This dataset is a small (30 cases) simulated outbreak originally used to illustrate outbreaker, and used for the same purposes in outbreaker2. This list contains the following:

fake_outbreak

Format

An object of class list of length 6.

Details

  • $onset: A vector of integers representing dates of onset.

  • $sample: A vector of integers representing the dates of isolation.

  • $dna: A DNAbin matrix of pathogen genome sequences.

  • $w: A numeric vector giving the empirical distribution of the generation time.

  • $ances: A vector of integers indicating, for each case, the true infectors. NA represents imported cases.

Examples

names(fake_outbreak)
#> [1] "onset" "sample" "dna" "w" "ances" "ctd"
fake_outbreak
#> $onset #> [1] 0 2 4 4 6 6 6 7 7 8 8 8 8 9 9 9 9 10 10 10 10 10 10 10 10 #> [26] 10 10 10 11 11 #> #> $sample #> [1] 3 5 6 6 7 9 8 9 9 9 11 10 10 10 10 11 11 12 11 13 12 13 11 12 11 #> [26] 11 13 12 14 14 #> #> $dna #> 30 DNA sequences in binary format stored in a matrix. #> #> All sequences of same length: 10000 #> #> Labels: #> ... #> #> Base composition: #> a c g t #> 0.251 0.242 0.251 0.256 #> (Total: 300 kb) #> #> $w #> [1] 0.04255319 0.21276596 0.42553191 0.31914894 #> #> $ances #> [1] NA 1 2 NA 3 4 4 5 6 6 7 8 9 5 5 7 7 8 9 10 11 11 13 13 13 #> [26] 17 17 NA 10 13 #> #> $ctd #> i j #> 1 4 7 #> 2 10 29 #> 3 13 30 #> 4 11 22 #> 5 13 25 #> 6 16 7 #> 7 13 23 #> 8 10 6 #> 9 18 8 #> 10 14 5 #> 11 17 26 #> 12 11 21 #> 13 3 5 #> 14 17 27 #> 15 2 3 #> 16 17 7 #> 17 19 9 #> 18 12 8 #> 19 22 6 #> 20 30 9 #> 21 17 20 #> 22 21 29 #> 23 11 14 #> 24 18 9 #> 25 25 29 #> 26 1 17 #> 27 23 7 #> 28 25 3 #> 29 3 9 #> 30 1 4 #> 31 13 4 #> 32 21 27 #> 33 16 2 #> 34 29 3 #> 35 21 5 #>