title: "Compare old and new code for US incidence survival curves" output: html_document: number_sections: yes toc: yes toc_depth: 2 html_notebook: number_sections: yes toc: yes toc_depth: 2
#-------------------------------------------------------------------------------- # Packages #-------------------------------------------------------------------------------- library(bcimodel) library(knitr) #-------------------------------------------------------------------------------- # Knitr #-------------------------------------------------------------------------------- opts_chunk$set(echo=FALSE, message=FALSE, warning=FALSE)
data(incratesf) # Compute survival from incidence/mortality databases newInc <- interpolate_cumsurv(incratesf, ratevar='Female.Rate.Per.100K', country='United States') newInc100 <- interpolate_cumsurv(incratesf, ratevar='Female.Rate.Per.100K', country='United States', maxage=100)
incfile <- '~/Documents/jbirnbau/archive/screentreat/data/bc_1975-1979_incidence.csv' format_clinical_incidence <- function( incfile ### Path to SEER clinical incidence table ) { # Read in data seer <- read.csv(incfile, stringsAsFactors=FALSE) seer <- within(seer, { Age <- gsub('[0-9]+=', '', Ages) Age <- as.character(gsub(' years', '', Age)) Age[Age=='85+'] <- 87 Age <- suppressWarnings(sapply(strsplit(Age, '-'), function(x) mean(as.numeric(x)))) }) seer <- seer[!is.nan(seer$Age),] seer <- seer[!is.na(seer$Age),] age_max <- max(seer$Age) incidence <- data.frame(age = 0:age_max, incidence_rate = with(seer, approx(Age, Crude.Rate, xout=0:age_max))$y/100000) incidence$incidencefree_rate <- 1-incidence$incidence_rate incidence_free_survival <- c() for(i in 1:(age_max+1)){ incidence_free_survival[i] <- prod(incidence$incidencefree_rate[1:i]) } incidence$incidencefree_survival <- incidence_free_survival rm(incidence_free_survival) return(incidence) } oldInc <- format_clinical_incidence(incfile)
plot(newInc100$age, newInc100$cumsurv, col='black', type='l') lines(newInc$age, newInc$cumsurv, col='red') lines(oldInc$age, oldInc$incidencefree_survival, col='green')
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