Working with fitdistrcens

Warning in .check.version(config): Your configuration is compatible with version 0.8 of the ProjectTemplate package.
  Please run ProjectTemplate::migrate.project() to migrate to the installed version 0.8.2.

So here’s what happens if we try to run fitdistrcens on a non-standard distribution:

library(rmutil)
temp <- filter(disperseLer, ID == "100_0")
cens_data <- cens_dispersal_data(temp, 7)
try(fitdistcens(cens_data, "ggamma", start = list(s = 5, m = 4, f = 2)), outFile = stdout())

Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg,  : 
  argument "hasnodefaultval" is missing, with no default

Does it work with fitdist, which doesn’t account for the censoring?

p1 <- fitdist(temp$Distance - 7, "ggamma", start = list(s = 5, m = 4, f = 2))

Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg, : Some parameter names have no starting/fixed value.

No, but gives a different error. I’ve traced this to the firstline of computegetparam, which has first line:

nonparaminR <- c("x", "p", "q", "n", "log", "log.p", "lower.tail", 
        "ncp")

However, the first argument of the distribution functions in rmutil is “y”. I can try to fix that here, but who knows whether the assumption of the first argument being x is baked in anywhere else!

The thing to try is to make a locally modified version of computegetparam and, if that works, fitdistccens. These will have to be sourced after fitdistrplus is loaded.

OK, I’ve made a modified version of computegetparam and put it in src/myfitdistrplus.R. Let’s try it:

source("src/myfitdistrplus.R")
p1 <- fitdist(temp$Distance - 7, "ggamma", start = list(s = 5, m = 4, f = 2))

Error in checkparamlist(arg_startfix$start.arg, arg_startfix$fix.arg, : Some parameter names have no starting/fixed value.

Shoot, it seems that the local function definition is not overriding the definition within the package. The same thing happens when I do it from the command line, so it’s not just a knitr thing.

I think the only solution (short of submitting a bug report and hoping for a fast update) is to download the package from its github mirror (https://github.com/cran/fitdistrplus) and build my own version.

Tried that, and so far generating the same error…