use only_linelist = TRUE at epicontacts::get_degree() #170
Description
At #169 we propose using epicontacts::get_degree()
Using only_linelist = TRUE helps us to get MERS and Ebola dispersion parameter estimates close to:
- https://community.appliedepi.org/t/estimating-the-degree-of-super-spreading-from-transmission-chain-data/103/2
- https://epiverse-trace.github.io/superspreading/articles/proportion_transmission.html
# Load packages -----------------------------------------------------------
library(epicontacts)
library(fitdistrplus)
#> Loading required package: MASS
#> Loading required package: survival
library(tidyverse)
# Create an epicontacts object -------------------------------------------
epi_contacts <-
epicontacts::make_epicontacts(
linelist = outbreaks::mers_korea_2015$linelist,
contacts = outbreaks::mers_korea_2015$contacts,
directed = TRUE
)
secondary_cases_false <- epicontacts::get_degree(
x = epi_contacts,
type = "out",
only_linelist = FALSE # default
)
secondary_cases_true <- epicontacts::get_degree(
x = epi_contacts,
type = "out",
only_linelist = TRUE
)
secondary_cases_true %>%
enframe(name = "from",value = "only_linelist_true") %>%
left_join(secondary_cases_false %>% enframe(name = "from", value = "only_linelist_false")) %>%
print(n = Inf)
#> Joining with `by = join_by(from)`
#> # A tibble: 162 × 3
#> from only_linelist_true only_linelist_false
#> <chr> <int> <int>
#> 1 SK_1 26 26
#> 2 SK_2 0 0
#> 3 SK_3 0 0
#> 4 SK_4 0 0
#> 5 SK_5 0 0
#> 6 SK_6 2 2
#> 7 SK_7 0 0
#> 8 SK_8 0 0
#> 9 SK_9 0 NA
#> 10 SK_10 0 0
#> 11 SK_11 1 1
#> 12 SK_12 1 1
#> 13 SK_13 0 0
#> 14 SK_14 38 38
#> 15 SK_15 4 4
#> 16 SK_16 21 21
#> 17 SK_17 0 0
#> 18 SK_18 0 0
#> 19 SK_19 0 0
#> 20 SK_20 0 0
#> 21 SK_21 0 0
#> 22 SK_22 0 0
#> 23 SK_23 0 0
#> 24 SK_24 0 0
#> 25 SK_25 0 NA
#> 26 SK_26 0 0
#> 27 SK_27 0 0
#> 28 SK_28 0 0
#> 29 SK_29 0 NA
#> 30 SK_30 0 0
#> 31 SK_31 0 0
#> 32 SK_32 0 0
#> 33 SK_33 0 0
#> 34 SK_34 0 0
#> 35 SK_35 0 0
#> 36 SK_36 0 NA
#> 37 SK_37 0 NA
#> 38 SK_38 0 0
#> 39 SK_39 0 0
#> 40 SK_40 0 0
#> 41 SK_41 0 0
#> 42 SK_42 0 NA
#> 43 SK_43 0 NA
#> 44 SK_44 0 NA
#> 45 SK_45 0 0
#> 46 SK_46 0 NA
#> 47 SK_47 0 0
#> 48 SK_48 0 0
#> 49 SK_49 0 NA
#> 50 SK_50 0 NA
#> 51 SK_51 0 NA
#> 52 SK_52 0 NA
#> 53 SK_53 0 NA
#> 54 SK_54 0 0
#> 55 SK_55 0 NA
#> 56 SK_56 0 NA
#> 57 SK_57 0 NA
#> 58 SK_58 0 NA
#> 59 SK_59 0 NA
#> 60 SK_60 0 NA
#> 61 SK_61 0 NA
#> 62 SK_62 0 NA
#> 63 SK_63 0 NA
#> 64 SK_64 0 NA
#> 65 SK_65 0 NA
#> 66 SK_66 0 NA
#> 67 SK_67 0 NA
#> 68 SK_68 0 NA
#> 69 SK_69 0 NA
#> 70 SK_70 0 NA
#> 71 SK_71 0 NA
#> 72 SK_72 0 NA
#> 73 SK_73 0 NA
#> 74 SK_74 0 NA
#> 75 SK_75 0 NA
#> 76 SK_76 2 2
#> 77 SK_77 0 NA
#> 78 SK_78 0 NA
#> 79 SK_79 0 NA
#> 80 SK_80 0 NA
#> 81 SK_81 0 NA
#> 82 SK_82 0 0
#> 83 SK_83 0 0
#> 84 SK_84 0 0
#> 85 SK_85 0 0
#> 86 SK_86 0 0
#> 87 SK_87 1 1
#> 88 SK_88 0 0
#> 89 SK_89 0 NA
#> 90 SK_90 0 NA
#> 91 SK_91 0 NA
#> 92 SK_92 0 0
#> 93 SK_93 0 0
#> 94 SK_94 0 0
#> 95 SK_95 0 NA
#> 96 SK_96 0 0
#> 97 SK_97 0 0
#> 98 SK_98 0 0
#> 99 SK_99 0 NA
#> 100 SK_100 0 0
#> 101 SK_101 0 NA
#> 102 SK_102 0 0
#> 103 SK_103 0 0
#> 104 SK_104 0 0
#> 105 SK_105 0 NA
#> 106 SK_106 0 0
#> 107 SK_107 0 0
#> 108 SK_108 0 0
#> 109 SK_109 0 NA
#> 110 SK_110 0 0
#> 111 SK_111 0 0
#> 112 SK_112 0 0
#> 113 SK_113 0 0
#> 114 SK_114 0 0
#> 115 SK_115 0 NA
#> 116 SK_116 0 0
#> 117 SK_117 0 0
#> 118 SK_118 1 1
#> 119 SK_119 0 NA
#> 120 SK_120 0 0
#> 121 SK_121 0 NA
#> 122 SK_122 0 0
#> 123 SK_123 1 1
#> 124 SK_124 0 0
#> 125 SK_125 0 0
#> 126 SK_126 0 0
#> 127 SK_127 0 0
#> 128 SK_128 0 0
#> 129 SK_129 0 0
#> 130 SK_130 0 0
#> 131 SK_131 0 0
#> 132 SK_132 0 0
#> 133 SK_133 0 0
#> 134 SK_134 0 0
#> 135 SK_135 0 0
#> 136 SK_136 0 0
#> 137 SK_137 0 0
#> 138 SK_138 0 0
#> 139 SK_139 0 0
#> 140 SK_140 0 0
#> 141 SK_141 0 NA
#> 142 SK_142 0 0
#> 143 SK_143 0 0
#> 144 SK_144 0 NA
#> 145 SK_145 0 0
#> 146 SK_146 0 0
#> 147 SK_147 0 0
#> 148 SK_148 0 NA
#> 149 SK_149 0 0
#> 150 SK_150 0 0
#> 151 SK_151 0 NA
#> 152 SK_152 0 NA
#> 153 SK_153 0 0
#> 154 SK_154 0 NA
#> 155 SK_155 0 NA
#> 156 SK_156 0 NA
#> 157 SK_157 0 NA
#> 158 SK_158 0 NA
#> 159 SK_159 0 NA
#> 160 SK_160 0 NA
#> 161 SK_161 0 NA
#> 162 SK_162 0 NACreated on 2025-04-03 with reprex v2.1.1