{vaccineff 1.0.0} refactors the package’s internal
structure for better maintainability.
estimate_vaccineff() replaces
effectiveness().
vaccineff.at parameter must always be provided for accurate
results.plot.vaccineff_data() replaces
plot_coverage().
cohortdata has been simplified and
reduced to improve examples and reduce computation time.
{vaccineff 0.0.4} simplifies data handling by using linelist
objects. Tags are assigned to the outcome, censoring, and vaccine dates
using the function make_vaccineff_data(), reducing
redundancy in function input parameters.
The new pipeline includes the following three functions and
complementary methods: summary and plot.
make_vaccineff_data(): This
function returns an S3 object of the class vaccineff_data()
with the study’s relevant information. It also allows the creation of a
matched cohort to control for confounding variables by setting
match = TRUE and passing the appropriate exact
and nearest arguments. The method summary()
can be used to check cohort characteristics, matching balance, and the
sizes of matched, excluded, and removed populations.
plot_coverage(): This function
returns a plot of the vaccine coverage or cumulative coverage. If the
population is matched, the plot includes the resulting count of doses
after matching.
effectiveness(): This function
provides methods for estimating VE using the \(HR\). A summary of the estimation is
available via summary(), and a graphical representation of
the methodology is generated by plot().
The following functions are no longer accessible to users, but they
are called within make_vaccineff_data():
make_immunization()match_cohort()The plot() method returns log-log and
survival type plots when receiving an object of type
effectiveness. This deprecates the functions
plot_survival() and plot_loglog().
This version introduces an iterative matching routine within
match_cohort(). After adjusting the exposure times of the
pairs, new pairs are created between the removed ones and the unmatched
population. The new matches with inconsistent exposure times are removed
again, and the procedure is repeated until no new pairs can be made. The
usage of all the functions remains unchanged by this update.
The number of functions and steps for computing vaccine effectiveness
has been drastically reduced in {vaccineff 0.0.2}. The new
pipeline for estimation now consists of three main functions:
make_immunization(): Prepares
information on immunization dates and vaccine status. It can handle
multiple columns for vaccine dates and custom vaccine statuses. In such
cases, it returns the name of the column selected as immunizing and the
custom name, if provided.
match_cohort(): This function has
been improved and generalized to reduce observation bias in cohorts. The
default matching strategy is static, based on nearest and exact
characteristics using Mahalanobis distance. The exposure times of the
pairs are adjusted after matching. In future releases, rolling calendar
matching will be introduced as a more accurate method to account for
exposure times. The function returns an S3 object of class
match, from which a summary and balance of the cohorts can
be printed using the summary() method. The matched cohort
can be extracted using the get_dataset() method. The
matched cohort contains all the necessary information to estimate
vaccine effectiveness.
effectiveness(): Receives a
(matched) cohort and estimates vaccine effectiveness using the Hazard
Ratio (HR). An S3 object of class effectiveness is
returned, compatible with the plot() and
summary() methods. Future releases will provide relative
risk (RR) as an alternative for cases where the proportional hazards
assumption is not satisfied.
The following functions are no longer accessible to users. However,
they are called within make_immunization():
get_immunization_date()get_immunization_dose()get_immunization_vaccine()set_status()Similarly, the effectiveness() function deprecates the
use of coh_eff_noconf(), and the plot() method
now returns a log-log plot, replacing the plot_loglog()
function.