Saves a subset of the National Seamless database or other nhdplusTools compatible data based on a specified collection of COMIDs. This function uses get_nhdplus for the "download" data source but returns data consistent with local data subsets in a subset file.

subset_nhdplus(
  comids = NULL,
  output_file = NULL,
  nhdplus_data = NULL,
  bbox = NULL,
  simplified = TRUE,
  overwrite = FALSE,
  return_data = TRUE,
  status = TRUE,
  flowline_only = NULL,
  streamorder = NULL,
  out_prj = 4269
)

Arguments

comids

integer vector of COMIDs to include.

output_file

character path to save the output to defaults to the directory of the nhdplus_data.

nhdplus_data

character path to the .gpkg or .gdb containing the national seamless database, a subset of NHDPlusHR, or "download" to use a web service to download NHDPlusV2.1 data. Not required if nhdplus_path has been set or the default has been adopted. See details for more.

bbox

object of class "bbox" as returned by sf::st_bbox in Latitude/Longitude. If no CRS is present, will be assumed to be in WGS84 Latitude Longitude.

simplified

boolean if TRUE (the default) the CatchmentSP layer will be included. Not relevant to the "download" option or NHDPlusHR data.

overwrite

boolean should the output file be overwritten

return_data

boolean if FALSE path to output file is returned silently otherwise data is returned in a list.

status

boolean should the function print status messages

flowline_only

boolean WARNING: experimental if TRUE only the flowline network and attributes will be returned

streamorder

integer only streams of order greater than or equal will be downloaded. Not implemented for local data.

out_prj

character override the default output CRS of NAD83 lat/lon (EPSG:4269)

Value

character path to the saved subset geopackage

Details

This function relies on the National Seamless Geodatabase or Geopackage. It can be downloaded here.

The "download" option of this function should be considered preliminary and subject to revision. It does not include as many layers and may not be available permenently.

Examples

# \donttest{

source(system.file("extdata/sample_data.R", package = "nhdplusTools"))

nhdplus_path(sample_data)

staged_nhdplus <- stage_national_data(output_path = tempdir())
#> Warning: attributes file exists
#> Warning: flowline file exists
#> Warning: catchment already exists.

sample_flines <- readRDS(staged_nhdplus$flowline)

geom_col <- attr(sample_flines, "sf_column")

plot(sample_flines[[geom_col]],
     lwd = 3)

start_point <- sf::st_sfc(sf::st_point(c(-89.362239, 43.090266)),
                          crs = 4326)

plot(start_point, cex = 1.5, lwd = 2, col = "red", add = TRUE)

start_comid <- discover_nhdplus_id(start_point)

comids <- get_UT(sample_flines, start_comid)

plot(dplyr::filter(sample_flines, COMID %in% comids)[[geom_col]],
     add=TRUE, col = "red", lwd = 2)

output_file <- tempfile(fileext = ".gpkg")

subset_nhdplus(comids = comids,
               output_file = output_file,
               nhdplus_data = sample_data,
               overwrite = TRUE,
               status = TRUE)
#> All intersections performed in latitude/longitude.
#> Reading NHDFlowline_Network
#> 168 comids of 168
#> Writing NHDFlowline_Network
#> Reading CatchmentSP
#> 168 comids of 168
#> Writing CatchmentSP
#> Reading NHDArea
#> Writing NHDArea
#> Reading NHDWaterbody
#> Writing NHDWaterbody
#> Reading NHDFlowline_NonNetwork
#> Writing NHDFlowline_NonNetwork
#> Reading Gage
#> Writing Gage
#> Reading Sink
#> No features to write in Sink
#> $NHDFlowline_Network
#> Simple feature collection with 168 features and 136 fields
#> Geometry type: LINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: -89.58537 ymin: 43.08521 xmax: -89.21254 ymax: 43.30179
#> Geodetic CRS:  NAD83
#> # A tibble: 168 x 137
#>       COMID FDATE               RESOLUTION GNIS_ID GNIS_NAME  LENGTHKM REACHCODE
#>  *    <int> <dttm>              <chr>      <chr>   <chr>         <dbl> <chr>    
#>  1 13293750 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    1.72  07090002~
#>  2 13293504 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    1.41  07090002~
#>  3 13294134 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    0.74  07090002~
#>  4 13294128 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    3.70  07090002~
#>  5 13294394 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    0.077 07090002~
#>  6 13293454 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    0.94  07090002~
#>  7 13293430 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    1.14  07090002~
#>  8 13293424 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    1.27  07090002~
#>  9 13294110 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    7.48  07090002~
#> 10 13293398 1999-10-29 00:00:00 Medium     1577073 Yahara Ri~    0.082 07090002~
#> # ... with 158 more rows, and 130 more variables: FLOWDIR <chr>,
#> #   WBAREACOMI <int>, FTYPE <chr>, FCODE <int>, Shape_Length <dbl>,
#> #   StreamLeve <int>, StreamOrde <int>, StreamCalc <int>, FromNode <dbl>,
#> #   ToNode <dbl>, Hydroseq <dbl>, LevelPathI <dbl>, Pathlength <dbl>,
#> #   TerminalPa <dbl>, ArbolateSu <dbl>, Divergence <int>, StartFlag <int>,
#> #   TerminalFl <int>, DnLevel <int>, UpLevelPat <dbl>, UpHydroseq <dbl>,
#> #   DnLevelPat <dbl>, DnMinorHyd <dbl>, DnDrainCou <int>, DnHydroseq <dbl>, ...
#> 
#> $CatchmentSP
#> Simple feature collection with 167 features and 6 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -89.60515 ymin: 43.03466 xmax: -89.20362 ymax: 43.36658
#> Geodetic CRS:  NAD83
#> # A tibble: 167 x 7
#>    GRIDCODE FEATUREID SOURCEFC    AreaSqKM Shape_Length Shape_Area
#>  *    <int>     <int> <chr>          <dbl>        <dbl>      <dbl>
#>  1  1085160  13293454 NHDFlowline   0.328       0.0256  0.0000364 
#>  2  1085219  13293750 NHDFlowline   6.69        0.148   0.000740  
#>  3  1085247  13294134 NHDFlowline   0.261       0.0307  0.0000288 
#>  4  1085414  13293570 NHDFlowline   0.0514      0.00963 0.00000569
#>  5  1085447  13293430 NHDFlowline   1.63        0.0780  0.000181  
#>  6  1085448  13293526 NHDFlowline   0.0690      0.0117  0.00000764
#>  7  1085463  13293588 NHDFlowline   0.429       0.0404  0.0000475 
#>  8  1085478  13293614 NHDFlowline   3.15        0.0953  0.000348  
#>  9  1085502  13294264 NHDFlowline  24.8         0.348   0.00275   
#> 10  1085509  13293384 NHDFlowline   0.291       0.0296  0.0000323 
#> # ... with 157 more rows, and 1 more variable: geom <POLYGON [°]>
#> 
#> $NHDArea
#> [1] "NHDArea"
#> 
#> $NHDWaterbody
#> [1] "NHDWaterbody"
#> 
#> $NHDFlowline_NonNetwork
#> [1] "NHDFlowline_NonNetwork"
#> 
#> $Gage
#> [1] "Gage"
#> 
#> $Sink
#> NULL
#> 

sf::st_layers(output_file)
#> Driver: GPKG 
#> Available layers:
#>               layer_name geometry_type features fields
#> 1    NHDFlowline_Network   Line String      168    136
#> 2            CatchmentSP       Polygon      167      6
#> 3                NHDArea       Polygon        1     14
#> 4           NHDWaterbody       Polygon       90     21
#> 5 NHDFlowline_NonNetwork   Line String       45     12
#> 6                   Gage         Point       33     19

catchment <- sf::read_sf(output_file, "CatchmentSP")

plot(catchment[[attr(catchment, "sf_column")]], add = TRUE)

waterbody <- sf::read_sf(output_file, "NHDWaterbody")

plot(waterbody[[attr(waterbody, "sf_column")]],
     col = rgb(0, 0, 1, alpha = 0.5), add = TRUE)


# Cleanup temp
sapply(staged_nhdplus, unlink)
#> attributes   flowline  catchment 
#>          0          0          0 
unlink(output_file)

# Download Option:
subset_nhdplus(comids = comids,
               output_file = output_file,
               nhdplus_data = "download",
               overwrite = TRUE,
               status = TRUE, flowline_only = FALSE)
#> All intersections performed in latitude/longitude.
#> Reading NHDFlowline_Network
#> Writing NHDFlowline_Network
#> Reading CatchmentSP
#> Writing CatchmentSP
#> $NHDFlowline_Network
#> Simple feature collection with 168 features and 138 fields
#> Geometry type: LINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: -89.58537 ymin: 43.08522 xmax: -89.21254 ymax: 43.30179
#> Geodetic CRS:  NAD83
#> # A tibble: 168 x 139
#>    id           comid fdate               resolution gnis_id gnis_name  lengthkm
#>  * <chr>        <int> <dttm>              <chr>      <chr>   <chr>         <dbl>
#>  1 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "           3.04 
#>  2 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "           1.44 
#>  3 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     "15770~ "Yahara R~    4.84 
#>  4 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "           4.40 
#>  5 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     "15770~ "Yahara R~    0.839
#>  6 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "           4.67 
#>  7 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     "15770~ "Yahara R~    0.402
#>  8 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "           1.08 
#>  9 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     "15770~ "Yahara R~    1.12 
#> 10 nhdflowli~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "           0.351
#> # ... with 158 more rows, and 132 more variables: reachcode <chr>,
#> #   flowdir <chr>, wbareacomi <int>, ftype <chr>, fcode <int>,
#> #   shape_length <dbl>, streamleve <int>, streamorde <int>, streamcalc <int>,
#> #   fromnode <dbl>, tonode <dbl>, hydroseq <dbl>, levelpathi <dbl>,
#> #   pathlength <dbl>, terminalpa <dbl>, arbolatesu <dbl>, divergence <int>,
#> #   startflag <int>, terminalfl <int>, dnlevel <int>, uplevelpat <dbl>,
#> #   uphydroseq <dbl>, dnlevelpat <dbl>, dnminorhyd <dbl>, dndraincou <int>, ...
#> 
#> $CatchmentSP
#> Simple feature collection with 167 features and 7 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -89.60574 ymin: 43.03405 xmax: -89.20332 ymax: 43.36719
#> Geodetic CRS:  NAD83
#> # A tibble: 167 x 8
#>    id             gridcode featureid sourcefc   areasqkm shape_length shape_area
#>  * <chr>             <int>     <int> <chr>         <dbl>        <dbl>      <dbl>
#>  1 catchmentsp.9~  1085512  13293376 NHDFlowli~  47.8          0.465  0.00530   
#>  2 catchmentsp.9~  1085714  13293378 NHDFlowli~   3.30         0.0899 0.000366  
#>  3 catchmentsp.9~  1085651  13293380 NHDFlowli~  19.1          0.247  0.00212   
#>  4 catchmentsp.9~  1085750  13293382 NHDFlowli~  12.1          0.197  0.00135   
#>  5 catchmentsp.9~  1085509  13293384 NHDFlowli~   0.291        0.0296 0.0000323 
#>  6 catchmentsp.9~  1085979  13293386 NHDFlowli~   9.94         0.175  0.00110   
#>  7 catchmentsp.9~  1085517  13293388 NHDFlowli~   0.154        0.0187 0.0000171 
#>  8 catchmentsp.9~  1085768  13293390 NHDFlowli~   1.41         0.0612 0.000157  
#>  9 catchmentsp.9~  1085605  13293392 NHDFlowli~   0.461        0.0393 0.0000511 
#> 10 catchmentsp.9~  1085893  13293394 NHDFlowli~   0.0796       0.0124 0.00000882
#> # ... with 157 more rows, and 1 more variable: geometry <POLYGON [°]>
#> 
#> $NHDArea
#> Simple feature collection with 1 feature and 15 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -89.40238 ymin: 43.14979 xmax: -89.36093 ymax: 43.18172
#> Geodetic CRS:  NAD83
#> # A tibble: 1 x 16
#>   id             comid fdate               resolution gnis_id gnis_name areasqkm
#> * <chr>          <int> <dttm>              <chr>      <chr>   <chr>        <dbl>
#> 1 nhdarea.5849  1.47e7 1999-10-28 23:00:00 Medium     " "     " "           1.36
#> # ... with 9 more variables: elevation <int>, ftype <chr>, fcode <int>,
#> #   shape_length <dbl>, shape_area <dbl>, onoffnet <int>, purpcode <chr>,
#> #   purpdesc <chr>, geometry <POLYGON [°]>
#> 
#> $NHDWaterbody
#> Simple feature collection with 90 features and 22 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -89.73095 ymin: 42.98903 xmax: -89.20938 ymax: 43.40565
#> Geodetic CRS:  NAD83
#> # A tibble: 90 x 23
#>    id          comid fdate               resolution gnis_id gnis_name   areasqkm
#>  * <chr>       <int> <dttm>              <chr>      <chr>   <chr>          <dbl>
#>  1 nhdwater~  1.47e7 1999-10-28 23:00:00 Medium     " "     " "            1.72 
#>  2 nhdwater~  1.36e7 1999-10-28 23:00:00 Medium     " "     " "            0.015
#>  3 nhdwater~  1.36e7 1999-10-28 23:00:00 Medium     "15769~ "Lake Wisc~   29.0  
#>  4 nhdwater~  1.36e7 1999-10-28 23:00:00 Medium     " "     " "            0.018
#>  5 nhdwater~  1.36e7 1999-10-28 23:00:00 Medium     " "     " "            0.016
#>  6 nhdwater~  1.36e7 1999-10-28 23:00:00 Medium     " "     " "            0.014
#>  7 nhdwater~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "            0.062
#>  8 nhdwater~  1.33e7 1999-10-28 23:00:00 Medium     "15737~ "Schoenber~    0.473
#>  9 nhdwater~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "            0.045
#> 10 nhdwater~  1.33e7 1999-10-28 23:00:00 Medium     " "     " "            0.123
#> # ... with 80 more rows, and 16 more variables: elevation <int>,
#> #   reachcode <chr>, ftype <chr>, fcode <int>, shape_length <dbl>,
#> #   shape_area <dbl>, onoffnet <int>, purpcode <chr>, purpdesc <chr>,
#> #   meandepth <dbl>, lakevolume <dbl>, maxdepth <dbl>, meandused <dbl>,
#> #   meandcode <chr>, lakearea <dbl>, geometry <POLYGON [°]>
#> 
#> $NHDFlowline_NonNetwork
#> Simple feature collection with 45 features and 13 fields
#> Geometry type: LINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: -89.62331 ymin: 43.04214 xmax: -89.25271 ymax: 43.35874
#> Geodetic CRS:  NAD83
#> # A tibble: 45 x 14
#>    id            comid fdate               resolution gnis_id gnis_name lengthkm
#>  * <chr>         <int> <dttm>              <chr>      <chr>   <chr>        <dbl>
#>  1 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           1.90
#>  2 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           1.80
#>  3 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           1.39
#>  4 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           2.36
#>  5 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           1.56
#>  6 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           2.87
#>  7 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           2.42
#>  8 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           2.12
#>  9 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           2.19
#> 10 nhdflowline~ 1.36e7 1999-10-28 19:00:00 Medium     " "     " "           1.29
#> # ... with 35 more rows, and 7 more variables: reachcode <chr>, flowdir <chr>,
#> #   wbareacomi <int>, ftype <chr>, fcode <int>, shape_length <dbl>,
#> #   geometry <LINESTRING [°]>
#> 

sf::st_layers(output_file)
#> Driver: GPKG 
#> Available layers:
#>               layer_name geometry_type features fields
#> 1    NHDFlowline_Network   Line String      168    138
#> 2            CatchmentSP       Polygon      167      7
#> 3                NHDArea       Polygon        1     15
#> 4           NHDWaterbody       Polygon       90     22
#> 5 NHDFlowline_NonNetwork   Line String       45     13

# NHDPlusHR
source(system.file("extdata/nhdplushr_data.R", package = "nhdplusTools"))

up_ids <- get_UT(hr_data$NHDFlowline, 15000500028335)

sub_gpkg <- file.path(work_dir, "sub.gpkg")
sub_nhdhr <- subset_nhdplus(up_ids, output_file = sub_gpkg,
                            nhdplus_data = hr_gpkg, overwrite = TRUE)
#> All intersections performed in latitude/longitude.
#> Reading NHDFlowline
#> 1000 comids of 1427
#> 1427 comids of 1427
#> Writing NHDFlowline
#> Reading NHDPlusCatchment
#> 1000 comids of 1427
#> 1427 comids of 1427
#> Found invalid geometry, attempting to fix.
#> Writing NHDPlusCatchment
#> Reading NHDArea
#> Writing NHDArea
#> Reading NHDWaterbody
#> Writing NHDWaterbody
#> Reading NHDPlusSink
#> No features to write in NHDPlusSink

sf::st_layers(sub_gpkg)
#> Driver: GPKG 
#> Available layers:
#>         layer_name geometry_type features fields
#> 1      NHDFlowline   Line String     1427     57
#> 2 NHDPlusCatchment Multi Polygon     1361      7
#> 3          NHDArea       Polygon        8     14
#> 4     NHDWaterbody       Polygon      741     15
names(sub_nhdhr)
#> [1] "NHDFlowline"      "NHDPlusCatchment" "NHDArea"          "NHDWaterbody"    
#> [5] "NHDPlusSink"     

plot(sf::st_geometry(hr_data$NHDFlowline), lwd = 0.5)
plot(sf::st_geometry(sub_nhdhr$NHDFlowline), lwd = 0.6, col = "red", add = TRUE)


unlink(output_file)
unlink(sub_gpkg)
# }