contact (version 1.2.4)

summarizeContacts: Summarize Contact Events

Description

This function takes the output from contactDur.all or contactDur.area and reports the number of durations when tracked individuals are in "contact" with one another (contactDur.all) or with specified fixed points/polygons (contactDur.area).

Usage

summarizeContacts(
  x,
  importBlocks = FALSE,
  avg = FALSE,
  parallel = FALSE,
  nCores = (parallel::detectCores()/2)
)

Arguments

x

Output from the contactDur.all or contactDur.area functions. Can be either a data frame or list of data frames.

importBlocks

Logical. If true, each block in x will be analyzed separately. Defaults to FALSE. Note that the "block" column must exist in x.

avg

Logical. If TRUE, summary output from all data frames contained in x will be averaged together. Output will produce an extra data frame containing the mean column values for each id (per block if importBlocks == TRUE). Defaults to FALSE.

parallel

Logical. If TRUE, sub-functions within the summarizeContacts wrapper will be parallelized. Note that the only sub-function parallelized here is called ONLY when importBlocks == TRUE.

nCores

Integer. Describes the number of cores to be dedicated to parallel processes. Defaults to half of the maximum number of cores available (i.e., (parallel::detectCores()/2)).

Value

Returns a data frame (or list of data frames if x is a list of data frames) with the following columns:

id

The unique ID of a tracked individual for which we will summarize to all other individuals/fixed locations observed in x.

id

Sum number of individuals/fixed locations observed in contact specific individuals.

id

Sum number of contacts associated with specific individuals.

contactDuration_...

Number of contacts between specific dyads.

If importBlocks == TRUE, the following columns are appended to the output data frame described above:

block

Integer ID describing unique blocks of time during which contacts occur.

block.start

The timepoint in x at which the block begins.

block.end

The timepoint in x at which the block ends.

numBlocks

Integer describing the total number of time blocks observed within x at which the block

Details

If x is a list, and avg == TRUE, this function will produce an extra data frame containing the mean column values for each id (per block if importBlocks == TRUE).

This is a sub-function found within the contactTest and ntwrkEdges function.

Examples

# NOT RUN {
data(calves)

calves.dateTime<-datetime.append(calves, date = calves$date, 
   time = calves$time) #create a dataframe with dateTime identifiers for location fixes

calves.agg<-tempAggregate(calves.dateTime, id = calves.dateTime$calftag, 
   dateTime = calves.dateTime$dateTime, point.x = calves.dateTime$x, 
   point.y = calves.dateTime$y, secondAgg = 300, extrapolate.left = FALSE, 
   extrapolate.right = FALSE, resolutionLevel = "reduced", parallel = FALSE, 
   na.rm = TRUE, smooth.type = 1) #smooth to 5-min fix intervals.

calves.dist<-dist2All_df(x = calves.agg, parallel = FALSE, 
   dataType = "Point", lonlat = FALSE) 
calves.contact.block<-contactDur.all(x = calves.dist, dist.threshold=1, 
   sec.threshold=10, blocking = TRUE, blockUnit = "hours", blockLength = 1, 
   equidistant.time = FALSE, parallel = FALSE, reportParameters = TRUE) 
   
calves.contactSumm.NOblock <- summarizeContacts(calves.contact.block)
head(calves.contactSumm.NOblock)

calves.contactSumm.block <- summarizeContacts(calves.contact.block, 
   importBlocks = TRUE)
head(calves.contactSumm.block)
# }