User-visible changes:
All changes specified for estimate_risk() also apply
to its synonym, est_risk(). There are no breaking changes,
only enhancements.
Users can now compare results with either the original Pooled
Cohort Equations (PCEs) released by the ACC/AHA in 2013 or the revised
PCEs released by Yadlowsky and colleagues in 2018. This is implemented
via expanding the set of valid input options for the existing argument
model within the estimate_risk() function. The
Shiny app has also been updated to permit estimation via the
PCEs.
Function arguments for estimate_risk() are now
semantically categorized as one of the following: required predictor
variable, optional predictor variable, optional behavior variable. This
is to help with clarity of documentation and additional features in the
package. Nothing has actually changed about which arguments are required
or the behavior of those arguments.
The function estimate_risk() gains the optional
behavior argument collapse, which allows users to collapse
the list of tibbles into a single tibble when relevant. To maintain
backwards compatibility, this is an opt-in feature, so the default of
collapse is FALSE.
The function estimate_risk() gains the optional
behavior arguments use_dat and add_to_dat,
which allow users to pass a data frame (as a data.frame, tibble, or
data.table) to the function to carry out risk estimation against a large
set of data in one function call, with the option (via
add_to_dat = TRUE) to append the results to the data frame
passed to the function. This is accompanied by
vignette("using-data-frame"), which gives many examples,
and also shows how to use a data frame for input even if you do not want
to use use_dat and add_to_dat.
The function estimate_risk() gains the optional
behavior argument progress, which gives users the option to
display a progress bar in the console when use_dat is a
data frame. This argument is independent of quiet.
All the above changes also have corresponding documentation within the relevant function and corresponding sections of the documentation.
Internal changes:
Minor edits to is_valid_* functions (adding
extra_text arg)
Addition of new is_valid_* functions in support of
estimating with other models
Expansion of verification for is_okay_type()
stemming from expansion of functionality with use_dat and
add_to_dat
Minor refactoring of some of the messaging functions within
estimate_risk(), including creation of new messaging for
other models and scenarios specific to the use_dat and
add_to_dat arguments
Considerable addition of other helper functions and capabilities
in support of estimating with other models and the use_dat
and add_to_dat arguments
Moving internal_call_* <- TRUE to inside relevant
sections and changing name to *_requested
Refactoring of method to return tibble of NAs when there are input problems
Many more tests for added functionality
User-visible changes:
Shiny app available online at https://martingmayer.shinyapps.io/prevent-equations/
or https://tiny.cc/prevent-equations,
and users can also access this via app()
Arguments egfr and bmi within the
estimate_risk() function (and its synonym
est_risk()) gain the ability to accept a call to a
corresponding, non-exported function rather than passing the
corresponding value directly; entering the value directly remains an
option (and there is no intent for that to change)
For egfr, the supported call is
calc_egfr() (or a synonym)
For bmi, the supported call is
calc_bmi() (or its synonym)
estimate_risk() and est_risk() now
advise 30-year risk prediction for people > 59 years is questionable
via two warnings:
In the console (that can be suppressed by setting
quiet = TRUE)
In the column input_problems of the return tibble
(quiet has no impact here)
All the above changes also have corresponding documentation within the relevant function
Internal changes:
Moved message_maybe(), warn_maybe(),
and valid to helpers
Added tests for new functionality