Merge pull request #25 from getwilds/test

Test

R/handle-screening.R

@@ -20,13 +20,18 @@ handle_screening <- function(screening) {
   screening <- tolower(screening)
 
   screening_mapping <- c(
-    "ever had colorectal endoscopy (sigmoidoscopy or colonoscopy), ages 50+" = "v09",
     "ever had fobt, ages 50-75" = "v304",
-    "fobt (1yr) / flex sig (5yr) / fobt (3yr) / colonoscopy (10yr), ages 50-75" = "v14",
     "guidance sufficient crc, ages 50-75" = "v303",
     "had colonoscopy in past 10 years, ages 50-75" = "v302",
-    "home-based fecal occult blood test (fobt) in past two years" = "v13",
-    "home-based fobt in the past two years or ever had a colorectal endoscopy" = "v59"
+
+    "home blood stool test in the past year, ages 45-75" = "v520",
+    "receieved at least one recommended crc test, ages 45-75" = "v521"
+
+    #removed from scp
+    # "ever had colorectal endoscopy (sigmoidoscopy or colonoscopy), ages 50+" = "v09",
+    # "fobt (1yr) / flex sig (5yr) / fobt (3yr) / colonoscopy (10yr), ages 50-75" = "v14",
+    # "home-based fecal occult blood test (fobt) in past two years" = "v13",
+    # "home-based fobt in the past two years or ever had a colorectal endoscopy" = "v59"
   )
 
   screening_code <- screening_mapping[screening]

R/risk-colorectal-screening.R

@@ -2,11 +2,11 @@
 #' 
 #' This function returns a data frame from Colorectal Screening in State Cancer Profiles
 #'
-#' @param screening One of the following values: "ever had colorectal endoscopy (sigmoidoscopy or colonoscopy), ages 50+", 
-#'                                                "fobt (1yr) / flex sig (5yr) / fobt (3yr) / colonoscopy (10yr), ages 50-75", 
-#'                                                "home-based fecal occult blood test (fobt) in past two years", 
-#'                                                "home-based fobt in the past two years or ever had a colorectal endoscopy", "ever had fobt, ages 50-75", 
-#'                                                "guidance sufficient crc, ages 50-75", "had colonoscopy in past 10 years, ages 50-75"
+#' @param screening One of the following values: "home blood stool test in the past year, ages 45-75",
+#'                                               "receieved at least one recommended crc test, ages 45-75",
+#'                                               "ever had fobt, ages 50-75",
+#'                                               "guidance sufficient crc, ages 50-75",
+#'                                               "had colonoscopy in past 10 years, ages 50-75"
 #' @param race One of the following values: "All Races (includes Hispanic)", "white (includes hispanic)",
 #'              "white non-hispanic","black","amer. indian/alaskan native (includes hispanic)",
 #'              "asian or pacific islander (includes hispanic)","hispanic (any race)
@@ -19,7 +19,7 @@
 #' 
 #' @examples
 #' \dontrun{
-#' risk_colorectal_screening("ever had colorectal endoscopy (sigmoidoscopy or colonoscopy), ages 50+",
+#' risk_colorectal_screening("home blood stool test in the past year, ages 45-75",
 #'                           "all races (includes hispanic)","both sexes")
 #' risk_colorectal_screening("ever had fobt, ages 50-75", area="usa")
 #' risk_colorectal_screening("ever had fobt, ages 50-75", area="wa")
@@ -28,10 +28,8 @@ risk_colorectal_screening <- function(screening, race=NULL, sex=NULL, area=NULL)
 
   req <- create_request("risk")
 
-  screening_type_1 = c("ever had colorectal endoscopy (sigmoidoscopy or colonoscopy), ages 50+",
-                       "fobt (1yr) / flex sig (5yr) / fobt (3yr) / colonoscopy (10yr), ages 50-75",
-                       "home-based fecal occult blood test (fobt) in past two years",
-                       "home-based fobt in the past two years or ever had a colorectal endoscopy")
+  screening_type_1 = c("home blood stool test in the past year, ages 45-75",
+                       "receieved at least one recommended crc test, ages 45-75")
 
   screening_type_2 = c("ever had fobt, ages 50-75",
                        "guidance sufficient crc, ages 50-75",

R/risk-diet-exercise.R

@@ -39,6 +39,14 @@ risk_diet_exercise <- function(diet_exercise, race, sex) {
 
   resp <- process_screening(resp)
 
-  resp %>% 
-    setNames(c("State", "FIPS", "Percent", "Lower_95%_CI", "Upper_95%_CI", "Number_of_Respondents"))
+  diet_exercise_type1 = c("bmi is overweight, high school survey",
+                          "bmi is obese, high school survey")
+
+  if (diet_exercise %in% diet_exercise_type1) {
+    resp %>% 
+      setNames(c("State", "FIPS", "Percent", "Lower_95%_CI", "Upper_95%_CI"))
+  } else {
+    resp %>% 
+      setNames(c("State", "FIPS", "Percent", "Lower_95%_CI", "Upper_95%_CI", "Number_of_Respondents"))
+  }
 }

tests/testthat/test-demo-crowding.R

@@ -1,22 +1,28 @@
-# test_that("demo-crowding", {
-#   test_crowding1 <- demo_crowding("WA", "hsa", "All Races (includes Hispanic)")
-# 
-# 
-#   # object, length, dimensions,
-#   # ranges -ex: greater than 10 rows
-#   # errors
-# 
-# 
-#   #expect_error() - catches an expected error
-# })
-
-
+#' Test demo-crowding
+#' 
+#' This testthat file test the demo-crowding function
+#' 
+#tests class and typeof output
 test_that("Output data type is correct", {
-  output <- demo_crowding("usa", "state", "All Races (includes Hispanic)")
-
-  expect_equal(class(output), "data.frame",
-               info = "Output should be a data frame")
+  output <- demo_crowding("wa", "hsa", "All Races (includes Hispanic)")
 
-  expect_equal(typeof(output), "list",
-               info = "Output should have list storage type (since data frames are lists)")
+  expect_true(inherits(output, "data.frame"))
+})
+
+#Ensures that variables are present and working on SCP
+test_that("demo-crowding returns non-empty data frame", {
+  crowding1 <- demo_crowding("wa", "hsa", "All Races (includes Hispanic)")
+  expect_true(is.data.frame(crowding1))
+})
+
+#demo-crowding must have 5 columns
+test_that("demo-crowding has correct number of columns", {
+  df <- demo_crowding("wa", "hsa", "All Races (includes Hispanic)")
+  expected_columns <- 5
+  expect_equal(ncol(df), expected_columns)
+})
+
+#parameter
+test_that("demo-crowding has correct parameters", {
+  expect_error(demo_crowding())
 })

tests/testthat/test-demo-poverty.R

@@ -11,10 +11,10 @@ test_that("Output data type is correct", {
 
 #Ensures that variables are present and working on SCP
 poverty_options <- list(
-  pov1 <- demo_poverty("wa", "county", "persistent poverty"),
-  pov2 <- demo_poverty("wa", "county", "families below poverty", "black"),
-  pov3 <- demo_poverty("wa", "county", "persons below poverty", "black", "both sexes"),
-  pov4 <- demo_poverty("wa", "county", "persons < 150% of poverty")
+  pov1 = demo_poverty("wa", "county", "persistent poverty"),
+  pov2 = demo_poverty("wa", "county", "families below poverty", "black"),
+  pov3 = demo_poverty("wa", "county", "persons below poverty", "black", "both sexes"),
+  pov4 = demo_poverty("wa", "county", "persons < 150% of poverty")
 )
 
 for (option_name in names(poverty_options)) {

tests/testthat/test-risk-alcohol.R

@@ -0,0 +1,34 @@
+#' Test risk-alcohol
+#' 
+#' This testthat file test the risk-alcohol function
+#' 
+#tests class and typeof output
+test_that("Output data type is correct", {
+  output <- risk_alcohol(paste("binge drinking (4+ drinks on one occasion for women,", 
+                               "5+ drinks for one occasion for men), ages 21+"), 
+                               "all races (includes hispanic)", "both sexes")
+
+  expect_true(inherits(output, "data.frame"))
+})
+
+#Ensures that variables are present and working on SCP
+test_that("risk-alcohol returns non-empty data frame", {
+  alcohol1 <- risk_alcohol(paste("binge drinking (4+ drinks on one occasion for women,", 
+                                 "5+ drinks for one occasion for men), ages 21+"), 
+                                 "all races (includes hispanic)", "both sexes")
+  expect_true(is.data.frame(alcohol1))
+})
+
+#risk-alcohol must have 5 columns
+test_that("risk-alcohol has correct number of columns", {
+  df <- risk_alcohol(paste("binge drinking (4+ drinks on one occasion for women,", 
+                           "5+ drinks for one occasion for men), ages 21+"), 
+                           "all races (includes hispanic)", "both sexes")
+  expected_columns <- 6
+  expect_equal(ncol(df), expected_columns)
+})
+
+#parameter
+test_that("risk-alcohol has correct parameters", {
+  expect_error(demo_alcohol())
+})

tests/testthat/test-risk-colorectal-screening.R

@@ -0,0 +1,57 @@
+#' Test risk-colorectal-screening
+#' 
+#' This testthat file test the risk-colorectal-screening function
+#' 
+#tests class and typeof output
+test_that("Output data type is correct", {
+  output <- risk_colorectal_screening("ever had fobt, ages 50-75", area="wa")
+
+  expect_true(inherits(output, "data.frame"))
+})
+
+#Ensures that variables are present and working on SCP
+screening_options <- list(
+  screening1 = risk_colorectal_screening("ever had fobt, ages 50-75", area = "wa"),
+  screening2 = risk_colorectal_screening("guidance sufficient crc, ages 50-75", area = "wa"),
+  screening3 = risk_colorectal_screening("had colonoscopy in past 10 years, ages 50-75", area = "wa"),
+  screening4 = risk_colorectal_screening("home blood stool test in the past year, ages 45-75",
+                                         "all races (includes hispanic)", "both sexes"),
+  screening5 = risk_colorectal_screening("receieved at least one recommended crc test, ages 45-75",
+                                         "all races (includes hispanic)", "both sexes")
+)
+
+for (option_name in names(screening_options)) {
+  test_that("risk-colorectal-screening returns non-empty data frame", {
+    option <- screening_options[[option_name]]
+    expect_true(is.data.frame(option))
+  })
+}
+
+#risk-colorectal-screening must have 5 columns
+test_that("risk-colorectal-screening has correct number of columns", {
+  df1 <- risk_colorectal_screening("ever had fobt, ages 50-75", area="wa")
+  df2 <- risk_colorectal_screening("home blood stool test in the past year, ages 45-75",
+                                   "all races (includes hispanic)","both sexes")
+  expected_columns1 <- 5
+  expected_columns2 <- 6
+  expect_equal(ncol(df1), expected_columns1)
+  expect_equal(ncol(df2), expected_columns2)
+})
+
+#test error handling
+test_that("risk-colorectal-screening handles invalid colorectal_screening parameters", {
+  expect_error(
+    risk_colorectal_screening("ever had fobt, ages 50-75", race="all races (includes hispanic)"),
+    "for this screening type, area must NOT be NULL and Race and Sex must be NULL"
+  )
+  expect_error(
+    risk_colorectal_screening("home blood stool test in the past year, ages 45-75",
+                              "all races (includes hispanic)"),
+    "For this screening type, Race and Sex must not be NULL"
+  )
+})
+
+#parameter
+test_that("risk-colorectal-screening has correct parameters", {
+  expect_error(risk_colorectal_screening())
+})

tests/testthat/test-risk-diet-exercise.R

@@ -0,0 +1,42 @@
+#' Test risk-diet-exercise
+#' 
+#' This testthat file test the risk-diet-exercise function
+#' 
+#tests class and typeof output
+test_that("Output data type is correct", {
+  output <- risk_diet_exercise("bmi is healthy, ages 20+", 
+                               "all races (includes hispanic)", "both sexes")
+
+  expect_true(inherits(output, "data.frame"))
+})
+
+#Ensures that variables are present and working on SCP
+diet_exercise_options <- c("bmi is healthy, ages 20+", "bmi is obese, ages 20+", 
+                           "bmi is obese, high school survey", "bmi is overweight, high school survey",
+                           "consumed 1 or more fruits per day", "consumed 1 or more vegetables per day",
+                           "no leisure time physical activity")
+
+for (option in diet_exercise_options) {
+  test_that("risk_diet_exercise returns non-empty data frame", {
+    result <- risk_diet_exercise(option, "all races (includes hispanic)", "both sexes")
+    expect_true(is.data.frame(result))
+  })
+}
+
+#risk-diet-exercise must have 5 columns
+test_that("risk-diet-exercise has correct number of columns", {
+  df1 <- risk_diet_exercise("bmi is healthy, ages 20+", 
+                           "all races (includes hispanic)", "both sexes")
+  df2 <- risk_diet_exercise("bmi is obese, high school survey", 
+                            "all races (includes hispanic)", "males")
+  expected_columns1 <- 6
+  expected_columns2 <- 5
+  expect_equal(ncol(df1), expected_columns1)
+  expect_equal(ncol(df2), expected_columns2)
+
+})
+
+#parameter
+test_that("risk-diet-exercise has correct parameters", {
+  expect_error(risk_diet_exercise())
+})

tests/testthat/test-risk-smoking.R

@@ -0,0 +1,3 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})

tests/testthat/test-risk-vaccines.R

@@ -0,0 +1,3 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})

tests/testthat/test-risk-womens-health.R

@@ -0,0 +1,42 @@
+#' Test risk-womens health
+#'
+#' This testthat file test the risk-womens health function
+#'
+#tests class and typeof output
+# test_that("Output data type is correct", {
+#   output <- risk_womens_health("bmi is healthy, ages 20+",
+#                                "all races (includes hispanic)", "both sexes")
+# 
+#   expect_true(inherits(output, "data.frame"))
+# })
+# 
+# #Ensures that variables are present and working on SCP
+# womens_health_options <- c("bmi is healthy, ages 20+", "bmi is obese, ages 20+",
+#                            "bmi is obese, high school survey", "bmi is overweight, high school survey",
+#                            "consumed 1 or more fruits per day", "consumed 1 or more vegetables per day",
+#                            "no leisure time physical activity")
+# 
+# for (option in womens_health_options) {
+#   test_that("risk_womens_health returns non-empty data frame", {
+#     result <- risk_womens_health(option, "all races (includes hispanic)", "both sexes")
+#     expect_true(is.data.frame(result))
+#   })
+# }
+# 
+# #risk-womens health must have 5 columns
+# test_that("risk-womens health has correct number of columns", {
+#   df1 <- risk_womens_health("bmi is healthy, ages 20+",
+#                             "all races (includes hispanic)", "both sexes")
+#   df2 <- risk_womens_health("bmi is obese, high school survey",
+#                             "all races (includes hispanic)", "males")
+#   expected_columns1 <- 6
+#   expected_columns2 <- 5
+#   expect_equal(ncol(df1), expected_columns1)
+#   expect_equal(ncol(df2), expected_columns2)
+# 
+# })
+# 
+# #parameter
+# test_that("risk-womens health has correct parameters", {
+#   expect_error(risk_womens_health())
+# })