More comprehensive seeding and vaccine schedules (#223)

* Add option for vaccinate_schedule to take a recurring or list schedule

Add tests for single action, multi-day, recurring and bespoke list vaccine schedules

* Allow Vaccine to be initiated with a MetaModel

* Add vaccines to the MetaModel

Basic version of vaccinate_schedule which allows the same schedule for all regions

* Inter-region migration infections are proportional to the tranmission_multipler of the strain

* Add pool transfers for central London regions where most infections are between other regions (i.e. 2 commuters)

* In MetaModel, extend vaccine schedule to work on a per region basis

* Additions to MetaModel plot function

Allow for a base_date to be given for date instead of time on x-axis

Allow strain speicific infecitons to be plotted

Allow for a denominator to be given so % of strain can be plotted

* Additions to MetaModel plot function

Allow for a base_date to be given for date instead of time on x-axis

Allow strain speicific infecitons to be plotted

Allow for a denominator to be given so % of strain can be plotted

* Don't add seed_infections to total infected at the point they are infected

Leads to discrepancy with total figures from model. No change in epidemic, but changes assumption to seed infections being at the very start of the following day as opposed to the very end of the current day.

* Change in MetaModel migration factor

Allow it to be updated during a simulation (required since it will decrease with social distancing measures)

* MetaModel - handle case of empty entry in vaccine schedule

* round_random when vaccinating a proportion of the population

gives the correct mean over time for small numbers

* Add seeding schedule to Model in R

* Add set_seeding_schedule to MetaModel

* Add seed_infect_by_indices

* Add long term migration matrix for England and option to blend

* Add long term migration matrix and ability to blend

Add regional infectious rate factors to England model

* In meta model move combine_run to be a private function

* Add using generation kernel for migration in meta model

Set default model for England metaModel

* Covnert param_list to list of lists (different R versions have different defaults if not specified)

* Add quarantine status to inidividual inforamtion which can be accessed via R/Python interfaces

Author: roberthinch

NAMESPACE

@@ -17,6 +17,7 @@ importFrom( "plotly", "animation_opts" )
 importFrom( "plotly", "colorbar" )
 importFrom( "plotly", "%>%" )
 importFrom( "stringr", "str_replace_all")
+importFrom( "utils", "read.csv")
 
 # R6 Classes
 export("Parameters")
@@ -35,6 +36,7 @@ export("MetaModel")
 export("Parameters.new")
 export("Parameters.get_param")
 export("Parameters.set_param")
+export("Parameters.default_param")
 export("Model.new")
 export("Model.one_time_step")
 export("Model.one_time_step_results")
@@ -59,5 +61,15 @@ export("VACCINE_STATUS")
 export("plot.value.total_infected")
 export("plot.value.new_infected")
 export("plot.values")
+export("plot.value.total_infected_strain_0")
+export("plot.value.new_infected_strain_0")
+export("plot.value.total_infected_strain_1")
+export("plot.value.new_infected_strain_1")
+export("plot.value.total_infected_strain_2")
+export("plot.value.new_infected_strain_2")
+export("plot.value.total_infected_strain_3")
+export("plot.value.new_infected_strain_3")
+export("plot.value.total_infected_strain_4")
+export("plot.value.new_infected_strain_4")
 
 useDynLib(OpenABMCovid19, .registration = TRUE)