Error(s) in re-building vignettes:
--- re-building 'TiPS.Rmd' using rmarkdown
Building the simulator ...
Compiling the simulator ...
Process complete.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Success!
Success!
Failure. You should try other parameter values.
Failure. You should try other parameter values.
Success!
Success!
Warning in Phylo$simulationTree() :
  Error : Cannot sample a compartment, the number of individuals is not sufficient.
Warning in Phylo$simulationTree() :
  Error: In compartment, variable activeNodes_ greater than compartment size.
Warning in Phylo$simulationTree() :
  Error: In compartment, variable activeNodes_ greater than compartment size.
Warning in Phylo$simulationTree() :
  Error: In compartment, variable activeNodes_ greater than compartment size.
Warning in Phylo$simulationTree() :
  Error: In compartment, variable activeNodes_ greater than compartment size.
Failure.
Warning in ape::plot.phylo(sir_tree, cex = 0.5) :
  found fewer than 2 tips in the tree
Building the simulator ...
Compiling the simulator ...
Process complete.
Success!
Warning in Phylo$simulationTree() :
  Error : Cannot sample a compartment, the number of individuals is not sufficient.
Warning in Phylo$simulationTree() :
  Error : Cannot sample a compartment, the number of individuals is not sufficient.
Warning in Phylo$simulationTree() :
  Error : Cannot sample a compartment, the number of individuals is not sufficient.
Failure.
Warning in ape::plot.phylo(bd_tree, root.edge = T, no.margin = F, align.tip.label = T) :
  found fewer than 2 tips in the tree
Quitting from lines 372-374 (TiPS.Rmd) 
Error: processing vignette 'TiPS.Rmd' failed with diagnostics:
object 'last_plot.phylo' not found
--- failed re-building 'TiPS.Rmd'

SUMMARY: processing the following file failed:
  'TiPS.Rmd'

Error: Vignette re-building failed.
Execution halted