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: 1. Users can now specify whether events are independent. For
non-independent events the data must be broken down by event frequency
and the function will perform an adjustment to the confidence interval
calculation. 2. The stdpoptype argument that was available in
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”. 3. Because of point
2 above, users can now calculate DSRs for groups containing different
numbers of age bands in a single execution (for example DSRs for all age
populations and DSRs for under 75s).
* 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