similar to: Likelihood ratio test between glm and glmer fits

I am currently running a generalized linear mixed effect model using glmer and I want to estimate how much of the variance is explained by my random factor. summary(glmer(cbind(female,male)~date+(1|dam),family=binomial,data= liz3")) Generalized linear mixed model fit by the Laplace approximation Formula: cbind(female, male) ~ date + (1 | dam) Data: liz3 AIC BIC logLik deviance 241.3

Hi all, I am trying to run a glm with mixed effects. My response variable is number of seedlings emerging; my fixed effects are the tree species and distance from the tree (in two classes - near and far).; my random effect is the individual tree itself (here called Plot). The command I've used is: mod <- glmer(number ~ Species + distance + offset(area) + (1|Plot), family = poisson)

Dear all, I found a problem with 'lme4'. Basically, once you load the package 'aod' (Analysis of Overdispersed Data), the functions 'lmer' and 'glmer' don't work anymore: library(lme4) (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) (gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd), family = binomial, data

Dear list, I have another (again possibly boneheaded) puzzle about importing, again encapsulated in a nearly trivial package. (The package is posted at <http://www.math.mcmaster.ca/bolker/misc/coefsumtest_0.001.tar.gz>.) The package consists (only) of the following S3 method definitions: coeftab <- function(object, ...) UseMethod("coeftab",object) coeftab.default <-

Hello, I am using glmer() from lmer(lme4) to run generalized linear mixed models. However, I am having a problem extracting the standard errors for the fixed effects. I have used: summary(model)$coef fixed.effects(model) coef(model) to get out the parameter estimates, but do not seem able to extract the se's. Anybody have a solution? Thanks, John

Hello, I need to perform a mixed-model (with nesting) MANCOVA, using Type III sums of squares. I know how to perform each of these types of tests individually, but I am not sure if performing a mixed-model MANCOVA is possible. Please let me know. Erika <>< <>< <>< <>< <>< <>< <>< Erika Crispo, PhD candidate

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 analysis on a different response variable every works great. Example using a simplified glmer model global model: mod<- glmer(cbind(st$X2.REP.LIVE,

Hi, after one month with gmirror and gjournal running on a 7.0-RELEASE #p2 amd64 (built from latest CVS source), the box hung a couple of times when on high disk load. Finally, while building some port it won't boot for no reason obvious to me. This is what I get with kernel.geom.mirror.debug=2: ata2-master: pio=PIO4 wdma=WDMA2 udma=UDMA133 cable=40 wire ad4: 476940MB <SAMSUNG HD501LJ

Hi, I've been following a similar and current thread about name resolution from LINUX side. I have exactly the opposite problem (running ubuntu 7.10 on a network with a mixture ubuntu 6.06, WinXP and WinVista boxes) The winboxes cannot see or mount this 7.10 box I can mount WinPC shares on this 7.10 box. I was wondering about firewalls, but I can ping this 7.10 from the WinBox by IP address

Hello everybody, Please, help to fix me a problem. I have a distributed-replicated volume between two servers. On each server I have 2 RAID-10 arrays, that replicated between servers. Brick gl1:/mnt/brick1/gm0 49153 0 Y 13910 Brick gl0:/mnt/brick0/gm0 N/A N/A N N/A Brick gl0:/mnt/brick1/gm0 N/A

I just did a source upgrade from 8.2 to 8.3. System boots but has this warning: GEOM_PART: integrity check failed (mirror/gm0, MBR) Google points to issues with FreeBSD 9 and the need to migrate to GPT but I wasn't expecting this with 8.3! Are there any quick fixes to eliminate this warning or is it safe to ignore please? sudo gpart list: Geom name: mirror/gm0 modified: false state:

Dear Ben, Perhaps I'm missing the point, but contrasts.arg is documented to be a list. From ?model.matrix: "contrasts.arg: A list, whose entries are values (numeric matrices or character strings naming functions) to be used as replacement values for the contrasts replacement function and whose names are the names of columns of data containing factors." This isn't entirely

Hi, community Please, help me with my trouble. I have 2 Gluster nodes, with 2 bricks on each. Configuration: Node1 brick1 replicated on Node0 brick0 Node0 brick1 replicated on Node1 brick0 Volume Name: gm0 Type: Distributed-Replicate Volume ID: 5e55f511-8a50-46e4-aa2f-5d4f73c859cf Status: Started Snapshot Count: 0 Number of Bricks: 2 x 2 = 4 Transport-type: tcp Bricks: Brick1:

Hi, We're using gmirror on our sun fire x2100 and FreeBSD 6.1-p10. Some days ago I found this in the logs: Apr 1 02:12:05 x2100 kernel: ad6: WARNING - WRITE_DMA48 UDMA ICRC error (retrying request) LBA=612960533 Apr 1 02:12:05 x2100 kernel: ad6: FAILURE - WRITE_DMA48 status=51<READY,DSC,ERROR> error=10<NID_NOT_FOUND> LBA=612960533 Apr 1 02:12:05 x2100 kernel: GEOM_MIRROR:

>>>>> Ben Bolker >>>>> on Thu, 21 Feb 2019 08:18:51 -0500 writes: > On Thu, Feb 21, 2019 at 7:49 AM Fox, John <jfox at mcmaster.ca> wrote: >> >> Dear Ben, >> >> Perhaps I'm missing the point, but contrasts.arg is documented to be a list. From ?model.matrix: "contrasts.arg: A list, whose entries are

Hi list, I'm working with gamm models of this sort, using Simon Wood's mgcv library: gm<- gamm(Z~te(x,y),data=DATA,random=list(Group=~1)) gm1<-gamm(Z~te(x,y,by=Factor)+Factor,data=DATA,random=list(Group=~1)) with a dataset of about 70000 rows and 110 levels for Group in order to test whether tensor product smooths vary across factor levels. I was wondering if comparing those two

I upgraded from 6.2 to 6.3 p5 last night. Upon rebooting, the second disk in the mirror is missing. # atacontrol status ar0 ar0: ATA RAID1 status: DEGRADED subdisks: 0 ad0 ONLINE 1 ---- MISSING # grep ata /var/run/dmesg.boot ad0: 238475MB <WDC WD2500AVJB-63UDA0 00.02C01> at ata0-master UDMA100 ad1: 238475MB <WDC WD2500AVJB-63UDA0 00.02C01> at ata0-slave UDMA100 ar0: disk0

Hi, I am working with gam models in the mgcv library. My response variable (Y) is binary (0/1), and my dataset contains repeated measures over 110 individuals (same number of 0/1 within a given individual: e.g. 345-zero and 345-one for individual A, 226-zero and 226-one for individual B, etc.). The variable Factor is separating the individuals in three groups according to mass (group 0,1,2),

>>>>> Fox, John >>>>> on Fri, 22 Feb 2019 17:40:15 +0000 writes: > Dear Martin and Ben, I agree that a warning is a good idea > (and perhaps that wasn't clear in my response to Ben's > post). > Also, it would be nice to correct the omission in the help > file, which as far as I could see doesn't mention that a

Dear all, I am running glmer() in R. How can I retrieve the estimates of fixed effects and the variance of the random effects from the result? Thank you so much. Joe ___________________________________________________ ±zªº¥Í¬¡§Y®É³q ¡Ð ·¾³q¡B®T¼Ö¡B¥Í¬¡¡B¤u§@¤@¦¸·d©w¡I [[alternative HTML version deleted]]