Multiple pathogen structure
Arguments
- case_timeseries
vector of total case data
- time
vector of labelled time data
- component_pathogen_timeseries
named list of each pathogen that has timeseries of case counts
- smoothing_structure
either `shared` (all pathogens have the same smoothing structure; tau[1]), `independent` (each pathogen has completely independent smoothing structure; tau[number of pathogens]), or `correlated` (smoothing structure is correlated among pathogens Sigma[number of pathogens, number of pathogens]). Case-insensitive.
- observation_noise
either `observation_noise_only` (only includes observation noise - the same between pathogens) or `pathogen_specific_noise` (includes noise in individual pathogens as well). Case-insensitive.
Value
named list including pathogen_structure, pathogen_names, data, and model_params of class `EpiStrainDynamics.pathogen_structure`
Examples
multiple(
case_timeseries = sarscov2$cases,
time = sarscov2$date,
component_pathogen_timeseries = list(
alpha = sarscov2$alpha,
delta = sarscov2$delta,
omicron = sarscov2$omicron,
other = sarscov2$other
),
smoothing_structure = 'independent',
observation_noise = 'observation_noise_only'
)
#> $pathogen_structure
#> [1] "multiple"
#>
#> $pathogen_names
#> [1] "alpha" "delta" "omicron" "other"
#>
#> $data
#> $data$case_timeseries
#> [1] 7096 7682 7318 6810 7023 9983 10366 12717 13357 13854
#> [11] 11667 11953 16753 17250 18573 18425 15893 12648 12202 19671
#> [21] 19116 19920 18606 17915 14882 14311 25872 25613 25714 23475
#> [31] 21694 16434 15895 26807 24351 23901 23614 22890 16673 15970
#> [41] 31925 25943 24027 24063 23659 18766 20244 31510 27789 27757
#> [51] 24826 24388 18223 16233 26952 23488 21076 18041 17100 12533
#> [61] 11895 19024 16679 16814 14761 14554 11086 10852 18198 16684
#> [71] 16676 15860 15834 12893 13731 21584 21065 21909 22916 24390
#> [81] 19588 22266 35197 34378 35427 34437 36419 25589 33066 48192
#> [91] 46475 42936 32392 14419 41110 48520 46408 83090 72161 53947
#> [101] 32482 61654 56335 77972 66638 58784 53187 48105 40035 37174
#> [111] 58592 50647 46509 43472 41452 31250 29592 45957 40525 35986
#> [121] 32502 30330 22344 17554 30737 27730 26303 24773 22434 17167
#> [131] 15783 22972 20265 19914 18493 16307 12320 11664 16194 14225
#> [141] 13899 13139 12573 9035 8995 14735 12939 11942 11793 10728
#> [151] 8313 8098 11657 9763 8847 8024 6782 4949 4873 7192
#> [161] 6918 6172 5937 5467 4628 4410 6890 6488 6250 5933
#> [171] 5717 4381 4425 6703 5863 5978 5632 5180 4247 5390
#> [181] 6459 5484 6224 5616 4567 3731 5030 4196 3779 3966
#> [191] 3674 2747 2508 2412 2744 3313 3253 3147 2953 2380
#> [201] 2376 2881 2495 2512 2345 2347 1722 2584 2738 2541
#> [211] 2708 2409 2020 1564 2119 2626 2178 2499 2230 1825
#> [221] 1433 1521 2084 2553 2569 2326 1982 1609 2307 2809
#> [231] 2329 2335 2182 1938 1628 1923 2858 2812 2813 2517
#> [241] 2367 2000 2326 3369 3427 3922 3747 3589 3000 3164
#> [251] 3897 5431 6168 6258 5861 4731 5534 7946 7896 8210
#> [261] 8043 7619 6284 7135 10362 10800 11052 11106 10320 8447
#> [271] 10087 16308 17402 18351 18714 18169 16301 18502 28418 28199
#> [281] 28923 28794 26339 24010 25170 34919 36060 38597 34020 32804
#> [291] 28379 30503 44511 47707 54910 62000 55264 38476 36182 47924
#> [301] 39876 35548 31278 27817 22852 22187 29981 29582 30237 28432
#> [311] 24749 20570 20985 29840 30473 32338 31660 28035 22540 22887
#> [321] 32162 31518 33350 31726 28974 25057 25327 36907 37920 38739
#> [331] 36501 32231 28536 28743 39715 37682 38777 37613 33745 27601
#> [341] 26136 34774 45212 43532 42328 38633 31810 31803 44929 38619
#> [351] 35849 33974 29187 23533 24060 34658 31435 30414 29710 29479
#> [361] 26645 31084 40768 38848 36756 35851 32108 28567 32083 41589
#> [371] 36548 34837 32604 29058 26316 32059 43733 39279 39264 38465
#> [381] 35612 32306 36418 50304 48321 47775 46419 43560 37878 43752
#> [391] 57743 52529 51661 45194 40664 35103 35764 47466 42124 43045
#> [401] 41391 40251 33569 34814 45109 38019 35986 33662 30318 27436
#> [411] 30586 44126 42246 42942 40999 37763 32885 35532 50948 46430
#> [421] 45895 44062 39606 35335 37250 50733 48197 46772 43425 39330
#> [431] 33303 39706 56289 55695 54820 50319 45667 38784 41051 59694
#> [441] 56258 58827 56995 52492 48594 53158 87169 102788 112703 106055
#> [451] 95897 88883 89133 133966 150293 161560 160633 137268 70363 116287
#> [461] 195011 212469 272798 236576 188567 118275 181068 229901 275647 222174
#> [471] 172980 120287 93615 95790 132959 115245 103219 96412 86325 77950
#> [481] 98097 131514 118857 111760 100324 91730 81733 102365 127364 113202
#> [491] 108668 96201 84026 73512 87702 105051 93949 88418 76644 63264
#> [501] 52305 60552 76483 69661 64339 52293 44559 37529 41755 54745
#> [511] 52502 51572 44716 33241 34647 37720 45132 39188 36477 30631
#> [521] 27837 25089 31360 44649 44795 46179 43761 41408 38759 49026
#> [531] 68520 70112 73531 70510 67030 62078 75739 99834 93708 91751
#> [541] 82853 75285 67417 81054 109286 99095 94185 82905 72430 61456
#> [551] 68336 92857 80126 73643 54791 47462 37592 42179 53727 49101
#> [561] 44750 38709 32988 27885 30952 37371 33771 31685 26639 21617
#> [571] 19925 20144 25223 25772 21457 18464 15703 13210 14714 17109
#> [581] 14560 13055 11608 10012 8354 9034 11907 13318 11672 10221
#> [591] 8954 7517 9062 10702 9748 8725 7642 6942 6120 7973
#> [601] 9417 8286 7638 6820 5821 5019 5997 7313 6679 6293
#> [611] 5753 5409 4988 5680 7115 7093 7011 6209 6635 7492
#> [621] 9815 11747 11411 11784 11319 10784 10077 12693 15272 15141
#> [631] 14837 14225 13919 13623 16997 19942 20896 20873 19590 18350
#> [641] 16800 20778 25104 25041 24601 24240 23650 21961 27780 33704
#> [651] 31415 29698 26454 24611 21246 25096 29826 26946 23856 21100
#> [661] 18359 15017 17236 18718 16670 16169 14158 12378 9934 11275
#> [671] 13299 11725 10544 9329 8508 7325 8426 9835 9170 8353
#> [681] 7296 6548 5420 6547 8068 7309 6748 6193 5339 4495
#> [691] 5363 6424 5559 5032 4564 4012 3502 4085 5224 4778
#> [701] 4554 3796 3451 3112 3439 4662 5226 4616 4350 3808
#> [711] 3417 4288 5125 4578 4235 3747 3553 3268 4347 5308
#> [721] 5148 4973 4634 4134 3521 4339 6166 7828 7553 6815
#> [731] 6485 5719 7240 8618 8255 8414 7895 7615 7065 9204
#> [741] 11692 10965 10231 9389 8950 7053 8558 10497 9461 8769
#> [751] 8134 7970 6442 7780 10005 8235 7598 6576 6297 4968
#> [761] 5523 6807 5665 5449 4855 4401 3583 4271 5129 4549
#> [771] 4014 3678 3107 2665 3267 4321 3829 3576 3205 2893
#> [781] 2433 2912 3923 3534 3260 3037 2773 2431 2890 3938
#> [791] 3805 3616 3329 2902 2551 3448 4639 4386 3980 3505
#> [801] 3596 2748 3786 5325 5241 5195 4537 4216 3570 4631
#> [811] 6986 7111 6533 6094 6084 4743 5772 9073 8631 7802
#> [821] 6877 5741 4132 3694 4950 6605 8419 7718 6126 4287
#>
#> $data$time
#> [1] "2020-09-23" "2020-09-24" "2020-09-25" "2020-09-26" "2020-09-27"
#> [6] "2020-09-28" "2020-09-29" "2020-09-30" "2020-10-01" "2020-10-02"
#> [11] "2020-10-03" "2020-10-04" "2020-10-05" "2020-10-06" "2020-10-07"
#> [16] "2020-10-08" "2020-10-09" "2020-10-10" "2020-10-11" "2020-10-12"
#> [21] "2020-10-13" "2020-10-14" "2020-10-15" "2020-10-16" "2020-10-17"
#> [26] "2020-10-18" "2020-10-19" "2020-10-20" "2020-10-21" "2020-10-22"
#> [31] "2020-10-23" "2020-10-24" "2020-10-25" "2020-10-26" "2020-10-27"
#> [36] "2020-10-28" "2020-10-29" "2020-10-30" "2020-10-31" "2020-11-01"
#> [41] "2020-11-02" "2020-11-03" "2020-11-04" "2020-11-05" "2020-11-06"
#> [46] "2020-11-07" "2020-11-08" "2020-11-09" "2020-11-10" "2020-11-11"
#> [51] "2020-11-12" "2020-11-13" "2020-11-14" "2020-11-15" "2020-11-16"
#> [56] "2020-11-17" "2020-11-18" "2020-11-19" "2020-11-20" "2020-11-21"
#> [61] "2020-11-22" "2020-11-23" "2020-11-24" "2020-11-25" "2020-11-26"
#> [66] "2020-11-27" "2020-11-28" "2020-11-29" "2020-11-30" "2020-12-01"
#> [71] "2020-12-02" "2020-12-03" "2020-12-04" "2020-12-05" "2020-12-06"
#> [76] "2020-12-07" "2020-12-08" "2020-12-09" "2020-12-10" "2020-12-11"
#> [81] "2020-12-12" "2020-12-13" "2020-12-14" "2020-12-15" "2020-12-16"
#> [86] "2020-12-17" "2020-12-18" "2020-12-19" "2020-12-20" "2020-12-21"
#> [91] "2020-12-22" "2020-12-23" "2020-12-24" "2020-12-25" "2020-12-26"
#> [96] "2020-12-27" "2020-12-28" "2020-12-29" "2020-12-30" "2020-12-31"
#> [101] "2021-01-01" "2021-01-02" "2021-01-03" "2021-01-04" "2021-01-05"
#> [106] "2021-01-06" "2021-01-07" "2021-01-08" "2021-01-09" "2021-01-10"
#> [111] "2021-01-11" "2021-01-12" "2021-01-13" "2021-01-14" "2021-01-15"
#> [116] "2021-01-16" "2021-01-17" "2021-01-18" "2021-01-19" "2021-01-20"
#> [121] "2021-01-21" "2021-01-22" "2021-01-23" "2021-01-24" "2021-01-25"
#> [126] "2021-01-26" "2021-01-27" "2021-01-28" "2021-01-29" "2021-01-30"
#> [131] "2021-01-31" "2021-02-01" "2021-02-02" "2021-02-03" "2021-02-04"
#> [136] "2021-02-05" "2021-02-06" "2021-02-07" "2021-02-08" "2021-02-09"
#> [141] "2021-02-10" "2021-02-11" "2021-02-12" "2021-02-13" "2021-02-14"
#> [146] "2021-02-15" "2021-02-16" "2021-02-17" "2021-02-18" "2021-02-19"
#> [151] "2021-02-20" "2021-02-21" "2021-02-22" "2021-02-23" "2021-02-24"
#> [156] "2021-02-25" "2021-02-26" "2021-02-27" "2021-02-28" "2021-03-01"
#> [161] "2021-03-02" "2021-03-03" "2021-03-04" "2021-03-05" "2021-03-06"
#> [166] "2021-03-07" "2021-03-08" "2021-03-09" "2021-03-10" "2021-03-11"
#> [171] "2021-03-12" "2021-03-13" "2021-03-14" "2021-03-15" "2021-03-16"
#> [176] "2021-03-17" "2021-03-18" "2021-03-19" "2021-03-20" "2021-03-21"
#> [181] "2021-03-22" "2021-03-23" "2021-03-24" "2021-03-25" "2021-03-26"
#> [186] "2021-03-27" "2021-03-28" "2021-03-29" "2021-03-30" "2021-03-31"
#> [191] "2021-04-01" "2021-04-02" "2021-04-03" "2021-04-04" "2021-04-05"
#> [196] "2021-04-06" "2021-04-07" "2021-04-08" "2021-04-09" "2021-04-10"
#> [201] "2021-04-11" "2021-04-12" "2021-04-13" "2021-04-14" "2021-04-15"
#> [206] "2021-04-16" "2021-04-17" "2021-04-18" "2021-04-19" "2021-04-20"
#> [211] "2021-04-21" "2021-04-22" "2021-04-23" "2021-04-24" "2021-04-25"
#> [216] "2021-04-26" "2021-04-27" "2021-04-28" "2021-04-29" "2021-04-30"
#> [221] "2021-05-01" "2021-05-02" "2021-05-03" "2021-05-04" "2021-05-05"
#> [226] "2021-05-06" "2021-05-07" "2021-05-08" "2021-05-09" "2021-05-10"
#> [231] "2021-05-11" "2021-05-12" "2021-05-13" "2021-05-14" "2021-05-15"
#> [236] "2021-05-16" "2021-05-17" "2021-05-18" "2021-05-19" "2021-05-20"
#> [241] "2021-05-21" "2021-05-22" "2021-05-23" "2021-05-24" "2021-05-25"
#> [246] "2021-05-26" "2021-05-27" "2021-05-28" "2021-05-29" "2021-05-30"
#> [251] "2021-05-31" "2021-06-01" "2021-06-02" "2021-06-03" "2021-06-04"
#> [256] "2021-06-05" "2021-06-06" "2021-06-07" "2021-06-08" "2021-06-09"
#> [261] "2021-06-10" "2021-06-11" "2021-06-12" "2021-06-13" "2021-06-14"
#> [266] "2021-06-15" "2021-06-16" "2021-06-17" "2021-06-18" "2021-06-19"
#> [271] "2021-06-20" "2021-06-21" "2021-06-22" "2021-06-23" "2021-06-24"
#> [276] "2021-06-25" "2021-06-26" "2021-06-27" "2021-06-28" "2021-06-29"
#> [281] "2021-06-30" "2021-07-01" "2021-07-02" "2021-07-03" "2021-07-04"
#> [286] "2021-07-05" "2021-07-06" "2021-07-07" "2021-07-08" "2021-07-09"
#> [291] "2021-07-10" "2021-07-11" "2021-07-12" "2021-07-13" "2021-07-14"
#> [296] "2021-07-15" "2021-07-16" "2021-07-17" "2021-07-18" "2021-07-19"
#> [301] "2021-07-20" "2021-07-21" "2021-07-22" "2021-07-23" "2021-07-24"
#> [306] "2021-07-25" "2021-07-26" "2021-07-27" "2021-07-28" "2021-07-29"
#> [311] "2021-07-30" "2021-07-31" "2021-08-01" "2021-08-02" "2021-08-03"
#> [316] "2021-08-04" "2021-08-05" "2021-08-06" "2021-08-07" "2021-08-08"
#> [321] "2021-08-09" "2021-08-10" "2021-08-11" "2021-08-12" "2021-08-13"
#> [326] "2021-08-14" "2021-08-15" "2021-08-16" "2021-08-17" "2021-08-18"
#> [331] "2021-08-19" "2021-08-20" "2021-08-21" "2021-08-22" "2021-08-23"
#> [336] "2021-08-24" "2021-08-25" "2021-08-26" "2021-08-27" "2021-08-28"
#> [341] "2021-08-29" "2021-08-30" "2021-08-31" "2021-09-01" "2021-09-02"
#> [346] "2021-09-03" "2021-09-04" "2021-09-05" "2021-09-06" "2021-09-07"
#> [351] "2021-09-08" "2021-09-09" "2021-09-10" "2021-09-11" "2021-09-12"
#> [356] "2021-09-13" "2021-09-14" "2021-09-15" "2021-09-16" "2021-09-17"
#> [361] "2021-09-18" "2021-09-19" "2021-09-20" "2021-09-21" "2021-09-22"
#> [366] "2021-09-23" "2021-09-24" "2021-09-25" "2021-09-26" "2021-09-27"
#> [371] "2021-09-28" "2021-09-29" "2021-09-30" "2021-10-01" "2021-10-02"
#> [376] "2021-10-03" "2021-10-04" "2021-10-05" "2021-10-06" "2021-10-07"
#> [381] "2021-10-08" "2021-10-09" "2021-10-10" "2021-10-11" "2021-10-12"
#> [386] "2021-10-13" "2021-10-14" "2021-10-15" "2021-10-16" "2021-10-17"
#> [391] "2021-10-18" "2021-10-19" "2021-10-20" "2021-10-21" "2021-10-22"
#> [396] "2021-10-23" "2021-10-24" "2021-10-25" "2021-10-26" "2021-10-27"
#> [401] "2021-10-28" "2021-10-29" "2021-10-30" "2021-10-31" "2021-11-01"
#> [406] "2021-11-02" "2021-11-03" "2021-11-04" "2021-11-05" "2021-11-06"
#> [411] "2021-11-07" "2021-11-08" "2021-11-09" "2021-11-10" "2021-11-11"
#> [416] "2021-11-12" "2021-11-13" "2021-11-14" "2021-11-15" "2021-11-16"
#> [421] "2021-11-17" "2021-11-18" "2021-11-19" "2021-11-20" "2021-11-21"
#> [426] "2021-11-22" "2021-11-23" "2021-11-24" "2021-11-25" "2021-11-26"
#> [431] "2021-11-27" "2021-11-28" "2021-11-29" "2021-11-30" "2021-12-01"
#> [436] "2021-12-02" "2021-12-03" "2021-12-04" "2021-12-05" "2021-12-06"
#> [441] "2021-12-07" "2021-12-08" "2021-12-09" "2021-12-10" "2021-12-11"
#> [446] "2021-12-12" "2021-12-13" "2021-12-14" "2021-12-15" "2021-12-16"
#> [451] "2021-12-17" "2021-12-18" "2021-12-19" "2021-12-20" "2021-12-21"
#> [456] "2021-12-22" "2021-12-23" "2021-12-24" "2021-12-25" "2021-12-26"
#> [461] "2021-12-27" "2021-12-28" "2021-12-29" "2021-12-30" "2021-12-31"
#> [466] "2022-01-01" "2022-01-02" "2022-01-03" "2022-01-04" "2022-01-05"
#> [471] "2022-01-06" "2022-01-07" "2022-01-08" "2022-01-09" "2022-01-10"
#> [476] "2022-01-11" "2022-01-12" "2022-01-13" "2022-01-14" "2022-01-15"
#> [481] "2022-01-16" "2022-01-17" "2022-01-18" "2022-01-19" "2022-01-20"
#> [486] "2022-01-21" "2022-01-22" "2022-01-23" "2022-01-24" "2022-01-25"
#> [491] "2022-01-26" "2022-01-27" "2022-01-28" "2022-01-29" "2022-01-30"
#> [496] "2022-01-31" "2022-02-01" "2022-02-02" "2022-02-03" "2022-02-04"
#> [501] "2022-02-05" "2022-02-06" "2022-02-07" "2022-02-08" "2022-02-09"
#> [506] "2022-02-10" "2022-02-11" "2022-02-12" "2022-02-13" "2022-02-14"
#> [511] "2022-02-15" "2022-02-16" "2022-02-17" "2022-02-18" "2022-02-19"
#> [516] "2022-02-20" "2022-02-21" "2022-02-22" "2022-02-23" "2022-02-24"
#> [521] "2022-02-25" "2022-02-26" "2022-02-27" "2022-02-28" "2022-03-01"
#> [526] "2022-03-02" "2022-03-03" "2022-03-04" "2022-03-05" "2022-03-06"
#> [531] "2022-03-07" "2022-03-08" "2022-03-09" "2022-03-10" "2022-03-11"
#> [536] "2022-03-12" "2022-03-13" "2022-03-14" "2022-03-15" "2022-03-16"
#> [541] "2022-03-17" "2022-03-18" "2022-03-19" "2022-03-20" "2022-03-21"
#> [546] "2022-03-22" "2022-03-23" "2022-03-24" "2022-03-25" "2022-03-26"
#> [551] "2022-03-27" "2022-03-28" "2022-03-29" "2022-03-30" "2022-03-31"
#> [556] "2022-04-01" "2022-04-02" "2022-04-03" "2022-04-04" "2022-04-05"
#> [561] "2022-04-06" "2022-04-07" "2022-04-08" "2022-04-09" "2022-04-10"
#> [566] "2022-04-11" "2022-04-12" "2022-04-13" "2022-04-14" "2022-04-15"
#> [571] "2022-04-16" "2022-04-17" "2022-04-18" "2022-04-19" "2022-04-20"
#> [576] "2022-04-21" "2022-04-22" "2022-04-23" "2022-04-24" "2022-04-25"
#> [581] "2022-04-26" "2022-04-27" "2022-04-28" "2022-04-29" "2022-04-30"
#> [586] "2022-05-01" "2022-05-02" "2022-05-03" "2022-05-04" "2022-05-05"
#> [591] "2022-05-06" "2022-05-07" "2022-05-08" "2022-05-09" "2022-05-10"
#> [596] "2022-05-11" "2022-05-12" "2022-05-13" "2022-05-14" "2022-05-15"
#> [601] "2022-05-16" "2022-05-17" "2022-05-18" "2022-05-19" "2022-05-20"
#> [606] "2022-05-21" "2022-05-22" "2022-05-23" "2022-05-24" "2022-05-25"
#> [611] "2022-05-26" "2022-05-27" "2022-05-28" "2022-05-29" "2022-05-30"
#> [616] "2022-05-31" "2022-06-01" "2022-06-02" "2022-06-03" "2022-06-04"
#> [621] "2022-06-05" "2022-06-06" "2022-06-07" "2022-06-08" "2022-06-09"
#> [626] "2022-06-10" "2022-06-11" "2022-06-12" "2022-06-13" "2022-06-14"
#> [631] "2022-06-15" "2022-06-16" "2022-06-17" "2022-06-18" "2022-06-19"
#> [636] "2022-06-20" "2022-06-21" "2022-06-22" "2022-06-23" "2022-06-24"
#> [641] "2022-06-25" "2022-06-26" "2022-06-27" "2022-06-28" "2022-06-29"
#> [646] "2022-06-30" "2022-07-01" "2022-07-02" "2022-07-03" "2022-07-04"
#> [651] "2022-07-05" "2022-07-06" "2022-07-07" "2022-07-08" "2022-07-09"
#> [656] "2022-07-10" "2022-07-11" "2022-07-12" "2022-07-13" "2022-07-14"
#> [661] "2022-07-15" "2022-07-16" "2022-07-17" "2022-07-18" "2022-07-19"
#> [666] "2022-07-20" "2022-07-21" "2022-07-22" "2022-07-23" "2022-07-24"
#> [671] "2022-07-25" "2022-07-26" "2022-07-27" "2022-07-28" "2022-07-29"
#> [676] "2022-07-30" "2022-07-31" "2022-08-01" "2022-08-02" "2022-08-03"
#> [681] "2022-08-04" "2022-08-05" "2022-08-06" "2022-08-07" "2022-08-08"
#> [686] "2022-08-09" "2022-08-10" "2022-08-11" "2022-08-12" "2022-08-13"
#> [691] "2022-08-14" "2022-08-15" "2022-08-16" "2022-08-17" "2022-08-18"
#> [696] "2022-08-19" "2022-08-20" "2022-08-21" "2022-08-22" "2022-08-23"
#> [701] "2022-08-24" "2022-08-25" "2022-08-26" "2022-08-27" "2022-08-28"
#> [706] "2022-08-29" "2022-08-30" "2022-08-31" "2022-09-01" "2022-09-02"
#> [711] "2022-09-03" "2022-09-04" "2022-09-05" "2022-09-06" "2022-09-07"
#> [716] "2022-09-08" "2022-09-09" "2022-09-10" "2022-09-11" "2022-09-12"
#> [721] "2022-09-13" "2022-09-14" "2022-09-15" "2022-09-16" "2022-09-17"
#> [726] "2022-09-18" "2022-09-19" "2022-09-20" "2022-09-21" "2022-09-22"
#> [731] "2022-09-23" "2022-09-24" "2022-09-25" "2022-09-26" "2022-09-27"
#> [736] "2022-09-28" "2022-09-29" "2022-09-30" "2022-10-01" "2022-10-02"
#> [741] "2022-10-03" "2022-10-04" "2022-10-05" "2022-10-06" "2022-10-07"
#> [746] "2022-10-08" "2022-10-09" "2022-10-10" "2022-10-11" "2022-10-12"
#> [751] "2022-10-13" "2022-10-14" "2022-10-15" "2022-10-16" "2022-10-17"
#> [756] "2022-10-18" "2022-10-19" "2022-10-20" "2022-10-21" "2022-10-22"
#> [761] "2022-10-23" "2022-10-24" "2022-10-25" "2022-10-26" "2022-10-27"
#> [766] "2022-10-28" "2022-10-29" "2022-10-30" "2022-10-31" "2022-11-01"
#> [771] "2022-11-02" "2022-11-03" "2022-11-04" "2022-11-05" "2022-11-06"
#> [776] "2022-11-07" "2022-11-08" "2022-11-09" "2022-11-10" "2022-11-11"
#> [781] "2022-11-12" "2022-11-13" "2022-11-14" "2022-11-15" "2022-11-16"
#> [786] "2022-11-17" "2022-11-18" "2022-11-19" "2022-11-20" "2022-11-21"
#> [791] "2022-11-22" "2022-11-23" "2022-11-24" "2022-11-25" "2022-11-26"
#> [796] "2022-11-27" "2022-11-28" "2022-11-29" "2022-11-30" "2022-12-01"
#> [801] "2022-12-02" "2022-12-03" "2022-12-04" "2022-12-05" "2022-12-06"
#> [806] "2022-12-07" "2022-12-08" "2022-12-09" "2022-12-10" "2022-12-11"
#> [811] "2022-12-12" "2022-12-13" "2022-12-14" "2022-12-15" "2022-12-16"
#> [816] "2022-12-17" "2022-12-18" "2022-12-19" "2022-12-20" "2022-12-21"
#> [821] "2022-12-22" "2022-12-23" "2022-12-24" "2022-12-25" "2022-12-26"
#> [826] "2022-12-27" "2022-12-28" "2022-12-29" "2022-12-30" "2022-12-31"
#>
#> $data$component_pathogens
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 10 7 9 15 5 6 23 54 32 15 23 8 35 39
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
#> [1,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 45 25 18 12 25 47 34 18 11 23 24 33
#> [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38]
#> [1,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 47 55 46 21 7 8 9 10 3 3 4 1
#> [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50]
#> [1,] 0 3 1 0 0 0 0 1 2 0 0 1
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 3 22 25 7 6 14 32 14 10 21 25 18
#> [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62]
#> [1,] 0 0 0 2 4 1 1 3 3 3 2 4
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 20 25 26 10 38 14 4 13 11 8 14 14
#> [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74]
#> [1,] 6 14 4 4 7 6 3 4 8 0 1 0
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 14 7 6 10 6 15 11 14 4 1 0 0
#> [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86]
#> [1,] 0 18 16 12 12 14 7 10 27 63 57 64
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 5 5 11 11 7 7 5 5 38 34 52 46
#> [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98]
#> [1,] 47 17 30 52 65 69 0 0 1 48 60 111
#> [2,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0 0 0
#> [4,] 34 21 16 29 32 29 0 0 0 27 21 41
#> [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108]
#> [1,] 68 15 0 35 50 125 93 67 50 55
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 13 14 0 22 18 39 28 21 9 15
#> [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118]
#> [1,] 40 48 81 75 70 38 46 43 45 67
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 11 17 10 18 18 4 2 12 4 7
#> [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
#> [1,] 54 53 39 34 29 17 19 51 53 44
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 4 17 2 6 5 4 6 1 4 4
#> [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138]
#> [1,] 39 22 47 36 26 24 31 18 29 2
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 5 3 5 4 0 1 1 0 1 0
#> [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
#> [1,] 33 25 29 23 20 10 8 22 26 17
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 1 2 1 1 0 2 1 0 0
#> [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158]
#> [1,] 6 5 6 8 13 16 13 11 10 7
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 1 0 1 0 0 1 0
#> [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
#> [1,] 11 10 14 15 11 4 9 6 13 6
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 1 2 0 3 0 0 1 0 0 0
#> [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177] [,178]
#> [1,] 11 10 15 12 8 20 6 6 12 4
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 1 0 0 0 0 0 2 0 0 0
#> [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187] [,188]
#> [1,] 7 8 11 8 8 13 4 8 8 10
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 1 0 0 0 0 0 0 1 0 1
#> [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198]
#> [1,] 11 9 8 5 3 0 5 7 8 2
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
#> [1,] 5 6 10 8 4 5 6 3 0 1
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217] [,218]
#> [1,] 5 7 3 2 3 3 1 3 4 2
#> [2,] 0 0 0 0 0 0 0 0 0 1
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 1 0 0 0 0 0 0 0
#> [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227] [,228]
#> [1,] 2 5 3 0 5 1 0 1 2 2
#> [2,] 0 0 0 0 0 0 0 0 0 1
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237] [,238]
#> [1,] 0 1 2 3 2 2 0 0 4 1
#> [2,] 0 0 0 0 0 0 0 0 0 10
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248]
#> [1,] 2 1 0 0 2 0 2 2 2 1
#> [2,] 0 0 4 2 1 4 3 3 0 1
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257] [,258]
#> [1,] 0 1 0 4 0 2 2 0 0 0
#> [2,] 10 2 3 7 6 2 10 6 3 6
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 1 0 0 0 0 0 0
#> [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267] [,268]
#> [1,] 0 1 2 1 1 0 2 1 1 0
#> [2,] 13 8 6 6 10 6 20 9 7 9
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277] [,278]
#> [1,] 1 0 0 0 2 0 2 0 0 1
#> [2,] 18 16 6 22 21 26 26 22 24 24
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 1 0 1 0 0 0 0
#> [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288]
#> [1,] 0 1 0 1 1 0 1 0 0 0
#> [2,] 37 29 40 30 39 21 23 55 61 83
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 61 63 55 42 73 80 66 94 60 58
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307] [,308]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 79 111 106 111 94 106 70 55 42 28
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 1 0
#> [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317] [,318]
#> [1,] 0 0 0 0 0 0 0 1 0 0
#> [2,] 37 54 70 49 49 66 85 70 94 56
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327] [,328]
#> [1,] 0 0 0 0 1 0 0 0 0 0
#> [2,] 40 39 48 64 86 71 64 49 56 70
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337] [,338]
#> [1,] 1 0 0 0 0 1 0 0 0 0
#> [2,] 97 86 49 58 74 65 68 92 80 73
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347] [,348]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 66 58 53 48 106 82 83 72 73 58
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357] [,358]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 74 93 107 101 74 66 50 99 86 75
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367] [,368]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 78 69 70 77 76 88 98 103 96 103
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377] [,378]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 93 102 119 113 100 104 111 118 127 112
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387] [,388]
#> [1,] 0 0 0 0 0 0 0 0 1 0
#> [2,] 143 122 134 141 87 103 124 161 145 151
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397] [,398]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 178 156 188 155 179 159 126 141 173 161
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407] [,408]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 161 184 147 110 94 149 122 150 148 148
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417] [,418]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 116 94 119 113 124 126 110 95 105 96
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426] [,427] [,428]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 131 166 123 93 116 106 119 119 147 150
#> [3,] 0 0 0 0 0 0 0 0 0 0
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,429] [,430] [,431] [,432] [,433] [,434] [,435] [,436] [,437] [,438]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 128 93 111 97 122 146 125 136 117 121
#> [3,] 0 0 0 0 2 0 0 0 1 2
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,439] [,440] [,441] [,442] [,443] [,444] [,445] [,446] [,447] [,448]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 108 95 137 106 123 85 81 84 95 117
#> [3,] 5 6 10 16 7 15 15 26 64 88
#> [4,] 0 0 0 0 0 0 0 0 0 2
#> [,449] [,450] [,451] [,452] [,453] [,454] [,455] [,456] [,457] [,458]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 133 111 94 72 70 122 112 87 55 0
#> [3,] 124 111 138 150 164 256 331 283 220 0
#> [4,] 0 0 0 0 0 0 1 0 0 0
#> [,459] [,460] [,461] [,462] [,463] [,464] [,465] [,466] [,467] [,468]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 38 37 28 29 15 0 12 15
#> [3,] 0 4 335 510 525 520 322 2 410 573
#> [4,] 0 0 1 0 0 0 0 0 0 0
#> [,469] [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477] [,478]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 22 13 10 6 5 13 7 7 5 2
#> [3,] 594 579 570 495 410 421 436 500 469 334
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,479] [,480] [,481] [,482] [,483] [,484] [,485] [,486] [,487] [,488]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 3 7 3 4 3 2 1 2 1 0
#> [3,] 337 348 341 411 452 329 258 321 327 295
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496] [,497] [,498]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 1 2 0 0 2 0 2 1 0 1
#> [3,] 408 450 425 352 303 356 388 475 517 501
#> [4,] 0 0 0 0 0 0 0 1 0 0
#> [,499] [,500] [,501] [,502] [,503] [,504] [,505] [,506] [,507] [,508]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 1 0 0 0 2 0 1 0
#> [3,] 398 372 319 359 423 400 417 346 281 316
#> [4,] 1 0 0 0 0 0 0 0 0 0
#> [,509] [,510] [,511] [,512] [,513] [,514] [,515] [,516] [,517] [,518]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 1 0 0 0 0 0 0 0 1
#> [3,] 255 282 329 308 275 201 226 269 265 272
#> [4,] 0 0 2 0 0 0 0 0 0 3
#> [,519] [,520] [,521] [,522] [,523] [,524] [,525] [,526] [,527] [,528]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 274 253 229 237 280 283 289 254 233 262
#> [4,] 1 1 0 0 0 1 0 0 0 0
#> [,529] [,530] [,531] [,532] [,533] [,534] [,535] [,536] [,537] [,538]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 2 0 0 0 0 0 0 0 0
#> [3,] 300 282 380 385 430 451 435 420 522 563
#> [4,] 0 0 1 0 3 2 2 1 5 3
#> [,539] [,540] [,541] [,542] [,543] [,544] [,545] [,546] [,547] [,548]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 1 0
#> [3,] 649 614 463 427 394 507 702 752 718 725
#> [4,] 3 7 3 0 4 7 6 3 5 2
#> [,549] [,550] [,551] [,552] [,553] [,554] [,555] [,556] [,557] [,558]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 590 662 560 831 860 811 673 489 474 479
#> [4,] 5 9 6 9 6 11 3 4 3 4
#> [,559] [,560] [,561] [,562] [,563] [,564] [,565] [,566] [,567] [,568]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 639 648 558 458 351 294 399 578 588 585
#> [4,] 6 4 6 2 2 4 1 3 4 3
#> [,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576] [,577] [,578]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 480 367 239 3 355 413 432 370 314 276
#> [4,] 4 0 1 0 4 6 4 1 9 2
#> [,579] [,580] [,581] [,582] [,583] [,584] [,585] [,586] [,587] [,588]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 204 252 285 196 183 152 133 101 157 166
#> [4,] 2 0 1 0 1 0 0 2 4 1
#> [,589] [,590] [,591] [,592] [,593] [,594] [,595] [,596] [,597] [,598]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 173 176 109 109 108 145 158 167 127 99
#> [4,] 0 0 2 2 3 1 4 0 0 7
#> [,599] [,600] [,601] [,602] [,603] [,604] [,605] [,606] [,607] [,608]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 101 88 139 131 154 150 106 78 83 110
#> [4,] 0 0 1 3 1 0 1 1 1 0
#> [,609] [,610] [,611] [,612] [,613] [,614] [,615] [,616] [,617] [,618]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 118 113 99 85 81 69 115 123 111 84
#> [4,] 0 0 1 0 1 1 0 0 3 0
#> [,619] [,620] [,621] [,622] [,623] [,624] [,625] [,626] [,627] [,628]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 1 116 103 171 206 190 170 192 119 121
#> [4,] 0 0 0 1 1 2 0 0 0 0
#> [,629] [,630] [,631] [,632] [,633] [,634] [,635] [,636] [,637] [,638]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 225 187 229 162 156 156 162 253 284 271
#> [4,] 0 2 0 0 0 1 0 1 1 0
#> [,639] [,640] [,641] [,642] [,643] [,644] [,645] [,646] [,647] [,648]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 245 256 208 228 330 322 325 297 270 229
#> [4,] 0 0 1 0 0 1 0 2 0 0
#> [,649] [,650] [,651] [,652] [,653] [,654] [,655] [,656] [,657] [,658]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 230 283 299 321 297 241 173 155 291 325
#> [4,] 0 0 0 0 0 1 1 0 0 0
#> [,659] [,660] [,661] [,662] [,663] [,664] [,665] [,666] [,667] [,668]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 283 312 268 226 151 287 334 373 348 336
#> [4,] 2 0 0 1 1 1 0 1 0 0
#> [,669] [,670] [,671] [,672] [,673] [,674] [,675] [,676] [,677] [,678]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 180 167 427 340 311 262 181 113 92 201
#> [4,] 0 0 4 1 0 0 2 0 0 0
#> [,679] [,680] [,681] [,682] [,683] [,684] [,685] [,686] [,687] [,688]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 138 101 118 97 49 27 171 112 69 95
#> [4,] 0 0 0 1 0 0 0 0 0 0
#> [,689] [,690] [,691] [,692] [,693] [,694] [,695] [,696] [,697] [,698]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 94 58 43 180 103 105 88 92 63 43
#> [4,] 0 0 0 0 0 0 0 0 2 0
#> [,699] [,700] [,701] [,702] [,703] [,704] [,705] [,706] [,707] [,708]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 162 116 105 64 75 31 23 72 114 42
#> [4,] 0 0 0 0 0 0 0 0 1 1
#> [,709] [,710] [,711] [,712] [,713] [,714] [,715] [,716] [,717] [,718]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 179 95 59 50 187 125 55 30 38 55
#> [4,] 0 0 0 0 0 0 0 0 0 0
#> [,719] [,720] [,721] [,722] [,723] [,724] [,725] [,726] [,727] [,728]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 55 182 95 114 119 106 69 22 57 228
#> [4,] 0 0 1 0 3 1 1 0 0 0
#> [,729] [,730] [,731] [,732] [,733] [,734] [,735] [,736] [,737] [,738]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 179 179 138 83 92 227 167 180 175 102
#> [4,] 0 0 0 1 1 4 2 0 0 0
#> [,739] [,740] [,741] [,742] [,743] [,744] [,745] [,746] [,747] [,748]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 61 95 274 237 262 301 246 126 90 369
#> [4,] 1 2 2 1 0 2 1 0 2 2
#> [,749] [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757] [,758]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 257 188 118 259 102 101 398 242 162 65
#> [4,] 1 1 2 3 1 4 12 9 7 2
#> [,759] [,760] [,761] [,762] [,763] [,764] [,765] [,766] [,767] [,768]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 247 105 56 207 78 254 170 177 70 68
#> [4,] 8 2 0 2 1 5 2 5 2 1
#> [,769] [,770] [,771] [,772] [,773] [,774] [,775] [,776] [,777] [,778]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 177 124 121 119 126 51 65 135 110 96
#> [4,] 6 5 4 5 2 2 2 6 2 4
#> [,779] [,780] [,781] [,782] [,783] [,784] [,785] [,786] [,787] [,788]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 103 98 55 42 119 75 64 72 64 54
#> [4,] 3 1 2 2 7 5 5 5 3 0
#> [,789] [,790] [,791] [,792] [,793] [,794] [,795] [,796] [,797] [,798]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 54 115 110 85 81 65 69 59 232 109
#> [4,] 6 10 8 8 8 4 5 2 16 3
#> [,799] [,800] [,801] [,802] [,803] [,804] [,805] [,806] [,807] [,808]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 77 65 150 70 63 218 216 187 153 92
#> [4,] 4 8 9 9 7 13 14 11 6 11
#> [,809] [,810] [,811] [,812] [,813] [,814] [,815] [,816] [,817] [,818]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 116 100 322 170 98 125 329 159 124 516
#> [4,] 17 8 32 16 10 13 39 13 12 39
#> [,819] [,820] [,821] [,822] [,823] [,824] [,825] [,826] [,827] [,828]
#> [1,] 0 0 0 0 0 0 0 0 0 0
#> [2,] 0 0 0 0 0 0 0 0 0 0
#> [3,] 401 300 165 73 22 7 21 165 451 396
#> [4,] 36 25 33 5 0 0 3 21 42 41
#> [,829] [,830]
#> [1,] 0 0
#> [2,] 0 0
#> [3,] 232 78
#> [4,] 29 3
#>
#>
#> $model_params
#> $model_params$cov_structure
#> [1] 1
#>
#> $model_params$noise_structure
#> [1] 0
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"