################################################################################
# APC_workshop_prep.R
#
# Created:  2010-04-07 by Caroline D
# Updated:  2010-04-19 by Caroline D
#
# Uses: breast_i_6206.txt
#
# Package: Epi (apc.fit, apc.frame, apc.lines)
# 
# Software: R 
#
# Aim: Exercise used ahead of APC workshop 
#
################################################################################


# Set working directory - change to your own!
# setwd("Z:/APC_workshop_2010/Data/Breast")

# Install and load the Epi-package, if not installed on your local computer
# install.packages("Epi", dependencies = TRUE)
library(Epi)


################################ 
# Breast cancer incidence
# for women in the Nordic
# countries, ages 30-74 
################################


########## 
# DENMARK
##########

# Read in data
t1 <- subset(	read.table( "http://staff.pubhealth.ku.dk/~bxc/APC/data/breast_i_6206.txt",
                          header = TRUE ),
              cou=="Denmark" & sex==2 & (A>=30 & A<=74) )

# Import t1 variables to R
attach(t1)

# Run apc.fit from the Epi package, for help type ?apc.fit in Console window
ex.t1 <- apc.fit( t1,          # Data
      dr.extr="Holford",       # How drift is extracted using Holford method
      parm="APC",              # What estimates to present [rates, RR, ...]
			                         # and also which effect to put to zero slope
      npar=c(5,6,10),          # Number of parameters (age,period,cohort)
      scale=10^5 )             # Scale to display rates
      
# Display rates
print(ex.t1)                                                      


########## 
# FINLAND
##########

# Read in data
t2 <- subset( read.table( "http://staff.pubhealth.ku.dk/~bxc/APC/data/breast_i_6206.txt",
                          header = TRUE ),
              cou=="Finland" & sex==2 & (A>=30 & A<=74) )

# Import t2 variables to R
attach(t2)

# Run apc.fit from the Epi package, for help type ?apc.fit in Console window
ex.t2 <- apc.fit( t2,          # Data
      dr.extr="Holford",       # How drift is extracted using Holford method
      parm="APC",              # What estimates to present [rates, RR, ...]
			                         # and also which effect to put to zero slope
      npar=c(5,6,10),          # Number of parameters (age,period,cohort)
      scale=10^5 )             # Scale to display rates

# Display rates
print(ex.t2)


########## 
# NORWAY
##########

# Read in data
t3 <- subset( read.table( "http://staff.pubhealth.ku.dk/~bxc/APC/data/breast_i_6206.txt",
                          header = TRUE ),
              cou=="Norway" & sex==2 & (A>=30 & A<=74) )

# Import t3 data to R
attach(t3)

# Run apc.fit from the Epi package, for help type ?apc.fit in Console window
ex.t3 <- apc.fit( t3,          # Data
      dr.extr="Holford",       # How drift is extracted using Holford method
      parm="APC",              # What estimates to present [rates, RR, ...]
			                         # and also which effect to put to zero slope
      npar=c(5,6,10),          # Number of parameters (age,period,cohort)
      scale=10^5 )             # Scale to display rates

# Display rates
print(ex.t3)


########## 
# SWEDEN
##########

# Read in data
t4 <- subset( read.table ( "http://staff.pubhealth.ku.dk/~bxc/APC/data/breast_i_6206.txt",
                          header = TRUE ),
              cou=="Sweden" & sex==2 & (A>=30 & A<=74))

# Import t4 data to R
attach(t4)

# Run apc.fit from the Epi package, for help type ?apc.fit in Console window
ex.t4 <- apc.fit( t4,          # Data
      dr.extr="Holford",       # How drift is extracted using Holford method
      parm="APC",              # What estimates to present [rates, RR, ...]
			                         # and also which effect to put to zero slope
      npar=c(5,6,10),          # Number of parameters (age,period,cohort)
      scale=10^5 )             # Scale to display rates

     
################################ 
# Plot the effects
################################

# Frame for graphical display, see ?par for help 
par( mfrow=c(2,2) )


########## 
# DENMARK
##########

# Create APC frame for the graph, type ?apc.frame for help
res <- apc.frame( 
    a.lab=c(30,45,60,75),                    # Num vector of labels for age axis
    cp.lab=c(seq(1885,2005,10)),             # Num vector of labels for cohort-period axis
    r.lab=c(1,2,5,10,20,50,100),             # Num vector of labels for rate axis
    a.tic=seq(30,75,5),                      # Location of add tick marks on age scale
    r.tic=c(1:10,1:5*10),                    # Location of add tick marks on rate scale
    gap=15,                                  # Gap between age scale and cohort-period scale
    a.txt="Denmark",                         # Text for age axis
    r.txt="",                                # Text for rate axis
    cp.txt="cohort slope set to zero")       # Text for cohort-period axis

# Create actual graph
apc.lines(  ex.t1, 
            frame.par=res, 
            col="blue",
            lwd=3)


########## 
# FINLAND
##########

# Create APC frame for the graph, type ?apc.frame for help
res <- apc.frame( 
    a.lab=c(30,45,60,75),                    # Num vector of labels for age axis
    cp.lab=c(seq(1885,2005,10)),             # Num vector of labels for cohort-period axis
    r.lab=c(1,2,5,10,20,50,100),             # Num vector of labels for rate axis
    a.tic=seq(30,75,5),                      # Location of add tick marks on age scale
    r.tic=c(1:10,1:5*10),                    # Location of add tick marks on rate scale
    gap=15,                                  # Gap between age scale and cohort-period scale
    a.txt="Finland",                         # Text for age axis
    r.txt="",                                # Text for rate axis
    cp.txt="cohort slope set to zero")       # Text for cohort-period axis

# Create actual graph
apc.lines( ex.t2,                            # Data
           frame.par=res,                    # Use frame created above
           col="red",                        # Line color
           lwd=3)                            # Line width


########## 
# NORWAY
##########

# Create APC frame for the graph, type ?apc.frame for help
res <- apc.frame( 
    a.lab=c(30,45,60,75),                    # Num vector of labels for age axis
    cp.lab=c(seq(1885,2005,10)),             # Num vector of labels for cohort-period axis
    r.lab=c(1,2,5,10,20,50,100),             # Num vector of labels for rate axis
    a.tic=seq(30,75,5),                      # Location of add tick marks on age scale
    r.tic=c(1:10,1:5*10),                    # Location of add tick marks on rate scale
    gap=15,                                  # Gap between age scale and cohort-period scale
    a.txt="Norway",                          # Text for age axis
    r.txt="",                                # Text for rate axis
    cp.txt="cohort slope set to zero")       # Text for cohort-period axis

# Create actual graph
apc.lines( ex.t3,                            # Data
           frame.par=res,                    # Use frame created above
           col="green",                      # Line color
           lwd=3)                            # Line width


########## 
# SWEDEN
##########

# Create APC frame for the graph, type ?apc.frame for help
res <- apc.frame( 
    a.lab=c(30,45,60,75),                    # Num vector of labels for age axis
    cp.lab=c(seq(1885,2005,10)),             # Num vector of labels for cohort-period axis
    r.lab=c(1,2,5,10,20,50,100),             # Num vector of labels for rate axis
    a.tic=seq(30,75,5),                      # Location of add tick marks on age scale
    r.tic=c(1:10,1:5*10),                    # Location of add tick marks on rate scale
    gap=15,                                  # Gap between age scale and cohort-period scale
    a.txt="Sweden",                          # Text for age axis
    r.txt="",                                # Text for rate axis
    cp.txt="cohort slope set to zero")       # Text for cohort-period axis

# Create actual graph
apc.lines( ex.t4,                            # Data
           frame.par=res,                    # Use frame created above
           col="black",                      # Line color
           lwd=3)                            # Line width