在 ggplot2 中绘制 nlme 对象

Question

I calculated a linear-mixed model using the nlme package. I was evaluating a psychological treatment and used treatment condition and measurement point as predictors. I did post-hoc comparisons using the emmans package. So far so good, everything worked out well and I am looking forward to finish my thesis. There is only one problem left. I am really really bad in plotting. I want to plot the emmeans for the four measurement points for each group. The emmip function in emmeans does this, but I am not that happy with the result. I used the following code to generate the result:

emmip(HLM_IPANAT_pos, Gruppe~TP, CIs=TRUE) + theme_bw() + labs(x = "Zeit", y = "IPANAT-PA")

I don't like the way the confidence intervals are presented. I would prefer a line bar with "normal" confidence bars, like the one below, which is taken from Ireland et al. (2017). I tried to do it in excel, but did not find out how to integrate seperate confidence intervals for each line. So I was wondering if there was the possibility to do it using ggplot2. However, I do not know how to integrate the values I obtained using emmeans in ggplot. As I said, I really have no idea about plotting. Does someone know how to do it?

Answer 1

I think it is possible. Rather than using emmip to create the plot, you could use emmeans to get the values for ggplot2 . With ggplot2 and the data, you might be able to better control the format of the plot. Since I do not have your data, I can only suggest a few steps.
First, after fitting the model HLM_IPANAT_pos , get values using emmeans . Second, broom::tidy this object. Third, ggplot the above broom::tidy object.

Using mtcars data as an example:

library(emmeans)
# mtcars data
mtcars$cyl = as.factor(mtcars$cyl)
# Model
mymodel <- lm(mpg ~ cyl * am, data = mtcars)

# using ggplot2 
library(tidyverse)
broom::tidy(emmeans(mymodel,  ~ am | cyl)) %>% 
  mutate(cyl_x = as.numeric(as.character(cyl)) + 0.1*am) %>% 
  ggplot(aes(x = cyl_x, y = estimate, color = as.factor(am))) + 
  geom_point() + 
  geom_line() +
  geom_errorbar(aes(ymin = conf.low, ymax = conf.high), width = 0.1)

^{Created on 2019-12-29 by the reprex package (v0.3.0)}