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incidence-vignette

Source: vignettes/incidence-vignette.Rmd
incidence-vignette.Rmd

Load the package

Retrieving Data

The Cancer Incidence category of cancerprof contains a single functions to pull data from the Incidence page of State Cancer Profile.

The function for retrieving incidence data is incidence_cancer()

Incidence Cancer

Incidence cancer has 23 cancer types to choose from. In total, incidence cancer has 8 arguments: area, areatype, cancer, race, sex, age, stage, year

Argument Details

  • The "latest single year (us by state)" argument for year can only be selected if area is "state"

  • For the following cancer types:

    • “breast (female in situ)”,
    • “childhood (ages <15, all sites)”,
    • “childhood (ages <20, all sites)”,
    • “leukemia”

    The stage argument must by "all stages"

  • For the following cancer types:

    • “breast (female)”,
    • “breast (female in situ)”,
    • “ovary”,
    • “uterus (corpus & uterus, nos)”

    The sex argument must by "females"

  • For "prostate" cancer, sex must be "males"

  • For "childhood (ages <15, all sites)", age must be "ages <15"

  • For "childhood (ages <20, all sites)", age must be "ages <20"

Examples 

incidence1 <- 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)"
)
head(incidence1, n = 3)
#>               State  FIPS Age_Adjusted_Incidence_Rate Lower_95%_CI Upper_95%_CI CI_Rank Lower_CI_Rank Upper_CI_Rank Annual_Average_Count
#> 1 US (SEER+NPCR)(1) 00000                       122.7        121.8        123.7      NA            NA            NA                65692
#> 2       Kentucky(3) 21000                       216.2        205.7        227.2       1             1             1                 1660
#> 3    Mississippi(2) 28000                       178.0        166.0        190.6       2             2             7                  868
#>   Percentage_of_Cases_with_Late_Stage
#> 1                                67.0
#> 2                                70.3
#> 3                                68.3

incidence2 <- incidence_cancer(
  area = "wa",
  areatype = "hsa",
  cancer = "ovary",
  race = "all races (includes hispanic)",
  sex = "females",
  age = "ages 50+",
  stage = "late stage (regional & distant)",
  year = "latest 5 year average"
)
head(incidence2, n = 3)
#>          Health_Service_Area HSA_Code Age_Adjusted_Incidence_Rate Lower_95%_CI Upper_95%_CI CI_Rank Lower_CI_Rank Upper_CI_Rank
#> 1              Washington(5)    53000                        20.5         19.4         21.6      NA             4            29
#> 2          US (SEER+NPCR)(1)    00000                        19.7         19.6         19.9      NA            NA            NA
#> 3 Lewis, WA - Pacific, WA(6)     0832                        28.4         19.2         40.5       1             1             9
#>   Annual_Average_Count Percentage_of_Cases_with_Late_Stage
#> 1                  278                                76.0
#> 2                11948                                73.5
#> 3                    7                                76.7

incidence3 <- 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"
)
head(incidence3, n = 3)
#>               County  FIPS Age_Adjusted_Incidence_Rate Lower_95%_CI Upper_95%_CI CI_Rank Lower_CI_Rank Upper_CI_Rank Annual_Average_Count
#> 1      Washington(5) 53000                      1926.6       1847.1       2008.6      NA             5            32                  493
#> 2  US (SEER+NPCR)(1) 00000                      1898.1       1892.4       1903.8      NA            NA            NA                89582
#> 3 Thurston County(7) 53067                      2720.3       2140.8       3408.4       2             1             8                   18
#>   Recent_Trend Recent_5_Year_Trend Trend_Lower_95%_CI Trend_Upper_95%_CI
#> 1      falling                -1.7               -2.4               -0.9
#> 2      falling                -0.5               -0.8               -0.2
#> 3         <NA>                  NA                 NA                 NA