Wastewater Model

.gitignore

@@ -122,6 +122,7 @@ target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
+*.ipynb
 
 # IPython
 profile_default/
@@ -387,5 +388,6 @@ poetry.lock
 
 notebooks/*_files/
 notebooks/*.md
+notebooks/*.quarto_ipynb
 
 nssp_demo/private_data/*

notebooks/data/fit/stan_data.json

@@ -1,16 +1,16 @@
 {
   "gt_max": 15,
   "hosp_delay_max": 55,
-  "inf_to_hosp": [0.0, 0.00469384736487552, 0.0145200073436112, 0.0278627741704387, 0.0423656492135518, 0.0558071445014868, 0.0665713169684116, 0.0737925805176124, 0.0772854627892072, 0.0773666390616176, 0.0746515449009948, 0.0698761436052596, 0.0637663813017696, 0.0569581929821651, 0.0499600186601535, 0.0431457477049282, 0.0367662806214046, 0.0309702535668237, 0.0258273785539499, 0.0213504646948306, 0.0175141661880584, 0.0142698211023571, 0.0115565159519833, 0.00930888979824423, 0.00746229206759214, 0.00595605679409682, 0.00473519993107751, 0.00375117728281842, 0.00296198928038098, 0.00233187862772459, 0.00183079868293457, 0.00143377454057296, 0.00107076258525208, 0.000773006742366448, 0.000539573690886396, 0.000364177599116743, 0.000237727628685579, 0.000150157714457011, 9.18283319498657e-05, 5.44079947589853e-05, 3.12548818921464e-05, 1.74202619730274e-05, 9.42698047424712e-06, 4.95614149002087e-06, 2.53275674485913e-06, 1.25854819834554e-06, 6.08116579596933e-07, 2.85572858589747e-07, 1.30129404249734e-07, 5.73280599448306e-08, 2.4219376577964e-08, 9.6316861194457e-09, 3.43804936850951e-09, 9.34806280366887e-10, 0.0],
+  "inf_to_hosp": [0.0, 0.00469384736487552, 0.0145200073436112, 0.0278627741704387, 0.0423656492135518, 0.0558071445014868, 0.0665713169684116, 0.0737925805176124, 0.0772854627892072, 0.0773666390616176, 0.0746515449009948, 0.0698761436052596, 0.0637663813017696, 0.0569581929821651, 0.0499600186601535, 0.0431457477049282, 0.0367662806214046, 0.0309702535668238, 0.0258273785539499, 0.0213504646948306, 0.0175141661880584, 0.0142698211023571, 0.0115565159519833, 0.00930888979824423, 0.00746229206759215, 0.00595605679409682, 0.00473519993107751, 0.00375117728281842, 0.00296198928038098, 0.00233187862772459, 0.00183079868293457, 0.00143377454057296, 0.00107076258525208, 0.000773006742366448, 0.000539573690886396, 0.000364177599116743, 0.000237727628685578, 0.000150157714457011, 9.18283319498657e-05, 5.44079947589853e-05, 3.12548818921464e-05, 1.74202619730274e-05, 9.42698047424712e-06, 4.95614149002087e-06, 2.53275674485913e-06, 1.25854819834554e-06, 6.08116579596933e-07, 2.85572858589747e-07, 1.30129404249734e-07, 5.73280599448305e-08, 2.4219376577964e-08, 9.6316861194457e-09, 3.43804936850951e-09, 9.34806280366887e-10, 0.0],
   "mwpd": 227000.0,
   "ot": 90,
   "n_subpops": 5,
   "n_ww_sites": 4,
   "n_ww_lab_sites": 5,
-  "owt": 88,
+  "owt": 98,
   "oht": 90,
-  "n_censored": 0,
-  "n_uncensored": 88,
+  "n_censored": 1,
+  "n_uncensored": 97,
   "uot": 50,
   "ht": 35,
   "n_weeks": 18,
@@ -322,17 +322,19 @@
   "generation_interval": [0.161701189933765, 0.320525743089203, 0.242198071982593, 0.134825252524032, 0.0689141939998525, 0.0346219683116734, 0.017497710736154, 0.00908172017279556, 0.00483656086299504, 0.00260732346885217, 0.00143298046642562, 0.00082002579123121, 0.0004729600977183, 0.000284420637980485, 0.000179877924728358],
   "ts": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
   "state_pop": 3000000.0,
-  "subpop_size": [400000.0, 200000.0, 100000.0, 50000.0, 2250000.0],
+  "subpop_size": [2250000.0, 400000.0, 200000.0, 100000.0, 50000.0],
   "norm_pop": 3000000.0,
-  "ww_sampled_times": [2, 5, 6, 6, 8, 9, 11, 12, 12, 13, 13, 13, 14, 14, 14, 15, 15, 18, 18, 18, 19, 20, 21, 22, 23, 23, 25, 26, 27, 29, 29, 29, 31, 32, 32, 33, 33, 34, 36, 36, 37, 37, 37, 39, 42, 42, 42, 43, 45, 45, 46, 47, 48, 51, 53, 58, 58, 59, 59, 63, 63, 64, 65, 65, 67, 70, 70, 73, 73, 74, 75, 76, 76, 76, 78, 80, 81, 82, 83, 83, 84, 87, 89, 91, 92, 93, 93, 95],
+  "ww_sampled_times": [2, 2, 2, 5, 6, 6, 8, 9, 11, 12, 12, 12, 13, 14, 14, 14, 15, 15, 16, 18, 18, 18, 19, 20, 21, 22, 22, 23, 23, 25, 26, 26, 27, 29, 29, 29, 31, 32, 32, 33, 33, 34, 36, 36, 37, 37, 39, 40, 42, 42, 42, 43, 45, 46, 46, 47, 48, 51, 52, 53, 56, 57, 58, 58, 59, 59, 63, 63, 64, 65, 65, 67, 70, 70, 73, 74, 75, 76, 76, 77, 78, 80, 81, 83, 83, 84, 86, 87, 89, 89, 90, 90, 92, 92, 92, 94, 94, 94],
   "hosp_times": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90],
-  "ww_sampled_lab_sites": [1, 5, 4, 5, 3, 2, 4, 1, 3, 2, 3, 5, 1, 3, 5, 3, 5, 2, 4, 5, 2, 3, 1, 2, 3, 5, 4, 3, 3, 2, 3, 4, 5, 1, 3, 3, 5, 5, 3, 4, 2, 3, 4, 2, 1, 3, 4, 4, 1, 5, 3, 2, 1, 4, 4, 2, 4, 1, 2, 1, 2, 4, 1, 3, 1, 1, 3, 4, 5, 1, 3, 2, 3, 4, 5, 4, 5, 5, 2, 4, 4, 4, 4, 3, 2, 3, 5, 1],
-  "ww_log_lod": [5.09434727489065, 4.9806950154474, 4.73771588167502, 4.9806950154474, 5.2940513994166, 4.76390186342314, 4.73771588167502, 5.09434727489065, 5.2940513994166, 4.76390186342314, 5.2940513994166, 4.9806950154474, 5.09434727489065, 5.2940513994166, 4.9806950154474, 5.2940513994166, 4.9806950154474, 4.76390186342314, 4.73771588167502, 4.9806950154474, 4.76390186342314, 5.2940513994166, 5.09434727489065, 4.76390186342314, 5.2940513994166, 4.9806950154474, 4.73771588167502, 5.2940513994166, 5.2940513994166, 4.76390186342314, 5.2940513994166, 4.73771588167502, 4.9806950154474, 5.09434727489065, 5.2940513994166, 5.2940513994166, 4.9806950154474, 4.9806950154474, 5.2940513994166, 4.73771588167502, 4.76390186342314, 5.2940513994166, 4.73771588167502, 4.76390186342314, 5.09434727489065, 5.2940513994166, 4.73771588167502, 4.73771588167502, 5.09434727489065, 4.9806950154474, 5.2940513994166, 4.76390186342314, 5.09434727489065, 4.73771588167502, 4.73771588167502, 4.76390186342314, 4.73771588167502, 5.09434727489065, 4.76390186342314, 5.09434727489065, 4.76390186342314, 4.73771588167502, 5.09434727489065, 5.2940513994166, 5.09434727489065, 5.09434727489065, 5.2940513994166, 4.73771588167502, 4.9806950154474, 5.09434727489065, 5.2940513994166, 4.76390186342314, 5.2940513994166, 4.73771588167502, 4.9806950154474, 4.73771588167502, 4.9806950154474, 4.9806950154474, 4.76390186342314, 4.73771588167502, 4.73771588167502, 4.73771588167502, 4.73771588167502, 5.2940513994166, 4.76390186342314, 5.2940513994166, 4.9806950154474, 5.09434727489065],
-  "ww_censored": [],
-  "ww_uncensored": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88],
-  "hosp": [6, 6, 7, 10, 10, 12, 12, 10, 8, 15, 8, 9, 9, 13, 17, 7, 12, 10, 13, 10, 12, 15, 19, 19, 22, 17, 19, 14, 17, 19, 18, 13, 24, 21, 35, 26, 25, 30, 26, 20, 29, 38, 35, 41, 30, 37, 35, 46, 38, 23, 38, 22, 28, 23, 31, 19, 23, 17, 23, 26, 17, 17, 12, 13, 9, 22, 12, 13, 17, 14, 12, 6, 10, 10, 4, 12, 9, 8, 9, 8, 6, 13, 7, 8, 13, 9, 9, 17, 7, 10],
+  "ww_sampled_subpops": [2, 4, 5, 4, 3, 4, 2, 2, 3, 2, 2, 5, 4, 2, 2, 4, 2, 4, 5, 2, 3, 4, 2, 2, 2, 2, 5, 2, 4, 3, 2, 5, 3, 2, 2, 3, 4, 2, 3, 3, 4, 4, 2, 3, 2, 3, 2, 5, 2, 2, 3, 3, 4, 2, 5, 2, 2, 4, 5, 4, 5, 5, 2, 4, 2, 5, 2, 5, 3, 2, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 3, 4, 2, 3, 3, 2, 3, 2, 4, 4, 5, 2, 4, 5, 2, 4, 5],
+  "lab_site_to_subpop_map": [2, 2, 3, 4, 5],
+  "ww_sampled_lab_sites": [1, 4, 5, 4, 3, 4, 2, 2, 3, 1, 2, 5, 4, 1, 2, 4, 2, 4, 5, 2, 3, 4, 1, 2, 1, 2, 5, 2, 4, 3, 2, 5, 3, 1, 2, 3, 4, 1, 3, 3, 4, 4, 2, 3, 2, 3, 1, 5, 1, 2, 3, 3, 4, 2, 5, 2, 1, 4, 5, 4, 5, 5, 1, 4, 1, 5, 1, 5, 3, 1, 2, 1, 1, 2, 4, 1, 2, 2, 4, 4, 4, 3, 4, 2, 3, 3, 1, 3, 1, 4, 4, 5, 2, 4, 5, 2, 4, 5],
+  "ww_log_lod": [4.81786386350134, 4.93524984908241, 4.78269939060126, 4.93524984908241, 5.01370230665543, 4.93524984908241, 5.14825526105204, 5.14825526105204, 5.01370230665543, 4.81786386350134, 5.14825526105204, 4.78269939060126, 4.93524984908241, 4.81786386350134, 5.14825526105204, 4.93524984908241, 5.14825526105204, 4.93524984908241, 4.78269939060126, 5.14825526105204, 5.01370230665543, 4.93524984908241, 4.81786386350134, 5.14825526105204, 4.81786386350134, 5.14825526105204, 4.78269939060126, 5.14825526105204, 4.93524984908241, 5.01370230665543, 5.14825526105204, 4.78269939060126, 5.01370230665543, 4.81786386350134, 5.14825526105204, 5.01370230665543, 4.93524984908241, 4.81786386350134, 5.01370230665543, 5.01370230665543, 4.93524984908241, 4.93524984908241, 5.14825526105204, 5.01370230665543, 5.14825526105204, 5.01370230665543, 4.81786386350134, 4.78269939060126, 4.81786386350134, 5.14825526105204, 5.01370230665543, 5.01370230665543, 4.93524984908241, 5.14825526105204, 4.78269939060126, 5.14825526105204, 4.81786386350134, 4.93524984908241, 4.78269939060126, 4.93524984908241, 4.78269939060126, 4.78269939060126, 4.81786386350134, 4.93524984908241, 4.81786386350134, 4.78269939060126, 4.81786386350134, 4.78269939060126, 5.01370230665543, 4.81786386350134, 5.14825526105204, 4.81786386350134, 4.81786386350134, 5.14825526105204, 4.93524984908241, 4.81786386350134, 5.14825526105204, 5.14825526105204, 4.93524984908241, 4.93524984908241, 4.93524984908241, 5.01370230665543, 4.93524984908241, 5.14825526105204, 5.01370230665543, 5.01370230665543, 4.81786386350134, 5.01370230665543, 4.81786386350134, 4.93524984908241, 4.93524984908241, 4.78269939060126, 5.14825526105204, 4.93524984908241, 4.78269939060126, 5.14825526105204, 4.93524984908241, 4.78269939060126],
+  "ww_censored": [66],
+  "ww_uncensored": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98],
+  "hosp": [14, 15, 11, 22, 13, 17, 26, 19, 21, 21, 18, 32, 22, 29, 15, 38, 30, 26, 26, 36, 37, 41, 38, 37, 50, 57, 56, 46, 55, 49, 53, 58, 58, 59, 63, 68, 66, 90, 71, 74, 90, 79, 66, 76, 91, 79, 94, 78, 93, 82, 100, 92, 61, 93, 60, 71, 62, 72, 53, 55, 49, 59, 68, 46, 50, 45, 36, 32, 56, 37, 41, 41, 35, 45, 37, 33, 27, 33, 34, 34, 38, 27, 43, 30, 33, 34, 35, 33, 35, 40],
   "day_of_week": [5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3, 4, 5, 6, 7, 1, 2, 3],
-  "log_conc": [7.84933755868547, 8.75878317201939, 7.94731683160414, 7.84271554481825, 6.84314706058328, 8.49580667918879, 8.70688802330958, 8.3080964891881, 7.51476199898784, 8.73263730516131, 7.67705894528627, 9.16138870419256, 8.2291748710282, 7.57842684442178, 8.7658468204119, 7.59564541757592, 8.6485267724375, 8.73847850883661, 8.53496849868392, 7.81189950945825, 8.72816004875312, 7.77632957957527, 8.35751634986049, 8.61237112259723, 7.14724348782869, 8.98381918138397, 9.71929374032385, 7.73223113044046, 7.64136587504144, 8.93727178027946, 7.69319599090821, 9.3539099812084, 9.77803780431265, 8.83676433943342, 7.80095273126195, 7.88428742699397, 10.6861051151009, 10.7177204634667, 7.86033075211836, 9.44031060901259, 9.19820314756664, 8.10945148438765, 9.47368587127031, 9.30021922706583, 8.71406234479695, 7.82242543443078, 8.73443519589195, 9.246306907259, 8.61154444152258, 10.8332932698813, 7.39925321859574, 9.06066397101092, 8.61830748102478, 8.86917291106784, 9.02943162748827, 8.42736799456162, 8.11764762377314, 8.03266723037298, 8.41720674557318, 7.98228105459503, 8.42950370265189, 8.47947015286844, 7.81419539933152, 6.95672231924945, 7.74818768373832, 7.66575220799484, 6.86777849754671, 7.76297112083073, 6.95229085580734, 7.56030545976231, 6.64452132423733, 7.65706249921245, 6.80982040079249, 8.28375427477922, 10.3920632090468, 8.17535318491482, 8.62625413957733, 7.21373104269779, 8.15256350454411, 8.38397288981646, 8.40418626057656, 8.23933140611506, 7.91321568315416, 6.89107975822161, 8.02468424809018, 6.87101220865236, 8.34645251673327, 7.62822976068377],
+  "log_conc": [7.66802724479397, 8.21650318956816, 6.4512477164068, 7.75785732441969, 9.04472643003972, 7.8876093738573, 8.85695271080419, 8.77448654283081, 9.25474422044025, 8.48197724221017, 9.18487615016851, 7.73586744786872, 9.15190271402333, 8.57063681753772, 9.22494958414535, 8.8811814139552, 8.95303168179479, 8.87479731488632, 7.04631257099227, 9.17451866263841, 9.81185744840712, 8.34692842110394, 8.56700168572782, 9.35764330055156, 8.64805057574179, 9.45079742597308, 7.30867303574344, 9.41472892758601, 9.12723564522376, 9.63427957851573, 9.4877830585957, 9.02899614473423, 9.86293199017148, 8.81668715131234, 9.35443062233028, 9.86957090190018, 8.95533551342666, 9.10840763554723, 9.89336595991182, 10.2035349739338, 8.51721998551749, 8.50763772111075, 9.68146528671227, 10.1267878546749, 9.82586519456221, 10.4562946689248, 9.39359538798059, 9.06912617169831, 9.13017806227903, 9.87195987699652, 10.1617885270518, 9.92070098259861, 9.04498782443653, 9.99736049469332, 7.8122356539209, 9.90761719216578, 9.19954542861679, 9.20908242423643, 7.53800674845928, 9.23810876627582, 8.74766338564374, 5.68405424571368, 8.94327722754565, 8.13815511398509, 8.72901851354369, 2.39134969530063, 8.55874357420902, 7.99413714656807, 8.70447685985134, 8.7648016157833, 9.28255076496634, 8.71171479812706, 8.80114398496407, 9.28818292020013, 7.6967588326828, 8.58440395540122, 8.89885558938604, 9.12890628468619, 7.639038061726, 7.70375332709297, 8.03272855574736, 8.59715668661873, 7.85031287265023, 8.95008137695999, 9.11122924030913, 9.12994052023167, 8.37562782560992, 8.46419130893256, 8.46685643123332, 8.15758459191837, 7.81253430699302, 6.6648633811922, 9.23344255196987, 8.06975580003644, 6.09213112399348, 8.97077401961493, 7.26054982586712, 8.02898834978338],
   "compute_likelihood": 1,
   "include_ww": 1,
   "include_hosp": 1,
@@ -341,8 +343,8 @@
   "viral_shedding_pars": [5.0, 1.0, 5.1, 0.5, 17.0, 3.0],
   "autoreg_rt_a": 2,
   "autoreg_rt_b": 40,
-  "autoreg_rt_site_a": 1,
-  "autoreg_rt_site_b": 4,
+  "autoreg_rt_subpop_a": 1,
+  "autoreg_rt_subpop_b": 4,
   "autoreg_p_hosp_a": 1,
   "autoreg_p_hosp_b": 100,
   "inv_sqrt_phi_prior_mean": 0.1,
@@ -351,8 +353,8 @@
   "r_prior_sd": 1,
   "log10_g_prior_mean": 12,
   "log10_g_prior_sd": 2,
-  "i_first_obs_over_n_prior_a": 1.0015,
-  "i_first_obs_over_n_prior_b": 5.9985,
+  "i_first_obs_over_n_prior_a": 1.00280952380952,
+  "i_first_obs_over_n_prior_b": 5.99719047619048,
   "hosp_wday_effect_prior_alpha": [5, 5, 5, 5, 5, 5, 5],
   "mean_initial_exp_growth_rate_prior_mean": 0,
   "mean_initial_exp_growth_rate_prior_sd": 0.01,
@@ -374,6 +376,10 @@
   "sigma_rt_prior": 0.1,
   "log_phi_g_prior_mean": -2.302585,
   "log_phi_g_prior_sd": 5,
-  "ww_sampled_sites": [1, 4, 3, 4, 2, 1, 3, 1, 2, 1, 2, 4, 1, 2, 4, 2, 4, 1, 3, 4, 1, 2, 1, 1, 2, 4, 3, 2, 2, 1, 2, 3, 4, 1, 2, 2, 4, 4, 2, 3, 1, 2, 3, 1, 1, 2, 3, 3, 1, 4, 2, 1, 1, 3, 3, 1, 3, 1, 1, 1, 1, 3, 1, 2, 1, 1, 2, 3, 4, 1, 2, 1, 2, 3, 4, 3, 4, 4, 1, 3, 3, 3, 3, 2, 1, 2, 4, 1],
-  "lab_site_to_site_map": [1, 1, 2, 3, 4]
+  "offset_ref_log_r_t_prior_mean": 0,
+  "offset_ref_log_r_t_prior_sd": 0.2,
+  "offset_ref_logit_i_first_obs_prior_mean": 0,
+  "offset_ref_logit_i_first_obs_prior_sd": 0.25,
+  "offset_ref_initial_exp_growth_rate_prior_mean": 0,
+  "offset_ref_initial_exp_growth_rate_prior_sd": 0.025
 }