Package: PAutilities 1.3.0

PAutilities: Streamline Physical Activity Research

Functions that support a broad range of common tasks in physical activity research, including but not limited to creation of Bland-Altman plots (<doi:10.1136/bmj.313.7049.106>), metabolic calculations such as basal metabolic rate predictions (<https://europepmc.org/article/med/4044297/reloa>), demographic calculations such as age-for-body-mass-index percentile (<https://www.cdc.gov/growthcharts/cdc_charts.htm>), and analysis of bout detection algorithm performance (<https://pubmed.ncbi.nlm.nih.gov/34258524/>).

Authors:Paul R. Hibbing [aut, cre], Centers for Disease Control and Prevention [ctb]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PAutilities/json (API)

# Install 'PAutilities' in R:

install.packages('PAutilities', repos = c('https://paulhibbing.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/paulhibbing/pautilities/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

ex_data - Example data for calculating bouts of moderate-to-vigorous physical activity

On CRAN:

cpp

5.24 score 1 stars 3 packages 39 scripts 598 downloads 31 exports 44 dependencies

Last updated from:bf4c74602d. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	224
linux-devel-x86_64	OK	166
source / vignettes	OK	207
linux-release-arm64	OK	172
linux-release-x86_64	OK	213
macos-release-arm64	OK	113
macos-release-x86_64	OK	208
macos-oldrel-arm64	OK	136
macos-oldrel-x86_64	OK	273
windows-devel	OK	133
windows-release	OK	189
windows-oldrel	OK	132
wasm-release	OK	174

Exports:ba_analysis ba_plot bout_mvpa cvd_risk descriptives df_continuous df_reorder epoch_length_sec full_days get_age get_bmi get_BMI_percentile get_bmr get_duration get_indices get_intensity get_kcal_vo2_conversion get_ree get_transition_info index_runs manage_procedure mean_sd paired_equivalence_test reintegrate residual_adjust rmr_sliding rolling_groups spurious_curve test_errors weight_status weir_equation

Dependencies:boot class cli cpp11 dplyr e1071 equivalence farver generics ggplot2 gld glue gtable isoband labeling lattice lazyeval lifecycle lmom lubridate magrittr MASS mvtnorm PairedData pillar pkgconfig plyr proxy R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr tibble tidyselect timechange utf8 vctrs viridisLite withr

The Transition Pairing Method

Rendered fromtpm.Rmdusingknitr::rmarkdown

Last update: 2025-06-07
Started: 2019-12-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
As("summaryTransition", "data.frame")	as
Perform Bland-Altman analysis on a data frame	ba_analysis
Create a Bland-Altman plot	ba_plot
Classify moderate-to-vigorous physical activity in bouts of a specific minimum length	bout_mvpa
Calculate risk of cardiovascular disease	cvd_risk cvd_risk.data.frame cvd_risk.default
Compute descriptive statistics for a variable in the metabolic data set	descriptives
Check if a dataframe is continuous	df_continuous
Reorder the columns of a data frame	df_reorder
Determine epoch length in seconds	epoch_length_sec
Example data for calculating bouts of moderate-to-vigorous physical activity	ex_data
Drop incomplete days from a dataset	full_days
Calculate age	get_age
Retrieve estimated basal metabolic rate for an individual	get_bmr
Retrieve indices for a rolling window analysis	get_indices
Classify activity intensity	get_intensity
Retrieve conversion factors from kilocalories to oxygen consumption	get_kcal_vo2_conversion
Calculate resting energy expenditure	get_ree
Run length encoding with indices	index_runs
Printing and timing utility for managing processes	get_duration manage_procedure
Compute the mean and standard deviation of a vector, returning a formatted string containing the values as `M +/- SD`	mean_sd mean_sd.data.frame mean_sd.default
Perform equivalence testing on paired samples	paired_equivalence_test paired_equivalence_test.data.frame paired_equivalence_test.default
PAutilities: Streamline Physical Activity Research	PAutilities-package PAutilities
Plot the outcome of a paired equivalence test	plot.paired_equivalence shaded_equivalence_plot unshaded_equivalence_plot
Plot a spurious curve	plot.spurious_curve
Plot the transitions and matchings from a 'transition' object	plot.transition
Reintegrate accelerometer data	reintegrate
Perform residual adjustment on an epidemiologic variable	residual_adjust
Calculate resting metabolic rate using a sliding window method	rmr_sliding
Loop along a vector, returning n elements at a time in a list	rolling_groups
Perform a spurious curve analysis	spurious_curve
An S4 class containing summary information about a 'transition' object	summaryTransition summaryTransition-class
Compare numeric variables in a data frame based on root-squared differences	test_errors
Determine weight status from body mass index	weight_status
Calculate energy expenditure using the Weir equation	weir_equation