Subtyped pathogen structure
Arguments
- case_timeseries
vector of total case data
- time
vector of labelled time data
- influenzaA_unsubtyped_timeseries
case timeseries data for unsubtyped influenzaA
- influenzaA_subtyped_timeseries
case timeseries data for subtyped influenzaA
- other_pathogen_timeseries
other pathogen case timeseries
- smoothing_structure
either `shared` (all pathogens have the same smoothing structure; tau[1]), `independent` (each pathogen has completely independent smoothing structure; tau[number of pathogens]), or `correlated` (smoothing structure is correlated among pathogens Sigma[number of pathogens, number of pathogens]). Case-insensitive.
- observation_noise
either `observation_noise_only` (only includes observation noise - the same between pathogens) or `pathogen_specific_noise` (includes noise in individual pathogens as well). Case-insensitive.
Value
named list including pathogen_structure, pathogen_names, data, and model_params of class `EpiStrainDynamics.pathogen_structure`
Examples
# Both integer and numeric inputs work consistently
subtyped(
case_timeseries = influenza$ili,
time = influenza$week,
influenzaA_unsubtyped_timeseries = influenza$inf_A,
influenzaA_subtyped_timeseries = list(
influenzaA.H3N2 = influenza$inf_H3N2,
influenzaA.H1N1 = influenza$inf_H1N1
),
other_pathogen_timeseries = list(
influenzaB = influenza$inf_B,
other = influenza$num_spec - influenza$inf_all
),
smoothing_structure = 'independent',
observation_noise = 'observation_noise_only'
)
#> $pathogen_structure
#> [1] "subtyped"
#>
#> $pathogen_names
#> [1] "influenzaA.H3N2" "influenzaA.H1N1" "influenzaB" "other"
#>
#> $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
#>
#> $data$time
#> [1] "2012-01-02" "2012-01-09" "2012-01-16" "2012-01-23" "2012-01-30"
#> [6] "2012-02-06" "2012-02-13" "2012-02-20" "2012-02-27" "2012-03-05"
#> [11] "2012-03-12" "2012-03-19" "2012-03-26" "2012-04-02" "2012-04-09"
#> [16] "2012-04-16" "2012-04-23" "2012-04-30" "2012-05-07" "2012-05-14"
#> [21] "2012-05-21" "2012-05-28" "2012-06-04" "2012-06-11" "2012-06-18"
#> [26] "2012-06-25" "2012-07-02" "2012-07-09" "2012-07-16" "2012-07-23"
#> [31] "2012-07-30" "2012-08-06" "2012-08-13" "2012-08-20" "2012-08-27"
#> [36] "2012-09-03" "2012-09-10" "2012-09-17" "2012-09-24" "2012-10-01"
#> [41] "2012-10-08" "2012-10-15" "2012-10-22" "2012-10-29" "2012-11-05"
#> [46] "2012-11-12" "2012-11-19" "2012-11-26" "2012-12-03" "2012-12-10"
#> [51] "2012-12-17" "2012-12-24" "2012-12-31" "2013-01-07" "2013-01-14"
#> [56] "2013-01-21" "2013-01-28" "2013-02-04" "2013-02-11" "2013-02-18"
#> [61] "2013-02-25" "2013-03-04" "2013-03-11" "2013-03-18" "2013-03-25"
#> [66] "2013-04-01" "2013-04-08" "2013-04-15" "2013-04-22" "2013-04-29"
#> [71] "2013-05-06" "2013-05-13" "2013-05-20" "2013-05-27" "2013-06-03"
#> [76] "2013-06-10" "2013-06-17" "2013-06-24" "2013-07-01" "2013-07-08"
#> [81] "2013-07-15" "2013-07-22" "2013-07-29" "2013-08-05" "2013-08-12"
#> [86] "2013-08-19" "2013-08-26" "2013-09-02" "2013-09-09" "2013-09-16"
#> [91] "2013-09-23" "2013-09-30" "2013-10-07" "2013-10-14" "2013-10-21"
#> [96] "2013-10-28" "2013-11-04" "2013-11-11" "2013-11-18" "2013-11-25"
#> [101] "2013-12-02" "2013-12-09" "2013-12-16" "2013-12-23" "2013-12-30"
#> [106] "2014-01-06" "2014-01-13" "2014-01-20" "2014-01-27" "2014-02-03"
#> [111] "2014-02-10" "2014-02-17" "2014-02-24" "2014-03-03" "2014-03-10"
#> [116] "2014-03-17" "2014-03-24" "2014-03-31" "2014-04-07" "2014-04-14"
#> [121] "2014-04-21" "2014-04-28" "2014-05-05" "2014-05-12" "2014-05-19"
#> [126] "2014-05-26" "2014-06-02" "2014-06-09" "2014-06-16" "2014-06-23"
#> [131] "2014-06-30" "2014-07-07" "2014-07-14" "2014-07-21" "2014-07-28"
#> [136] "2014-08-04" "2014-08-11" "2014-08-18" "2014-08-25" "2014-09-01"
#> [141] "2014-09-08" "2014-09-15" "2014-09-22" "2014-09-29" "2014-10-06"
#> [146] "2014-10-13" "2014-10-20" "2014-10-27" "2014-11-03" "2014-11-10"
#> [151] "2014-11-17" "2014-11-24" "2014-12-01" "2014-12-08" "2014-12-15"
#> [156] "2014-12-22" "2014-12-29" "2015-01-05" "2015-01-12" "2015-01-19"
#> [161] "2015-01-26" "2015-02-02" "2015-02-09" "2015-02-16" "2015-02-23"
#> [166] "2015-03-02" "2015-03-09" "2015-03-16" "2015-03-23" "2015-03-30"
#> [171] "2015-04-06" "2015-04-13" "2015-04-20" "2015-04-27" "2015-05-04"
#> [176] "2015-05-11" "2015-05-18" "2015-05-25" "2015-06-01" "2015-06-08"
#> [181] "2015-06-15" "2015-06-22" "2015-06-29" "2015-07-06" "2015-07-13"
#> [186] "2015-07-20" "2015-07-27" "2015-08-03" "2015-08-10" "2015-08-17"
#> [191] "2015-08-24" "2015-08-31" "2015-09-07" "2015-09-14" "2015-09-21"
#> [196] "2015-09-28" "2015-10-05" "2015-10-12" "2015-10-19" "2015-10-26"
#> [201] "2015-11-02" "2015-11-09" "2015-11-16" "2015-11-23" "2015-11-30"
#> [206] "2015-12-07" "2015-12-14" "2015-12-21" "2015-12-28" "2016-01-04"
#> [211] "2016-01-11" "2016-01-18" "2016-01-25" "2016-02-01" "2016-02-08"
#> [216] "2016-02-15" "2016-02-22" "2016-02-29" "2016-03-07" "2016-03-14"
#> [221] "2016-03-21" "2016-03-28" "2016-04-04" "2016-04-11" "2016-04-18"
#> [226] "2016-04-25" "2016-05-02" "2016-05-09" "2016-05-16" "2016-05-23"
#> [231] "2016-05-30" "2016-06-06" "2016-06-13" "2016-06-20" "2016-06-27"
#> [236] "2016-07-04" "2016-07-11" "2016-07-18" "2016-07-25" "2016-08-01"
#> [241] "2016-08-08" "2016-08-15" "2016-08-22" "2016-08-29" "2016-09-05"
#> [246] "2016-09-12" "2016-09-19" "2016-09-26" "2016-10-03" "2016-10-10"
#> [251] "2016-10-17" "2016-10-24" "2016-10-31" "2016-11-07" "2016-11-14"
#> [256] "2016-11-21" "2016-11-28" "2016-12-05" "2016-12-12" "2016-12-19"
#> [261] "2016-12-26" "2017-01-02" "2017-01-09" "2017-01-16" "2017-01-23"
#> [266] "2017-01-30" "2017-02-06" "2017-02-13" "2017-02-20" "2017-02-27"
#> [271] "2017-03-06" "2017-03-13" "2017-03-20" "2017-03-27" "2017-04-03"
#> [276] "2017-04-10" "2017-04-17" "2017-04-24" "2017-05-01" "2017-05-08"
#> [281] "2017-05-15" "2017-05-22" "2017-05-29" "2017-06-05" "2017-06-12"
#> [286] "2017-06-19" "2017-06-26" "2017-07-03" "2017-07-10" "2017-07-17"
#> [291] "2017-07-24" "2017-07-31" "2017-08-07" "2017-08-14" "2017-08-21"
#> [296] "2017-08-28" "2017-09-04" "2017-09-11" "2017-09-18" "2017-09-25"
#> [301] "2017-10-02" "2017-10-09" "2017-10-16" "2017-10-23" "2017-10-30"
#> [306] "2017-11-06" "2017-11-13" "2017-11-20" "2017-11-27" "2017-12-04"
#> [311] "2017-12-11" "2017-12-18" "2017-12-25" "2018-01-01" "2018-01-08"
#> [316] "2018-01-15" "2018-01-22" "2018-01-29" "2018-02-05" "2018-02-12"
#> [321] "2018-02-19" "2018-02-26" "2018-03-05" "2018-03-12" "2018-03-19"
#> [326] "2018-03-26" "2018-04-02" "2018-04-09" "2018-04-16" "2018-04-23"
#> [331] "2018-04-30" "2018-05-07" "2018-05-14" "2018-05-21" "2018-05-28"
#> [336] "2018-06-04" "2018-06-11" "2018-06-18" "2018-06-25" "2018-07-02"
#> [341] "2018-07-09" "2018-07-16" "2018-07-23" "2018-07-30" "2018-08-06"
#> [346] "2018-08-13" "2018-08-20" "2018-08-27" "2018-09-03" "2018-09-10"
#> [351] "2018-09-17" "2018-09-24" "2018-10-01" "2018-10-08" "2018-10-15"
#> [356] "2018-10-22" "2018-10-29" "2018-11-05" "2018-11-12" "2018-11-19"
#> [361] "2018-11-26" "2018-12-03" "2018-12-10" "2018-12-17" "2018-12-24"
#> [366] "2018-12-31" "2019-01-07" "2019-01-14" "2019-01-21" "2019-01-28"
#> [371] "2019-02-04" "2019-02-11" "2019-02-18" "2019-02-25" "2019-03-04"
#> [376] "2019-03-11" "2019-03-18" "2019-03-25" "2019-04-01" "2019-04-08"
#> [381] "2019-04-15" "2019-04-22" "2019-04-29" "2019-05-06" "2019-05-13"
#> [386] "2019-05-20" "2019-05-27" "2019-06-03" "2019-06-10" "2019-06-17"
#> [391] "2019-06-24" "2019-07-01" "2019-07-08" "2019-07-15" "2019-07-22"
#> [396] "2019-07-29" "2019-08-05" "2019-08-12" "2019-08-19" "2019-08-26"
#> [401] "2019-09-02" "2019-09-09" "2019-09-16" "2019-09-23" "2019-09-30"
#> [406] "2019-10-07" "2019-10-14" "2019-10-21" "2019-10-28" "2019-11-04"
#> [411] "2019-11-11" "2019-11-18" "2019-11-25" "2019-12-02" "2019-12-09"
#> [416] "2019-12-16" "2019-12-23" "2019-12-30" "2020-01-06" "2020-01-13"
#> [421] "2020-01-20" "2020-01-27" "2020-02-03" "2020-02-10" "2020-02-17"
#> [426] "2020-02-24"
#>
#> $data$component_pathogens
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,] 4 4 13 6 3 1 2 4 6 4 12 9 14 8
#> [2,] 3 1 8 5 2 7 10 9 13 10 19 12 8 5
#> [3,] 278 219 238 187 228 274 278 266 327 324 346 333 322 317
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
#> [1,] 9 16 13 14 12 15 27 33 56 95 95 182
#> [2,] 6 4 4 10 7 12 11 8 18 23 30 72
#> [3,] 326 378 328 379 403 481 524 637 509 512 701 644
#> [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38]
#> [1,] 264 310 280 311 318 274 295 187 153 89 63 44
#> [2,] 90 129 111 122 117 114 90 100 97 50 46 28
#> [3,] 675 949 903 775 874 844 783 897 686 813 707 508
#> [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50]
#> [1,] 17 12 10 9 4 0 10 10 0 3 7 2
#> [2,] 15 12 7 6 3 2 3 1 2 1 0 0
#> [3,] 524 450 433 433 367 324 352 374 359 319 357 292
#> [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62]
#> [1,] 3 1 5 8 11 11 10 15 15 8 15 8
#> [2,] 2 0 3 5 6 4 3 3 2 2 1 7
#> [3,] 258 205 153 177 171 171 185 198 198 240 246 260
#> [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74]
#> [1,] 18 25 10 6 4 4 3 1 2 4 9 5
#> [2,] 3 2 0 2 1 0 0 0 2 3 1 0
#> [3,] 285 305 250 248 289 272 303 296 284 282 378 339
#> [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86]
#> [1,] 8 4 4 7 23 26 48 37 71 87 80 105
#> [2,] 1 3 1 3 6 10 20 8 10 17 19 23
#> [3,] 317 393 330 370 425 423 441 471 459 469 507 566
#> [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98]
#> [1,] 127 102 116 113 109 59 64 46 38 39 26 17
#> [2,] 32 14 24 12 16 14 18 7 4 8 6 8
#> [3,] 561 611 509 586 549 461 430 467 321 322 277 269
#> [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108]
#> [1,] 10 19 12 22 7 11 20 22 23 17
#> [2,] 4 13 5 9 1 2 1 1 2 9
#> [3,] 244 254 217 229 239 119 142 170 173 201
#> [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118]
#> [1,] 18 29 25 13 20 18 18 10 14 15
#> [2,] 1 2 1 3 13 3 3 7 2 6
#> [3,] 160 179 122 197 237 152 254 211 211 280
#> [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
#> [1,] 12 16 6 5 12 12 15 13 12 16
#> [2,] 7 1 2 4 4 7 4 1 2 3
#> [3,] 229 232 238 231 294 269 310 309 280 329
#> [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138]
#> [1,] 19 44 83 118 172 176 204 268 237 293
#> [2,] 4 7 8 7 12 12 13 9 31 27
#> [3,] 316 339 374 435 481 451 508 527 631 640
#> [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
#> [1,] 246 187 162 128 92 51 41 17 17 14
#> [2,] 25 30 25 22 18 21 17 12 11 10
#> [3,] 548 532 541 532 524 398 424 357 374 354
#> [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158]
#> [1,] 7 21 1 2 6 9 5 10 2 19
#> [2,] 18 5 7 4 6 6 2 4 1 1
#> [3,] 312 294 312 247 216 232 223 146 68 197
#> [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
#> [1,] 19 15 11 22 17 25 17 17 17 14
#> [2,] 4 3 5 2 5 5 3 5 3 5
#> [3,] 169 177 175 172 175 216 213 231 214 248
#> [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177] [,178]
#> [1,] 19 32 13 15 28 23 10 17 21 12
#> [2,] 9 5 9 10 11 18 15 25 26 29
#> [3,] 236 267 226 274 291 256 301 295 330 349
#> [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187] [,188]
#> [1,] 22 25 23 23 35 42 40 49 61 78
#> [2,] 41 46 49 59 111 88 92 106 93 125
#> [3,] 349 373 421 403 456 485 502 542 592 549
#> [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198]
#> [1,] 72 114 74 91 86 102 117 68 58 49
#> [2,] 103 137 111 79 73 79 72 45 27 19
#> [3,] 619 624 622 563 560 549 491 385 387 338
#> [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
#> [1,] 27 19 24 31 9 9 22 29 15 20
#> [2,] 14 8 6 4 3 2 2 2 2 3
#> [3,] 321 323 314 277 286 275 295 265 254 183
#> [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217] [,218]
#> [1,] 6 27 17 11 16 21 22 16 24 21
#> [2,] 0 0 2 1 1 2 8 3 3 8
#> [3,] 108 253 223 207 197 212 222 221 250 273
#> [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227] [,228]
#> [1,] 22 16 21 7 14 15 8 6 14 19
#> [2,] 4 6 7 5 6 8 4 5 5 12
#> [3,] 258 267 241 269 284 316 319 306 367 389
#> [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237] [,238]
#> [1,] 30 26 35 39 52 63 92 99 121 239
#> [2,] 14 7 12 9 12 14 24 33 55 41
#> [3,] 405 860 805 746 788 897 950 1052 1075 1075
#> [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248]
#> [1,] 243 284 342 488 479 541 539 372 317 236
#> [2,] 54 67 91 81 75 70 63 61 62 37
#> [3,] 1078 1235 1227 1456 1367 1572 1587 1404 1409 1255
#> [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257] [,258]
#> [1,] 185 128 65 46 48 20 22 27 12 13
#> [2,] 41 27 17 15 12 14 4 5 8 6
#> [3,] 1250 1163 1017 954 877 848 722 634 607 582
#> [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267] [,268]
#> [1,] 17 20 9 30 30 25 37 49 40 30
#> [2,] 4 10 4 6 2 3 2 2 1 3
#> [3,] 557 522 429 326 352 309 275 263 231 288
#> [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277] [,278]
#> [1,] 42 25 18 30 34 32 15 17 7 10
#> [2,] 8 2 2 2 2 8 6 1 4 4
#> [3,] 316 381 344 310 509 652 596 593 734 675
#> [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288]
#> [1,] 21 16 28 26 20 24 32 61 59 125
#> [2,] 6 3 4 15 7 7 19 27 23 45
#> [3,] 717 719 725 789 905 781 842 989 947 1114
#> [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298]
#> [1,] 225 363 359 471 610 652 654 584 709 663
#> [2,] 59 74 69 148 207 249 222 220 251 206
#> [3,] 1238 1150 1283 1137 1088 1653 1765 1796 1832 1927
#> [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307] [,308]
#> [1,] 502 329 221 132 76 48 40 29 29 13
#> [2,] 219 200 126 96 52 30 36 33 20 22
#> [3,] 1817 1691 1488 1377 1087 1058 1028 987 929 746
#> [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317] [,318]
#> [1,] 21 19 17 17 18 38 19 24 34 36
#> [2,] 22 11 15 13 11 9 11 12 22 17
#> [3,] 752 671 641 606 525 428 429 364 337 384
#> [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327] [,328]
#> [1,] 26 55 37 23 27 16 18 22 23 14
#> [2,] 10 18 16 14 5 6 10 3 7 0
#> [3,] 326 336 331 368 373 345 544 504 621 678
#> [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337] [,338]
#> [1,] 20 16 26 28 29 18 20 25 37 39
#> [2,] 3 2 5 4 4 6 4 0 7 2
#> [3,] 702 669 749 815 933 980 945 1094 1085 1188
#> [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347] [,348]
#> [1,] 70 64 89 70 80 71 114 145 186 201
#> [2,] 2 3 7 3 8 0 5 9 14 9
#> [3,] 1163 1244 1427 1422 1408 1399 1341 1476 1457 1440
#> [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357] [,358]
#> [1,] 155 238 232 158 176 105 74 56 39 47
#> [2,] 19 14 8 12 7 13 9 3 4 6
#> [3,] 1719 1412 1469 1332 1360 1234 1076 941 936 960
#> [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367] [,368]
#> [1,] 63 105 110 186 124 138 103 84 99 123
#> [2,] 7 8 7 3 5 7 6 3 3 2
#> [3,] 943 933 984 843 857 828 664 646 790 717
#> [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377] [,378]
#> [1,] 95 107 104 103 124 132 95 105 67 76
#> [2,] 2 3 2 1 1 2 2 6 7 5
#> [3,] 688 778 669 784 876 887 868 884 983 892
#> [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387] [,388]
#> [1,] 94 142 174 196 213 245 363 640 655 844
#> [2,] 4 2 4 14 9 12 22 46 52 68
#> [3,] 1095 1176 1129 1271 1267 1327 1556 2041 2178 2207
#> [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397] [,398]
#> [1,] 746 782 862 749 567 511 364 294 303 274
#> [2,] 96 109 140 118 95 96 97 87 118 154
#> [3,] 2478 2433 2563 2671 2712 2573 2297 2245 2294 2350
#> [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407] [,408]
#> [1,] 338 256 182 159 130 127 79 78 52 38
#> [2,] 138 103 112 65 51 32 28 22 4 7
#> [3,] 2239 2247 2202 1882 2011 1923 1767 1725 1518 1563
#> [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417] [,418]
#> [1,] 29 20 25 23 36 51 37 18 25 41
#> [2,] 5 2 0 3 4 3 5 0 1 1
#> [3,] 1367 1226 1219 1202 1107 1160 1142 805 852 979
#> [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426]
#> [1,] 58 54 103 72 74 62 55 69
#> [2,] 2 2 10 12 6 5 7 3
#> [3,] 1059 891 1057 1290 1290 1193 1293 1513
#>
#> $data$influenzaA_subtyped
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
#> [1,] 4 4 13 3 3 1 0 3 4 4 10 9 14 7
#> [2,] 0 0 0 2 0 0 2 1 2 0 2 0 0 0
#> [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
#> [1,] 6 13 12 13 11 13 26 28 39 63 79 175
#> [2,] 3 3 1 1 1 2 1 2 1 1 2 5
#> [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37] [,38]
#> [1,] 250 306 272 304 308 268 291 180 148 88 61 43
#> [2,] 11 4 7 5 9 6 3 6 4 1 2 0
#> [,39] [,40] [,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48] [,49] [,50]
#> [1,] 15 12 8 9 4 0 8 8 0 1 4 1
#> [2,] 0 0 2 0 0 0 0 1 0 2 3 0
#> [,51] [,52] [,53] [,54] [,55] [,56] [,57] [,58] [,59] [,60] [,61] [,62]
#> [1,] 1 0 3 2 7 8 6 11 9 7 13 6
#> [2,] 2 1 2 5 3 3 4 3 6 1 1 2
#> [,63] [,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72] [,73] [,74]
#> [1,] 7 7 7 4 2 2 1 1 1 4 7 3
#> [2,] 11 18 3 1 2 2 2 0 1 0 1 1
#> [,75] [,76] [,77] [,78] [,79] [,80] [,81] [,82] [,83] [,84] [,85] [,86]
#> [1,] 4 3 4 5 16 19 40 28 58 65 61 74
#> [2,] 4 1 0 2 5 7 7 8 12 21 18 30
#> [,87] [,88] [,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96] [,97] [,98]
#> [1,] 70 49 75 70 65 29 32 30 21 22 14 10
#> [2,] 55 52 40 42 42 30 30 15 17 14 11 7
#> [,99] [,100] [,101] [,102] [,103] [,104] [,105] [,106] [,107] [,108]
#> [1,] 6 12 8 21 6 10 14 15 12 10
#> [2,] 3 5 4 1 1 1 5 7 11 7
#> [,109] [,110] [,111] [,112] [,113] [,114] [,115] [,116] [,117] [,118]
#> [1,] 14 24 18 9 11 12 7 2 8 9
#> [2,] 4 5 7 3 9 6 11 8 6 6
#> [,119] [,120] [,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
#> [1,] 7 15 5 4 6 3 4 6 2 1
#> [2,] 4 1 1 1 5 9 9 7 10 13
#> [,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136] [,137] [,138]
#> [1,] 3 12 25 14 33 48 82 110 81 91
#> [2,] 14 30 54 104 131 125 110 148 136 168
#> [,139] [,140] [,141] [,142] [,143] [,144] [,145] [,146] [,147] [,148]
#> [1,] 73 65 52 57 36 27 21 16 11 7
#> [2,] 152 104 98 60 46 18 17 1 6 7
#> [,149] [,150] [,151] [,152] [,153] [,154] [,155] [,156] [,157] [,158]
#> [1,] 3 12 1 2 3 7 4 10 2 17
#> [2,] 4 8 0 0 2 2 1 0 0 2
#> [,159] [,160] [,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
#> [1,] 16 14 8 18 14 20 11 14 17 11
#> [2,] 3 1 3 3 3 5 6 3 0 2
#> [,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176] [,177] [,178]
#> [1,] 14 29 12 13 22 19 10 14 18 10
#> [2,] 5 2 1 2 6 4 0 3 2 2
#> [,179] [,180] [,181] [,182] [,183] [,184] [,185] [,186] [,187] [,188]
#> [1,] 21 17 23 19 32 36 36 38 52 63
#> [2,] 1 7 0 3 3 6 4 7 8 11
#> [,189] [,190] [,191] [,192] [,193] [,194] [,195] [,196] [,197] [,198]
#> [1,] 63 98 64 80 73 92 103 54 51 44
#> [2,] 6 12 7 8 7 6 12 10 5 5
#> [,199] [,200] [,201] [,202] [,203] [,204] [,205] [,206] [,207] [,208]
#> [1,] 20 15 23 30 9 8 17 13 4 8
#> [2,] 5 4 1 1 0 1 5 16 11 12
#> [,209] [,210] [,211] [,212] [,213] [,214] [,215] [,216] [,217] [,218]
#> [1,] 4 16 3 5 2 4 2 3 6 0
#> [2,] 2 11 14 6 14 17 20 13 18 21
#> [,219] [,220] [,221] [,222] [,223] [,224] [,225] [,226] [,227] [,228]
#> [1,] 4 4 11 3 2 4 4 3 9 8
#> [2,] 18 12 10 4 12 11 4 3 5 11
#> [,229] [,230] [,231] [,232] [,233] [,234] [,235] [,236] [,237] [,238]
#> [1,] 12 7 6 9 10 19 22 22 41 94
#> [2,] 18 14 18 13 26 17 26 25 21 37
#> [,239] [,240] [,241] [,242] [,243] [,244] [,245] [,246] [,247] [,248]
#> [1,] 131 188 221 242 236 293 291 216 196 146
#> [2,] 17 24 17 17 14 11 10 11 7 7
#> [,249] [,250] [,251] [,252] [,253] [,254] [,255] [,256] [,257] [,258]
#> [1,] 118 94 43 26 32 12 13 15 8 6
#> [2,] 6 5 0 1 0 0 0 0 1 0
#> [,259] [,260] [,261] [,262] [,263] [,264] [,265] [,266] [,267] [,268]
#> [1,] 10 18 3 23 19 18 22 37 32 21
#> [2,] 1 0 0 2 2 1 3 2 0 0
#> [,269] [,270] [,271] [,272] [,273] [,274] [,275] [,276] [,277] [,278]
#> [1,] 34 21 14 19 18 15 9 6 2 4
#> [2,] 1 0 2 2 5 3 1 2 4 0
#> [,279] [,280] [,281] [,282] [,283] [,284] [,285] [,286] [,287] [,288]
#> [1,] 9 6 8 7 8 9 12 13 11 29
#> [2,] 8 7 11 8 5 4 8 15 17 15
#> [,289] [,290] [,291] [,292] [,293] [,294] [,295] [,296] [,297] [,298]
#> [1,] 54 59 57 65 95 115 142 135 238 217
#> [2,] 18 18 13 16 14 30 18 26 34 37
#> [,299] [,300] [,301] [,302] [,303] [,304] [,305] [,306] [,307] [,308]
#> [1,] 167 109 93 69 52 36 31 19 16 6
#> [2,] 34 33 28 17 4 4 6 2 3 5
#> [,309] [,310] [,311] [,312] [,313] [,314] [,315] [,316] [,317] [,318]
#> [1,] 9 12 6 7 13 13 6 12 10 20
#> [2,] 6 3 4 5 1 14 6 5 8 4
#> [,319] [,320] [,321] [,322] [,323] [,324] [,325] [,326] [,327] [,328]
#> [1,] 12 26 18 13 14 8 8 8 6 6
#> [2,] 4 13 4 5 4 7 8 11 8 5
#> [,329] [,330] [,331] [,332] [,333] [,334] [,335] [,336] [,337] [,338]
#> [1,] 3 5 5 12 6 1 2 8 3 2
#> [2,] 7 8 10 6 6 5 11 12 27 24
#> [,339] [,340] [,341] [,342] [,343] [,344] [,345] [,346] [,347] [,348]
#> [1,] 6 9 7 5 5 4 8 7 15 14
#> [2,] 41 48 66 44 44 44 68 92 93 112
#> [,349] [,350] [,351] [,352] [,353] [,354] [,355] [,356] [,357] [,358]
#> [1,] 23 26 25 29 55 29 18 24 7 8
#> [2,] 100 107 144 81 61 46 26 21 21 25
#> [,359] [,360] [,361] [,362] [,363] [,364] [,365] [,366] [,367] [,368]
#> [1,] 13 5 14 28 23 28 33 29 39 60
#> [2,] 39 78 73 136 91 92 43 30 51 53
#> [,369] [,370] [,371] [,372] [,373] [,374] [,375] [,376] [,377] [,378]
#> [1,] 47 23 47 33 45 48 23 29 13 17
#> [2,] 26 29 28 28 29 26 25 21 15 13
#> [,379] [,380] [,381] [,382] [,383] [,384] [,385] [,386] [,387] [,388]
#> [1,] 24 73 84 108 104 162 204 390 394 471
#> [2,] 21 13 24 17 21 12 19 15 6 9
#> [,389] [,390] [,391] [,392] [,393] [,394] [,395] [,396] [,397] [,398]
#> [1,] 365 345 355 314 178 150 110 60 40 33
#> [2,] 5 10 3 4 8 6 6 3 3 4
#> [,399] [,400] [,401] [,402] [,403] [,404] [,405] [,406] [,407] [,408]
#> [1,] 52 18 27 23 7 9 5 6 9 7
#> [2,] 6 9 5 1 1 1 3 2 2 4
#> [,409] [,410] [,411] [,412] [,413] [,414] [,415] [,416] [,417] [,418]
#> [1,] 1 0 2 1 0 1 1 0 0 3
#> [2,] 4 5 6 6 9 13 14 0 0 11
#> [,419] [,420] [,421] [,422] [,423] [,424] [,425] [,426]
#> [1,] 3 2 2 5 3 2 7 11
#> [2,] 11 21 37 28 22 16 17 22
#>
#>
#> $model_params
#> $model_params$cov_structure
#> [1] 1
#>
#> $model_params$noise_structure
#> [1] 0
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"
# NOTE: smoothing_structure and observation_noise are case insensitive, so
# these will work
# subtyped(
# ...
# smoothing_structure = 'Independent',
# observation_noise = 'OBSERVATION_NOISE_ONLY'
# )