Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
palette(c("#0073C2", "#EFC000", "#868686", "#CD534C"))
library(lattice)
## ----load_opa-----------------------------------------------------------------
library(opa)
## ----str_data-----------------------------------------------------------------
str(pituitary)
## ----plot_data, fig.width=6, fig.height=6-------------------------------------
xyplot(distance ~ age | individual, pituitary, type = c("g", "p", "l"),
groups = sex, cex = 1.2, pch = 21,
fill = c("#EFC00070", "#0073C270"), col = c("#EFC000", "#0073C2"),
scales = list(x = list(at = c(8, 10, 12, 14))),
xlab = "Age (years)", ylab = "Distance (mm)",
main = "Pituitary-Pterygomaxillary Fissure Distance",
key = list(space = "bottom", columns = 2,
text = list(c("Female", "Male")),
lines = list(col = c("#EFC000", "#0073C2")),
points = list(pch = 21, fill = c("#EFC00070", "#0073C270"),
col = c("#EFC000", "#0073C2"))))
## ----reshape_data-------------------------------------------------------------
dat_wide <- reshape(data = pituitary,
direction = "wide",
idvar = c("individual", "sex"),
timevar = "age",
v.names = "distance")
## -----------------------------------------------------------------------------
head(dat_wide)
## ----define_h1----------------------------------------------------------------
h1 <- hypothesis(c(1, 2, 3, 4), type = "pairwise")
## ----print_h1-----------------------------------------------------------------
print(h1)
## ----plot_h1, fig.width=4, fig.height=4---------------------------------------
plot(h1)
## ----fit_model1---------------------------------------------------------------
m1 <- opa(dat_wide[,3:6], h1)
## ----summary_model1-----------------------------------------------------------
summary(m1)
## ----plot_model1, fig.width=7, fig.height=5-----------------------------------
plot(m1)
## ----compare_conds_model1-----------------------------------------------------
compare_conditions(m1)
## ----define_h2----------------------------------------------------------------
h2 <- hypothesis(c(2, 1, 3, 4))
## ----plot_h2, fig.width=4, fig.height=4---------------------------------------
plot(h2)
## ----print_h2-----------------------------------------------------------------
print(h2)
## ----fit_model2---------------------------------------------------------------
m2 <- opa(dat_wide[,3:6], h2)
## ----compare_hypotheses-------------------------------------------------------
(comp_h1_h2 <- compare_hypotheses(m1, m2))
## -----------------------------------------------------------------------------
plot(comp_h1_h2)
## ----fit_model3---------------------------------------------------------------
m3 <- opa(dat_wide[,3:6], h1, group = dat_wide$sex)
## ----plot_model3--------------------------------------------------------------
plot(m3)
## ----compare_groups-----------------------------------------------------------
(comp_m_f <- compare_groups(m3, "M", "F"))
## -----------------------------------------------------------------------------
plot(comp_m_f)
## ----fit_model4---------------------------------------------------------------
m4 <- opa(dat_wide[,3:6], h1, group = dat_wide$sex, diff_threshold = 1)
## ----diff_threshold_results---------------------------------------------------
group_results(m4)
## ----compare_groups_with_diff_threshold---------------------------------------
compare_groups(m4, "M", "F")
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