fitting a Rayleigh distribution

[dagmorga]

I am using Rstudio (release 1.2.5019 running R 4.05) on a Windows 10 machine to follow the instructions on this page:

Finding the parameters of a (possibly) Rayleigh distributed data set

It's quite simple: load two libraries, create a small data set in vector x, fit to a Rayleigh distribution with this command:

fit <- fitdist(x, "rayleigh", start = list(sigma = 1))

When I do this in RStudio, I get this error:
Error in fitdistr(x, "rayleigh", start = list(sigma = 1)) :
unsupported distribution

When I type exactly the same commands into a command window started from the R 4.05 installation running on this machine, the fitting works.

Any thoughts as to why it fails inside RStudio but not in the terminal window?

Thanks in advance...

[nirgrahamuk]

are you using library(extraDistr) in addition to library(fitdistrplus) ?

[dagmorga]

Yes, those are the two libraries in the example I'm following.

[nirgrahamuk]

ok, please provide the results you receive when you run.

packageVersion("fitdistrplus")
packageVersion("extraDistr")

[dagmorga]

I get 1.1.8 for fitdistrplus and 1.9.1 for extraDistr. Those versions are identical when run inside RStudio (where the fitting fails) and in the R command window (where it works).

[nirgrahamuk]

in the library(MASS) there is a function fitdistr that can complain 'unsupported distribution'
I am not aware that fitdist would throw that.
Is there any possibility you have a typo in the code you are trying for Rstudio, but not in R command ?

[dagmorga]

No. I cut and pasted across the two. I also just tested whether also loading MASS had any effect on whether the R terminal window works or not. It still works even when MASS is loaded.

When I have a bit more time, I will look to see exactly which packages are loaded in the two environments.

[nirgrahamuk]

Its quite curious.
I wonder what happens when you try binom instead of rayleigh
i.e.

fit <- fitdist(x, "binom", start = list(sigma = 1))
fit <- fitdistr(x, "binom", start = list(sigma = 1))

I get errors on both, but they are quite different :

# fitdistrplus:
> fit <- fitdist(x, "binom", start = list(sigma = 1))
Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg,  : 
  'start' must specify names which are arguments to 'distr'.

# MASS
> fit <- fitdistr(x, "binom", start = list(sigma = 1))
Error in fitdistr(x, "binom", start = list(sigma = 1)) : 
  unsupported distribution
>

[dagmorga]

I haven't had time to check that the packages are comparable and won't get to that today. I don't know whether package order matters, but I have both MASS and fitdistrplus loaded in both RStudio and my R terminal. I get different results:

RStudio

fit2 <- fitdistr( x, "rayleigh", start = list(sigma = 1) )
Error in fitdistr(x, "rayleigh", start = list(sigma = 1)) :
unsupported distribution
fit2 <- fitdistr( x, "binom", start = list(sigma = 1) )
Error in fitdistr(x, "binom", start = list(sigma = 1)) :
unsupported distribution

R terminal:

fit2 <- fitdist(x, "rayleigh", start = list(sigma = 1))
fit2 <- fitdist(x, "binom", start = list(sigma = 1))
Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg, :
'start' must specify names which are arguments to 'distr'.

Whatever that means...

[nirgrahamuk]

According to this post, in rstudio you tested fitdistr twice whereas in the terminal you tested fitdist twice

[dagmorga]

When I saw your note late yesterday, I assumed that I had simply been an idiot and my problem really was as simple as a typo. However, when I had a chance to test it, I find:

RStudio:

fit2 <- fitdistr( x, "rayleigh", start = list(sigma = 1) )
Error in fitdistr(x, "rayleigh", start = list(sigma = 1)) :
unsupported distribution
fit2 <- fitdistr( x, "binom", start = list(sigma = 1) )
Error in fitdistr(x, "binom", start = list(sigma = 1)) :
unsupported distribution

fit2 <- fitdist( x, "rayleigh", start = list(sigma = 1) )
Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg, :
'start' must specify names which are arguments to 'distr'.
fit2 <- fitdist( x, "binom", start = list(sigma = 1) )
Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg, :
'start' must specify names which are arguments to 'distr'.

R terminal:

fit2 <- fitdistr( x, "rayleigh", start = list(sigma = 1) )
Error in fitdistr(x, "rayleigh", start = list(sigma = 1)) :
unsupported distribution
fit2 <- fitdistr( x, "binom", start = list(sigma = 1) )
Error in fitdistr(x, "binom", start = list(sigma = 1)) :
unsupported distribution

fit2 <- fitdist( x, "rayleigh", start = list(sigma = 1) )
fit2 <- fitdist( x, "binom", start = list(sigma = 1) )
Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg, :
'start' must specify names which are arguments to 'distr'.

Again, the R Terminal can do the Rayleigh fit using fitdist while RStudio cannot...

And thanks for your help and patience.