Debug curve plot

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.2.0.9022
+Version: 1.2.0.9023
 Authors@R: c(
     person("Peter", "Teunis", , "p.teunis@emory.edu", role = c("aut", "cph"),
            comment = "Author of the method and original code."),

NEWS.md

@@ -2,6 +2,8 @@
 
 ## New features
 
+* Fixed a bug in computing the antibody response curve when $r=1$ (#323)
+
 * Added example datasets with documentation for examples and testing (#314)
 
 * Improved error messaging for `autoplot.pop_data()` (#234).

R/ab0.R

@@ -1,19 +1,26 @@
 # uses r > 1 scale for shape
-ab0 <- function(
-    t,
-    curve_params) {
+ab0 <- function(t, curve_params) {
   y0 <- curve_params[["y0"]]
   y1 <- curve_params[["y1"]]
   t1 <- curve_params[["t1"]]
   alpha <- curve_params[["alpha"]]
-  shape <- curve_params[["r"]]
+  r <- curve_params[["r"]]
 
   beta <- bt(y0, y1, t1)
 
   yt <- 0
 
   yt_phase_1 <- y0 * exp(beta * t)
-  yt_phase_2 <- (y1^(1 - shape) - (1 - shape) * alpha * (t - t1))^(1 / (1 - shape))
+  if (r == 1) {
+    yt_phase_2 <- y1 * exp(-alpha * (t - t1))
+    # see wolfram alpha result: https://bit.ly/3ZB69Yn
+    # this is a version the product-limit characterization of the
+    # exponential function
+  } else {
+    yt_phase_2 <-
+      (y1^(1 - r) - (1 - r) * alpha * (t - t1))^(1 / (1 - r))
+  }
+
   yt <- dplyr::if_else(t <= t1, yt_phase_1, yt_phase_2)
   return(yt)
 }

tests/testthat/_snaps/ab0.md

@@ -0,0 +1,16 @@
+# `ab0()` produces consistent results
+
+    9298.67465260527
+
+---
+
+    9990.00499833375
+
+---
+
+    9298.67465260527
+
+---
+
+    909.090909090912
+

tests/testthat/test-ab0.R

@@ -0,0 +1,43 @@
+test_that("`ab0()` produces consistent results", {
+  params1 <-
+    data.frame(
+      y0 = 10,
+      y1 = 10^4,
+      t1 = 9.5,
+      alpha = 0.01,
+      r = 1,
+      antigen_iso = "test"
+    ) |>
+    as_curve_params()
+
+  calc1 <-
+    ab0(curve_params = params1, t = 9.4)
+
+  expect_snapshot_value(calc1, style = "deparse")
+
+  calc2 <-
+    ab0(curve_params = params1, t = 9.6)
+
+  expect_snapshot_value(calc2, style = "deparse")
+
+  params2 <-
+    data.frame(
+      y0 = 10,
+      y1 = 10^4,
+      t1 = 9.5,
+      alpha = 0.01,
+      r = 2,
+      antigen_iso = "test"
+    ) |>
+    as_curve_params()
+
+  calc3 <-
+    ab0(curve_params = params2, t = 9.4)
+
+  expect_snapshot_value(calc3, style = "deparse")
+
+  calc4 <-
+    ab0(curve_params = params2, t = 9.6)
+
+  expect_snapshot_value(calc4, style = "deparse")
+})

tests/testthat/test-plot_curve_params_one_ab.R

@@ -0,0 +1,23 @@
+test_that("`plot_curve_params_one_ab()` produces consistent results", {
+  params <-
+    data.frame(
+      y0 = 10,
+      y1 = 10 ^ 4,
+      t1 = 9.5,
+      alpha = 0.01,
+      r = 1,
+      antigen_iso = "test"
+    ) |>
+    as_curve_params()
+
+
+  fig1 <-
+    params |>
+    plot_curve_params_one_ab(n_points = 10 ^ 5,
+                             xlim = c(0, 25),
+                             log_y = FALSE)
+
+  fig1 |>
+    vdiffr::expect_doppelganger(title = "curve_r1")
+
+})