River Distance Between Sequential Observations

Returns a matrix of distances traveled by unique fish, between sequential surveys. A plotting method is also provided for the output; see plotseq

riverdistanceseq(unique, survey, seg, vert, rivers, logical = NULL,
  stopiferror = TRUE, algorithm = NULL)

Arguments

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.
logical	A boolean vector that can be used for subsetting. If used, riverdistanceseq() will only return pairwise distances in which a specified condition is met.
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 data frame of distances (numeric), with rows defined by unique fish and columns defined by observation increment (1 to 2, 2 to 3, etc.)

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, plotseq

Examples

data(Gulk, fakefish)
riverdistanceseq(unique=fakefish$fish.id, survey=fakefish$flight,
      seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk)
#>      1 to 2    2 to 3   3 to 4    4 to 5    5 to 6    6 to 7    7 to 8
#> 1  95083.92        NA       NA  31716.70        NA        NA        NA
#> 3        NA 98874.073       NA        NA 161737.19 136260.65 78484.316
#> 4        NA  8851.529       NA        NA  14155.61  14839.50        NA
#> 6        NA        NA       NA        NA        NA  62068.00        NA
#> 7  65807.27 12711.061 66917.81  24371.74        NA        NA        NA
#> 8        NA        NA       NA        NA        NA        NA 62652.317
#> 9  49426.77 33738.885 83233.47        NA        NA        NA        NA
#> 10       NA        NA       NA  32212.19        NA        NA        NA
#> 11       NA        NA       NA        NA        NA        NA        NA
#> 13       NA        NA       NA 112786.74 166903.42  52140.91        NA
#> 14       NA        NA 33037.94  41936.11 132315.85  93566.45        NA
#> 15       NA 70005.435       NA        NA 123847.49        NA        NA
#> 16       NA        NA       NA        NA        NA        NA  1777.165
#> 17       NA        NA       NA        NA 140074.17        NA        NA
#> 18       NA  3419.247 67104.32        NA        NA        NA        NA
#> 19       NA        NA       NA        NA        NA        NA        NA
#> 20       NA        NA       NA        NA 125131.75  38174.45 75305.374
#>       8 to 9   9 to 10
#> 1  54220.046  36142.97
#> 3   3810.189  88381.02
#> 4         NA        NA
#> 6         NA        NA
#> 7         NA        NA
#> 8   9037.607  31666.38
#> 9         NA        NA
#> 10  6621.268        NA
#> 11 93415.847  95830.80
#> 13        NA        NA
#> 14        NA  69776.53
#> 15        NA        NA
#> 16 69473.303 109142.02
#> 17        NA        NA
#> 18        NA        NA
#> 19 67213.962        NA
#> 20        NA        NA

seqbysurvey <- riverdistanceseq(unique=fakefish$fish.id, survey=fakefish$flight.date,
      seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk)
seqbysurvey
#>    2015-04-01 to 2015-04-19 2015-04-19 to 2015-06-01 2015-06-01 to 2015-06-21
#> 1                  95083.92                       NA                       NA
#> 3                        NA                98874.073                       NA
#> 4                        NA                 8851.529                       NA
#> 6                        NA                       NA                       NA
#> 7                  65807.27                12711.061                 66917.81
#> 8                        NA                       NA                       NA
#> 9                  49426.77                33738.885                 83233.47
#> 10                       NA                       NA                       NA
#> 11                       NA                       NA                       NA
#> 13                       NA                       NA                       NA
#> 14                       NA                       NA                 33037.94
#> 15                       NA                70005.435                       NA
#> 16                       NA                       NA                       NA
#> 17                       NA                       NA                       NA
#> 18                       NA                 3419.247                 67104.32
#> 19                       NA                       NA                       NA
#> 20                       NA                       NA                       NA
#>    2015-06-21 to 2015-07-07 2015-07-07 to 2015-08-11 2015-08-11 to 2015-09-05
#> 1                  31716.70                       NA                       NA
#> 3                        NA                161737.19                136260.65
#> 4                        NA                 14155.61                 14839.50
#> 6                        NA                       NA                 62068.00
#> 7                  24371.74                       NA                       NA
#> 8                        NA                       NA                       NA
#> 9                        NA                       NA                       NA
#> 10                 32212.19                       NA                       NA
#> 11                       NA                       NA                       NA
#> 13                112786.74                166903.42                 52140.91
#> 14                 41936.11                132315.85                 93566.45
#> 15                       NA                123847.49                       NA
#> 16                       NA                       NA                       NA
#> 17                       NA                140074.17                       NA
#> 18                       NA                       NA                       NA
#> 19                       NA                       NA                       NA
#> 20                       NA                125131.75                 38174.45
#>    2015-09-05 to 2015-09-20 2015-09-20 to 2015-10-29 2015-10-29 to 2015-11-25
#> 1                        NA                54220.046                 36142.97
#> 3                 78484.316                 3810.189                 88381.02
#> 4                        NA                       NA                       NA
#> 6                        NA                       NA                       NA
#> 7                        NA                       NA                       NA
#> 8                 62652.317                 9037.607                 31666.38
#> 9                        NA                       NA                       NA
#> 10                       NA                 6621.268                       NA
#> 11                       NA                93415.847                 95830.80
#> 13                       NA                       NA                       NA
#> 14                       NA                       NA                 69776.53
#> 15                       NA                       NA                       NA
#> 16                 1777.165                69473.303                109142.02
#> 17                       NA                       NA                       NA
#> 18                       NA                       NA                       NA
#> 19                       NA                67213.962                       NA
#> 20                75305.374                       NA                       NA
plotseq(seqbysurvey)