# R/printPod.R In markusboenn/POD: Probability of Detection for Qualitative PCR Methods

#### Documented in print.pod

```#' @title Summary of POD objects
#'
#' @description Generate nicely formatted output of the POD object
#'
#' @param x An object of class 'pod'
#' @param ... Other parameters, not supported yet.
#' @return Nothing is returned.
#'
#' @export
#' @name print.pod
#'
#' @examples
#' x <- cbind(
#'  X=c( 0.1,1,2,5,10,20 ),
#'  S=c( 0,5,6,6,6,6 ),
#'  N=c( 6,6,6,6,6,6 )
#' )
#' obj <- analyzeSingleLab(x=x)
#' print(obj)
#'
#' obj <- analyzeSingleLab(x=x, qLOD=c(50, 70, 95))
#' print(obj)

print.pod <- function(x, ...){
obj <- x
.shift <- function(k){ return( c( " ", "  ", "   ", "    ", "     ", "      " )[k] ) }

cat("\n#######################\nSummary of POD analysis\n#######################\n\n")
cat("Data:\n")
print(round(obj\$x,3))
cat("\n")

HEAD <- c("Full GLM", "Simplified GLM (setting 'b' to fixed value)")
OBJ <- list(obj\$fit.glm.full, obj\$fit.glm.simple)
for( i in 1:2 ){
fit <- OBJ[[i]]
tmp <- round(unlist(fit\$LOD), 3)
k <- 2
if(nrow(tmp)>1){
k <- 4
cat(.shift(2), "LOD:\n", sep="")
}
for(rn in rownames(tmp)){
tmp0 <- tmp[rn,]
cat(.shift(k), "LOD", rn, " [95% CI]: ", sprintf("%.3f [%.3f;%.3f]", tmp0[1], tmp0[2], tmp0[3]), "\n", sep="")
}

cat(.shift(2), sprintf("lambda=%.3f; b=%.3f", fit\$lambda, fit\$b), "\n", sep="")
cat(.shift(2), "Warnings:\n", sep=""); for(w in fit\$warn){cat(.shift(4), w, "\n", sep="")}
cat("\n")
}
cat("#######################\n\n")
}
```
markusboenn/POD documentation built on April 6, 2019, 2:18 a.m.