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Created with Raphaël 2.2.030Jan11Dec954324Jun171164324Apr17Jan11Dec7530Nov27Merge branch 'devel-reconcile-v4' into 'master'mastermasterForce writing output of all mosquito compartments (6 instead of 3) to be in accordance with Output_overview.Rdevel-reconcile…devel-reconcile-v4Update README.mdv3v3Delete compiled model that should not be part of the git repo (and update .gitignore to avoid that in the future)Add newly-generated model_output.txt files that serves as exampleUpdate README.md with instructions related to peri-domestic and occupational mosquito populations and adjust default outputs.Replace parameter files by new versions that can be used for running the modelRefactored equilibrium calculation and peri-domestic vs occupational exposure calculations.Change default value for number of equilibrium setupAdapted Source.cpp 2/2: Added reference to peri-domestic EIR and switched population initialisation routine to the new 3-step version.Adapted Source.cpp 1/n: Removed references to N_spec and S_spec_max for N_mosq and related indexes from g to v(ector).Adapted Simulation.h 1/1: Added references to both EIR and age and gender stratified counts.Adapted Simulation.cpp 4/4: Update available outputs with age and gender stratified data (among other things).Adapted Simulation.cpp 3/n: Split EIR into two different values in both inputs and outputs.Adapted Simulation.cpp 2/n: Changed BS_ prefixes by CQ_ prefixes for consistency with other drugsAdapted Simulation.cpp 1/n: Change references from N_spec to N_mosq and related indexes from g to v(ector).Adapted Population.cpp: Split calculation of equilibrium into 3 different functions and now account for new '3 gender' method of modelling occupational vs. peri-domestic exposureAdapted Population.cpp 3/n: Update structure of output data to include age/gender stratified data.Adapted Population.cpp 2/n: Introduced 2 values of EIR (and 3 gender) and accounted for such modifications in calculating the quilibrium state.Adapted Population.cpp 1/n: Change reference from N_spec to N_mosq and related indexes from g to v(ector).Adapted Population.h 6/6: Finished accounting for different EIRs into equilibrium calculation and added some indicator indexes for occupational age boundaries and pregnancy age boundaries.Adapted Population.h 5/n: Account for the two distinct EIR (peri-domestic and occupational) in setting-up the equilibrium state.Adapted Population.h 4/n: Replace BS (bloodstage) references by CQ (chloroquine) to be consistent with other naming. Also allow to count and export number of detected cases in different age groups.Adapted Population.h 3/n: Account for two distinct EIR (peri-domestic and occupational).Adapted Population.h 2/n: Split equilibrium initialization into three separate functions that will be defined in Population.cpp at a later stageAdapted Population.h 1/n: Replaced variable N_spec by N_mosq for consistency across all source code...Adapted Params.cpp 8/8: Removed unnecessary reference to normalizing proportion of mosquito species and related parameters.Adapted Params.cpp 7/n: Removed all default vaues for intervention parameters, as these are read in from the interventions input fileAdapted Params.cpp 6/n : Some more refactoring for CM_ related variables, to read in parameter values from parameters input file...Adapted Params.cpp 5/n: Started refactoring CM_ related variables (efficacy, prophylaxis, G6PD diagnotic tool). This particular commit introduces a lot fo redundancy but is needed to keep track of changes. The upcoming commit(s) will pursue these changes.Adapted Params.cpp 4/n: Introduced calculation of rate of pregnancy from proportion of pregnant women in observational data, and allowed pregnancy age range to be modified.dapted Params.cpp 3/n: Removed some (not all) references to mosquito species data and added occupational vs. peri-domestic EIR with introduction of a relative risk factor.Adapted Params.cpp 2/n: Changed fixed pregnancy probability to rate derived from observational data.Adapted Params.cpp 1/n: Changed reference from both (redundant) N_spec and N_spec_max to N_mosq, and index g to v(ector) to remain consisten with the rest of source code.Adapted Params.h 20/20: Change variable name for daily rate of pregnancy (which will get derived from observed rate of pregnancy in women in age range) + small cleanup.Adapted Params.h 19/n: Cleanup for spaces and empty lines...Adapted Params.h 18/n: Tidied up and renamed STAT2_ parameters for consistency.Adapted Params.h 17/n: Tidied up and renamed STAT1_ parameters for consistency.Adapted Params.h 16/n: Tidied up and renamed MSAT2_ parameters for consistency.Adapted Params.h 15/n: Tidied up and renamed MSAT1_ parameters for consistency.