#R Program to Calculate Survival Probability of Kidney Carcinoma Patients using Hypertabastic Proportional Hazards Model

  #'Time: Continuous (in months)
  #'Age: Continuous (in years)
  #'Gender: 
  #'  0=Female 1=Male 
  #'Race: 
  #'  0=White 1=Hispanic 2=Asian 3=Black
  #'Histology: 
  #'  0=Other 1=Adeno 2=Papillary 3=Clear 4=Renal 
  #'       5=Chromophobe  6=Sarcomatoid 7=Granular 
  #'Region:
  #'  0=Southwest 1=East 2=North 3=Pacific
  #'Stage:
  #'  0=Regional 1=Localized 2=Distant
  #'Grade:
  #'  0=Undifferentiated 1=Well 2=Moderate 3=Poor
  #'Site:
  #'  0=Other 1=No_Surgery 2=Cryo13 3=Thermal 4=Cryo23 5=Part_Neph/Part_Uret 
  #'     6=Complete_Neph 7=Radical 8=Any_Neph 

#Read in Function
Survival_Probability <- function(Time,Age,Gender,Race,Histology,Region,Stage,Grade,Site){
  
  start = c(2,5,12,15,17,20) #Initialize
  input = c(Race,Histology,Region,Stage,Grade,Site) #Record part of input
  
  B = c(Age,Gender,integer(27)) #Create vector of parameters
  place = start + input #Set location in vector to be changed
  
  for(i in 1:6){if(input[i] == 0){}else{B[place[i]] = 1}} #Set vector locations = 1
  
  Beta = -sum(B*c(-0.011576,-0.016056,-0.081035,-0.041793,-0.13937,0.228189,0.532579,0.565283,
                 0.323947,1.187381,-0.280902,0.376178,0.015638,0.068913,0.050401,1.221175,
                 -1.420683,1.176737,0.999862,0.419985,-1.167472,0.736603,0.487928,0.440444,
                 1.012776,0.090548,-0.094567,-0.270463,-0.135374)) #Set beta values
  
  return(1/cosh(0.104941*(1-(Time)^0.331843*1/tanh((Time)^0.331843))/0.331843)^exp(Beta)) #Output
}

#Answer to Proposed Question
Survival_Probability(Time = 60,Age=55,Gender=1,Race=0,Histology=1,
                     Region=2,Stage=2,Grade=3,Site=7)