Trajectory definition

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 ecosystem states..

sites

A character vector indicating the site corresponding to each ecosystem state (other types are converted to character).

surveys

An integer vector indicating the survey corresponding to each ecosystem 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 ecosystem states

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

  • sites: A character vector indicating the site corresponding to each ecosystem state.

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

  • times: A numeric vector indicating survey times.

See also

subsetTrajectories

Examples

#Description of sites and surveys
sites <- 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, sites, 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"