Merge pull request #29 from getwilds/test

completed incidence tests

R/incidence-cancer.R

@@ -102,3 +102,10 @@ incidence_cancer <- function(area, areatype, cancer, race, sex=NULL, age, stage,
       setNames(c(areatype_title, "FIPS", "Age Adjusted Incidence Rate", "Lower 95% CI", "Upper 95% CI", "CI Rank", "Lower CI Rank", "Upper CI Rank", "Annual Average Count", "Percentage of Cases with Late Stage"))
   }
 }
+
+
+
+
+
+
+

R/process-incidence.R

@@ -44,5 +44,6 @@ process_incidence <- function(resp) {
   if(column %in% c("Health.Service.Area", "County")) {
       resp <- resp %>%
         filter(!(!!sym(column) %in% state.name))
-    }
+  }
+  resp
 }

tests/testthat/test-incidence-cancer.R

@@ -0,0 +1,72 @@
+#' Test incidence Cancer
+#'
+#' This testthat file test the incidence_cancer function
+#'
+# tests class and typeof output
+test_that("Output data type is correct", {
+  output <- incidence_cancer("wa", "county", "all cancer sites", "black (non-hispanic)", 
+                             "both sexes", "ages 65+", "all stages")
+
+  expect_true(inherits(output, "data.frame"))
+})
+
+#Ensures that variables are present and working on SCP
+cancer_options <- c("all cancer sites","bladder", "brain & ons", "colon & rectum", 
+                    "esophagus", "kidney & renal pelvis", "leukemia", "liver & bile duct", 
+                    "lung & bronchus", "melanoma of the skin", "non-hodgkin lymphoma", 
+                    "oral cavity & pharynx", "pancreas", "stomach", "thyroid")
+
+for (option in cancer_options) {
+  test_that("incidence cancer returns non-empty data frame", {
+    result <- incidence_cancer("wa", "county", option, "all races (includes hispanic)", 
+                               "both sexes", "all ages", "all stages")
+    expect_true(is.data.frame(result))
+  })
+}
+
+female_cancer_options <- c("breast (female)", "breast (female in situ)", 
+                           "cervix", "ovary", "uterus (corpus & uterus, nos)")
+
+for (option in female_cancer_options) {
+  test_that("incidence female cancer returns non-empty data frame", {
+    result <- incidence_cancer("wa", "county", option, 
+                               "all races (includes hispanic)", "females", 
+                               "ages 50+", "all stages")
+
+    expect_true(is.data.frame(result))
+  })
+}
+
+childhood_male_cancer_options <- list(
+  childhood15 = incidence_cancer("ca", "hsa", "childhood (ages <20, all sites)", "all races (includes hispanic)", 
+                                 "males", "ages <20", "all stages"),
+  childhood20 = incidence_cancer("ca", "hsa", "childhood (ages <20, all sites)", "all races (includes hispanic)", 
+                                 "males", "ages <20", "all stages"),
+  prostate = incidence_cancer("usa", "state", "prostate", "all races (includes hispanic)", 
+                              "males", "ages 50+", "all stages")
+)
+
+for (option_name in names(childhood_male_cancer_options)) {
+  test_that("incidence cancer returns non-empty data frame", {
+    option <- childhood_male_cancer_options[[option_name]]
+    expect_true(is.data.frame(option))
+  })
+}
+
+#incidence_cancer must have 14 columns
+test_that("incidence_cancer has correct number of columns", {
+  df1 <- incidence_cancer("wa", "county", "all cancer sites", "black (non-hispanic)", 
+                         "both sexes", "ages 65+", "all stages")
+  df2 <- incidence_cancer("usa", "state", "lung & bronchus", "all races (includes hispanic)", "males", 
+                         "ages 50+", "late stage (regional & distant)")
+  expected_columns1 <- 13
+  expected_columns2 <- 10
+  expect_equal(ncol(df1), expected_columns1)
+  expect_equal(ncol(df2), expected_columns2)
+
+})
+
+#parameter
+test_that("incidence_cancer has correct parameters", {
+  expect_error(incidence_cancer())
+})