Load packages required for analysis
Load the fitted model and prior draws.
## Wrapper around LibBi
## ======================
## Model: Baseline
## Run time: 14214.12 seconds
## Number of samples: 1000
## State trajectories recorded: E H L P S T_E T_P YearlyAgeCases YearlyDeaths YearlyECases YearlyEPulCases YearlyPCases YearlyPulCases
## Noise trajectories recorded: NoiseNUKCases
## Parameters recorded: beta_young_adult c_eff c_hist_half c_hist M_young_adult M meas_error meas_std non_uk_scaling older_adult_activation_scaling- Get overall acceptance rate
## [1] 0.03403403- Get the rejection rates of parameters
## M non_uk_scaling
## 0.965966 0.965966
## c_eff c_hist
## 0.965966 0.965966
## c_hist_half beta_young_adult
## 0.965966 0.965966
## M_young_adult older_adult_activation_scaling
## 0.965966 0.965966
## meas_error meas_std
## 0.965966 0.965966- Evaluate Posterior Traces
- Plot overview of prior and posterior densities
- Table of priors and posteriors
| Parameter | Prior | Posterior | latex_param |
|---|---|---|---|
| beta_young_adult | 4.88 (0.35, 9.74) | 5.72 (5.72, 5.72) | \(\beta_{\text{young adult}}\) |
| c_eff | 1.22 (0.09, 3.13) | 0.06 (0.06, 0.06) | \(c_{\text{eff}}\) |
| c_hist | 10.50 (1.38, 19.36) | 1.28 (1.28, 1.28) | \(c^{\text{hist}}_{\text{eff}}\) |
| c_hist_half | 5.95 (0.53, 15.80) | 4.34 (4.34, 4.34) | \(c^{\text{hist}}_{\text{half}}\) |
| M | 1.22 (0.08, 3.07) | 0.71 (0.71, 0.71) | \(M\) |
| M_young_adult | 5.19 (0.23, 9.76) | 9.98 (9.98, 9.98) | \(M_{\text{young adult}}\) |
| meas_error | 0.90 (0.82, 0.98) | 0.90 (0.90, 0.90) | \(E_{\text{syst}}\) |
| meas_std | 0.01 (0.00, 0.02) | 0.02 (0.02, 0.02) | \(E_{\text{noise}}\) |
| non_uk_scaling | 100.27 (3.34, 196.54) | 192.90 (192.90, 192.90) | \(\iota_{\text{scale}}\) |
| older_adult_activation_scaling | 2.01 (1.18, 2.98) | 2.19 (2.19, 2.19) | \(\epsilon^{\text{older-adult}}_L\) |
Get observations values predicted by the model
Calculate incidence sensitivity to parameters at the maximum time fitted to.
| Parameter | gamma | p.value | latex_param |
|---|---|---|---|
| beta_young_adult | 0.0265486 | 0.4016722 | \(\beta_{\text{young adult}}\) |
| c_eff | 0.0242696 | 0.4433042 | \(c_{\text{eff}}\) |
| meas_std | -0.0175489 | 0.5793779 | \(E_{\text{noise}}\) |
| meas_error | 0.0169607 | 0.5921586 | \(E_{\text{syst}}\) |
| non_uk_scaling | 0.0130079 | 0.6811834 | \(\iota_{\text{scale}}\) |
| older_adult_activation_scaling | -0.0111673 | 0.7243063 | \(\epsilon^{\text{older-adult}}_L\) |
| c_hist_half | -0.0108391 | 0.7320915 | \(c^{\text{hist}}_{\text{half}}\) |
| M_young_adult | 0.0075882 | 0.8105908 | \(M_{\text{young adult}}\) |
| M | -0.0059983 | 0.8497431 | \(M\) |
| c_hist | 0.0053200 | 0.8665632 | \(c^{\text{hist}}_{\text{eff}}\) |
- Plot incidence sensitivity to parameters
- Plot an overview of states
- Plot an overview of states zoomed into 1990 onwards
- Plot fitted observed states.
- Table fitted states
| Observation | Year | Observed Incidence | Predicted Incidence |
|---|---|---|---|
| UK born TB cases | 2000 | 1803 | 372 (129, 657) |
| 2001 | 1866 | 358 (130, 640) | |
| 2002 | 1833 | 353 (124, 623) | |
| 2003 | 1685 | 345 (131, 608) | |
| 2004 | 1776 | 337 (132, 597) |
| Year | Age | Observed Incidence | Predicted Incidence |
|---|---|---|---|
| 2000 | 0-4 | 75 | 3 (3, 4) |
| 5-9 | 59 | 2 (2, 3) | |
| 10-14 | 75 | 2 (2, 3) | |
| 15-19 | 112 | 3 (3, 4) | |
| 20-24 | 133 | 5 (4, 6) | |
| 25-29 | 116 | 6 (4, 8) | |
| 30-34 | 147 | 4 (2, 6) | |
| 35-39 | 99 | 5 (2, 10) | |
| 40-44 | 83 | 8 (3, 15) | |
| 45-49 | 105 | 13 (5, 24) | |
| 50-69 | 428 | 154 (50, 271) | |
| 70-89 | 371 | 158 (51, 336) | |
| 2001 | 0-4 | 113 | 4 (3, 4) |
| 5-9 | 65 | 3 (2, 3) | |
| 10-14 | 51 | 2 (2, 3) | |
| 15-19 | 130 | 3 (3, 4) | |
| 20-24 | 145 | 5 (4, 6) | |
| 25-29 | 127 | 6 (5, 8) | |
| 30-34 | 122 | 4 (2, 6) | |
| 35-39 | 128 | 5 (2, 9) | |
| 40-44 | 107 | 8 (3, 14) | |
| 45-49 | 101 | 13 (4, 22) | |
| 50-69 | 386 | 147 (46, 261) | |
| 70-89 | 391 | 153 (50, 322) | |
| 2002 | 0-4 | 102 | 5 (4, 5) |
| 5-9 | 62 | 3 (3, 3) | |
| 10-14 | 64 | 3 (2, 3) | |
| 15-19 | 129 | 4 (3, 4) | |
| 20-24 | 148 | 5 (4, 7) | |
| 25-29 | 120 | 7 (5, 9) | |
| 30-34 | 112 | 4 (2, 6) | |
| 35-39 | 127 | 5 (2, 9) | |
| 40-44 | 98 | 7 (3, 13) | |
| 45-49 | 89 | 12 (4, 21) | |
| 50-69 | 398 | 141 (45, 249) | |
| 70-89 | 384 | 150 (48, 318) | |
| 2003 | 0-4 | 74 | 5 (5, 6) |
| 5-9 | 46 | 4 (3, 4) | |
| 10-14 | 59 | 3 (3, 4) | |
| 15-19 | 102 | 4 (4, 5) | |
| 20-24 | 116 | 6 (5, 8) | |
| 25-29 | 137 | 8 (6, 10) | |
| 30-34 | 118 | 4 (2, 6) | |
| 35-39 | 113 | 5 (2, 9) | |
| 40-44 | 109 | 7 (3, 13) | |
| 45-49 | 83 | 11 (4, 20) | |
| 50-69 | 386 | 135 (45, 241) | |
| 70-89 | 342 | 146 (47, 310) | |
| 2004 | 0-4 | 112 | 6 (5, 6) |
| 5-9 | 71 | 4 (3, 4) | |
| 10-14 | 81 | 3 (3, 4) | |
| 15-19 | 111 | 5 (4, 5) | |
| 20-24 | 120 | 7 (6, 8) | |
| 25-29 | 136 | 8 (7, 11) | |
| 30-34 | 129 | 4 (2, 7) | |
| 35-39 | 103 | 5 (2, 9) | |
| 40-44 | 128 | 7 (3, 12) | |
| 45-49 | 94 | 11 (4, 19) | |
| 50-69 | 379 | 130 (42, 230) | |
| 70-89 | 312 | 142 (45, 301) |
- Plot age distributed cases.
