Run infectious disease models models
run_infectiousdisease_model.RdRun infectious disease models models
Arguments
- time
vector of time units over which to run model
- init
initial population size of population
- params
vector of beta (infection rate), m (natural birth/death rate), and gamma (recovery rate)
- model_type
which type of model to run? (should be one of
SIR,SIR_ft,SEIR,SEIR_ft,SIRD,SIRD_ft,SIS, orSIS_ft)
See also
plot_infectiousdisease_time() to plot trajectories over time, and
plot_infectiousdisease_portrait() to plot pairwise portrait diagrams
Examples
# Run the SIR model
params_vec <- c(m = .1, beta = .01, v = .2, gamma = 0)
init_vec <- c(S = 100, I = 1, R = 0)
time_vec <- seq(0, 10, 0.1)
run_infectiousdisease_model(time = time_vec, init = init_vec, params =
params_vec, model_type = "SIR")
#> time S I R
#> 1 0.0 100.00000 1.000000 0.0000000
#> 2 0.1 99.70499 1.094015 0.2009934
#> 3 0.2 99.40350 1.196509 0.3999868
#> 4 0.3 99.09479 1.308208 0.5970002
#> 5 0.4 98.77806 1.429887 0.7920533
#> 6 0.5 98.45245 1.562382 0.9851656
#> 7 0.6 98.11705 1.706590 1.1763564
#> 8 0.7 97.77088 1.863473 1.3656448
#> 9 0.8 97.41289 2.034062 1.5530498
#> 10 0.9 97.04195 2.219459 1.7385900
#> 11 1.0 96.65688 2.420839 1.9222841
#> 12 1.1 96.25640 2.639454 2.1041504
#> 13 1.2 95.83916 2.876635 2.2842071
#> 14 1.3 95.40373 3.133794 2.4624723
#> 15 1.4 94.94861 3.412422 2.6389636
#> 16 1.5 94.47221 3.714093 2.8136988
#> 17 1.6 93.97284 4.040461 2.9866954
#> 18 1.7 93.44877 4.393261 3.1579707
#> 19 1.8 92.89816 4.774301 3.3275417
#> 20 1.9 92.31911 5.185460 3.4954255
#> 21 2.0 91.70968 5.628684 3.6616388
#> 22 2.1 91.06783 6.105971 3.8261982
#> 23 2.2 90.39151 6.619367 3.9891202
#> 24 2.3 89.67863 7.170949 4.1504212
#> 25 2.4 88.92707 7.762808 4.3101172
#> 26 2.5 88.13474 8.397034 4.4682242
#> 27 2.6 87.29955 9.075689 4.6247579
#> 28 2.7 86.41948 9.800787 4.7797342
#> 29 2.8 85.49257 10.574259 4.9331684
#> 30 2.9 84.51700 11.397928 5.0850759
#> 31 3.0 83.49106 12.273468 5.2354719
#> 32 3.1 82.41326 13.202371 5.3843715
#> 33 3.2 81.28231 14.185902 5.5317894
#> 34 3.3 80.09720 15.225063 5.6777406
#> 35 3.4 78.85722 16.320545 5.8222395
#> 36 3.5 77.56201 17.472688 5.9653006
#> 37 3.6 76.21162 18.681438 6.1069382
#> 38 3.7 74.80653 19.946307 6.2471665
#> 39 3.8 73.34766 21.266340 6.3859995
#> 40 3.9 71.83647 22.640082 6.5234511
#> 41 4.0 70.27491 24.065557 6.6595350
#> 42 4.1 68.66548 25.540252 6.7942649
#> 43 4.2 67.01123 27.061111 6.9276542
#> 44 4.3 65.31574 28.624541 7.0597163
#> 45 4.4 63.58310 30.226432 7.1904643
#> 46 4.5 61.81791 31.862182 7.3199113
#> 47 4.6 60.02519 33.526743 7.4480703
#> 48 4.7 58.21037 35.214671 7.5749542
#> 49 4.8 56.37923 36.920196 7.7005755
#> 50 4.9 54.53777 38.637288 7.8249468
#> 51 5.0 52.69217 40.359744 7.9480806
#> 52 5.1 50.84874 42.081275 8.0699893
#> 53 5.2 49.01372 43.795591 8.1906849
#> 54 5.3 47.19333 45.496491 8.3101796
#> 55 5.4 45.39356 47.177953 8.4284853
#> 56 5.5 43.62017 48.834211 8.5456138
#> 57 5.6 41.87859 50.459833 8.6615769
#> 58 5.7 40.17383 52.049781 8.7763861
#> 59 5.8 38.51048 53.599466 8.8900530
#> 60 5.9 36.89262 55.104794 9.0025888
#> 61 6.0 35.32381 56.562188 9.1140049
#> 62 6.1 33.80708 57.968612 9.2243124
#> 63 6.2 32.34490 59.321574 9.3335223
#> 64 6.3 30.93924 60.619119 9.4416456
#> 65 6.4 29.59149 61.859818 9.5486930
#> 66 6.5 28.30258 63.042742 9.6546753
#> 67 6.6 27.07297 64.167430 9.7596030
#> 68 6.7 25.90265 65.233859 9.8634867
#> 69 6.8 24.79126 66.242398 9.9663367
#> 70 6.9 23.73806 67.193772 10.0681634
#> 71 7.0 22.74201 68.089015 10.1689768
#> 72 7.1 21.80178 68.929428 10.2687872
#> 73 7.2 20.91586 69.716538 10.3676044
#> 74 7.3 20.08250 70.452057 10.4654384
#> 75 7.4 19.29986 71.137845 10.5622989
#> 76 7.5 18.56593 71.775873 10.6581956
#> 77 7.6 17.87867 72.368194 10.7531382
#> 78 7.7 17.23595 72.916911 10.8471360
#> 79 7.8 16.63565 73.424153 10.9401986
#> 80 7.9 16.07561 73.892054 11.0323351
#> 81 8.0 15.55371 74.322733 11.1235549
#> 82 8.1 15.06786 74.718277 11.2138670
#> 83 8.2 14.61599 75.080728 11.3032806
#> 84 8.3 14.19612 75.412073 11.3918044
#> 85 8.4 13.80632 75.714234 11.4794474
#> 86 8.5 13.44472 75.989063 11.5662184
#> 87 8.6 13.10954 76.238335 11.6521259
#> 88 8.7 12.79907 76.463747 11.7371787
#> 89 8.8 12.51170 76.666915 11.8213852
#> 90 8.9 12.24587 76.849374 11.9047538
#> 91 9.0 12.00013 77.012574 11.9872929
#> 92 9.1 11.77310 77.157888 12.0690107
#> 93 9.2 11.56348 77.286609 12.1499154
#> 94 9.3 11.37003 77.399952 12.2300150
#> 95 9.4 11.19162 77.499058 12.3093177
#> 96 9.5 11.02717 77.584996 12.3878313
#> 97 9.6 10.87567 77.658767 12.4655637
#> 98 9.7 10.73617 77.721304 12.5425226
#> 99 9.8 10.60780 77.773480 12.6187158
#> 100 9.9 10.48974 77.816107 12.6941508
#> 101 10.0 10.38122 77.849943 12.7688353