Changes in version 1.1.3 (2024-06-21)                  

  - Fix: add extra checks to avoid segfaults in move_alpha and
    move_swap_alpha

                 Changes in version 1.1.2 (2024-03-26)                  

  - Resubmission following CRAN archive

                 Changes in version 1.1.1 (2023-12-12)                  

  - Fix: Update Rcpp to remove warnings

                 Changes in version 1.1.0 (2021-09-11)                  

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.

                        Changes in version 1.0.2                        

  - Fix: "f_dens" refers to the "incubation period", not the
    "colonization time"

                 Changes in version 1.0.1 (2020-09-25)                  

  - 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.

                 Changes in version 1.0.0 (2020-08-26)                  

  - initial release