tests/testthat/test_inverseSurv.R

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

test_that("inverseSurv works at high parameters", {

#library(paleotree)

# let's simulate some taxon ranges from an imperfectly sampled fossil record
set.seed(444)
record <- simFossilRecord(p = 0.1, q = 0.1, nruns = 1,
	nTotalTaxa = c(30,40), nExtant = 0)
taxa <- fossilRecord2fossilTaxa(record)
rangesCont <- sampleRanges(taxa,r = 0.5)

#bin the ranges into discrete time intervals
rangesDisc <- binTimeData(rangesCont,int.length = 5)

#apply make_inverseSurv
likFun <- make_inverseSurv(rangesDisc)

#use constrainParPaleo to make the model time-homogeneous
  	#match.all ~ match.all will match parameters so only 2 pars: p = q and r

constrFun <- constrainParPaleo(likFun, match.all~match.all)

#unconstrained function with ALL of the 225 possible parameters!!!
    # this will take forever to converge	
res <- optim(parInit(likFun),likFun,
      lower = parLower(likFun), upper = parUpper(likFun),
      method = "L-BFGS-B", control = list(maxit = 3))
	  
expect_false(any(is.na(res)))

})