FE_versus_Mixed_Models.R

library(easystats)
library(palmerpenguins)
library(lme4)
library(ggplot2)


# data generation -----------------------

data(penguins)
d <- penguins |>
  # rename variables (we remove the “_mm”)
  data_rename(
    pattern = c("bill_length_mm", "bill_depth_mm", "flipper_length_mm"),
    replacement = c("bill_length", "bill_depth", "flipper_length")
  )
# create de meaned variables
penguin_demean <- demean(d, select = "bill_length", group = "species")

# “bind colums”, i.e. merge original data frame
# and data frame with demeaned variables
d <- cbind(d, penguin_demean)



# plot setup -----------------------

theme_set(theme_modern())
fontsize <- theme(plot.title = element_text(size = 20),
  axis.title = element_text(size = 16),
  legend.text = element_text(size = 14),
  legend.title = element_text(size = 15)
)



# figure 1: raw data  ------

ggplot(d, aes(bill_length, bill_depth)) +
  geom_point(colour = "#555555", size = 2.5, alpha = 0.5) +
  labs(title = "Penguin bill dimensions (omit species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)") +
  fontsize



# figure 2: Relationship between typing errors and typing speed ------

ggplot(d, aes(bill_length, bill_depth)) +
  geom_point(colour = "#555555", size = 2.5, alpha = 0.5) +
  see::theme_modern() +
  geom_smooth(method = "lm", se = F, colour = "#555555") +
  labs(title = "Penguin bill dimensions (omit species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)") +
  fontsize

m1 <- lm(bill_depth ~ bill_length, data = d)
model_parameters(m1, digits = 3)




# figure 3: Relationship between typing errors and typing speed ------

ggplot(d, aes(bill_length, bill_depth)) +
  geom_point(mapping = aes(colour = species), size = 2.5, alpha = 0.5) +
  geom_smooth(method = "lm", se = F, colour = "#555555") +
  labs(title = "Penguin bill dimensions (omit species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)",
       colour = "Species") +
  fontsize +
  see::scale_color_flat()




# figure 4: Within-effect of typing-speed ------

ggplot(d, aes(bill_length, bill_depth)) +
  geom_smooth(mapping = aes(colour = species), method = "lm", se = FALSE) +
  geom_point(mapping = aes(colour = species), size = 2.2, alpha = 0.6) +
  labs(title = "Penguin bill dimensions by species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)",
       colour = "Species") +
  fontsize +
  see::scale_color_flat()

m2 <- lm(bill_depth ~ 0 + bill_length_within + species, data = d)
model_parameters(m2, digits = 3)[1, ]




# figure 5: Between-effect of typing-speed ------

ggplot(d, aes(bill_length, bill_depth)) +
  geom_smooth(mapping = aes(x = bill_length_between, y = bill_depth_between), method = "lm", se = F, colour = "#444444") +
  geom_point(mapping = aes(colour = species), size = 2.2, alpha = 0.6) +
  labs(title = "Penguin bill dimensions by species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)",
       colour = "Species") +
  fontsize +
  see::scale_color_flat()


m3 <- lm(bill_depth ~ bill_length_between, data = d)
model_parameters(m3, digits = 3)



ggplot(d, aes(bill_length, bill_depth)) +
  geom_smooth(mapping = aes(x = bill_length_between, y = bill_depth_between), method = "lm", se = F, colour = "#444444") +
  geom_point(mapping = aes(colour = species), size = 2.2, alpha = 0.6) +
  labs(title = "Penguin bill dimensions by species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)",
       colour = "Species") +
  fontsize +
  see::scale_color_flat() +
  # geom_density_2d(colour = "#444444") +
  geom_density_2d(mapping = aes(colour = species)) +
  see::geom_point2(x = mean(d$bill_length, na.rm = TRUE), y = mean(d$bill_depth, na.rm = TRUE), colour = "black", size = 5)




# figure 6: Within- and between-effect of typing-speed ------

ggplot(d, aes(bill_length, bill_depth)) +
  geom_smooth(mapping = aes(colour = species), method = "lm", se = FALSE) +
  geom_point(mapping = aes(colour = species), size = 2.2, alpha = 0.6) +
  geom_smooth(mapping = aes(x = bill_length_between, y = bill_depth_between), method = "lm", se = F, colour = "#444444") +
  labs(title = "Penguin bill dimensions by species)",
       x = "Bill length (mm)",
       y = "Bill depth (mm)",
       colour = "Species") +
  fontsize +
  see::scale_color_flat()

m4 <- lmer(bill_depth ~ bill_length_between + bill_length_within + (1 | species), data = d)
model_parameters(m4, digits = 3)



# figure 7: Within- and between-effect of typing-speed ------

m5 <- lmer(bill_depth ~ bill_length_between + bill_length_within + (1 + bill_length_within | species), data = d)
model_parameters(m5, digits = 3)




model_parameters(m1)
model_parameters(m2)[1, ]
model_parameters(m3)
model_parameters(m4)
model_parameters(m5)