Calculation of crude age-specific incidence rate and confidence intervals
The crude age-specific incidence rate is computed by dividing the the number of new cancer cases diagnosed for persons in a 5-year age group by the population at risk, and then multiplied by 100,000. The rates are computed for both time periods 2000-2003 and 2010-2013. The number of cancer cases and the susceptible population are from the geographical regions given by the 17 selected SEER cancer registries (omitting Alaska).
The difficulty in computing the age-specific rate is for the ‘oldest old’ category, where the population for the 5-year age groups older than 85 years has to be inferred using the Census data from the 17 registries.
The two-sided confidence intervals were computed as in Harding et al. (2008): “Where x is the count of new diagnoses and n is the person-years at risk, +/- 34.1% two-sided confidence intervals for incidence rates were calculated according to the normal distribution (for x > 10), according to the Poisson distribution (for x < 10 and n > 1000), and by exact binomial proportion (for x < 10 and n < 1,000).”).”
Processing Steps
The following script is called to compute the crude incidence rate and the confidence intervals in R, called from the working directory scripts/incidence-seer-tgca. Note: At the top of the script, the variable startyear should be defined as either 2000 or 2010, indicating which time period is to be computed. In addition, data files were saved with the system date as a prefix in the filename, and thus scripts which load that data may need to be updated with the correct date.
The processed tables and output are saved in the outputs/seer-tcga/count-data directory.
source('seerTCGACounts.R')
The seerTCGACounts.R script loops over every TGCA cancer type and calls three scripts, in order.
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seerTCGACounts19Groups.R: Creates tables (data frames) of the number of case counts and population for 5-year categories up to “85+” category (i.e. 19 age grouped data, excluding the ‘oldest old’) for one cancer type. -
seerTCGACountsOlder.R: Creates tables (data frames) of the number of case counts and population for 5-year categories for ages 85-90, 90-95, …, 110+, i.e. the ‘oldest old’ age categories for one cancer type. -
seerTCGACountsPopCombine.R: Combines the data from the 19 age groups and the oldest old, creating a table (data frame) for the given cancer type.
The tables from the different cancer types are concatenated to create one large table denoted sumcounts, with the columns Site, Sex, Age, Counts, Population and Crude Rate. Then (still within the script seerTCGACounts.R, at the end):
seerTCGAErrorCalculation.Ris called to compute confidence intervals for the crude age-specific rate and add columns indicating the lower and upper intervals to thesumcountstable.