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PHEindicatormethods

This is an R package to support analysts in the execution of statistical methods approved for use in the production of PHE indicators such as those presented via Fingertips. It provides functions for the generation of Proportions, Rates, DSRs, ISRs, Means, Life Expectancy and Slope Index of Inequality including confidence intervals for these statistics, and a function for assigning data to quantiles.

In October 2021 Public Health England (PHE) was disbanded and as a result this package is now owned by the Department of Health and Social Care. It will continue to be supported and to prevent breaking changes there are currently no immediate plans to rename the package or its functions in light of this organisational change.

Any feedback would be appreciated and can be provided using the Issues section of the PHEindicatormethods GitHub repository.

Installation

Install from CRAN

Install the latest release version of PHEindicatormethods directly from CRAN with:

install.packages("PHEindicatormethods")

Install a development version from GitHub using remotes package

You can install a development version of PHEindicatormethods from GitHub with:

if (!require(remotes)) install.packages("remotes")

remotes::install_github("ukhsa-collaboration/PHEindicatormethods",
                         build_vignettes = TRUE,
                         dependencies = TRUE,
                         build_opts = c("--no-resave-data"))

Package Versioning

Following installation of this package, type ‘packageVersion(“PHEindicatormethods”)’ in the R console to show the package version. If it is suffixed with a 9000 number then you are using an unapproved development version.

Released versions of this package will have version numbers consisting of three parts:

major.minor.patch

In-development versions of this package will have a fourth component, the development version number, which will increment from 9000.

See https://r-pkgs.org/lifecycle.html for further information on package versioning

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Version

Install

install.packages('PHEindicatormethods')

Monthly Downloads

467

Version

2.1.0

License

GPL-3

Maintainer

Anderson Georgina

Last Published

December 12th, 2024

Functions in PHEindicatormethods (2.1.0)

calculate_ISRate

Calculate Indirectly Standardised Rates using calculate_ISRate
calculate_ISRatio

Calculate Indirectly standardised ratios using calculate_ISRatio
phe_sii

Calculate Slope Index of Inequality using phe_sii
prevalence_data

SII test datasets - Prevalence
calculate_funnel_points

For rate-based funnels: Derive rate and annual population values for charting based. Process removes rates where the rate type is dsr and the number of observed events are below 10.
esp2013

European Standard Population 2013
phe_dsr

Calculate Directly Standardised Rates using phe_dsr
phe_life_expectancy

Calculate Life Expectancy using phe_life_expectancy
DSR_data

SII test datasets - DSR
LE_data

SII test datasets - Life Expectancy
PHEindicatormethods-package

PHEindicatormethods: Common Public Health Statistics and their Confidence Intervals
phe_mean

Calculate Means using phe_mean
phe_proportion

Calculate Proportions using phe_proportion
assign_funnel_significance

Identifies whether each value in a dataset falls outside of 95 and/or 99.8 percent control limits based on the aggregated average value across the whole dataset as an indicator of statistically significant difference.
phe_quantile

Assign Quantiles using phe_quantile
phe_rate

Calculate Rates using phe_rate
calculate_dsr

Calculate Directly Standardised Rates using calculate_dsr
calculate_funnel_limits

Calculate control limits for funnel plots