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Merge pull request #74 from dblodgett-usgs/master
match levelpaths and create outlets for dendritic catchments
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,264 @@ | ||
| #' Get linked points | ||
| #' @description Given matched levelpaths, finds outlets of catchments along level paths. | ||
| #' @param hu_lp data.frame as returned by `match_levelpaths` | ||
| #' @param net sf data.frame ... | ||
| #' @param wbd sf data.frame ... | ||
| #' @param exclude character vector of HUs to exclude from consideration | ||
| #' @param cores numeric (optional) number of cores to use in paralel evaluation | ||
| #' | ||
| #' This function is preliminary and subject to revision. It has been tested thoroughly | ||
| #' but complete methods description have not yet been published. | ||
| #' | ||
| #' @importFrom dplyr bind_rows bind_cols | ||
| #' @importFrom sf st_coordinates st_as_sf st_crs<- st_transform st_point st_geometry<- st_intersection | ||
| #' @importFrom stats setNames | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' library(dplyr) | ||
| #' library(sf) | ||
| #' | ||
| #' source(system.file("extdata/new_hope_data.R", package = "nhdplusTools")) | ||
| #' suppressWarnings(net_prep <- prepare_nhdplus(new_hope_flowline, 20, 0, 10) %>% | ||
| #' left_join(select(new_hope_flowline, COMID, DnLevelPat, | ||
| #' AreaSqKM), by = "COMID") %>% | ||
| #' st_sf() %>% | ||
| #' group_by(LevelPathI) %>% | ||
| #' arrange(Hydroseq) %>% | ||
| #' mutate(DnLevelPat = DnLevelPat[1]) %>% | ||
| #' ungroup()) | ||
| #' | ||
| #' net_prep["denTotalAreaSqKM"] <- | ||
| #' calculate_total_drainage_area(select(st_set_geometry(net_prep, NULL), | ||
| #' ID = COMID, toID = toCOMID, | ||
| #' area = AreaSqKM)) | ||
| #' | ||
| #' wbd <- select(new_hope_wbd, HUC12 = HUC_12, TOHUC = HU_12_DS) %>% | ||
| #' st_transform(st_crs(net_prep)) | ||
| #' | ||
| #' net_prep <- st_join(net_prep, wbd) %>% | ||
| #' st_set_geometry(NULL) | ||
| #' | ||
| #' outlet_comid <- 8897784 | ||
| #' | ||
| #' hu_lp <- match_levelpaths(net_prep, outlet_comid) | ||
| #' | ||
| #' linked_points <- get_linked_points(hu_lp, new_hope_flowline, wbd, exclude = c()) | ||
| #' | ||
| #' lps <- filter(new_hope_flowline, LevelPathI %in% linked_points$LevelPathI) | ||
| #' | ||
| #' plot(st_geometry(new_hope_flowline), lwd = 0.4, col = "blue") | ||
| #' plot(st_geometry(lps), col = "blue", add = TRUE) | ||
| #' plot(linked_points$geometry, col = "red", pch = 19, add = TRUE) | ||
| #' plot(st_transform(new_hope_wbd$geom, | ||
| #' st_crs(linked_points)), lwd = 1.5, add = TRUE) | ||
|
|
||
| get_linked_points <- function(hu_lp, net, wbd, exclude, cores = NA) { | ||
|
|
||
| lp_points <- suppressWarnings(get_points_out(hu_lp, net, wbd, exclude) %>% | ||
| get_lp_hu_points(st_crs(wbd))) | ||
|
|
||
| lp_points <- lp_points %>% | ||
| filter(!hu12 %in% exclude) %>% | ||
| mutate(lp = as.numeric(lp)) %>% | ||
| group_by(hu12) %>% | ||
| filter(lp == min(lp)) %>% | ||
| ungroup() | ||
|
|
||
| filter_na <- is.na(unname(st_coordinates(lp_points)[, 1])) | ||
| na_points <- filter(lp_points, filter_na) | ||
| lp_points <- filter(lp_points, !filter_na) | ||
|
|
||
| na_points <- st_set_geometry(na_points, NULL) | ||
|
|
||
| na_points <- distinct(na_points) | ||
|
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||
| both <- filter(na_points, na_points$hu12 %in% lp_points$hu12) # Only broken border HUs included. | ||
|
|
||
| na_points <- filter(na_points, !hu12 %in% both) | ||
| lp_points <- filter(lp_points, !hu12 %in% both) | ||
|
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||
| na_outlets <- net %>% | ||
| filter(LevelPathI %in% na_points$lp) %>% | ||
| group_by(LevelPathI) %>% | ||
| filter(Hydroseq == min(Hydroseq)) %>% | ||
| ungroup() %>% | ||
| left_join(na_points, by = c("LevelPathI" = "lp")) | ||
|
|
||
| problem_na <- filter(na_outlets, FromMeas != 0) | ||
|
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||
| na_outlets <- filter(na_outlets, FromMeas == 0) | ||
|
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| lp_list <- unique(lp_points$lp) | ||
|
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||
| net <- select(net, COMID, LevelPathI, REACHCODE, ToMeas, FromMeas, Hydroseq) %>% | ||
| filter(LevelPathI %in% lp_list) | ||
|
|
||
| in_list_fun <- function(lp_search, net, lp_points) { | ||
| list(lp_search = lp_search, | ||
| lp_geom = filter(net, LevelPathI == lp_search), | ||
| hu_points = filter(lp_points, lp == lp_search)) | ||
| } | ||
|
|
||
| in_list <- lapply(lp_list, in_list_fun, net = net, lp_points = lp_points) | ||
|
|
||
| if(is.na(cores)) { | ||
| linked <- lapply(in_list, par_linker) | ||
| } else { | ||
| cl <- parallel::makeCluster(rep("localhost", cores), | ||
| type = "SOCK", outfile = "par.log") | ||
|
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||
| linked <- snow::parLapply(cl, in_list, par_linker) | ||
|
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| parallel::stopCluster(cl) | ||
| } | ||
|
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| linked <- st_sf(do.call(rbind, linked), crs = st_crs(lp_points)) %>% | ||
| select(COMID, REACHCODE, REACH_meas, offset, HUC12 = hu12, LevelPathI = lp) | ||
|
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||
| if(nrow(na_outlets) > 0) { | ||
| na_outlet_coords <- st_coordinates(na_outlets) %>% | ||
| as.data.frame() %>% | ||
| group_by(L2) %>% | ||
| filter(row_number() == n()) %>% | ||
| ungroup() %>% | ||
| select(-L1, -L2) %>% | ||
| bind_cols(st_set_geometry(na_outlets, NULL)) %>% | ||
| st_as_sf(coords = c("X", "Y"), crs = st_crs(na_outlets)) %>% | ||
| rename(geom = geometry) | ||
|
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| na_outlet_coords$REACH_meas <- 0 | ||
| na_outlet_coords$offset <- 0 | ||
|
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| na_outlet_coords <- select(na_outlet_coords, | ||
| COMID, REACHCODE, REACH_meas, | ||
| offset, HUC12 = hu12, LevelPathI) | ||
|
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||
| names(linked)[names(linked) == attr(linked, "sf_column")] <- | ||
| names(na_outlet_coords)[names(na_outlet_coords) == attr(na_outlet_coords, "sf_column")] | ||
|
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| attr(linked, "sf_column") <- attr(na_outlet_coords, "sf_column") | ||
|
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| linked <- rbind(linked, na_outlet_coords) %>% | ||
| st_sf() | ||
| } | ||
|
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| return(linked) | ||
| } | ||
|
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| hu_points_fun <- function(hp) { | ||
| if(length(unlist(hp)) > 0) { | ||
| out <- do.call(rbind, | ||
| lapply(1:length(hp), | ||
| function(x) { | ||
| if(length(unlist(hp[[x]])) > 0) { | ||
| o <- lapply(1:length(hp[[x]]), | ||
| function(y) st_cast(hp[[x]][y], "POINT")) | ||
| o <- data.frame(geometry = do.call(c, o)) | ||
| o[["hu12"]] <- names(hp[x]) | ||
| } else { | ||
| o <- data.frame(hu12 = names(hp[x]), stringsAsFactors = FALSE) | ||
| o[["geometry"]] <- list(st_point()) | ||
| } | ||
| return(o) | ||
| })) | ||
| } else { | ||
| out <- data.frame(hu12 = names(hp), stringsAsFactors = FALSE) | ||
| out[["geometry"]] <- list(st_point()) | ||
| } | ||
|
|
||
| return(out) | ||
| } | ||
|
|
||
| run_lp <- function(lp_id, net, hu_lp, wbd) { | ||
| out <- NULL | ||
| tryCatch({ | ||
| lp <- filter(net, LevelPathI == lp_id) %>% | ||
| st_geometry() | ||
|
|
||
| hu_ids <- filter(hu_lp, corrected_LevelPathI == lp_id) | ||
| hus <- filter(wbd, HUC12 %in% hu_ids$HUC12) | ||
| st_geometry(hus) <- st_cast(st_geometry(hus), "MULTILINESTRING") | ||
|
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||
| out <- setNames(lapply(1:nrow(hus), | ||
| function(i, lp, hus) { | ||
| suppressMessages( | ||
| st_intersection(lp, st_geometry(hus)[i]) | ||
| ) | ||
| }, | ||
| lp = lp, hus = hus), | ||
| hus$HUC12) | ||
| }, | ||
| error = function(e) { | ||
| warning(paste(lp_id, e)) | ||
| }, | ||
| warning = function(w) { | ||
| warning(paste(lp_id, w)) | ||
| }) | ||
| return(out) | ||
| } | ||
|
|
||
| par_linker <- function(lp_list) { | ||
| library(nhdplusTools) | ||
| library(dplyr) | ||
| library(sf) | ||
| linked <- NULL | ||
| tryCatch({ | ||
| linked <- get_flowline_index(lp_list$lp_geom, lp_list$hu_points, search_radius = 1000) %>% | ||
| bind_cols(lp_list$hu_points) %>% | ||
| left_join(select(st_set_geometry(lp_list$lp_geom, NULL), COMID, Hydroseq), by = "COMID") %>% | ||
| group_by(hu12) %>% | ||
| filter(Hydroseq == min(Hydroseq)) | ||
|
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||
| if(any(group_size(linked) > 1)) { | ||
| linked <- linked %>% | ||
| group_by(hu12, REACHCODE) %>% | ||
| filter(REACH_meas == min(REACH_meas)) | ||
| } | ||
|
|
||
| linked <- ungroup(linked) | ||
| }, | ||
| error = function(e) warning(paste(lp_list$lp_search, e)), | ||
| warning = function(w) warning(paste(lp_list$lp_search, w))) | ||
| return(linked) | ||
| } | ||
|
|
||
| get_points_out <- function(hu_lp, net, wbd, exclude) { | ||
|
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||
| hu_lp <- group_by(hu_lp, HUC12) %>% | ||
| filter(corrected_LevelPathI == min(corrected_LevelPathI)) %>% | ||
| ungroup() | ||
|
|
||
| wbd <- filter(wbd, !HUC12 %in% exclude) | ||
| hu_lp <- filter(hu_lp, !HUC12 %in% exclude) | ||
|
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| lp_ids <- unique(hu_lp$corrected_LevelPathI) | ||
|
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| if(st_crs(net) != st_crs(wbd)) { | ||
| net <- st_transform(net, st_crs(wbd)) | ||
| } | ||
|
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| points <- setNames(lapply(X = lp_ids, | ||
| FUN = run_lp, | ||
| net = net, hu_lp = hu_lp, wbd = wbd), | ||
| lp_ids) | ||
|
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| return(points) | ||
| } | ||
|
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| get_lp_hu_points <- function(points, prj) { | ||
| lp_points <- lapply(names(points), | ||
| function(lp, points) { | ||
| hu_points <- bind_rows(lapply(points[lp], hu_points_fun)) | ||
|
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| hu_points[["lp"]] <- lp | ||
|
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| return(hu_points) | ||
| }, points = points) %>% | ||
| bind_rows() %>% | ||
| st_sf() | ||
|
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| st_crs(lp_points) <- prj | ||
|
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||
| return(lp_points) | ||
| } |
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