Single 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.- 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
formatted list with pathogen structure and data of class
EpiStrainDynamics.pathogen_structure.
See also
Other pathogen_structure:
multiple(),
subtyped()
Examples
# Using a data frame
single(
data = sarscov2,
case_timeseries = "cases",
time = "date"
)
#> $pathogen_structure
#> [1] "single"
#>
#> $pathogen_names
#> [1] "cases"
#>
#> $validated_tsbl
#> # A tsibble: 830 x 2 [1D]
#> date case_timeseries
#> <date> <dbl>
#> 1 2020-09-23 7096
#> 2 2020-09-24 7682
#> 3 2020-09-25 7318
#> 4 2020-09-26 6810
#> 5 2020-09-27 7023
#> 6 2020-09-28 9983
#> 7 2020-09-29 10366
#> 8 2020-09-30 12717
#> 9 2020-10-01 13357
#> 10 2020-10-02 13854
#> # 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
#>
#>
#> 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")], order.by = sarscov2$date)
single(
data = sarscov2_xts,
case_timeseries = "cases"
)
#> $pathogen_structure
#> [1] "single"
#>
#> $pathogen_names
#> [1] "cases"
#>
#> $validated_tsbl
#> # A tsibble: 830 x 2 [1D]
#> index case_timeseries
#> <date> <dbl>
#> 1 2020-09-23 7096
#> 2 2020-09-24 7682
#> 3 2020-09-25 7318
#> 4 2020-09-26 6810
#> 5 2020-09-27 7023
#> 6 2020-09-28 9983
#> 7 2020-09-29 10366
#> 8 2020-09-30 12717
#> 9 2020-10-01 13357
#> 10 2020-10-02 13854
#> # 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
#>
#>
#> attr(,"class")
#> [1] "EpiStrainDynamics.pathogen_structure"
#> [2] "list"