SEERaBomb (version 2015.2)

seerSet: Join SEER cancers and PY

Description

Creates a sex-specific list of cancer and population person year (PY) data frames, possibly specific to a race and interval of ages at diagnosis.

Usage

seerSet(canc,popsa,Sex, Race="pooled",ageStart=15,ageEnd=85)

Arguments

canc

Data frame of cancers that includes agedx, sex, race, yrdx, modx, surv and cancer.

popsa

Data frame of population PY at 1-year age resolution.

Sex

"male" or "female".

Race

"white", "black", "other", or "pooled" (default).

ageStart,ageEnd

canc and popsa will be reduced to ages in ageEnd>age>=ageStart.

Value

• A list containing sex specific subsets of canc and popsa and information regarding how they were reduced.

Details

In the output: 1) 0.5 years is added to ages at diagnosis (agedx) to reverse SEER flooring to integers; 2) 0.5 months is added to survival months (again, to reverse flooring) before dividing by 12 to convert to years; 3) year of diagnosis integers are converted to reals by adding to them the month of diagnosis (modx) - 0.5 divided by 12 (note that a modx of 1 represents anytime in the month of January). If ageEnd>85, popsae (extended to ages up to 99) should be used as the input for popsa. If popsa is used, the age86 column of popsa will be replaced by an age column. The age86 and yrbrth columns of a canc are not used and will be removed if they happen to be present; users should manually remove any other columns not needed to minimize seerSet object sizes. Sex and race columns in inputs are removed from outputs as they are specified in other (scalar) seerSet elements. Also removed from canc are cancer factor levels not present for that sex.

See Also

SEERaBomb-package, mk2D, plot2D

Examples

library(SEERaBomb)
simSeerSet() # without data, a simulated seerSet
#  else, with data ...
load("~/data/SEER/mrgd/cancDef.RData") #load in canc
load("~/data/SEER/mrgd/popsae.RData") # load in popsae
# trim columns
library(dplyr)  
canc=canc%>%select(-reg,-recno,-agerec,-numprims,-COD,
          -age19,-age86,-radiatn,-ICD9,-db,-histo3) 
popsae=popsae%>%select(-reg,-db)   
seerSet(canc,popsae,Sex="male",ageStart=0,ageEnd=100)