CODEWITHSUNDEEP
rggplot2broom
giac
giac

Reputation: 4299

R - tidy augment confidence interval

I am wondering how I can compute confidence interval using the broom package.

What I am trying to do is simple and standard : 

set.seed(1)
x <- runif(50)
y <- 2.5 + (3 * x) + rnorm(50, mean = 2.5, sd = 2)
dat <- data.frame(x = x, y = y)
mod <- lm(y ~ x, data = dat)

Using visreg I can plot regression models with CI very simply with : 

library(visreg)
visreg(mod, 'x',  overlay=TRUE)

enter image description here

I am interesting in reproducing this using broom and ggplot2, so far I only achieved this : 

 library(broom) 

 dt = lm(y ~ x, data = dat) %>% augment(conf.int = TRUE)  
 ggplot(data = dt, aes(x, y, colour = y)) + 
  geom_point() + geom_line(data = dt, aes(x, .fitted, colour = .fitted))

enter image description here

The augment funciton doesn't compute conf.int. Any clue how I can add some smooth confidence invervals ? 

 geom_smooth(data=dt, aes(x, y, ymin=lcl, ymax=ucl), size = 1.5, 
        colour = "red", se = TRUE, stat = "smooth")

Upvotes: 1

Views: 2356

Answers (3)

Matifou
Matifou

Reputation: 8880

Note that the broom::augment() version does not have (at least in version 1.0.6) a conf.int argument, but it has an interval argument that will add columns .lower and .upper.

Here's the complete reproducible code:

library(ggplot2)
library(broom)
set.seed(1)
x <- runif(50)
y <- 2.5 + (3 * x) + rnorm(50, mean = 2.5, sd = 2)
dat <- data.frame(x = x, y = y)
mod <- lm(y ~ x, data = dat)

broom::augment(mod, interval = "confidence") |>
  ggplot(aes(x=x, y=y))+
  geom_ribbon(aes(ymin=.lower, ymax=.upper), alpha=0.2, color="grey")+
  geom_line(aes(y=.fitted), color="blue")+
  geom_point()

Created on 2024-08-23 with reprex v2.1.1

Upvotes: 0

Sandipan Dey
Sandipan Dey

Reputation: 23101

Just do this (with your original dataset dat):

ggplot(data = dat, aes(x, y, colour = y)) + 
  geom_point(size=2) + geom_smooth(method='lm', se = TRUE) + theme_bw()

enter image description here

Upvotes: 0

eipi10
eipi10

Reputation: 93811

Using the broom output, you can do something like this:

ggplot(data = dt, aes(x, y)) + 
  geom_ribbon(aes(ymin=.fitted-1.96*.se.fit, ymax=.fitted+1.96*.se.fit), alpha=0.2) +
  geom_point(aes(colour = y)) + 
  geom_line(aes(x, .fitted, colour = .fitted)) +
  theme_bw()

I moved colour=y into geom_point() because you can't apply a colour aesthetic to geom_ribbon.

enter image description here

Upvotes: 7

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