Multiple pathogen structure
Arguments
- data
dataframe containing columns with all relevant data, or a time series object (ts, xts, zoo, tsibble, etc.)
- case_timeseries
Column name containing case counts. Must be numeric or a
unitsobject from the units package.- component_pathogen_timeseries
vector of column names with additional pathogen case count timeseries to model. Must be numeric or a
unitsobject from the units package.- time
Column name with time data. Required for non-time-series input data. Flexible format - can be date, index, or others, accepted as
indexidentifiers in thetsibbletime format. Optional whendatais a time series class object (ts, mts, xts, zoo, zooreg, tsibble) as the time index will be automatically detected.
Value
named list including pathogen_structure, pathogen_names, and data
of class EpiStrainDynamics.pathogen_structure
See also
Other pathogen_structure:
single(),
subtyped()
Examples
# Using a data frame
multiple(
data = sarscov2,
case_timeseries = "cases",
component_pathogen_timeseries = c("alpha", "delta", "omicron", "other"),
time = "date"
)
#> $pathogen_structure
#> [1] "multiple"
#>
#> $pathogen_names
#> [1] "alpha" "delta" "omicron" "other"
#>
#> $validated_tsbl
#> # A tsibble: 830 x 6 [1D]
#> date case_timeseries alpha delta omicron other
#> <date> <dbl> <int> <int> <int> <int>
#> 1 2020-09-23 7096 0 0 0 10
#> 2 2020-09-24 7682 0 0 0 7
#> 3 2020-09-25 7318 0 0 0 9
#> 4 2020-09-26 6810 0 0 0 15
#> 5 2020-09-27 7023 0 0 0 5
#> 6 2020-09-28 9983 0 0 0 6
#> 7 2020-09-29 10366 0 0 0 23
#> 8 2020-09-30 12717 0 0 0 54
#> 9 2020-10-01 13357 0 0 0 32
#> 10 2020-10-02 13854 0 0 0 15
#> # ℹ 820 more rows
#>
#> $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
#>
#> $data$component_pathogens
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> alpha 0 0 0 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0 0
#> other 10 7 9 15 5 6 23 54 32 15 23 8 35
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> alpha 0 0 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 39 45 25 18 12 25 47 34 18 11 23 24
#> [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
#> alpha 0 0 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 33 47 55 46 21 7 8 9 10 3 3 4
#> [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49]
#> alpha 0 0 3 1 0 0 0 0 1 2 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 1 3 22 25 7 6 14 32 14 10 21 25
#> [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61]
#> alpha 1 0 0 0 2 4 1 1 3 3 3 2
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 18 20 25 26 10 38 14 4 13 11 8 14
#> [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73]
#> alpha 4 6 14 4 4 7 6 3 4 8 0 1
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 14 14 7 6 10 6 15 11 14 4 1 0
#> [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85]
#> alpha 0 0 18 16 12 12 14 7 10 27 63 57
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 0 5 5 11 11 7 7 5 5 38 34 52
#> [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97]
#> alpha 64 47 17 30 52 65 69 0 0 1 48 60
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 46 34 21 16 29 32 29 0 0 0 27 21
#> [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107]
#> alpha 111 68 15 0 35 50 125 93 67 50
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 41 13 14 0 22 18 39 28 21 9
#> [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117]
#> alpha 55 40 48 81 75 70 38 46 43 45
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 15 11 17 10 18 18 4 2 12 4
#> [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127]
#> alpha 67 54 53 39 34 29 17 19 51 53
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 7 4 17 2 6 5 4 6 1 4
#> [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
#> alpha 44 39 22 47 36 26 24 31 18 29
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 4 5 3 5 4 0 1 1 0 1
#> [,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147]
#> alpha 2 33 25 29 23 20 10 8 22 26
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 1 2 1 1 0 2 1 0
#> [,148] [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157]
#> alpha 17 6 5 6 8 13 16 13 11 10
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 1 0 1 0 0 1
#> [,158] [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167]
#> alpha 7 11 10 14 15 11 4 9 6 13
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 1 2 0 3 0 0 1 0 0
#> [,168] [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177]
#> alpha 6 11 10 15 12 8 20 6 6 12
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 1 0 0 0 0 0 2 0 0
#> [,178] [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187]
#> alpha 4 7 8 11 8 8 13 4 8 8
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 1 0 0 0 0 0 0 1 0
#> [,188] [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197]
#> alpha 10 11 9 8 5 3 0 5 7 8
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 1 0 0 0 0 0 0 0 0 0
#> [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207]
#> alpha 2 5 6 10 8 4 5 6 3 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,208] [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217]
#> alpha 1 5 7 3 2 3 3 1 3 4
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 1 0 0 0 0 0 0
#> [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227]
#> alpha 2 2 5 3 0 5 1 0 1 2
#> delta 1 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237]
#> alpha 2 0 1 2 3 2 2 0 0 4
#> delta 1 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,238] [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247]
#> alpha 1 2 1 0 0 2 0 2 2 2
#> delta 10 0 0 4 2 1 4 3 3 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,248] [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257]
#> alpha 1 0 1 0 4 0 2 2 0 0
#> delta 1 10 2 3 7 6 2 10 6 3
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 1 0 0 0 0 0
#> [,258] [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267]
#> alpha 0 0 1 2 1 1 0 2 1 1
#> delta 6 13 8 6 6 10 6 20 9 7
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,268] [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277]
#> alpha 0 1 0 0 0 2 0 2 0 0
#> delta 9 18 16 6 22 21 26 26 22 24
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 1 0 1 0 0 0
#> [,278] [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287]
#> alpha 1 0 1 0 1 1 0 1 0 0
#> delta 24 37 29 40 30 39 21 23 55 61
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,288] [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 83 61 63 55 42 73 80 66 94 60
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,298] [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 58 79 111 106 111 94 106 70 55 42
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 1
#> [,308] [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317]
#> alpha 0 0 0 0 0 0 0 0 1 0
#> delta 28 37 54 70 49 49 66 85 70 94
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,318] [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327]
#> alpha 0 0 0 0 0 1 0 0 0 0
#> delta 56 40 39 48 64 86 71 64 49 56
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,328] [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337]
#> alpha 0 1 0 0 0 0 1 0 0 0
#> delta 70 97 86 49 58 74 65 68 92 80
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,338] [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 73 66 58 53 48 106 82 83 72 73
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,348] [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 58 74 93 107 101 74 66 50 99 86
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,358] [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 75 78 69 70 77 76 88 98 103 96
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,368] [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 103 93 102 119 113 100 104 111 118 127
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,378] [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387]
#> alpha 0 0 0 0 0 0 0 0 0 1
#> delta 112 143 122 134 141 87 103 124 161 145
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,388] [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 151 178 156 188 155 179 159 126 141 173
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 161 161 184 147 110 94 149 122 150 148
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,408] [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 148 116 94 119 113 124 126 110 95 105
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,418] [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426] [,427]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 96 131 166 123 93 116 106 119 119 147
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,428] [,429] [,430] [,431] [,432] [,433] [,434] [,435] [,436] [,437]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 150 128 93 111 97 122 146 125 136 117
#> omicron 0 0 0 0 0 2 0 0 0 1
#> other 0 0 0 0 0 0 0 0 0 0
#> [,438] [,439] [,440] [,441] [,442] [,443] [,444] [,445] [,446] [,447]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 121 108 95 137 106 123 85 81 84 95
#> omicron 2 5 6 10 16 7 15 15 26 64
#> other 0 0 0 0 0 0 0 0 0 0
#> [,448] [,449] [,450] [,451] [,452] [,453] [,454] [,455] [,456] [,457]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 117 133 111 94 72 70 122 112 87 55
#> omicron 88 124 111 138 150 164 256 331 283 220
#> other 2 0 0 0 0 0 0 1 0 0
#> [,458] [,459] [,460] [,461] [,462] [,463] [,464] [,465] [,466] [,467]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 38 37 28 29 15 0 12
#> omicron 0 0 4 335 510 525 520 322 2 410
#> other 0 0 0 1 0 0 0 0 0 0
#> [,468] [,469] [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 15 22 13 10 6 5 13 7 7 5
#> omicron 573 594 579 570 495 410 421 436 500 469
#> other 0 0 0 0 0 0 0 0 0 0
#> [,478] [,479] [,480] [,481] [,482] [,483] [,484] [,485] [,486] [,487]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 2 3 7 3 4 3 2 1 2 1
#> omicron 334 337 348 341 411 452 329 258 321 327
#> other 0 0 0 0 0 0 0 0 0 0
#> [,488] [,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496] [,497]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 1 2 0 0 2 0 2 1 0
#> omicron 295 408 450 425 352 303 356 388 475 517
#> other 0 0 0 0 0 0 0 0 1 0
#> [,498] [,499] [,500] [,501] [,502] [,503] [,504] [,505] [,506] [,507]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 1 0 0 1 0 0 0 2 0 1
#> omicron 501 398 372 319 359 423 400 417 346 281
#> other 0 1 0 0 0 0 0 0 0 0
#> [,508] [,509] [,510] [,511] [,512] [,513] [,514] [,515] [,516] [,517]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 1 0 0 0 0 0 0 0
#> omicron 316 255 282 329 308 275 201 226 269 265
#> other 0 0 0 2 0 0 0 0 0 0
#> [,518] [,519] [,520] [,521] [,522] [,523] [,524] [,525] [,526] [,527]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 1 0 0 0 0 0 0 0 0 0
#> omicron 272 274 253 229 237 280 283 289 254 233
#> other 3 1 1 0 0 0 1 0 0 0
#> [,528] [,529] [,530] [,531] [,532] [,533] [,534] [,535] [,536] [,537]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 2 0 0 0 0 0 0 0
#> omicron 262 300 282 380 385 430 451 435 420 522
#> other 0 0 0 1 0 3 2 2 1 5
#> [,538] [,539] [,540] [,541] [,542] [,543] [,544] [,545] [,546] [,547]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 1
#> omicron 563 649 614 463 427 394 507 702 752 718
#> other 3 3 7 3 0 4 7 6 3 5
#> [,548] [,549] [,550] [,551] [,552] [,553] [,554] [,555] [,556] [,557]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 725 590 662 560 831 860 811 673 489 474
#> other 2 5 9 6 9 6 11 3 4 3
#> [,558] [,559] [,560] [,561] [,562] [,563] [,564] [,565] [,566] [,567]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 479 639 648 558 458 351 294 399 578 588
#> other 4 6 4 6 2 2 4 1 3 4
#> [,568] [,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576] [,577]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 585 480 367 239 3 355 413 432 370 314
#> other 3 4 0 1 0 4 6 4 1 9
#> [,578] [,579] [,580] [,581] [,582] [,583] [,584] [,585] [,586] [,587]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 276 204 252 285 196 183 152 133 101 157
#> other 2 2 0 1 0 1 0 0 2 4
#> [,588] [,589] [,590] [,591] [,592] [,593] [,594] [,595] [,596] [,597]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 166 173 176 109 109 108 145 158 167 127
#> other 1 0 0 2 2 3 1 4 0 0
#> [,598] [,599] [,600] [,601] [,602] [,603] [,604] [,605] [,606] [,607]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 99 101 88 139 131 154 150 106 78 83
#> other 7 0 0 1 3 1 0 1 1 1
#> [,608] [,609] [,610] [,611] [,612] [,613] [,614] [,615] [,616] [,617]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 110 118 113 99 85 81 69 115 123 111
#> other 0 0 0 1 0 1 1 0 0 3
#> [,618] [,619] [,620] [,621] [,622] [,623] [,624] [,625] [,626] [,627]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 84 1 116 103 171 206 190 170 192 119
#> other 0 0 0 0 1 1 2 0 0 0
#> [,628] [,629] [,630] [,631] [,632] [,633] [,634] [,635] [,636] [,637]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 121 225 187 229 162 156 156 162 253 284
#> other 0 0 2 0 0 0 1 0 1 1
#> [,638] [,639] [,640] [,641] [,642] [,643] [,644] [,645] [,646] [,647]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 271 245 256 208 228 330 322 325 297 270
#> other 0 0 0 1 0 0 1 0 2 0
#> [,648] [,649] [,650] [,651] [,652] [,653] [,654] [,655] [,656] [,657]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 229 230 283 299 321 297 241 173 155 291
#> other 0 0 0 0 0 0 1 1 0 0
#> [,658] [,659] [,660] [,661] [,662] [,663] [,664] [,665] [,666] [,667]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 325 283 312 268 226 151 287 334 373 348
#> other 0 2 0 0 1 1 1 0 1 0
#> [,668] [,669] [,670] [,671] [,672] [,673] [,674] [,675] [,676] [,677]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 336 180 167 427 340 311 262 181 113 92
#> other 0 0 0 4 1 0 0 2 0 0
#> [,678] [,679] [,680] [,681] [,682] [,683] [,684] [,685] [,686] [,687]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 201 138 101 118 97 49 27 171 112 69
#> other 0 0 0 0 1 0 0 0 0 0
#> [,688] [,689] [,690] [,691] [,692] [,693] [,694] [,695] [,696] [,697]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 95 94 58 43 180 103 105 88 92 63
#> other 0 0 0 0 0 0 0 0 0 2
#> [,698] [,699] [,700] [,701] [,702] [,703] [,704] [,705] [,706] [,707]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 43 162 116 105 64 75 31 23 72 114
#> other 0 0 0 0 0 0 0 0 0 1
#> [,708] [,709] [,710] [,711] [,712] [,713] [,714] [,715] [,716] [,717]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 42 179 95 59 50 187 125 55 30 38
#> other 1 0 0 0 0 0 0 0 0 0
#> [,718] [,719] [,720] [,721] [,722] [,723] [,724] [,725] [,726] [,727]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 55 55 182 95 114 119 106 69 22 57
#> other 0 0 0 1 0 3 1 1 0 0
#> [,728] [,729] [,730] [,731] [,732] [,733] [,734] [,735] [,736] [,737]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 228 179 179 138 83 92 227 167 180 175
#> other 0 0 0 0 1 1 4 2 0 0
#> [,738] [,739] [,740] [,741] [,742] [,743] [,744] [,745] [,746] [,747]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 102 61 95 274 237 262 301 246 126 90
#> other 0 1 2 2 1 0 2 1 0 2
#> [,748] [,749] [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 369 257 188 118 259 102 101 398 242 162
#> other 2 1 1 2 3 1 4 12 9 7
#> [,758] [,759] [,760] [,761] [,762] [,763] [,764] [,765] [,766] [,767]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 65 247 105 56 207 78 254 170 177 70
#> other 2 8 2 0 2 1 5 2 5 2
#> [,768] [,769] [,770] [,771] [,772] [,773] [,774] [,775] [,776] [,777]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 68 177 124 121 119 126 51 65 135 110
#> other 1 6 5 4 5 2 2 2 6 2
#> [,778] [,779] [,780] [,781] [,782] [,783] [,784] [,785] [,786] [,787]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 96 103 98 55 42 119 75 64 72 64
#> other 4 3 1 2 2 7 5 5 5 3
#> [,788] [,789] [,790] [,791] [,792] [,793] [,794] [,795] [,796] [,797]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 54 54 115 110 85 81 65 69 59 232
#> other 0 6 10 8 8 8 4 5 2 16
#> [,798] [,799] [,800] [,801] [,802] [,803] [,804] [,805] [,806] [,807]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 109 77 65 150 70 63 218 216 187 153
#> other 3 4 8 9 9 7 13 14 11 6
#> [,808] [,809] [,810] [,811] [,812] [,813] [,814] [,815] [,816] [,817]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 92 116 100 322 170 98 125 329 159 124
#> other 11 17 8 32 16 10 13 39 13 12
#> [,818] [,819] [,820] [,821] [,822] [,823] [,824] [,825] [,826] [,827]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 516 401 300 165 73 22 7 21 165 451
#> other 39 36 25 33 5 0 0 3 21 42
#> [,828] [,829] [,830]
#> alpha 0 0 0
#> delta 0 0 0
#> omicron 396 232 78
#> other 41 29 3
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"
# Using a time series object (time argument is optional)
sarscov2_xts <- xts::xts(
sarscov2[, c("cases", "alpha", "delta", "omicron", "other")],
order.by = sarscov2$date
)
multiple(
data = sarscov2_xts,
case_timeseries = "cases",
component_pathogen_timeseries = c("alpha", "delta", "omicron", "other")
)
#> $pathogen_structure
#> [1] "multiple"
#>
#> $pathogen_names
#> [1] "alpha" "delta" "omicron" "other"
#>
#> $validated_tsbl
#> # A tsibble: 830 x 6 [1D]
#> index case_timeseries alpha delta omicron other
#> <date> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2020-09-23 7096 0 0 0 10
#> 2 2020-09-24 7682 0 0 0 7
#> 3 2020-09-25 7318 0 0 0 9
#> 4 2020-09-26 6810 0 0 0 15
#> 5 2020-09-27 7023 0 0 0 5
#> 6 2020-09-28 9983 0 0 0 6
#> 7 2020-09-29 10366 0 0 0 23
#> 8 2020-09-30 12717 0 0 0 54
#> 9 2020-10-01 13357 0 0 0 32
#> 10 2020-10-02 13854 0 0 0 15
#> # ℹ 820 more rows
#>
#> $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
#>
#> $data$component_pathogens
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> alpha 0 0 0 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0 0
#> other 10 7 9 15 5 6 23 54 32 15 23 8 35
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> alpha 0 0 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 39 45 25 18 12 25 47 34 18 11 23 24
#> [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
#> alpha 0 0 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 33 47 55 46 21 7 8 9 10 3 3 4
#> [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49]
#> alpha 0 0 3 1 0 0 0 0 1 2 0 0
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 1 3 22 25 7 6 14 32 14 10 21 25
#> [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61]
#> alpha 1 0 0 0 2 4 1 1 3 3 3 2
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 18 20 25 26 10 38 14 4 13 11 8 14
#> [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73]
#> alpha 4 6 14 4 4 7 6 3 4 8 0 1
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 14 14 7 6 10 6 15 11 14 4 1 0
#> [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85]
#> alpha 0 0 18 16 12 12 14 7 10 27 63 57
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 0 5 5 11 11 7 7 5 5 38 34 52
#> [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97]
#> alpha 64 47 17 30 52 65 69 0 0 1 48 60
#> delta 0 0 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0 0 0
#> other 46 34 21 16 29 32 29 0 0 0 27 21
#> [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107]
#> alpha 111 68 15 0 35 50 125 93 67 50
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 41 13 14 0 22 18 39 28 21 9
#> [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117]
#> alpha 55 40 48 81 75 70 38 46 43 45
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 15 11 17 10 18 18 4 2 12 4
#> [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127]
#> alpha 67 54 53 39 34 29 17 19 51 53
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 7 4 17 2 6 5 4 6 1 4
#> [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
#> alpha 44 39 22 47 36 26 24 31 18 29
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 4 5 3 5 4 0 1 1 0 1
#> [,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147]
#> alpha 2 33 25 29 23 20 10 8 22 26
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 1 2 1 1 0 2 1 0
#> [,148] [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157]
#> alpha 17 6 5 6 8 13 16 13 11 10
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 1 0 1 0 0 1
#> [,158] [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167]
#> alpha 7 11 10 14 15 11 4 9 6 13
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 1 2 0 3 0 0 1 0 0
#> [,168] [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177]
#> alpha 6 11 10 15 12 8 20 6 6 12
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 1 0 0 0 0 0 2 0 0
#> [,178] [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187]
#> alpha 4 7 8 11 8 8 13 4 8 8
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 1 0 0 0 0 0 0 1 0
#> [,188] [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197]
#> alpha 10 11 9 8 5 3 0 5 7 8
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 1 0 0 0 0 0 0 0 0 0
#> [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207]
#> alpha 2 5 6 10 8 4 5 6 3 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,208] [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217]
#> alpha 1 5 7 3 2 3 3 1 3 4
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 1 0 0 0 0 0 0
#> [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227]
#> alpha 2 2 5 3 0 5 1 0 1 2
#> delta 1 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237]
#> alpha 2 0 1 2 3 2 2 0 0 4
#> delta 1 0 0 0 0 0 0 0 0 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,238] [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247]
#> alpha 1 2 1 0 0 2 0 2 2 2
#> delta 10 0 0 4 2 1 4 3 3 0
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,248] [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257]
#> alpha 1 0 1 0 4 0 2 2 0 0
#> delta 1 10 2 3 7 6 2 10 6 3
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 1 0 0 0 0 0
#> [,258] [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267]
#> alpha 0 0 1 2 1 1 0 2 1 1
#> delta 6 13 8 6 6 10 6 20 9 7
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,268] [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277]
#> alpha 0 1 0 0 0 2 0 2 0 0
#> delta 9 18 16 6 22 21 26 26 22 24
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 1 0 1 0 0 0
#> [,278] [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287]
#> alpha 1 0 1 0 1 1 0 1 0 0
#> delta 24 37 29 40 30 39 21 23 55 61
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,288] [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 83 61 63 55 42 73 80 66 94 60
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,298] [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 58 79 111 106 111 94 106 70 55 42
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 1
#> [,308] [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317]
#> alpha 0 0 0 0 0 0 0 0 1 0
#> delta 28 37 54 70 49 49 66 85 70 94
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,318] [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327]
#> alpha 0 0 0 0 0 1 0 0 0 0
#> delta 56 40 39 48 64 86 71 64 49 56
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,328] [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337]
#> alpha 0 1 0 0 0 0 1 0 0 0
#> delta 70 97 86 49 58 74 65 68 92 80
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,338] [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 73 66 58 53 48 106 82 83 72 73
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,348] [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 58 74 93 107 101 74 66 50 99 86
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,358] [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 75 78 69 70 77 76 88 98 103 96
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,368] [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 103 93 102 119 113 100 104 111 118 127
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,378] [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387]
#> alpha 0 0 0 0 0 0 0 0 0 1
#> delta 112 143 122 134 141 87 103 124 161 145
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,388] [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 151 178 156 188 155 179 159 126 141 173
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 161 161 184 147 110 94 149 122 150 148
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,408] [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 148 116 94 119 113 124 126 110 95 105
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,418] [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426] [,427]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 96 131 166 123 93 116 106 119 119 147
#> omicron 0 0 0 0 0 0 0 0 0 0
#> other 0 0 0 0 0 0 0 0 0 0
#> [,428] [,429] [,430] [,431] [,432] [,433] [,434] [,435] [,436] [,437]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 150 128 93 111 97 122 146 125 136 117
#> omicron 0 0 0 0 0 2 0 0 0 1
#> other 0 0 0 0 0 0 0 0 0 0
#> [,438] [,439] [,440] [,441] [,442] [,443] [,444] [,445] [,446] [,447]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 121 108 95 137 106 123 85 81 84 95
#> omicron 2 5 6 10 16 7 15 15 26 64
#> other 0 0 0 0 0 0 0 0 0 0
#> [,448] [,449] [,450] [,451] [,452] [,453] [,454] [,455] [,456] [,457]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 117 133 111 94 72 70 122 112 87 55
#> omicron 88 124 111 138 150 164 256 331 283 220
#> other 2 0 0 0 0 0 0 1 0 0
#> [,458] [,459] [,460] [,461] [,462] [,463] [,464] [,465] [,466] [,467]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 38 37 28 29 15 0 12
#> omicron 0 0 4 335 510 525 520 322 2 410
#> other 0 0 0 1 0 0 0 0 0 0
#> [,468] [,469] [,470] [,471] [,472] [,473] [,474] [,475] [,476] [,477]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 15 22 13 10 6 5 13 7 7 5
#> omicron 573 594 579 570 495 410 421 436 500 469
#> other 0 0 0 0 0 0 0 0 0 0
#> [,478] [,479] [,480] [,481] [,482] [,483] [,484] [,485] [,486] [,487]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 2 3 7 3 4 3 2 1 2 1
#> omicron 334 337 348 341 411 452 329 258 321 327
#> other 0 0 0 0 0 0 0 0 0 0
#> [,488] [,489] [,490] [,491] [,492] [,493] [,494] [,495] [,496] [,497]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 1 2 0 0 2 0 2 1 0
#> omicron 295 408 450 425 352 303 356 388 475 517
#> other 0 0 0 0 0 0 0 0 1 0
#> [,498] [,499] [,500] [,501] [,502] [,503] [,504] [,505] [,506] [,507]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 1 0 0 1 0 0 0 2 0 1
#> omicron 501 398 372 319 359 423 400 417 346 281
#> other 0 1 0 0 0 0 0 0 0 0
#> [,508] [,509] [,510] [,511] [,512] [,513] [,514] [,515] [,516] [,517]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 1 0 0 0 0 0 0 0
#> omicron 316 255 282 329 308 275 201 226 269 265
#> other 0 0 0 2 0 0 0 0 0 0
#> [,518] [,519] [,520] [,521] [,522] [,523] [,524] [,525] [,526] [,527]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 1 0 0 0 0 0 0 0 0 0
#> omicron 272 274 253 229 237 280 283 289 254 233
#> other 3 1 1 0 0 0 1 0 0 0
#> [,528] [,529] [,530] [,531] [,532] [,533] [,534] [,535] [,536] [,537]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 2 0 0 0 0 0 0 0
#> omicron 262 300 282 380 385 430 451 435 420 522
#> other 0 0 0 1 0 3 2 2 1 5
#> [,538] [,539] [,540] [,541] [,542] [,543] [,544] [,545] [,546] [,547]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 1
#> omicron 563 649 614 463 427 394 507 702 752 718
#> other 3 3 7 3 0 4 7 6 3 5
#> [,548] [,549] [,550] [,551] [,552] [,553] [,554] [,555] [,556] [,557]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 725 590 662 560 831 860 811 673 489 474
#> other 2 5 9 6 9 6 11 3 4 3
#> [,558] [,559] [,560] [,561] [,562] [,563] [,564] [,565] [,566] [,567]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 479 639 648 558 458 351 294 399 578 588
#> other 4 6 4 6 2 2 4 1 3 4
#> [,568] [,569] [,570] [,571] [,572] [,573] [,574] [,575] [,576] [,577]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 585 480 367 239 3 355 413 432 370 314
#> other 3 4 0 1 0 4 6 4 1 9
#> [,578] [,579] [,580] [,581] [,582] [,583] [,584] [,585] [,586] [,587]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 276 204 252 285 196 183 152 133 101 157
#> other 2 2 0 1 0 1 0 0 2 4
#> [,588] [,589] [,590] [,591] [,592] [,593] [,594] [,595] [,596] [,597]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 166 173 176 109 109 108 145 158 167 127
#> other 1 0 0 2 2 3 1 4 0 0
#> [,598] [,599] [,600] [,601] [,602] [,603] [,604] [,605] [,606] [,607]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 99 101 88 139 131 154 150 106 78 83
#> other 7 0 0 1 3 1 0 1 1 1
#> [,608] [,609] [,610] [,611] [,612] [,613] [,614] [,615] [,616] [,617]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 110 118 113 99 85 81 69 115 123 111
#> other 0 0 0 1 0 1 1 0 0 3
#> [,618] [,619] [,620] [,621] [,622] [,623] [,624] [,625] [,626] [,627]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 84 1 116 103 171 206 190 170 192 119
#> other 0 0 0 0 1 1 2 0 0 0
#> [,628] [,629] [,630] [,631] [,632] [,633] [,634] [,635] [,636] [,637]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 121 225 187 229 162 156 156 162 253 284
#> other 0 0 2 0 0 0 1 0 1 1
#> [,638] [,639] [,640] [,641] [,642] [,643] [,644] [,645] [,646] [,647]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 271 245 256 208 228 330 322 325 297 270
#> other 0 0 0 1 0 0 1 0 2 0
#> [,648] [,649] [,650] [,651] [,652] [,653] [,654] [,655] [,656] [,657]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 229 230 283 299 321 297 241 173 155 291
#> other 0 0 0 0 0 0 1 1 0 0
#> [,658] [,659] [,660] [,661] [,662] [,663] [,664] [,665] [,666] [,667]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 325 283 312 268 226 151 287 334 373 348
#> other 0 2 0 0 1 1 1 0 1 0
#> [,668] [,669] [,670] [,671] [,672] [,673] [,674] [,675] [,676] [,677]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 336 180 167 427 340 311 262 181 113 92
#> other 0 0 0 4 1 0 0 2 0 0
#> [,678] [,679] [,680] [,681] [,682] [,683] [,684] [,685] [,686] [,687]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 201 138 101 118 97 49 27 171 112 69
#> other 0 0 0 0 1 0 0 0 0 0
#> [,688] [,689] [,690] [,691] [,692] [,693] [,694] [,695] [,696] [,697]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 95 94 58 43 180 103 105 88 92 63
#> other 0 0 0 0 0 0 0 0 0 2
#> [,698] [,699] [,700] [,701] [,702] [,703] [,704] [,705] [,706] [,707]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 43 162 116 105 64 75 31 23 72 114
#> other 0 0 0 0 0 0 0 0 0 1
#> [,708] [,709] [,710] [,711] [,712] [,713] [,714] [,715] [,716] [,717]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 42 179 95 59 50 187 125 55 30 38
#> other 1 0 0 0 0 0 0 0 0 0
#> [,718] [,719] [,720] [,721] [,722] [,723] [,724] [,725] [,726] [,727]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 55 55 182 95 114 119 106 69 22 57
#> other 0 0 0 1 0 3 1 1 0 0
#> [,728] [,729] [,730] [,731] [,732] [,733] [,734] [,735] [,736] [,737]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 228 179 179 138 83 92 227 167 180 175
#> other 0 0 0 0 1 1 4 2 0 0
#> [,738] [,739] [,740] [,741] [,742] [,743] [,744] [,745] [,746] [,747]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 102 61 95 274 237 262 301 246 126 90
#> other 0 1 2 2 1 0 2 1 0 2
#> [,748] [,749] [,750] [,751] [,752] [,753] [,754] [,755] [,756] [,757]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 369 257 188 118 259 102 101 398 242 162
#> other 2 1 1 2 3 1 4 12 9 7
#> [,758] [,759] [,760] [,761] [,762] [,763] [,764] [,765] [,766] [,767]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 65 247 105 56 207 78 254 170 177 70
#> other 2 8 2 0 2 1 5 2 5 2
#> [,768] [,769] [,770] [,771] [,772] [,773] [,774] [,775] [,776] [,777]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 68 177 124 121 119 126 51 65 135 110
#> other 1 6 5 4 5 2 2 2 6 2
#> [,778] [,779] [,780] [,781] [,782] [,783] [,784] [,785] [,786] [,787]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 96 103 98 55 42 119 75 64 72 64
#> other 4 3 1 2 2 7 5 5 5 3
#> [,788] [,789] [,790] [,791] [,792] [,793] [,794] [,795] [,796] [,797]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 54 54 115 110 85 81 65 69 59 232
#> other 0 6 10 8 8 8 4 5 2 16
#> [,798] [,799] [,800] [,801] [,802] [,803] [,804] [,805] [,806] [,807]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 109 77 65 150 70 63 218 216 187 153
#> other 3 4 8 9 9 7 13 14 11 6
#> [,808] [,809] [,810] [,811] [,812] [,813] [,814] [,815] [,816] [,817]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 92 116 100 322 170 98 125 329 159 124
#> other 11 17 8 32 16 10 13 39 13 12
#> [,818] [,819] [,820] [,821] [,822] [,823] [,824] [,825] [,826] [,827]
#> alpha 0 0 0 0 0 0 0 0 0 0
#> delta 0 0 0 0 0 0 0 0 0 0
#> omicron 516 401 300 165 73 22 7 21 165 451
#> other 39 36 25 33 5 0 0 3 21 42
#> [,828] [,829] [,830]
#> alpha 0 0 0
#> delta 0 0 0
#> omicron 396 232 78
#> other 41 29 3
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"