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_pathhas 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 × 137
#> COMID FDATE RESOLU…¹ GNIS_ID GNIS_…² LENGT…³ REACH…⁴ FLOWDIR
#> * <int> <dttm> <chr> <chr> <chr> <dbl> <chr> <chr>
#> 1 13293750 1999-10-29 00:00:00 Medium 1577073 Yahara… 1.72 070900… With D…
#> 2 13293504 1999-10-29 00:00:00 Medium 1577073 Yahara… 1.41 070900… With D…
#> 3 13294134 1999-10-29 00:00:00 Medium 1577073 Yahara… 0.74 070900… With D…
#> 4 13294128 1999-10-29 00:00:00 Medium 1577073 Yahara… 3.70 070900… With D…
#> 5 13294394 1999-10-29 00:00:00 Medium 1577073 Yahara… 0.077 070900… With D…
#> 6 13293454 1999-10-29 00:00:00 Medium 1577073 Yahara… 0.94 070900… With D…
#> 7 13293430 1999-10-29 00:00:00 Medium 1577073 Yahara… 1.14 070900… With D…
#> 8 13293424 1999-10-29 00:00:00 Medium 1577073 Yahara… 1.27 070900… With D…
#> 9 13294110 1999-10-29 00:00:00 Medium 1577073 Yahara… 7.48 070900… With D…
#> 10 13293398 1999-10-29 00:00:00 Medium 1577073 Yahara… 0.082 070900… With D…
#> # … with 158 more rows, 129 more variables: 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>, FromMeas <dbl>, ToMeas <dbl>, …
#>
#> $CatchmentSP
#> Simple feature collection with 167 features and 6 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: -89.60479 ymin: 43.03507 xmax: -89.20378 ymax: 43.36607
#> Geodetic CRS: NAD83
#> # A tibble: 167 × 7
#> GRIDCODE FEATUREID SOURCEFC AreaS…¹ Shape…² Shape…³ geom
#> * <int> <int> <chr> <dbl> <dbl> <dbl> <MULTIPOLYGON [°]>
#> 1 1085160 13293454 NHDFlow… 0.328 0.0256 3.64e-5 (((-89.34777 43.20671, -…
#> 2 1085219 13293750 NHDFlow… 6.69 0.148 7.40e-4 (((-89.38126 43.07518, -…
#> 3 1085247 13294134 NHDFlow… 0.261 0.0307 2.88e-5 (((-89.35547 43.18545, -…
#> 4 1085414 13293570 NHDFlow… 0.0514 0.00963 5.69e-6 (((-89.41468 43.15295, -…
#> 5 1085447 13293430 NHDFlow… 1.63 0.0780 1.81e-4 (((-89.35208 43.20989, -…
#> 6 1085448 13293526 NHDFlow… 0.0690 0.0117 7.64e-6 (((-89.34975 43.16686, -…
#> 7 1085463 13293588 NHDFlow… 0.429 0.0404 4.75e-5 (((-89.42608 43.14793, -…
#> 8 1085478 13293614 NHDFlow… 3.15 0.0953 3.48e-4 (((-89.58446 43.13534, -…
#> 9 1085502 13294264 NHDFlow… 24.8 0.348 2.75e-3 (((-89.53449 43.05226, -…
#> 10 1085509 13293384 NHDFlow… 0.291 0.0296 3.23e-5 (((-89.33033 43.27117, -…
#> # … with 157 more rows, and abbreviated variable names ¹AreaSqKM,
#> # ²Shape_Length, ³Shape_Area
#>
#> $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 crs_name
#> 1 NHDFlowline_Network Line String 168 136 NAD83
#> 2 CatchmentSP Multi Polygon 167 6 NAD83
#> 3 NHDArea Polygon 1 14 NAD83
#> 4 NHDWaterbody Polygon 90 21 NAD83
#> 5 NHDFlowline_NonNetwork Line String 45 12 NAD83
#> 6 Gage Point 33 19 NAD83
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
#> Spherical geometry (s2) switched off
#> Spherical geometry (s2) switched on
#> Writing NHDFlowline_Network
#> Reading CatchmentSP
#> Spherical geometry (s2) switched off
#> Spherical geometry (s2) switched on
#> Writing CatchmentSP
#> Spherical geometry (s2) switched off
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#> Spherical geometry (s2) switched on
#> Spherical geometry (s2) switched off
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#> Spherical geometry (s2) switched on
#> Spherical geometry (s2) switched off
#> although coordinates are longitude/latitude, st_intersects assumes that they
#> are planar
#> Spherical geometry (s2) switched on
#> $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 × 139
#> id comid fdate resol…¹ gnis_id gnis_…² lengt…³ reach…⁴
#> * <chr> <int> <dttm> <chr> <chr> <chr> <dbl> <chr>
#> 1 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium " " " " 3.04 070900…
#> 2 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium " " " " 1.44 070900…
#> 3 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium "15770… "Yahar… 4.84 070900…
#> 4 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium " " " " 4.40 070900…
#> 5 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium "15770… "Yahar… 0.839 070900…
#> 6 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium " " " " 4.67 070900…
#> 7 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium "15770… "Yahar… 0.402 070900…
#> 8 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium " " " " 1.08 070900…
#> 9 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium "15770… "Yahar… 1.12 070900…
#> 10 nhdflowli… 1.33e7 1999-10-28 23:00:00 Medium " " " " 0.351 070900…
#> # … with 158 more rows, 131 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>, frommeas <dbl>, …
#>
#> $CatchmentSP
#> Simple feature collection with 167 features and 7 fields
#> Geometry type: MULTIPOLYGON
#> Dimension: XY
#> Bounding box: xmin: -89.60479 ymin: 43.03507 xmax: -89.20378 ymax: 43.36607
#> Geodetic CRS: NAD83
#> # A tibble: 167 × 8
#> id gridcode featureid sourcefc areasqkm shape_le…¹ shape…²
#> * <chr> <int> <int> <chr> <dbl> <dbl> <dbl>
#> 1 catchmentsp.948294 1085512 13293376 NHDFlowline 47.8 0.465 5.30e-3
#> 2 catchmentsp.948495 1085714 13293378 NHDFlowline 3.30 0.0899 3.66e-4
#> 3 catchmentsp.948432 1085651 13293380 NHDFlowline 19.1 0.247 2.12e-3
#> 4 catchmentsp.948531 1085750 13293382 NHDFlowline 12.1 0.197 1.35e-3
#> 5 catchmentsp.948291 1085509 13293384 NHDFlowline 0.291 0.0296 3.23e-5
#> 6 catchmentsp.948759 1085979 13293386 NHDFlowline 9.94 0.175 1.10e-3
#> 7 catchmentsp.948299 1085517 13293388 NHDFlowline 0.154 0.0187 1.71e-5
#> 8 catchmentsp.948549 1085768 13293390 NHDFlowline 1.41 0.0612 1.57e-4
#> 9 catchmentsp.948386 1085605 13293392 NHDFlowline 0.461 0.0393 5.11e-5
#> 10 catchmentsp.948674 1085893 13293394 NHDFlowline 0.0796 0.0124 8.82e-6
#> # … with 157 more rows, 1 more variable: geometry <MULTIPOLYGON [°]>, and
#> # abbreviated variable names ¹shape_length, ²shape_area
#>
#> $NHDArea
#> Simple feature collection with 1 feature and 15 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: -89.40194 ymin: 43.15016 xmax: -89.36131 ymax: 43.18112
#> Geodetic CRS: NAD83
#> # A tibble: 1 × 16
#> id comid fdate resol…¹ gnis_id gnis_…² areas…³ eleva…⁴ ftype
#> * <chr> <int> <dttm> <chr> <chr> <chr> <dbl> <int> <chr>
#> 1 nhda… 1.47e7 1999-10-28 23:00:00 Medium " " " " 1.36 0 Stre…
#> # … with 7 more variables: fcode <int>, shape_length <dbl>, shape_area <dbl>,
#> # onoffnet <int>, purpcode <chr>, purpdesc <chr>, geometry <POLYGON [°]>, and
#> # abbreviated variable names ¹resolution, ²gnis_name, ³areasqkm, ⁴elevation
#>
#> $NHDWaterbody
#> Simple feature collection with 90 features and 22 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: -89.72879 ymin: 42.9897 xmax: -89.20939 ymax: 43.40395
#> Geodetic CRS: NAD83
#> # A tibble: 90 × 23
#> id comid fdate resol…¹ gnis_id gnis_…² areas…³ eleva…⁴
#> * <chr> <int> <dttm> <chr> <chr> <chr> <dbl> <int>
#> 1 nhdwaterb… 1.47e7 1999-10-28 23:00:00 Medium " " " " 1.72 0
#> 2 nhdwaterb… 1.36e7 1999-10-28 23:00:00 Medium " " " " 0.015 0
#> 3 nhdwaterb… 1.36e7 1999-10-28 23:00:00 Medium "15769… "Lake … 29.0 236
#> 4 nhdwaterb… 1.36e7 1999-10-28 23:00:00 Medium " " " " 0.018 0
#> 5 nhdwaterb… 1.36e7 1999-10-28 23:00:00 Medium " " " " 0.016 0
#> 6 nhdwaterb… 1.36e7 1999-10-28 23:00:00 Medium " " " " 0.014 0
#> 7 nhdwaterb… 1.33e7 1999-10-28 23:00:00 Medium " " " " 0.062 0
#> 8 nhdwaterb… 1.33e7 1999-10-28 23:00:00 Medium "15737… "Schoe… 0.473 0
#> 9 nhdwaterb… 1.33e7 1999-10-28 23:00:00 Medium " " " " 0.045 0
#> 10 nhdwaterb… 1.33e7 1999-10-28 23:00:00 Medium " " " " 0.123 0
#> # … with 80 more rows, 15 more variables: 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 [°]>, and abbreviated variable names ¹resolution,
#> # ²gnis_name, ³areasqkm, ⁴elevation
#>
#> $NHDFlowline_NonNetwork
#> Simple feature collection with 45 features and 13 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: -89.62331 ymin: 43.04214 xmax: -89.25271 ymax: 43.35874
#> Geodetic CRS: NAD83
#> # A tibble: 45 × 14
#> id comid fdate resol…¹ gnis_id gnis_…² lengt…³ reach…⁴
#> * <chr> <int> <dttm> <chr> <chr> <chr> <dbl> <chr>
#> 1 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 1.90 070700…
#> 2 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 1.80 070700…
#> 3 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 1.39 070700…
#> 4 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 2.36 070700…
#> 5 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 1.56 070700…
#> 6 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 2.87 070700…
#> 7 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 2.42 070700…
#> 8 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 2.12 070700…
#> 9 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 2.19 070700…
#> 10 nhdflowli… 1.36e7 1999-10-28 19:00:00 Medium " " " " 1.29 070700…
#> # … with 35 more rows, 6 more variables: flowdir <chr>, wbareacomi <int>,
#> # ftype <chr>, fcode <int>, shape_length <dbl>, geometry <LINESTRING [°]>,
#> # and abbreviated variable names ¹resolution, ²gnis_name, ³lengthkm,
#> # ⁴reachcode
#>
sf::st_layers(output_file)
#> Driver: GPKG
#> Available layers:
#> layer_name geometry_type features fields crs_name
#> 1 NHDFlowline_Network Line String 168 138 NAD83
#> 2 CatchmentSP Multi Polygon 167 7 NAD83
#> 3 NHDArea Polygon 1 15 NAD83
#> 4 NHDWaterbody Polygon 90 22 NAD83
#> 5 NHDFlowline_NonNetwork Line String 45 13 NAD83
# NHDPlusHR
source(system.file("extdata/nhdplushr_data.R", package = "nhdplusTools"))
up_ids <- get_UT(hr_data$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 crs_name
#> 1 NHDFlowline Line String 1427 57 NAD83
#> 2 NHDPlusCatchment Multi Polygon 1361 7 NAD83
#> 3 NHDArea Polygon 8 14 NAD83
#> 4 NHDWaterbody Polygon 740 15 NAD83
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)
# }