Index of "interesting" elements for the lancelot model. This function conforms to the mcstate interface.
lancelot_index(
info,
rt = TRUE,
cum_admit = TRUE,
diagnoses_admitted = TRUE,
cum_infections_disag = TRUE,
cum_n_vaccinated = TRUE,
D_all = TRUE,
D_hosp = TRUE,
infections_inc_per_strain = TRUE,
severity = FALSE,
protected = FALSE
)The result of running the $info() method on an
initialised basic model
Logical, whether to output trajectories required for calculating Rt (default = TRUE)
Logical, whether to output cumulative admissions by age (default = TRUE)
Logical, whether to output cumulative combined confirmed admissions and inpatient diagnoses by age and vaccine class (default = TRUE)
Logical, whether to output cumulative infections by age and vaccine class (default = TRUE)
Logical, whether to output cumulative number vaccinated by age and vaccine class (default = TRUE)
Logical, whether to output all deaths by age and vaccine class (default = TRUE)
Logical, whether to output hospital deaths by age (default = TRUE)
Logical, whether to output infections incidence per strain (default = TRUE)
Logical, whether to output severity calculations (default = FALSE)
Logical, whether to output protected levels
A list with element run, indicating the locations of (in
order) (1) ICU, (2) general, (3) deaths in community, (4) deaths
in hospital, (5) total deaths, (6) cumulative confirmed
admissions,(7) cumulative confirmed new admissions, (8)
probability of a positive sero test, (9) probability of a positive
pillar 2 test, and with element state containing the same values
followed by 17 S compartments (one per age group, then one for
carehome workers and carehome residents respectively) and 17
"cumulative admission" compartments.
p <- lancelot_parameters(sircovid_date("2020-02-07"), "england")
mod <- lancelot$new(p, 0, 10)
lancelot_index(mod$info())
#> $run
#> time icu
#> 1 22
#> general deaths_carehomes_inc
#> 23 45
#> deaths_comm_inc deaths_comm_0_49_inc
#> 35 36
#> deaths_comm_50_54_inc deaths_comm_55_59_inc
#> 37 38
#> deaths_comm_60_64_inc deaths_comm_65_69_inc
#> 39 40
#> deaths_comm_70_74_inc deaths_comm_75_79_inc
#> 41 42
#> deaths_comm_80_plus_inc deaths_hosp_inc
#> 43 48
#> deaths_hosp_0_49_inc deaths_hosp_50_54_inc
#> 49 50
#> deaths_hosp_55_59_inc deaths_hosp_60_64_inc
#> 51 52
#> deaths_hosp_65_69_inc deaths_hosp_70_74_inc
#> 53 54
#> deaths_hosp_75_79_inc deaths_hosp_80_plus_inc
#> 55 56
#> admitted_inc all_admission_0_9_inc
#> 2 4
#> all_admission_10_19_inc all_admission_20_29_inc
#> 5 6
#> all_admission_30_39_inc all_admission_40_49_inc
#> 7 8
#> all_admission_50_59_inc all_admission_60_69_inc
#> 9 10
#> all_admission_70_79_inc all_admission_80_plus_inc
#> 11 12
#> diagnoses_inc sero_pos_1
#> 3 57
#> sero_pos_2 sympt_cases_inc
#> 58 69
#> sympt_cases_non_variant_inc sympt_cases_over25_inc
#> 70 71
#> sympt_cases_under15_inc sympt_cases_15_24_inc
#> 73 74
#> sympt_cases_25_49_inc sympt_cases_50_64_inc
#> 75 76
#> sympt_cases_65_79_inc sympt_cases_80_plus_inc
#> 77 78
#> sympt_cases_non_variant_over25_inc ons_pos
#> 72 79
#> react_pos react_5_24_pos
#> 80 81
#> react_25_34_pos react_35_44_pos
#> 82 83
#> react_45_54_pos react_55_64_pos
#> 84 85
#> react_65_plus_pos
#> 86
#>
#> $state
#> icu general
#> 22 23
#> deaths_carehomes_inc deaths_comm_inc
#> 45 35
#> deaths_comm_0_49_inc deaths_comm_50_54_inc
#> 36 37
#> deaths_comm_55_59_inc deaths_comm_60_64_inc
#> 38 39
#> deaths_comm_65_69_inc deaths_comm_70_74_inc
#> 40 41
#> deaths_comm_75_79_inc deaths_comm_80_plus_inc
#> 42 43
#> deaths_hosp_inc deaths_hosp_0_49_inc
#> 48 49
#> deaths_hosp_50_54_inc deaths_hosp_55_59_inc
#> 50 51
#> deaths_hosp_60_64_inc deaths_hosp_65_69_inc
#> 52 53
#> deaths_hosp_70_74_inc deaths_hosp_75_79_inc
#> 54 55
#> deaths_hosp_80_plus_inc admitted_inc
#> 56 2
#> all_admission_0_9_inc all_admission_10_19_inc
#> 4 5
#> all_admission_20_29_inc all_admission_30_39_inc
#> 6 7
#> all_admission_40_49_inc all_admission_50_59_inc
#> 8 9
#> all_admission_60_69_inc all_admission_70_79_inc
#> 10 11
#> all_admission_80_plus_inc diagnoses_inc
#> 12 3
#> sero_pos_1 sero_pos_2
#> 57 58
#> sympt_cases_inc sympt_cases_non_variant_inc
#> 69 70
#> sympt_cases_over25_inc sympt_cases_under15_inc
#> 71 73
#> sympt_cases_15_24_inc sympt_cases_25_49_inc
#> 74 75
#> sympt_cases_50_64_inc sympt_cases_65_79_inc
#> 76 77
#> sympt_cases_80_plus_inc sympt_cases_non_variant_over25_inc
#> 78 72
#> ons_pos react_pos
#> 79 80
#> react_5_24_pos react_25_34_pos
#> 81 82
#> react_35_44_pos react_45_54_pos
#> 83 84
#> react_55_64_pos react_65_plus_pos
#> 85 86
#> hosp admitted
#> 24 16
#> diagnoses deaths
#> 17 46
#> deaths_inc infections
#> 47 13
#> infections_inc susceptible
#> 14 87
#> recovered1 effective_susceptible_1
#> 191 190
#> S_0 S_5
#> 540 541
#> S_10 S_15
#> 542 543
#> S_20 S_25
#> 544 545
#> S_30 S_35
#> 546 547
#> S_40 S_45
#> 548 549
#> S_50 S_55
#> 550 551
#> S_60 S_65
#> 552 553
#> S_70 S_75
#> 554 555
#> S_80 S_CHW
#> 556 557
#> S_CHR R_0
#> 558 711
#> R_5 R_10
#> 712 713
#> R_15 R_20
#> 714 715
#> R_25 R_30
#> 716 717
#> R_35 R_40
#> 718 719
#> R_45 R_50
#> 720 721
#> R_55 R_60
#> 722 723
#> R_65 R_70
#> 724 725
#> R_75 R_80
#> 726 727
#> R_CHW R_CHR
#> 728 729
#> prob_strain cum_admit_0
#> 189 151
#> cum_admit_5 cum_admit_10
#> 152 153
#> cum_admit_15 cum_admit_20
#> 154 155
#> cum_admit_25 cum_admit_30
#> 156 157
#> cum_admit_35 cum_admit_40
#> 158 159
#> cum_admit_45 cum_admit_50
#> 160 161
#> cum_admit_55 cum_admit_60
#> 162 163
#> cum_admit_65 cum_admit_70
#> 164 165
#> cum_admit_75 cum_admit_80
#> 166 167
#> cum_admit_CHW cum_admit_CHR
#> 168 169
#> diagnoses_admitted_0 diagnoses_admitted_5
#> 483 484
#> diagnoses_admitted_10 diagnoses_admitted_15
#> 485 486
#> diagnoses_admitted_20 diagnoses_admitted_25
#> 487 488
#> diagnoses_admitted_30 diagnoses_admitted_35
#> 489 490
#> diagnoses_admitted_40 diagnoses_admitted_45
#> 491 492
#> diagnoses_admitted_50 diagnoses_admitted_55
#> 493 494
#> diagnoses_admitted_60 diagnoses_admitted_65
#> 495 496
#> diagnoses_admitted_70 diagnoses_admitted_75
#> 497 498
#> diagnoses_admitted_80 diagnoses_admitted_CHW
#> 499 500
#> diagnoses_admitted_CHR cum_infections_disag_0
#> 501 502
#> cum_infections_disag_5 cum_infections_disag_10
#> 503 504
#> cum_infections_disag_15 cum_infections_disag_20
#> 505 506
#> cum_infections_disag_25 cum_infections_disag_30
#> 507 508
#> cum_infections_disag_35 cum_infections_disag_40
#> 509 510
#> cum_infections_disag_45 cum_infections_disag_50
#> 511 512
#> cum_infections_disag_55 cum_infections_disag_60
#> 513 514
#> cum_infections_disag_65 cum_infections_disag_70
#> 515 516
#> cum_infections_disag_75 cum_infections_disag_80
#> 517 518
#> cum_infections_disag_CHW cum_infections_disag_CHR
#> 519 520
#> cum_n_vaccinated_0 cum_n_vaccinated_5
#> 350 351
#> cum_n_vaccinated_10 cum_n_vaccinated_15
#> 352 353
#> cum_n_vaccinated_20 cum_n_vaccinated_25
#> 354 355
#> cum_n_vaccinated_30 cum_n_vaccinated_35
#> 356 357
#> cum_n_vaccinated_40 cum_n_vaccinated_45
#> 358 359
#> cum_n_vaccinated_50 cum_n_vaccinated_55
#> 360 361
#> cum_n_vaccinated_60 cum_n_vaccinated_65
#> 362 363
#> cum_n_vaccinated_70 cum_n_vaccinated_75
#> 364 365
#> cum_n_vaccinated_80 cum_n_vaccinated_CHW
#> 366 367
#> cum_n_vaccinated_CHR D_all_0
#> 368 521
#> D_all_5 D_all_10
#> 522 523
#> D_all_15 D_all_20
#> 524 525
#> D_all_25 D_all_30
#> 526 527
#> D_all_35 D_all_40
#> 528 529
#> D_all_45 D_all_50
#> 530 531
#> D_all_55 D_all_60
#> 532 533
#> D_all_65 D_all_70
#> 534 535
#> D_all_75 D_all_80
#> 536 537
#> D_all_CHW D_all_CHR
#> 538 539
#> D_hosp_0 D_hosp_5
#> 559 560
#> D_hosp_10 D_hosp_15
#> 561 562
#> D_hosp_20 D_hosp_25
#> 563 564
#> D_hosp_30 D_hosp_35
#> 565 566
#> D_hosp_40 D_hosp_45
#> 567 568
#> D_hosp_50 D_hosp_55
#> 569 570
#> D_hosp_60 D_hosp_65
#> 571 572
#> D_hosp_70 D_hosp_75
#> 573 574
#> D_hosp_80 D_hosp_CHW
#> 575 576
#> D_hosp_CHR infections_inc_strain_1
#> 577 92
#>