'R: Prevent "~." in a linear mixed effect model from running an independent variable as both a fixed and random effect
I seem to be running into some issues when I run the code below:
library(lme4)
columns <- c("disp", "hp", "wt", "qsec", "vs")
X <- mtcars[,c(columns, 'cyl', 'carb', 'gear')] # data
rf <- lmer(cyl~ (carb | gear) +., data = X)
rf
### The output that I don't want (lists 'carb' and 'gear' as fixed variables):
Linear mixed model fit by REML ['lmerMod']
Formula: cyl ~ (carb | gear) + .
Data: X
REML criterion at convergence: 76.9662
Random effects:
Groups Name Std.Dev. Corr
gear (Intercept) 0.2887
carb 0.2039 -1.00
Residual 0.5202
Number of obs: 32, groups: gear, 3
Fixed Effects:
(Intercept) carb gear disp hp wt
10.179140 0.025990 -0.873174 0.003883 0.008190 0.089656
qsec vs
-0.159582 -0.779400
As you can see, it is counting 'carb' and 'gear' as fixed variables when I only need them to be used for my random effect variable.
My goal is to keep the code in a similar format and also be able to run the model without the variables 'carb' and 'gear' being taken in as fixed effects (only as random effects).
How can I prevent "~." in the first model from selecting 'carb' and 'gear' as fixed variables so that it may produce the same output as the second model below?
The output that I need: (ONLY 'carb' and 'gear' listed as random effects):
> el <- lmer(cyl~ disp + hp + wt + qsec + vs + (carb | gear), data = mtcars)
> el
Linear mixed model fit by REML ['lmerMod']
Formula: cyl ~ disp + hp + wt + qsec + vs + (carb | gear)
Data: mtcars
REML criterion at convergence: 79.7548
Random effects:
Groups Name Std.Dev. Corr
gear (Intercept) 0.9932
carb 0.1688 -0.82
Residual 0.5263
Number of obs: 32, groups: gear, 3
Fixed Effects:
(Intercept) disp hp wt qsec vs
6.848103 0.004024 0.006929 0.172789 -0.169145 -0.785878
Any help at all is greatly appreciated!
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