---
layout: post
title: "Anthropometric Birthday Cards"
tags: [rstats, stats, obesity, nonparametrics]
comments: yes
---

 <!-- bibliography: /Users/hoehle/Literature/Bibtex/jabref.bib -->

```{r,include=FALSE,echo=FALSE,message=FALSE}
##If default fig.path, then set it.
if (knitr::opts_chunk$get("fig.path") == "figure/") {
  knitr::opts_knit$set( base.dir = '/Users/hoehle/Sandbox/Blog/')
  knitr::opts_chunk$set(fig.path="figure/source/2022-06-11-refpop/")
}
fullFigPath <- paste0(knitr::opts_knit$get("base.dir"),knitr::opts_chunk$get("fig.path"))
filePath <- file.path("","Users","hoehle","Sandbox", "Blog", "figure", "source", "2022-06-11-refpop")

knitr::opts_chunk$set(echo = FALSE, fig.width=8, fig.height=4, fig.cap='', fig.align='center', dpi=72*2)#, global.par = TRUE)
options(width=150, scipen=1e3)

suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(scales))
suppressPackageStartupMessages(library(knitr))
# Non CRAN packages
# devtools::install_github("hadley/emo")

##Configuration
options(knitr.table.format = "html")
theme_set(theme_minimal())
#if there are more than n rows in the tibble, print only the first m rows.
options(tibble.print_max = 10, tibble.print_min = 5)

# Fix seed value for the post
set.seed(20220610)
```


## Abstract:

We visualize children reference populations for height, weight and body mass index by plotting percentiles of the population as a function of age. Besides the epidemiological interest in these anthropometric curves, they have dual-use potential for reproducible birthday cards.

<center>
```{r,results='asis',echo=FALSE}
cat(paste0("![]({{ site.baseurl }}/",knitr::opts_chunk$get("fig.path"),"make_bmi_plot-1.png"),")")
```
</center>

<br>
<a rel="license" href="http://creativecommons.org/licenses/by-sa/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by-sa/4.0/88x31.png"/></a>
This work is licensed under a <a rel="license"
href="http://creativecommons.org/licenses/by-sa/4.0/">Creative Commons
Attribution-ShareAlike 4.0 International License</a>.
The [R-markdown source code](`r paste0("https://raw.githubusercontent.com/hoehleatsu/hoehleatsu.github.io/master/_source/",current_input())`) of this blog is available under a [GNU General Public License (GPL v3)](https://www.gnu.org/licenses/gpl-3.0.html) license from GitHub.

## Introduction

Percentiles of a reference population at a given age are often used to assess under- and overweight of children. As an example, the WHO defines 
obesity for children under 5 years of age when the [weight-for-height](https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/cht-wfl-girls-z-0-2.pdf?sfvrsn=a683172c_11) of a child is greater than 3 standard deviations above [WHO Child Growth Standards median for that age](https://www.who.int/news-room/fact-sheets/detail/obesity-and-overweight) (see also the WHO R package [anthro](https://cran.r-project.org/web/packages/anthro/index.html)).

In order to estimate these percentiles, data from a sample of the reference population is often fitted using flexible regression models such as GAMLSS [@rigby_stasinopoulos2005] or quantile regression [@koenker2005]. This allows for a flexible modelling of the percentiles as smooth functions of age [@fenske_etal2013]. The reference curves used in Germany are based on the Box-Cox Cole and Green distribution [@KromeyerHauschild_etal2001] (aka. the LMS method).
The [childsds](https://cran.r-project.org/web/packages/childsds/index.html) R package contains an implementation of these curves as `data(kro.ref)`. Furthermore, the package contains similar reference curves for several other countries as well as the WHO reference. 

In what follows, we will re-purpose the package as work-horse for generating individualized birthday cards for children.

## Results

Quantiles of the reference population are obtained with the `childsds::make_percentile_tab` function. As an example, let's get the 5th, 50th and 95th percentile of the height distribution for the population of girls in Germany aged 0 and 4 years, respectively.

```{r, echo=TRUE, message=FALSE}
library(childsds)
data(kro.ref)
childsds::make_percentile_tab(
  ref = kro.ref, item = "height", age=c(0,4),
  perc=c(5,50,95), include.pars= FALSE
) %>% filter(sex == "female") 
```


The main result of this short blog post is a [Rmd file](https://github.com/hoehleatsu/hoehleatsu.github.io/blob/master/figure/source/2022-06-11-refpop/birth_stats.Rmd), which contains a visualization of an imaginary child's growth trajectory: Albert B. Cook born on 2018-06-11. The data of Albert are stored in a [CSV file]({{ site.baseurl }}/figure/source/2022-06-11-refpop/kid_measurements.csv). We show the trajectories for height, weight and BMI and compare to 5 quantiles of the German reference population, i.e. the 2.5%, 5%, 50%, 95% and 97.5% quantile. The resulting visualization looks as follows:

<hr>
```{r make_birth_report, child=file.path(filePath, "birth_stats.Rmd")}
```
<hr>

The Rmd file can be obtained from GitHub and serves as a template for creating [html based congratulation cards]({{ site.baseurl }}/figure/source/2022-06-11-refpop/birth_stats.html) in response to news of newborn (which usually are annotated with birth height and birth weight) or to track the growth of your own kids.

## Discussion

Percentile curves for longitudinal trajectories in populations can also be used in very different contexts than anthropometry. As an example consider the development of your [solve time for the 3x3x3 Rubik's cube as a function of time since first WCA competition](https://staff.math.su.se/hoehle/blog/2019/05/06/wcamining.html). 


## Literature