I am a quite beginner of random effect modelling.
Sorry for my ignorant question.
No problem, but this question is more appropriate for
the r-sig-mixed-mod...@r-project.org mailing list ...
My question is about the values of lme function.
It
Danielle Duncan dlduncan2 at alaska.edu writes:
Greetings, I have a question that I'd like to get input on. I have a
classic toxicology study where I artificially fertilized and exposed
embryos to a chemical and counted defects. In addition, I kept track of
male-female pairs that I used to
how.
-- Evelyn Hall and Simon 'Yoda' Blomberg
R-help (April 2005)
Yes, although if you really wanted to compute (symbolic) indefinite integrals,
it would be awfully hard. R is Turing-complete so of course you could do
it ... but ...
Ben Bolker
On 11-11-30 11:32 AM, peter dalgaard wrote:
On Nov 29, 2011, at 23:19 , Ben Bolker wrote:
rch4 rch4 at geneseo.edu writes:
We need help
We are doing a project for a statistical class in and we are
looking at world record times in different running events over
time. We
in R until recently
(see a long thread referenced at http://glmm.wikidot.com/faq on
degrees of freedom, but has recently been implemented in
(an experimental version of?) the 'doBy' package.
You might also get more answers if you show what you have
tried so far.
Ben Bolker
approach.
Please re-post to the r-sig-mixed-mod...@r-project.org list.
Your basic approach looks reasonable; you should be able to
use (1|Subject/Session) [check whether the results are identical]
for this nested analysis. May provide more comments in
the other forum.
Ben Bolker
rch4 rch4 at geneseo.edu writes:
We need help
We are doing a project for a statistical class in and we are looking at
world record times in different running events over time. We are trying to
fit the data with a negative exponential but we just cant seem to get a
function that works
sirilkt jankee2010 at hotmail.com writes:
Hi All,
When we run the command : summary ( newmod-gam(Dlq~ formula,family,,data) )
in R, the output would the effect of smoothness in R.
As of now to calculate the probability I am following the below approach:
1) Run the plot of the
John Kane jrkrideau at yahoo.ca writes:
There are probably lots of better aproaches but this seems to work.
I just combined the lines into one vector
and assighed a dummy variable to mark the diffferent lines
ibrary(ggplot2)
mydata - data.frame(xrange - c(100, 200, 300, 400, 500, 600,
zloncaric zloncaric at biologija.unios.hr writes:
Is it posible to apply /cumsum()/ along the 3rd dimension of 3D array?
Something like matrlab function - /cumsum (*A*,dim)/ which returns the
cumulative sum of the elements along the dimension of *A* specified by
scalar dim.
Check out the
Michael Clawson michael.v.clawson at 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
Alessio Unisi franceschi6 at unisi.it writes:
Dear R-users,
i need help for this topic!
I'm trying to determine if the reproductive success
(0=fail, 1=success) of a species of bird
is related to a list of covariates.
These are the covariates:
§elev: elevation of nest (meters)
syrvn mentor_ at gmx.net writes:
Hello,
can anyone recommend an R package which can deal with nested random-effects
ANOVA models?
Cheers
Syrvn
lme in the nlme package; lmer in the lme4 package; and/or visit
the r-sig-mixed-models list.
Ben Bolker
Tyler Rinker tyler_rinker at hotmail.com writes:
try: library(pscl)
There's a zeroinfl for zero inflated neg. binom.
Tyler
Dear All,
I am trying to fit some data both as a negative binomial and a zero
inflated binomial.
For the first case, I have no particular problems,
Peter Minting peter_minting at hotmail.com writes:
Dear R help,
I am trying to work out if I am justified in
log-transforming data and specifying Gamma in the same glm.
Does it have to be one or the other?
No, but I've never seen it done.
I have attached an R script and the datafile
Fischer, Felix Felix.Fischer at charite.de writes:
Hello,
i use ggplot to plot some measures including CIs as horizontal
errorbars. I get an error when the scale
limits are narrower than the boundaries of the error bar and
hence the CIs are not plotted.
library(ggplot2)
df -
approved channels.
Ben Bolker
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(when posting non-homework questions)
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sincerely
Ben Bolker
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Neotropical bat risk assessments neotropical.bats at gmail.com writes:
Issue with sos package
I am now using R 2.14 and the sos package did work with 2.13
library(sos)
Loading required package: brew
Attaching package: 'sos'
The following object(s) are masked from 'package:JGR':
Myriam fantasmita1948 at yahoo.fr writes:
Dear Mr. Baddeley I just graduated from a Masters in
Applied Mathematics on Jun19th. My thesis was about spatial
distribution /a nalysis of some trees in a part of the Congo Basic
Forest. In my thesis I used your spatial package in R, and today
, I'm sure lots
of people here will be happy to help.
sincerely
Ben Bolker
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arunkumar akpbond007 at gmail.com writes:
Hi
can we perform logistic regression using lmer function. Please help me with
this
Yes.
library(lme4)
glmer([reponse]~[fixed effects (covariates)]+(1|[grouping variable]),
data=[data frame], family=binomial)
Further questions
Hans W Borchers hwborchers at googlemail.com writes:
Ben Bolker bbolker at gmail.com writes:
Simulated annealing and other stochastic global optimization
methods are also possible solutions, although they may or may not
work better than the many-starting-points solution
Jun Ji junj at stanford.edu writes:
Is there any encryption package of R? For instance, 3DES or AES algorithm
package or whatever...
Thanks a lot in advance.
library(sos)
findFn(encryption)
finds a partial AES implementation, but not much else.
Rolf Turner rolf.turner at xtra.co.nz writes:
On 11/11/11 08:55, Dimitri Liakhovitski wrote:
Bert,
that's exactly where I started. I found optim in the first paragraph
under General Purpose Continuous Solvers and used bounded BFGS for a
constrained optimization for a situation with
David Winsemius dwinsemius at comcast.net writes:
On Nov 9, 2011, at 2:59 PM, Nathan Miller wrote:
Hello,
This is a pretty simple question, but after spending quite a bit of
time
looking at Hmisc and using Google, I can't find the answer.
If I use
arunkumar akpbond007 at gmail.com writes:
I'm getting the intercepts of the Random effects as 0. Please help me to
understand why this is coming Zero
This is my R code
Data- read.csv(C:/FE and RE.csv)
Formula=Y~X2+X3+X4 + (1|State) + (0+X5|State)
David Winsemius dwinsemius at comcast.net writes:
From that hand waving description it would be difficult to tell. Sounds like a
reinvention of the Pareto
Index, for which you can find many packages that provide facilities:
Davg davidgrimsey at hotmail.com writes:
I am trying to compare negative binomial models for the prediction of sports
games (I know that Poisson models would be better but I'm just trying
Negative Binomial at the moment).
But, to compare the models I need them to have the same theta value.
on http://glmm.wikidot.com/faq about this ... ?
If you look at it and still can't work it out I would suggest that requesting
help on the r-sig-mixed-models list will be more useful ...
Ben Bolker
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ethan.shepherd someguy235 at gmail.com writes:
I'm getting errors when running what seems to be a simple Weibull
distribution function:
[snip]
If I change the data to this:
[snip]
I get the error Error in fitdistr(x, weibull): optimization failed
I can run a Weibull
Scott Raynaud scott.raynaud at yahoo.com writes:
Is there a package that will perform power calculations
for mixed model ordinal logistic regression? I
searched and came up with nothing.
Didn't you ask this question, and get an answer, on this list
yesterday ... ??
robgriffin247 robgriffin247 at hotmail.com writes:
Hi,
I'm sure there is a pretty simple answer to this but I have had my head
buried in the R book and on help pages for a while now and I've not made any
progress.
In simple terms:
I have 2 columns of data, column A and column B. I want
Bert Gunter gunter.berton at gene.com writes:
If I understand you correctly, it sounds like you need to do some reading.
?lm and ?formula tell you how to specify linear models for glm or glmnet.
However, if you do not have sufficient statistical background, It probably
will be
with glmnet but you are familiar with GLMs in
general may I suggest bigglm() in the biglm package?
On Tue, Oct 25, 2011 at 12:34 PM, Marc Schwartz marc_schwa...@me.com wrote:
On Oct 25, 2011, at 11:16 AM, Ben Bolker wrote:
Bert Gunter gunter.berton at gene.com writes:
If I understand you
Adrienne Wootten amwootte at ncsu.edu writes:
R-listers,
I have noticed several posts on issues with difftime producing NA's
but they have been for older versions of R. Here's the issue
associated with difftime that I am dealing with in R 2.12.2.
difftime(strptime(03/11/2007
to
r-sig-mixed-mod...@r-project.org (the special interest
group on mixed models)
Ben Bolker
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Md Desa, Zairul Nor Deana Binti zndeana at ku.edu writes:
Hello,
Does anyone knows how to deal with zero subscript in R.
Try the Oarray package (that's a capital letter O).
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R. Michael Weylandt michael.weylandt at gmail.com writes:
It seems like the relevant plot would depend on what you are trying to
investigate, but usually a scatterplot would well work for bivariate
data with no other assumptions needed. I usually find ecdf() plots
rather hard to interpret
Henri Mone henriMone at gmail.com writes:
I want to fit to my data an exponential function with following
functional form:
y=exp(a*x)
I used the function nls but this gives me exponential fits with
following functional form:
y=l*exp(a*x)
With l being an scaling factor. What do I need
problem exactly.
That fix is 18 months old, so updating might be a good idea ...
Ben Bolker
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you can't solve
analytically).
Ben Bolker
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Lucas Merrill Brown lucas.merrill.brown at gmail.com writes:
I've been programming maximum likelihood estimation models using the
function optim. My current research requires modeling a particular
parameter as a categorical variable (what R calls a factor), not as a
continuous parameter.
D_Tomas tomasmeca at hotmail.com writes:
Hi,
I am trying to fi a glm-poisson model to 400.000 records. I have tried biglm
and glmulti but i have problems... can it really be the case that 400.000
are too many records???
I am thinking of using random samples of my dataset.
I
in addition to
WinBUGS, and the addition of BRugs, R2OpenBUGS, rjags, R2jags
interfaces to the R2WinBUGS interface). I don't know of any systematic
comparisons, though.
good luck,
Ben Bolker
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Jonas Fransson jf at iva.dk writes:
I have a dataframe with two columns,
where NUMBER is the number of occurrences of DEPTH:
a-data.frame(c(2,3,2,5),c(1,2,3,1))
colnames(a)=c(DEPTH,NUMBER)
I want a column or a vector where all the DEPTHs are listed: 2, 3, 3, 2, 2, 2,
5 (NUMBER=1 in
emmarosenfeld emmarosenfeld at hotmail.co.uk writes:
Dear all,
I am having some problems trying to run a GLMM model with zero-inflation
using the alpha version of glmmADMB (0.6.4) using R (2.13.1) in Windows and
I would greatly appreciate some help.
My count response variable (number of
D_Tomas tomasmeca at hotmail.com writes:
I have fitted a Negative Binomial model (glm.nb) and a Poisson model (glm
family=poisson) to some count data. Both have the same explanatory variables
dataset
When I call sum(fitted(model.poisson)) for my GLM-Poisson model, I obtain
exactly the
value)
out of the elements in the integrand.
Ben Bolker
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to set lower and upper bounds.) [See section 6.6.1 of
the book for more details.]
Note that I have included ReedfrogFuncresp in the data list.
I now regret using attach() in the book examples.
Ben Bolker
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Paul Hiemstra paul.hiemstra at knmi.nl writes:
Hi,
When using ggplot, take a look at facet_wrap and geom_histogram.
regards,
More specifically, try something along the lines of
d - data.frame(f=factor(paste(chr,rep(c(1,2,3,7,9,22),each=50),sep=)),
v=runif(300))
library(ggplot2)
-mail easily).
Ben Bolker
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[cc'ed back to r-help]
I've started to take a look, and there's nothing immediately obvious
about the problem with the fit (the warnings and errors are about a
non-positive-definite Hessian, which usually means an
overfitted/poorly identified model) -- still working on whether there's
a way to
list.
Ben Bolker
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(e.g. if family were gaussian or Gamma).
Ben Bolker
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lincoln miseno77 at hotmail.com writes:
Hi all,
I have run a (glm) analysis where the dependent variable is the gender
(family=binomial) and the predictors are percentages.
I get a warning saying fitted probabilities numerically 0 or 1 occurred
that is indicating that quasi-separation or
Steve Lianoglou mailinglist.honeypot at gmail.com writes:
Hi,
On Wed, Oct 12, 2011 at 11:23 AM, Akram Khaleghei Ghosheh balagh
a.khaleghei at gmail.com wrote:
Hello;
Does anybody knows that R have a function for Generelized Negative Binomial
model, something like gnbreg in STATA
nqueralt at clinic.ub.es writes:
I am facing the problem that comes up when an ExpressionSet
object is intended to be created parsing a matrix
expression data with duplicate row names:
You might have more luck with this question on the BioConductor mailing
list ...
(library(sos); findFn({delta method})).
More text to try to make gmane happy
Ben Bolker
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collegegurl69 gunnerman4000 at hotmail.com writes:
I have this error and I can't figure out whats wrong:
invalid or not-yet-implemented 'Matrix' subsetting
it pops up when I try to run this line of code:
S - B[indices.mod,union(mir.e.nc,mir.negatives.nc)]
Could we have a reproducible
shardman samuelhardman at hotmail.com writes:
Hi,
I'm trying to analyse some data I have imported into R from a .csv file but
when I carry out the aov command the results show only one degree of freedom
when there should be 14. Does anyone know why? I'd really appreciate some
help, the
Heverkuhn Heverkuhn heverkuhn at gmail.com writes:
[snip]
when I launch findFn from RStudio ( but not from R
console)
the table of results does not pop in the browser and I got a warning.
findFn(test)
found 9914 matches; retrieving 20 pages, 400 matches.
2 3 4 5 6 7 8 9 10 11 12 13 14
florencia bonatto mfbonatto at yahoo.com.ar writes:
I have a linear
mixed-effects model (from the package
nlme) with a random effect; Is there something like
an r squared for the whole
model which I can state? I´d like to kown: How would I do anova for a linear
mixed-effects model?
Marcus Drescher drescher at tum.de writes:
Hi all,
is there a way to calculate standard error of random effect
from the estimated model in lme?
Search in http://glmm.wikidot.com/faq , and post follow-up
questions to the r-sig-mixed-models mailing list.
Ben Bolker
Joyce Flynt dr.joyceflynt at yahoo.com writes:
Im doing a project using Rcommander. I have a dataset with 5 variables,
BMI being one of them. I would like to
find the variance, standard deviation, range, median, etc of BMI.
However, everytime I type a command
into the script window,
Karel V karel.viaene at ugent.be writes:
Dear all,
I’m analyzing this dataset containing biodiversity indices, measured over
time (Week), and at various contaminant concentrations (Treatment). We have
two replicates (Replicate) per treatment.
I’m looking for the effects of time (Week)
Kevin Wright kw.stat at gmail.com writes:
Generally, the only way to estimate f1:f2 is if you have all combinations of
data present for these two factors.
Well, he said it was unbalanced, he didn't say how unbalanced --
i.e. it's not clear (to me) whether there are any completely missing
saber fallahpour s_fallahpour at yahoo.com writes:
Hi
I want to do simulation on quasi-binomial distribution with some covariates.
Does anyone have an idea how to do that?
There is no such thing as a quasi-binomial distribution, but if you
parameterized the beta-binomial distribution
Bert Gunter gunter.berton at gene.com writes:
Below.
On Tue, Oct 4, 2011 at 7:34 AM, Panagiotis pat2 at hi.is wrote:
Hi,
I applied a linear mixed effect model in my data using the nlme package.
lme2-lme(distance~temperature*condition, random=~+1|trial, data) and then
anova.
I
for practical
purposes than the well-tested existing RNG algorithms described in
?RNGkind ...
Ben Bolker
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on that list if you can't find
a suitable answer.
Ben Bolker
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Duncan Murdoch murdoch.duncan at gmail.com writes:
On 11-10-02 1:11 PM, Kerry wrote:
I have 3 columns of data and want to plot each row as a point in a
scatter plot and want one column to be represented as a color gradient
(e.g. larger values being more red). Anyone know the command or
of my
post.
Sorry.
Ben Bolker
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sincerely
Ben Bolker
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Meredith Jantzen mjantzen at uwo.ca writes:
Hello everyone, Apologies in advance, as this is partially a stats
question and partially an R question. I have been using a GAM to
model the activity level of bats going into and coming out from a
forested edge. I had eight microphones set up
importing the
whole thing and *then* selecting the relevant columns.
If the original poster is trying to avoid importing the whole
data set because (for example) it's got a gigantic number of
columns and will be very slow and/or tax their system, then this
idiom won't help.
Ben Bolker
阮铮 rz1991 at foxmail.com writes:
I encounters some codes in ggplot2 manual and confused with one of
its lm syntax.
[snip]
mod - lm(lprice2 ~ lcarat * color, data = d)
# *** what puzzled me is the
last statement marked with ***. How does R deal with lcarat * color,
since color is not of
Spencer Graves spencer.graves at structuremonitoring.com writes:
On 9/25/2011 9:57 AM, Berend Hasselman wrote:
Joshua Wiley-2 wrote:
So we have at least three people interested, maybe not call for a
totally new system. What about a PDF form that could be filled out
digitally, saved,
Joseph Park jpark.us at att.net writes:
Perhaps this question is inappropriate or posted to the wrong list?
Any guidance would be appreciated. Thanks.
[snip]
This seems like a perfectly reasonable question.
Sometimes people just don't bite.
Ben Bolker
Allan Carson acarson at unbc.ca writes:
[snip]
When I try to conduct a
multiple comparison, I get an error (See below):
fm3- lme(abovegroundbiomass.m.2~medium*amelioration*fertilizer*treatment,
random=~1|block/medium/amelioration/fertilizer)
tukeytest-glht(fm3,
Diviya Smith diviya.smith at gmail.com writes:
I dont think *r* is related to the problem. I am not trying to
estimate *r* and
so basically I am giving the model the correct value of *r* and so log(1-r)
should not go to infinity.
For test data, I generate data from the same model and
Andrey A avakoa at gmail.com writes:
Hello I performed a linear regression, my equation is Y = âo+ â1A + â2B +
â3AB.
Is there a way to separate interaction terms, say â3AB and plot it against a
certain variable?
Thanks, Andrew
Not quite sure what you mean here. Possibly something like
Atle Torvik Kristiansen atletorvik at gmail.com writes:
I have a dataset where the residual variance decreases with on one of
the predictors (population size).
Currently, the full model looks like this:
prior-list(R=list(V=1e-16, nu=-2),G1=list(V=diag(2), nu=2))
rjswift rosejswift at gmail.com writes:
I'm trying to select a model under PCA using independent contrasts. Since
PICs need to be forced through the origin I've been using lmorigin for the
original regression, but it doesn't appear that stepAIC recognizes it. I
keep receiving an error
for everyone's skepticism is that matrix multiplication
is a *very* basic part of R, tested at least thousands and possibly
millions of times a day by thousands of users on all different platforms --
so it's surprising that it is failing for you.
Ben Bolker
Xavier Fernández i Marín xfim.ll at gmail.com writes:
More elements: In python the same algorithm does not show this strange
behaviour.
Is Python using the same BLAS/LAPACK?
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It's your choice which venue you prefer.
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varunshivashankar varunshivashankar at gmail.com writes:
I have a dataset
X Y1
1200 1.375
4000 0.464
1333.33 0.148
444.440.047
148.148 0.014
49.3830.005
16.4610.004
I have to find a curve fit for the above dataset based on a 4-parameter
jonas garcia garcia.jonas80 at googlemail.com writes:
I am trying to fit some mixed models using packages lme4 and nlme.
I did the model selection using lmer but I suspect that I may have some
autocorrelation going on in my data so I would like to have a look using the
handy correlation
at http://prof.beuth-hochschule.de/groemping/relaimpo/ it seems that
you can't legally install that version of the package because of
conflicts with http://www.patentstorm.us/patents/6640204.html.
Would some of the other results of
library(sos)
findFn({relative importance})
work for you?
Ben
joerg stephan stephanj at rhrk.uni-kl.de writes:
Hi,
I tried to do a nested Anova with the attached Data. My response
variable is survivors and I would like to know the effect of
(insect-egg clutch) size, position (of clutch on twig) and clone
(/plant genotype) on the survival of eggs
eeadie eeadie at unm.edu writes:
Now I have a new problem with the same model that I've been working on. Here
is the model and the error message:
modelnbbb-glmmadmb(total_bites_rounded~age_class_back+
(1|focal_individual)+(1|food.dif.id)+
easier in your case since the means
line up in the order you want.
Just a thought.
Ben Bolker
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