Return an _opts List per Region

Source: R/opts.R

[Maturing] Define a list of _opts() to pass to regional_epinow _opts() accepting arguments. This is useful when different settings are needed between regions within a single regional_epinow call. Using opts_list the defaults can be applied to all regions present with an override passed to regions as necessary (either within opts_list or externally).

opts_list(opts, reported_cases, ...)

Arguments

opts

An _opts() function call such as rt_opts()

reported_cases

A data frame containing a region variable indicating the target regions

...

Optional override for region defaults. See the examples for use case.

Value

A named list of options per region which can be passed to the _optaccepting arguments of regional_epinow

See also

regional_epinow rt_opts

Examples

# uses example case vector
cases <- example_confirmed[1:40]
cases <- data.table::rbindlist(list(
  data.table::copy(cases)[, region := "testland"],
  cases[, region := "realland"]
))

# default settings
opts_list(rt_opts(), cases)
#> $testland
#> $testland$prior
#> $testland$prior$mean
#> [1] 1
#> 
#> $testland$prior$sd
#> [1] 1
#> 
#> 
#> $testland$use_rt
#> [1] TRUE
#> 
#> $testland$rw
#> [1] 0
#> 
#> $testland$use_breakpoints
#> [1] TRUE
#> 
#> $testland$future
#> [1] "latest"
#> 
#> $testland$pop
#> [1] 0
#> 
#> $testland$gp_on
#> [1] "R_t-1"
#> 
#> 
#> $realland
#> $realland$prior
#> $realland$prior$mean
#> [1] 1
#> 
#> $realland$prior$sd
#> [1] 1
#> 
#> 
#> $realland$use_rt
#> [1] TRUE
#> 
#> $realland$rw
#> [1] 0
#> 
#> $realland$use_breakpoints
#> [1] TRUE
#> 
#> $realland$future
#> [1] "latest"
#> 
#> $realland$pop
#> [1] 0
#> 
#> $realland$gp_on
#> [1] "R_t-1"
#> 
#> 

# add a weekly random walk in realland
opts_list(rt_opts(), cases, realland = rt_opts(rw = 7))
#> $testland
#> $testland$prior
#> $testland$prior$mean
#> [1] 1
#> 
#> $testland$prior$sd
#> [1] 1
#> 
#> 
#> $testland$use_rt
#> [1] TRUE
#> 
#> $testland$rw
#> [1] 0
#> 
#> $testland$use_breakpoints
#> [1] TRUE
#> 
#> $testland$future
#> [1] "latest"
#> 
#> $testland$pop
#> [1] 0
#> 
#> $testland$gp_on
#> [1] "R_t-1"
#> 
#> 
#> $realland
#> $realland$prior
#> $realland$prior$mean
#> [1] 1
#> 
#> $realland$prior$sd
#> [1] 1
#> 
#> 
#> $realland$use_rt
#> [1] TRUE
#> 
#> $realland$rw
#> [1] 7
#> 
#> $realland$use_breakpoints
#> [1] TRUE
#> 
#> $realland$future
#> [1] "latest"
#> 
#> $realland$pop
#> [1] 0
#> 
#> $realland$gp_on
#> [1] "R_t-1"
#> 
#> 

# add a weekly random walk externally
rt <- opts_list(rt_opts(), cases)
rt$realland$rw <- 7
rt
#> $testland
#> $testland$prior
#> $testland$prior$mean
#> [1] 1
#> 
#> $testland$prior$sd
#> [1] 1
#> 
#> 
#> $testland$use_rt
#> [1] TRUE
#> 
#> $testland$rw
#> [1] 0
#> 
#> $testland$use_breakpoints
#> [1] TRUE
#> 
#> $testland$future
#> [1] "latest"
#> 
#> $testland$pop
#> [1] 0
#> 
#> $testland$gp_on
#> [1] "R_t-1"
#> 
#> 
#> $realland
#> $realland$prior
#> $realland$prior$mean
#> [1] 1
#> 
#> $realland$prior$sd
#> [1] 1
#> 
#> 
#> $realland$use_rt
#> [1] TRUE
#> 
#> $realland$rw
#> [1] 7
#> 
#> $realland$use_breakpoints
#> [1] TRUE
#> 
#> $realland$future
#> [1] "latest"
#> 
#> $realland$pop
#> [1] 0
#> 
#> $realland$gp_on
#> [1] "R_t-1"
#> 
#>