Verify map output

R/app.R

@@ -10,7 +10,6 @@
 ## TODO:
 ## make Shiny app run when you call "oncarto" from the R console
 ## fill out additional tabs / background
-## confirm that presented data are correctly updating
 
 # Call required libraries / packages
 library(pak)

R/incidenceByState.qmd

@@ -330,8 +330,8 @@ merge_all_incidence <- function(cancer_types, race, sex, age, stage, year, con){
 }
 ```
 
-
 # Step 1. Ingest incidence data from {cancerprof}
+
 ```{r}
 # Create a new DuckDB database, corresponding to incidence data from US states
 con <- dbConnect(duckdb::duckdb(), "cancer-incidence-usa-state.duckdb")
@@ -359,7 +359,6 @@ for (cancer in cancer_types) {
 dbListTables(con)
 ```
 
-
 # Step 2. Merge DB data into a wide table
 
 ```{r}
@@ -375,8 +374,6 @@ incidence_by_cancer_type = merge_all_incidence(
 dbDisconnect(con)
 ```
 
-
-
 # Step 3. Visualize incidence data in a choropleth map
 
 NOTE: the following code will likely be replaced for the full-scale Shiny app
@@ -442,5 +439,3 @@ leaflet(incidence_by_type_with_shape) %>%
     title = "Cancer Incidence (All Sites)"
   )
 ```
-
-

R/incidenceByWAHSA.qmd

@@ -193,16 +193,19 @@ cancer_types = c(
 )
 ```
 
+Test code
 ```{r}
-cancerprof::incidence_cancer(
-      "WA", "hsa",
-      "all cancer sites",
+test_data = cancerprof::incidence_cancer(
+      "USA", "state",
+      "bladder",
       "All Races (includes Hispanic)",
-      "males",
+      "both sexes",
       "all ages",
       "all stages",
       "latest 5 year average"
     )
+
+test_data
 ```
 
 ```{r}