## ----include = FALSE----------------------------------------------------------
library(tanner)
# render at plot_stadia()'s native A4-landscape device size (matching
# README.qmd) since plot_stadia_general() places text at hardcoded
# coordinates tuned for that size; scale down only the displayed image
# (out.width), not the R graphics device itself, to fit the page column
knitr::opts_chunk$set(
  fig.width = 11.67,
  fig.height = 8.27,
  dpi = 150,
  out.width = "100%"
)

## ----multi-stage-boy----------------------------------------------------------
boy <- data.frame(
  id = 1,
  age = c(9.1, 10.2, 11.3, 12.1, 12.9, 13.8, 14.6, 15.2),
  sex = "M",
  gen = c(1, 1, 2, 3, 3, 4, 4, 5),
  phb = c(1, 1, 1, 2, 3, 4, 4, 5),
  tv = c(2, 3, 4, 8, 10, 12, 15, 20)
)

plot_stadia(
  data = boy,
  persons = 1,
  type = c(TRUE, TRUE, TRUE),
  plotline = c(FALSE, FALSE, FALSE),
  colors = c("#0060A0", "#00A000", "#A00000"),
  title = "Boy 1: genital, pubic hair & testicular volume",
  padid = FALSE
)

## ----overlay-boys-------------------------------------------------------------
boys <- data.frame(
  id = rep(c(1, 2), each = 4),
  age = c(9, 11, 13, 15, 10, 12, 14, 16),
  sex = "M",
  gen = c(1, 2, 3, 5, 1, 1, 3, 4),
  phb = c(1, 2, 3, 5, 1, 2, 3, 4),
  tv = NA
)

plot_stadia(
  data = boys,
  persons = c(1, 2),
  type = c(TRUE, FALSE, FALSE),
  plotline = c(TRUE, FALSE, FALSE),
  overlay = TRUE,
  ovsex = "M",
  title = "Genital stage, two boys overlaid",
  padid = FALSE
)

## ----tv-interpolation---------------------------------------------------------
# 11ml is strictly between the T10 and T12 Prader bead curves; age must
# be supplied per stage value (no recycling), so it's repeated here
calculate_sds(age = c(13, 13, 13), stage = c(10, 11, 12), type = "tv")

## ----ref-shape----------------------------------------------------------------
head(tanner::nl1997$gen)