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)
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 and Means including confidence intervals for these statistics.
Any feedback would be appreciated and can be provided using the Issues section of the GitHub repository, or by emailing [email protected]
You can install the latest version of PHEindicatormethods from GitHub with:
if (!require(devtools)) install.packages("devtools")devtools::install_github("PublicHealthEngland/PHEindicatormethods",build_vignettes = TRUE,dependencies = "suggests")
Some users may receive a Lazy Load error following installation and loading of this package using devtools in RStudio. In these cases, please close and re-open RStudio and then re-load the package using the library command.
Download this repository from GitHub and either build from source or do:
source <- devtools:::source_pkg("C:/path/to/PHEindicatormethods-master")devtools::install(source)
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: .. 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
The package contains the following functions, datasets and vignettes - see individual item documentation for full details
Functions:
- byars_lower
- byars_upper
- phe_dsr
- phe_isr
- phe_mean
- phe_proportion
- phe_rate
- phe_smr
- wilson_lower
- wilson_upper
Datasets:
- esp2013
Vignettes:
- Vignette for calculating DSRs for multiple geographies and time
periods
(type ‘browseVignettes(“PHEindicatormethods”)’ to view in HTML)
The following changes may affect backwards compatibility with earlier versions of the package:
phe_proportion: Replaced logical PERCENTAGE argument with a numeric MULTIPLIER argument to enable proportions to be expressed more flexibly (eg per 1000). Default is now multiplier = 1 which gives equivalent output to the previous default of percentage = FALSE. There is loss of backwards compatibility where the percentage argument has previously been specified in the function call - please replace 'percentage=TRUE' with 'multiplier=100' and 'percentage=FALSE' with 'multiplier=1'.
all functions using the TYPE argument: Altered the default value for the TYPE argument from 'standard' to 'full'. This may affect backwards compatibility with earlier versions of the package - where type has not been specified output will now contain additional metadata columns - to remove these please specify type = "standard" as a function argument.
byars_lower()
, byars_upper()
, wilson_lower()
and wilson_upper()
functions have been moved to the package utilities and are less readily available to be used as stand-alone functions within the package. These functions are intended to be called using other 'phe-' prefixed package functions.
The following changes will not affect backwards compatibility with earlier versions of the package:
phe_life_expectancy()
function added for calculation of life expectancy at different ages based on population and death data
phe_quantile()
function added for assigning data to quantiles
phe_sii()
function added for calculation of slope index of inequality and relative index of inequality
phe_proportion()
and phe_rate()
functions now return aggregate data when grouped data is passed
Altered handling of NA values in phe_proportion()
, phe_rate()
and phe_mean()
functions to enable results to be returned for the records which do not contain invalid NAs
Altered handling of NA values in phe_dsr()
function such that NA values in the age-specific count data are assumed to be equal to zero and no longer cause the function to error
Altered handling of NA values in phe_isr()
and phe_smr()
functions such that NA values in the age-specific count, age-specific population and/or reference count data are assumed to be equal to zero and no longer cause the functions to error
This is the first release of this package to CRAN