Author: dblodgett@usgs.gov

# Working with NHDPlusHR

#### dblodgett@usgs.gov

## TL;DR;

Most functions in `nhdplusTools` work with NHDPlus High Res (HR) the same as they do with medium res. The demo below shows how to get a single four-digit hydrologic unit worth of HR data, index a point to it, subset it, and plot the results.

Note: For consistency, identifiers from NHDPlusV2 are used with HiRes data. A future release of nhdplusTools may alter this behavior.

    library(nhdplusTools)
    library(sf)

    work_dir <- file.path(nhdplusTools_data_dir(), "hr_v_cache")

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

    hr_gpkg <- file.path(work_dir, "hr_data.gpkg")

    # Make a plot and get some background NHDPlusV2 data.
    plot_data <- plot_nhdplus(list("nwissite", "USGS-05428500"), streamorder = 3,
                              nhdplus_data = sample_data)

    # Find the HU04 we are interested in.
    hu04 <- unique(substr(plot_data$flowline$reachcode, 1, 4))

    # Download some NHDPlusHR Data
    hr_data_dir <- download_nhdplushr(work_dir, hu04)

    # Projection and simplification for demo purposes.
    hr <- get_nhdplushr(work_dir, out_gpkg = hr_gpkg,
                        proj = 3857)

    (start_index <- get_flowline_index(st_transform(hr$NHDFlowline, 5070),
                                       st_transform(plot_data$outlets, 5070),
                                       search_radius = 200)) # meters albers eq area
    #> defaulting to comid rather than permanent_identifier
    #> Warning in check_search_radius(search_radius, points): search_radius units not
    #> set, trying units of points CRS.
    #> Warning in force_linestring(x): converting to LINESTRING, this may be slow,
    #> check results
    #>   id          COMID      REACHCODE REACH_meas   offset
    #> 1  1 22001000032700 07090002006114    37.6572 87.71874

    ids <- get_UT(hr$NHDFlowline, start_index$COMID)
    #> defaulting to comid rather than permanent_identifier

    hr_subset <- subset_nhdplus(ids, nhdplus_data = hr_gpkg)

Now that we have both a four digit hydrologic unit worth of NHDPlusHR data and a subset upstream of a point of interest, we can plot things up and see what it looks like. This plot uses NHDPlusV2 as returned by `plot_nhdplus()` as a base layer and adds NHDPlusHR data on top of it.

    plot_nhdplus(list("nwissite", "USGS-05428500"), streamorder = 2,
                 nhdplus_data = sample_data, overwrite = TRUE,
                 plot_config = list(flowline = list(lwd = 2.5),
                                    basin = list(lwd = 3)))

    plot(st_geometry(hr$NHDPlusCatchment), lwd = 0.25, add = TRUE)
    plot(st_geometry(hr$NHDFlowline), col = "blue", lwd = 0.5, add = TRUE)

    plot(st_geometry(st_transform(hr_subset$NHDFlowline, 3857)),
         col = "cyan", lwd = 1, add = TRUE)

## Download

NHDPlusHR support in nhdplusTools begins with the function `download_nhdplushr()`. The NHDPlusHR can be downloaded in four digit hydrologic unit code subsets here. `download_nhdplushr()` facilitates downloading these subsets for as few or as many as you need. It takes a directory you want to save your output into and a vector of four digit (HU04) or two digit (HU02) hydrologic units. There is also an option to just return the URLs of the data that would be downloaded for you to use in some other process. Since the TL;DR; above already downloaded some data. The code below shows how to just get the URLs for a whole HU02 and what the output looks like on disk.

Note: Data for each HU02 are put in their own output folder.

    (hr_urls <- download_nhdplushr(work_dir, "06", download_files = FALSE))
    #> [1] "https://prd-tnm.s3.amazonaws.com/StagedProducts/Hydrography/NHDPlusHR/VPU/Current/GDB/NHDPLUS_H_0601_HU4_20220418_GDB.zip"
    #> [2] "https://prd-tnm.s3.amazonaws.com/StagedProducts/Hydrography/NHDPlusHR/VPU/Current/GDB/NHDPLUS_H_0602_HU4_20220418_GDB.zip"
    #> [3] "https://prd-tnm.s3.amazonaws.com/StagedProducts/Hydrography/NHDPlusHR/VPU/Current/GDB/NHDPLUS_H_0603_HU4_20220418_GDB.zip"
    #> [4] "https://prd-tnm.s3.amazonaws.com/StagedProducts/Hydrography/NHDPlusHR/VPU/Current/GDB/NHDPLUS_H_0604_HU4_20220418_GDB.zip"

    # already downloaded:
    list.files(hr_data_dir)
    #> [1] "NHDPLUS_H_0709_HU4_GDB.gdb" "NHDPLUS_H_0709_HU4_GDB.jpg"
    #> [3] "NHDPLUS_H_0709_HU4_GDB.xml"

## Basic functionality

The second part of nhdplusTools support for NHDPlusHR is a bit more involved. The entry point is a function called `get_nhdplushr()`. At it’s core, it will take a collection of NHDPlusHR subsets, open them up one by one and build a single output table for later use. It also 1. joins flowline attributes to the flowline geometry, 1. can return one or more selected layers, 1. can save the result to a standalone geopackage for later use, and 1. can make some attributes of a subset look like they are part of a standalone network rather than having references to downstream data that aren’t in the subset.

Using the data we downloaded in the TL;DR; intro, the code below demonstrates a few behaviors of `get_nhdplushr()`

First, if we just give it a directory containing HR data, it will give us back a list with flowlines and catchments as sf data.frames.

    hr <- get_nhdplushr(hr_data_dir)
    sapply(hr, class)
    #>      NHDFlowline  NHDPlusCatchment
    #> [1,] "sf"         "sf"
    #> [2,] "tbl_df"     "tbl_df"
    #> [3,] "tbl"        "tbl"
    #> [4,] "data.frame" "data.frame"
    plot(st_geometry(hr$NHDFlowline), lwd = (hr$NHDFlowline$StreamOrde / 6))

If we want more data, we can get any of the layer options listed in the `get_nhdplushr()` documentation.

    hr <- get_nhdplushr(hr_data_dir, layers = c("NHDFlowline", "NHDWaterbody", "NHDArea"))
    sapply(hr, class)
    #>      NHDFlowline  NHDWaterbody NHDArea
    #> [1,] "sf"         "sf"         "sf"
    #> [2,] "tbl_df"     "tbl_df"     "tbl_df"
    #> [3,] "tbl"        "tbl"        "tbl"
    #> [4,] "data.frame" "data.frame" "data.frame"
    sapply(hr, nrow)
    #>  NHDFlowline NHDWaterbody      NHDArea
    #>        34532        11444          499
    plot(st_geometry(hr$NHDFlowline), lwd = (hr$NHDFlowline$StreamOrde / 6), col = "blue")

    plot(c(st_geometry(hr$NHDWaterbody), st_geometry(hr$NHDArea)),
         col = "cyan", border = "cyan", lwd = 0.25, add = TRUE)

Since this function can work over large amounts of data and we don’t want to keep running it again and again, there is an option to save the results to a standalone database for later use.

    demo_gpkg <- file.path(work_dir, "demo.gpkg")
    hr <- get_nhdplushr(hr_data_dir, out_gpkg = demo_gpkg)
    st_layers(demo_gpkg)
    #> Driver: GPKG
    #> Available layers:
    #>         layer_name     geometry_type features fields crs_name
    #> 1      NHDFlowline Multi Line String    34532     57    NAD83
    #> 2 NHDPlusCatchment     Multi Polygon    42300      7    NAD83

## HR modification and filtering

Since NHDPlusHR data can be very large, `get_nhdplushr()` offers the ability to subset the data using a few filter options. Most of the filters are described in the manual page of the `get_hr_data()` utility function. 1. `min_size_sqkm` will remove flowlines under a certain size threshold. 1. `sim` will simplify all geometry to a given tolerance using `sf::st_simplify()`. 1. `proj` will project the output into the desired projection. 1. `keep_cols` is used to specify which attributes are desired in the output. 1. `rename` controls whether output is automatically renamed to be compatible with `nhdplusTools` functions.

Note: These options only operate on the flowline network.

    demo <- get_nhdplushr(hr_data_dir, layers = "NHDFlowline",
                                   min_size_sqkm = 50)
    plot(st_geometry(demo$NHDFlowline),
         lwd = demo$NHDFlowline$StreamOrde/4, col = "blue")

    demo <- get_nhdplushr(hr_data_dir, layers = "NHDFlowline",
                          min_size_sqkm = 100,
                          proj = "+init=epsg:5070", simp = 200,
                          keep_cols = c("COMID", "StreamOrde"))
    #> Warning in CPL_crs_from_input(x): GDAL Message 1: +init=epsg:XXXX syntax is
    #> deprecated. It might return a CRS with a non-EPSG compliant axis order. Further
    #> messages of this type will be suppressed.
    names(demo$NHDFlowline)
    #> [1] "COMID"      "StreamOrde" "Shape"
    plot(st_geometry(demo$NHDFlowline),
         lwd = demo$NHDFlowline$StreamOrde/4, col = "blue")

## Make Standalone Basins

The NHDPlus data model has some shared identifiers that can span very large distances. For example, the “Level Path Identifier” identifies an entire river from headwater to outlet using the “hydrologic sequence identifier” of the outlet. Similarly, the “Terminal Path Identifier” identifies an entire basin using the hydrologic sequence identifier of the terminal flowline (to the ocean or an inland sink). When creating subsets of NHDPlus data, many times, these attributes can identify flowlines that are not included in the subset. For most applications, this is not a problem, but in some cases, it is advantageous to adjust identifiers such that the subset appears to be a complete drainage basin with a true terminal outlet. `make_standalone()` accomplishes this task.

On a one by one basis, this may seam insignificant, but for workflows that need to work with arbitrary subsets and start from basin outlets, this functionality is useful. It has little impact on the data and is applied by default.

The example below shows how the outlet is modified. As described in the documentation os `make_standalone()` all related attributes upstream are also fixed such that the network is intact for further use.

    demo <- get_nhdplushr(hr_data_dir, layers = "NHDFlowline",
                        min_size_sqkm = 100, check_terminals = FALSE)

    # Create a standalone basin with the results for comparison.
    standalone_demo <- make_standalone(demo$NHDFlowline)

    demo_outlet <- dplyr::filter(demo$NHDFlowline, TotDASqKM == max(TotDASqKM))

    standalone_demo_outlet <- dplyr::filter(standalone_demo, TotDASqKM == max(TotDASqKM))

    broken_outlet <- dplyr::select(st_drop_geometry(demo_outlet),
                                   Hydroseq, TerminalPa, TerminalFl, LevelPathI)
    fixed_outlet <- dplyr::select(st_drop_geometry(standalone_demo_outlet),
                                  Hydroseq, TerminalPa, TerminalFl, LevelPathI)

    print(data.frame(broken_outlet))
    #>         Hydroseq     TerminalPa TerminalFl     LevelPathI
    #> 1 22001000000414 22000100000212          0 22000300045683
    print(data.frame(fixed_outlet))
    #>         Hydroseq     TerminalPa TerminalFl     LevelPathI
    #> 1 22001000000414 22001000000414          1 22001000000414

    (broken <- dplyr::filter(demo$NHDFlowline, TerminalPa == demo_outlet$Hydroseq))
    #> Simple feature collection with 0 features and 57 fields
    #> Geometry type: MULTILINESTRING
    #> Bounding box:  xmin: NA ymin: NA xmax: NA ymax: NA
    #> Geodetic CRS:  NAD83
    #> # A tibble: 0 × 58
    #> # ℹ 58 variables: Permanent_Identifier <chr>, FDate <dttm>, Resolution <int>,
    #> #   GNIS_ID <chr>, GNIS_Name <chr>, LENGTHKM <dbl>, REACHCODE <chr>,
    #> #   FlowDir <int>, WBArea_Permanent_Identifier <chr>, FTYPE <int>, FCODE <int>,
    #> #   MainPath <int>, InNetwork <int>, VisibilityFilter <int>,
    #> #   Shape_Length <dbl>, COMID <dbl>, VPUID <chr>, Enabled <int>,
    #> #   Shape <MULTILINESTRING [°]>, StreamLeve <int>, StreamOrde <int>,
    #> #   StreamCalc <int>, FromNode <dbl>, ToNode <dbl>, Hydroseq <dbl>, …
    (standalone <- dplyr::filter(standalone_demo, TerminalPa == standalone_demo_outlet$Hydroseq))
    #> Simple feature collection with 5358 features and 57 fields
    #> Geometry type: MULTILINESTRING
    #> Dimension:     XY
    #> Bounding box:  xmin: -90.68076 ymin: 41.27482 xmax: -88.1999 ymax: 43.74949
    #> Geodetic CRS:  NAD83
    #> # A tibble: 5,358 × 58
    #>    Permanent_Identifier FDate               Resolution GNIS_ID  GNIS_Name
    #>  * <chr>                <dttm>                   <int> <chr>    <chr>
    #>  1 156038282            2012-03-19 01:32:25          2 00415503 Pecatonica River
    #>  2 155714162            2014-10-28 19:00:00          2 00424882 Fairfield Ditch…
    #>  3 156035374            2012-03-19 01:35:08          2 01561947 Gordon Creek
    #>  4 145600320            2012-03-19 01:34:47          2 00416806 Rock Creek
    #>  5 155712981            2012-03-19 02:05:44          2 <NA>     <NA>
    #>  6 137417698            2012-03-18 13:07:31          2 01575030 Sugar River
    #>  7 156037500            2012-03-19 01:33:10          2 <NA>     <NA>
    #>  8 145599800            2012-03-19 01:34:47          2 00414599 North Fork Kent…
    #>  9 143246785            2012-03-18 12:56:43          2 00416824 Rock River
    #> 10 155712415            2012-03-19 02:05:51          2 00424170 Willow Creek
    #> # ℹ 5,348 more rows
    #> # ℹ 53 more variables: LENGTHKM <dbl>, REACHCODE <chr>, FlowDir <int>,
    #> #   WBArea_Permanent_Identifier <chr>, FTYPE <int>, FCODE <int>,
    #> #   MainPath <int>, InNetwork <int>, VisibilityFilter <int>,
    #> #   Shape_Length <dbl>, COMID <dbl>, VPUID <chr>, Enabled <int>,
    #> #   Shape <MULTILINESTRING [°]>, StreamLeve <int>, StreamOrde <int>,
    #> #   StreamCalc <int>, FromNode <dbl>, ToNode <dbl>, Hydroseq <dbl>, …

    plot(st_geometry(standalone))