Saya ingin menghitung CI dalam model campuran, binomial negatif nol, dan model rintangan. Kode saya untuk model rintangan terlihat seperti ini (x1, x2 kontinu, x3 kategorikal):
m1 <- glmmTMB(count~x1+x2+x3+(1|year/class),
data = bd, zi = ~x2+x3+(1|year/class), family = truncated_nbinom2,
)
Saya menggunakan confint
, dan saya mendapatkan hasil ini:
ci <- confint(m1,parm="beta_")
ci
2.5 % 97.5 % Estimate
cond.(Intercept) 1.816255e-01 0.448860094 0.285524861
cond.x1 9.045278e-01 0.972083366 0.937697401
cond.x2 1.505770e+01 26.817439186 20.094998772
cond.x3high 1.190972e+00 1.492335046 1.333164894
cond.x3low 1.028147e+00 1.215828654 1.118056377
cond.x3reg 1.135515e+00 1.385833853 1.254445909
class:year.cond.Std.Dev.(Intercept)2.256324e+00 2.662976154 2.441845815
year.cond.Std.Dev.(Intercept) 1.051889e+00 1.523719169 1.157153015
zi.(Intercept) 1.234418e-04 0.001309705 0.000402085
zi.x2 2.868578e-02 0.166378014 0.069084606
zi.x3high 8.972025e-01 1.805832900 1.272869874
Apakah saya menghitung intervalnya dengan benar? Mengapa hanya ada satu kategori di x3 untuk zi? Jika memungkinkan, saya juga ingin tahu apakah CI ini dapat diplot.
Terima kasih!
Datanya terlihat seperti ini:
class id year count x1 x2 x3
956 5 3002 2002 3 15.6 47.9 high
957 5 4004 2002 3 14.3 47.9 low
958 5 6021 2002 3 14.2 47.9 high
959 4 2030 2002 3 10.5 46.3 high
960 4 2031 2002 3 15.3 46.3 high
961 4 2034 2002 3 15.2 46.3 reg
dengan x1 dan x2 kontinu, x3 variabel kategori tiga tingkat (faktor)
Ringkasan model:
summary(m1)
'giveCsparse' has been deprecated; setting 'repr = "T"' for you'giveCsparse' has been deprecated; setting 'repr = "T"' for you'giveCsparse' has been deprecated; setting 'repr = "T"' for you
Family: truncated_nbinom2 ( log )
Formula: count ~ x1 + x2 + x3 + (1 | year/class)
Zero inflation: ~x2 + x3 + (1 | year/class)
Data: bd
AIC BIC logLik deviance df.resid
37359.7 37479.7 -18663.8 37327.7 13323
Random effects:
Conditional model:
Groups Name Variance Std.Dev.
class:year(Intercept) 0.79701 0.8928
year (Intercept) 0.02131 0.1460
Number of obs: 13339, groups: class:year, 345; year, 15
Zero-inflation model:
Groups Name Variance Std.Dev.
dpto:year (Intercept) 1.024e+02 1.012e+01
year (Intercept) 7.842e-07 8.856e-04
Number of obs: 13339, groups: class:year, 345; year, 15
Overdispersion parameter for truncated_nbinom2 family (): 1.02
Conditional model:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.25343 0.23081 -5.431 5.62e-08 ***
x1 -0.06433 0.01837 -3.501 0.000464 ***
x2 3.00047 0.14724 20.378 < 2e-16 ***
x3high 0.28756 0.05755 4.997 5.82e-07 ***
x3low 0.11159 0.04277 2.609 0.009083 **
x3reg 0.22669 0.05082 4.461 8.17e-06 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Zero-inflation model:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -7.8188 0.6025 -12.977 < 2e-16 ***
x2 -2.6724 0.4484 -5.959 2.53e-09 ***
x3high 0.2413 0.1784 1.352 0.17635
x3low -0.1325 0.1134 -1.169 0.24258
x3reg -0.3806 0.1436 -2.651 0.00802 **
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
CI dengan sapu.campuran
> broom.mixed::tidy(m1, effects="fixed", conf.int=TRUE)
# A tibble: 12 x 9
effect component term estimate std.error statistic p.value conf.low conf.high
<chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 fixed cond (Intercept) -1.25 0.231 -5.43 5.62e- 8 -1.71 -0.801
2 fixed cond x1 -0.0643 0.0184 -3.50 4.64e- 4 -0.100 -0.0283
3 fixed cond x2 3.00 0.147 20.4 2.60e-92 2.71 3.29
4 fixed cond x3high 0.288 0.0575 5.00 5.82e- 7 0.175 0.400
5 fixed cond x3low 0.112 0.0428 2.61 9.08e- 3 0.0278 0.195
6 fixed cond x3reg 0.227 0.0508 4.46 8.17e- 6 0.127 0.326
7 fixed zi (Intercept) -9.88 1.32 -7.49 7.04e-14 -12.5 -7.30
8 fixed zi x1 0.214 0.120 1.79 7.38e- 2 -0.0206 0.448
9 fixed zi x2 -2.69 0.449 -6.00 2.01e- 9 -3.57 -1.81
10 fixed zi x3high 0.232 0.178 1.30 1.93e- 1 -0.117 0.582
11 fixed zi x3low -0.135 0.113 -1.19 2.36e- 1 -0.357 0.0878
12 fixed zi x4reg -0.382 0.144 -2.66 7.74e- 3 -0.664 -0.101
broom.mixed::tidy(m1, effects="fixed", conf.int=TRUE)
untuk mendapatkan data dalam format yang sesuai untukggplot2
(atau bahkandotwhisker::dwplot(m1, effects="fixed")
) - person Ben Bolker   schedule 12.04.2021confint
hanya melaporkan satu. Bagaimanapun, saya akan mencoba sapu.campur. - person MKie45   schedule 12.04.2021summary(m1)
serta pesan peringatan apa saja yang mungkin tercetak...? - person Ben Bolker   schedule 12.04.2021levels(bd$x3)
? (2) sebagai cross check, apa hasilbroom.mixed::tidy(bd, effects="fixed", conf.int=TRUE)
? - person Ben Bolker   schedule 13.04.2021