remove use of :: in source #12

NAMESPACE

@@ -65,12 +65,14 @@ export(sort_network)
 export(st_compatibalize)
 importFrom(RANN,nn2)
 importFrom(data.table,as.data.table)
+importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,setnames)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,as_tibble)
+importFrom(dplyr,between)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
@@ -92,6 +94,9 @@ importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
+importFrom(fastmap,fastqueue)
+importFrom(fastmap,faststack)
+importFrom(methods,as)
 importFrom(pbapply,pbapply)
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pboptions)
@@ -110,11 +115,22 @@ importFrom(sf,st_intersects)
 importFrom(sf,st_is_longlat)
 importFrom(sf,st_join)
 importFrom(sf,st_linestring)
+importFrom(sf,st_point)
 importFrom(sf,st_reverse)
 importFrom(sf,st_segmentize)
 importFrom(sf,st_sf)
+importFrom(sf,st_sfc)
 importFrom(sf,st_transform)
 importFrom(sf,st_zm)
+importFrom(stats,na.omit)
+importFrom(stats,setNames)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,replace_na)
+importFrom(tidyr,unnest)
+importFrom(units,as_units)
+importFrom(units,set_units)
+importFrom(utils,adist)
 importFrom(utils,combn)
+importFrom(utils,setTxtProgressBar)
 importFrom(utils,tail)
+importFrom(utils,txtProgressBar)

R/00_hydroloom.R

@@ -107,7 +107,7 @@ hnd$point_id <- "identifier of hydrologic location point"
 hnd$offset <- "offset distance from point to line in units of linear reference analysis units"
 hnd$levelpath_outlet_id <- "id of outlet catchment of a levelpath"
 
-hydroloom_name_definitions <- stats::setNames(as.character(hnd), names(hnd))
+hydroloom_name_definitions <- setNames(as.character(hnd), names(hnd))
 class(hydroloom_name_definitions) <- c("hydroloom_names", class(hydroloom_name_definitions))
 
 #' @export
@@ -193,14 +193,22 @@ get_outlet_value <- function(x) {
 }
 
 #' @importFrom dplyr filter select left_join right_join all_of any_of bind_rows group_by
-#' @importFrom dplyr ungroup n rename row_number arrange desc distinct mutate summarise
+#' @importFrom dplyr ungroup n rename row_number between arrange desc distinct mutate summarise
 #' @importFrom dplyr everything as_tibble pull group_split tibble bind_cols lag case_when
+#' @importFrom data.table copy data.table as.data.table setnames
+#' @importFrom tidyr unnest replace_na pivot_wider
 #' @importFrom rlang :=
 #' @importFrom sf "st_geometry<-" st_drop_geometry st_geometry st_geometry_type st_intersects
 #' @importFrom sf st_cast st_linestring st_is_longlat st_transform st_segmentize st_buffer
 #' @importFrom sf st_as_sf st_sf st_zm st_coordinates st_crs st_join st_reverse
+#' @importFrom sf st_point st_sfc
 #' @importFrom pbapply pblapply pbsapply pbapply pboptions
 #' @importFrom RANN nn2
+#' @importFrom stats setNames na.omit
+#' @importFrom fastmap fastqueue faststack
+#' @importFrom utils txtProgressBar setTxtProgressBar adist combn tail
+#' @importFrom units set_units as_units
+#' @importFrom methods as
 
 .data <- NULL
 
@@ -266,7 +274,7 @@ hy <- function(x, clean = FALSE) {
     x <- as_tibble(x)
   }
 
-  attr(x, "orig_names") <- stats::setNames(names(x), keep_names)
+  attr(x, "orig_names") <- setNames(names(x), keep_names)
 
   class(x) <- c("hy", class(x))
 

R/add_divergence.R

@@ -123,7 +123,7 @@ add_divergence.hy <- function(x, coastal_outlet_ids, inland_outlet_ids,
 
   x <- make_fromids(make_index_ids(x), return_list = TRUE)
 
-  paths <- pbapply::pblapply(term, function(i, net) {
+  paths <- pblapply(term, function(i, net) {
     try(navigate_network_dfs(x = net, starts = i,
                              direction = "up",
                              reset = FALSE))
@@ -133,8 +133,8 @@ add_divergence.hy <- function(x, coastal_outlet_ids, inland_outlet_ids,
                          paths = I(unlist(paths,
                                           recursive = FALSE))) |>
     mutate(coastal = id %in% coastal_outlet_ids) |>
-    tidyr::unnest(cols = c(paths)) |>
-    tidyr::unnest(cols = c(paths)) |>
+    unnest(cols = c(paths)) |>
+    unnest(cols = c(paths)) |>
     select(all_of(c(id = "paths", "coastal"))) |>
     distinct() |>
     group_by(id) |>

R/add_levelpaths.R

@@ -156,7 +156,7 @@ add_levelpaths.hy <- function(x, name_attribute, weight_attribute,
     x$done[pathids$ind] <- rep(TRUE, nrow(pathids))
 
     # grab everything that goes to the path we just followed
-    outlet_ind <- stats::na.omit(as.numeric(from_ind$froms[, pathids$ind]))
+    outlet_ind <- na.omit(as.numeric(from_ind$froms[, pathids$ind]))
     # remove the path we just follwed
     outlet_ind <- x[outlet_ind[!outlet_ind %in% pathids$ind],]
 
@@ -218,7 +218,7 @@ get_path <- function(x, tailid, from_ind, status, wat) {
 
   while(keep_going) {
     tryCatch({
-      next_tails <- x[stats::na.omit(from_ind$froms[,tailid]), ]
+      next_tails <- x[na.omit(from_ind$froms[,tailid]), ]
 
       if(nrow(next_tails) > 1) {
 

R/add_pfafstetter.R

@@ -92,7 +92,6 @@ add_pfafstetter.hy <- function(x, max_level = 2, status = FALSE) {
 }
 
 #' @noRd
-#' @importFrom dplyr arrange left_join
 get_pfaf_9 <- function(x, mainstem, max_level, pre_pfaf = 0, assigned = NA, status = FALSE) {
 
   if(!levelpath_outlet_id %in% names(x)) {
@@ -149,7 +148,7 @@ get_pfaf_9 <- function(x, mainstem, max_level, pre_pfaf = 0, assigned = NA, stat
   out[["pfaf"]] <- out$p_id + pre_pfaf * 10
 
   if(all(sapply(out$members, function(x) all(is.na(x))))) out$members[[1]] <- mainstem$id
-  out <- unnest(out, "members")
+  out <- simple_unnest(out, "members")
   out <- list(out[!is.na(out$members), ])
 
   if(nrow(out[[1]]) == 0 | all(out[[1]]$members %in% mainstem$id)) {
@@ -174,8 +173,6 @@ apply_fun <- function(p, p9, x, max_level, status) {
   }
 }
 
-#' @importFrom tidyr pivot_wider
-#' @importFrom dplyr select
 #' @noRd
 cleanup_pfaf <- function(pfaf) {
   # Add level number
@@ -187,8 +184,8 @@ cleanup_pfaf <- function(pfaf) {
   # Deduplicate problem tributaries
   remove <- do.call(c, lapply(1:length(unique(pfaf$level)), function(l, pfaf) {
     check <- pfaf[pfaf$level == l, ]
-    check <- dplyr::group_by(check, .data$id)
-    check <- dplyr::filter(check, n() > 1 & .data$pfaf < max(.data$pfaf))$uid
+    check <- group_by(check, .data$id)
+    check <- filter(check, n() > 1 & .data$pfaf < max(.data$pfaf))$uid
   }, pfaf = pfaf))
 
   pfaf <- pivot_wider(select(pfaf[!pfaf$uid %in% remove, ], -"uid"),

R/add_toids.R

@@ -41,7 +41,6 @@ add_toids.data.frame <- function(x, return_dendritic = TRUE) {
 }
 
 .datatable.aware=TRUE
-#' @importFrom data.table data.table
 #' @name add_toids
 #' @export
 add_toids.hy <- function(x, return_dendritic = TRUE) {

R/align_names.R

@@ -74,7 +74,7 @@ align_names <- function(x) {
 
   }
 
-  x <- rename(x, any_of(stats::setNames(names(replace_names), unname(replace_names))))
+  x <- rename(x, any_of(setNames(names(replace_names), unname(replace_names))))
 
   switch_back <- !names(x) %in% good_names
 

R/check_hy_graph.R

@@ -41,7 +41,7 @@ check_hy_graph <- function(x, loop_check = FALSE) {
              data.table(drop_geometry(x)),
              by.x = "toid", by.y = "id", all.x = TRUE)
 
-  x <- dplyr::as_tibble(x)
+  x <- as_tibble(x)
 
   check <- x$id == x$toid.y
 
@@ -91,11 +91,11 @@ check_hy_graph_internal <- function(g, all_starts) {
   f <- make_fromids(g)
 
   # used to track which path tops we need to go back to
-  to_visit_queue <- fastmap::fastqueue(missing_default = 0)
+  to_visit_queue <- fastqueue(missing_default = 0)
 
   lapply(all_starts, function(x) to_visit_queue$add(x))
 
-  out_stack <- fastmap::faststack()
+  out_stack <- faststack()
 
   # to track where we've been
   visited_tracker <- rep(FALSE, ncol(g$to))
@@ -106,7 +106,7 @@ check_hy_graph_internal <- function(g, all_starts) {
   # trigger for making a new path
   new_path <- FALSE
 
-  pb = utils::txtProgressBar(0, ncol(g$to), style = 3)
+  pb = txtProgressBar(0, ncol(g$to), style = 3)
   on.exit(close(pb))
   n <- 0
 
@@ -119,7 +119,7 @@ check_hy_graph_internal <- function(g, all_starts) {
     visited_tracker[node] <- TRUE
 
     if(!n %% 100)
-      utils::setTxtProgressBar(pb, n)
+      setTxtProgressBar(pb, n)
 
 
     # now look at what's downtream and add to a queue
@@ -185,7 +185,7 @@ check_hy_graph_internal <- function(g, all_starts) {
 
   }
 
-  utils::setTxtProgressBar(pb, n)
+  setTxtProgressBar(pb, n)
 
   # if we got this far, Cool!
   unique(g$to_list$id[as.integer(out_stack$as_list())])
@@ -195,7 +195,7 @@ check_hy_graph_internal <- function(g, all_starts) {
 loop_search_dfs <- function(g, node, visited_tracker) {
 
   # stack to track stuff we need to visit
-  to_visit_stack <- fastmap::faststack(missing_default = 0)
+  to_visit_stack <- faststack(missing_default = 0)
 
   # while we still have nodes to check
   while(node != 0) {

R/disambiguate.R

@@ -51,7 +51,7 @@ disambiguate_indexes <- function(indexes, flowpath, hydro_location) {
 
   indexes <- align_names(indexes)
 
-  renamer <- stats::setNames(names(indexes), orig_index_names)
+  renamer <- setNames(names(indexes), orig_index_names)
 
   call_rename <- FALSE
   if(!is.hy(flowpath, silent = TRUE)) call_rename <- TRUE
@@ -107,7 +107,7 @@ disambiguate_indexes <- function(indexes, flowpath, hydro_location) {
 }
 
 string_score <- function(x) {
-  raw_score <- as.numeric(utils::adist(x[[1]], x[[2]], ignore.case = TRUE))
+  raw_score <- as.numeric(adist(x[[1]], x[[2]], ignore.case = TRUE))
 
   (1 - (raw_score) / max(c(nchar(x[[1]]), nchar(x[[2]]))))
 }

R/get_hydro_location.R

@@ -41,7 +41,7 @@ get_hydro_location <- function(indexes, flowpath) {
 
 get_hydro_location_single <- function(x) {
 
-  coords <- sf::st_coordinates(x[[2]]) |>
+  coords <- st_coordinates(x[[2]]) |>
     add_index() |>
     add_len()
 
@@ -58,15 +58,15 @@ get_hydro_location_single <- function(x) {
 
   if(nds == nus) {
     return(
-      sf::st_sfc(sf::st_point(c(coords$X[nds], coords$Y[nds])),
-                 crs = sf::st_crs(x[[2]]))
+      st_sfc(st_point(c(coords$X[nds], coords$Y[nds])),
+                 crs = st_crs(x[[2]]))
     )}
 
   new_m <- rescale_measures(m, coords$id_measure[nds], coords$id_measure[nus])
 
   new <- interp_meas(new_m, coords$X[nds], coords$Y[nds], coords$X[nus], coords$Y[nus])
 
-  return(sf::st_sfc(sf::st_point(c(new[[1]], new[[2]])), crs = sf::st_crs(x[[2]])))
+  return(st_sfc(st_point(c(new[[1]], new[[2]])), crs = st_crs(x[[2]])))
 }
 
 interp_meas <- function(m, x1, y1, x2, y2) {

R/index_points_to_lines.R

@@ -28,7 +28,7 @@ matcher <- function(coords, points, search_radius, max_matches = 1) {
 
   # Now limit to max matches per point
   matched <- group_by(matched, .data$point_id) |>
-    filter(dplyr::row_number() <= max_matches) |>
+    filter(row_number() <= max_matches) |>
     ungroup() |>
     as.data.frame()
 
@@ -39,18 +39,18 @@ check_search_radius <- function(search_radius, points) {
 
   if(is.null(search_radius)) {
     if(st_is_longlat(points)) {
-      search_radius <- units::set_units(0.01, "degrees")
+      search_radius <- set_units(0.01, "degrees")
     } else {
-      search_radius <- units::set_units(200, "m")
+      search_radius <- set_units(200, "m")
 
-      units(search_radius) <- units::as_units(
+      units(search_radius) <- as_units(
         st_crs(points, parameters = TRUE)$ud_unit)
     }
   }
 
   if(!inherits(search_radius, "units")) {
     warning("search_radius units not set, trying units of points.")
-    units(search_radius) <- units::as_units(
+    units(search_radius) <- as_units(
       st_crs(points, parameters = TRUE)$ud_unit)
   }
 
@@ -89,9 +89,9 @@ add_index <- function(x) {
 
 add_len <- function(x) {
   x |>
-    mutate(len  = sqrt( ( (.data$X - (dplyr::lag(.data$X))) ^ 2) +
-                          ( ( (.data$Y - (dplyr::lag(.data$Y))) ^ 2)))) |>
-    mutate(len = tidyr::replace_na(.data$len, 0)) |>
+    mutate(len  = sqrt( ( (.data$X - (lag(.data$X))) ^ 2) +
+                          ( ( (.data$Y - (lag(.data$Y))) ^ 2)))) |>
+    mutate(len = replace_na(.data$len, 0)) |>
     mutate(len = cumsum(.data$len)) |>
     mutate(id_measure = 100 - (100 * .data$len / max(.data$len)))
 }
@@ -199,8 +199,8 @@ index_points_to_lines.hy <- function(x, points,
 
   point_buffer <- st_buffer(points, search_radius)
 
-  if(units(search_radius) == units(units::as_units("degrees"))) {
-    if(st_is_longlat(in_crs) & search_radius > units::set_units(1, "degree")) {
+  if(units(search_radius) == units(as_units("degrees"))) {
+    if(st_is_longlat(in_crs) & search_radius > set_units(1, "degree")) {
       warning("search radius is large for lat/lon input, are you sure?")
     }
   }
@@ -223,7 +223,7 @@ index_points_to_lines.hy <- function(x, points,
 
   fline_atts <- drop_geometry(x)
 
-  if(sf::st_geometry_type(x, by_geometry = FALSE) != "LINESTRING") {
+  if(st_geometry_type(x, by_geometry = FALSE) != "LINESTRING") {
     warning("converting to LINESTRING, this may be slow, check results")
   }
 
@@ -273,7 +273,7 @@ index_points_to_lines.hy <- function(x, points,
     x <- x |>
       mutate(index = seq_len(nrow(x))) |>
       st_cast("LINESTRING", warn = FALSE) |>
-      st_segmentize(dfMaxLength = units::as_units(precision, "m"))
+      st_segmentize(dfMaxLength = as_units(precision, "m"))
 
     fline_atts <- right_join(fline_atts,
                              select(drop_geometry(x),
@@ -354,8 +354,6 @@ index_points_to_lines.hy <- function(x, points,
 #' \link[units]{set_units}.
 #' @return data.frame with two columns, COMID, in_wb_COMID, near_wb_COMID,
 #' near_wb_dist, and outlet_fline_COMID. Distance is in units of provided projection.
-#' @importFrom sf st_join st_geometry_type
-#' @importFrom dplyr select mutate bind_cols
 #' @export
 #' @examples
 #'
@@ -451,7 +449,7 @@ rename_indexed <- function(x, matched) {
   orig_aggregate_id <- names(attr(x, "orig_names")[attr(x, "orig_names") == aggregate_id])
   new_aggregate_measure <- paste0(orig_aggregate_id, "_measure")
 
-  rename(matched, any_of(stats::setNames(c(id, aggregate_id, aggregate_id_measure),
+  rename(matched, any_of(setNames(c(id, aggregate_id, aggregate_id_measure),
                                          c(orig_id, orig_aggregate_id, new_aggregate_measure))))
 }