Upstream Distance Between Sequential Observations

Returns a matrix of distance with direction by unique fish between sequential surveys. The mouth (lowest point) segment and vertex must be specified (see setmouth). A plotting method is provided for the output; see plotseq.

upstreamseq(unique, survey, seg, vert, rivers, logical = NULL,
  flowconnected = FALSE, net = FALSE, 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, `upstreamseq()` will only return pairwise distances in which a specified condition is met.
flowconnected	If `TRUE`, only returns distance if the input segments are flow-connected. Defaults to `FALSE`.
net	Whether to calculate net upstream distance (net=TRUE) or total distance (net=FALSE, default).
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 upstream distances (numeric), with rows defined by unique fish and columns defined by observation increment (1 to 2, 2 to 3, etc.) See upstream for additional information.

Note

Returns either net upstream distance (net=TRUE) or total distance (net=FALSE, default). See upstream.

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

Examples

data(Gulk, fakefish)

# Mouth must be specified
Gulk$mouth$mouth.seg <- 1
Gulk$mouth$mouth.vert <- 1

upstreamseq(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 <- upstreamseq(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)

Upstream Distance Between Sequential Observations

Arguments

Value

Note

See also

Examples

Contents

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