library(fitdistrplus)

visualize <- FALSE # TRUE for manual tests with visualization of results

# (1) Plot various distributions fitted to bacterial contamination data
#
data(smokedfish)
Clog10 <- log10(smokedfish)

fitsfn <- fitdistcens(Clog10,"norm")
fitsfl <- fitdistcens(Clog10,"logis")

dgumbel <- function(x,a,b) 1/b*exp((a-x)/b)*exp(-exp((a-x)/b))
pgumbel <- function(q,a,b) exp(-exp((a-q)/b))
qgumbel <- function(p,a,b) a-b*log(-log(p))
fitsfg <- fitdistcens(Clog10, "gumbel", start=list(a=-3,b=3))

cdfcompcens(list(fitsfn,fitsfl,fitsfg))
cdfcompcens(list(fitsfn,fitsfl,fitsfg), fitlty=1, fitlwd=3)

# Same plot in y logscale
cdfcompcens(list(fitsfn, fitsfl, fitsfg), NPMLE.method = "Turnbull",
            ylogscale = TRUE, ylim=c(.5, .99))
cdfcompcens(list(fitsfn, fitsfl, fitsfg), NPMLE.method = "Wang",
            ylogscale = TRUE, ylim=c(.5, .99))

if (requireNamespace ("ggplot2", quietly = TRUE)) {
  cdfcompcens(list(fitsfn,fitsfl,fitsfg), plotstyle = "ggplot")
  cdfcompcens(list(fitsfn,fitsfl,fitsfg), plotstyle = "ggplot", fitlty=1, fitlwd=3)
  cdfcompcens(list(fitsfn,fitsfl,fitsfg), datacol="grey", 
              legendtext=c("normal","logistic","Gumbel"),
              main="bacterial contamination fits",
              xlab="bacterial concentration (CFU/g)", ylab="F",
              xlegend = "center", lines01 = TRUE, plotstyle = "ggplot")
  
  # Same plot in y logscale
  cdfcompcens(list(fitsfn, fitsfl, fitsfg), NPMLE.method = "Wang",
              ylogscale = TRUE, ylim=c(.5, .99), plotstyle = "ggplot")
}

# Use of x logscale
if (visualize)
{
  if(any(installed.packages()[,"Package"] == "actuar"))
  {
    require(actuar)
    data(smokedfish)
    fln <- fitdistcens(smokedfish,"lnorm")
    fll <- fitdistcens(smokedfish,"llogis")
    cdfcompcens(list(fln, fll))
    cdfcompcens(list(fln, fll), xlogscale = TRUE)
    cdfcompcens(list(fln, fll), xlogscale = TRUE, xlim = c(0.01, 1000))
    cdfcompcens(list(fln, fll), NPMLE.method = "Turnbull",
                xlogscale = TRUE, xlim = c(0.01, 1000))
    
    if (requireNamespace ("ggplot2", quietly = TRUE)) {
      cdfcompcens(list(fln, fll), plotstyle = "ggplot")
      cdfcompcens(list(fln, fll), xlogscale = TRUE, plotstyle = "ggplot")
      cdfcompcens(list(fln, fll), xlogscale = TRUE, xlim = c(0.01, 1000), plotstyle = "ggplot")
    }
  }
  # same plot using argument add
  cdfcompcens(fitsfn, addlegend = FALSE, fitcol = "red")
  cdfcompcens(fitsfl, addlegend = FALSE, fillrect = NA, fitcol = "green", add = TRUE)
  cdfcompcens(fitsfg, addlegend = FALSE, fillrect = NA, fitcol = "blue", add = TRUE)
  
  cdfcompcens(list(fitsfn, fitsfl, fitsfg), addlegend = FALSE, fitcol = 2:4, fitlty = 1, plotstyle = "ggplot")
  cdfcompcens(list(fitsfn, fitsfl, fitsfg), addlegend = FALSE, fitcol = 2:4, fitlty = 1, plotstyle = "ggplot")
}

# Test on the salinity data set
#
data(salinity)
log10LC50 <-log10(salinity)
plotdistcens(log10LC50)
plotdistcens(log10LC50, NPMLE = FALSE)
fn <- fitdistcens(log10LC50,"norm")
fl <- fitdistcens(log10LC50,"logis")
plot(fn)
plot(fl)
cdfcompcens(list(fn, fl))

if (requireNamespace("ggplot2", quietly = TRUE)) {
  cdfcompcens(list(fn, fl), plotstyle = "ggplot")
}