Generate a infectivity profile matrix from a long format

This converts a long format infectivity profile to something that will work with EpiEstim. In general ggoutbreak will do the conversion internally. This is provided as a utility for examples mostly.

Usage

omega_matrix(ip = i_discrete_ip, epiestim_compat = TRUE)

Arguments

ip

long format infectivity profile - a dataframe with columns:

boot (anything + default(1)) - a bootstrap identifier
probability (proportion) - the probability of new event during this period.
tau (integer + complete) - the days since the index event.

Minimally grouped by: boot (and other groupings allowed).

epiestim_compat

ensure the matrix works with EpiEstim's si_from_sample method by making probability at time zero equal to zero.

Value

a matrix with 0:max(tau) rows and 1:max(boot) columns.

Examples

omega_matrix(example_ip())
#>             boot.1       boot.2       boot.3       boot.4       boot.5
#>  [1,] 0.000000e+00 0.000000e+00 0.0000000000 0.000000e+00 0.000000e+00
#>  [2,] 7.677533e-03 4.184484e-04 0.0140500744 3.879250e-04 7.526397e-03
#>  [3,] 9.291725e-02 1.813812e-02 0.1046338997 2.227981e-02 9.442324e-02
#>  [4,] 2.043664e-01 9.230062e-02 0.1809500713 1.229569e-01 2.100911e-01
#>  [5,] 2.268502e-01 1.796117e-01 0.1898102498 2.309453e-01 2.318273e-01
#>  [6,] 1.833768e-01 2.112346e-01 0.1605625298 2.425320e-01 1.844411e-01
#>  [7,] 1.241137e-01 1.846491e-01 0.1206750683 1.800831e-01 1.221454e-01
#>  [8,] 7.504208e-02 1.331164e-01 0.0841748031 1.066530e-01 7.198976e-02
#>  [9,] 4.197525e-02 8.388998e-02 0.0557756827 5.393305e-02 3.915034e-02
#> [10,] 2.218114e-02 4.788837e-02 0.0355981082 2.428026e-02 2.007592e-02
#> [11,] 1.122399e-02 2.534381e-02 0.0220801720 1.000047e-02 9.843690e-03
#> [12,] 5.488918e-03 1.263459e-02 0.0133909251 3.839760e-03 4.659313e-03
#> [13,] 2.611286e-03 6.001426e-03 0.0079749802 1.392949e-03 2.143457e-03
#> [14,] 1.214373e-03 2.739158e-03 0.0046788999 4.821980e-04 9.631838e-04
#> [15,] 5.540821e-04 1.209025e-03 0.0027108306 1.604913e-04 4.243777e-04
#> [16,] 2.487464e-04 5.186508e-04 0.0015538888 5.166060e-05 1.838752e-04
#> [17,] 1.101234e-04 2.170966e-04 0.0008825539 1.615724e-05 7.852955e-05
#> [18,] 4.816494e-05 8.895148e-05 0.0004972622 4.928334e-06 3.312050e-05
#>             boot.6       boot.7       boot.8       boot.9      boot.10
#>  [1,] 0.0000000000 0.000000e+00 0.0000000000 0.000000e+00 0.000000e+00
#>  [2,] 0.0010693021 2.789247e-03 0.0285487735 8.376028e-05 8.544732e-04
#>  [3,] 0.0296756651 5.225867e-02 0.1470322686 1.150323e-02 2.968015e-02
#>  [4,] 0.1156510062 1.559865e-01 0.1997222056 9.883226e-02 1.272837e-01
#>  [5,] 0.1908943929 2.135242e-01 0.1835657684 2.354013e-01 2.136520e-01
#>  [6,] 0.2041656160 1.999387e-01 0.1439792770 2.708088e-01 2.207492e-01
#>  [7,] 0.1698309920 1.507670e-01 0.1036320670 1.990858e-01 1.717519e-01
#>  [8,] 0.1201387928 9.897287e-02 0.0706750878 1.088086e-01 1.112291e-01
#>  [9,] 0.0759332148 5.902414e-02 0.0464475760 4.826935e-02 6.339668e-02
#> [10,] 0.0441850007 3.280974e-02 0.0297126245 1.835557e-02 3.289873e-02
#> [11,] 0.0241363367 1.728467e-02 0.0186207185 6.202430e-03 1.589089e-02
#> [12,] 0.0125435084 8.728618e-03 0.0114823561 1.909109e-03 7.253581e-03
#> [13,] 0.0062612434 4.259719e-03 0.0069887070 5.448888e-04 3.162964e-03
#> [14,] 0.0030231308 2.021013e-03 0.0042081345 1.461239e-04 1.328154e-03
#> [15,] 0.0014194912 9.364489e-04 0.0025110990 3.719014e-05 5.403237e-04
#> [16,] 0.0006508702 4.252645e-04 0.0014869791 9.053479e-06 2.139743e-04
#> [17,] 0.0002923972 1.898053e-04 0.0008747341 2.121144e-06 8.279348e-05
#> [18,] 0.0001290395 8.344685e-05 0.0005116233 4.806800e-07 3.139542e-05
#>            boot.11      boot.12      boot.13      boot.14      boot.15
#>  [1,] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.0000000000
#>  [2,] 1.479224e-02 9.300358e-03 1.640893e-03 1.521200e-03 0.0377552540
#>  [3,] 1.283081e-01 1.087101e-01 5.246507e-02 3.721842e-02 0.1732055051
#>  [4,] 2.264344e-01 2.268979e-01 1.945690e-01 1.323704e-01 0.2143386747
#>  [5,] 2.208562e-01 2.365227e-01 2.694367e-01 2.035060e-01 0.1842008757
#>  [6,] 1.656469e-01 1.787775e-01 2.236164e-01 2.057033e-01 0.1368963546
#>  [7,] 1.074576e-01 1.129017e-01 1.376763e-01 1.632791e-01 0.0940719937
#>  [8,] 6.360375e-02 6.361613e-02 6.991054e-02 1.109443e-01 0.0615473547
#>  [9,] 3.534588e-02 3.313576e-02 3.105330e-02 6.767128e-02 0.0389351166
#> [10,] 1.875894e-02 1.629650e-02 1.250444e-02 3.813506e-02 0.0240339379
#> [11,] 9.612912e-03 7.671727e-03 4.671849e-03 2.022915e-02 0.0145614312
#> [12,] 4.792060e-03 3.489304e-03 1.645437e-03 1.023103e-02 0.0086937687
#> [13,] 2.336244e-03 1.543515e-03 5.525431e-04 4.978718e-03 0.0051293915
#> [14,] 1.118259e-03 6.673163e-04 1.783935e-04 2.346940e-03 0.0029969673
#> [15,] 5.270889e-04 2.830151e-04 5.572854e-05 1.077202e-03 0.0017367682
#> [16,] 2.452119e-04 1.180844e-04 1.692792e-05 4.833170e-04 0.0009994866
#> [17,] 1.127993e-04 4.858121e-05 5.019407e-06 2.126548e-04 0.0005717524
#> [18,] 5.138252e-05 1.974386e-05 1.457434e-06 9.198772e-05 0.0003253670
#>            boot.16      boot.17      boot.18      boot.19      boot.20
#>  [1,] 0.0000000000 0.0000000000 0.0000000000 0.000000e+00 0.000000e+00
#>  [2,] 0.0016996564 0.0030047001 0.0027652700 1.833881e-03 4.693477e-03
#>  [3,] 0.0421750530 0.0496607178 0.0484661289 4.252390e-02 7.348588e-02
#>  [4,] 0.1476610154 0.1414855294 0.1423502263 1.444289e-01 1.898801e-01
#>  [5,] 0.2190799925 0.1949704849 0.1983680681 2.129348e-01 2.306766e-01
#>  [6,] 0.2112228185 0.1897617177 0.1929463796 2.071615e-01 1.952382e-01
#>  [7,] 0.1588181831 0.1516238691 0.1529676100 1.586827e-01 1.346719e-01
#>  [8,] 0.1017696394 0.1067990890 0.1064040924 1.042406e-01 8.152930e-02
#>  [9,] 0.0583627852 0.0689381600 0.0676049868 6.155395e-02 4.509957e-02
#> [10,] 0.0308539946 0.0417436034 0.0401961525 3.361555e-02 2.335448e-02
#> [11,] 0.0153281770 0.0240727610 0.0227190657 1.729437e-02 1.150021e-02
#> [12,] 0.0072508299 0.0133584958 0.0123383387 8.488602e-03 5.442797e-03
#> [13,] 0.0032967261 0.0071860114 0.0064879552 4.010986e-03 2.494760e-03
#> [14,] 0.0014507365 0.0037677404 0.0033219873 1.836715e-03 1.113695e-03
#> [15,] 0.0006211428 0.0019334406 0.0016633724 8.192254e-04 4.862795e-04
#> [16,] 0.0002598173 0.0009741615 0.0008172012 3.573067e-04 2.083650e-04
#> [17,] 0.0001065185 0.0004831534 0.0003949683 1.528643e-04 8.784574e-05
#> [18,] 0.0000429137 0.0002363644 0.0001881968 6.431105e-05 3.651654e-05
#>            boot.21     boot.22      boot.23      boot.24      boot.25
#>  [1,] 0.000000e+00 0.000000000 0.000000e+00 0.000000e+00 0.000000e+00
#>  [2,] 9.332891e-03 0.061318962 1.043755e-04 4.953968e-03 1.252013e-03
#>  [3,] 1.022630e-01 0.199145058 1.039234e-02 7.643928e-02 3.453768e-02
#>  [4,] 2.108509e-01 0.203906705 8.062162e-02 1.946379e-01 1.309865e-01
#>  [5,] 2.254156e-01 0.164201659 1.937563e-01 2.330544e-01 2.073971e-01
#>  [6,] 1.784158e-01 0.120852859 2.432313e-01 1.945087e-01 2.110390e-01
#>  [7,] 1.194171e-01 0.084780913 2.058114e-01 1.323573e-01 1.662299e-01
#>  [8,] 7.186652e-02 0.057721180 1.343050e-01 7.907024e-02 1.110168e-01
#>  [9,] 4.019370e-02 0.038500931 7.302394e-02 4.317168e-02 6.611007e-02
#> [10,] 2.130787e-02 0.025300425 3.470205e-02 2.206989e-02 3.619138e-02
#> [11,] 1.084434e-02 0.016438228 1.487331e-02 1.073000e-02 1.857881e-02
#> [12,] 5.344630e-03 0.010585353 5.875369e-03 5.014514e-03 9.065872e-03
#> [13,] 2.566658e-03 0.006767470 2.172649e-03 2.269804e-03 4.246174e-03
#> [14,] 1.206515e-03 0.004300988 7.608025e-04 1.000720e-03 1.922639e-03
#> [15,] 5.570719e-04 0.002719866 2.544992e-04 4.315662e-04 8.462041e-04
#> [16,] 2.533191e-04 0.001712725 8.188276e-05 1.826527e-04 3.635528e-04
#> [17,] 1.136904e-04 0.001074593 2.547630e-05 7.606466e-05 1.529787e-04
#> [18,] 5.044528e-05 0.000672083 7.698555e-06 3.123428e-05 6.321765e-05
#>            boot.26      boot.27      boot.28      boot.29      boot.30
#>  [1,] 0.000000e+00 0.0000000000 0.0000000000 0.0000000000 0.000000e+00
#>  [2,] 2.988272e-03 0.0135707237 0.0179566678 0.0402588554 4.567568e-03
#>  [3,] 5.523195e-02 0.1057634618 0.1201794161 0.1873784565 6.726541e-02
#>  [4,] 1.622191e-01 0.1863079560 0.1923028668 0.2280479740 1.723622e-01
#>  [5,] 2.181213e-01 0.1951537305 0.1916760482 0.1892171342 2.153630e-01
#>  [6,] 2.005066e-01 0.1631645607 0.1563404997 0.1346937915 1.914548e-01
#>  [7,] 1.483967e-01 0.1204994695 0.1142674235 0.0882754684 1.404381e-01
#>  [8,] 9.560509e-02 0.0822843205 0.0779384577 0.0549355488 9.113485e-02
#>  [9,] 5.595302e-02 0.0532389949 0.0506921566 0.0329958915 5.433696e-02
#> [10,] 3.052232e-02 0.0331165792 0.0318470835 0.0193127945 3.045016e-02
#> [11,] 1.577951e-02 0.0199909124 0.0194861514 0.0110838915 1.627602e-02
#> [12,] 7.819782e-03 0.0117859063 0.0116775678 0.0062636049 8.381656e-03
#> [13,] 3.744961e-03 0.0068172510 0.0068815503 0.0034957200 4.188330e-03
#> [14,] 1.743627e-03 0.0038817296 0.0039995207 0.0019310008 2.041613e-03
#> [15,] 7.928448e-04 0.0021812883 0.0022976703 0.0010575085 9.746877e-04
#> [16,] 3.533331e-04 0.0012120708 0.0013070089 0.0005749114 4.571588e-04
#> [17,] 1.547592e-04 0.0006670327 0.0007371851 0.0003105822 2.111772e-04
#> [18,] 6.677013e-05 0.0003640121 0.0004127257 0.0001668659 9.626445e-05
#>            boot.31      boot.32      boot.33      boot.34      boot.35
#>  [1,] 0.000000e+00 0.000000e+00 0.0000000000 0.000000e+00 0.0000000000
#>  [2,] 1.417077e-03 2.412331e-03 0.0211305326 2.446991e-03 0.0075158077
#>  [3,] 3.940577e-02 5.691140e-02 0.1441701765 4.902957e-02 0.0733248095
#>  [4,] 1.465270e-01 1.839975e-01 0.2226805305 1.524307e-01 0.1534941737
#>  [5,] 2.232736e-01 2.468026e-01 0.2070594694 2.135372e-01 0.1822258210
#>  [6,] 2.162484e-01 2.127856e-01 0.1550747283 2.023052e-01 0.1679003577
#>  [7,] 1.610723e-01 1.422368e-01 0.1031730163 1.532527e-01 0.1343810383
#>  [8,] 1.012998e-01 8.074469e-02 0.0637113101 1.005913e-01 0.0983682387
#>  [9,] 5.664363e-02 4.092744e-02 0.0373785848 5.978244e-02 0.0677068298
#> [10,] 2.905692e-02 1.909285e-02 0.0211255405 3.303549e-02 0.0445517138
#> [11,] 1.395536e-02 8.360138e-03 0.0116048964 1.726853e-02 0.0283262985
#> [12,] 6.363241e-03 3.482399e-03 0.0062338508 8.639930e-03 0.0175296524
#> [13,] 2.782177e-03 1.393251e-03 0.0032887119 4.172468e-03 0.0106137617
#> [14,] 1.175040e-03 5.391861e-04 0.0017093406 1.957026e-03 0.0063116143
#> [15,] 4.820654e-04 2.029259e-04 0.0008774244 8.957036e-04 0.0036969851
#> [16,] 1.929421e-04 7.458232e-05 0.0004456354 4.014982e-04 0.0021378152
#> [17,] 7.559750e-05 2.685758e-05 0.0002242747 1.767712e-04 0.0012225965
#> [18,] 2.907691e-05 9.501334e-06 0.0001119767 7.662322e-05 0.0006924862
#>            boot.36      boot.37      boot.38      boot.39      boot.40
#>  [1,] 0.000000e+00 0.000000e+00 0.0000000000 0.000000e+00 0.000000e+00
#>  [2,] 4.221589e-04 3.417375e-04 0.0216662535 1.707855e-03 2.956394e-03
#>  [3,] 2.997143e-02 1.855140e-02 0.1369282354 4.910111e-02 5.571837e-02
#>  [4,] 1.685429e-01 1.032911e-01 0.2072318946 1.772741e-01 1.647513e-01
#>  [5,] 2.879235e-01 2.036781e-01 0.1966275009 2.514619e-01 2.211080e-01
#>  [6,] 2.543035e-01 2.305500e-01 0.1533208246 2.209869e-01 2.018093e-01
#>  [7,] 1.509454e-01 1.876168e-01 0.1074073789 1.470776e-01 1.478327e-01
#>  [8,] 6.908274e-02 1.231284e-01 0.0703383454 8.183818e-02 9.407353e-02
#>  [9,] 2.636236e-02 6.952865e-02 0.0439781763 4.021280e-02 5.430354e-02
#> [10,] 8.801320e-03 3.515025e-02 0.0265835975 1.803772e-02 2.918667e-02
#> [11,] 2.652881e-03 1.632749e-02 0.0156610044 7.546862e-03 1.485508e-02
#> [12,] 7.377023e-04 7.093867e-03 0.0090413860 2.988998e-03 7.242976e-03
#> [13,] 1.921998e-04 2.919882e-03 0.0051351455 1.132487e-03 3.411063e-03
#> [14,] 4.745650e-05 1.149393e-03 0.0028775288 4.136813e-04 1.561113e-03
#> [15,] 1.120155e-05 4.358228e-04 0.0015943388 1.465499e-04 6.975174e-04
#> [16,] 2.544647e-06 1.600713e-04 0.0008749207 5.058037e-05 3.053570e-04
#> [17,] 5.593218e-07 5.720059e-05 0.0004761722 1.706990e-05 1.313486e-04
#> [18,] 1.194669e-07 1.995807e-05 0.0002572965 5.649381e-06 5.564166e-05
#>            boot.41      boot.42      boot.43      boot.44      boot.45
#>  [1,] 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000
#>  [2,] 0.0062119371 0.0120302656 0.0079254705 0.0014207590 0.0159815693
#>  [3,] 0.0776312520 0.1062153209 0.0886392063 0.0344882007 0.1169328389
#>  [4,] 0.1799199426 0.1976598642 0.1903707465 0.1237705479 0.1959319089
#>  [5,] 0.2130218150 0.2076292787 0.2146188303 0.1941669151 0.1977873929
#>  [6,] 0.1846521690 0.1693290583 0.1801367838 0.2015815424 0.1605818484
#>  [7,] 0.1343795504 0.1200553063 0.1282324686 0.1649792465 0.1156798254
#>  [8,] 0.0875020731 0.0779092756 0.0822228039 0.1158693553 0.0772790618
#>  [9,] 0.0527668997 0.0475692070 0.0490536507 0.0731768348 0.0490156605
#> [10,] 0.0300833240 0.0277801377 0.0277629469 0.0427501241 0.0299340191
#> [11,] 0.0164322682 0.0156824522 0.0150942831 0.0235310824 0.0177610373
#> [12,] 0.0086781213 0.0086198284 0.0079509835 0.0123581733 0.0103017587
#> [13,] 0.0044598904 0.0046368077 0.0040825557 0.0062485485 0.0058666691
#> [14,] 0.0022411342 0.0024503003 0.0020525496 0.0030619678 0.0032908416
#> [15,] 0.0011051735 0.0012756911 0.0010138696 0.0014615329 0.0018227083
#> [16,] 0.0005363318 0.0006557902 0.0004933369 0.0006821888 0.0009987217
#> [17,] 0.0002567110 0.0003334594 0.0002369657 0.0003123464 0.0005421754
#> [18,] 0.0001214066 0.0001679563 0.0001125482 0.0001406341 0.0002919626
#>            boot.46      boot.47      boot.48      boot.49      boot.50
#>  [1,] 0.0000000000 0.000000e+00 0.000000e+00 0.0000000000 0.000000e+00
#>  [2,] 0.0018773139 1.524538e-03 2.059709e-04 0.0009855786 2.028305e-03
#>  [3,] 0.0397419551 4.182723e-02 1.363647e-02 0.0244255135 5.200704e-02
#>  [4,] 0.1312207973 1.529669e-01 8.633563e-02 0.0930564741 1.772187e-01
#>  [5,] 0.1959704564 2.286534e-01 1.873558e-01 0.1590805019 2.458145e-01
#>  [6,] 0.1980750426 2.169874e-01 2.279365e-01 0.1825622141 2.162951e-01
#>  [7,] 0.1600705387 1.582693e-01 1.961192e-01 0.1665061439 1.463133e-01
#>  [8,] 0.1120589939 9.744165e-02 1.345290e-01 0.1309828278 8.357605e-02
#>  [9,] 0.0710131127 5.332932e-02 7.874304e-02 0.0929728958 4.245488e-02
#> [10,] 0.0418339482 2.677263e-02 4.100591e-02 0.0611967776 1.978934e-02
#> [11,] 0.0233079185 1.258266e-02 1.952524e-02 0.0380229598 8.638224e-03
#> [12,] 0.0124275680 5.614014e-03 8.662403e-03 0.0225733599 3.580558e-03
#> [13,] 0.0063949121 2.401727e-03 3.629367e-03 0.0129168951 1.423389e-03
#> [14,] 0.0031955804 9.924760e-04 1.450475e-03 0.0071700830 5.466717e-04
#> [15,] 0.0015580524 3.983726e-04 5.571518e-04 0.0038798557 2.039745e-04
#> [16,] 0.0007439169 1.559973e-04 2.069115e-04 0.0020543812 7.425865e-05
#> [17,] 0.0003488500 5.979923e-05 7.464080e-05 0.0010676458 2.646829e-05
#> [18,] 0.0001610429 2.250235e-05 2.625348e-05 0.0005458923 9.262077e-06
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