This release makes changes to the DSR function
calculate_dsr function added to replace phe_dsr. The new calculate_dsr function has three new features:phe_dsr is not available in calculate_dsr and the user is now required to provide the standard populations as a field in the input dataframe. This is to negate the risk of incorrectly joining the standard population vector by position that was possible when using the function with stdpoptype = "vector".phe_dsr has been soft deprecated - please replace all calls to this function with calculate_dsr before September 2025, after which date the phe_dsr function will be removed from the package. Previous calls to phe_dsr with stdpoptype set to "field" can be replaced directly with calculate_dsr, however, the stdpoptype argument has been deprectaed so will need to be removed and the stdpop argument no longer has a default so this column name will need to be provided explicitly. For previous calls to phe_dsr with stdpoptype = "vector", the user will need to append the standard populations to their input data frame before calling the calculate_dsr function and provide the stdpop argument explicitly.phe_sii amended to allow data to be transformed prior to calculation of the SII, and to allow the intercept value to be output.calculate_ISRate and calculate_ISRatio updated so observed events can be passed as total without age breakdownsphe_smr and phe_isr functions which were previously soft-deprecated have now been removed - see NEWS from release version 1.4.0 for replacements for these functions.phe_proportion amended so option to request no confidence intervals is allowed.calculate_funnel_limits(), assign_funnel_significance() and prepare_funnel_plot() functions added. This provides ability to calculate funnel plot lines and significance for provided data in line with Fingertips published technical guidance.calculate_ISRate and calculate_ISRatio functions replace phe_isr and phe_smr respectively. phe_isr and phe_smr functions remain available in this release but are lifecycle badged as deprecated and function documentation signposts users to the new replacement functions. This is purely a renaming exercise to overcome ambiguous acronyms used in the original function names and there is no change to the functionality of the code. phe_isr and phe_smr are scheduled to be removed in a future release of the package, not before December 2022.phe_life_expectancy now forces suppression of LEs when the 95% confidence interval is greater than 20 years.phe_dsr, phe_isr, phe_mean, phe_proportion, phe_rate, phe_smr, phe_life_expectancy amended so output data frame has the same grouping attributes as the input data frame.
phe_proportion, phe_rate, phe_quantile, phe_life_expectancy, phe_sii:
Functions amended to ensure continued compatibility with dplyr when v1.0.0 is released.
These changes will not be noticeable to end users.
phe_life_expectancy: dropped population and death columns from output as these are no longer applicable to the final LE statistic. Added pops_used and dths_used columns to output when type = 'full' which reflect the cumulative populations and deaths used in each LE calculation (ie the pops and deaths for all ages equal to or above the Life_Expectancy_At age)
phe_sii function updated to be able to output multiple confidence intervalsphe_life_expectancy() function previously calculated life expectancy and confidence levels inaccurately when the number of deaths in all age groups except the final one was 40% or more of the size of the population in any age group (apart from the 1–4 age group where it’s 50%). It had an affect in very few scenarios, but was inaccurate nonetheless. This has now been corrected to agree with the published methodologyphe_life_expectancy() now accepts a numeric vector as an input to the confidence argument so users can calculate multiple confidence limits in one commandphe_dsr The standardised_pop output variable added in v1.2.0 has been removed as this was not providing a meaningful value. This may result in some backwards incompatibility if code has been written to reference (eg drop) this column as it will no longer be included in the phe_dsr output.The following changes may affect backwards compatibility with earlier versions of the package:
The following changes will not affect backwards compatibility with earlier versions of the package:
Amended functions to use new embrace interpolation features of rlang 0.4.0: dsr, isr, smr, rate, proportion, mean, quantile. Package dependencies now require Rlang version 0.4.0 or higher
Added ability to output both 95% and 99.8% confidence intervals in a single execution to dsr, isr, smr, rate, proportion, mean functions
Amended phe_dsr to also output the standardised population used in the calculation when type="full"
Some warnings that occurred with phe_life_expectancy() have been fixed
phe_sii function updated to be compatible with nest and unnest functions from tidyr version 1.0
No significant changes. Removed confusing line of commented out code from phe_life_expectancy calculation Amended vignette title
Minor amendments to package testing scripts to work on platforms using clang as compiler.
Updates will not affect end users using other platforms.
Minor amendments to package testing scripts to work on platforms using clang as compiler. Updates will not affect end users using other platforms.
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