Package index • growthcleanr

Overview

Package overview

growthcleanr-package growthcleanr: growthcleanr: a data cleaner for anthropometric measurements

Main function

cleangrowth() cleans growth data. Start here.

cleangrowth(): Clean growth measurements (main growthcleanr function)

Other cleaning functions

Other ways to run growthcleanr

gc_runtrial(): Trial run of growthcleanr on a sample of your data
growthcleanr_app(): Run the growthcleanr Shiny application
run_gc_cli(): Run growthcleanr from the command line (CSV in, CSV out)

User utilities

User functions for related tasks. ext_bmiz() computes Z-scores and percentiles for pediatric subjects using the methods in the cdcanthro package (https://CRAN.R-project.org/package=cdcanthro).

permissiveness_presets(): Return preset setting values for each permissiveness level
gc_cli_path(): Path to the growthcleanr command-line driver script
longwide(): Transform data in growthcleanr format into wide structure for BMI calculation
simple_bmi(): Compute BMI using standard formula
ext_bmiz(): Calculate extended BMI measures
recode_sex(): Recode binary sex variable for compatibility

Support functions

Functions used within the cleaning process. Users can call them directly (for example, for checkpointed, partial, or repeated runs), but most users will not need to.

cleangrowth_checkpoint(): Run cleangrowth() with automatic checkpointing (deprecated wrapper)
cleangrowth_checkpoint_combine(): Combine saved checkpoint files from a checkpointed cleangrowth() run
gc_preload_refs(): Pre-load growthcleanr reference closures
gc_partial_run(): Incremental (partial) growthcleanr run
ewma(): Exponentially Weighted Moving Average (EWMA)
read_anthro(): Function to calculate z-scores and csd-scores based on anthro tables.

Datasets

Reference data and additional sources

CDCref_d: CDC BMI reference data
syngrowth: syngrowth
tanner_ht_vel: Tanner Growth Velocity Table
child_z3_reference: Child unit-error-range reference values
who_ht_maxvel: WHO Maximum Height Velocity for (3\(\sigma\))
who_ht_vel_3sd: WHO Height Velocity for (3\(\sigma\))
fent_foraga: Approximated Fenton Median Weights by Gestational Age
fenton2025_ms_lookup_smoothed: Approximated Fenton CSD Values (M, S_upper, S_lower)
growth_cdc_ext_infants: CDC Growth Reference Table
growth_who_ext: WHO Growth Reference Table
rc-reference-medians: Recentering reference medians
who_hc_maxvel: WHO Maximum Head Circumference Velocity for (3\(\sigma\))
who_hc_vel_3sd: WHO Head Circumference Velocity for (3\(\sigma\))