NEWS.md

In MGDrivE2: Mosquito Gene Drive Explorer 2

MGDrivE2 2.1.0

New features:

1. Decoupled/Imperial sampling can now calculate malaria-induced severe disease and mortality. See human_Imperial_ODE function for implementation details.
2. equilibrium_Imperial_decoupled updated to calculate the total number of mosquitoes given human population parameters.

Bugfixes:

1. human_Imperial_ODE updated to correctly calculate the per-capita force of infection. Does not fail with suppression constructs anymore due to divide-by-zero error.
2. base_female_Imperial updated with correct mosquito density equations to begin the mosquito population at equilibrium, based on epi parameters.

MGDrivE2 2.0.0

New features

1. Decoupled epi-mosquito dynamics now implemented with Imperial model of malaria transmission. See Vignettes for details.
2. add_interventions allows mosquito lifecycle parameters to vary in the presence of LLINs and IRS.

MGDrivE2 1.2.0

New features:

1. Function batch_migration now takes an additional argument stages to allow simulation of batch migration where only one of egg, larval, or pupal stages experiences batch migration events.
2. Stuff about decoupled epi-mosquito dynamics

Bugfixes, miscellaneous:

1. If tracking events using sim_trajectory_base_CSV, write to file called "Tracking.csv" instead of "Events.csv" to avoid clashes with summary function split_aggregate_CSV.

MGDrivE2 1.1.0

New features:

1. Update to include batch migration, see new file R/auxiliary-batch.R and user-facing function batch_migration which sets up the batch migration events. Functions sim_trajectory_R and sim_trajectory_CSV now take an additional argument batch which may be set to NULL if no batch migration is to be simulated.
2. Added function get_shape to get the shape parameter (number of bins) for Erlang developmental delays, given rate parameter q and coefficient of variation cv.

Bugfixes, miscellaneous:

1. In sim_trajectory_base_CSV and sim_trajectory_base_R the hazards are now correctly evaluated at the start of the time step rather than at the end; [times[i-1],times[i]). Both functions no longer need the (extraneous) argument dt.
2. Remove argument t0 from sim_trajectory_base_CSV and sim_trajectory_base_R, all simulations are assumed to start at time 0. Change named argument tt to tmax.
3. In sim_trajectory_base_CSV and sim_trajectory_base_R testing for whether to preform a release is now based on a <= check, rather than equality.
4. Add argument n to function spn_T_lifecycle_network to allow simulation of multiple nodes with no migration between them. Useful for debugging as well as for simulation of landscapes where nodes are far enough apart that batch migration is the only way for mosquitoes to travel between nodes.

MGDrivE2 1.0.1

Small fixes to address CRAN comments:

1. R/hazard-functions-mosy.R: function make_move_male_haz has a fix such that the origin/destination probability is correctly calculated.
2. R/equilibrium-lifecycle.R: function basic_eq_life modified to not use the <<- global assignment operator.
3. vignettes/output-storage.Rmd: replaced absolute path for files with tempdir() to conform to the CRAN standard.
4. Edit DESCRIPTION to conform to CRAN standard.
5. Remove dontrun code from examples where not necessary and direct users to appropriate vignettes, otherwise run examples.

MGDrivE2 1.0.0

Initial release & CRAN submission.

MGDrivE2 documentation built on March 7, 2023, 6:44 p.m.