I have an generalized mixed effects model such as the following:
library(lme4)
mod1<-glmer(resp~var1 (var1||group1) (1|group2), family=binomial, data=testdata,
control=glmerControl(optimizer="bobyqa", optCtrl=list(maxfun=2e6)),nAGQ=0)
AIC BIC logLik deviance df.resid
1112.4 1140.6 -550.2 1100.4 814
Scaled residuals:
Min 1Q Median 3Q Max
-1.8083 -0.9033 -0.5787 0.9235 1.7280
Random effects:
Groups Name Variance Std.Dev.
group2 var1 0.0000 0.0000
group2.1 (Intercept) 0.2059 0.4538
group1 var1 0.0000 0.0000
group1.1 (Intercept) 0.1071 0.3272
Number of obs: 820, groups: group2, 74; group1, 7
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.08061 0.35577 3.037 0.002387 **
var1 -0.08115 0.02308 -3.516 0.000438 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr)
var1 -0.900
When I look at ranef plot, the var 1 which I modeled as a random slope is centered around 0. I haven't been able to find any similar looking ranef plots, I haven't been able to dwell too deep into mixed effect models as my background is not really mathematical heavy. I am not sure what to think of this plot, what does it mean in terms of var 1?
lattice::dotplot(ranef(mod1,which="group1", condVar=TRUE))
my data is
testdata<-structure(list(group2 = c(27, 27, 27, 27, 27, 27, 27, 27, 27,
27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10,
10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16,
16, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 19, 19,
19, 19, 19, 19, 19, 19, 19, 56, 56, 56, 56, 56, 56, 56, 56, 56,
56, 56, 56, 56, 56, 56, 65, 65, 65, 65, 65, 65, 65, 65, 65, 65,
65, 65, 65, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 66, 66,
66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 66, 67, 67, 67,
67, 67, 67, 67, 67, 67, 67, 67, 67, 68, 68, 68, 68, 68, 68, 68,
68, 68, 68, 68, 68, 68, 68, 68, 69, 69, 69, 69, 69, 69, 69, 69,
69, 69, 69, 69, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70,
71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 72, 72, 72, 72, 72,
72, 72, 72, 72, 72, 72, 72, 72, 72, 73, 73, 74, 74, 74, 74, 74,
74, 74, 74, 74, 74, 74, 74, 74, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 64, 64, 64, 64, 64, 64, 64, 64, 64, 63, 63, 63, 63,
63, 63, 63, 63, 63, 63, 63, 63, 63, 62, 62, 62, 62, 62, 62, 62,
62, 62, 62, 62, 62, 62, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61,
61, 61, 61, 61, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 59,
59, 58, 58, 58, 58, 58, 58, 58, 58, 57, 57, 57, 57, 57, 57, 21,
21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23,
23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24,
25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26,
26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9,
9, 9, 9, 9, 12, 12, 12, 12, 13, 13, 13, 13, 13, 13, 14, 14, 14,
14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15,
52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 53, 53, 53, 53,
53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 54, 54, 54, 54, 54, 54,
54, 54, 54, 54, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,
55, 55, 55, 55, 51, 51, 51, 51, 51, 51, 51, 51, 51, 50, 50, 50,
50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 30,
30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31,
31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 33, 33, 33, 35, 35,
35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 37, 37, 37,
37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 39, 39, 39, 39, 39, 39,
39, 39, 39, 39, 39, 39, 39, 39, 41, 41, 41, 41, 41, 41, 41, 41,
41, 41, 41, 41, 41, 43, 43, 43, 43, 43, 42, 42, 42, 42, 42, 45,
45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20,
20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28,
28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29,
29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 47, 47, 47, 47, 47,
47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 32, 32, 32, 32, 32,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 34, 34, 34, 34,
34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 36,
36, 36, 36, 36, 36, 36, 36, 36, 38, 38, 38, 38, 38, 38, 38, 38,
38, 38, 38, 38, 38, 38, 38, 38, 38, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 44, 44, 44, 44, 44, 44, 44, 44,
44, 44, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46,
46, 46, 46, 46, 46, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49,
49, 49, 49, 49, 49), group1 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7), resp = c(0, 1, 1, 1, 1,
0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0,
1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1,
0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1,
1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0,
0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1,
0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1,
0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0,
0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1,
0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0,
1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1,
1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1,
1, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0,
0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0,
0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1,
1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1,
1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1,
0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0,
0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0,
1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1,
0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1,
0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1,
1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0,
0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1,
1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0,
0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1,
0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0,
1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 1,
0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1,
0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), var1 = c(18.8679622641132,
18.8679622641132, 21.2132034355964, 20.976176963403, 20.7364413533277,
19.2353840616713, 19.2353840616713, 19.2353840616713, 19.2353840616713,
19.2353840616713, 19.2353840616713, 18.8679622641132, 18.8679622641132,
18.8679622641132, 15.8113883008419, 15.8113883008419, 15.8113883008419,
20.976176963403, 20.976176963403, 20.976176963403, 22.9128784747792,
22.9128784747792, 22.9128784747792, 22.9128784747792, 22.9128784747792,
22.9128784747792, 22.9128784747792, 22.9128784747792, 22.9128784747792,
22.9128784747792, 22.9128784747792, 22.9128784747792, 17.606816861659,
18.1659021245849, 18.1659021245849, 18.1659021245849, 18.1659021245849,
18.1659021245849, 17.0293863659264, 17.0293863659264, 17.0293863659264,
21.095023109729, 21.095023109729, 21.095023109729, 20.2484567313166,
20.2484567313166, 22.9128784747792, 22.9128784747792, 18.4390889145858,
22.9128784747792, 22.9128784747792, 22.9128784747792, 20.976176963403,
20.7364413533277, 20.7364413533277, 20.7364413533277, 20.7364413533277,
20.7364413533277, 18.3030052177231, 17.8885438199983, 17.8885438199983,
14.142135623731, 20.4939015319192, 20.4939015319192, 20.4939015319192,
20.7364413533277, 20.7364413533277, 18.8414436814168, 20.7364413533277,
20.7364413533277, 20.7364413533277, 20.2484567313166, 20.1246117974981,
20.1246117974981, 20, 20, 20, 20, 20.976176963403, 17.606816861659,
19.2353840616713, 19.7484176581315, 20.4939015319192, 20.4939015319192,
20.2484567313166, 20.2484567313166, 20.2484567313166, 13.1909059582729,
16.9705627484771, 10.4880884817015, 11.4891252930761, 11.8743420870379,
11.8743420870379, 11.8743420870379, 11.8743420870379, 9.48683298050514,
11.4017542509914, 11.4017542509914, 11.4017542509914, 12.6491106406735,
11.4017542509914, 11.4017542509914, 16.9115345252878, 9.53939201416946,
12.6491106406735, 11.4891252930761, 11.1803398874989, 14.0356688476182,
14.0356688476182, 14.0356688476182, 14.0356688476182, 14.0356688476182,
14.0356688476182, 14.0356688476182, 14.0356688476182, 14.5258390463339,
10.0995049383621, 12.1243556529821, 15.4272486205415, 11.1803398874989,
10.4403065089106, 9.64365076099295, 9.64365076099295, 11.7473401244707,
11.7473401244707, 11.7473401244707, 13.7840487520902, 10.4880884817015,
10.4880884817015, 11.8743420870379, 11.8743420870379, 11.8743420870379,
11.8743420870379, 11.8743420870379, 11.8743420870379, 11.8743420870379,
11.8743420870379, 11.8743420870379, 11.8743420870379, 11.8743420870379,
11.8743420870379, 11.8743420870379, 11.8743420870379, 11.8743420870379,
14.4913767461894, 14.4913767461894, 14.4913767461894, 14.4913767461894,
14.4913767461894, 14.4913767461894, 14.4913767461894, 14.4913767461894,
14.4913767461894, 14.4913767461894, 16.1245154965971, 12.8840987267251,
8.24621125123532, 8.83176086632785, 14.0712472794703, 17.8044938147649,
17.8044938147649, 17.8044938147649, 17.8044938147649, 17.8044938147649,
17.8044938147649, 17.8044938147649, 17.8044938147649, 17.8044938147649,
11.8321595661992, 9.59166304662544, 14.8660687473185, 13.0384048104053,
11.8743420870379, 13.3790881602597, 13.3790881602597, 13.3790881602597,
13.3790881602597, 15.4272486205415, 12.0415945787923, 12.0415945787923,
13.0384048104053, 13.0384048104053, 13.114877048604, 7.14142842854285,
7.14142842854285, 7.14142842854285, 7.14142842854285, 7.14142842854285,
7.14142842854285, 9.64365076099295, 9.64365076099295, 9.64365076099295,
6.70820393249937, 6.32455532033676, 6.32455532033676, 16.5227116418583,
5.56776436283002, 6.70820393249937, 7.81024967590665, 9.21954445729289,
9.21954445729289, 9.53939201416946, 9.32737905308882, 9.4339811320566,
9.4339811320566, 7.28010988928052, 8.12403840463596, 8.12403840463596,
9.89949493661167, 9.4339811320566, 9.4339811320566, 9.4339811320566,
9.4339811320566, 9.4339811320566, 9.4339811320566, 9.4339811320566,
9.4339811320566, 10.2469507659596, 10, 9.53939201416946, 15.556349186104,
13.7113092008021, 12.4096736459909, 12.9614813968157, 16.1554944214035,
16.1554944214035, 16.1554944214035, 16.1554944214035, 16.1554944214035,
16.1554944214035, 16.1554944214035, 16.1554944214035, 16.1554944214035,
12.6491106406735, 12.6491106406735, 11.6189500386223, 11.6189500386223,
11.6189500386223, 11.6189500386223, 11.6189500386223, 11.6189500386223,
11.6189500386223, 11.6189500386223, 11.6189500386223, 11.6189500386223,
9.69535971483266, 12.6491106406735, 14.4913767461894, 12.1655250605964,
8.94427190999916, 8.94427190999916, 8.94427190999916, 8.94427190999916,
8.94427190999916, 8.36660026534076, 18.7082869338697, 18.7082869338697,
18.7082869338697, 19.8746069143518, 19.8746069143518, 19.8746069143518,
15.1657508881031, 17.1755640373177, 17.1755640373177, 17.1755640373177,
17.1755640373177, 17.1755640373177, 18.1659021245849, 15.1657508881031,
15.1657508881031, 15.1657508881031, 19.8746069143518, 22.4722050542442,
19.8746069143518, 19.8746069143518, 19.8746069143518, 19.8746069143518,
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CodePudding user response：
It is plotting everything at 0 because the variance term is exactly zero.
summary(mod1)
Generalized linear mixed model fit by maximum likelihood (Adaptive
Gauss-Hermite Quadrature, nAGQ = 0) [glmerMod]
Family: binomial ( logit )
Formula: resp ~ var1 (var1 || group1) (1 | group2)
Data: testdata
Control:
glmerControl(optimizer = "bobyqa", optCtrl = list(maxfun = 2e 06))
AIC BIC logLik deviance df.resid
1110.4 1133.9 -550.2 1100.4 815
Scaled residuals:
Min 1Q Median 3Q Max
-1.8083 -0.9033 -0.5787 0.9235 1.7280
Random effects:
Groups Name Variance Std.Dev.
group2 (Intercept) 0.2059 0.4538
group1 var1 0.0000 0.0000
group1.1 (Intercept) 0.1071 0.3272
Number of obs: 820, groups: group2, 74; group1, 7
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 1.08061 0.35577 3.037 0.002386 **
var1 -0.08115 0.02308 -3.516 0.000438 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr)
var1 -0.900
I'm not sure why the singular fit warning is not showing up automatically, but when I fit the model and run the following we see that it is one, and the model has not been able to estimate the random slope:
isSingular(mod1)
[1] TRUE
I would recommend looking at the different approaches to dealing with the singularity here: https://bbolker.github.io/mixedmodels-misc/glmmFAQ.html#singular-models-random-effect-variances-estimated-as-zero-or-correlations-estimated-as---1