Use autoplot for curve params in methodology vignette

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.4.0.9009
+Version: 1.4.0.9010
 Authors@R: c(
     person("Kristina", "Lai", , "kwlai@ucdavis.edu", role = c("aut", "cre")),
     person("Chris", "Orwa", role = "aut"),

NEWS.md

@@ -7,6 +7,10 @@
   - Provides clear tables comparing old and new function names
   - Includes code examples showing how to update existing code
   - Accessible as a prominent tab in the website navigation
+
+## Documentation
+
+* Updated the methodology vignette to plot curve parameters via the `autoplot()` method.
 ## New features
 
 * Added `cluster_var` and `stratum_var` parameters to `est_seroincidence()` and 

R/plot_curve_params_one_ab.R

@@ -6,7 +6,7 @@
 #' @param n_curves how many curves to plot (see details).
 #' @param n_points Number of points to interpolate along the x axis
 #' (passed to [ggplot2::geom_function()])
-#' @param iters_to_graph which MCMC iterations in `curve_params` to plot
+#' @param iters_to_graph which rows of `object` to plot
 #' (overrides `n_curves`).
 #' @param alpha (passed to [ggplot2::geom_function()])
 #' how transparent the curves should be:
@@ -71,8 +71,8 @@ plot_curve_params_one_ab <- function(
                              minor_breaks = NULL)
   }
 
-  layer_function <- function(cur_iter) {
-    cur_params <- object |> filter(.data$iter == cur_iter)
+  layer_function <- function(cur_row) {
+    cur_params <- object[cur_row, ]
     ggplot2::geom_function(
       alpha = alpha,
       fun = ab0,

tests/testthat/test-plot_curve_params_one_ab.R

@@ -22,3 +22,31 @@ test_that("`plot_curve_params_one_ab()` produces consistent results", {
     vdiffr::expect_doppelganger(title = "curve_r1")
 
 })
+
+test_that(
+  "`plot_curve_params_one_ab()` works when `iter` does not start at 1",
+  {
+    # Regression test: previously, layer_function filtered by
+    # `iter == cur_iter`, where cur_iter was a row index (1, 2, ...).
+    # When iter values didn't start at 1, the filter returned 0 rows,
+    # causing `r` to be numeric(0).
+    params <-
+      data.frame(
+        y0 = 10,
+        y1 = 10 ^ 4,
+        t1 = 9.5,
+        alpha = 0.01,
+        r = 1,
+        iter = 5,
+        antigen_iso = "test"
+      ) |>
+      as_sr_params()
+
+    expect_no_error(
+      params |>
+        plot_curve_params_one_ab(n_points = 100,
+                                 xlim = c(0, 25),
+                                 log_y = FALSE)
+    )
+  }
+)

vignettes/articles/_antibody-response-model.qmd

@@ -122,8 +122,10 @@ curve1 <-
 library(ggplot2)
 
 curve1 |>
-  serocalculator:::plot_curve_params_one_ab(
-    log_y = FALSE
+  autoplot(
+    quantiles = NULL,
+    log_y = FALSE,
+    n_curves = 1
   ) +
   xlim(0, 100) +
   theme_minimal() +