Fix: add extra checks to avoid segfaults in move_alpha and
move_swap_alpha
o2geosocial 1.1.2
Resubmission following CRAN archive
o2geosocial 1.1.1
Fix: Update Rcpp to remove warnings
o2geosocial 1.1.0
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
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$outlier_relative == T”, the same threshold of
plausibility is used in R/outbreaker_find_imports.R and
R/outbreaker_move.R.
Add “cpp_gen_tree()” in src/internals.cpp: function for internal use
that calculates the genotype reported in a given tree.
Bug Fixes
Fix: In R/outbreaker_find_imports.R, if “max(data$is_cluster)” was
equal to 1, “list_influences” was initialised as a matrix, now it is
always a list.
Fix: In R/outbreaker_data.R: modify “final_index” to change how the
tail of “w_dens” is calculated and avoid log(w_dens) = -Inf.
Fix: In R/custom_likelihoods.R: Change the number of arguments
needed to customise likelihood functions.
Fix: In certain situations, some of the initial trees (generated by
“create_config()”) contained more than one genotype reported per
tree.
Fix: In R/outbreaker_find_imports.R and R/outbreaker_move.R, change
the calculation of “n_measures”
Fix various typos.
o2geosocial 1.0.2
Fix: “f_dens” refers to the “incubation period”, not the
“colonization time”
o2geosocial 1.0.1
Fix: Remove dependencies to unused packages in DESCRIPTION
File.
Fix: Remove checks in cpp_move_swap_cases.
Fix: Consensus tree for imported cases in “summary()”: the value of
the column “from” for an imported case is now NA.