From a460362209428ce1b80bc58cac5dc8b8f1eafcdc Mon Sep 17 00:00:00 2001
From: SkylarMarvel <57526164+SkylarMarvel@users.noreply.github.com>
Date: Tue, 22 Oct 2024 15:06:05 -0600
Subject: [PATCH] Added some unit tests (#66)

---
 R/calc_invitro_concentration.R             |   2 +-
 R/compute_sensitivity.R                    |  10 ++
 R/sample_Css.R                             |   4 +-
 R/sensitivity_analysis.R                   |   3 +-
 R/simulate_exposure.R                      |   8 +-
 tests/testthat/test-check_lengths.R        |   7 +
 tests/testthat/test-check_names.R          |  10 ++
 tests/testthat/test-compute_sensitivity.R  |  67 +++++++++
 tests/testthat/test-fit_hill.R             |  37 +++++
 tests/testthat/test-get_fixed_css.R        |  25 ++++
 tests/testthat/test-get_fixed_params.R     |  27 ++--
 tests/testthat/test-sample_Css.R           |   1 +
 tests/testthat/test-sensitivity_analysis.R |  41 ++++++
 tests/testthat/test-simulate_exposure.R    |  63 +++++++--
 tests/testthat/test-simulate_obesity.R     |  15 +++
 tests/testthat/test-simulate_population.R  | 150 ++++++++++++++++-----
 16 files changed, 406 insertions(+), 64 deletions(-)
 create mode 100644 tests/testthat/test-check_lengths.R
 create mode 100644 tests/testthat/test-check_names.R
 create mode 100644 tests/testthat/test-compute_sensitivity.R
 create mode 100644 tests/testthat/test-get_fixed_css.R
 create mode 100644 tests/testthat/test-sensitivity_analysis.R

diff --git a/R/calc_invitro_concentration.R b/R/calc_invitro_concentration.R
index 85d0a51..bc8fc88 100644
--- a/R/calc_invitro_concentration.R
+++ b/R/calc_invitro_concentration.R
@@ -30,5 +30,5 @@ calc_invitro_concentration <- function(D_int, C_ss = NULL) {
 }
 
 .calc_invitro_concentration <- function(D_int, C_ss) {
-  D_int * C_ss
+  as.matrix(D_int * C_ss)
 }
diff --git a/R/compute_sensitivity.R b/R/compute_sensitivity.R
index 9ad04ad..9f2960e 100644
--- a/R/compute_sensitivity.R
+++ b/R/compute_sensitivity.R
@@ -23,9 +23,16 @@ compute_sensitivity <- function(x,
     tp_b_mult <- x$par$resp$tp_b_mult
   }
   
+  if (is.null(x$age)) {
+    stop("GeoTox 'age' field is not set.", call. = FALSE)
+  }
+  
   if (vary == "age") {
     age <- x$age
     IR <- x$IR
+    if (is.null(IR)) {
+      stop("GeoTox 'IR' field is not set.", call. = FALSE)
+    }
   } else {
     age <- lapply(x$age, function(x) rep(stats::median(x),
                                          length.out = length(x)))
@@ -34,6 +41,9 @@ compute_sensitivity <- function(x,
   
   if (vary == "C_ext") {
     C_ext <- x$C_ext
+    if (is.null(C_ext)) {
+      stop("GeoTox 'C_ext' field is not set.", call. = FALSE)
+    }
   } else {
     # Set exposure sd = NA (or 0)
     exposure <- lapply(x$exposure, \(x) x |> dplyr::mutate(sd = NA))
diff --git a/R/sample_Css.R b/R/sample_Css.R
index faf73ec..b5485eb 100644
--- a/R/sample_Css.R
+++ b/R/sample_Css.R
@@ -28,8 +28,8 @@ sample_Css <- function(simulated_css, age, obesity) {
     stop("Names and lengths of 'age' and 'obesity' fields must be equal",
          call. = FALSE)
   }
-  if (length(age) == 0) {
-    stop("'age' and 'obesity' data has not been simulated", call. = FALSE)
+  if (length(age[[1]]) == 0) {
+    stop("'age' and 'obesity' data have not been simulated", call. = FALSE)
   }
 
   mapply(
diff --git a/R/sensitivity_analysis.R b/R/sensitivity_analysis.R
index d850cc0..ce77d2c 100644
--- a/R/sensitivity_analysis.R
+++ b/R/sensitivity_analysis.R
@@ -27,8 +27,7 @@ sensitivity_analysis <- function(x,
     stop("Input 'x' must be a GeoTox object.", call. = FALSE)
   }
   if (length(tp_b_mult) != 5) {
-    stop("Input 'tp_b_mult' must be a numeric vector of length 5.",
-         call. = FALSE)
+    stop("Input 'tp_b_mult' must have a length of 5.", call. = FALSE)
   }
   
   x$sensitivity <- list(
diff --git a/R/simulate_exposure.R b/R/simulate_exposure.R
index 3c02db4..adc848d 100644
--- a/R/simulate_exposure.R
+++ b/R/simulate_exposure.R
@@ -36,14 +36,14 @@ simulate_exposure <- function(x,
                               n = 1e3) {
 
   if (!any(c("data.frame", "list") %in% class(x))) {
-    stop("x must be a data.frame or list")
+    stop("'x' must be a data.frame or list", call. = FALSE)
   }
   
   if (is.data.frame(x)) x <- list(x)
 
   if (.check_names(x, c(expos_mean, expos_sd))) {
-    stop("x data frames must contain columns named by 'expos_mean' and ",
-         "'expos_sd'")
+    stop("'x' data frames must contain columns named by 'expos_mean' and ",
+         "'expos_sd'", call. = FALSE)
   }
   
   lapply(x, function(df) {
@@ -53,7 +53,7 @@ simulate_exposure <- function(x,
       # Have consistent output order
       out <- out[, order(colnames(out)), drop = FALSE]
     } else if (nrow(df) > 1) {
-      stop("x data frames must contain a column named by 'expos_label'",
+      stop("'x' data frames must contain a column named by 'expos_label'",
            call. = FALSE)
     }
     out
diff --git a/tests/testthat/test-check_lengths.R b/tests/testthat/test-check_lengths.R
new file mode 100644
index 0000000..8d897a4
--- /dev/null
+++ b/tests/testthat/test-check_lengths.R
@@ -0,0 +1,7 @@
+test_that("results", {
+  # TRUE means different lengths
+  expect_true(.check_lengths(list(1:5),
+                             list(6:9)))
+  expect_false(.check_lengths(list(1:5),
+                              list(6:10)))
+})
diff --git a/tests/testthat/test-check_names.R b/tests/testthat/test-check_names.R
new file mode 100644
index 0000000..c1060f4
--- /dev/null
+++ b/tests/testthat/test-check_names.R
@@ -0,0 +1,10 @@
+test_that("results", {
+  # TRUE means names not found
+  names <- "a"
+  expect_true(.check_names(c(), names = names))
+  expect_true(.check_names(list(c()), names = names))
+  expect_true(.check_names(list(c("a" = 1),
+                                c()), names = names))
+  expect_false(.check_names(c("a" = 1), names = names))
+  expect_false(.check_names(list(c("a" = 1)), names = names))
+})
diff --git a/tests/testthat/test-compute_sensitivity.R b/tests/testthat/test-compute_sensitivity.R
new file mode 100644
index 0000000..6a099cc
--- /dev/null
+++ b/tests/testthat/test-compute_sensitivity.R
@@ -0,0 +1,67 @@
+test_that("bad inputs", {
+  
+  # Age field not set
+  expect_error(compute_sensitivity(GeoTox()))
+  
+  # IR field not set
+  geoTox <- GeoTox()
+  geoTox$age <- list(1)
+  expect_error(compute_sensitivity(geoTox))
+  
+  # C_ext field not set
+  geoTox <- GeoTox()
+  geoTox$age <- list(1)
+  expect_error(compute_sensitivity(geoTox, vary = "C_ext"))
+})
+
+test_that("results", {
+  
+  # Similar to "test-sensitivity_analysis.R"
+  
+  geoTox <- GeoTox()
+  
+  expect_null(geoTox$sensitivity)
+  
+  geoTox$par$n <- 1
+  geoTox$hill_params <- data.frame(resp_max = 5,
+                                   tp = 5,
+                                   tp.sd = 1,
+                                   logc_min = -1,
+                                   logc_max = 1,
+                                   logAC50 = 0,
+                                   logAC50.sd = 1)
+  geoTox$age <- list(2)
+  geoTox$IR <- list(0.5)
+  geoTox$obesity <- list("Normal")
+  geoTox$exposure <- list(data.frame(mean = 1, sd = 0))
+  geoTox$C_ext <- list(1)
+  geoTox$css_sensitivity <- list(age = list(matrix(5)),
+                                 obesity = list(matrix(10)),
+                                 params = list(matrix(15)),
+                                 other = list(7))
+  
+  out <- compute_sensitivity(geoTox, "age", NULL)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+  
+  out <- compute_sensitivity(geoTox, "obesity", 1.1)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+  
+  out <- compute_sensitivity(geoTox, "css_params", 1.2)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+  
+  out <- compute_sensitivity(geoTox, "fit_params", 1.3)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+  
+  out <- compute_sensitivity(geoTox, "C_ext", 1.4)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+})
diff --git a/tests/testthat/test-fit_hill.R b/tests/testthat/test-fit_hill.R
index 506b398..32e3c83 100644
--- a/tests/testthat/test-fit_hill.R
+++ b/tests/testthat/test-fit_hill.R
@@ -1,3 +1,17 @@
+test_that("bad inputs", {
+  # Input should be a data frame
+  expect_error(fit_hill(c()))
+  # Expected required column names
+  expect_error(fit_hill(data.frame(x = 0, y = 0)))
+  # Expected optional column names
+  expect_error(fit_hill(data.frame(logc = c(-1, 1),
+                                   resp = c(100, 0)),
+                        chem = "missing"))
+  expect_error(fit_hill(data.frame(logc = c(-1, 1),
+                                   resp = c(100, 0)),
+                        assay = "missing"))
+})
+
 test_that("output column names", {
   df <- data.frame(
     logc = -3:3,
@@ -22,3 +36,26 @@ test_that("output column names", {
   expect_equal(names(fit_hill(df, chem = "chem_col", assay = "assay_col")),
                c("assay", "chem", colnames))
 })
+
+test_that("internal", {
+  
+  x <- data.frame(logc = c(-1, 0, 1), resp = c(10, 5, 0))
+  
+  out <- .fit_hill(x)
+  
+  expect_equal(as.numeric(out$par["slope"]),
+               1)
+  
+  out <- .fit_hill(x, fixed_slope = FALSE)
+  
+  expect_true(as.numeric(out$par["slope"]) > 1)
+  
+  res <- .extract_hill_params(out)
+  
+  colnames <- c("tp", "tp.sd", "logAC50", "logAC50.sd", "slope", "slope.sd",
+                "logc_min", "logc_max", "resp_min", "resp_max",
+                "AIC", "tp.sd.imputed", "logAC50.sd.imputed")
+  
+  expect_equal(names(res),
+               colnames)
+})
diff --git a/tests/testthat/test-get_fixed_css.R b/tests/testthat/test-get_fixed_css.R
new file mode 100644
index 0000000..d146783
--- /dev/null
+++ b/tests/testthat/test-get_fixed_css.R
@@ -0,0 +1,25 @@
+test_that("errors", {
+  expect_error(get_fixed_css(age = c(1, 2), obesity = c("Normal")))
+})
+
+test_that("results", {
+  simulated_css <- list(tibble::tibble(age_min = 1,
+                                       age_median_css = 5,
+                                       weight = "Normal",
+                                       weight_median_css = 10,
+                                       css = list(c(15, 15))))
+  C_ss <- list(matrix(7))
+  age <- 2
+  obesity <- "Normal"
+
+  out <- get_fixed_css(simulated_css = simulated_css,
+                       C_ss = C_ss,
+                       age = age,
+                       obesity = obesity)
+  
+  expect_equal(out,
+               list(age = list(matrix(5)),
+                    params = list(matrix(15)),
+                    obesity = list(matrix(10)),
+                    other = list(7)))
+})
diff --git a/tests/testthat/test-get_fixed_params.R b/tests/testthat/test-get_fixed_params.R
index 0c0482a..c554d2d 100644
--- a/tests/testthat/test-get_fixed_params.R
+++ b/tests/testthat/test-get_fixed_params.R
@@ -9,13 +9,22 @@ test_that("expected results", {
   })
   simulated_css <- list("chem1" = x, "chem2" = y)
   
-  expect_equal(
-    get_fixed_params(simulated_css, list(c(1, 27, 30), c(15, 60))),
-    list(matrix(c(4, 4, 4, 2, 2, 2),
-                ncol = 2,
-                dimnames = list(NULL, c("chem1", "chem2"))),
-         matrix(c(6, 6, 3, 3),
-                ncol = 2,
-                dimnames = list(NULL, c("chem1", "chem2"))))
-  )
+  # Age list
+  out <- get_fixed_params(simulated_css, list(c(1, 27, 30), c(15, 60)))
+  
+  expect_equal(out,
+               list(matrix(c(4, 4, 4, 2, 2, 2),
+                           ncol = 2,
+                           dimnames = list(NULL, c("chem1", "chem2"))),
+                    matrix(c(6, 6, 3, 3),
+                           ncol = 2,
+                           dimnames = list(NULL, c("chem1", "chem2")))))
+  
+  # Age vector
+  out <- get_fixed_params(simulated_css, c(1, 27, 30))
+  
+  expect_equal(out,
+               list(matrix(c(4, 4, 4, 2, 2, 2),
+                           ncol = 2,
+                           dimnames = list(NULL, c("chem1", "chem2")))))
 })
diff --git a/tests/testthat/test-sample_Css.R b/tests/testthat/test-sample_Css.R
index c077e95..7a5711a 100644
--- a/tests/testthat/test-sample_Css.R
+++ b/tests/testthat/test-sample_Css.R
@@ -1,6 +1,7 @@
 test_that("bad inputs", {
   # Missing age/obesity data
   expect_error(sample_Css(age = c(), obesity = c()))
+  expect_error(sample_Css(age = NULL, obesity = NULL))
   # Age/obesity data do not match lengths
   expect_error(sample_Css(age = 1:3, obesity = c("Normal", "Obese")))
   # Age/obesity data do not match names
diff --git a/tests/testthat/test-sensitivity_analysis.R b/tests/testthat/test-sensitivity_analysis.R
new file mode 100644
index 0000000..5856d84
--- /dev/null
+++ b/tests/testthat/test-sensitivity_analysis.R
@@ -0,0 +1,41 @@
+test_that("bad inputs", {
+  expect_error(sensitivity_analysis(list()))
+  expect_error(sensitivity_analysis(GeoTox(), 1:3))
+})
+
+test_that("results", {
+  
+  # Similar to "test-compute_sensitivity.R"
+  
+  geoTox <- GeoTox()
+  
+  expect_null(geoTox$sensitivity)
+  
+  geoTox$par$n <- 1
+  geoTox$hill_params <- data.frame(resp_max = 5,
+                                   tp = 5,
+                                   tp.sd = 1,
+                                   logc_min = -1,
+                                   logc_max = 1,
+                                   logAC50 = 0,
+                                   logAC50.sd = 1)
+  geoTox$age <- list(2)
+  geoTox$IR <- list(0.5)
+  geoTox$obesity <- list("Normal")
+  geoTox$exposure <- list(data.frame(mean = 1, sd = 0))
+  geoTox$C_ext <- list(1)
+  geoTox$css_sensitivity <- list(age = list(matrix(5)),
+                                 obesity = list(matrix(10)),
+                                 params = list(matrix(15)),
+                                 other = list(7))
+  
+  geoTox <- sensitivity_analysis(geoTox, list(NULL, 1.1, 1.2, 1.3, 1.4))
+  
+  geoTox$sensitivity
+
+  expect_false(is.null(geoTox$sensitivity$age))
+  expect_false(is.null(geoTox$sensitivity$obesity))
+  expect_false(is.null(geoTox$sensitivity$css_params))
+  expect_false(is.null(geoTox$sensitivity$fit_params))
+  expect_false(is.null(geoTox$sensitivity$C_ext))
+})
diff --git a/tests/testthat/test-simulate_exposure.R b/tests/testthat/test-simulate_exposure.R
index e1ac862..819677b 100644
--- a/tests/testthat/test-simulate_exposure.R
+++ b/tests/testthat/test-simulate_exposure.R
@@ -3,18 +3,30 @@ test_that("bad inputs", {
   expect_error(simulate_exposure(c()))
   # Need columns named by "expos_mean" and "expos_sd"
   expect_error(simulate_exposure(data.frame(x = 0, y = 0)))
+  expect_error(simulate_exposure(list(data.frame(x = 0, y = 0),
+                                      data.frame(mean = 0, sd = 0))))
   # Need column named by "expos_label" if nrows > 1
   expect_error(simulate_exposure(data.frame(mean = c(0, 0), sd = c(0, 0))))
 })
 
-test_that("single data frame", {
+test_that("single row", {
   
-  out <- simulate_exposure(
-    data.frame(mean = 1:3,
-               sd = (1:3) / 10,
-               casn = letters[1:3]),
-    n = 5)
+  out <- simulate_exposure(data.frame(mean = 10, sd = 1), n = 5)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+  expect_equal(dim(out[[1]]), c(5, 1))
+  expect_equal(colnames(out[[1]]), NULL)
+  
+})
 
+test_that("single data frame", {
+  
+  out <- simulate_exposure(data.frame(mean = 1:3,
+                                      sd = (1:3) / 10,
+                                      casn = letters[1:3]),
+                           n = 5)
+  
   expect_type(out, "list")
   expect_length(out, 1)
   expect_equal(dim(out[[1]]), c(5, 3))
@@ -30,7 +42,7 @@ test_that("two data frames", {
                            casn = letters[1:3]),
          loc2 = data.frame(mean = 4:7,
                            sd = 0.1,
-                           casn = letters[4:7])),
+                           casn = letters[c(4, 7, 6, 5)])),
     n = 5)
   
   expect_type(out, "list")
@@ -69,9 +81,7 @@ test_that("custom column names", {
 
 test_that("internal", {
   
-  out <- .simulate_exposure(data.frame(mean = 1:3,
-                                       sd = (1:3) / 10,
-                                       casn = letters[1:3]),
+  out <- .simulate_exposure(data.frame(mean = 1:3, sd = (1:3) / 10),
                             mean = "mean",
                             sd = "sd",
                             n = 5)
@@ -82,3 +92,36 @@ test_that("internal", {
   expect_true(all(out >= 0))
   
 })
+
+test_that("internal special cases", {
+  
+  out <- .simulate_exposure(data.frame(mean = c(), sd = c()),
+                            mean = "mean",
+                            sd = "sd",
+                            n = 5)
+  
+  # Output is a matrix, so type == "double" with 2 dimensions
+  expect_type(out, "double")
+  expect_equal(dim(out), c(5, 0))
+  
+  out <- .simulate_exposure(data.frame(mean = 0, sd = 0),
+                            mean = "mean",
+                            sd = "sd",
+                            n = 5)
+  
+  # Output is a matrix, so type == "double" with 2 dimensions
+  expect_type(out, "double")
+  expect_equal(dim(out), c(5, 1))
+  expect_true(all(out == 0))
+  
+  out <- .simulate_exposure(data.frame(mean = 1, sd = NA),
+                            mean = "mean",
+                            sd = "sd",
+                            n = 5)
+  
+  # Output is a matrix, so type == "double" with 2 dimensions
+  expect_type(out, "double")
+  expect_equal(dim(out), c(5, 1))
+  expect_true(all(out == 1))
+  
+})
diff --git a/tests/testthat/test-simulate_obesity.R b/tests/testthat/test-simulate_obesity.R
index 4ab2494..1ebe18f 100644
--- a/tests/testthat/test-simulate_obesity.R
+++ b/tests/testthat/test-simulate_obesity.R
@@ -8,6 +8,21 @@ test_that("bad inputs", {
                                            OBESITY_SD = c(0, 0))))
 })
 
+test_that("single row", {
+  
+  x <- data.frame(OBESITY_CrudePrev = 50,
+                  OBESITY_SD = 5)
+  
+  out <- simulate_obesity(x, n = 5)
+  
+  expect_type(out, "list")
+  expect_length(out, 1)
+  expect_equal(names(out), NULL)
+  expect_equal(length(out[[1]]), 5)
+  expect_true(all(out[[1]] %in% c("Normal", "Obese")))
+
+})
+
 test_that("default column names", {
   
   x <- data.frame(OBESITY_CrudePrev = c(20, 50, 80),
diff --git a/tests/testthat/test-simulate_population.R b/tests/testthat/test-simulate_population.R
index 6b2a07e..004ac70 100644
--- a/tests/testthat/test-simulate_population.R
+++ b/tests/testthat/test-simulate_population.R
@@ -1,3 +1,91 @@
+test_that("errors", {
+  # If IR_params is input, then age must be input or already exist
+  expect_error(GeoTox() |> simulate_population(IR_params = "test"))
+})
+
+test_that("populate fields - age", {
+
+  geoTox <- GeoTox()
+  age <- data.frame(AGEGRP = 0:18, TOT_POP = 0)
+  age$TOT_POP[c(1, 10)] <- 100
+  
+  expect_null(geoTox$age)
+  expect_null(geoTox$IR)
+  
+  geoTox <- geoTox |> simulate_population(age = age, n = 5)
+  
+  expect_false(is.null(geoTox$age))
+  expect_false(is.null(geoTox$IR))
+})
+
+test_that("populate fields - IR_params", {
+  
+  geoTox <- GeoTox()
+  IR_params <- data.frame("age" = c(20, 0, 50),
+                          "mean" = c(0.3, 0.5, 0.2),
+                          "sd" = 0)
+  
+  expect_null(geoTox$IR)
+  
+  geoTox$age <- list(seq(10, 90, by = 10))
+  geoTox <- geoTox |> simulate_population(IR_params = IR_params)
+  
+  expect_false(is.null(geoTox$IR))
+})
+
+test_that("populate fields - obesity", {
+  
+  geoTox <- GeoTox()
+  obesity <- data.frame(OBESITY_CrudePrev = c(20, 50, 80),
+                        OBESITY_SD = c(5, 5, 5),
+                        FIPS = c("c", "a", "b"))
+  
+  expect_null(geoTox$obesity)
+  
+  geoTox <- geoTox |> simulate_population(obesity = obesity, n = 5)
+
+  expect_false(is.null(geoTox$obesity))
+})
+
+test_that("populate fields - exposure", {
+  
+  geoTox <- GeoTox()
+  exposure <- data.frame(mean = 10, sd = 1)
+  
+  expect_null(geoTox$exposure)
+  expect_null(geoTox$C_ext)
+  
+  geoTox <- geoTox |> simulate_population(exposure = exposure, n = 5)
+  
+  expect_false(is.null(geoTox$exposure))
+  expect_false(is.null(geoTox$C_ext))
+})
+
+test_that("populate fields - simulated_css", {
+  
+  geoTox <- GeoTox()
+  x <- y <- expand.grid(age_min = seq(0, 50, 10), weight = c("Normal", "Obese"))
+  x$css <- lapply(1:nrow(x), function(i) {
+    rep(x$age_min[i] / 5 + as.integer(x$weight[i] == "Obese"), 2)
+  })
+  x$age_median_css <- x$weight_median_css <- 10
+  y$css <- lapply(1:nrow(y), function(i) {
+    rep(y$age_min[i] / 10 + as.integer(y$weight[i] == "Obese") / 2, 2)
+  })
+  y$age_median_css <- y$weight_median_css <- 10
+  simulated_css <- list("chem1" = x, "chem2" = y)
+
+  expect_null(geoTox$C_ss)
+  expect_null(geoTox$css_sensitivity)
+  
+  geoTox$age <- seq(5, 50, by = 5)
+  geoTox$obesity <- rep("Normal", 10)
+  geoTox <- geoTox |> simulate_population(simulated_css = simulated_css)
+  
+  expect_false(is.null(geoTox$C_ss))
+  expect_false(is.null(geoTox$css_sensitivity))
+})
+
 test_that("clear downstream - age", {
   
   # Simulate GeoTox age field
@@ -43,24 +131,19 @@ test_that("default params", {
   
   geoTox <- GeoTox()
   
-  expect_equal(
-    geoTox$par,
-    list(
-      n = 1e3,
-      IR_params = NULL,
-      obesity = list(obes_prev  = "OBESITY_CrudePrev",
-                     obes_sd    = "OBESITY_SD",
-                     obes_label = "FIPS"),
-      exposure = list(expos_mean  = "mean",
-                      expos_sd    = "sd",
-                      expos_label = "casn"),
-      internal_dose = list(time    = 1,
-                           BW      = 1,
-                           scaling = 1),
-      resp = list(tp_b_mult = 1.5)
-    )
-  )
-  
+  expect_equal(geoTox$par,
+               list(n = 1e3,
+                    IR_params = NULL,
+                    obesity = list(obes_prev  = "OBESITY_CrudePrev",
+                                   obes_sd    = "OBESITY_SD",
+                                   obes_label = "FIPS"),
+                    exposure = list(expos_mean  = "mean",
+                                    expos_sd    = "sd",
+                                    expos_label = "casn"),
+                    internal_dose = list(time    = 1,
+                                         BW      = 1,
+                                         scaling = 1),
+                    resp = list(tp_b_mult = 1.5)))
 })
 
 test_that("update params", {
@@ -93,22 +176,17 @@ test_that("update params", {
                         expos_sd = expos_sd,
                         expos_label = expos_label)
   
-  expect_equal(
-    geoTox$par,
-    list(
-      n = n,
-      IR_params = IR_params,
-      obesity = list(obes_prev  = obes_prev,
-                     obes_sd    = obes_sd,
-                     obes_label = obes_label),
-      exposure = list(expos_mean  = expos_mean,
-                      expos_sd    = expos_sd,
-                      expos_label = expos_label),
-      internal_dose = list(time    = 1,
-                           BW      = 1,
-                           scaling = 1),
-      resp = list(tp_b_mult = 1.5)
-    )
-  )
-  
+  expect_equal(geoTox$par,
+               list(n = n,
+                    IR_params = IR_params,
+                    obesity = list(obes_prev  = obes_prev,
+                                   obes_sd    = obes_sd,
+                                   obes_label = obes_label),
+                    exposure = list(expos_mean  = expos_mean,
+                                    expos_sd    = expos_sd,
+                                    expos_label = expos_label),
+                    internal_dose = list(time    = 1,
+                                         BW      = 1,
+                                         scaling = 1),
+                    resp = list(tp_b_mult = 1.5)))
 })