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Trajectory definition

Source: R/defineTrajectories.R
defineTrajectories.Rd

Defines data structures for trajectory analysis

Usage

defineTrajectories(d, sites, surveys = NULL, times = NULL)

Arguments

d

A symmetric matrix or an object of class dist containing the distance values between pairs of ecological states..

sites

A character vector indicating the ecological entity (site, individual, community) corresponding to each ecological state (other types are converted to character).

surveys

An integer vector indicating the survey corresponding to each ecological state (only necessary when surveys are not in order and times is not provided).

times

A numeric vector indicating survey times.

Value

An object (list) of class trajectories with the following elements:

  • d: An object of class dist containing relationships between ecological states

  • metadata: A data frame describing trajectory states, with the following columns:

    • sites: A character vector indicating the ecological entity corresponding to each ecological state.

    • surveys: An integer vector indicating the survey corresponding to each ecological state.

    • times: A numeric vector indicating survey times.

Details

If surveys is not provided, but times is available, surveys will be taken as the order of times. Otherwise, surveys will be assumed to be in order for all the occurrences of the same value of sites. If times is not provided, then it is made equal to surveys.

See also

subsetTrajectories

Examples

#Description of entities (sites) and surveys
entities <- c("1","1","1","2","2","2")
surveys <- c(1,2,3,1,2,3)
  
#Raw data table
xy<-matrix(0, nrow=6, ncol=2)
xy[2,2]<-1
xy[3,2]<-2
xy[4:6,1] <- 0.5
xy[4:6,2] <- xy[1:3,2]
xy[6,1]<-1

d <- dist(xy)

# Defines trajectories
x <- defineTrajectories(d, entities, surveys)
x
#> $d
#>          1        2        3        4        5
#> 2 1.000000                                    
#> 3 2.000000 1.000000                           
#> 4 0.500000 1.118034 2.061553                  
#> 5 1.118034 0.500000 1.118034 1.000000         
#> 6 2.236068 1.414214 1.000000 2.061553 1.118034
#> 
#> $metadata
#>   sites surveys times
#> 1     1       1     1
#> 2     1       2     2
#> 3     1       3     3
#> 4     2       1     1
#> 5     2       2     2
#> 6     2       3     3
#> 
#> attr(,"class")
#> [1] "trajectories" "list"