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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.

Any feedback would be appreciated and can be provided using the Issues section of the GitHub repository https://github.com/PublicHealthEngland/PHEindicatormethods, or by emailing PHDS@phe.gov.uk

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("PublicHealthEngland/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#version for further information on package versioning

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Version

Install

install.packages('PHEindicatormethods')

Monthly Downloads

513

Version

1.4.2

License

GPL-3

Maintainer

Anderson Georgina

Last Published

December 1st, 2022

Functions in PHEindicatormethods (1.4.2)

byars_lower

byars_lower
byars_upper

byars_upper
LE_data

SII test datasets - Life Expectancy
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.
phe_quantile

Assign Quantiles using phe_quantile
phe_mean

Calculate Means using phe_mean
phe_proportion

Calculate Proportions using phe_proportion
phe_rate

Calculate Rates using phe_rate
esp2013

European Standard Population 2013
DSR_data

SII test datasets - DSR
phe_life_expectancy

Calculate Life Expectancy using phe_life_expectancy
phe_sii

Calculate Slope Index of Inequality using phe_sii
wilson_lower

wilson_lower
prevalence_data

SII test datasets - Prevalence
phe_dsr

Calculate Directly Standardised Rates using phe_dsr
phe_smr

Calculate Indirectly Standardised Ratio (Standardised Mortality Ratio or Standardised Admission Ratio) using calculate_ISRatio
phe_isr

Calculate Indirectly Standardised Rates using calculate_ISRate
wilson_upper

wilson_upper
calculate_ISRate

Calculate Indirectly Standardised Rates using calculate_ISRate
calculate_ISRatio

Calculate Standardised Mortality Ratios using calculate_ISRatio
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.
calculate_funnel_limits

Calculate control limits for funnel plots
PHEindicatormethods

PHEindicatormethods: A package for performing standard statistics for public health indicators