From b36d6b281d7d4e7116592ccb02c460fd4cbc5b08 Mon Sep 17 00:00:00 2001
From: Ron Keizer <ron@insight-rx.com>
Date: Wed, 1 Apr 2026 10:53:00 -0700
Subject: [PATCH] Ensure AMT is always coerced to numeric in
 get_initial_estimates_from_data
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Uses as.numeric(as.character()) to handle character and factor AMT columns
correctly — as.numeric(factor) returns level codes, not values.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 DESCRIPTION                                   |  2 +-
 R/get_initial_estimates_from_data.R           |  2 +
 .../test-get_initial_estimates_from_data.R    | 61 +++++++++++++++++++
 3 files changed, 64 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a1eb597..df092ab 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pharmr.extra
 Title: Extension of pharmr (Pharmpy) functionality
-Version: 0.0.0.9032
+Version: 0.0.0.9033
 Authors@R: c(
     person("Ron", "Keizer", email = "ron@insight-rx.com", role = c("cre", "aut")),
     person("Michael", "McCarthy", email = "michael.mccarthy@insight-rx.com", role = "ctb"),
diff --git a/R/get_initial_estimates_from_data.R b/R/get_initial_estimates_from_data.R
index e35854f..821d005 100644
--- a/R/get_initial_estimates_from_data.R
+++ b/R/get_initial_estimates_from_data.R
@@ -29,6 +29,7 @@ get_initial_estimates_from_data <- function(
   suppressWarnings(
     data <- data |>
       dplyr::mutate(
+        AMT = as.numeric(as.character(.data$AMT)),
         DV = as.numeric(.data$DV),
         TIME = as.numeric(.data$TIME)
       ) |>
@@ -134,6 +135,7 @@ get_initial_estimates_from_individual_data <- function(
     est$V <- dose / max(obs$DV, na.rm=TRUE)
     est$CL <- KEL * est$V
   } else { # more crude estimation
+    
     if(length(tmp$DV) > 0) {
       est$V <- dose / (max(tmp$DV, na.rm=TRUE) * 5)
       est$CL <- est$V / 10
diff --git a/tests/testthat/test-get_initial_estimates_from_data.R b/tests/testthat/test-get_initial_estimates_from_data.R
index 8ca39da..2630e32 100644
--- a/tests/testthat/test-get_initial_estimates_from_data.R
+++ b/tests/testthat/test-get_initial_estimates_from_data.R
@@ -258,3 +258,64 @@ test_that("get_initial_estimates_from_data errors on non-existent CSV file", {
     "`data` file does not exist"
   )
 })
+
+test_that("get_initial_estimates_from_data works when AMT is character", {
+  test_data <- data.frame(
+    ID = c(1, 1, 1, 1),
+    TIME = c(0, 1, 4, 8),
+    DV = c(0, 100, 50, 25),
+    EVID = c(1, 0, 0, 0),
+    MDV = c(1, 0, 0, 0),
+    AMT = c("1000", "0", "0", "0"),
+    stringsAsFactors = FALSE
+  )
+
+  result <- get_initial_estimates_from_data(test_data, n_cmt = 1)
+
+  expect_type(result, "list")
+  expect_named(result, c("V", "CL"))
+  expect_true(all(result > 0))
+  expect_equal(result$V, 10, tolerance = 0.1)
+})
+
+test_that("get_initial_estimates_from_data works when AMT is factor", {
+  test_data <- data.frame(
+    ID = c(1, 1, 1, 1),
+    TIME = c(0, 1, 4, 8),
+    DV = c(0, 100, 50, 25),
+    EVID = c(1, 0, 0, 0),
+    MDV = c(1, 0, 0, 0),
+    AMT = factor(c("1000", "0", "0", "0"))
+  )
+
+  result <- get_initial_estimates_from_data(test_data, n_cmt = 1)
+
+  expect_type(result, "list")
+  expect_named(result, c("V", "CL"))
+  expect_true(all(result > 0))
+  expect_equal(result$V, 10, tolerance = 0.1)
+})
+
+test_that("get_initial_estimates_from_data gives same result regardless of AMT column type", {
+  base_data <- data.frame(
+    ID = c(1, 1, 1, 1),
+    TIME = c(0, 1, 4, 8),
+    DV = c(0, 100, 50, 25),
+    EVID = c(1, 0, 0, 0),
+    MDV = c(1, 0, 0, 0),
+    AMT = c(1000, 0, 0, 0)
+  )
+
+  result_numeric   <- get_initial_estimates_from_data(base_data, n_cmt = 1)
+  result_character <- get_initial_estimates_from_data(
+    transform(base_data, AMT = as.character(AMT)), n_cmt = 1
+  )
+  result_factor    <- get_initial_estimates_from_data(
+    transform(base_data, AMT = as.factor(AMT)), n_cmt = 1
+  )
+
+  expect_equal(result_numeric$V,  result_character$V,  tolerance = 1e-6)
+  expect_equal(result_numeric$CL, result_character$CL, tolerance = 1e-6)
+  expect_equal(result_numeric$V,  result_factor$V,     tolerance = 1e-6)
+  expect_equal(result_numeric$CL, result_factor$CL,    tolerance = 1e-6)
+})