Merge pull request #38 from getwilds/documentation

edited incidence and mortality docs

R/demo-crowding.R

@@ -4,22 +4,35 @@
 #'
 #' @param area A state/territory abbreviation or USA.
 #' @param areatype Either "county", "hsa" (Health service area), or "state"
-#' @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)
+#' @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)"
 #' 
 #' @importFrom httr2 req_url_query req_perform
 #' @importFrom stats setNames
 #' 
-#' @returns A data frame with the following columns "County", "FIPS", "Percent", "Households", "Rank"
+#' @returns A data frame with the following columns Area, Area Code, "Percent", "Households", "Rank"
 #' 
 #' @export
 #' 
 #' @examples
 #' \dontrun{
-#' demo_crowding("WA", "hsa", "All Races (includes Hispanic)")
-#' demo_crowding("usa", "state", "All Races (includes Hispanic)")
-#' demo_crowding("pr", "hsa", "black")
+#' demo_crowding(area = "WA", 
+#'               areatype = "hsa", 
+#'               race = "All Races (includes Hispanic)")
+#'              
+#' demo_crowding(area = "usa",
+#'               areatype = "state",
+#'               race = "All Races (includes Hispanic)")
+#'
+#' demo_crowding(area = "pr",
+#'               areatype = "hsa",
+#'               race = "black")
 #' }
 demo_crowding <- function(area, areatype, race) {
 

R/incidence-cancer.R

@@ -17,26 +17,43 @@
 #' @param stage Either "all stages" or "late stage (regional & distant)"
 #' @param year Either "latest 5 year average", "latest single year (us by state)"
 #' 
-#' @returns A data frame with the following columns "State", "FIPS", "Percent", "Lower 95% CI", "Upper 95% CI", "Number of Respondents"
+#' @returns A data frame with the following columns Areatype, Area Code, "Met Healthy People Objective of ***?",
+#'                                                  "Age Adjusted Death Rate", "Lower 95% CI Rate", "Upper 95% CI Rate", 
+#'                                                  "CI Rank", "Lower CI Rank", "Upper CI Rank", "Annual Average Count", 
+#'                                                  "Recent Trend", "Recent 5 Year Trend", "Lower 95% CI Trend", "Upper 95% CI Trend"
 #' 
 #' @export
 #' 
 #' @examples
 #' \dontrun{
-#' incidence_cancer("wa", "county", "all cancer sites", "black (non-hispanic)", 
-#'                  "both sexes", "ages 65+", "all stages")
-#' incidence_cancer("wa", "county", "lung & bronchus", "all races (includes hispanic)", "males", 
-#'                  "ages 50+", "late stage (regional & distant)")
-#' incidence_cancer("usa", "state", "lung & bronchus", "all races (includes hispanic)", "males", 
-#'                  "ages 50+", "late stage (regional & distant)")
-#' incidence_cancer(area="wa", areatype="county", cancer="ovary", race="all races (includes hispanic)", 
-#'                  sex="females", age="ages 50+", stage="late stage (regional & distant)")
-#' incidence_cancer("ca", "hsa", "prostate", "all races (includes hispanic)", "males", 
-#'                  "ages 50+", "all stages")
-#' incidence_cancer("ca", "hsa", "childhood (ages <20, all sites)", "all races (includes hispanic)", 
-#'                  "males", "ages <20", "all stages")
+#' incidence_cancer(area = "wa",
+#'                  areatype = "county",
+#'                  cancer = "all cancer sites",
+#'                  race = "black (non-hispanic)",
+#'                  sex = "both sexes",
+#'                  age = "ages 65+",
+#'                  stage = "all stages",
+#'                  year = "latest 5 year average")
+#'                  
+#' incidence_cancer(area = "usa",
+#'                  areatype = "state",
+#'                  cancer = "lung & bronchus",
+#'                  race = "all races (includes hispanic)",
+#'                  sex = "males",
+#'                  age = "ages 50+",
+#'                  stage = "late stage (regional & distant)",
+#'                  year = "latest single year (us by state)")
+#'                  
+#' incidence_cancer(area = "wa",
+#'                  areatype = "county",
+#'                  cancer = "ovary",
+#'                  race = "all races (includes hispanic)",
+#'                  sex = "females",
+#'                  age = "ages 50+",
+#'                  stage = "late stage (regional & distant)",
+#'                  year = "latest 5 year average")
 #' }
-incidence_cancer <- function(area, areatype, cancer, race, sex=NULL, age, stage, year="latest 5 year average") {
+incidence_cancer <- function(area, areatype, cancer, race, sex, age, stage, year) {
 
   allstage_cancer <- c("all cancer sites", "breast (female in situ)", "childhood (ages <15, all sites)", 
                        "childhood (ages <20, all sites)", "leukemia")
@@ -45,6 +62,10 @@ incidence_cancer <- function(area, areatype, cancer, race, sex=NULL, age, stage,
 
   childhood_cancer <- c("childhood (ages <15, all sites)", "childhood (ages <20, all sites)")
 
+  if ((areatype == "county" || areatype == "hsa") && year == "latest single year (us by state)") {
+    cli_abort("For year latest single year (us by state), areatype must be state")
+  }
+
   if ((cancer %in% allstage_cancer) && stage == "late stage (regional & distant)") {
     cli_abort("For this cancer type, stage must be all stages")
   }

R/mortality-cancer.R

@@ -14,32 +14,52 @@
 #' @param race One of the following values: "all races (includes hispanic)", "white (non-hispanic)", 
 #'                                          "black (non-hispanic)", "amer. indian / ak native (non-hispanic)", 
 #'                                          "asian / pacific islander (non-hispanic)","hispanic (any race)"
-#' @param sex Either "both sexes", "males", "females"
+#' @param sex Defaulted to NULL. Specify either "both sexes", "males", "females" if necessary
 #' @param age Either "all ages", "ages <50", "ages 50+", "ages <65", "ages 65+", ages <15, ages <20
 #' @param year Either "latest 5 year average", "latest single year (us by state)"
 #' 
-#' @returns A data frame with the following columns "State", "FIPS", "Percent", "Lower 95% CI", "Upper 95% CI", "Number of Respondents"
+#' @returns A data frame with the following columns Areatype, Area Code, "Met Healthy People Objective of ***?",
+#'                                                  "Age Adjusted Death Rate", "Lower 95% CI Rate", "Upper 95% CI Rate", 
+#'                                                  "CI Rank", "Lower CI Rank", "Upper CI Rank", "Annual Average Count", 
+#'                                                  "Recent Trend", "Recent 5 Year Trend", "Lower 95% CI Trend", "Upper 95% CI Trend"
 #' 
 #' @export
 #' 
 #' @examples
 #' \dontrun{
-#' mortality_cancer("wa", "county", "all cancer sites", "black (non-hispanic)", 
-#'                  "both sexes", "ages 65+")
-#' mortality_cancer("ca", "hsa", "lung & bronchus", "all races (includes hispanic)", 
-#'                  "males", "ages 50+")
-#' mortality_cancer("usa", "state", "prostate", "all races (includes hispanic)", 
-#'                  "males", "ages 50+")
-#' mortality_cancer(area="wa", areatype="county", cancer="ovary", race="all races (includes hispanic)", 
-#'                  sex="females", age="ages 50+")
-#' mortality_cancer("ca", "hsa", "childhood (ages <20, all sites)", "all races (includes hispanic)", 
-#'                  "males", "ages <20")
+#' mortality_cancer(area = "wa",
+#'                  areatype = "county",
+#'                  cancer = "all cancer sites",
+#'                  race = "black (non-hispanic)",
+#'                  sex = "both sexes",
+#'                  age = "ages 65+",
+#'                  year = "latest 5 year average")
+#'
+#' mortality_cancer(area = "usa",
+#'                  areatype = "state",
+#'                  cancer = "prostate",
+#'                  race = "all races (includes hispanic)",
+#'                  sex = "males",
+#'                  age = "ages 50+",
+#'                  year = "latest single year (us by state)")
+#'                  
+#' mortality_cancer(area = "wa",
+#'                  areatype = "hsa",
+#'                  cancer = "ovary",
+#'                  race = "all races (includes hispanic)",
+#'                  sex = "females",
+#'                  age = "ages 50+",
+#'                  year = "latest 5 year average")
 #' }
-mortality_cancer <- function(area, areatype, cancer, race, sex=NULL, age, year="latest 5 year average") {
+mortality_cancer <- function(area, areatype, cancer, race, sex, age, year) {
   female_cancer <- c("breast (female)", "ovary", "uterus (corpus & uterus, nos)")
 
   childhood_cancer <- c("childhood (ages <15, all sites)", "childhood (ages <20, all sites)")
 
+  if ((areatype == "county" || areatype == "hsa") && year == "latest single year (us by state)") {
+    cli_abort("For year latest single year (us by state), areatype must be state")
+  }
+
   if ((cancer %in% female_cancer) && (sex == "males" || sex == "both sexes")) {
     cli_abort("For this cancer type, sex must be females")
   } else if (cancer == "prostate" && (sex == "females" || sex == "both sexes")) {

README.md

@@ -18,6 +18,6 @@ You can install the development version of `rcromwell` from [GitHub](https://git
 pak::pak("getwilds/cancerprof")
 ```
 
+## Support
 
-## Contact
-For questions, feedback, or inquiries, please contact Brian Park: [email protected]
+For questions, bugs, or feature requests, please reach out to Brian Park at [email protected], or open an issue on our [issue tracker](https://github.com/getwilds/cancerprof/issues)