Parameters for the "carehomes" model.
carehomes_parameters( start_date, region, beta_date = NULL, beta_value = NULL, severity = NULL, p_death_carehome = 0.7, p_specificity = 0.9, progression = NULL, eps = 0.1, C_1 = 4e-06, C_2 = 5e-05, pillar2_specificity = 0.99, pillar2_sensitivity = 0.99, prop_noncovid_sympt = 0.01, exp_noise = 1e+06 )
| start_date | Thee start date, as a |
|---|---|
| region | 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 thee 7 NHS regions (e.g., "midlands"). These names are case insensitive. |
| beta_date | A vector of dates for changes in beta (the
contact rate parameter), or |
| beta_value | A vector of values for beta (the contact rate
parameter). If not given, and if |
| severity | Severity data, via Bob Verity's |
| p_death_carehome | Probability of death within carehomes (conditional on having an "inflenza-like-illness") |
| p_specificity | Specificity of the serology test |
| progression | Progression data |
| eps | Change in contact rate for carehome residents |
| C_1 | Contact rate between carehome workers and either residents or workers |
| C_2 | Contact rate between carehome residents |
| pillar2_specificity | Specificity of the Pillar 2 test |
| pillar2_sensitivity | Sensitivity of the Pillar 2 test |
| prop_noncovid_sympt | Proportion of population who do not have covid but have covid-like symptoms |
| exp_noise | 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 |
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.
#> $hosp_transmission #> [1] 0.1 #> #> $ICU_transmission #> [1] 0.05 #> #> $comm_D_transmission #> [1] 0.05 #> #> $dt #> [1] 0.25 #> #> $initial_step #> [1] 128 #> #> $N_age #> [1] 19 #> #> $beta_step #> [1] 0.08 #> #> $population #> [1] 3857263 4149852 3953866 3656968 4153080 4514249 4497132 4395667 4019539 #> [10] 4402122 4661015 4405908 3755185 3368199 3318867 2325296 3362599 #> #> $carehome_beds #> [1] 537521 #> #> $carehome_residents #> [1] 398841 #> #> $carehome_workers #> [1] 398841 #> #> $m #> [0,4) [5,9) [10,14) [15,19) [20,24) #> [0,4) 4.966707e-07 1.980202e-07 1.146078e-07 7.547886e-08 1.138137e-07 #> [5,9) 1.980202e-07 1.599396e-06 2.972491e-07 1.352721e-07 1.101069e-07 #> [10,14) 1.146078e-07 2.972491e-07 1.733225e-06 3.334453e-07 6.026086e-08 #> [15,19) 7.547886e-08 1.352721e-07 3.334453e-07 1.836025e-06 3.278825e-07 #> [20,24) 1.138137e-07 1.101069e-07 6.026086e-08 3.278825e-07 6.244090e-07 #> [25,29) 1.819153e-07 1.626085e-07 8.744544e-08 1.819264e-07 3.222430e-07 #> [30,34) 1.940880e-07 2.332740e-07 1.297928e-07 1.120304e-07 1.882853e-07 #> [35,39) 2.235471e-07 2.784775e-07 2.396054e-07 1.996738e-07 1.624326e-07 #> [40,44) 9.944949e-08 2.332186e-07 2.679243e-07 2.341623e-07 1.838660e-07 #> [45,49) 6.175863e-08 8.096090e-08 1.519569e-07 2.467186e-07 2.148012e-07 #> [50,54) 8.214138e-08 7.752704e-08 8.335625e-08 1.392241e-07 1.530723e-07 #> [55,59) 6.104769e-08 5.013907e-08 8.513107e-08 7.833919e-08 1.178128e-07 #> [60,64) 6.057159e-08 9.418311e-08 5.929099e-08 5.863294e-08 8.866898e-08 #> [65,69) 4.767006e-08 7.402091e-08 6.898452e-08 9.552015e-08 7.226646e-08 #> [70,74) 2.100618e-08 2.893729e-08 5.503570e-08 9.539437e-08 5.468746e-08 #> [75,79) 2.100618e-08 2.893729e-08 5.503570e-08 9.539437e-08 5.468746e-08 #> [80,100) 2.100618e-08 2.893729e-08 5.503570e-08 9.539437e-08 5.468746e-08 #> CHW 1.220055e-07 1.511359e-07 1.374799e-07 1.571202e-07 1.808205e-07 #> CHR 2.100618e-09 2.893729e-09 5.503570e-09 9.539437e-09 5.468746e-09 #> [25,29) [30,34) [35,39) [40,44) [45,49) #> [0,4) 1.819153e-07 1.940880e-07 2.235471e-07 9.944949e-08 6.175863e-08 #> [5,9) 1.626085e-07 2.332740e-07 2.784775e-07 2.332186e-07 8.096090e-08 #> [10,14) 8.744544e-08 1.297928e-07 2.396054e-07 2.679243e-07 1.519569e-07 #> [15,19) 1.819264e-07 1.120304e-07 1.996738e-07 2.341623e-07 2.467186e-07 #> [20,24) 3.222430e-07 1.882853e-07 1.624326e-07 1.838660e-07 2.148012e-07 #> [25,29) 4.054957e-07 2.389792e-07 1.870791e-07 1.918110e-07 2.005309e-07 #> [30,34) 2.389792e-07 3.706066e-07 2.728896e-07 2.145623e-07 1.654374e-07 #> [35,39) 1.870791e-07 2.728896e-07 3.412451e-07 3.032663e-07 2.149544e-07 #> [40,44) 1.918110e-07 2.145623e-07 3.032663e-07 3.370632e-07 3.085384e-07 #> [45,49) 2.005309e-07 1.654374e-07 2.149544e-07 3.085384e-07 4.254147e-07 #> [50,54) 1.882440e-07 1.671228e-07 1.606864e-07 1.873283e-07 1.702589e-07 #> [55,59) 1.560297e-07 1.454919e-07 1.379231e-07 1.451614e-07 1.482183e-07 #> [60,64) 1.189756e-07 1.374885e-07 1.668294e-07 1.791329e-07 1.414642e-07 #> [65,69) 1.147535e-07 8.979643e-08 1.540697e-07 1.348771e-07 8.620090e-08 #> [70,74) 4.760237e-08 3.516410e-08 4.653274e-08 1.307023e-07 1.059467e-07 #> [75,79) 4.760237e-08 3.516410e-08 4.653274e-08 1.307023e-07 1.059467e-07 #> [80,100) 4.760237e-08 3.516410e-08 4.653274e-08 1.307023e-07 1.059467e-07 #> CHW 2.133559e-07 2.156373e-07 2.227971e-07 2.326728e-07 2.217800e-07 #> CHR 4.760237e-09 3.516410e-09 4.653274e-09 1.307023e-08 1.059467e-08 #> [50,54) [55,59) [60,64) [65,69) [70,74) #> [0,4) 8.214138e-08 6.104769e-08 6.057159e-08 4.767006e-08 2.100618e-08 #> [5,9) 7.752704e-08 5.013907e-08 9.418311e-08 7.402091e-08 2.893729e-08 #> [10,14) 8.335625e-08 8.513107e-08 5.929099e-08 6.898452e-08 5.503570e-08 #> [15,19) 1.392241e-07 7.833919e-08 5.863294e-08 9.552015e-08 9.539437e-08 #> [20,24) 1.530723e-07 1.178128e-07 8.866898e-08 7.226646e-08 5.468746e-08 #> [25,29) 1.882440e-07 1.560297e-07 1.189756e-07 1.147535e-07 4.760237e-08 #> [30,34) 1.671228e-07 1.454919e-07 1.374885e-07 8.979643e-08 3.516410e-08 #> [35,39) 1.606864e-07 1.379231e-07 1.668294e-07 1.540697e-07 4.653274e-08 #> [40,44) 1.873283e-07 1.451614e-07 1.791329e-07 1.348771e-07 1.307023e-07 #> [45,49) 1.702589e-07 1.482183e-07 1.414642e-07 8.620090e-08 1.059467e-07 #> [50,54) 1.592838e-07 2.060829e-07 1.178586e-07 9.108480e-08 9.232320e-08 #> [55,59) 2.060829e-07 2.647960e-07 1.998500e-07 1.379069e-07 8.128181e-08 #> [60,64) 1.178586e-07 1.998500e-07 1.734975e-07 1.674043e-07 1.041277e-07 #> [65,69) 9.108480e-08 1.379069e-07 1.674043e-07 2.089258e-07 1.332611e-07 #> [70,74) 9.232320e-08 8.128181e-08 1.041277e-07 1.332611e-07 1.493131e-07 #> [75,79) 9.232320e-08 8.128181e-08 1.041277e-07 1.332611e-07 1.493131e-07 #> [80,100) 9.232320e-08 8.128181e-08 1.041277e-07 1.332611e-07 1.493131e-07 #> CHW 1.703607e-07 1.754236e-07 1.533259e-07 1.206750e-07 7.932803e-08 #> CHR 9.232320e-09 8.128181e-09 1.041277e-08 1.332611e-08 1.493131e-08 #> [75,79) [80,100) CHW CHR #> [0,4) 2.100618e-08 2.100618e-08 1.220055e-07 2.100618e-09 #> [5,9) 2.893729e-08 2.893729e-08 1.511359e-07 2.893729e-09 #> [10,14) 5.503570e-08 5.503570e-08 1.374799e-07 5.503570e-09 #> [15,19) 9.539437e-08 9.539437e-08 1.571202e-07 9.539437e-09 #> [20,24) 5.468746e-08 5.468746e-08 1.808205e-07 5.468746e-09 #> [25,29) 4.760237e-08 4.760237e-08 2.133559e-07 4.760237e-09 #> [30,34) 3.516410e-08 3.516410e-08 2.156373e-07 3.516410e-09 #> [35,39) 4.653274e-08 4.653274e-08 2.227971e-07 4.653274e-09 #> [40,44) 1.307023e-07 1.307023e-07 2.326728e-07 1.307023e-08 #> [45,49) 1.059467e-07 1.059467e-07 2.217800e-07 1.059467e-08 #> [50,54) 9.232320e-08 9.232320e-08 1.703607e-07 9.232320e-09 #> [55,59) 8.128181e-08 8.128181e-08 1.754236e-07 8.128181e-09 #> [60,64) 1.041277e-07 1.041277e-07 1.533259e-07 1.041277e-08 #> [65,69) 1.332611e-07 1.332611e-07 1.206750e-07 1.332611e-08 #> [70,74) 1.493131e-07 1.493131e-07 7.932803e-08 1.493131e-08 #> [75,79) 1.493131e-07 1.493131e-07 7.932803e-08 1.493131e-08 #> [80,100) 1.493131e-07 1.493131e-07 7.932803e-08 1.493131e-08 #> CHW 7.932803e-08 7.932803e-08 4.000000e-06 4.000000e-06 #> CHR 1.493131e-08 1.493131e-08 4.000000e-06 5.000000e-05 #> #> $N_tot #> [1] 3857263 4149852 3953866 3656968 4153080 4462289 4445369 4345072 3973273 #> [10] 4351452 4607365 4355195 3711962 3348257 3298925 2265470 3063468 398841 #> [19] 398841 #> #> $N_tot_15_64 #> [1] 42062025 #> #> $p_specificity #> [1] 0.9 #> #> $pillar2_specificity #> [1] 0.99 #> #> $pillar2_sensitivity #> [1] 0.99 #> #> $prop_noncovid_sympt #> [1] 0.01 #> #> $observation #> $observation$phi_ICU #> [1] 1 #> #> $observation$k_ICU #> [1] 2 #> #> $observation$phi_general #> [1] 1 #> #> $observation$k_general #> [1] 2 #> #> $observation$phi_hosp #> [1] 1 #> #> $observation$k_hosp #> [1] 2 #> #> $observation$phi_death_hosp #> [1] 1 #> #> $observation$k_death_hosp #> [1] 2 #> #> $observation$phi_death_comm #> [1] 1 #> #> $observation$k_death_comm #> [1] 2 #> #> $observation$k_death #> [1] 2 #> #> $observation$phi_admitted #> [1] 1 #> #> $observation$k_admitted #> [1] 2 #> #> $observation$phi_new #> [1] 1 #> #> $observation$k_new #> [1] 2 #> #> $observation$phi_new_admitted #> [1] 1 #> #> $observation$k_new_admitted #> [1] 2 #> #> $observation$phi_pillar2_cases #> [1] 1 #> #> $observation$k_pillar2_cases #> [1] 2 #> #> $observation$rho_pillar2_tests #> [1] 0.1 #> #> $observation$exp_noise #> [1] 1e+06 #> #> #> $p_admit_conf #> [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 0.2 0.2 #> #> $p_asympt #> [1] 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 #> [16] 0.34 0.34 0.34 0.34 #> #> $p_death_comm #> [1] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.7 #> #> $p_death_hosp_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 0.2603941 0.4820000 #> #> $p_death_ICU #> [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 0.5234896 0.5234896 #> #> $p_hosp_ILI #> [1] 0.001772051 0.001510059 0.002681536 0.005482996 0.010801921 0.020789645 #> [7] 0.030033884 0.043195770 0.050353126 0.067162222 0.084808192 0.106382665 #> [13] 0.131365666 0.151247633 0.169503156 0.204930342 0.200036782 0.065630479 #> [19] 0.200036782 #> #> $p_ICU_hosp #> [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 0.22030943 #> [19] 0.01673267 #> #> $p_seroconversion #> [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 0.8212394 0.8212394 #> #> $p_sympt_ILI #> [1] 0.2356449 0.2356449 0.2450545 0.2450545 0.2777233 0.2777233 0.3033047 #> [8] 0.3033047 0.3225450 0.3225450 0.3819877 0.3819877 0.4339815 0.4339815 #> [15] 0.4836359 0.4836359 0.5049071 0.3393986 0.5049071 #> #> $psi_hosp_ILI #> [1] 0.008647088 0.007368644 0.013085111 0.026755414 0.052710207 0.101447374 #> [7] 0.146556549 0.210782695 0.245708497 0.327731957 0.413839119 0.519116224 #> [13] 0.641025944 0.738044114 0.827125720 1.000000000 0.976120865 0.320257500 #> [19] 0.976120865 #> #> $p_hosp_ILI_step #> [1] 0.2049303 #> #> $psi_ICU_hosp #> [1] 0.16360021 0.16360021 0.16360021 0.16360021 0.16360021 0.16360021 #> [7] 0.16360021 0.17334653 0.19461564 0.24301727 0.33751521 0.48675845 #> [13] 0.72894974 1.00000000 0.25133371 0.07512036 0.02311000 0.30427599 #> [19] 0.02311000 #> #> $p_ICU_hosp_step #> [1] 0.7240447 #> #> $psi_death_ICU #> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> #> $p_death_ICU_step #> [1] 0.5234896 #> #> $psi_death_hosp_D #> [1] 0.2611893 0.2543846 0.2814790 0.3167383 0.3616246 0.4028795 0.4343604 #> [8] 0.4656277 0.4917293 0.5349130 0.6034743 0.6654854 0.7522070 0.8111317 #> [15] 0.8737583 0.9285184 1.0000000 0.5402367 1.0000000 #> #> $p_death_hosp_D_step #> [1] 0.482 #> #> $psi_death_comm #> [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 #> #> $p_death_comm_step #> [1] 0.7 #> #> $psi_admit_conf #> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> #> $p_admit_conf_step #> [1] 0.2 #> #> $s_E #> [1] 2 #> #> $s_asympt #> [1] 1 #> #> $s_mild #> [1] 1 #> #> $s_ILI #> [1] 1 #> #> $s_comm_D #> [1] 2 #> #> $s_hosp_D #> [1] 2 #> #> $s_hosp_R #> [1] 2 #> #> $s_ICU_D #> [1] 2 #> #> $s_ICU_R #> [1] 2 #> #> $s_triage #> [1] 2 #> #> $s_stepdown #> [1] 2 #> #> $s_PCR_pos #> [1] 2 #> #> $gamma_E #> [1] 0.4357298 #> #> $gamma_asympt #> [1] 0.4784689 #> #> $gamma_mild #> [1] 0.4784689 #> #> $gamma_ILI #> [1] 0.25 #> #> $gamma_comm_D #> [1] 0.4 #> #> $gamma_hosp_D #> [1] 0.4 #> #> $gamma_hosp_R #> [1] 0.2 #> #> $gamma_ICU_D #> [1] 0.4 #> #> $gamma_ICU_R #> [1] 0.2 #> #> $gamma_triage #> [1] 2 #> #> $gamma_stepdown #> [1] 0.4 #> #> $gamma_R_pre_1 #> [1] 0.2 #> #> $gamma_R_pre_2 #> [1] 0.1 #> #> $gamma_test #> [1] 0.3 #> #> $gamma_PCR_pos #> [1] 0.2 #>