An analysis of change in Egyptian skull sizes from -4000 to 150. Post: http://emilkirkegaard.dk/en/?p=5933

egyptian_skull_size_change.R

### EGYPTIAN SKULLS ANALYSIS

# libs --------------------------------------------------------------------
library(pacman)
p_load(ggplot2, ade4, magrittr, reshape2, kirkegaard, plyr, psych)


# data --------------------------------------------------------------------
#load
data(skulls)
d_skulls = skulls

#period
d_skulls$period = rep(c(-4000, -3300, -1850, -200, 150), each = 30)

#rename
colnames(d_skulls) = c("maximum_breadth", "basibregmatic_height", "basialveolar_length", "nasal_height", "period")

#factor
fa(d_skulls[-5])

#long format
d_skulls_long = melt(d_skulls, id.vars = "period")

#means
d_skulls_means = ddply(d_skulls_long, .variables = .(period, variable), .fun = summarize,
                       "mean" = mean(value),
                       "se" = sqrt(var(value)/length(value)))

# plot --------------------------------------------------------------------

ggplot() + geom_point(data = d_skulls_long, aes(period, value, color = variable)) + ylab("size (mm)") + xlab("year") +
  geom_line(data = d_skulls_means, aes(period, mean, color = variable)) +
  geom_errorbar(data = d_skulls_means, aes(period, ymax = mean + 1.96 * se, ymin = mean - 1.96 * se), color = "red") +
  scale_color_discrete(name = "Skull measurement") +
  ggtitle("Change in Egyptian skull sizes: -4000 to 150")

ggsave("egyptian_skull_sizes.png")