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wepp_mapper.R
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wepp_mapper.R
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#' Calculate spatial entities required for WEPP
#'
#' This function takes backup data frame output from [flow_mapper()] and
#' [form_mapper()] calculates hillslope, channel segments and impoundment
#' spatial entities required for input in to WEPP (Water Erosion and Prediction
#' Project) (among other metrics). Based on FacetMapR by R. A. (Bob) MacMillan,
#' LandMapper Environmental Solutions.
#'
#' @param folder Character. Location of [flow_mapper()] output
#' @param chan_length Numeric. Channel length maximum length. Used to split
#' channels into segments
#' @param upslope_threshold Numeric. Threshold of upslope cells to define
#' channel cells. #' Cells with an upslope value larger than this are
#' considered channel cells
#'
#' @inheritParams args
#'
#' @examples
#'
#' \dontrun{
#' # First need to run flow_mapper()
#' flow_mapper(file = system.file("extdata", "testELEV.dbf", package = "LITAP"),
#' out_folder = "./testELEV/", nrow = 90, ncol = 90, grid = 5)
#'
#' # Now can run wepp_mapper()
#' wepp_mapper(folder = "./testELEV/")
#' }
#'
#' @export
wepp_mapper <- function(folder,
chan_length = 200,
upslope_threshold = 300,
clean = FALSE,
resume = NULL,
log = TRUE,
verbose = FALSE, quiet = FALSE, debug = FALSE) {
# Setup -------------------------------------------------------------------
# Get resume options
if(is.null(resume)) resume <- ""
resume_options <- c("", "mark_chan", "cut_chan", "merge_chan", "new_ups",
"remark_chan", "mark_pits", "split_segments", "flow2_chan",
"calc_segs", "order_segs", "redo_ddir",
"find_upsegs", "hill_sheds", "renum_segs", "build_stru",
"wepp_form", "wepp_len", "hill_stats", "chan_stats",
"new_ups_final")
check_resume(resume, resume_options)
# Get out format
out_format <- get_format(folder, where = "flow")
# Get backup fill dem
db <- get_previous(folder, step = "fill", where = "flow")
if("ldir" %in% names(db)) db <- dplyr::rename(db, "ddir" = "ldir")
db <- dplyr::select(db, "seqno", "x", "y", "row", "col", "elev", "drec",
"ddir", "upslope", "fill_shed") %>%
add_buffer()
grid <- calc_grid(db)
check_grid(grid)
# Get fill file
fill <- get_previous(folder, step = "fill", where = "flow", type = "stat") %>%
dplyr::mutate_at(dplyr::vars(dplyr::matches("row|col")), ~ . + 1) %>%
dplyr::mutate_at(dplyr::vars(dplyr::contains("seqno")),
~ seqno_to_buffer(., db$seqno[!db$buffer]))
# Get out locs
out_locs <- locs_create(folder, which = "wepp", clean = clean)
# Messaging
if(quiet) verbose <- FALSE
# Setup Log
log_file <- log_setup(folder, which = "wepp", log)
start <- Sys.time()
# File details to log
log_write("Run options:\n", log = log_file)
log_write(" Input folder = ", normalizePath(folder), "\n",
" grid = ", grid, "\n",
" chan_length = ", chan_length, "\n",
" upslope_threshold = ", upslope_threshold, "\n",
log = log_file)
# Run start to log
log_write("\nRun started: ", start, "\n", log = log_file)
# Mark Channels -----------------------------------------------------------
task <- "Marking channels and channel junction"
if(resume == "" || resume == "mark_chan"){
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
db_marked <- mark_chan(db, upslope_threshold = upslope_threshold)
save_output(data = db_marked, name = "marked", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Cut Channels ------------------------------------------------------------
task <- "Cut channels fix elevation"
if(resume == "" || resume == "cut_chan"){
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_marked")) {
db_marked <- get_previous(folder, step = "marked", where = "wepp") %>%
add_buffer()
}
db_cut <- cut_chan(db_marked, upslope_threshold)
save_output(data = db_cut, name = "cut", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Merge Channels -----------------------------------------------------------
task <- "Merge/thin adjacent channels"
if(resume == "" || resume == "merge_chan"){
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_cut")) {
db_cut <- get_previous(folder, step = "cut", where = "wepp") %>%
add_buffer()
}
db_merged <- merge_chan(db_cut)
save_output(data = db_merged, name = "merged", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Recalculate Upslopes ----------------------------------------------------
task <- "Re-calculate upslopes"
if(resume == "" || resume == "new_ups") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_merged")) {
db_merged <- get_previous(folder, step = "merged", where = "wepp") %>%
add_buffer()
}
db_ups <- dplyr::mutate(db_merged, shedno = fill_shed) %>%
calc_upslopes()
save_output(data = db_ups, name = "ups", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Re-mark Upslopes ----------------------------------------------------
task <- "Re-mark Channels"
if(resume == "" || resume == "remark_chan") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_ups")) {
db_ups <- get_previous(folder, step = "ups", where = "wepp") %>%
add_buffer()
}
db_remarked <- remark_chan(db_ups, upslope_threshold = upslope_threshold)
save_output(data = db_remarked, name = "remarked", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Mark Pits ----------------------------------------------------
task <- "Mark Pits"
if(resume == "" || resume == "mark_pits") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_remarked")) {
db_remarked <- get_previous(folder, step = "remarked", where = "wepp") %>%
add_buffer()
}
db_pits <- mark_pits(db_remarked, fill)
save_output(data = db_pits, name = "pits", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Split Segments ----------------------------------------------------
task <- "Split Segments"
if(resume == "" || resume == "split_segments") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_pits")) {
db_pits <- get_previous(folder, step = "pits", where = "wepp") %>%
add_buffer()
}
db_split <- split_segments(db_pits, grid, chan_length)
save_output(data = db_split, name = "split", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Flow to channels ----------------------------------------------------
task <- "Flow to channels"
if(resume == "" || resume == "flow2_chan") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_split")) {
db_split <- get_previous(folder, step = "split", where = "wepp") %>%
add_buffer()
}
db_flow <- flow_to_channels(db_split)
save_output(data = db_flow, name = "flow", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Calculate Segments ----------------------------------------------------
task <- "Calculate segments"
if(resume == "" || resume == "calc_segs") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_flow")) {
db_flow <- get_previous(folder, step = "flow", where = "wepp") %>%
add_buffer()
}
db_segs <- calc_segments(db_flow, grid = grid)
segs <- db_segs$segs
db_segs <- db_segs$db
save_output(data = db_segs, stats = segs, name = "first_segs", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
save_output(data = db_segs, name = "first_segs", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Order Segments ----------------------------------------------------
task <- "Order segments"
if(resume == "" || resume == "order_segs") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_segs") | !exists("segs")) {
db_segs <- get_previous(folder, step = "first_segs", where = "wepp") %>%
add_buffer()
segs <- get_previous(folder, step = "first_segs", where = "wepp", type = "stats") %>%
add_buffer(db = db_segs, stats = .)
}
db_ordered <- order_segments(db_segs, segs)
segs_ordered <- db_ordered$segs
db_ordered <- db_ordered$db
save_output(data = db_ordered, stats = segs_ordered, name = "ordered",
locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
save_output(data = db_ordered, name = "ordered", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Redo ddir ----------------------------------------------------
task <- "Redo and Add ddir"
if(resume == "" || resume == "redo_ddir") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_ordered") | !exists("segs_ordered")) {
db_ordered <- get_previous(folder, step = "ordered", where = "wepp") %>%
add_buffer()
segs_ordered <- get_previous(folder, step = "ordered", where = "wepp", type = "stats") %>%
add_buffer(db = db_ordered, stats = .)
}
db_ddir <- redo_ddir(db_ordered, segs_ordered)
segs_ddir <- db_ddir$segs
db_ddir <- db_ddir$db
save_output(data = db_ddir, stats = segs_ddir, name = "ddir2", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
save_output(data = db_ddir, name = "ddir2", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Find upsegs ----------------------------------------------------
task <- "Find upslope segments"
if(resume == "" || resume == "find_upsegs") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("segs_ordered")) {
db_ddir <- get_previous(folder, step = "ddir2", where = "wepp") %>%
add_buffer()
segs_ddir <- get_previous(folder, step = "ddir2", where = "wepp",
type = "stats") %>%
add_buffer(db_ddir, stats = .)
}
segs_upsegs <- find_upsegs(segs_ddir)
save_output(data = db_ddir, stats = segs_upsegs, name = "upsegs", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Hillslope segs ----------------------------------------------------
task <- "Compute and label hillslope segments"
if(resume == "" || resume == "hill_sheds") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_ddir")) {
db_ddir <- get_previous(folder, step = "ddir2", where = "wepp") %>%
add_buffer()
}
db_hillsheds <- hill_sheds(db_ddir)
save_output(data = db_hillsheds, name = "hillsheds", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Renumber segments ----------------------------------------------------
task <- "Renumber segments"
if(resume == "" || resume == "renum_segs") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_hillsheds") | !exists("segs_upsegs")) {
db_hillsheds <- get_previous(folder, step = "hillsheds", where = "wepp") %>%
add_buffer()
segs_upsegs <- get_previous(folder, step = "upsegs", where = "wepp", type = "stats") %>%
add_buffer(db_hillsheds, stats = .)
}
db_renum <- renum_segs(db_hillsheds, segs_upsegs)
segs_renum <- db_renum$segs
db_renum <- db_renum$db
save_output(data = db_renum, stats = segs_renum, name = "renum", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
save_output(data = db_renum, name = "renum", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Build WEPP structure file ----------------------------------------------------
task <- "Build WEPP structure file"
if(resume == "" || resume == "build_stru") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_renum") | !exists("segs_renum")) {
db_renum <- get_previous(folder, step = "renum", where = "wepp") %>%
add_buffer()
segs_renum <- get_previous(folder, step = "renum", where = "wepp",
type = "stats") %>%
add_buffer(db_renum, stats = .)
}
struct <- build_stru(db_renum, segs_renum)
segs_struct <- struct$segs %>%
dplyr::mutate(flow2crow = 0, chan_shape = 0, width_m = 0) %>%
dplyr::select(-"upside", -"not_equal", -"num_down")
struct <- struct$struct
save_basic(data = struct, name = "struct", locs = out_locs,
out_format = out_format, where = "wepp")
save_basic(data = remove_buffer(db_renum, segs_struct),
name = "segs", locs = out_locs,
out_format = out_format, where = "wepp")
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Compute aspect and slope for WEPP -----------------------------------------
task <- "Compute aspect and slope for WEPP"
if(resume == "" || resume == "wepp_form") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_renum")) {
db_renum <- get_previous(folder, step = "renum", where = "wepp") %>%
add_buffer()
}
db_wepp_form <- wepp_form(db_renum, grid)
save_output(data = db_wepp_form, name = "wepp_form", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Measures of channel length ------------------------------------------------
task <- "Calcualte 3 measures of channel length"
if(resume == "" || resume == "wepp_len") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_wepp_form")) {
db_wepp_form <- get_previous(folder, step = "wepp_form", where = "wepp") %>%
add_buffer()
}
db_wepp_len <- wepp_len(db_wepp_form, grid)
save_output(data = db_wepp_len, name = "wepp", locs = out_locs,
out_format = out_format, where = "wepp", debug = debug)
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Hill Stats (profiles) -------------------------------------------------------------------
task <- "Calculate hill profiles"
if(resume == "" || resume == "hill_stats") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_wepp_len") | !exists("segs_struct")) {
db_wepp_len <- get_previous(folder, step = "wepp", where = "wepp") %>%
add_buffer()
segs_struct <- get_previous(folder, step = "stats_segs", where = "wepp",
type = "stats") %>%
add_buffer(db_wepp_len, stats = .)
}
db_hill_stats <- hill_stats(db_wepp_len, segs_struct, grid)
save_basic(data = db_hill_stats$hill, name = "hill", locs = out_locs,
out_format = out_format, where = "wepp")
save_basic(data = db_hill_stats$prof, name = "prof", locs = out_locs,
out_format = out_format, where = "wepp")
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Chan Stats -------------------------------------------------------------------
task <- "Calculate channel stats"
if(resume == "" || resume == "chan_stats") {
announce(task, quiet)
sub_start <- Sys.time()
log_start(task, sub_start, log_file)
if(!exists("db_wepp_len") | !exists("segs_struct")) {
db_wepp_len <- get_previous(folder, step = "wepp_len", where = "wepp") %>%
add_buffer()
segs_struct <- get_previous(folder, step = "struct", where = "wepp",
type = "stats") %>%
add_buffer(db_wepp_len, stats = .)
}
db_chan_stats <- chan_stats(db_wepp_len, segs_struct, grid)
save_basic(data = db_chan_stats, name = "chan", locs = out_locs,
out_format = out_format, where = "wepp")
log_time(sub_start, log_file)
resume <- ""
} else skip_task(task, log_file, quiet)
# Clean up
if(!debug) remove_output(locs = out_locs, out_format = out_format,
where = "wepp")
# Save final time
run_time(start, log_file, quiet)
}