PHEindicatormethods v1.1.5

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Common Public Health Statistics and their Confidence Intervals

Functions to calculate commonly used public health statistics and their confidence intervals using methods approved for use in the production of Public Health England indicators such as those presented via Fingertips (<http://fingertips.phe.org.uk/>). It provides functions for the generation of proportions, crude rates, means, directly standardised rates, indirectly standardised rates, standardised mortality ratios, slope and relative index of inequality and life expectancy. Statistical methods are referenced in the following publications. Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>. Dobson et al (1991) <doi:10.1002/sim.4780100317>. Armitage P, Berry G (2002) <doi:10.1002/9780470773666>. Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>. Altman DG et al (2000, ISBN: 978-0-727-91375-3). Chiang CL. (1968, ISBN: 978-0-882-75200-6). Newell C. (1994, ISBN: 978-0-898-62451-9). Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>. Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>. Low and Low (2004) <doi:10.1093/pubmed/fdh175>.

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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, SMRs, Means, Life Expectancy and Slope Index of Inequaltiy 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 http://r-pkgs.had.co.nz/description.html for further information on package versioning



Package Contents

The package contains the following functions, datasets and vignettes - see individual item documentation for full details

Functions:

  • phe_dsr
  • phe_isr
  • phe_mean
  • phe_proportion
  • phe_quantile
  • phe_rate
  • phe_smr
  • phe_quantile
  • phe_life_expectancy
  • phe_sii

Datasets:

  • esp2013
  • LE_data (for use with SII vignette)
  • DSR_data (for use with SII vignette)
  • prevalence_data (for use with SII vignette)

Vignettes:

  • Vignette to introduce the package functions included in the original package release
  • Vignette for calculating DSRs for multiple geographies and time periods
  • Vignette showing worked examples of the phe_sii function

(type ‘browseVignettes(“PHEindicatormethods”)’ to view in HTML)

Functions in PHEindicatormethods

Name Description
SimulationFunc SimulationFunc
FindXValues FindXValues
byars_upper byars_upper
PHEindicatormethods PHEindicatormethods: A package for performing standard statistics for public health indicators
DSR_data SII test datasets - DSR
na.zero Convert NAs to zeros using na.zero
phe_dsr Calculate Directly Standardised Rates using phe_dsr
LE_data SII test datasets - Life Expectancy
esp2013 European Standard Population 2013
phe_quantile Assign Quantiles using phe_quantile
phe_sii Calculate Slope Index of Inequality using phe_sii
phe_smr Calculate Standardised Mortality Ratios using phe_smr
prevalence_data SII test datasets - Prevalence
phe_rate Calculate Rates using phe_rate
phe_life_expectancy Calculate Life Expectancy using phe_life_expectancy
phe_isr Calculate Indirectly Standardised Rates using phe_isr
wilson_lower wilson_lower
wilson_upper wilson_upper
phe_proportion Calculate Proportions using phe_proportion
phe_mean Calculate Means using phe_mean
byars_lower byars_lower
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Vignettes of PHEindicatormethods

Name
DSR-vignette.Rmd
Introduction_to_PHEindicatormethods.Rmd
PHElogo.png
WorkedExamples_phe_sii.Rmd
bluestrip.png
phe-white-48.png
quotes-close.jpg
quotes.jpg
style.css
whitestrip.png
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Details

Type Package
BugReports https://github.com/PublicHealthEngland/PHEindicatormethods/issues
License GPL-3
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2019-09-05 20:28:57 UTC; Georgina.Anderson
Repository CRAN
Date/Publication 2019-09-11 11:50:02 UTC

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