Major changes:
- Change the calculation and format of the connectivity matrix ("param$log_s_dens"): param$log_s_dens now contains the probability of connection between regions (rather than the log-probability) if "kappa = 1". If there is a missing generation between two connected cases (i.e. "kappa = 2"), the spatial likelihood is computed in src/likelihoods.cpp.
- Speed up the exploration of potential infectors (in "cpp_move_alpha()" and "cpp_move_ancestors()") by computing the genotype reported in each tree.
- In R/outbreaker_find_imports.R: imported cases do not influence the computation of "threshold" (i.e. the threshold of plausibility of a connection between cases) since they are by definition not infected by any case (and their likelihood is de facto smaller).
Minor changes:
- Update Rcpp and remove warnings
- Fix runtime error stemming from delta being set as Inf or -Inf
- Add parameter "outlier_plot" to "create_config()": if TRUE, the likelihoods of connection are plotted after the first short run ("outbreaker_find_imports()")
- Add a message to indicate how many imports were added after the first run (in R/outbreaker_find_imports.R)
- If "config$outlier_relative == T", the same threshold of plausibility is used in R/outbreaker_find_imports.R and R/outbreaker_move.R.
Add "cpp_gen_tree()" in src/internals.cpp: function for internal use that calculates the genotype reported in a given tree.