Merge pull request #324 from DOI-USGS/hydroloom

Hydroloom - tracking PR

.Rbuildignore

@@ -8,14 +8,12 @@ inst/doc/*.html
 docs
 _pkgdown.yml
 data-raw
-vignettes/rosm.cache
 DISCLAIMER.md
 code.json
 ^doc$
 ^Meta$
 .Renviron
 tests/testthat/data/03
-rosm.cache
 pkgdown
 .gitlab-ci.yml
 .github

.dockerignore

@@ -3,7 +3,6 @@
 pkgdown
 docs
 data-raw
-rosm.cache
 .Renviron
 .Rproj.user
 .Rhistory

.github/workflows/R-CMD-check.yaml

@@ -32,7 +32,6 @@ jobs:
         with:
             r-version: ${{ matrix.config.r }}
             use-public-rspm: true
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck, any::covr

.gitignore

@@ -17,3 +17,4 @@ pkgdown
 cran-comments.md
 .Renviron
 CRAN-SUBMISSION
+temp.R

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: nhdplusTools
 Type: Package
 Title: NHDPlus Tools
-Version: 0.7.0
+Version: 1.0.0
 Authors@R: c(person(given = "David", 
                     family = "Blodgett", 
                     role = c("aut", "cre"), 
@@ -18,14 +18,18 @@ Authors@R: c(person(given = "David",
             person(given = "Josh", 
                    family = "Erickson", 
                    role = "ctb", 
-                   email = "[email protected]"))
+                   email = "[email protected]"),
+            person(given = "Lauren",
+                   family = "Koenig",
+                   role = "ctb",
+                   comment = c(ORCID = "0000-0002-7790-330X")))
 Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
 URL: https://doi-usgs.github.io/nhdplusTools/ https://github.com/doi-usgs/nhdplusTools/
 BugReports: https://github.com/doi-usgs/nhdplusTools/issues/
 Depends:
     R (>= 4.0)
-Imports: dplyr, rlang, sf, RANN, units, magrittr, jsonlite, httr, xml2, R.utils, utils, tidyr, methods, rosm, prettymapr, fst, dataRetrieval, tools, zip, pbapply, arrow
-Suggests: testthat, knitr, rmarkdown, markdown, ggmap, ggplot2, sp, lwgeom, devtools, codetools, data.table, parallel, s2, gifski, leaflet, httptest
+Imports: hydroloom, dplyr, sf, units, magrittr, jsonlite, httr, xml2, R.utils, utils, tidyr, methods, maptiles, mapsf, fst, arrow, dataRetrieval, tools, zip, pbapply, future.apply
+Suggests: testthat, knitr, rmarkdown, markdown, ggmap, ggplot2, sp, lwgeom, devtools, codetools, data.table, parallel, s2, gifski, leaflet, httptest, future
 License: CC0
 Encoding: UTF-8
 RoxygenNote: 7.2.3

NAMESPACE

@@ -7,6 +7,7 @@ export(calculate_total_drainage_area)
 export(disambiguate_flowline_indexes)
 export(discover_nhdplus_id)
 export(discover_nldi_characteristics)
+export(download_nhd)
 export(download_nhdplushr)
 export(download_nhdplusv2)
 export(download_rf1)
@@ -71,18 +72,15 @@ export(rename_geometry)
 export(rescale_catchment_characteristics)
 export(rescale_measures)
 export(st_compatibalize)
-export(stage_national_data)
 export(subset_nhdplus)
 export(subset_rpu)
 export(subset_vpu)
-importFrom(RANN,nn2)
 importFrom(arrow,open_dataset)
 importFrom(arrow,s3_bucket)
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
-importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,collect)
 importFrom(dplyr,desc)
@@ -91,17 +89,13 @@ importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_split)
-importFrom(dplyr,lag)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
-importFrom(dplyr,n)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
 importFrom(dplyr,right_join)
-importFrom(dplyr,row_number)
 importFrom(dplyr,select)
 importFrom(dplyr,starts_with)
-importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(fst,metadata_fst)
@@ -111,33 +105,52 @@ importFrom(httr,POST)
 importFrom(httr,RETRY)
 importFrom(httr,progress)
 importFrom(httr,write_disk)
+importFrom(hydroloom,accumulate_downstream)
+importFrom(hydroloom,add_levelpaths)
+importFrom(hydroloom,add_pathlength)
+importFrom(hydroloom,add_pfafstetter)
+importFrom(hydroloom,add_streamlevel)
+importFrom(hydroloom,add_streamorder)
+importFrom(hydroloom,add_toids)
+importFrom(hydroloom,disambiguate_indexes)
+importFrom(hydroloom,fix_flowdir)
+importFrom(hydroloom,get_hydro_location)
+importFrom(hydroloom,get_node)
+importFrom(hydroloom,get_partial_length)
+importFrom(hydroloom,hy)
+importFrom(hydroloom,index_points_to_lines)
+importFrom(hydroloom,index_points_to_waterbodies)
+importFrom(hydroloom,make_fromids)
+importFrom(hydroloom,make_index_ids)
+importFrom(hydroloom,navigate_connected_paths)
+importFrom(hydroloom,navigate_hydro_network)
+importFrom(hydroloom,rename_geometry)
+importFrom(hydroloom,rescale_measures)
+importFrom(hydroloom,sort_network)
+importFrom(hydroloom,st_compatibalize)
 importFrom(jsonlite,fromJSON)
-importFrom(magrittr,"%>%")
+importFrom(magrittr,`%>%`)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(pbapply,pbapply)
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pboptions)
-importFrom(rlang,.data)
 importFrom(sf,"st_geometry<-")
 importFrom(sf,read_sf)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_as_sfc)
 importFrom(sf,st_bbox)
 importFrom(sf,st_buffer)
 importFrom(sf,st_cast)
-importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
 importFrom(sf,st_distance)
 importFrom(sf,st_drop_geometry)
 importFrom(sf,st_filter)
 importFrom(sf,st_geometry)
 importFrom(sf,st_geometry_type)
-importFrom(sf,st_join)
 importFrom(sf,st_layers)
 importFrom(sf,st_multilinestring)
 importFrom(sf,st_nearest_feature)
-importFrom(sf,st_reverse)
 importFrom(sf,st_sf)
 importFrom(sf,st_simplify)
 importFrom(sf,st_transform)
@@ -146,6 +159,7 @@ importFrom(sf,write_sf)
 importFrom(stats,weighted.mean)
 importFrom(tidyr,contains)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,replace_na)
 importFrom(tools,R_user_dir)
 importFrom(utils,combn)
 importFrom(utils,download.file)

NEWS.md

@@ -1,3 +1,58 @@
+nhdplusTools 1.0.0
+==========
+
+## `hydroloom` 
+
+v1.0.0 should be backward compatible with v0.7 but deprecation warnings have been added and one previously deprecated function has been removed. 
+
+This release evolves `nhdplusTools` to use [`hydroloom`](https://doi-usgs.github.io/hydroloom/articles/hydroloom.html) as a core dependency. `nhdplusTools` now depends on `hydroloom` for all network navigation and indexing functionality that is not specific to the nhdplus data model or specific to a US-context.
+
+Specific functions imported from [`hydroloom`](https://doi-usgs.github.io/hydroloom/articles/hydroloom.html) include:
+
+- hy
+- accumulate_downstream
+- add_levelpaths
+- add_pathlength
+- add_pfafstetter
+- add_streamlevel
+- add_streamorder
+- add_toids
+- disambiguate_indexes
+- fix_flowdir
+- get_hydro_location
+- get_node
+- get_partial_length
+- index_points_to_lines
+- index_points_to_waterbodies
+- make_fromids
+- make_index_ids
+- navigate_connected_paths
+- navigate_hydro_network
+- rename_geometry
+- rescale_measures
+- sort_network
+- st_compatibalize
+
+[See the `hydroloom` reference list for details about these functions.](https://doi-usgs.github.io/hydroloom/reference/index.html)
+
+With these functions migrated to hydroloom, a number of `nhdplusTools` functions are now deprecated in favor of the `hyroloom` implementation.
+
+- `make_node_topology()`
+- `get_pfaf()`
+- `get_path_members()`
+- `get_path_lengths()`
+- `get_levelpaths()`
+- `get_terminal()`
+- `make_node_topology()`
+
+In v1.0.0, the `download_nhd()` function was added.
+
+In v1.0.0, the stage_national_data (previously deprecated) function was removed.
+
+nhdplusTools 0.7.1
+==========
+This release fixes a minor example issue for CRAN checks
+
 nhdplusTools 0.7.0
 ==========
 This release adds three new functions.

R/A_nhdplusTools.R

@@ -3,7 +3,7 @@ vaa_hydroshare <-
   'https://www.hydroshare.org/resource/6092c8a62fac45be97a09bfd0b0bf726/data/contents/nhdplusVAA.fst'
 
 vaa_sciencebase <-
-  'https://www.sciencebase.gov/catalog/file/get/60c92503d34e86b9389df1c9?name=enhd_nhdplusatts.fst'
+  'https://www.sciencebase.gov/catalog/file/get/63cb311ed34e06fef14f40a3?name=enhd_nhdplusatts.fst'
 
 nhdplusTools_env <- new.env()
 
@@ -249,10 +249,11 @@ default_nhdplus_path <- "../NHDPlusV21_National_Seamless.gdb"
 
 assign("default_nhdplus_path", default_nhdplus_path, envir = nhdplusTools_env)
 
-nhdhr_bucket <- "https://prd-tnm.s3.amazonaws.com/"
+nhd_bucket <- "https://prd-tnm.s3.amazonaws.com/"
 nhdhr_file_list <- "?prefix=StagedProducts/Hydrography/NHDPlusHR/Beta/GDB/"
+nhd_file_list <- "?prefix=StagedProducts/Hydrography/NHD/HU4/GDB/"
 
-assign("nhdhr_bucket", nhdhr_bucket, envir = nhdplusTools_env)
+assign("nhd_bucket", nhd_bucket, envir = nhdplusTools_env)
 assign("nhdhr_file_list", nhdhr_file_list, envir = nhdplusTools_env)
 
 assign("nhdpt_dat_dir",
@@ -391,65 +392,6 @@ align_nhdplus_names <- function(x){
 
 }
 
-# TODO: deprecate moved to hydroloom
-drop_geometry <- function(x) {
-  if("sf" %in% class(x)) {
-    sf::st_drop_geometry(x)
-  } else {
-    x
-  }
-}
-
-# TODO: deprecate moved to hydroloom
-#' make spatial inputs compatible
-#' @description makes sf1 compatible with sf2 by projecting into
-#' the projection of 2 and ensuring that the geometry columns are the
-#' same name.
-#' @param sf1 sf data.frame
-#' @param sf2 sf data.frame
-#' @export
-#' @examples
-#'
-#' source(system.file("extdata", "sample_flines.R", package = "nhdplusTools"))
-#'
-#' (one <- dplyr::select(sample_flines))
-#' (two <- sf::st_transform(one, 5070))
-#'
-#' attr(one, "sf_column") <- "geotest"
-#' names(one)[names(one) == "geom"] <- "geotest"
-#'
-#' st_compatibalize(one, two)
-#'
-st_compatibalize <- function(sf1, sf2) {
-
-  sf1 <- st_transform(sf1, st_crs(sf2))
-
-  rename_geometry(sf1, attr(sf2, "sf_column"))
-
-}
-
-# TODO: deprecate moved to hydroloom
-#' rename_geometry
-#' @description correctly renames the geometry column
-#' of a sf object.
-#' @param g sf data.table
-#' @param name character name to be used for geometry
-#' @export
-#' @examples
-#'
-#' (g <- sf::st_sf(a=3, geo = sf::st_sfc(sf::st_point(1:2))))
-#' rename_geometry(g, "geometry")
-#'
-rename_geometry <- function(g, name){
-  current = attr(g, "sf_column")
-
-  names(g)[names(g)==current] = name
-
-  attr(g, "sf_column") <- name
-
-  g
-}
-
 get_cl <- function(cl) {
   if(!is.null(cl)) {
     if(!requireNamespace("parallel", quietly = TRUE)) {
@@ -465,3 +407,31 @@ get_cl <- function(cl) {
   }
   return(cl)
 }
+
+#' @importFrom hydroloom st_compatibalize
+#' @export
+hydroloom::st_compatibalize
+
+#' @importFrom hydroloom rename_geometry
+#' @export
+hydroloom::rename_geometry
+
+#' @importFrom hydroloom get_node
+#' @export
+hydroloom::get_node
+
+#' @importFrom hydroloom fix_flowdir
+#' @export
+hydroloom::fix_flowdir
+
+#' @importFrom hydroloom rescale_measures
+#' @export
+hydroloom::rescale_measures
+
+#' @importFrom hydroloom get_hydro_location
+#' @export
+hydroloom::get_hydro_location
+
+#' @importFrom hydroloom get_partial_length
+#' @export
+hydroloom::get_partial_length