Small simulated outbreak

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.

Author

Thibaut Jombart thibautjombart@gmail.com

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
#>