Single pathogen structure
Value
formatted list with pathogen structure and data of class `EpiStrainDynamics.pathogen_structure`.
Examples
single(
case_timeseries = sarscov2$cases,
time = sarscov2$date,
pathogen_name = 'SARS-COV-2' # preserved as provided
)
#> $pathogen_structure
#> [1] "single"
#>
#> $pathogen_names
#> [1] "SARS-COV-2"
#>
#> $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"
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"
single(
case_timeseries = sarscov2$cases,
time = sarscov2$date,
pathogen_name = 'sarscov2' # preserved as provided
)
#> $pathogen_structure
#> [1] "single"
#>
#> $pathogen_names
#> [1] "sarscov2"
#>
#> $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"
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"
single(
case_timeseries = sarscov2$cases,
time = sarscov2$date
)
#> $pathogen_structure
#> [1] "single"
#>
#> $pathogen_names
#> [1] "default"
#>
#> $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"
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#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"