In hafen/hbgd: Healthy birth, growth & development

Introduction

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

library(hbgd)

The growth velocity function allows you to apply a function to the first derivative of growth trajectories. For example, taking the mean of the first derivative. Since the function depends on growth trajectories, they need to be generated first; see documentation for HBGD package.

smc <- get_smocc_data()[1:500,]
smc_haz_wandfit <- get_fit(smc, y_var = "haz", method = "wand")
smc_tr <- fit_all_trajectories(smc, smc_haz_wandfit)

Calling the function

Suppose we assign the trajectories to a variable named traj. We call the growth velocity method as follows:

traj_velocity <- get_traj_velocity(all_traj = smc_tr)

The result of this call will be a tibble. Each row of this tibble has the subject ID and growth velocity.

print(traj_velocity)

Options and Defaults

all_traj The returned value from calling fit_all_trajectories function. This is mandatory.
z_score = TRUE will use the z-scores, e.g., haz. The default value is TRUE.
agedays_floor = 0.00 specifies the minimum agedays to use. The default value is zero. This parameter, combined with agedays_limit, extracts the required ranges of the fitted trajectory. Note that times depends heavily on the the number of grid points used to generate the trajectories, which is specified by the xg parameter for the functions hbgd::fit_trajectory and hbgd::fit_all_trajectories. This is because the function supplied by FUN will be applied to derivative data with x-axis grid value less than agedays_limit; the x-axis grid values are set up by xg parameter of the functions hbgd::fit_trajectory and hbgd::fit_all_trajectories.
agedays_limit = 365 specifies the maximum agedays to use. The default value is one year (365 days). This parameter, combined with agedays_floor, extracts the required ranges of the fitted trajectory. Note that times depends heavily on the the number of grid points used to generate the trajectories, which is specified by the xg parameter for the functions hbgd::fit_trajectory and hbgd::fit_all_trajectories. This is because the function supplied by FUN will be applied to derivative data with x-axis grid value less than agedays_limit; the x-axis grid values are set up by xg parameter of the functions hbgd::fit_trajectory and hbgd::fit_all_trajectories.
FUN argument takes a function specified by the user that will be apply on the growth trajectory data. This function should only receive one argument, a vector containing the first derivative of the growth trajectory. Since the first derivative can contain NA value (e.g., derivative for the first growth data), the supplied function should be able to handle NA values. The default for this argument is an internal function that simply calculates the mean.