---
title: "Charts"
output: markdown::html_format
vignette: >
  %\VignetteIndexEntry{Charts}
  %\VignetteEngine{knitr::knitr}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", echo = FALSE)
library(peditools2)
```

The charts in this version of peditools2 (data `r paste(growth_data_version(), collapse = ", ")`), generated from
`growth_charts()` and `growth_references()`. Coverage: the range of x, in the chart's x units; sexes: "both" for
one table used for both sexes. Each chart's full sources are on the PediTools Sources and methods page
(`sources_url`).

```{r, results = "asis"}
charts <- growth_charts()
refs <- growth_references()
clinical <- refs[refs$role == "clinical" & refs$position == 1, ]
fmt <- function(v) format(signif(v, 6), drop0trailing = TRUE, trim = TRUE)
rows <- lapply(split(charts, charts$chart), function(t) {
  per_measure <- lapply(split(t, t$measure), function(m) {
    sexes <- if (all(is.na(m$sex))) "both" else paste(sort(m$sex), collapse = ", ")
    range <- if (length(unique(m$x_min)) == 1 && length(unique(m$x_max)) == 1) {
      paste0(fmt(m$x_min[1]), "–", fmt(m$x_max[1]))
    } else {
      paste(paste0(m$sex, " ", fmt(m$x_min), "–", fmt(m$x_max)), collapse = "; ")
    }
    data.frame(
      measure = paste0(m$measure[1], " (", m$measure_units[1], ")"),
      x = paste0(m$x_label[1], ", ", range, " ", m$x_units[1]),
      sexes = sexes, method = m$z_method[1], family = m$family[1]
    )
  })
  out <- do.call(rbind, per_measure)
  ref <- clinical$short[clinical$chart == t$chart[1]][1]
  cbind(
    chart = c(paste0("`", t$chart[1], "`"), rep("", nrow(out) - 1)), out,
    website = c(if (t$on_website[1]) "yes" else "no", rep("", nrow(out) - 1)),
    publication = c(if (is.na(ref)) "" else ref, rep("", nrow(out) - 1))
  )
})
table <- do.call(rbind, rows)
rownames(table) <- NULL
cat(knitr::kable(table, format = "pipe"), sep = "\n")
```

Method: `lms` the LMS method; `sd23` WHO's restricted LMS method beyond ±3 SD; `cdf` the INTERGROWTH-21st models
($Z = \Phi^{-1}(F(y))$). On `cdc_2000_bmi`, CDC's extended method applies above the 95th percentile. Website: whether
a PediTools calculator uses the chart. See `vignette("methods", package = "peditools2")`.