diff --git a/posts/vaccineff_v1.0.0/index.qmd b/posts/vaccineff_v1.0.0/index.qmd new file mode 100644 index 00000000..be13347b --- /dev/null +++ b/posts/vaccineff_v1.0.0/index.qmd @@ -0,0 +1,96 @@ +--- +title: "vaccineff v1.0.0" +author: + - name: "The Epiverse-TRACE development team" +date: "2024-12-02" +categories: [new-release] +--- + +We are very excited to announce the release of a new [vaccineff](https://epiverse-trace.github.io/vaccineff/) version v1.0.0. +The package offers tools for estimating vaccine effectiveness (VE) and related +metrics, with features such as: + +* Estimation in a cohort study design via the Cox model for Proportional Hazards +* Controlling for confounders through an iterative matching algorithm +* A detailed vignette with illustrative examples + +Two main functions compose `{vaccineff 1.0.0}`: + +1. `make_vaccineff_data()`: Constructs the `vaccineff_data` class, managing key +features for preparing, visualizing, and organizing cohort data. + +2. `estimate_vaccineff()`: Constructs the `vaccineff` class, enabling estimation +of VE and assessment of results and model performance. + +Both classes support `plot()` and `summary()` methods, providing visualizations +and detailed reports. + +## Breaking Changes + +`{vaccineff 1.0.0}` refactors the package's internal structure for better +maintainability. + +* **`estimate_vaccineff()`** replaces `effectiveness()`. + * It returns an object of class `vaccineff`. + * The `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. + +## Quick start + +To start with `{vaccineff}` 1.0.0, run the following example. +This example estimates VE using the package's example dataset, adjusted +for confounders (age and sex) via the iterative matching strategy. + +The `summary()` method for the `vaccineff_data` object provides details +on cohort balance and composition before and after applying the matching +strategy, as well as general cohort features. + +When called on the `vaccineff` object (`ve`), the `summary()` method +returns the estimation summary, including results from the Schoenfeld +test for proportional hazards. + +```{r} +library(vaccineff) + +# Create `vaccineff_data` +data(cohortdata) +vaccineff_data <- make_vaccineff_data( + data_set = cohortdata, + outcome_date_col = "death_date", + censoring_date_col = "death_other_causes", + vacc_date_col = "vaccine_date_2", + vaccinated_status = "v", + unvaccinated_status = "u", + immunization_delay = 15, + end_cohort = as.Date("2021-12-31"), + match = TRUE, + exact = "sex", + nearest = c(age = 1) +) +summary(vaccineff_data) + +# Estimate VE +ve <- estimate_vaccineff(vaccineff_data, at = 180) +summary(ve) +``` + +## Acknowledgements + +```{r ctbs, results='asis', echo=FALSE, message = FALSE} +releases <- gh::gh("GET /repos/{owner}/{repo}/releases", + owner = "epiverse-trace", + repo = "vaccineff") |> + purrr::discard(~ grepl("\\d+\\.\\d+\\.[1-9]\\d*$", .x$tag_name)) + +ctbs <- usethis::use_tidy_thanks( + "epiverse-trace/vaccineff", + from = releases[[2]][["tag_name"]], + to = "v1.0.0" +) +ctbs <- ctbs[grep("github-actions\\[bot\\]", ctbs, invert = TRUE)] +cat(glue::glue("[@{ctbs}](https://github.com/{ctbs})")) +```