get checks working, rename nexus_topology file (ignored by roxygen?)

.Rbuildignore

@@ -1,7 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 LICENSE
-.travis.yml
 .lintr
 inst/doc/*.html
 docs
@@ -19,6 +18,9 @@ Dockerfile
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-runners
-dead
 ^LICENSE\.md$
+^data/raw-data$
+^data/derived-data$
+^outputs$
+^figures$
+^analyses$

DESCRIPTION

@@ -19,6 +19,7 @@ Imports:
     dplyr,
     glue,
     httr,
+    hydroloom,
     igraph,
     logger,
     lwgeom,
@@ -30,15 +31,15 @@ Imports:
     rmapshaper,
     rvest,
     sf,
+    stats,
     terra,
     tibble,
     tidyr,
     units,
     utils,
     yyjsonr
 Suggests: 
-    testthat,
-    knitr
+    testthat
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -10,13 +10,16 @@ export(add_lookup_table)
 export(add_mapped_hydrolocations)
 export(add_measures)
 export(add_nonnetwork_divides)
+export(add_nonnetwork_nexus_location)
+export(add_prefix)
 export(agg_length_area)
 export(aggregate_along_mainstems)
 export(aggregate_network_to_outlets)
 export(aggregate_sets)
 export(aggregate_to_distribution)
 export(aggregate_to_outlets)
 export(append_style)
+export(apply_nexus_topology)
 export(assign_global_identifiers)
 export(assign_id)
 export(build_collapse_table)
@@ -47,6 +50,7 @@ export(pinch_sides)
 export(prep_split_events)
 export(prepare_network)
 export(read_hydrofabric)
+export(realign_topology)
 export(reconcile_catchment_divides)
 export(reconcile_collapsed_flowlines)
 export(refactor)
@@ -124,6 +128,7 @@ importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
 importFrom(pbapply,pblapply)
 importFrom(rlang,":=")
+importFrom(rlang,`:=`)
 importFrom(rlang,sym)
 importFrom(rmapshaper,check_sys_mapshaper)
 importFrom(rmapshaper,ms_dissolve)
@@ -164,6 +169,7 @@ importFrom(sf,st_make_valid)
 importFrom(sf,st_multipolygon)
 importFrom(sf,st_nearest_feature)
 importFrom(sf,st_point)
+importFrom(sf,st_point_on_surface)
 importFrom(sf,st_precision)
 importFrom(sf,st_read)
 importFrom(sf,st_segmentize)

R/nexus_topology.R → R/topo.R

@@ -1,3 +1,28 @@
+#' Add small area to crosswalk
+#' @param crosswalk an existing crosswalk table
+#' @param comid the shared ID
+#' @return data.frame
+#' @importFrom rlang `:=`
+#' @export
+
+add_areasqkm_to_crosswalk = function(crosswalk, comid = "hf_id"){
+  get_vaa('areasqkm') %>% 
+    select(s_areasqkm = areasqkm, !!comid := comid) %>% 
+    right_join(crosswalk, by = eval(comid)) 
+}
+
+
+#' @title Add Prefixes to Topological Data
+#' @description This function adds specified prefixes to the `id` and `toid` columns of a topological data frame based on the type of topology and its context (e.g., network or nexus).
+#' @param topo A data frame containing topological data. Must include columns `topo_type`, `type`, `id`, and `toid`.
+#' @param hf_prefix A character string to prefix `id` values in rows where `topo_type == "network"`. Default is `"cat-"`.
+#' @param nexus_prefix A character string to prefix `toid` values in rows where `type` does not match specific cases (`terminal`, `coastal`, or `internal`). Default is `"nex-"`.
+#' @param terminal_nexus_prefix A character string to prefix `toid` values where `type == "terminal"`. Default is `"tnx-"`.
+#' @param coastal_nexus_prefix A character string to prefix `toid` values where `type == "coastal"`. Default is `"cnx-"`.
+#' @param internal_nexus_prefix A character string to prefix `toid` values where `type == "internal"`. Default is `"inx-"`.
+#' @return A data frame with updated `id` and `toid` values, including appropriate prefixes based on the type of topology and the `type` column. The resulting data frame contains the columns `id`, `toid`, `type`, and any additional columns with names containing `"vpu"`.
+#' @export
+
 add_prefix = function(topo,
                       hf_prefix = "cat-",
                       nexus_prefix = "nex-",
@@ -33,7 +58,15 @@ add_prefix = function(topo,
 
 }
 
-
+#' @title Remove Prefixes from Columns
+#' @description This function removes prefixes from specified columns in a data frame by extracting the numeric portion of the values after the last `-` character.
+#' @param input A data frame containing the columns to be processed.
+#' @param col A character vector specifying the names of the columns from which to remove prefixes.
+#' @return The input data frame with the specified columns updated. The values in these columns are converted to numeric, retaining only the portion after the last `-` character.
+#' @details 
+#' - The function processes each specified column by removing the prefix up to and including the last `-` character using a regular expression.
+#' - The updated columns are converted to numeric values.
+#' @export
 
 flush_prefix	 = function (input, col) {
   for (i in col) {
@@ -42,6 +75,23 @@ flush_prefix	 = function (input, col) {
   input
 }
 
+#' @title Add Non-Network Nexus Locations
+#' @description This function generates spatial points for non-network nexus locations (coastal and internal) based on the provided divides. It assigns unique identifiers and links them to waterbody identifiers.
+#' @param divides A spatial data frame (e.g., `sf` object) containing polygons representing divides. Must include columns `type`, `divide_id`, and `toid`.
+#' @param coastal_nexus_prefix A character string to prefix `divide_id` values for coastal nexus locations. Default is `"cnx-"`.
+#' @param internal_nexus_prefix A character string to prefix `divide_id` values for internal nexus locations. Default is `"inx-"`.
+#' @param waterbody_prefix A character string to prefix `toid` values for non-network nexus locations. Default is `"wb-"`.
+#' @return A spatial data frame (e.g., `sf` object) containing the non-network nexus locations. The resulting data frame includes the columns:
+#' - `id`: Unique identifier for each nexus location (prefixed with `coastal_nexus_prefix` or `internal_nexus_prefix`).
+#' - `toid`: Linked waterbody identifier (prefixed with `waterbody_prefix`).
+#' - `type`: The type of nexus (`coastal` or `internal`).
+#' - `geometry`: The spatial location of each nexus.
+#' @details
+#' - For each divide of type `coastal` or `internal`, the function calculates a representative point using `st_point_on_surface`.
+#' - Prefixes are applied to `divide_id` and `toid` values using `flush_prefix` and `mutate`.
+#' - The output retains only the columns `id`, `toid`, `type`, and geometry.
+#' @export
+
 add_nonnetwork_nexus_location  = function(divides,
                                           coastal_nexus_prefix = "cnx-",
                                           internal_nexus_prefix = "inx-",
@@ -69,7 +119,7 @@ add_nonnetwork_nexus_location  = function(divides,
 }
 
 
-#' Realign Topology to a nexus network
+#' @title Realign Topology to a nexus network
 #' @param network_list          list containing flowpath and catchment `sf` objects
 #' @param nexus_prefix          character prefix for nexus IDs
 #' @param terminal_nexus_prefix character prefix for terminal nexus IDs
@@ -82,12 +132,6 @@ add_nonnetwork_nexus_location  = function(divides,
 #' @importFrom  dplyr select mutate left_join bind_rows group_by mutate ungroup filter distinct bind_rows slice_max rename case_when
 #' @importFrom  nhdplusTools rename_geometry get_node
 #' @importFrom  sf st_drop_geometry st_intersects st_as_sf
-# 
-# filter(network_list$flowpaths, id == 3548) %>% 
-#   mutate(l = add_lengthkm(.)) |> 
-#   mapview::mapview()
-# 
-# filter(topo, id == 3548)
 
 realign_topology = function(network_list,
                             nexus_prefix = NULL,
@@ -104,7 +148,7 @@ realign_topology = function(network_list,
     st_drop_geometry() 
 
   if(is.null(term_filter)){
-
+    
     if(is.null(term_add)){
       term_net = filter(net, toid == 0 )
     } else {
@@ -136,10 +180,10 @@ realign_topology = function(network_list,
 
   # Get all start and end node geometries
   starts_ends = bind_rows(get_node(iso, "start"), get_node(iso, "end"))
- # write_sf(starts_ends, "test.gpkg")
+  # write_sf(starts_ends, "test.gpkg")
   # Find the locations where the end points intersect with starting/ending points
   emap     = st_intersects(ends, starts_ends)
-
+  
   # If more then one intersection occurs its a nexus,
   #  otherwise it is a junction
   ends$type = ifelse(lengths(emap) > 1, "nex", "jun")
@@ -273,20 +317,20 @@ realign_topology = function(network_list,
     mutate(topo_type = "network") |> 
     select(id, toid, topo_type, type) |> 
     distinct()
-
+  
 
   ## NEW!!! ##
   xx =  select(topo, toid, type) %>%
     group_by(toid) %>%
     mutate(type = ifelse(any(type == 'terminal'), "terminal", type)) %>%
     slice(1) %>%
     ungroup()
-
+  
   topo = topo %>%
     mutate(type = NULL) %>%
     left_join(xx, by = "toid", multiple = "all") %>%
     filter(id != toid)
-
+  
   # We'll use the fl --> nex topo to modify the input flow network toIDs
   # Additionally we will add the NextGen required prefixes.
   fl =  left_join(select(network_list$flowpaths, -toid), 
@@ -298,7 +342,7 @@ realign_topology = function(network_list,
            toid = paste0(ifelse(type == "terminal", terminal_nexus_prefix, nexus_prefix), toid),
            realized_catchment = gsub(waterbody_prefix, catchment_prefix, id)) |> 
     filter(!duplicated(id))
-
+  
 
 
   divide =  left_join(select(network_list$catchments, -toid),
@@ -368,15 +412,15 @@ realign_topology = function(network_list,
       distinct()
   })
 
-
+  
 
   if(sum(!divide$toid %in% nex$id) != 0){
     stop('Divides flow to nexus locations that do not exist!\n',
          paste(st_drop_geometry(divide[which(!divide$toid %in% nex$id),"divide_id"]),"-->", st_drop_geometry(divide[which(!divide$toid %in% nex$id),"toid"]), "\n"), call. = FALSE)
   }
 
- filter(divide, divide_id == 'cat-212673')
- filter(divide, divide_id == 'cat-212675')
+  filter(divide, divide_id == 'cat-212673')
+  filter(divide, divide_id == 'cat-212675')
 
   if(sum(!fl$toid %in% nex$id) != 0 ){
     stop('Flowpaths flow to nexus locations that do not exist!\n',
@@ -418,9 +462,9 @@ realign_topology = function(network_list,
 #' @param enforce_dm            should the data model be validated prior to writing?
 #' @param export_gpkg           file path to write new data. If NULL list object is returned
 #' @return list or file path
+#' @export
 #' @importFrom sf read_sf st_point_on_surface
 #' @importFrom dplyr select mutate left_join everything distinct contains slice n
-#' @export
 
 apply_nexus_topology = function(gpkg,
                                 catchments = NULL,
@@ -481,7 +525,7 @@ apply_nexus_topology = function(gpkg,
 
 
   if(layer_exists(gpkg, "pois")){
-      
+
     x = read_sf(gpkg, "pois") |>
       select(poi_id) |> 
       mutate(poi_id = as.integer(poi_id)) 
@@ -517,7 +561,7 @@ apply_nexus_topology = function(gpkg,
     t = st_drop_geometry(ngen_flows$pois) |> 
       select(id, poi_id) |> 
       distinct()
-      
+
     network = left_join(network, t, by = "id", relationship = "many-to-many")
   }
 
@@ -539,7 +583,7 @@ apply_nexus_topology = function(gpkg,
       left_join(select(tmp, -id), by = 'divide_id') %>%
       mutate(vpuid = as.character(vpu),
              poi_id = as.integer(poi_id))
-      
+
 
     ngen_flows$network  = filter(network, !type %in% c(c('coastal', "internal"))) %>%
       left_join(select(tmp, id, hf_source, hf_id, hf_id_part, hydroseq), by = 'id', relationship = "many-to-many") %>%
@@ -576,7 +620,7 @@ apply_nexus_topology = function(gpkg,
   if(!is.null(export_gpkg)){
     write_sf(baddies, export_gpkg, "error")
   }
-
+  
   if(nrow(baddies) > 0){
     message("Foiled again ... ID/toIDs: \n\t",
             paste(paste0(baddies$id, "-->", baddies$toid), collapse = "\n\t"))

README.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R CMD Check](https://github.com/mikejohnson51/hydrofab/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/mikejohnson51/hydrofab/actions/workflows/R-CMD-check.yml)
-[![Dependencies](https://img.shields.io/badge/dependencies-18/71-red?style=flat)](#)
+[![Dependencies](https://img.shields.io/badge/dependencies-19/70-red?style=flat)](#)
 [![License: Apache License (>= 2)](https://img.shields.io/badge/License-Apache%20License%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/apache-2.0/)
 <!-- badges: end -->
 

data-raw/boundary_data.R

@@ -37,10 +37,9 @@ rpu = get_vaa(c("rpuid", "vpuid")) |>
   ms_simplify(keep = .001)
 
 ######## ----
-usethis::use_data(rpu_boundaries, overwrite =TRUE)
+usethis::use_data(rpu_boundaries, overwrite = TRUE)
 ######## ----
 
-
 files = list.files("data", recursive = TRUE, full.names = TRUE)
 bad_files = files[!grepl(".rda$", files)]
 

data/derived-data/README.md

@@ -0,0 +1,3 @@
+# README
+
+**{{ PLEASE DESCRIBE THE CONTENT OF THIS FOLDER}}**

data/raw-data/README.md

@@ -0,0 +1,3 @@
+# README
+
+**{{ PLEASE DESCRIBE THE CONTENT OF THIS FOLDER}}**

inst/logo.R

@@ -1,8 +1,6 @@
 
 library(hexSticker)
 
-
-
 imgurl <- "inst/figures/logo.png"
 library(showtext)
 font_add_google("Gochi Hand", "gochi")