Subtyped pathogen structure
Usage
subtyped(
data,
case_timeseries,
unsubtyped_timeseries,
subtyped_timeseries,
other_pathogen_timeseries,
time = NULL
)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.- unsubtyped_timeseries
vector of column names with additional unsubtyped pathogen case count timeseries. Must be numeric or a
unitsobject from the units package.- subtyped_timeseries
vector of column names with additional subtyped pathogen case count timeseries. Must be numeric or a
unitsobject from the units package.- other_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
name of column 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:
multiple(),
single()
Examples
# Using a data frame
subtyped(
data = influenza,
case_timeseries = "ili",
unsubtyped_timeseries = "inf_A",
subtyped_timeseries = c("inf_H3N2", "inf_H1N1"),
other_pathogen_timeseries = c("inf_B", "other"),
time = "week"
)
#> $pathogen_structure
#> [1] "subtyped"
#>
#> $pathogen_names
#> [1] "inf_H3N2" "inf_H1N1" "inf_B" "other"
#>
#> $validated_tsbl
#> # A tsibble: 426 x 7 [7D]
#> week case_timeseries inf_A inf_H3N2 inf_H1N1 inf_B other
#> <date> <int> <int> <int> <int> <int> <int>
#> 1 2012-01-02 29 4 4 0 3 278
#> 2 2012-01-09 38 4 4 0 1 219
#> 3 2012-01-16 42 13 13 0 8 238
#> 4 2012-01-23 58 6 3 2 5 187
#> 5 2012-01-30 45 3 3 0 2 228
#> 6 2012-02-06 60 1 1 0 7 274
#> 7 2012-02-13 30 2 0 2 10 278
#> 8 2012-02-20 52 4 3 1 9 266
#> 9 2012-02-27 33 6 4 2 13 327
#> 10 2012-03-05 26 4 4 0 10 324
#> # ℹ 416 more rows
#>
#> $data
#> $data$case_timeseries
#> [1] 29 38 42 58 45 60 30 52 33 26 75 65 71 92 71 75 73 39
#> [19] 57 94 140 144 218 234 176 265 370 389 469 465 434 496 441 399 359 255
#> [37] 198 195 156 105 78 48 48 77 69 58 64 80 69 60 50 63 41 54
#> [55] 64 55 53 64 61 68 81 66 81 89 76 100 86 106 39 57 65 64
#> [73] 80 83 136 125 140 113 133 171 168 166 204 181 245 216 202 236 220 188
#> [91] 211 157 105 40 58 128 83 106 70 98 106 32 25 45 48 69 60 79
#> [109] 49 49 81 70 84 107 104 99 110 137 92 98 71 124 114 73 67 98
#> [127] 96 136 148 153 179 173 158 213 306 328 381 410 411 336 341 269 186 166
#> [145] 107 121 47 116 110 110 106 75 59 62 65 34 48 61 61 26 11 11
#> [163] 19 22 28 49 40 39 46 48 36 57 62 66 117 99 118 117 131 141
#> [181] 177 202 220 226 231 246 292 327 384 492 375 340 303 242 206 140 80 88
#> [199] 54 55 55 44 31 40 32 28 15 11 13 21 34 17 13 15 22 30
#> [217] 31 38 31 25 28 44 68 57 59 62 68 55 94 91 123 94 110 109
#> [235] 106 116 131 157 178 229 257 315 247 239 260 241 172 118 95 97 73 52
#> [253] 55 49 50 28 38 37 41 20 19 24 34 28 33 22 20 39 38 55
#> [271] 47 41 51 69 57 49 49 51 57 57 58 57 71 89 71 82 114 160
#> [289] 154 186 243 392 464 540 554 475 508 424 374 308 202 171 132 100 93 83
#> [307] 49 72 46 32 37 49 21 19 36 16 42 20 38 50 44 40 58 33
#> [325] 52 53 43 68 74 54 45 64 85 103 101 83 94 110 79 103 109 123
#> [343] 129 120 129 130 146 152 148 153 134 93 85 98 90 76 54 52 54 41
#> [361] 58 46 51 30 14 32 32 45 24 25 34 30 53 56 50 53 73 88
#> [379] 129 160 95 102 207 209 264 320 330 320 285 283 283 280 319 262 274 246
#> [397] 259 273 242 215 225 150 146 101 89 42 55 37 37 41 37 37 39 35
#> [415] 31 19 7 21 26 19 31 37 45 28 38 33
#>
#> $data$component_pathogens
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> inf_A 4 4 13 6 3 1 2 4 6 4 12 9 14
#> inf_B 3 1 8 5 2 7 10 9 13 10 19 12 8
#> other 278 219 238 187 228 274 278 266 327 324 346 333 322
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> inf_A 8 9 16 13 14 12 15 27 33 56 95 95
#> inf_B 5 6 4 4 10 7 12 11 8 18 23 30
#> other 317 326 378 328 379 403 481 524 637 509 512 701
#> [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
#> inf_A 182 264 310 280 311 318 274 295 187 153 89 63
#> inf_B 72 90 129 111 122 117 114 90 100 97 50 46
#> other 644 675 949 903 775 874 844 783 897 686 813 707
#> [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49]
#> inf_A 44 17 12 10 9 4 0 10 10 0 3 7
#> inf_B 28 15 12 7 6 3 2 3 1 2 1 0
#> other 508 524 450 433 433 367 324 352 374 359 319 357
#> [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61]
#> inf_A 2 3 1 5 8 11 11 10 15 15 8 15
#> inf_B 0 2 0 3 5 6 4 3 3 2 2 1
#> other 292 258 205 153 177 171 171 185 198 198 240 246
#> [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73]
#> inf_A 8 18 25 10 6 4 4 3 1 2 4 9
#> inf_B 7 3 2 0 2 1 0 0 0 2 3 1
#> other 260 285 305 250 248 289 272 303 296 284 282 378
#> [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85]
#> inf_A 5 8 4 4 7 23 26 48 37 71 87 80
#> inf_B 0 1 3 1 3 6 10 20 8 10 17 19
#> other 339 317 393 330 370 425 423 441 471 459 469 507
#> [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97]
#> inf_A 105 127 102 116 113 109 59 64 46 38 39 26
#> inf_B 23 32 14 24 12 16 14 18 7 4 8 6
#> other 566 561 611 509 586 549 461 430 467 321 322 277
#> [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107]
#> inf_A 17 10 19 12 22 7 11 20 22 23
#> inf_B 8 4 13 5 9 1 2 1 1 2
#> other 269 244 254 217 229 239 119 142 170 173
#> [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117]
#> inf_A 17 18 29 25 13 20 18 18 10 14
#> inf_B 9 1 2 1 3 13 3 3 7 2
#> other 201 160 179 122 197 237 152 254 211 211
#> [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127]
#> inf_A 15 12 16 6 5 12 12 15 13 12
#> inf_B 6 7 1 2 4 4 7 4 1 2
#> other 280 229 232 238 231 294 269 310 309 280
#> [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
#> inf_A 16 19 44 83 118 172 176 204 268 237
#> inf_B 3 4 7 8 7 12 12 13 9 31
#> other 329 316 339 374 435 481 451 508 527 631
#> [,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147]
#> inf_A 293 246 187 162 128 92 51 41 17 17
#> inf_B 27 25 30 25 22 18 21 17 12 11
#> other 640 548 532 541 532 524 398 424 357 374
#> [,148] [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157]
#> inf_A 14 7 21 1 2 6 9 5 10 2
#> inf_B 10 18 5 7 4 6 6 2 4 1
#> other 354 312 294 312 247 216 232 223 146 68
#> [,158] [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167]
#> inf_A 19 19 15 11 22 17 25 17 17 17
#> inf_B 1 4 3 5 2 5 5 3 5 3
#> other 197 169 177 175 172 175 216 213 231 214
#> [,168] [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177]
#> inf_A 14 19 32 13 15 28 23 10 17 21
#> inf_B 5 9 5 9 10 11 18 15 25 26
#> other 248 236 267 226 274 291 256 301 295 330
#> [,178] [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187]
#> inf_A 12 22 25 23 23 35 42 40 49 61
#> inf_B 29 41 46 49 59 111 88 92 106 93
#> other 349 349 373 421 403 456 485 502 542 592
#> [,188] [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197]
#> inf_A 78 72 114 74 91 86 102 117 68 58
#> inf_B 125 103 137 111 79 73 79 72 45 27
#> other 549 619 624 622 563 560 549 491 385 387
#> [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207]
#> inf_A 49 27 19 24 31 9 9 22 29 15
#> inf_B 19 14 8 6 4 3 2 2 2 2
#> other 338 321 323 314 277 286 275 295 265 254
#> [,208] [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217]
#> inf_A 20 6 27 17 11 16 21 22 16 24
#> inf_B 3 0 0 2 1 1 2 8 3 3
#> other 183 108 253 223 207 197 212 222 221 250
#> [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227]
#> inf_A 21 22 16 21 7 14 15 8 6 14
#> inf_B 8 4 6 7 5 6 8 4 5 5
#> other 273 258 267 241 269 284 316 319 306 367
#> [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237]
#> inf_A 19 30 26 35 39 52 63 92 99 121
#> inf_B 12 14 7 12 9 12 14 24 33 55
#> other 389 405 860 805 746 788 897 950 1052 1075
#> [,238] [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247]
#> inf_A 239 243 284 342 488 479 541 539 372 317
#> inf_B 41 54 67 91 81 75 70 63 61 62
#> other 1075 1078 1235 1227 1456 1367 1572 1587 1404 1409
#> [,248] [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257]
#> inf_A 236 185 128 65 46 48 20 22 27 12
#> inf_B 37 41 27 17 15 12 14 4 5 8
#> other 1255 1250 1163 1017 954 877 848 722 634 607
#> [,258] [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267]
#> inf_A 13 17 20 9 30 30 25 37 49 40
#> inf_B 6 4 10 4 6 2 3 2 2 1
#> other 582 557 522 429 326 352 309 275 263 231
#> [,268] [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277]
#> inf_A 30 42 25 18 30 34 32 15 17 7
#> inf_B 3 8 2 2 2 2 8 6 1 4
#> other 288 316 381 344 310 509 652 596 593 734
#> [,278] [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287]
#> inf_A 10 21 16 28 26 20 24 32 61 59
#> inf_B 4 6 3 4 15 7 7 19 27 23
#> other 675 717 719 725 789 905 781 842 989 947
#> [,288] [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297]
#> inf_A 125 225 363 359 471 610 652 654 584 709
#> inf_B 45 59 74 69 148 207 249 222 220 251
#> other 1114 1238 1150 1283 1137 1088 1653 1765 1796 1832
#> [,298] [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307]
#> inf_A 663 502 329 221 132 76 48 40 29 29
#> inf_B 206 219 200 126 96 52 30 36 33 20
#> other 1927 1817 1691 1488 1377 1087 1058 1028 987 929
#> [,308] [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317]
#> inf_A 13 21 19 17 17 18 38 19 24 34
#> inf_B 22 22 11 15 13 11 9 11 12 22
#> other 746 752 671 641 606 525 428 429 364 337
#> [,318] [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327]
#> inf_A 36 26 55 37 23 27 16 18 22 23
#> inf_B 17 10 18 16 14 5 6 10 3 7
#> other 384 326 336 331 368 373 345 544 504 621
#> [,328] [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337]
#> inf_A 14 20 16 26 28 29 18 20 25 37
#> inf_B 0 3 2 5 4 4 6 4 0 7
#> other 678 702 669 749 815 933 980 945 1094 1085
#> [,338] [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347]
#> inf_A 39 70 64 89 70 80 71 114 145 186
#> inf_B 2 2 3 7 3 8 0 5 9 14
#> other 1188 1163 1244 1427 1422 1408 1399 1341 1476 1457
#> [,348] [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357]
#> inf_A 201 155 238 232 158 176 105 74 56 39
#> inf_B 9 19 14 8 12 7 13 9 3 4
#> other 1440 1719 1412 1469 1332 1360 1234 1076 941 936
#> [,358] [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367]
#> inf_A 47 63 105 110 186 124 138 103 84 99
#> inf_B 6 7 8 7 3 5 7 6 3 3
#> other 960 943 933 984 843 857 828 664 646 790
#> [,368] [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377]
#> inf_A 123 95 107 104 103 124 132 95 105 67
#> inf_B 2 2 3 2 1 1 2 2 6 7
#> other 717 688 778 669 784 876 887 868 884 983
#> [,378] [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387]
#> inf_A 76 94 142 174 196 213 245 363 640 655
#> inf_B 5 4 2 4 14 9 12 22 46 52
#> other 892 1095 1176 1129 1271 1267 1327 1556 2041 2178
#> [,388] [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
#> inf_A 844 746 782 862 749 567 511 364 294 303
#> inf_B 68 96 109 140 118 95 96 97 87 118
#> other 2207 2478 2433 2563 2671 2712 2573 2297 2245 2294
#> [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407]
#> inf_A 274 338 256 182 159 130 127 79 78 52
#> inf_B 154 138 103 112 65 51 32 28 22 4
#> other 2350 2239 2247 2202 1882 2011 1923 1767 1725 1518
#> [,408] [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417]
#> inf_A 38 29 20 25 23 36 51 37 18 25
#> inf_B 7 5 2 0 3 4 3 5 0 1
#> other 1563 1367 1226 1219 1202 1107 1160 1142 805 852
#> [,418] [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426]
#> inf_A 41 58 54 103 72 74 62 55 69
#> inf_B 1 2 2 10 12 6 5 7 3
#> other 979 1059 891 1057 1290 1290 1193 1293 1513
#>
#> $data$subtyped
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> inf_H3N2 4 4 13 3 3 1 0 3 4 4 10 9 14
#> inf_H1N1 0 0 0 2 0 0 2 1 2 0 2 0 0
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
#> inf_H3N2 7 6 13 12 13 11 13 26 28 39 63
#> inf_H1N1 0 3 3 1 1 1 2 1 2 1 1
#> [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35]
#> inf_H3N2 79 175 250 306 272 304 308 268 291 180 148
#> inf_H1N1 2 5 11 4 7 5 9 6 3 6 4
#> [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46]
#> inf_H3N2 88 61 43 15 12 8 9 4 0 8 8
#> inf_H1N1 1 2 0 0 0 2 0 0 0 0 1
#> [,47] [,48] [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57]
#> inf_H3N2 0 1 4 1 1 0 3 2 7 8 6
#> inf_H1N1 0 2 3 0 2 1 2 5 3 3 4
#> [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68]
#> inf_H3N2 11 9 7 13 6 7 7 7 4 2 2
#> inf_H1N1 3 6 1 1 2 11 18 3 1 2 2
#> [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
#> inf_H3N2 1 1 1 4 7 3 4 3 4 5 16
#> inf_H1N1 2 0 1 0 1 1 4 1 0 2 5
#> [,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90]
#> inf_H3N2 19 40 28 58 65 61 74 70 49 75 70
#> inf_H1N1 7 7 8 12 21 18 30 55 52 40 42
#> [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101]
#> inf_H3N2 65 29 32 30 21 22 14 10 6 12 8
#> inf_H1N1 42 30 30 15 17 14 11 7 3 5 4
#> [,102] [,103] [,104] [,105] [,106] [,107] [,108] [,109] [,110] [,111]
#> inf_H3N2 21 6 10 14 15 12 10 14 24 18
#> inf_H1N1 1 1 1 5 7 11 7 4 5 7
#> [,112] [,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120] [,121]
#> inf_H3N2 9 11 12 7 2 8 9 7 15 5
#> inf_H1N1 3 9 6 11 8 6 6 4 1 1
#> [,122] [,123] [,124] [,125] [,126] [,127] [,128] [,129] [,130] [,131]
#> inf_H3N2 4 6 3 4 6 2 1 3 12 25
#> inf_H1N1 1 5 9 9 7 10 13 14 30 54
#> [,132] [,133] [,134] [,135] [,136] [,137] [,138] [,139] [,140] [,141]
#> inf_H3N2 14 33 48 82 110 81 91 73 65 52
#> inf_H1N1 104 131 125 110 148 136 168 152 104 98
#> [,142] [,143] [,144] [,145] [,146] [,147] [,148] [,149] [,150] [,151]
#> inf_H3N2 57 36 27 21 16 11 7 3 12 1
#> inf_H1N1 60 46 18 17 1 6 7 4 8 0
#> [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159] [,160] [,161]
#> inf_H3N2 2 3 7 4 10 2 17 16 14 8
#> inf_H1N1 0 2 2 1 0 0 2 3 1 3
#> [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170] [,171]
#> inf_H3N2 18 14 20 11 14 17 11 14 29 12
#> inf_H1N1 3 3 5 6 3 0 2 5 2 1
#> [,172] [,173] [,174] [,175] [,176] [,177] [,178] [,179] [,180] [,181]
#> inf_H3N2 13 22 19 10 14 18 10 21 17 23
#> inf_H1N1 2 6 4 0 3 2 2 1 7 0
#> [,182] [,183] [,184] [,185] [,186] [,187] [,188] [,189] [,190] [,191]
#> inf_H3N2 19 32 36 36 38 52 63 63 98 64
#> inf_H1N1 3 3 6 4 7 8 11 6 12 7
#> [,192] [,193] [,194] [,195] [,196] [,197] [,198] [,199] [,200] [,201]
#> inf_H3N2 80 73 92 103 54 51 44 20 15 23
#> inf_H1N1 8 7 6 12 10 5 5 5 4 1
#> [,202] [,203] [,204] [,205] [,206] [,207] [,208] [,209] [,210] [,211]
#> inf_H3N2 30 9 8 17 13 4 8 4 16 3
#> inf_H1N1 1 0 1 5 16 11 12 2 11 14
#> [,212] [,213] [,214] [,215] [,216] [,217] [,218] [,219] [,220] [,221]
#> inf_H3N2 5 2 4 2 3 6 0 4 4 11
#> inf_H1N1 6 14 17 20 13 18 21 18 12 10
#> [,222] [,223] [,224] [,225] [,226] [,227] [,228] [,229] [,230] [,231]
#> inf_H3N2 3 2 4 4 3 9 8 12 7 6
#> inf_H1N1 4 12 11 4 3 5 11 18 14 18
#> [,232] [,233] [,234] [,235] [,236] [,237] [,238] [,239] [,240] [,241]
#> inf_H3N2 9 10 19 22 22 41 94 131 188 221
#> inf_H1N1 13 26 17 26 25 21 37 17 24 17
#> [,242] [,243] [,244] [,245] [,246] [,247] [,248] [,249] [,250] [,251]
#> inf_H3N2 242 236 293 291 216 196 146 118 94 43
#> inf_H1N1 17 14 11 10 11 7 7 6 5 0
#> [,252] [,253] [,254] [,255] [,256] [,257] [,258] [,259] [,260] [,261]
#> inf_H3N2 26 32 12 13 15 8 6 10 18 3
#> inf_H1N1 1 0 0 0 0 1 0 1 0 0
#> [,262] [,263] [,264] [,265] [,266] [,267] [,268] [,269] [,270] [,271]
#> inf_H3N2 23 19 18 22 37 32 21 34 21 14
#> inf_H1N1 2 2 1 3 2 0 0 1 0 2
#> [,272] [,273] [,274] [,275] [,276] [,277] [,278] [,279] [,280] [,281]
#> inf_H3N2 19 18 15 9 6 2 4 9 6 8
#> inf_H1N1 2 5 3 1 2 4 0 8 7 11
#> [,282] [,283] [,284] [,285] [,286] [,287] [,288] [,289] [,290] [,291]
#> inf_H3N2 7 8 9 12 13 11 29 54 59 57
#> inf_H1N1 8 5 4 8 15 17 15 18 18 13
#> [,292] [,293] [,294] [,295] [,296] [,297] [,298] [,299] [,300] [,301]
#> inf_H3N2 65 95 115 142 135 238 217 167 109 93
#> inf_H1N1 16 14 30 18 26 34 37 34 33 28
#> [,302] [,303] [,304] [,305] [,306] [,307] [,308] [,309] [,310] [,311]
#> inf_H3N2 69 52 36 31 19 16 6 9 12 6
#> inf_H1N1 17 4 4 6 2 3 5 6 3 4
#> [,312] [,313] [,314] [,315] [,316] [,317] [,318] [,319] [,320] [,321]
#> inf_H3N2 7 13 13 6 12 10 20 12 26 18
#> inf_H1N1 5 1 14 6 5 8 4 4 13 4
#> [,322] [,323] [,324] [,325] [,326] [,327] [,328] [,329] [,330] [,331]
#> inf_H3N2 13 14 8 8 8 6 6 3 5 5
#> inf_H1N1 5 4 7 8 11 8 5 7 8 10
#> [,332] [,333] [,334] [,335] [,336] [,337] [,338] [,339] [,340] [,341]
#> inf_H3N2 12 6 1 2 8 3 2 6 9 7
#> inf_H1N1 6 6 5 11 12 27 24 41 48 66
#> [,342] [,343] [,344] [,345] [,346] [,347] [,348] [,349] [,350] [,351]
#> inf_H3N2 5 5 4 8 7 15 14 23 26 25
#> inf_H1N1 44 44 44 68 92 93 112 100 107 144
#> [,352] [,353] [,354] [,355] [,356] [,357] [,358] [,359] [,360] [,361]
#> inf_H3N2 29 55 29 18 24 7 8 13 5 14
#> inf_H1N1 81 61 46 26 21 21 25 39 78 73
#> [,362] [,363] [,364] [,365] [,366] [,367] [,368] [,369] [,370] [,371]
#> inf_H3N2 28 23 28 33 29 39 60 47 23 47
#> inf_H1N1 136 91 92 43 30 51 53 26 29 28
#> [,372] [,373] [,374] [,375] [,376] [,377] [,378] [,379] [,380] [,381]
#> inf_H3N2 33 45 48 23 29 13 17 24 73 84
#> inf_H1N1 28 29 26 25 21 15 13 21 13 24
#> [,382] [,383] [,384] [,385] [,386] [,387] [,388] [,389] [,390] [,391]
#> inf_H3N2 108 104 162 204 390 394 471 365 345 355
#> inf_H1N1 17 21 12 19 15 6 9 5 10 3
#> [,392] [,393] [,394] [,395] [,396] [,397] [,398] [,399] [,400] [,401]
#> inf_H3N2 314 178 150 110 60 40 33 52 18 27
#> inf_H1N1 4 8 6 6 3 3 4 6 9 5
#> [,402] [,403] [,404] [,405] [,406] [,407] [,408] [,409] [,410] [,411]
#> inf_H3N2 23 7 9 5 6 9 7 1 0 2
#> inf_H1N1 1 1 1 3 2 2 4 4 5 6
#> [,412] [,413] [,414] [,415] [,416] [,417] [,418] [,419] [,420] [,421]
#> inf_H3N2 1 0 1 1 0 0 3 3 2 2
#> inf_H1N1 6 9 13 14 0 0 11 11 21 37
#> [,422] [,423] [,424] [,425] [,426]
#> inf_H3N2 5 3 2 7 11
#> inf_H1N1 28 22 16 17 22
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"
# Using a time series object (time argument is optional)
influenza_xts <- xts::xts(
influenza[, c("ili", "inf_A", "inf_H3N2", "inf_H1N1", "inf_B", "other")],
order.by = influenza$week
)
subtyped(
data = influenza_xts,
case_timeseries = "ili",
unsubtyped_timeseries = "inf_A",
subtyped_timeseries = c("inf_H3N2", "inf_H1N1"),
other_pathogen_timeseries = c("inf_B", "other")
)
#> $pathogen_structure
#> [1] "subtyped"
#>
#> $pathogen_names
#> [1] "inf_H3N2" "inf_H1N1" "inf_B" "other"
#>
#> $validated_tsbl
#> # A tsibble: 426 x 7 [7D]
#> index case_timeseries inf_A inf_H3N2 inf_H1N1 inf_B other
#> <date> <int> <int> <int> <int> <int> <int>
#> 1 2012-01-02 29 4 4 0 3 278
#> 2 2012-01-09 38 4 4 0 1 219
#> 3 2012-01-16 42 13 13 0 8 238
#> 4 2012-01-23 58 6 3 2 5 187
#> 5 2012-01-30 45 3 3 0 2 228
#> 6 2012-02-06 60 1 1 0 7 274
#> 7 2012-02-13 30 2 0 2 10 278
#> 8 2012-02-20 52 4 3 1 9 266
#> 9 2012-02-27 33 6 4 2 13 327
#> 10 2012-03-05 26 4 4 0 10 324
#> # ℹ 416 more rows
#>
#> $data
#> $data$case_timeseries
#> [1] 29 38 42 58 45 60 30 52 33 26 75 65 71 92 71 75 73 39
#> [19] 57 94 140 144 218 234 176 265 370 389 469 465 434 496 441 399 359 255
#> [37] 198 195 156 105 78 48 48 77 69 58 64 80 69 60 50 63 41 54
#> [55] 64 55 53 64 61 68 81 66 81 89 76 100 86 106 39 57 65 64
#> [73] 80 83 136 125 140 113 133 171 168 166 204 181 245 216 202 236 220 188
#> [91] 211 157 105 40 58 128 83 106 70 98 106 32 25 45 48 69 60 79
#> [109] 49 49 81 70 84 107 104 99 110 137 92 98 71 124 114 73 67 98
#> [127] 96 136 148 153 179 173 158 213 306 328 381 410 411 336 341 269 186 166
#> [145] 107 121 47 116 110 110 106 75 59 62 65 34 48 61 61 26 11 11
#> [163] 19 22 28 49 40 39 46 48 36 57 62 66 117 99 118 117 131 141
#> [181] 177 202 220 226 231 246 292 327 384 492 375 340 303 242 206 140 80 88
#> [199] 54 55 55 44 31 40 32 28 15 11 13 21 34 17 13 15 22 30
#> [217] 31 38 31 25 28 44 68 57 59 62 68 55 94 91 123 94 110 109
#> [235] 106 116 131 157 178 229 257 315 247 239 260 241 172 118 95 97 73 52
#> [253] 55 49 50 28 38 37 41 20 19 24 34 28 33 22 20 39 38 55
#> [271] 47 41 51 69 57 49 49 51 57 57 58 57 71 89 71 82 114 160
#> [289] 154 186 243 392 464 540 554 475 508 424 374 308 202 171 132 100 93 83
#> [307] 49 72 46 32 37 49 21 19 36 16 42 20 38 50 44 40 58 33
#> [325] 52 53 43 68 74 54 45 64 85 103 101 83 94 110 79 103 109 123
#> [343] 129 120 129 130 146 152 148 153 134 93 85 98 90 76 54 52 54 41
#> [361] 58 46 51 30 14 32 32 45 24 25 34 30 53 56 50 53 73 88
#> [379] 129 160 95 102 207 209 264 320 330 320 285 283 283 280 319 262 274 246
#> [397] 259 273 242 215 225 150 146 101 89 42 55 37 37 41 37 37 39 35
#> [415] 31 19 7 21 26 19 31 37 45 28 38 33
#>
#> $data$component_pathogens
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> inf_A 4 4 13 6 3 1 2 4 6 4 12 9 14
#> inf_B 3 1 8 5 2 7 10 9 13 10 19 12 8
#> other 278 219 238 187 228 274 278 266 327 324 346 333 322
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
#> inf_A 8 9 16 13 14 12 15 27 33 56 95 95
#> inf_B 5 6 4 4 10 7 12 11 8 18 23 30
#> other 317 326 378 328 379 403 481 524 637 509 512 701
#> [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
#> inf_A 182 264 310 280 311 318 274 295 187 153 89 63
#> inf_B 72 90 129 111 122 117 114 90 100 97 50 46
#> other 644 675 949 903 775 874 844 783 897 686 813 707
#> [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49]
#> inf_A 44 17 12 10 9 4 0 10 10 0 3 7
#> inf_B 28 15 12 7 6 3 2 3 1 2 1 0
#> other 508 524 450 433 433 367 324 352 374 359 319 357
#> [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61]
#> inf_A 2 3 1 5 8 11 11 10 15 15 8 15
#> inf_B 0 2 0 3 5 6 4 3 3 2 2 1
#> other 292 258 205 153 177 171 171 185 198 198 240 246
#> [,62] [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73]
#> inf_A 8 18 25 10 6 4 4 3 1 2 4 9
#> inf_B 7 3 2 0 2 1 0 0 0 2 3 1
#> other 260 285 305 250 248 289 272 303 296 284 282 378
#> [,74] [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85]
#> inf_A 5 8 4 4 7 23 26 48 37 71 87 80
#> inf_B 0 1 3 1 3 6 10 20 8 10 17 19
#> other 339 317 393 330 370 425 423 441 471 459 469 507
#> [,86] [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97]
#> inf_A 105 127 102 116 113 109 59 64 46 38 39 26
#> inf_B 23 32 14 24 12 16 14 18 7 4 8 6
#> other 566 561 611 509 586 549 461 430 467 321 322 277
#> [,98] [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107]
#> inf_A 17 10 19 12 22 7 11 20 22 23
#> inf_B 8 4 13 5 9 1 2 1 1 2
#> other 269 244 254 217 229 239 119 142 170 173
#> [,108] [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117]
#> inf_A 17 18 29 25 13 20 18 18 10 14
#> inf_B 9 1 2 1 3 13 3 3 7 2
#> other 201 160 179 122 197 237 152 254 211 211
#> [,118] [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127]
#> inf_A 15 12 16 6 5 12 12 15 13 12
#> inf_B 6 7 1 2 4 4 7 4 1 2
#> other 280 229 232 238 231 294 269 310 309 280
#> [,128] [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137]
#> inf_A 16 19 44 83 118 172 176 204 268 237
#> inf_B 3 4 7 8 7 12 12 13 9 31
#> other 329 316 339 374 435 481 451 508 527 631
#> [,138] [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147]
#> inf_A 293 246 187 162 128 92 51 41 17 17
#> inf_B 27 25 30 25 22 18 21 17 12 11
#> other 640 548 532 541 532 524 398 424 357 374
#> [,148] [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157]
#> inf_A 14 7 21 1 2 6 9 5 10 2
#> inf_B 10 18 5 7 4 6 6 2 4 1
#> other 354 312 294 312 247 216 232 223 146 68
#> [,158] [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167]
#> inf_A 19 19 15 11 22 17 25 17 17 17
#> inf_B 1 4 3 5 2 5 5 3 5 3
#> other 197 169 177 175 172 175 216 213 231 214
#> [,168] [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177]
#> inf_A 14 19 32 13 15 28 23 10 17 21
#> inf_B 5 9 5 9 10 11 18 15 25 26
#> other 248 236 267 226 274 291 256 301 295 330
#> [,178] [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187]
#> inf_A 12 22 25 23 23 35 42 40 49 61
#> inf_B 29 41 46 49 59 111 88 92 106 93
#> other 349 349 373 421 403 456 485 502 542 592
#> [,188] [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197]
#> inf_A 78 72 114 74 91 86 102 117 68 58
#> inf_B 125 103 137 111 79 73 79 72 45 27
#> other 549 619 624 622 563 560 549 491 385 387
#> [,198] [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207]
#> inf_A 49 27 19 24 31 9 9 22 29 15
#> inf_B 19 14 8 6 4 3 2 2 2 2
#> other 338 321 323 314 277 286 275 295 265 254
#> [,208] [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217]
#> inf_A 20 6 27 17 11 16 21 22 16 24
#> inf_B 3 0 0 2 1 1 2 8 3 3
#> other 183 108 253 223 207 197 212 222 221 250
#> [,218] [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227]
#> inf_A 21 22 16 21 7 14 15 8 6 14
#> inf_B 8 4 6 7 5 6 8 4 5 5
#> other 273 258 267 241 269 284 316 319 306 367
#> [,228] [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237]
#> inf_A 19 30 26 35 39 52 63 92 99 121
#> inf_B 12 14 7 12 9 12 14 24 33 55
#> other 389 405 860 805 746 788 897 950 1052 1075
#> [,238] [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247]
#> inf_A 239 243 284 342 488 479 541 539 372 317
#> inf_B 41 54 67 91 81 75 70 63 61 62
#> other 1075 1078 1235 1227 1456 1367 1572 1587 1404 1409
#> [,248] [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257]
#> inf_A 236 185 128 65 46 48 20 22 27 12
#> inf_B 37 41 27 17 15 12 14 4 5 8
#> other 1255 1250 1163 1017 954 877 848 722 634 607
#> [,258] [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267]
#> inf_A 13 17 20 9 30 30 25 37 49 40
#> inf_B 6 4 10 4 6 2 3 2 2 1
#> other 582 557 522 429 326 352 309 275 263 231
#> [,268] [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277]
#> inf_A 30 42 25 18 30 34 32 15 17 7
#> inf_B 3 8 2 2 2 2 8 6 1 4
#> other 288 316 381 344 310 509 652 596 593 734
#> [,278] [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287]
#> inf_A 10 21 16 28 26 20 24 32 61 59
#> inf_B 4 6 3 4 15 7 7 19 27 23
#> other 675 717 719 725 789 905 781 842 989 947
#> [,288] [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297]
#> inf_A 125 225 363 359 471 610 652 654 584 709
#> inf_B 45 59 74 69 148 207 249 222 220 251
#> other 1114 1238 1150 1283 1137 1088 1653 1765 1796 1832
#> [,298] [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307]
#> inf_A 663 502 329 221 132 76 48 40 29 29
#> inf_B 206 219 200 126 96 52 30 36 33 20
#> other 1927 1817 1691 1488 1377 1087 1058 1028 987 929
#> [,308] [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317]
#> inf_A 13 21 19 17 17 18 38 19 24 34
#> inf_B 22 22 11 15 13 11 9 11 12 22
#> other 746 752 671 641 606 525 428 429 364 337
#> [,318] [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327]
#> inf_A 36 26 55 37 23 27 16 18 22 23
#> inf_B 17 10 18 16 14 5 6 10 3 7
#> other 384 326 336 331 368 373 345 544 504 621
#> [,328] [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337]
#> inf_A 14 20 16 26 28 29 18 20 25 37
#> inf_B 0 3 2 5 4 4 6 4 0 7
#> other 678 702 669 749 815 933 980 945 1094 1085
#> [,338] [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347]
#> inf_A 39 70 64 89 70 80 71 114 145 186
#> inf_B 2 2 3 7 3 8 0 5 9 14
#> other 1188 1163 1244 1427 1422 1408 1399 1341 1476 1457
#> [,348] [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357]
#> inf_A 201 155 238 232 158 176 105 74 56 39
#> inf_B 9 19 14 8 12 7 13 9 3 4
#> other 1440 1719 1412 1469 1332 1360 1234 1076 941 936
#> [,358] [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367]
#> inf_A 47 63 105 110 186 124 138 103 84 99
#> inf_B 6 7 8 7 3 5 7 6 3 3
#> other 960 943 933 984 843 857 828 664 646 790
#> [,368] [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377]
#> inf_A 123 95 107 104 103 124 132 95 105 67
#> inf_B 2 2 3 2 1 1 2 2 6 7
#> other 717 688 778 669 784 876 887 868 884 983
#> [,378] [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387]
#> inf_A 76 94 142 174 196 213 245 363 640 655
#> inf_B 5 4 2 4 14 9 12 22 46 52
#> other 892 1095 1176 1129 1271 1267 1327 1556 2041 2178
#> [,388] [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397]
#> inf_A 844 746 782 862 749 567 511 364 294 303
#> inf_B 68 96 109 140 118 95 96 97 87 118
#> other 2207 2478 2433 2563 2671 2712 2573 2297 2245 2294
#> [,398] [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407]
#> inf_A 274 338 256 182 159 130 127 79 78 52
#> inf_B 154 138 103 112 65 51 32 28 22 4
#> other 2350 2239 2247 2202 1882 2011 1923 1767 1725 1518
#> [,408] [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417]
#> inf_A 38 29 20 25 23 36 51 37 18 25
#> inf_B 7 5 2 0 3 4 3 5 0 1
#> other 1563 1367 1226 1219 1202 1107 1160 1142 805 852
#> [,418] [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426]
#> inf_A 41 58 54 103 72 74 62 55 69
#> inf_B 1 2 2 10 12 6 5 7 3
#> other 979 1059 891 1057 1290 1290 1193 1293 1513
#>
#> $data$subtyped
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
#> inf_H3N2 4 4 13 3 3 1 0 3 4 4 10 9 14
#> inf_H1N1 0 0 0 2 0 0 2 1 2 0 2 0 0
#> [,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
#> inf_H3N2 7 6 13 12 13 11 13 26 28 39 63
#> inf_H1N1 0 3 3 1 1 1 2 1 2 1 1
#> [,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35]
#> inf_H3N2 79 175 250 306 272 304 308 268 291 180 148
#> inf_H1N1 2 5 11 4 7 5 9 6 3 6 4
#> [,36] [,37] [,38] [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46]
#> inf_H3N2 88 61 43 15 12 8 9 4 0 8 8
#> inf_H1N1 1 2 0 0 0 2 0 0 0 0 1
#> [,47] [,48] [,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56] [,57]
#> inf_H3N2 0 1 4 1 1 0 3 2 7 8 6
#> inf_H1N1 0 2 3 0 2 1 2 5 3 3 4
#> [,58] [,59] [,60] [,61] [,62] [,63] [,64] [,65] [,66] [,67] [,68]
#> inf_H3N2 11 9 7 13 6 7 7 7 4 2 2
#> inf_H1N1 3 6 1 1 2 11 18 3 1 2 2
#> [,69] [,70] [,71] [,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
#> inf_H3N2 1 1 1 4 7 3 4 3 4 5 16
#> inf_H1N1 2 0 1 0 1 1 4 1 0 2 5
#> [,80] [,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88] [,89] [,90]
#> inf_H3N2 19 40 28 58 65 61 74 70 49 75 70
#> inf_H1N1 7 7 8 12 21 18 30 55 52 40 42
#> [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98] [,99] [,100] [,101]
#> inf_H3N2 65 29 32 30 21 22 14 10 6 12 8
#> inf_H1N1 42 30 30 15 17 14 11 7 3 5 4
#> [,102] [,103] [,104] [,105] [,106] [,107] [,108] [,109] [,110] [,111]
#> inf_H3N2 21 6 10 14 15 12 10 14 24 18
#> inf_H1N1 1 1 1 5 7 11 7 4 5 7
#> [,112] [,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120] [,121]
#> inf_H3N2 9 11 12 7 2 8 9 7 15 5
#> inf_H1N1 3 9 6 11 8 6 6 4 1 1
#> [,122] [,123] [,124] [,125] [,126] [,127] [,128] [,129] [,130] [,131]
#> inf_H3N2 4 6 3 4 6 2 1 3 12 25
#> inf_H1N1 1 5 9 9 7 10 13 14 30 54
#> [,132] [,133] [,134] [,135] [,136] [,137] [,138] [,139] [,140] [,141]
#> inf_H3N2 14 33 48 82 110 81 91 73 65 52
#> inf_H1N1 104 131 125 110 148 136 168 152 104 98
#> [,142] [,143] [,144] [,145] [,146] [,147] [,148] [,149] [,150] [,151]
#> inf_H3N2 57 36 27 21 16 11 7 3 12 1
#> inf_H1N1 60 46 18 17 1 6 7 4 8 0
#> [,152] [,153] [,154] [,155] [,156] [,157] [,158] [,159] [,160] [,161]
#> inf_H3N2 2 3 7 4 10 2 17 16 14 8
#> inf_H1N1 0 2 2 1 0 0 2 3 1 3
#> [,162] [,163] [,164] [,165] [,166] [,167] [,168] [,169] [,170] [,171]
#> inf_H3N2 18 14 20 11 14 17 11 14 29 12
#> inf_H1N1 3 3 5 6 3 0 2 5 2 1
#> [,172] [,173] [,174] [,175] [,176] [,177] [,178] [,179] [,180] [,181]
#> inf_H3N2 13 22 19 10 14 18 10 21 17 23
#> inf_H1N1 2 6 4 0 3 2 2 1 7 0
#> [,182] [,183] [,184] [,185] [,186] [,187] [,188] [,189] [,190] [,191]
#> inf_H3N2 19 32 36 36 38 52 63 63 98 64
#> inf_H1N1 3 3 6 4 7 8 11 6 12 7
#> [,192] [,193] [,194] [,195] [,196] [,197] [,198] [,199] [,200] [,201]
#> inf_H3N2 80 73 92 103 54 51 44 20 15 23
#> inf_H1N1 8 7 6 12 10 5 5 5 4 1
#> [,202] [,203] [,204] [,205] [,206] [,207] [,208] [,209] [,210] [,211]
#> inf_H3N2 30 9 8 17 13 4 8 4 16 3
#> inf_H1N1 1 0 1 5 16 11 12 2 11 14
#> [,212] [,213] [,214] [,215] [,216] [,217] [,218] [,219] [,220] [,221]
#> inf_H3N2 5 2 4 2 3 6 0 4 4 11
#> inf_H1N1 6 14 17 20 13 18 21 18 12 10
#> [,222] [,223] [,224] [,225] [,226] [,227] [,228] [,229] [,230] [,231]
#> inf_H3N2 3 2 4 4 3 9 8 12 7 6
#> inf_H1N1 4 12 11 4 3 5 11 18 14 18
#> [,232] [,233] [,234] [,235] [,236] [,237] [,238] [,239] [,240] [,241]
#> inf_H3N2 9 10 19 22 22 41 94 131 188 221
#> inf_H1N1 13 26 17 26 25 21 37 17 24 17
#> [,242] [,243] [,244] [,245] [,246] [,247] [,248] [,249] [,250] [,251]
#> inf_H3N2 242 236 293 291 216 196 146 118 94 43
#> inf_H1N1 17 14 11 10 11 7 7 6 5 0
#> [,252] [,253] [,254] [,255] [,256] [,257] [,258] [,259] [,260] [,261]
#> inf_H3N2 26 32 12 13 15 8 6 10 18 3
#> inf_H1N1 1 0 0 0 0 1 0 1 0 0
#> [,262] [,263] [,264] [,265] [,266] [,267] [,268] [,269] [,270] [,271]
#> inf_H3N2 23 19 18 22 37 32 21 34 21 14
#> inf_H1N1 2 2 1 3 2 0 0 1 0 2
#> [,272] [,273] [,274] [,275] [,276] [,277] [,278] [,279] [,280] [,281]
#> inf_H3N2 19 18 15 9 6 2 4 9 6 8
#> inf_H1N1 2 5 3 1 2 4 0 8 7 11
#> [,282] [,283] [,284] [,285] [,286] [,287] [,288] [,289] [,290] [,291]
#> inf_H3N2 7 8 9 12 13 11 29 54 59 57
#> inf_H1N1 8 5 4 8 15 17 15 18 18 13
#> [,292] [,293] [,294] [,295] [,296] [,297] [,298] [,299] [,300] [,301]
#> inf_H3N2 65 95 115 142 135 238 217 167 109 93
#> inf_H1N1 16 14 30 18 26 34 37 34 33 28
#> [,302] [,303] [,304] [,305] [,306] [,307] [,308] [,309] [,310] [,311]
#> inf_H3N2 69 52 36 31 19 16 6 9 12 6
#> inf_H1N1 17 4 4 6 2 3 5 6 3 4
#> [,312] [,313] [,314] [,315] [,316] [,317] [,318] [,319] [,320] [,321]
#> inf_H3N2 7 13 13 6 12 10 20 12 26 18
#> inf_H1N1 5 1 14 6 5 8 4 4 13 4
#> [,322] [,323] [,324] [,325] [,326] [,327] [,328] [,329] [,330] [,331]
#> inf_H3N2 13 14 8 8 8 6 6 3 5 5
#> inf_H1N1 5 4 7 8 11 8 5 7 8 10
#> [,332] [,333] [,334] [,335] [,336] [,337] [,338] [,339] [,340] [,341]
#> inf_H3N2 12 6 1 2 8 3 2 6 9 7
#> inf_H1N1 6 6 5 11 12 27 24 41 48 66
#> [,342] [,343] [,344] [,345] [,346] [,347] [,348] [,349] [,350] [,351]
#> inf_H3N2 5 5 4 8 7 15 14 23 26 25
#> inf_H1N1 44 44 44 68 92 93 112 100 107 144
#> [,352] [,353] [,354] [,355] [,356] [,357] [,358] [,359] [,360] [,361]
#> inf_H3N2 29 55 29 18 24 7 8 13 5 14
#> inf_H1N1 81 61 46 26 21 21 25 39 78 73
#> [,362] [,363] [,364] [,365] [,366] [,367] [,368] [,369] [,370] [,371]
#> inf_H3N2 28 23 28 33 29 39 60 47 23 47
#> inf_H1N1 136 91 92 43 30 51 53 26 29 28
#> [,372] [,373] [,374] [,375] [,376] [,377] [,378] [,379] [,380] [,381]
#> inf_H3N2 33 45 48 23 29 13 17 24 73 84
#> inf_H1N1 28 29 26 25 21 15 13 21 13 24
#> [,382] [,383] [,384] [,385] [,386] [,387] [,388] [,389] [,390] [,391]
#> inf_H3N2 108 104 162 204 390 394 471 365 345 355
#> inf_H1N1 17 21 12 19 15 6 9 5 10 3
#> [,392] [,393] [,394] [,395] [,396] [,397] [,398] [,399] [,400] [,401]
#> inf_H3N2 314 178 150 110 60 40 33 52 18 27
#> inf_H1N1 4 8 6 6 3 3 4 6 9 5
#> [,402] [,403] [,404] [,405] [,406] [,407] [,408] [,409] [,410] [,411]
#> inf_H3N2 23 7 9 5 6 9 7 1 0 2
#> inf_H1N1 1 1 1 3 2 2 4 4 5 6
#> [,412] [,413] [,414] [,415] [,416] [,417] [,418] [,419] [,420] [,421]
#> inf_H3N2 1 0 1 1 0 0 3 3 2 2
#> inf_H1N1 6 9 13 14 0 0 11 11 21 37
#> [,422] [,423] [,424] [,425] [,426]
#> inf_H3N2 5 3 2 7 11
#> inf_H1N1 28 22 16 17 22
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"