混合 model 绘图与 R - 显示数据点

Question

I have run a mixed effects binary model using the following code:

model = glmer(A ~ B + (1|C), data = data, family = "binomial")
summary(model)

I am now plotting the marginal fixed effects for a variable of interest (B). I have taken the code from the nice page on: https://cran.r-project.org/web/packages/ggeffects/vignettes/practical_logisticmixedmodel.html

To produce the graph I have used:

ggpredict(model, "B")
plot(ggpredict(model, "B"))

The following is created which I like. But I want also the data points from the variable B to show on the graph. How can I add these in? Thanks.

Answer 1

welcome to stackoverflow:)

Sadly, I dont know how to (/whether it is possible) to add points to your plot of the ggpredict-object, since I am no good with ggplots:/ But I can do a workaround with baseplot. Only thing missing are the grey confidence intervals...which may bw crucial for good looks? :D

Cheers

#using the example data from the link you provided:

library(magrittr)
library(ggeffects)
library(sjmisc)
library(lme4)
library(splines)

set.seed(123)

#creating the data:

dat <- data.frame(
  outcome = rbinom(n = 100, size = 1, prob = 0.35),
  var_binom = as.factor(rbinom(n = 100, size = 1, prob = 0.2)),
  var_cont = rnorm(n = 100, mean = 10, sd = 7),
  group = sample(letters[1:4], size = 100, replace = TRUE)
)

dat$var_cont <- sjmisc::std(dat$var_cont)

#model creation:
m1 <- glmer( outcome ~ var_binom + var_cont + (1 | group), 
             data = dat, 
  family = binomial(link = "logit")
)

#save results:
m1_results <- ggpredict(m1, "var_cont")

#same plot you did:
plot(m1_results)

#workaround using baseplot:
#plotting the raw data:
plot(dat$outcome~dat$var_cont,
     pch = 16,
     ylab = "outcome",
     xlab = "var_cont",
     yaxt = "n")
#adding yaxis with percentages:
axis(2, at = pretty(dat$outcome), lab=paste0(pretty(dat$outcome) * 100," %"), las = TRUE)
#adding the model taken from ggpredict:
lines(m1_results$predicted~m1_results$x, 
      type = "l")
#upper and lower conf intervals:
lines(m1_results$conf.low~m1_results$x, 
      lty=2)
lines(m1_results$conf.high~m1_results$x, 
      lty=2)