Parameters for the "basic" model.
basic_parameters(
start_date,
region,
beta_date = NULL,
beta_value = NULL,
beta_type = "piecewise-linear",
severity = NULL,
exp_noise = 1e+06,
initial_seed_size = 30,
initial_seed_pattern = 1
)The start date, as a sircovid_date() (i.e.,
the number of days into 2020)
The region to run the model for. This will bee used to get population data, which is currently fixed within the package and is limited to "uk", the four constituent nations ("england", "wales", "scotland", "northern_ireland") and the 7 NHS regions (e.g., "midlands"). These names are case insensitive.
A vector of dates (each as a sircovid_date())
for changes in beta (the contact rate parameter), or NULL if
a single value is used for all times (see
sircovid_parameters_piecewise_linear() or
sircovid_parameters_piecewise_constant(), where
this is passed as date). If beta_type = "piecewise-constant",
then the first date must be 0.
A vector of values for beta (the contact rate
parameter). If not given, and if beta_date is NULL then a
value of 0.1 will be used through the whole simulation,
otherwise if beta_date is NULL this must be a scalar. If
beta_date is given then beta_date and beta_value must have
the same length (see sircovid_parameters_piecewise_linear() or
sircovid_parameters_piecewise_constant(), where this is passed
as value).
The type of form used for beta (the contact rate
parameter), which currently can be "piecewise-linear" or
"piecewise-constant"
Severity data, via Bob Verity's markovid
package. This needs to be NULL (use the default bundled data
version in the package), a data.frame object (for raw severity
data) or a list (for data that has already been processed by
sircovid for use). New severity data comes from Bob Verity
via the markovid package, and needs to be carefully calibrated
with the progression parameters.
Rate of exponential noise used in the compare
function - typically set to a large value so that noise is small
but non-zero. If set to Inf then there is no noise in the
observation process (not realistic but useful for testing).
Initial size of seeding from the S to E
compartment; all seeding is in the 15-19 year old group from
start_date according to initial_seed_pattern. The default is 30.
A vector of seeding weights for the initial
seeding. The length represents the number of steps to seed over from the
start_date, and the initial_seed_size is split over these steps
according to those weights. If start_date is not a multiple of the step
size (and thus falls between two steps) then we weight over an additional
step and adjust the weights according to how far the start_date is from
the previous full step.
A list of inputs to the model, many of which are fixed and
represent data. These correspond largely to user() calls
within the odin code, though some are also used in processing
just before the model is run.
basic_parameters(sircovid_date("2020-02-01"), "uk")
#> $hosp_transmission
#> [1] 0
#>
#> $ICU_transmission
#> [1] 0
#>
#> $G_D_transmission
#> [1] 0
#>
#> $dt
#> [1] 0.25
#>
#> $steps_per_day
#> [1] 4
#>
#> $n_age_groups
#> [1] 17
#>
#> $beta_step
#> [1] 0.1
#>
#> $population
#> [1] 3782330 4147413 4045114 3683680 4133158 4476630 4521975 4404100 4091543
#> [10] 4303967 4616017 4510851 3855818 3355381 3363906 2403759 3385592
#>
#> $seed_step_start
#> [1] 128
#>
#> $seed_value
#> [1] 30
#>
#> $m
#> [0,4) [5,9) [10,14) [15,19) [20,24)
#> [0,4) 5.065104e-07 1.997490e-07 1.142840e-07 7.576677e-08 1.152515e-07
#> [5,9) 1.997490e-07 1.600336e-06 2.935787e-07 1.349839e-07 1.103265e-07
#> [10,14) 1.142840e-07 2.935787e-07 1.694128e-06 3.280779e-07 5.961244e-08
#> [15,19) 7.576677e-08 1.349839e-07 3.280779e-07 1.822711e-06 3.268613e-07
#> [20,24) 1.152515e-07 1.103265e-07 5.961244e-08 3.268613e-07 6.274186e-07
#> [25,29) 1.845218e-07 1.632727e-07 8.698579e-08 1.818952e-07 3.243075e-07
#> [30,34) 1.952085e-07 2.326886e-07 1.280368e-07 1.113148e-07 1.881822e-07
#> [35,39) 2.254526e-07 2.783622e-07 2.371701e-07 1.988849e-07 1.626312e-07
#> [40,44) 9.887255e-08 2.310936e-07 2.625822e-07 2.312508e-07 1.827198e-07
#> [45,49) 6.308239e-08 8.236923e-08 1.514590e-07 2.475631e-07 2.178102e-07
#> [50,54) 8.341645e-08 7.794834e-08 8.286894e-08 1.389614e-07 1.540431e-07
#> [55,59) 6.076487e-08 4.961125e-08 8.319027e-08 7.716537e-08 1.171382e-07
#> [60,64) 6.016292e-08 9.333274e-08 5.786570e-08 5.761025e-08 8.832882e-08
#> [65,69) 4.838958e-08 7.411618e-08 6.788907e-08 9.515620e-08 7.258711e-08
#> [70,74) 2.115025e-08 2.881885e-08 5.386913e-08 9.465172e-08 5.467673e-08
#> [75,79) 2.115025e-08 2.881885e-08 5.386913e-08 9.465172e-08 5.467673e-08
#> [80,100) 2.115025e-08 2.881885e-08 5.386913e-08 9.465172e-08 5.467673e-08
#> [25,29) [30,34) [35,39) [40,44) [45,49)
#> [0,4) 1.845218e-07 1.952085e-07 2.254526e-07 9.887255e-08 6.308239e-08
#> [5,9) 1.632727e-07 2.326886e-07 2.783622e-07 2.310936e-07 8.236923e-08
#> [10,14) 8.698579e-08 1.280368e-07 2.371701e-07 2.625822e-07 1.514590e-07
#> [15,19) 1.818952e-07 1.113148e-07 1.988849e-07 2.312508e-07 2.475631e-07
#> [20,24) 3.243075e-07 1.881822e-07 1.626312e-07 1.827198e-07 2.178102e-07
#> [25,29) 4.089032e-07 2.391542e-07 1.875372e-07 1.905722e-07 2.037410e-07
#> [30,34) 2.391542e-07 3.685705e-07 2.720147e-07 2.121539e-07 1.663500e-07
#> [35,39) 1.875372e-07 2.720147e-07 3.405917e-07 3.002888e-07 2.167891e-07
#> [40,44) 1.905722e-07 2.121539e-07 3.002888e-07 3.311315e-07 3.091782e-07
#> [45,49) 2.037410e-07 1.663500e-07 2.167891e-07 3.091782e-07 4.351166e-07
#> [50,54) 1.899482e-07 1.671856e-07 1.611473e-07 1.861135e-07 1.728174e-07
#> [55,59) 1.554527e-07 1.433145e-07 1.363783e-07 1.422542e-07 1.489368e-07
#> [60,64) 1.184181e-07 1.356357e-07 1.652679e-07 1.754511e-07 1.411386e-07
#> [65,69) 1.155679e-07 8.948746e-08 1.540300e-07 1.332215e-07 8.780807e-08
#> [70,74) 4.777273e-08 3.488339e-08 4.611959e-08 1.284464e-07 1.068351e-07
#> [75,79) 4.777273e-08 3.488339e-08 4.611959e-08 1.284464e-07 1.068351e-07
#> [80,100) 4.777273e-08 3.488339e-08 4.611959e-08 1.284464e-07 1.068351e-07
#> [50,54) [55,59) [60,64) [65,69) [70,74)
#> [0,4) 8.341645e-08 6.076487e-08 6.016292e-08 4.838958e-08 2.115025e-08
#> [5,9) 7.794834e-08 4.961125e-08 9.333274e-08 7.411618e-08 2.881885e-08
#> [10,14) 8.286894e-08 8.319027e-08 5.786570e-08 6.788907e-08 5.386913e-08
#> [15,19) 1.389614e-07 7.716537e-08 5.761025e-08 9.515620e-08 9.465172e-08
#> [20,24) 1.540431e-07 1.171382e-07 8.832882e-08 7.258711e-08 5.467673e-08
#> [25,29) 1.899482e-07 1.554527e-07 1.184181e-07 1.155679e-07 4.777273e-08
#> [30,34) 1.671856e-07 1.433145e-07 1.356357e-07 8.948746e-08 3.488339e-08
#> [35,39) 1.611473e-07 1.363783e-07 1.652679e-07 1.540300e-07 4.611959e-08
#> [40,44) 1.861135e-07 1.422542e-07 1.754511e-07 1.332215e-07 1.284464e-07
#> [45,49) 1.728174e-07 1.489368e-07 1.411386e-07 8.780807e-08 1.068351e-07
#> [50,54) 1.608365e-07 2.050266e-07 1.170549e-07 9.178605e-08 9.246504e-08
#> [55,59) 2.050266e-07 2.586356e-07 1.949070e-07 1.358154e-07 7.969682e-08
#> [60,64) 1.170549e-07 1.949070e-07 1.689694e-07 1.646502e-07 1.016733e-07
#> [65,69) 9.178605e-08 1.358154e-07 1.646502e-07 2.097239e-07 1.329549e-07
#> [70,74) 9.246504e-08 7.969682e-08 1.016733e-07 1.329549e-07 1.469234e-07
#> [75,79) 9.246504e-08 7.969682e-08 1.016733e-07 1.329549e-07 1.469234e-07
#> [80,100) 9.246504e-08 7.969682e-08 1.016733e-07 1.329549e-07 1.469234e-07
#> [75,79) [80,100)
#> [0,4) 2.115025e-08 2.115025e-08
#> [5,9) 2.881885e-08 2.881885e-08
#> [10,14) 5.386913e-08 5.386913e-08
#> [15,19) 9.465172e-08 9.465172e-08
#> [20,24) 5.467673e-08 5.467673e-08
#> [25,29) 4.777273e-08 4.777273e-08
#> [30,34) 3.488339e-08 3.488339e-08
#> [35,39) 4.611959e-08 4.611959e-08
#> [40,44) 1.284464e-07 1.284464e-07
#> [45,49) 1.068351e-07 1.068351e-07
#> [50,54) 9.246504e-08 9.246504e-08
#> [55,59) 7.969682e-08 7.969682e-08
#> [60,64) 1.016733e-07 1.016733e-07
#> [65,69) 1.329549e-07 1.329549e-07
#> [70,74) 1.469234e-07 1.469234e-07
#> [75,79) 1.469234e-07 1.469234e-07
#> [80,100) 1.469234e-07 1.469234e-07
#>
#> $p_star
#> [1] 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
#>
#> $p_C
#> [1] 0.1809 0.1809 0.1809 0.1809 0.2241 0.2241 0.2241 0.2241 0.3054 0.3054
#> [11] 0.3054 0.3054 0.3546 0.3546 0.3546 0.3546 0.6456
#>
#> $p_G_D
#> [1] 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
#> [16] 0.05 0.05
#>
#> $p_H_D
#> [1] 0.1258933 0.1226134 0.1356729 0.1526679 0.1743031 0.1941879 0.2093617
#> [8] 0.2244326 0.2370135 0.2578281 0.2908746 0.3207640 0.3625638 0.3909655
#> [15] 0.4211515 0.4475459 0.4820000
#>
#> $p_ICU_D
#> [1] 0.5234896 0.5234896 0.5234896 0.5234896 0.5234896 0.5234896 0.5234896
#> [8] 0.5234896 0.5234896 0.5234896 0.5234896 0.5234896 0.5234896 0.5234896
#> [15] 0.5234896 0.5234896 0.5234896
#>
#> $p_W_D
#> [1] 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05
#> [16] 0.05 0.05
#>
#> $p_ICU
#> [1] 0.11845387 0.11845387 0.11845387 0.11845387 0.11845387 0.11845387
#> [7] 0.11845387 0.12551064 0.14091042 0.17595537 0.24437611 0.35243489
#> [13] 0.52779221 0.72404472 0.18197685 0.05439050 0.01673267
#>
#> $p_sero_pos_1
#> [1] 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394
#> [8] 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394
#> [15] 0.8212394 0.8212394 0.8212394
#>
#> $p_sero_pos_2
#> [1] 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394
#> [8] 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394 0.8212394
#> [15] 0.8212394 0.8212394 0.8212394
#>
#> $p_H
#> [1] 0.000632689 0.000539148 0.000995640 0.002035807 0.004545371 0.008748134
#> [7] 0.013802147 0.019850725 0.024607803 0.032822485 0.049084367 0.061571007
#> [13] 0.086379194 0.099452536 0.124208801 0.150169192 0.153030303
#>
#> $p_R
#> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>
#> $p_recov_ICU
#> [1] 0.4765104 0.4765104 0.4765104 0.4765104 0.4765104 0.4765104 0.4765104
#> [8] 0.4765104 0.4765104 0.4765104 0.4765104 0.4765104 0.4765104 0.4765104
#> [15] 0.4765104 0.4765104 0.4765104
#>
#> $p_recov_hosp
#> [1] 0.7705654 0.7734568 0.7619442 0.7469624 0.7278899 0.7103605 0.6969841
#> [8] 0.6782255 0.6554737 0.6115828 0.5358321 0.4398496 0.3010024 0.1680663
#> [15] 0.4735115 0.5224059 0.5093325
#>
#> $p_death_hosp
#> [1] 0.1109807 0.1080894 0.1196019 0.1345838 0.1536562 0.1711856 0.1845620
#> [8] 0.1962639 0.2036158 0.2124618 0.2197918 0.2077156 0.1712054 0.1078890
#> [15] 0.3445117 0.4232036 0.4739349
#>
#> $p_recov_sympt
#> [1] 0.9993673 0.9994609 0.9990044 0.9979642 0.9954546 0.9912519 0.9861979
#> [8] 0.9801493 0.9753922 0.9671775 0.9509156 0.9384290 0.9136208 0.9005475
#> [15] 0.8757912 0.8498308 0.8469697
#>
#> $k_E
#> [1] 2
#>
#> $k_A
#> [1] 1
#>
#> $k_C
#> [1] 1
#>
#> $k_hosp
#> [1] 2
#>
#> $k_ICU
#> [1] 2
#>
#> $k_rec
#> [1] 2
#>
#> $gamma_E
#> [1] 0.4357298
#>
#> $gamma_A
#> [1] 0.4784689
#>
#> $gamma_C
#> [1] 0.25
#>
#> $gamma_hosp
#> [1] 2
#>
#> $gamma_ICU
#> [1] 0.4
#>
#> $gamma_rec
#> [1] 0.4
#>
#> $phi_ICU
#> [1] 0.95
#>
#> $kappa_ICU
#> [1] 2
#>
#> $phi_death
#> [1] 0.9087341
#>
#> $kappa_death
#> [1] 2
#>
#> $exp_noise
#> [1] 1e+06
#>