In Class Code

# Generate the probabilities of default

# Clear workspace and graphs

if(!is.null(dev.list())) dev.off()

rm(list = ls())

library("caret")

library("data.table")

load("01_data/biofilm.Rdata")

setDT(biofilm_data)

names(biofilm_data)

thefiles <- unique(biofilm_data$file)

onefile <- biofilm_data[thefiles[30]==file,]

plot(onefile$mz,onefile$int,type="h")

biofilm_data[,mz:=round(mz,1)]

setkeyv(biofilm_data,cols=c("file","indicator","mz"))

biofilm_data[,.(int=sum(int)),by=c("file","indicator","mz")]

biofilm_data_wide <- dcast(biofilm_data, file + indicator ~ mz, value.var = "int")

trainIndex <- createDataPartition(biofilm_data_wide$indicator,list=FALSE,p=0.8)

trainSet <- biofilm_data_wide[trainIndex,]

testSet <- biofilm_data_wide[-trainIndex,]

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