R Under development (unstable) (2024-07-10 r86888 ucrt) -- "Unsuffered Consequences"
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> library(fitdistrplus)
Loading required package: MASS
Loading required package: survival
> 
> 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))
Warning message:
In cdfcompcens(list(fitsfn, fitsfl, fitsfg), NPMLE.method = "Turnbull",  :
  Turnbull is now a deprecated option for NPMLE.method. You should use Turnbull.middlepoints
            of Turnbull.intervals. It was here fixed as Turnbull.middlepoints, equivalent to former Turnbull.
> 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")
+ }
Warning messages:
1: In ggplot2::scale_y_continuous(trans = "log10") :
  log-10 transformation introduced infinite values.
2: In ggplot2::scale_y_continuous(trans = "log10") :
  log-10 transformation introduced infinite values.
3: In ggplot2::scale_y_continuous(trans = "log10") :
  log-10 transformation introduced infinite values.
4: In ggplot2::scale_y_continuous(trans = "log10") :
  log-10 transformation introduced infinite values.
> 
> # 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")
+ }
> 
> 
> proc.time()
   user  system elapsed 
   3.62    0.35    3.96