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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).

times

A numeric vector indicating survey times (if missing, survey times are made equal to surveys).

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.

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"