River Distance Matrix of All Observations of an Individual

Returns a matrix of network distances between all observations of one unique fish.

riverdistancematbysurvey(indiv, unique, survey, seg, vert, rivers,
  full = TRUE, stopiferror = TRUE, algorithm = NULL)

Arguments

indiv	The unique identifier of the fish in question.
unique	A vector of identifiers for each fish.
survey	A vector of identifiers for each survey. It is recommended to use a numeric or date format (see as.Date) to preserve survey order.
seg	A vector of river locations (segment component).
vert	A vector of river locations (vertex component).
rivers	The river network object to use.
full	Whether to return the full matrix, with NA values for missing data (TRUE), or a the subset of rows and columns corresponding to successful observations. Defaults to TRUE.
stopiferror	Whether or not to exit with an error if a route cannot be found. If this is set to FALSE and a route cannot be found, the function will return NA in the appropriate entry. Defaults to TRUE. See detectroute.
algorithm	Which route detection algorithm to use ("Dijkstra", "sequential", or "segroutes"). If left as NULL (the default), the function will automatically make a selection. See detectroute for more details.

Value

A matrix of distances (numeric), with rows and columns defined by survey.

Note

Building routes from the river mouth to each river network segment and/or distance lookup tables will greatly reduce computation time (see buildsegroutes).

See also

riverdistance

Examples

data(Gulk, fakefish)
riverdistancematbysurvey(indiv=1, unique=fakefish$fish.id, survey=fakefish$flight,
      seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk)
#>            1         2  3          4         5  6  7         8        9
#> 1       0.00 95083.922 NA 104647.183 136363.88 NA NA  79431.13 74981.17
#> 2   95083.92     0.000 NA   9563.261  41279.96 NA NA  74322.80 20102.75
#> 3         NA        NA NA         NA        NA NA NA        NA       NA
#> 4  104647.18  9563.261 NA      0.000  31716.70 NA NA  83886.06 29666.01
#> 5  136363.88 41279.962 NA  31716.701      0.00 NA NA 115602.76 61382.72
#> 6         NA        NA NA         NA        NA NA NA        NA       NA
#> 7         NA        NA NA         NA        NA NA NA        NA       NA
#> 8   79431.13 74322.799 NA  83886.060 115602.76 NA NA      0.00 54220.05
#> 9   74981.17 20102.754 NA  29666.015  61382.72 NA NA  54220.05     0.00
#> 10  38838.20 56245.722 NA  65808.983  97525.68 NA NA  40592.93 36142.97
#>          10
#> 1  38838.20
#> 2  56245.72
#> 3        NA
#> 4  65808.98
#> 5  97525.68
#> 6        NA
#> 7        NA
#> 8  40592.93
#> 9  36142.97
#> 10     0.00

riverdistancematbysurvey(indiv=1, unique=fakefish$fish.id, survey=fakefish$flight,
      seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk, full=FALSE)
#>            1         2          4         5         8        9       10
#> 1       0.00 95083.922 104647.183 136363.88  79431.13 74981.17 38838.20
#> 2   95083.92     0.000   9563.261  41279.96  74322.80 20102.75 56245.72
#> 4  104647.18  9563.261      0.000  31716.70  83886.06 29666.01 65808.98
#> 5  136363.88 41279.962  31716.701      0.00 115602.76 61382.72 97525.68
#> 8   79431.13 74322.799  83886.060 115602.76      0.00 54220.05 40592.93
#> 9   74981.17 20102.754  29666.015  61382.72  54220.05     0.00 36142.97
#> 10  38838.20 56245.722  65808.983  97525.68  40592.93 36142.97     0.00