Movatterモバイル変換

o2geosocial 1.1.3

Change the calculation and format of the connectivity matrix(“param$log_s_dens"):param$log_s_dens now contains the probability of connectionbetween regions (rather than the log-probability) if”kappa = 1”. Ifthere 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 genotypereported in each tree.
In R/outbreaker_find_imports.R: imported cases do not influence thecomputation of “threshold” (i.e. the threshold of plausibility of aconnection between cases) since they are by definition not infected byany case (and their likelihood is de facto smaller).

Add parameter “outlier_plot” to “create_config()”: if TRUE, thelikelihoods of connection are plotted after the first short run(“outbreaker_find_imports()”)
Add a message to indicate how many imports were added after thefirst run (in R/outbreaker_find_imports.R)
If “config$outlier_relative == T”, the same threshold ofplausibility is used in R/outbreaker_find_imports.R andR/outbreaker_move.R.
Add “cpp_gen_tree()” in src/internals.cpp: function for internal usethat calculates the genotype reported in a given tree.

Fix: In R/outbreaker_find_imports.R, if “max(data$is_cluster)” wasequal to 1, “list_influences” was initialised as a matrix, now it isalways a list.
Fix: In R/outbreaker_data.R: modify “final_index” to change how thetail of “w_dens” is calculated and avoid log(w_dens) = -Inf.
Fix: In R/custom_likelihoods.R: Change the number of argumentsneeded to customise likelihood functions.
Fix: In certain situations, some of the initial trees (generated by“create_config()”) contained more than one genotype reported pertree.
Fix: In R/outbreaker_find_imports.R and R/outbreaker_move.R, changethe calculation of “n_measures”
Fix various typos.

Fix: Remove dependencies to unused packages in DESCRIPTIONFile.
Fix: Remove checks in cpp_move_swap_cases.
Fix: Consensus tree for imported cases in “summary()”: the value ofthe column “from” for an imported case is now NA.