Perhaps you are looking for the effects package, which can plot effects
(predicted values) for terms in mer objects from lme4?
library(effects)
?effect
library(lme4)
data(cake, package="lme4")
fm1 <- lmer(angle ~ recipe * temperature + (1|recipe:replicate), cake,
REML = FALSE)
plot(effect("recipe:temperature", fm1), grid=TRUE)
plot(Effect(c("recipe", "temperature"), fm1)) # equivalent
On 10/10/2013 12:52 AM, Rebecca Stirnemann wrote:
Thanks Jim for helping,
Your sample data actually looks like my dataset. The one I put up looks
strange for some reason so please ignore that.
I have three landusenumb variables 1 2 and 3. is rep (1,2,3) correct?
When I run the following code I am getting:
mod1 <- glmer(frat ~ flandusenumb + ground.cover_lo + (1|fsite) ,family =
binomial, data= mao1)
#Calculate predicted values
newdata1 <- data.frame(ground.cover_lo = c(25,50,100), flandusenumb =
rep(1,2,3))
pred34 <- predict(mod1,newdata=newdata1,type="response")
Error in UseMethod("predict") :
no applicable method for 'predict' applied to an object of class "mer"
Can you see what I am doing wrong?
What I am aiming for is a graph which looks like this.
Thanks
Rebecca
On Thu, Oct 10, 2013 at 5:33 PM, Jim Lemon <j...@bitwrit.com.au> wrote:
On 10/10/2013 08:35 AM, Rebecca Stirnemann wrote:
Dear R wizards,
Though I hate to do it after weeks of my code not working I need some help
since I cant find an example which seems to work.
I am trying to create a graph which show the probability of predation of a
nest on one side (either 1 to 0) or (0% to 100%) on one side
and grass height at the bottom. I want to then add my predicted lines from
my glmr onto the graph for three habitat types.
I would like to repeat this procedure 3 times for three different grass
heights 25- 50- 100 to see the effect size.
My data:
landusenumb landuse sitename rat ground.cover_lo 1 plantation
far.leftroad_LHS 0 60 1 plantation far.leftroad_LHS 1 70 1 plantation
far.leftroad_LHS 1 10 1 plantation far.leftroad_LHS 1 30 1 plantation
far.leftroad_LHS 1 50 1 plantation far.leftroad_LHS 0 20 1 plantation
far.leftroad_LHS 0 70 1 plantation far.leftroad_LHS 0 100 1 plantation
far.leftroad_LHS 0 90
#Graph
#Fit model
mod1<- glmer(frat ~ flandusenumb + ground.cover_lo + (1|fsite) ,family =
binomial, data= mao1)
#Calculate predicted values
newdata1<- data.frame(ground.cover_lo = seq(0,10,length=100), flandusenumb
= rep(1,2,3))
pred34<- predict(mod1,newdata=newdata1,**type="response")
#Plot model predicted curves
plot(c(0,100),c(0,1),type="n",**xlab="grasscover",ylab="**Probability of
predation")
lines(newdata1$frat,pred34,**lwd=3,col="blue")
Hi Rebecca,
First, your sample data are a bit mangled, and should look like this:
mao1
landusenumb landuse sitename rat ground.cover_lo
1 plantation far.leftroad_LHS 0 60
1 plantation far.leftroad_LHS 1 70
1 plantation far.leftroad_LHS 1 10
1 plantation far.leftroad_LHS 1 30
1 plantation far.leftroad_LHS 1 50
1 plantation far.leftroad_LHS 0 20
1 plantation far.leftroad_LHS 0 70
1 plantation far.leftroad_LHS 0 100
1 plantation far.leftroad_LHS 0 90
If you want the predicted values with ground cover as above, then:
ground.cover_lo = c(25,50,100)
The variable names in the first model don't match those in the data frame,
but I assume these were typos. What does "pred34" look like? This will tell
you what function you should be using to plot it.
Jim
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele Street Web: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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