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
> 
> # (1) Plot of an empirical censored distribution (censored data) as a CDF
> # using the default Turnbull method
> #
> data(smokedfish)
> plotdistcens(smokedfish)
> plotdistcens(data.frame(right=smokedfish$right, left=smokedfish$left))
> d1 <- as.data.frame(log10(smokedfish))
> plotdistcens(d1)
> 
> #test on first arg
> try(plotdistcens(list(left=smokedfish$left, right=smokedfish$right)))
Error in plotdistcens(list(left = smokedfish$left, right = smokedfish$right)) : 
  datacens must be a dataframe with two columns named 'left' and 'right' and more than one line
> try(plotdistcens(cbind(left=smokedfish$left, right=smokedfish$right)))
Error in plotdistcens(cbind(left = smokedfish$left, right = smokedfish$right)) : 
  datacens must be a dataframe with two columns named 'left' and 'right' and more than one line
> d2 <- data.frame(left=smokedfish$right, right=smokedfish$left)
> try(plotdistcens(d2))
Error in plotdistcens(d2) : 
  some rows in censdata have left values strictly greater than right values
> 
> # (2) Add the CDF of a normal distribution and QQ and PP plots
> #
> plotdistcens(smokedfish,"lnorm", para=list(meanlog=-3.6,sdlog=3.5))
> plotdistcens(d1,"norm", para=list(mean=-1.6,sd=1.5))
> 
> # (3) Various plots of the same empirical distribution 
> #
> # default Wang plot
> plotdistcens(d1, NPMLE = TRUE, NPMLE.method = "Wang")
> plotdistcens(d1, NPMLE = TRUE, NPMLE.method = "Wang", lwd = 3, main = "Wang ECDF plot")
> # Turnbull plot
> plotdistcens(d1, NPMLE = TRUE, NPMLE.method = "Turnbull", col = "red", 
+              main = "Turnbull ECDF plot")
Warning message:
In plotdistcens(d1, NPMLE = TRUE, NPMLE.method = "Turnbull", col = "red",  :
  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.
> plotdistcens(d1,Turnbull = TRUE) # deprecated way to do it
Warning message:
In plotdistcens(d1, Turnbull = TRUE) :
  When Turnbull.confint is TRUE NPMLE.method is forced to Turnbull.middlepoints.
> # Turnbull plot with confidence intervals
> plotdistcens(d1,NPMLE = TRUE, NPMLE.method = "Turnbull", Turnbull.confint = TRUE)
Warning message:
In plotdistcens(d1, NPMLE = TRUE, NPMLE.method = "Turnbull", Turnbull.confint = TRUE) :
  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.
> plotdistcens(d1,Turnbull = TRUE,Turnbull.confint = TRUE) # deprecated way to do it
Warning messages:
1: In plotdistcens(d1, Turnbull = TRUE, Turnbull.confint = TRUE) :
  When Turnbull.confint is TRUE NPMLE.method is forced to Turnbull.middlepoints.
2: In plot.window(...) : "Turnbull" is not a graphical parameter
3: In plot.xy(xy, type, ...) : "Turnbull" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
  "Turnbull" is not a graphical parameter
5: In axis(side = side, at = at, labels = labels, ...) :
  "Turnbull" is not a graphical parameter
6: In box(...) : "Turnbull" is not a graphical parameter
7: In title(...) : "Turnbull" is not a graphical parameter
> # with intervals and points
> plotdistcens(d1,NPMLE = FALSE)
> plotdistcens(d1,NPMLE = FALSE, col = "red", lwd = 2)
> plotdistcens(d1,rightNA=3, NPMLE = FALSE)
> plotdistcens(d1,rightNA=3, Turnbull = FALSE) # deprecated way to do it
> # with intervals and points
> # defining a minimum value for left censored values
> plotdistcens(d1,leftNA=-3, NPMLE = FALSE)
> 
> # (4) Goodness-of-fit plots for the same dataset after logarithmic transformation
> #   with a lognormal distribution, successively using the three proposed methods
> #
> d3 <- smokedfish
> plotdistcens(d3,"lnorm",para=list(meanlog=-3.6,sdlog=3.5), main = "Wang plot")
> plotdistcens(d3,"lnorm",para=list(meanlog=-3.6,sdlog=3.5), 
+              NPMLE.method = "Turnbull", main = "Turnbull plot")
Warning messages:
1: In plotdistcens(d3, "lnorm", para = list(meanlog = -3.6, sdlog = 3.5),  :
  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.
2: In plotdistcens(d3, "lnorm", para = list(meanlog = -3.6, sdlog = 3.5),  :
  Q-Q plot and P-P plot are available only  
            with the arguments NPMLE.method at Wang (default value) or Turnbull.intervals.
> plotdistcens(d3,"lnorm",para=list(meanlog=-3.6,sdlog=3.5),
+              NPMLE = FALSE, leftNA=0, main = "Plot of ordered intervals")
Warning message:
In plotdistcens(d3, "lnorm", para = list(meanlog = -3.6, sdlog = 3.5),  :
  When NPMLE is FALSE the nonparametric maximum likelihood estimation 
            of the cumulative distribution function is not computed.
            Q-Q plot and P-P plot are available only with the arguments NPMLE.method at Wang 
            (default value) or Turnbull.intervals.
> 
> # Test with the salinity data set
> #
> data(salinity)
> log10LC50 <-log10(salinity)
> plotdistcens(log10LC50)
> plotdistcens(log10LC50, NPMLE.method = "Turnbull")
Warning message:
In plotdistcens(log10LC50, 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.
> plotdistcens(log10LC50, NPMLE = FALSE)
> fn <- fitdistcens(log10LC50,"norm")
> fl <- fitdistcens(log10LC50,"logis")
> plot(fn)
> plot(fl)
> 
> proc.time()
   user  system elapsed 
   2.31    0.28    2.57