Remove Hmisc dependency

CITATION.cff

@@ -190,19 +190,6 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2025'
-- type: software
-  title: Hmisc
-  abstract: 'Hmisc: Harrell Miscellaneous'
-  notes: Imports
-  url: https://hbiostat.org/R/Hmisc/
-  repository: https://CRAN.R-project.org/package=Hmisc
-  authors:
-  - family-names: Harrell Jr
-    given-names: Frank E
-    email: [email protected]
-    orcid: https://orcid.org/0000-0002-8271-5493
-  year: '2025'
-  doi: 10.32614/CRAN.package.Hmisc
 - type: software
   title: loo
   abstract: 'loo: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models'

DESCRIPTION

@@ -42,7 +42,6 @@ Imports:
     ggplot2,
     glue,
     graphics,
-    Hmisc,
     loo,
     Matrix,
     methods,

R/plot_seromodel.R

@@ -17,22 +17,25 @@ prepare_serosurvey_for_plotting <- function( #nolint
   serosurvey,
   alpha = 0.05
   ) {
-
-  serosurvey <- cbind(
+  # The binomial confidence interval calculation is based on:
+  # https://forum.posit.co/t/apply-binomial-test-for-each-row-in-a-data-table/32112/2 #nolint
+  serosurvey$seroprev <- serosurvey$n_seropositive / serosurvey$n_sample
+  serosurvey <- dplyr::mutate(
     serosurvey,
-    Hmisc::binconf(
-      serosurvey$n_seropositive,
-      serosurvey$n_sample,
-      alpha = alpha,
-      method = "exact",
-      return.df = TRUE
+    binconf = purrr::pmap(
+      .l = serosurvey,
+      .f = purrr::lift_vd(..f = function(dat) {
+        ci <- stats::binom.test(
+          x = dat["n_seropositive"],
+          n = dat["n_sample"],
+          p = dat["seroprev"],
+          conf.level = 1 - alpha)$conf.int
+        names(x = ci) <- c("seroprev_lower", "seroprev_upper")
+        return(ci)
+      })
     )
   ) |>
-    dplyr::rename(
-      seroprev = "PointEst",
-      seroprev_lower = "Lower",
-      seroprev_upper = "Upper"
-    ) |>
+  tidyr::unnest_wider(.data$binconf) |>
     dplyr::arrange(.data$age_group) |>
     dplyr::relocate(!!dplyr::sym("age_group"))