Package: DRpower 1.0.2

Bob Verity

DRpower: Study design and analysis for pfhrp2/3 deletion prevalence studies

This package can be used in the design and/or analysis stages of Plasmodium falciparum pfhrp2/3 deletion prevalence studies. We assume that the study takes the form of a clustered prevalence survey, meaning the data consists of a numerator (number of deletions found) and denominator (number tested) over multiple clusters. We are interested in estimating the study-level prevalence, i.e. over all clusters, while accounting for the possibility of high intra-cluster correlation. The analysis approach uses a Bayesian random effects model to estimate prevalence and intra-cluster correlation. The approach to power analysis is simulation-based, running the analysis many times on simulated data and estimating empirical power. This method can be used to establish a minimum sample size required to achieve a given target power.

Authors:Bob Verity [aut, cre], Shazia Ruybal [aut]

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DRpower.pdf |DRpower.html✨
DRpower/json (API)

# Install DRpower in R:

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

Bug tracker:https://github.com/mrc-ide/drpower/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

df_sim - Summary of simulations from the threshold analysis
df_ss - Minimum sample sizes for the threshold analysis
historical_data - Data from historical pfhrp2 studies that passed filters for inclusion into an ICC analysis.

On CRAN:

18 exports 1 stars 0.82 score 41 dependencies

Last updated 7 months agofrom:250c08a6aa457c5b5a0be099b315fd1523f27970

Exports:%>%check_DRpower_loaded get_ICC get_joint get_margin get_margin_Bayesian get_margin_CP get_power_presence get_power_threshold get_prevalence get_sample_size_margin get_sample_size_margin_CP get_sample_size_presence get_sample_size_table plot_ICC plot_joint plot_power plot_prevalence

Dependencies:cli colorspace cpp11 dplyr extraDistr fansi farver generics ggplot2 glue gtable isoband knitrProgressBar labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig purrr R.methodsS3 R.oo R6 RColorBrewer Rcpp rlang scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Articles and/or reference manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Check that DRpower package has loaded successfully	check_DRpower_loaded
Summary of simulations from the threshold analysis	df_sim
Minimum sample sizes for the threshold analysis	df_ss
The DRpower app for design and analysis of Plasmodium falciparum pfhrp2/3 data	DRpower
Get posterior distribution of both prevalence and the ICC on a grid	get_joint
Margin of error calculations using the Bayesian DRpower model when estimating prevalence from a clustered survey	get_margin_Bayesian
Margin of error calculations when estimating prevalence from a clustered survey	get_margin get_margins get_margin_CP get_sample_size_margin get_sample_size_margin_CP
Estimate prevalence and intra-cluster correlation from raw counts	get_ICC get_posterior get_prevalence
Calculate power when testing for presence of deletions	get_power_presence
Estimate power when testing prevalence against a threshold	get_power_threshold
Get minimum sample size when testing for presence of deletions	get_sample_size_presence
Get pre-computed sample size tables	get_sample_size_table
Data from historical pfhrp2 studies that passed filters for inclusion into an ICC analysis.	historical_data
Contour plot of joint posterior distribution of prevalence and ICC	plot_joint
Plot posterior distribution of prevalence and ICC	plot_ICC plot_posterior plot_prevalence
Plot a power curve using pre-computed values	plot_power

Package: DRpower 1.0.2

DRpower: Study design and analysis for pfhrp2/3 deletion prevalence studies

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