![[Deprecated]](figures/lifecycle-deprecated.svg)
Function calculates the distribution of genetic distances in a population of viruses
with the given parameters
gen_dists(
mut_rate,
mean_gens_pdf,
max_link_gens = 1,
max_gens = NULL,
max_dist = NULL
)Arguments
- mut_rate
mean number of mutations per generation, assumed to be Poisson distributed
- mean_gens_pdf
the density distribution of the mean number of generations between cases; the index of this vector is assumed to be the discrete distance between cases
- max_link_gens
the maximum generations of separation for linked pairs
- max_gens
the maximum number of generations to consider, if
NULL(default) value is set to the highest number of generations in mean_gens_pdf with a non-zero probability- max_dist
the maximum distance to calculate, if
NULL(default) value is set to max_gens * 99.9th percentile of mut_rate Poisson distribution
Value
a data frame with distances and probabilities
See also
Other mutrate_functions:
get_optim_roc(),
sens_spec_calc(),
sens_spec_roc()
Examples
# ebola-like pathogen
R <- 1.5
mut_rate <- 1
# use simulated generation distributions from the provided 'genDistSim' data object
data('genDistSim')
mean_gens_pdf <- as.numeric(genDistSim[genDistSim$R == R, -(1:2)])
# get theoretical genetic distance dist based on mutation rate and generation parameters
gen_dists(mut_rate = mut_rate,
mean_gens_pdf = mean_gens_pdf,
max_link_gens = 1)
#> Warning: `gen_dists()` was deprecated in phylosamp 1.0.0.
#> ℹ Please use `gendist_distribution()` instead.
#> dist linked_prob unlinked_prob
#> [1,] 0 3.678794e-01 7.090339e-04
#> [2,] 1 3.678794e-01 2.120973e-03
#> [3,] 2 1.839397e-01 3.810662e-03
#> [4,] 3 6.131324e-02 5.612427e-03
#> [5,] 4 1.532831e-02 7.590688e-03
#> [6,] 5 3.065662e-03 9.833909e-03
#> [7,] 6 5.109437e-04 1.238470e-02
#> [8,] 7 7.299195e-05 1.524673e-02
#> [9,] 8 9.123994e-06 1.839695e-02
#> [10,] 9 1.013777e-06 2.178995e-02
#> [11,] 10 1.013777e-07 2.535940e-02
#> [12,] 11 9.216156e-09 2.902012e-02
#> [13,] 12 7.680130e-10 3.267160e-02
#> [14,] 13 5.907792e-11 3.620293e-02
#> [15,] 14 4.219851e-12 3.949867e-02
#> [16,] 15 2.813234e-13 4.244516e-02
#> [17,] 16 1.758271e-14 4.493683e-02
#> [18,] 17 1.034277e-15 4.688211e-02
#> [19,] 18 5.745985e-17 4.820856e-02
#> [20,] 19 3.024203e-18 4.886693e-02
#> [21,] 20 1.512101e-19 4.883396e-02
#> [22,] 21 7.200483e-21 4.811368e-02
#> [23,] 22 3.272947e-22 4.673709e-02
#> [24,] 23 1.423020e-23 4.476029e-02
#> [25,] 24 5.929251e-25 4.226109e-02
#> [26,] 25 2.371700e-26 3.933435e-02
#> [27,] 26 9.121925e-28 3.608642e-02
#> [28,] 27 3.378491e-29 3.262913e-02
#> [29,] 28 1.206604e-30 2.907367e-02
#> [30,] 29 4.160703e-32 2.552495e-02
#> [31,] 30 1.386901e-33 2.207678e-02
#> [32,] 31 4.473874e-35 1.880814e-02
#> [33,] 32 1.398086e-36 1.578079e-02
#> [34,] 33 4.236623e-38 1.303827e-02
#> [35,] 34 1.246066e-39 1.060613e-02
#> [36,] 35 3.560187e-41 8.493426e-03
#> [37,] 36 9.889410e-43 6.694922e-03
#> [38,] 37 2.672813e-44 5.193965e-03
#> [39,] 38 7.033720e-46 3.965563e-03
#> [40,] 39 1.803518e-47 2.979420e-03
#> [41,] 40 4.508795e-49 2.202706e-03
#> [42,] 41 1.099706e-50 1.602374e-03
#> [43,] 42 2.618348e-52 1.146955e-03
#> [44,] 43 6.089180e-54 8.078007e-04
#> [45,] 44 1.383905e-55 5.598156e-04
#> [46,] 45 3.075344e-57 3.817538e-04
#> [47,] 46 6.685530e-59 2.561771e-04
#> [48,] 47 1.422453e-60 1.691776e-04
#> [49,] 48 2.963444e-62 1.099572e-04
#> [50,] 49 6.047845e-64 7.034279e-05
#> [51,] 50 1.209569e-65 4.429686e-05
#> [52,] 51 2.371704e-67 2.746180e-05
#> [53,] 52 4.560969e-69 1.676242e-05
#> [54,] 53 8.605602e-71 1.007507e-05
#> [55,] 54 1.593630e-72 5.963713e-06
#> [56,] 55 2.897509e-74 3.476958e-06
#> [57,] 56 5.174123e-76 1.996890e-06
#> [58,] 57 9.077409e-78 1.129900e-06
#> [59,] 58 1.565071e-79 6.299665e-07
#> [60,] 59 2.652662e-81 3.461366e-07
#> [61,] 60 4.421103e-83 1.874529e-07
#> [62,] 61 7.247710e-85 1.000721e-07
#> [63,] 62 1.168986e-86 5.267117e-08
#> [64,] 63 1.855533e-88 2.733592e-08
#> [65,] 64 2.899270e-90 1.399128e-08
#> [66,] 65 4.460415e-92 7.063281e-09
#> [67,] 66 6.758204e-94 3.517564e-09
#> [68,] 67 1.008687e-95 1.728324e-09
#> [69,] 68 1.483364e-97 8.379472e-10
#> [70,] 69 2.149802e-99 4.009374e-10
#> [71,] 70 3.071146e-101 1.893496e-10
#> [72,] 71 4.325558e-103 8.827521e-11
#> [73,] 72 6.007719e-105 4.063104e-11
#> [74,] 73 8.229753e-107 1.846628e-11
#> [75,] 74 1.112129e-108 8.288191e-12
#> [76,] 75 1.482838e-110 3.674133e-12
#> [77,] 76 1.951103e-112 1.608867e-12
#> [78,] 77 2.533900e-114 6.960005e-13
#> [79,] 78 3.248590e-116 2.974932e-13
#> [80,] 79 4.112139e-118 1.256537e-13
#> [81,] 80 5.140174e-120 5.245135e-14
#> [82,] 81 6.345893e-122 2.164074e-14
#> [83,] 82 7.738894e-124 8.826172e-15
#> [84,] 83 9.323969e-126 3.558829e-15
#> [85,] 84 1.109996e-127 1.418813e-15
#> [86,] 85 1.305878e-129 5.593391e-16
#> [87,] 86 1.518463e-131 2.180742e-16
#> [88,] 87 1.745360e-133 8.409295e-17
#> [89,] 88 1.983363e-135 3.207649e-17
#> [90,] 89 2.228498e-137 1.210407e-17
#> [91,] 90 2.476109e-139 4.518956e-18
#> [92,] 91 2.720999e-141 1.669362e-18
#> [93,] 92 2.957607e-143 6.102565e-19
#> [94,] 93 3.180223e-145 2.207832e-19
#> [95,] 94 3.383216e-147 7.905933e-20
#> [96,] 95 3.561280e-149 2.802304e-20
#> [97,] 96 3.709666e-151 9.833158e-21
#> [98,] 97 3.824398e-153 3.416066e-21
#> [99,] 98 3.902447e-155 1.175045e-21
#> [100,] 99 3.941866e-157 4.002361e-22
#> [101,] 100 3.941866e-159 1.350050e-22
#> [102,] 101 3.902838e-161 4.510172e-23
#> [103,] 102 3.826311e-163 1.492391e-23
#> [104,] 103 3.714865e-165 4.891647e-24
#> [105,] 104 3.571986e-167 1.588351e-24
#> [106,] 105 3.401891e-169 5.109656e-25
#> [107,] 106 3.209332e-171 1.628643e-25
#> [108,] 107 2.999375e-173 5.143790e-26
#> [109,] 108 2.777199e-175 1.609895e-26
#> [110,] 109 2.547889e-177 4.993466e-27
#> [111,] 110 2.316263e-179 1.535075e-27
#> [112,] 111 2.086723e-181 4.677484e-28
#> [113,] 112 1.863146e-183 1.412804e-28
#> [114,] 113 1.648802e-185 4.230289e-29
#> [115,] 114 1.446317e-187 1.255762e-29
#> [116,] 115 1.257667e-189 3.695934e-30
#> [117,] 116 1.084196e-191 1.078576e-30
#> [118,] 117 9.266631e-194 3.121161e-31
#> [119,] 118 7.853077e-196 8.956737e-32
#> [120,] 119 6.599225e-198 2.549062e-32
#> [121,] 120 5.499354e-200 7.195089e-33
#> [122,] 121 4.544921e-202 2.014396e-33
#> [123,] 122 3.725345e-204 5.594150e-34
#> [124,] 123 3.028736e-206 1.541100e-34
#> [125,] 124 2.442529e-208 4.211744e-35
#> [126,] 125 1.954023e-210 1.141967e-35
#> [127,] 126 1.550812e-212 3.072074e-36
#> [128,] 127 1.221112e-214 8.200150e-37
#> [129,] 128 9.539935e-217 2.171948e-37
#> [130,] 129 7.395299e-219 5.708725e-38
#> [131,] 130 5.688691e-221 1.489072e-38
#> [132,] 131 4.342512e-223 3.854812e-39
#> [133,] 132 3.289782e-225 9.904341e-40
#> [134,] 133 2.473520e-227 2.525843e-40
#> [135,] 134 1.845911e-229 6.393945e-41
#> [136,] 135 1.367341e-231 1.606704e-41
#> [137,] 136 1.005398e-233 4.008023e-42
#> [138,] 137 7.338672e-236 9.925992e-43
#> [139,] 138 5.317878e-238 2.440559e-43
#> [140,] 139 3.825811e-240 5.957964e-44
#> [141,] 140 2.732722e-242 1.444180e-44
#> [142,] 141 1.938101e-244 3.476005e-45
#> [143,] 142 1.364860e-246 8.308000e-46
#> [144,] 143 9.544475e-249 1.971923e-46
#> [145,] 144 6.628107e-251 4.648162e-47
#> [146,] 145 4.571109e-253 1.088154e-47
#> [147,] 146 3.130896e-255 2.530098e-48
#> [148,] 147 2.129861e-257 5.843076e-49
#> [149,] 148 1.439096e-259 1.340363e-49
#> [150,] 149 9.658359e-262 3.054212e-50
#> [151,] 150 6.438906e-264 6.913382e-51
#> [152,] 151 4.264176e-266 1.554588e-51
#> [153,] 152 2.805379e-268 3.472894e-52
#> [154,] 153 1.833581e-270 7.707930e-53
#> [155,] 154 1.190637e-272 1.699698e-53
#> [156,] 155 7.681530e-275 3.724015e-54
#> [157,] 156 4.924058e-277 8.107262e-55
#> [158,] 157 3.136342e-279 1.753789e-55
#> [159,] 158 1.985027e-281 3.769971e-56
#> [160,] 159 1.248445e-283 8.053285e-57
#> [161,] 160 7.802778e-286 1.709619e-57
#> [162,] 161 4.846446e-288 3.606891e-58
#> [163,] 162 2.991633e-290 7.562942e-59
#> [164,] 163 1.835358e-292 1.576117e-59
#> [165,] 164 1.119121e-294 3.264693e-60
#> [166,] 165 6.782550e-297 6.721526e-61
#> [167,] 166 4.085873e-299 1.375564e-61
#> [168,] 167 2.446631e-301 2.798312e-62
#> [169,] 168 1.456328e-303 5.658868e-63
#> [170,] 169 8.617324e-306 1.137617e-63
#> [171,] 170 5.069014e-308 2.273580e-64