From 86f97fa558126d7190cbc74ef40f049162d7c83f Mon Sep 17 00:00:00 2001
From: Jiayuan Zhu <jiayuanz0322@gmail.com>
Date: Wed, 4 Oct 2023 19:53:43 +0100
Subject: [PATCH] add NZ relaxed params

---
 .../NewZealand_parameters_relaxed.json        | 515 ++++++++++++++++++
 1 file changed, 515 insertions(+)
 create mode 100644 python_examples/NZ_example/NewZealand_parameters_relaxed.json

diff --git a/python_examples/NZ_example/NewZealand_parameters_relaxed.json b/python_examples/NZ_example/NewZealand_parameters_relaxed.json
new file mode 100644
index 00000000..10f74fc1
--- /dev/null
+++ b/python_examples/NZ_example/NewZealand_parameters_relaxed.json
@@ -0,0 +1,515 @@
+{
+    "basic_reproduction_num": 3.28,
+    "do_CovidSim": false,
+    "mcell_num_per_cell": 81,
+    "ave_places_per_mcell": 5,
+    "infection_radius": 5,
+    "latent_period": 4.59,
+    "asympt_infect_period": 14,
+    "mean_mild_to_recov": 7,
+    "mean_gp_to_recov": 7,
+    "mean_gp_to_hosp": 5,
+    "mean_gp_to_death": 7,
+    "mean_hosp_to_recov": 1,
+    "mean_hosp_to_icu": 1,
+    "mean_hosp_to_death": 1,
+    "mean_icu_to_icurecov": 1,
+    "mean_icu_to_death": 1,
+    "mean_icurecov_to_recov": 1,
+    "latent_period_iCDF": [
+        0,
+        0.098616903,
+        0.171170649,
+        0.239705594,
+        0.307516598,
+        0.376194441,
+        0.446827262,
+        0.520343677,
+        0.597665592,
+        0.679808341,
+        0.767974922,
+        0.863671993,
+        0.968878064,
+        1.086313899,
+        1.219915022,
+        1.37573215,
+        1.563841395,
+        1.803041398,
+        2.135346254,
+        2.694118208,
+        3.964172493
+    ],
+    "asympt_infect_icdf": [
+        0,
+        0.171566836,
+        0.424943468,
+        0.464725594,
+        0.50866631,
+        0.55773764,
+        0.613298069,
+        0.67732916,
+        0.752886568,
+        0.843151261,
+        0.895791527,
+        0.955973422,
+        1.026225109,
+        1.110607115,
+        1.216272375,
+        1.336349102,
+        1.487791911,
+        1.701882384,
+        1.865779085,
+        2.126940581,
+        2.524164972
+    ],
+    "mild_to_recov_icdf": [
+        0,
+        0.341579599,
+        0.436192391,
+        0.509774887,
+        0.574196702,
+        0.633830053,
+        0.690927761,
+        0.74691114,
+        0.802830695,
+        0.859578883,
+        0.918015187,
+        0.97906363,
+        1.043815683,
+        1.113669859,
+        1.190557274,
+        1.277356871,
+        1.378761429,
+        1.50338422,
+        1.670195767,
+        1.938414132,
+        2.511279379
+    ],
+    "gp_to_recov_icdf": [
+        0,
+        0.341579599,
+        0.436192391,
+        0.509774887,
+        0.574196702,
+        0.633830053,
+        0.690927761,
+        0.74691114,
+        0.802830695,
+        0.859578883,
+        0.918015187,
+        0.97906363,
+        1.043815683,
+        1.113669859,
+        1.190557274,
+        1.277356871,
+        1.378761429,
+        1.50338422,
+        1.670195767,
+        1.938414132,
+        2.511279379
+    ],
+    "gp_to_hosp_icdf": [
+        0,
+        0.341579599,
+        0.436192391,
+        0.509774887,
+        0.574196702,
+        0.633830053,
+        0.690927761,
+        0.74691114,
+        0.802830695,
+        0.859578883,
+        0.918015187,
+        0.97906363,
+        1.043815683,
+        1.113669859,
+        1.190557274,
+        1.277356871,
+        1.378761429,
+        1.50338422,
+        1.670195767,
+        1.938414132,
+        2.511279379
+    ],
+    "gp_to_death_icdf": [
+        0,
+        2.257735908,
+        3.171065856,
+        3.924183798,
+        4.608738224,
+        5.260437017,
+        5.898728066,
+        6.53669783,
+        7.184755068,
+        7.852438367,
+        8.549591424,
+        9.287408763,
+        10.07967529,
+        10.94457146,
+        11.90769274,
+        13.00769447,
+        14.3081531,
+        15.92655201,
+        18.12320384,
+        21.71626849,
+        29.58154704
+    ],
+    "hosp_to_recov_icdf": [
+        0,
+        0.634736097,
+        1.217461548,
+        1.805695261,
+        2.41206761,
+        3.044551205,
+        3.71010552,
+        4.415905623,
+        5.170067405,
+        5.982314035,
+        6.864787504,
+        7.833196704,
+        8.908589322,
+        10.12027655,
+        11.51100029,
+        13.14682956,
+        15.13821107,
+        17.69183155,
+        21.27093904,
+        27.35083955,
+        41.35442157
+    ],
+    "hosp_to_icu_icdf": [
+        0,
+        0.108407687,
+        0.220267228,
+        0.337653773,
+        0.46159365,
+        0.593106462,
+        0.733343356,
+        0.88367093,
+        1.045760001,
+        1.221701998,
+        1.414175806,
+        1.62669998,
+        1.864032461,
+        2.132837436,
+        2.442868902,
+        2.809242289,
+        3.257272257,
+        3.834402667,
+        4.647120033,
+        6.035113821,
+        9.253953212
+    ],
+    "hosp_to_death_icdf": [
+        0,
+        1.703470233,
+        2.39742257,
+        2.970367222,
+        3.491567676,
+        3.988046604,
+        4.474541783,
+        4.960985883,
+        5.455292802,
+        5.964726999,
+        6.496796075,
+        7.06004732,
+        7.665014091,
+        8.325595834,
+        9.061367792,
+        9.901900127,
+        10.8958347,
+        12.133068,
+        13.81280888,
+        16.56124574,
+        22.5803431
+    ],
+    "icu_to_icurecov_icdf": [
+        0,
+        1.308310071,
+        1.87022015,
+        2.338694632,
+        2.76749788,
+        3.177830401,
+        3.581381361,
+        3.986127838,
+        4.398512135,
+        4.824525291,
+        5.270427517,
+        5.743406075,
+        6.252370864,
+        6.809125902,
+        7.430338867,
+        8.141231404,
+        8.983341913,
+        10.03350866,
+        11.46214198,
+        13.80540164,
+        18.95469153
+    ],
+    "icu_to_death_icdf": [
+        0,
+        1.60649128,
+        2.291051747,
+        2.860938008,
+        3.382077741,
+        3.880425012,
+        4.37026577,
+        4.861330415,
+        5.361460943,
+        5.877935626,
+        6.4183471,
+        6.991401405,
+        7.607881726,
+        8.282065409,
+        9.034104744,
+        9.894486491,
+        10.91341144,
+        12.18372915,
+        13.9113346,
+        16.74394356,
+        22.96541429
+    ],
+    "icurecov_to_recov": [
+        0,
+        0.133993315,
+        0.265922775,
+        0.402188416,
+        0.544657341,
+        0.694774487,
+        0.853984373,
+        1.023901078,
+        1.206436504,
+        1.403942719,
+        1.619402771,
+        1.856711876,
+        2.121118605,
+        2.419957988,
+        2.763950408,
+        3.169692564,
+        3.664959893,
+        4.301777536,
+        5.196849239,
+        6.7222126,
+        10.24997697
+    ],
+    "CDF_RES": 20,
+    "time_steps_per_day": 1,
+    "prob_symptomatic": 0.66,
+    "sympt_infectiousness": 1.5,
+    "asympt_infectiousness": 1,
+    "latent_to_sympt_delay": 0.5,
+    "infectiousness_prof": [0.487464241, 1, 1.229764827, 1.312453175,
+        1.307955665, 1.251658756, 1.166040358, 1.065716869,
+        0.960199498, 0.855580145, 0.755628835, 0.662534099,
+        0.577412896, 0.500665739, 0.432225141, 0.371729322,
+        0.318643018, 0.272340645, 0.232162632, 0.19745264,
+        0.167581252, 0.141960133, 0.120049578, 0.101361532,
+        0.085459603, 0.071957123, 0.060514046, 0.050833195,
+        0.04265624, 0.035759641, 0.029950735, 0.025064045,
+        0.02095788, 0.017511251, 0.014621091, 0.012199802,
+        0.010173075, 0.008477992, 0.007061366, 0.005878301,
+        0.00489096, 0.004067488, 0.003381102, 0.00280931,
+        0.002333237, 0.001937064, 0.001607543, 0.001333589,
+        0.001105933, 0.00091683, 0.000759816, 0.000629496,
+        0.000521372, 0.000431695, 0.000357344, 0.000295719,
+        0.000244659],
+    "max_infectious_steps": 2550,
+    "infprof_res": 56,
+    "place_params": {
+        "age_group1_min_age": [5, 11, 18, 16, 25],
+        "age_group1_max_age": [11, 16, 65, 18, 64],
+        "age_group1_prop": [
+            0.976396125, 0.98390173, 0, 0.37097869299999997, 0.0115
+        ],
+        "age_group2_min_age": [3, 16, 18, 18, 65],
+        "age_group2_max_age": [5, 18, 21, 21, 80],
+        "age_group2_prop": [
+            1, 0.959727307, 0.629021307, 0.040272693000000026, 0.0113
+        ],
+        "age_group3_min_age": [21, 21, 21, 21, 80],
+        "age_group3_max_age": [65, 65, 65, 65, 1000],
+        "age_group3_prop": [
+            0.005292966, 0.006331515, 0.064144615, 0.742058813, 0.123
+        ],
+        "nearest_places": [3, 3, 6, 0, 0],
+        "mean_size": [230, 1010, 3300, 14.28, 40],
+        "max_size": [0, 0, 0, 5927, 0],
+        "size_power": [0, 0, 0, 1.34, 0],
+        "size_offset": [0, 0, 0, 5.35, 0],
+        "mean_group_size": [25, 25, 100, 10, 20],
+        "place_transmission": 0.1
+    },
+    "household_transmission": 0.1,
+    "household_size_distribution": [0.228400, 0.252600, 0.252600, 0.110500,
+                                	0.110400, 0.020000, 0.015000, 0.005500,
+                                    0.002500, 0.002500],
+    "false_positive_rate": 0,
+    "place_transmission": 0.1,
+    "use_ages": 1,
+    "age_proportions": [0.060664682, 0.063339685, 0.062279914, 0.058834798, 
+                        0.067008987, 0.075176065, 0.074907299, 0.070626696,
+                        0.062933599, 0.065106245, 0.061568308, 0.060744568,
+                        0.055552253, 0.048511717, 0.042487527, 0.029830204,
+                        0.040427453],
+    "age_contact": [0.6, 0.7, 0.75, 1, 1, 1, 1, 1,
+                    1, 1, 1, 1, 1, 1, 1, 0.75, 0.5],
+    "host_progression_lists": {
+        "prob_gp_to_hosp": [0.001896, 0.001616, 0.002981, 0.006083,
+                            0.013513, 0.025793, 0.040294, 0.057278,
+                            0.070361, 0.092402, 0.13409, 0.164461,
+                            0.220964, 0.248858, 0.298479, 0.346454,
+                            0.351508],
+        "prob_gp_to_recov": [0.998104, 0.998384, 0.997019, 0.993917,
+                                0.986487, 0.974207, 0.959706, 0.942722,
+                                0.929639, 0.907598, 0.86591, 0.835539,
+                                0.779036, 0.751142, 0.701521, 0.653546,
+                                0.648492],
+
+        "prob_exposed_to_asympt": [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, 0.34, 0.34],
+        "prob_exposed_to_gp": [0.220278, 0.220237, 0.220438, 0.220896,
+                                0.222, 0.223849, 0.226073, 0.228734,
+                                0.230827, 0.234442, 0.241597, 0.247091,
+                                0.258007, 0.263759, 0.274652, 0.286074,
+                                0.287333],
+        "prob_exposed_to_mild": [0.439722, 0.439763, 0.439562, 0.43910,
+                                    0.438, 0.436151, 0.433927, 0.431266,
+                                    0.429173, 0.425558, 0.418403, 0.41291,
+                                    0.401993, 0.396241, 0.385348,
+                                    0.373926, 0.372667],
+
+        "prob_hosp_to_death": [0.110981, 0.108089, 0.119602, 0.134584,
+                                0.153656, 0.171186, 0.184562, 0.196264,
+                                0.203616, 0.212462, 0.219792, 0.207716,
+                                0.171205, 0.107889, 0.344512, 0.423204,
+                                0.473935],
+        "prob_hosp_to_recov": [0.770565, 0.773457, 0.761945, 0.746962,
+                                0.72789, 0.710361, 0.696984, 0.678225,
+                                0.655474, 0.611583, 0.535832, 0.43985,
+                                0.301002, 0.168066, 0.473511, 0.522406,
+                                0.509332],
+        "prob_hosp_to_icu": [0.118454, 0.118454, 0.118453, 0.118454,
+                                0.118454, 0.118454, 0.118454, 0.125511,
+                                0.14091, 0.175955, 0.244376, 0.352435,
+                                0.527792, 0.724045, 0.181977, 0.054391,
+                                0.016733],
+
+        "prob_icu_to_death": [0.52349, 0.52349, 0.52349, 0.52349,
+                                0.52349, 0.52349, 0.52349, 0.52349,
+                                0.52349, 0.52349, 0.52349, 0.52349,
+                                0.52349, 0.52349, 0.52349, 0.52349,
+                                0.52349],
+        "prob_icu_to_icurecov": [0.47651, 0.47651, 0.47651, 0.47651,
+                                    0.47651, 0.47651, 0.47651, 0.47651,
+                                    0.47651, 0.47651, 0.47651, 0.47651,
+                                    0.47651, 0.47651, 0.47651, 0.47651,
+                                    0.47651]
+    },
+    "max_household_size": 10,
+    "household_age_params": {
+        "mean_child_age_gap": 2,
+        "min_adult_age": 19,
+        "max_MF_partner_age_gap": 5,
+        "min_parent_age_gap": 19,
+        "max_FM_partner_age_gap": 5,
+        "max_parent_age_gap": 44,
+        "max_child_age": 20,
+        "one_child_two_pers_prob": 0.08,
+        "two_child_three_pers_prob": 0.11,
+        "one_pers_house_prob_old": 0.5,
+        "two_pers_house_prob_old": 0.5,
+        "one_pers_house_prob_young": 0.23,
+        "two_pers_house_prob_young": 0.23,
+        "one_child_prob_youngest_child_under_five": 0.5,
+        "two_children_prob_youngest_under_five": 0.0,
+        "prob_youngest_child_under_five": 0.0,
+        "zero_child_three_pers_prob": 0.25,
+        "one_child_four_pers_prob": 0.2,
+        "young_and_single_slope": 0.7,
+        "young_and_single": 36,
+        "no_child_pers_age": 44,
+        "old_pers_age": 60,
+        "three_child_five_pers_prob": 0.5,
+        "older_gen_gap": 19,
+        "prop_other_parent_away": 0.0
+    },
+    "carehome_params": {
+      "carehome_minimum_age": 65,
+      "carehome_allow_initial_infections": 0,
+      "carehome_resident_household_scaling": 1,
+      "carehome_resident_place_scaling": 1,
+      "carehome_resident_spatial_scaling": 1,
+      "carehome_worker_group_scaling": 1,
+      "carehome_rel_prob_hosp": 1
+    },
+    "travel_params": {
+        "ratio_introduce_cases": 0.0,
+        "constant_introduce_cases": [1],
+        "duration_travel_stay": [14, 30],
+        "prob_existing_household": 0.25
+    },
+    "intervention_params": {
+        "case_isolation": {
+            "start_time": 0,
+            "policy_duration": 90,
+            "case_threshold": 0,
+            "isolation_delay": 0,
+            "isolation_duration": 14,
+            "isolation_probability": 1,
+            "use_testing": 0,
+            "isolation_effectiveness": 0.25,
+            "isolation_house_effectiveness": 0.5
+        },
+        "place_closure": {
+            "start_time": 25,
+            "policy_duration": 49,
+            "case_threshold": 0,
+            "closure_delay": 0,
+            "closure_duration": 49,
+            "closure_place_type": [1, 2, 3, 4, 6],
+            "closure_household_infectiousness": 1.5,
+            "closure_spatial_params": 1.25,
+            "case_microcell_threshold": 0
+        },
+        "household_quarantine": {
+            "start_time": 0,
+            "policy_duration": 90,
+            "case_threshold": 0,
+            "quarantine_delay": 0,
+            "quarantine_duration": 14,
+            "quarantine_house_compliant": 0.75,
+            "quarantine_individual_compliant": 1.0,
+            "quarantine_house_effectiveness": 1.5,
+            "quarantine_spatial_effectiveness": 0.25,
+            "quarantine_place_effectiveness": [0.25, 0.25, 0.25, 0.25, 0.25, 0.25]
+        },
+        "social_distancing": {
+            "start_time": 49,
+            "policy_duration": 90,
+            "case_threshold": 0,
+            "distancing_delay": 0,
+            "distancing_duration": 90,
+            "case_microcell_threshold": 0,
+            "distancing_enhanced_prob": [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.3, 0.3, 0.5, 0.5, 0.8, 0.8, 0.8, 0.8],
+            "distancing_house_enhanced_susc": 1,
+            "distancing_place_enhanced_susc": [0.25, 0.25, 0.25, 0.25, 0.25, 0.25],
+            "distancing_spatial_enhanced_susc": 0.25,
+            "distancing_house_susc": 1.25,
+            "distancing_place_susc": [0.5, 0.5, 0.5, 0.5, 0.75, 0.75],
+            "distancing_spatial_susc": 0.25
+        },
+        "travel_isolation": {
+            "start_time": 14,
+            "policy_duration": 365,
+            "case_threshold": 0,
+            "isolation_delay": 0,
+            "isolation_duration": 14,
+            "isolation_probability": 1.0,
+            "use_testing": 0,
+            "hotel_isolate": 1,
+            "isolation_effectiveness": 0.1,
+            "isolation_house_effectiveness": 0.5
+        }
+    }
+}