Read linelist and contact data

This function reads data stored as data.frame containing linelist (case information, where each row corresponds to a unique patient), and contacts between patients. Common identifiers should be used in the two data sources for matching to be achieved.

make_epicontacts(
  linelist,
  contacts,
  id = 1L,
  from = 1L,
  to = 2L,
  directed = FALSE
)

Arguments

linelist	a data.frame with at least one column providing unique patient identifiers
contacts	a data.frame that needs at least two columns indicating patients between which cases take place; these need not be referenced in the linelist
id	an index or name indicating which column in linelist contains unique identifiers; default is first column in linelist data frame
from	an index or name indicating which column in contacts contains the first case of a contact
to	an index or name indicating which column in contacts contains the second case of a contact
directed	a logical indicating if contacts are directed or not; default is FALSE but note that contacts will be indicated as 'from' and 'to' even in non-directed contacts

Value

An epicontacts object in list format with three elements:

• linelist: data.frame of cases with first column 'id' containing character vector of unique identifiers

• contacts: data.frame of contacts with first two columns named 'from' and 'to' indicating unique pairs of contact between individuals

• directed: indicator as to whether or not the contacts are to be considered directed or not

Details

An epicontacts object can be created from two components:

• a linelist provided as a data.frame where columns are different variables describing cases, and where each row is a different case. and a contact list.

• a contact list provided as a data.frame where each row contains unique pairs of contacts with unique features of contact in columns. The line list and contact list should share an identification scheme for individuals.

References

https://foodborne.unl.edu/public/role/epidemiologist/lineLists.html

Author

Thibaut Jombart (thibautjombart@gmail.com)

Examples

if (require(outbreaks)) {
## make epicontacts object from simulated Ebola data
x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts)

## test reordering of columns
linelist <- ebola_sim$linelist[,rev(seq_len(ncol(ebola_sim$linelist)))]
contacts <- ebola_sim$contacts[,rev(seq_len(ncol(ebola_sim$contacts)))]
head(linelist)
head(contacts)

## make object
x <- make_epicontacts(linelist, contacts, id = "case_id",
                       to = "case_id", from = "infector")
head(x$linelist)
head(x$contacts)
}
#>      from     to  source
#> 2  d1fafd 53371b   other
#> 3  cac51e f5c3d8 funeral
#> 5  f5c3d8 0f58c4   other
#> 8  0f58c4 881bd4   other
#> 11 8508df 40ae5f   other
#> 12 127d83 f547d6 funeral