tests/testthat/_snaps/snapshots.md

In bbolker/McMasterPandemic: Pandemic Model

basic examples_snapshot

Code
  tail(s0, 10)
Output
        t        S        E       Ia        Ip       Im        Is         H
  91   91 762.8436 766.8565 4686.631 53.891857 9594.649 216.09582 2028.2646
  92   92 752.9350 629.2927 4066.269 44.423085 8327.026 183.05932 1854.1502
  93   93 744.4529 516.7570 3525.713 36.255473 7222.388 154.96517 1693.0578
  94   94 737.1840 424.6495 3055.165 29.995424 6259.939 131.06384 1544.3418
  95   95 730.9491 349.2211 2645.934 24.446826 5423.013 110.79018 1407.3217
  96   96 725.5969 287.4154 2290.330 20.325111 4695.039  93.57259 1281.3099
  97   97 720.9997 236.7404 1981.564 16.523013 4063.181  79.00235 1165.6116
  98   98 717.0488 195.1643 1713.659 13.828325 3514.319  66.64478 1059.5473
  99   99 713.6519 161.0295 1481.361 11.192742 3038.713  56.21048  962.4474
  100 100 710.7305 132.9838 1280.060  9.452072 2626.011  47.36844  873.6712
            H2     ICUs      ICUd        D        R         foi
  91  299.2287 965.8891 199.97718 3288.415 977137.3 0.012989057
  92  287.6774 922.1281 179.51351 3313.412 979440.1 0.011265355
  93  276.2484 879.8621 160.91473 3335.852 981453.5 0.009764084
  94  264.9918 839.1200 144.05140 3355.966 983213.5 0.008457775
  95  253.9494 799.9136 128.79457 3373.972 984751.7 0.007322206
  96  243.1552 762.2422 115.01952 3390.072 986095.9 0.006335823
  97  232.6363 726.0932 102.60514 3404.449 987270.6 0.005479749
  98  222.4137 691.4459  91.43689 3417.275 988297.2 0.004737231
  99  212.5032 658.2717  81.40542 3428.704 989194.5 0.004093690
  100 202.9162 626.5374  72.40898 3438.880 989979.0 0.003536206

Code
  tail(s1, 10)
Output
           date        S         E        I        H      ICU        R    death
  84 2020-05-23 901.9129 3108.3803 38491.91 4026.425 1711.831 948740.5 55.54473
  85 2020-05-24 870.9142 2541.6136 33600.75 3740.425 1623.957 954552.6 50.65579
  86 2020-05-25 844.7857 2078.9702 29296.72 3468.472 1539.117 959656.1 46.08073
  87 2020-05-26 822.6886 1701.2654 25516.64 3211.043 1457.539 964133.2 41.82103
  88 2020-05-27 803.9468 1392.8407 22202.40 2968.344 1379.372 968057.6 37.87283
  89 2020-05-28 788.0116 1140.9220 19301.23 2740.347 1304.695 971495.1 34.22833
  90 2020-05-29 774.4337  935.0918 16765.19 2526.847 1233.533 974504.3 30.87655
  91 2020-05-30 762.8436  766.8565 14551.27 2327.493 1165.866 977137.3 27.80441
  92 2020-05-31 752.9350  629.2927 12620.78 2141.828 1101.642 979440.1 24.99715
  93 2020-06-01 744.4529  516.7570 10939.32 1969.306 1040.777 981453.5 22.43919
            D         foi incidence    report   cumRep
  84 3019.076 0.034369924 30.998677 25.753719 99822.44
  85 3069.731 0.030001204 26.128474 19.863299 99842.30
  86 3115.812 0.026157082 22.097129 15.528549 99857.83
  87 3157.633 0.022781097 18.741749 12.290202 99870.12
  88 3195.506 0.019821304 15.935275  9.835656 99879.96
  89 3229.734 0.017230525 13.577853  7.949571 99887.91
  90 3260.611 0.014965921 11.590114  6.481688 99894.39
  91 3288.415 0.012989057  9.908619  5.325753 99899.72
  92 3313.412 0.011265355  8.482080  4.405621 99904.12
  93 3335.852 0.009764084  7.268901  3.665996 99907.79

params methods_snapshot

Code
  summary(params)
Output
          r0         R0       Gbar    CFR_gen   dbl_time 
   0.2278149  6.5180089 12.1897402  0.0352000  3.0425898

time-varying snapshot

Code
  tail(resICU_t, 10)
Output
           date        S        E        I        H       ICU         R
  59 2020-05-23 998915.4 38.07728 65.29358 2.579514 1.1064881  974.3035
  60 2020-05-24 998909.6 37.27880 63.92462 2.528612 1.0881608  982.3696
  61 2020-05-25 998903.8 36.49706 62.58433 2.478555 1.0699772  990.2670
  62 2020-05-26 998898.2 35.73170 61.27212 2.429344 1.0519462  997.9993
  63 2020-05-27 998892.7 34.98237 59.98740 2.380976 1.0340762 1005.5699
  64 2020-05-28 998887.3 34.24875 58.72959 2.333448 1.0163746 1012.9821
  65 2020-05-29 998882.1 33.53050 57.49813 2.286755 0.9988482 1020.2392
  66 2020-05-30 998876.9 32.82731 56.29247 2.240892 0.9815031 1027.3445
  67 2020-05-31 998871.8 32.13885 55.11208 2.195854 0.9643448 1034.3012
  68 2020-06-01 998866.9 31.46482 53.95642 2.151631 0.9473780 1041.1122
          death        D          foi incidence    report   cumRep
  59 0.03431694 3.190419 5.869413e-06  5.863047 0.7151511 100.6168
  60 0.03360271 3.224022 5.746353e-06  5.740087 0.7001551 101.3170
  61 0.03290280 3.256924 5.625871e-06  5.619704 0.6854733 102.0024
  62 0.03221701 3.289141 5.507913e-06  5.501844 0.6710991 102.6735
  63 0.03154509 3.320687 5.392426e-06  5.386455 0.6570261 103.3306
  64 0.03088683 3.351573 5.279358e-06  5.273484 0.6432481 103.9738
  65 0.03024199 3.381815 5.168659e-06  5.162881 0.6297587 104.6036
  66 0.02961033 3.411426 5.060279e-06  5.054596 0.6165521 105.2201
  67 0.02899162 3.440417 4.954170e-06  4.948581 0.6036222 105.8237
  68 0.02838561 3.468803 4.850285e-06  4.844789 0.5909632 106.4147

time-varying with ndt>1

Code
  tail(resICU_t2, 10)
Output
            date        S        E        I        H      ICU        R      death
  581 2020-05-23 998165.1 39.82512 71.36003 3.326391 1.542409 1713.140 0.04440598
  591 2020-05-24 998158.8 38.62289 69.20612 3.231869 1.505601 1722.864 0.04307513
  601 2020-05-25 998152.7 37.45694 67.11720 3.139789 1.469423 1732.295 0.04178330
  611 2020-05-26 998146.8 36.32617 65.09130 3.050110 1.433880 1741.443 0.04052943
  621 2020-05-27 998141.0 35.22953 63.12652 2.962787 1.398976 1750.315 0.03931252
  631 2020-05-28 998135.5 34.16599 61.22102 2.877778 1.364713 1758.920 0.03813156
  641 2020-05-29 998130.1 33.13454 59.37302 2.795036 1.331093 1767.266 0.03698554
  651 2020-05-30 998124.9 32.13422 57.58078 2.714516 1.298115 1775.361 0.03587352
  661 2020-05-31 998119.8 31.16410 55.84261 2.636171 1.265778 1783.212 0.03479452
  671 2020-06-01 998114.9 30.22325 54.15690 2.559954 1.234082 1790.827 0.03374762
             D          foi incidence    report   cumRep
  581 5.754946 6.378334e-06  6.366630 0.8493616 158.8170
  591 5.798022 6.185812e-06  6.174423 0.8237222 159.6407
  601 5.839805 5.999099e-06  5.988017 0.7988564 160.4396
  611 5.880334 5.818019e-06  5.807237 0.7747410 161.2143
  621 5.919647 5.642402e-06  5.631913 0.7513533 161.9657
  631 5.957778 5.472084e-06  5.461882 0.7286713 162.6943
  641 5.994764 5.306905e-06  5.296982 0.7066739 163.4010
  651 6.030637 5.146710e-06  5.137059 0.6853403 164.0863
  661 6.065432 4.991349e-06  4.981964 0.6646505 164.7510
  671 6.099180 4.840676e-06  4.831550 0.6445852 165.3956

ndt>1

Code
  tail(s2, 10)
Output
        t        S        E       Ia       Ip        Im       Is        H
  91   91 999474.0 300.6302 48.37322 17.08642  81.93509 3.489647 1.290286
  92   92 999447.1 316.0054 50.84536 17.96032  86.12793 3.668352 1.357212
  93   93 999418.8 332.1663 53.44398 18.87889  90.53516 3.856190 1.427548
  94   94 999389.0 349.1533 56.17556 19.84442  95.16773 4.053626 1.501470
  95   95 999357.7 367.0084 59.04687 20.85930 100.03715 4.261153 1.579159
  96   96 999324.8 385.7760 62.06505 21.92605 105.15555 4.479285 1.660809
  97   97 999290.3 405.5027 65.23761 23.04733 110.53563 4.708565 1.746623
  98   98 999253.9 426.2372 68.57243 24.22590 116.19076 4.949563 1.836813
  99   99 999215.7 448.0312 72.07780 25.46470 122.13501 5.202877 1.931604
  100 100 999175.6 470.9386 75.76242 26.76680 128.38314 5.469137 2.031230
              H2      ICUs      ICUd          D         R          foi
  91  0.02510128 0.2352986 0.1907828 0.08648955  72.65309 0.0001347600
  92  0.02645021 0.2475875 0.2006551 0.09125912  76.40300 0.0001416535
  93  0.02786808 0.2605033 0.2110304 0.09627550  80.34472 0.0001488996
  94  0.02935839 0.2740781 0.2219345 0.10155126  84.48808 0.0001565161
  95  0.03092484 0.2883456 0.2333944 0.10709963  88.84337 0.0001645222
  96  0.03257130 0.3033411 0.2454385 0.11293448  93.42145 0.0001729376
  97  0.03430186 0.3191019 0.2580967 0.11907045  98.23370 0.0001817833
  98  0.03612080 0.3356671 0.2714005 0.12552286 103.29210 0.0001910812
  99  0.03803264 0.3530778 0.2853829 0.13230788 108.60923 0.0002008545
  100 0.04004211 0.3713773 0.3000786 0.13944245 114.19832 0.0002111274

Code
  tail(s3, 10)
Output
            date        S         E         I         H        ICU          R
  201 2020-03-11 999925.6  42.82681  21.52276 0.1652520 0.05311803   9.787678
  221 2020-03-12 999903.9  55.22406  27.73878 0.2211672 0.07119874  12.812219
  241 2020-03-13 999875.9  71.20875  35.75585 0.2930341 0.09446204  16.710644
  261 2020-03-14 999839.8  91.81894  46.09487 0.3854114 0.12438907  21.736206
  281 2020-03-15 999793.3 118.39277  59.42746 0.5041949 0.16289483  28.215383
  301 2020-03-16 999733.2 152.65511  76.61953 0.6570005 0.21245262  36.569069
  321 2020-03-17 999655.9 196.82909  98.78734 0.8536583 0.27625458  47.339888
  341 2020-03-18 999556.1 253.77974 127.36986 1.1068505 0.35841879  61.227395
  361 2020-03-19 999427.5 327.19871 164.22174 1.4329335 0.46425621  79.133429
  381 2020-03-20 999261.6 421.84171 211.73317 1.8529971 0.60061469 102.220556
            death           D          foi incidence    report    cumRep
  201 0.002610712 0.008215352 1.919536e-05  19.19393        NA 0.0000000
  221 0.003503658 0.011719010 2.475130e-05  24.74892        NA 0.0000000
  241 0.004649356 0.016368366 3.191541e-05  31.91145        NA 0.0000000
  261 0.006119965 0.022488330 4.115302e-05  41.14643        NA 0.0000000
  281 0.008008907 0.030497237 5.306408e-05  53.05311        NA 0.0000000
  301 0.010436929 0.040934166 6.842205e-05  68.40380 0.7819422 0.7819422
  321 0.013559934 0.054494100 8.822404e-05  88.19368 1.0071995 1.7891417
  341 0.017579092 0.072073192 1.137553e-04 113.70484 1.2981554 3.0872971
  361 0.022753872 0.094827064 1.466725e-04 146.58857 1.6735728 4.7608699
  381 0.029418848 0.124245912 1.891106e-04 188.97096 2.1577653 6.9186352

Code
  tail(s3B, 10)
Output
           date        S         E         I         H        ICU         R
  11 2020-03-11 999943.1  32.87921  16.54283 0.1201598 0.03847274  7.357600
  12 2020-03-12 999928.3  41.30698  20.73595 0.1596571 0.05120529  9.432949
  13 2020-03-13 999909.8  51.86001  26.05897 0.2067331 0.06642125 11.988331
  14 2020-03-14 999886.6  65.14294  32.69002 0.2677910 0.08616275 15.245756
  15 2020-03-15 999857.4  81.79331  41.07352 0.3418788 0.11015936 19.286749
  16 2020-03-16 999820.7 102.73258  51.54815 0.4367754 0.14089976 24.409712
  17 2020-03-17 999774.7 128.99746  64.75736 0.5533537 0.17870518 30.794419
  18 2020-03-18 999716.9 162.00908  81.29224 0.7015736 0.22677251 38.860370
  19 2020-03-19 999644.3 203.43268 102.11062 0.8851455 0.28634358 48.941688
  20 2020-03-20 999553.1 255.47674 128.20074 1.1174849 0.36173752 61.649431
           death           D          foi incidence    report    cumRep
  11 0.001688610 0.004996085 1.475154e-05  14.75070        NA 0.0000000
  12 0.002230748 0.007226833 1.849800e-05  18.49668        NA 0.0000000
  13 0.002951569 0.010178402 2.325811e-05  23.25601        NA 0.0000000
  14 0.003804320 0.013982722 2.918116e-05  29.17785        NA 0.0000000
  15 0.004912853 0.018895575 3.667398e-05  36.66875        NA 0.0000000
  16 0.006252024 0.025147600 4.602940e-05  46.02115 0.6476299 0.6476299
  17 0.007970496 0.033118095 5.783186e-05  57.81883 0.8126009 1.4602308
  18 0.010076228 0.043194323 7.259975e-05  72.57919 1.0202383 2.4804691
  19 0.012757220 0.055951543 9.119817e-05  91.16573 1.2811118 3.7615809
  20 0.016072819 0.072024362 1.145004e-04 114.44919 1.6088300 5.3704109

var-specific obsdisp

Code
  tail(s0, 10)
Output
           date       S     E         I   H ICU     R hosp   X death D foi
  34 2020-04-22 1349361  4129  2159.890   0   8   384    1  18     1 1   0
  35 2020-04-23 1120588  5678  2710.089  21   2  4506    1   2     1 2   0
  36 2020-04-24  118715  6374  3399.520  57  37   814    2  22     0 2   0
  37 2020-04-25  231303  9009  4263.221   6  66   792   15  88     0 2   0
  38 2020-04-26   88319 10323  5344.271  34  17  3186    2  74     1 3   0
  39 2020-04-27  107589 14223  6696.500  78  23  2206   27 160     1 4   0
  40 2020-04-28 1133210 17043  8385.920  17  21  2880    0 107     0 4   0
  41 2020-04-29  466589 20727 10494.117 224 127 18947   19 235     3 7   0
  42 2020-04-30  497808 26305 13120.356 116  52  2990    8  51     2 9   0
  43 2020-05-01 1122972 31791 16385.500   3 127  1538    3  66     0 9   0
     incidence report cumRep
  34        57      5     67
  35       129      7     74
  36       107     83    157
  37       876     48    205
  38      7274     15    220
  39     12003     50    270
  40     19693     13    283
  41     12370    153    436
  42      1452    125    561
  43      4085    407    968

Code
  tail(s1, 10)
Output
           date       S     E         I   H ICU    R hosp   X death D foi
  34 2020-04-22 1272771  6081  3096.854   0  32  142   14   2     1 3   0
  35 2020-04-23 1774740  7988  3884.129 134   1 6057    9  18     0 3   0
  36 2020-04-24  819699 10011  4869.861  43   9 4185    6  77     0 3   0
  37 2020-04-25   87127 12179  6103.256  89  12  595    0  46     0 3   0
  38 2020-04-26  143844 14724  7644.968  62   6  290    4  71     0 3   0
  39 2020-04-27  444731 18799  9569.889  46  92 1168   28 190     0 3   0
  40 2020-04-28 1252011 24030 11969.589  10   0 1023  129  38     0 3   0
  41 2020-04-29  312546 27562 14955.707 211  12 5269  135 137     2 5   0
  42 2020-04-30  523809 37306 18662.782  12   0 2859   26 276     1 6   0
  43 2020-05-01  405233 44563 23251.568 906  70 9172   71 119     1 7   0
     incidence report cumRep
  34      2101      2    298
  35       191     31    329
  36       207     74    403
  37      3667    142    545
  38      7157    270    815
  39     17100     49    864
  40      4566     37    901
  41     14443     74    975
  42     17692    128   1103
  43       972    410   1513

bbolker/McMasterPandemic documentation built on Aug. 25, 2024, 6:35 p.m.