Displaying 20 results from an estimated 200 matches similar to: "Calculating the percentage of explained deviance in lmer"
2010 Jul 22
5
choosing a random sample by precentage
hi all
i have found the follwoing way to choose a random sample by sample size (200):
ten_per_T2000 <- F_T2000_All[sample(nrow(F_T2000_All), 200), ]
but i wondered if there is a way to choose a sample size by
precentage (10% etc..)
thx
ethan
2004 Oct 19
1
barchart fails when grouping variable has more than 7 levels (PR#7293)
Full_Name: Andreas Kiermeier
Version: 2.0.0
OS: Windows XP
Submission from: (NULL) (203.26.122.12)
I've struck a problem drawing barcharts after installing R 2.0.0. Previously
I've used the following command
print(barchart(100*result ~ sample,
groups=congener,
data=dioxin.2003.fresh.ub.p, stack=TRUE, ylim=c(0,102)))
to draw a stacked barchart of the
2009 Nov 10
1
phase determination
Hi,
I'm trying to determine the phase of irregularly sampled data. Is there any
particular reason why both spec.pgram and spec.ls return phase<-NULL for
vectors?
Thank you.
Lisandro
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxx
Lisandro Benedetti-Cecchi
Associate Professor in Ecology
Department of Biology - University of Pisa
Via
2011 Nov 10
1
Sum of the deviance explained by each term in a gam model does not equal to the deviance explained by the full model.
Dear R users,
I read your methods of extracting the variance explained by each
predictor in different places. My question is: using the method you
suggested, the sum of the deviance explained by all terms is not equal to
the deviance explained by the full model. Could you tell me what caused
such problem?
> set.seed(0)
> n<-400
> x1 <- runif(n, 0, 1)
> ## to see problem
2017 Oct 05
0
fraction of null deviance explained by each node/variable in regression trees
I have used packages rpart, mvpart and tree for classification and
regression trees. I want to calculate fraction of null deviance explained
by each node and variable in the tree. For instance, at the first split,
this would be (1 - (sum of residual deviance in each of the two
leaves)/deviance at the root). In the subsequent splits, this formula is
slightly different.
There probably is a function
2005 Jul 08
1
explained deviance in multinom
Hi:
I'm working with multinomial models with library nnet, and I'm trying to get the explained deviance (pseudo R^2) of my models.
I am assuming that:
pseudo R^2= 1 - dev(model) / dev (null)
where dev(model) is the deviance for the fitted model and dev(null) is the deviance for the null model (with the intercept only).
library(nnet)
full.model<- multinom(cbind(factor1,
2006 Apr 23
1
lme: null deviance, deviance due to the random effects, residual deviance
A maybe trivial and stupid question:
In the case of a lm or glm fit, it is quite informative (to me) to have
a look to the null deviance and the residual deviance of a model. This
is generally provided in the print method or the summary, eg:
Null Deviance: 658.8
Residual Deviance: 507.3
and (a bit simpled minded) I like to think that the proportion of
deviance 'explained' by the
2010 Jul 30
2
svydesign syntax and deviance!
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Nom : non disponible
URL : <https://stat.ethz.ch/pipermail/r-help/attachments/20100731/ac3b9e43/attachment.pl>
2012 Jan 10
0
rpart vs. tree and deviance calculations
Hi Everyone,
I'm working on building some classification trees, and up to this point
I've been using rpart. However, I recently discovered the tree package,
and found that it had some useful functions (in particular deviance(),
which I would really like to use for my project). I can't seem to find
an equivalent function for rpart. I've considered using tree() in place
of
2008 Jan 10
0
Residual deviance in glm
I'm running a categorical data analysis with a two-way design of
nominal by ordinal structure like the Political Ideology Example
(Table 9.5) in Agresti's book Categorical Data Analysis. The nominal
variable is Method while the ordinal variable is Quality (Bad,
Moderate, Good, Excellent). I rank/quantify Quality with another
variable QualityR (1, 2, 3, 4), and run the following:
2006 Nov 30
0
Standardized deviance residuals in plot.lm
It seems that the standardized deviance residulas, that one gets on
plots of a glm.object x with plot(x) are calculated as
r <- residuals(x)
s <- sqrt(deviance(x)/df.residual(x))
w <- weights(x)
hii <- lm.influence(x)$hat
r.w <- if (is.null(w)) r else (sqrt(w) * r)
rs <- r.w/(s * sqrt(1 - hii))
This implies that, for example, for binomial B(ni,pi) data the devaince
residials
2012 Nov 26
0
R jags clear deviance
Hi all,
I'd like to fit different models using a loop together with the jags
package.
to do this, I load the following packages "runjags", "R2jags" and "coda"
and use the function "jags" to fit my models.
The problem is that the following a windowx with the following message
appear between each model fitting inside my loop : the following objects in
2011 Aug 17
0
How to calculate residual mean deviance in rpart
Hi,
I am doing a regression tree using the package 'rpart' but could not able to
calculate the residual mean deviance.
Please help.
Narayan
[[alternative HTML version deleted]]
2002 Feb 28
1
get deviance from glm() for given parameter values
Dear all,
I would like to get glm() return its results (at least the deviance) for
some given parameter values (ie without actually fitting the model). I
tried to set `maxit = 0' but this does not work, eg:
> glm(y ~ x, start = c(1, 1), maxit = 0)
Error in glm.control(...) : maximum number of iterations must be > 0
Any idea?
Thanks in advance.
Emmanuel Paradis
2007 Nov 21
0
How to extract the Deviance of a glm fit result
dear List:
glm(a~b+c,family=binomial,data=x)->fit
deviance(fit) returns the same as the residual deviance.
I don't not know much about logistic regression.Some book tells that:
"
Deviance (likelihood ratio statistic):
Deviance = -2log( likelihoodof the currentmodel /likelihoodof thesaturated
model)
Note:
(1). The current model is the model of interest.
(2). The saturated model
2009 Jan 07
0
Residual deviance (cross-post from sci.stat.consult)
Dear all,
I'm trying to fit a statistical model to series of measurements.
Unfortunately, my knowledge of statistics is rather limited, so I'm a
bit at loss of what is going on with the model.
First of all, I've prepared a histogram. Then, I've tried to fit a Poisson model to express the relation between the middle points of
classes (mids) and the corresponding frequencies
2009 May 27
1
Deviance explined in GAMM, library mgcv
Dear R-users,
To obtain the percentage of deviance explained when fitting a gam model using the mgcv library is straightforward:
summary(object.gam) $dev.expl
or alternatively, using the deviance (deviance(object.gam)) of the null and the fitted models, and then using 1 minus the quotient of deviances.
However, when a gamm (generalizad aditive mixed model) is fitted, the
2011 Jul 12
2
Deviance of zeroinfl/hurdle models
Dear list, I'm wondering if anyone can help me calculate the deviance
of either a zeroinfl or hurdle model from package pscl?
Even if someone could point me to the correct formula for calculating
the deviance, I could do the rest on my own.
I am trying to calculate a pseudo-R-squared measure based on the
R^{2}_{DEV} of [1], so I need to be able to calculate the deviance of
the full and null
2012 Jan 13
1
deviance and variance - GAM models
Hi all,
This is pretty basic but I am not an expert and I couldn't find anything in
the forum or my statistics book about it. I was reading a paper and the
authors were using both "explained deviance" and "explained variance" as
synonyms. They were describing a GAM regression. Is that right? I performed
an analysis in R to take a look to the output of GAM regression and I
2013 Feb 12
0
Deviance and AIC in weighted NLS
Dear All,
I encounter some discrepancies when comparing the deviance of a weighted and
unweigthed model with the AIC values. A general example (from 'nls'):
DNase1 <- subset(DNase, Run == 1)
fm1DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1)
Now for a weighted fit:
fm2DNase1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal),