indToPair: Transforms a dataset of individuals to a dataset of pairs
In nbTransmission: Naive Bayes Transmission Analysis

Description Usage Arguments Details Value Examples

The function indToPair takes a dataset of observations (such as individuals in an infectious disease outbreak) and transforms it into a dataset of pairs.

indToPair(
  indData,
  indIDVar,
  separator = "_",
  dateVar = NULL,
  units = c("mins", "hours", "days", "weeks"),
  ordered = FALSE
)

`indData`	An individual-level dataframe.
`indIDVar`	The name (in quotes) of the column with the individual ID.
`separator`	The character to be used to separate the individual IDs when creating the pairID.
`dateVar`	The name (in quotes) of the column with the dates that the individuals are observed (optional unless `ordered = TRUE`). This column must be a date or date-time (POSIXt) object. If supplied, the time difference between individuals will be calculated in the units specified.
`units`	The units for the time difference, only necessary if `dateVar` is supplied. Must be one of `"mins", "hours", "days", "weeks"`.
`ordered`	A logical indicating if a set of ordered pairs should be returned (`<dateVar>.1` before `<dateVar>.2` or `<dateVar>.1` = `<dateVar>.2`). If FALSE a dataframe of all pairs will be returned

The function requires an id column: indIDVar to identify the individual observations. The resulting pair-level dataframe will have a pairID column which combines the individual IDs for that pair.

The function can either output all possible pairs (ordered = FALSE) or only ordered pairs (ordered = TRUE) where the ordered is determined by a date variable (dateVar). If orded = TRUE, then dateVar must be provided and if ordered = FALSE, it is optional. In both cases, if dateVar is provided, the output will include the time difference between the individuals in the pair in the units specified ("mins", "hours", "days", "weeks").

A dataframe of either all possible pairs of individuals (ordered = FALSE) or ordered pairs of individuals (ordered = TRUE). The dataframe will have all of the original variables with suffixes ".1" and ".2" corresponding to the original values of <indIDVar>.1 and <indIDVar>.2.

Added to the dataframe will be a column called pairID which is <indIDVar>.1 and <indIDVar>.2 separated by separator.

If dateVar is provided the dataframe will also include variables <dateVar>.Diff giving the difference of time of dateVar for <indIDVar>.1 and <indIDVar>.2 in the units specified

## Create a dataset of all pairs with no date variable
pairU <- indToPair(indData = indData, indIDVar = "individualID")

## Create a dataset of all pairs with a date variable
pairUD <- indToPair(indData = indData, indIDVar = "individualID",
                      dateVar = "infectionDate", units = "days")

## Create a dataset of ordered pairs
pairO <- indToPair(indData = indData, indIDVar = "individualID",
                     dateVar = "infectionDate", units = "days", ordered = TRUE)