getConfFromData {babsim.hospital} | R Documentation |
getConfFromData
Description
Generate a configuration list for babsimTools based on the data file and the
vector of resources.
This function returns the default configuration settings of the babsimTools functions
used to run babsimHospital
.
Usage
getConfFromData(conf, simData, fieldData)
Arguments
conf |
Configuration. Default: |
simData |
Simulation data. Default: |
fieldData |
Field (real) data. Default: |
Details
Configuration conf
is a list of the following settings.
seed
(int) Initial seed. Default: 123
simRepeats
(int) Number of
simmer
simulation runs. Default: 1parallel
(logical) Use parallel simulations based on
mclapply
. Default: FALSEperCores
(num) Percentage of cores used, if
parallel == TRUE
. Default: 0.5ICU
(logical) Use ICU (RKI) data. Default: FALSE.
logLevel
(int) 0 = no logging, >= 1 logging. Default: 0. If larger than 10, shown detailed simmer output.
maxCapacity
(num) Maximum capacity used for
babsimHospital
resources. Default: 1e6.dataset
(chr) 'GA' or 'ICU'. Default: 'GA'.
simulationDates
List with the following entries:
StartDate
(chr) Start date of the simulation data (infection data used to generate arrival times), first day. Default: '2020-03-03'
EndDate
(chr) End date of the simulation data, last day. Default: '2020-06-24'
fieldDates
List with the following entries:
StartDate
(chr) Start date of the field (resources) data, first day. Default: '2020-03-03'
EndDate
(chr) End date of the field data, last day. Default: '2020-06-24'
simulationData
(data frame) Data used for the simulation. Default
dataCovidBeds20200624
- bed
int 2 2 3 3 3 3 3 3 4 4 ...
- intensiveBed
int 0 0 0 0 0 0 0 0 0 0 ...
- intensiveBedVentilation
int 0 0 0 0 0 0 0 0 0 0 ...
- Day
Date, format: '2020-03-03' '2020-03-04' '2020-03-05' '2020-03-06' ...
- Infected
num 5 0 0 0 0 0 0 7 2 5 ...
- Sick
num 5 5 5 5 5 5 5 12 14 19 ...
fieldEvents
(data frame) Data used for evalution of the simulation. Default
GABeds220200624
- ressource
chr 'bed' 'bed' 'bed' 'bed' ...
- time
int 1 2 3 4 5 6 7 8 9 10 ...
- med
int 2 2 3 3 3 3 3 3 4 4 ...
- source
int 2 2 3 3 3 3 3 3 4 4 ...
- date
Date, format: '2020-03-03' '2020-03-04' '2020-03-05' '2020-03-06' ...
resource
(vector) Resources used in the simulation. Default:
c('bed', 'intensiveBed', 'intensiveBedVentilation')
. For ICU data use:c('bed', 'intensiveBedVentilation')
- ressource
chr 'bed' 'bed' 'bed' 'bed' ...
- time
int 1 2 3 4 5 6 7 8 9 10 ...
- med
int 2 2 3 3 3 3 3 3 4 4 ...
- source
int 2 2 3 3 3 3 3 3 4 4 ...
- date
Date, format: '2020-03-03' '2020-03-04' '2020-03-05' '2020-03-06' ...
Value
a list
Examples
conf <- babsimToolsConf()
simData <- babsim.hospital::dataCovidBeds20200624
fieldData <- babsim.hospital::dataCovidBeds20200624
conf <- getConfFromData(
conf = conf,
simData = simData,
fieldData = fieldData
)
# turn on parallel simulation:
conf$parallel <- TRUE
# Change the start date of the simulations
conf$simulationDates$StartDate <- "2020-01-01"