Merge pull request #12 from getwilds/bugsquash

resolved errors in incident

NAMESPACE

@@ -36,6 +36,5 @@ importFrom(rlang,":=")
 importFrom(rlang,sym)
 importFrom(stats,setNames)
 importFrom(stringr,str_pad)
-importFrom(tibble,rownames_to_column)
 importFrom(utils,data)
 importFrom(utils,read.csv)

R/incidence-cancer.R

@@ -36,18 +36,6 @@
 #' incidence_cancer("ca", "hsa", "childhood (ages <20, all sites)", "all races (includes hispanic)", 
 #'                  "males", "ages <20", "all stages")
 #' }
-
-
-# incidence_cancer("wa", "county", "all cancer sites", "black (non-hispanic)", "both sexes", "ages 65+", "all stages")
-# 
-# area = "wa"
-# areatype = "county"
-# cancer = "all cancer sites"
-# race = "black (non-hispanic)"
-# sex = "both sexes"
-# age = "ages 65+"
-# stage = "all stages"
-
 incidence_cancer <- function(area, areatype, cancer, race, sex=NULL, age, stage, year="latest 5 year average") {
 
   allstage_cancer <- c("all cancer sites", "breast (female in situ)", "childhood (ages <15, all sites)", 

R/process-incidence.R

@@ -8,17 +8,13 @@
 #' @importFrom dplyr mutate_all na_if filter mutate rename
 #' @importFrom rlang sym :=
 #' @importFrom utils read.csv data
-#' @importFrom tibble rownames_to_column
 #' 
 #' @returns A processed response data frame
 #' 
 #' @examples
 #' \dontrun{
 #' process_incidence(resp)
 #' }
-
-
-#Health.Service.Area.HSA_Code State.FIPS
 process_incidence <- function(resp) {
 
   nenv <- new.env()
@@ -37,27 +33,15 @@ process_incidence <- function(resp) {
     (\(x) read.csv(textConnection(x), header=TRUE, colClasses = "character"))()
 
 
-  column <- c("Health.Service.Area", "County", "State")[c("Health.Service.Area.HSA_Code", "County.FIPS", "State.FIPS") %in% colnames(resp)]
-
-  old_column2 <- c("Health.Service.Area.HSA_Code", "County.FIPS", "State.FIPS")[c("Health.Service.Area.HSA_Code", "County.FIPS", "State.FIPS") %in% colnames(resp)]
-
-  column2 <- c("HSA Code", "FIPS", "FIPS")[c("Health.Service.Area.HSA_Code", "County.FIPS", "State.FIPS") %in% colnames(resp)]
-
-  # column <- c("Health.Service.Area.HSA_Code", "County.FIPS", "State.FIPS")[c("Health.Service.Area.HSA_Code", "County.FIPS", "State.FIPS") %in% colnames(resp)]
-
+  column <- c("County", "Health.Service.Area", "State")[c("County", "Health.Service.Area", "State") %in% colnames(resp)]
 
   resp <- resp %>% 
-    rownames_to_column(column) %>% 
-    rename(!!column2 := !!sym(old_column2)) %>% 
-    filter(!!sym(column) != "US (SEER+NPCR)(1)") %>% 
-    mutate_all(\(x) na_if(x, "N/A")) %>% 
-    mutate_all(\(x) na_if(x, "data not available")) %>%
-    mutate_all(\(x) na_if(x, "*")) %>% 
-    mutate(!!column := sub("\\(\\d+\\)", "", !!sym(column)))
+    filter(!!sym(column) != "US (SEER+NPCR)(1)") %>%
+    mutate(!!sym(column) := str_replace_all(!!sym(column), "\\(\\d+\\)", ""))
+
 
   if(column %in% c("Health.Service.Area", "County")) {
-    resp <- resp %>%
-      filter(!(!!sym(column) %in% state.name))
-  }
-  resp
+      resp <- resp %>%
+        filter(!(!!sym(column) %in% state.name))
+    }
 }

R/risk-colorectal-screening.R

@@ -21,7 +21,11 @@
 #' \dontrun{
 #' risk_colorectal_screening("ever had colorectal endoscopy (sigmoidoscopy or colonoscopy), ages 50+",
 #'                           "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")
+#' risk_colorectal_screening("fobt (1yr) / flex sig (5yr) / fobt (3yr) / colonoscopy (10yr), ages 50-75", 
+#'                           "all races (includes hispanic)", "males" )
+
 #' }
 risk_colorectal_screening <- function(screening, race=NULL, sex=NULL, area=NULL) {