# risk and odds chapter
install.packages("epitools", dependencies=TRUE)
library(epitools)
############ skiers
## matrix(c( column  . . . . column), nrow , ncol)  coloumnwise data
thedata <- matrix(c(40, 20, 60, 80 ),nrow = 2 , ncol = 2)
# now give the row then columns names - opposite way round to the matrix command)
dimnames(thedata) <- list("group" = c("case", "control"), "outcome" = c("injury", "no_injury"))
thedata
epitab(thedata)

################ the aspirin data  
thedata <- matrix(c(55, 96, 5376, 5392),2 , 2)
dimnames(thedata) <- list("group" = c("aspirin", "placebo"), "outcome" = c("heart_attack", "no_heart_attack"))
thedata
install.packages("epitools", dependencies=TRUE)
library(epitools)
epitab(thedata)
##################
# different odd ratios CI estimates:

oddsratio(thedata)
oddsratio.midp(thedata) 
oddsratio.fisher(thedata)
oddsratio.wald(thedata)
oddsratio.small (thedata)

#############################
# Risk ratios 
# need to make the control the 
#reference group
########
riskratio(thedata, rev = "both")
riskratio.wald(thedata, rev = "both")
riskratio.small(thedata, rev = "both") 
riskratio.boot(thedata, rev = "both")
###
## can also use: riskratio(method = "boot", rev = "both")  etc
detach("package:epitools")

install.packages("epibasix", dependencies=TRUE)
library(epibasix)

summary(epi2x2(thedata))
############## table of recipricals
result <- matrix(seq(.5,10,.5), 2)
result
for (val in seq(1,10,.5)) 
  {
x<-1/val
print(x)
}

val <- seq(.5,10,.5)
recip <- round(1/val, 3)
mydata <- data.frame(val,recip)
names(mydata) <- c("value","reciprical") # variable names
mydata