Use outputs from cloud2trees() to generate inputs for LANL TREES program

cloud2trees_to_lanl_trees() uses the output from cloud2trees() to generate inputs for LANL TREES program as a pathway to fire modeling with Quic-Fire

The primary input is a directory with outputs from cloud2trees(). The default directory written by cloud2trees() is point_cloud_processing_delivery which must contain (at a minimum):

• DTM raster with a name formatted as: "dtm_xx.tif"

• Tree list data with the name formatted as : "final_detected_tree_tops.gpkg" (tree points) or "final_detected_crowns.gpkg" (tree crowns)

• A study area spatial file that can be read with the sf package (see sf::st_drivers())

Usage

cloud2trees_to_lanl_trees(
  input_dir,
  study_boundary = NA,
  bbox_aoi = T,
  buffer = 0,
  topofile = "flat",
  cbd_method = "landfire",
  output_dir = tempdir(),
  fuel_litter = list(ilitter = 0, lrho = 4.667, lmoisture = 0.06, lss = 5e-04, ldepth =
    0.06),
  fuel_grass = list(igrass = 0, grho = 1.17, gmoisture = 0.06, gss = 5e-04, gdepth =
    0.27)
)

Arguments

input_dir

directory with outputs from cloud2trees(). The default directory written by cloud2trees() is point_cloud_processing_delivery

study_boundary

sf. The boundary of the study area which is used to determine the outputs

bbox_aoi

logical. Should the study_boundary be transformed to a bounding box instead of it's original shape for determining the objects within the boundary?

buffer

numeric. Buffer to be applied to the study area prior to determining objects within the boundary. Units are determined by the horizontal CRS settings of the tree list data

topofile

character. one of "flat" or "dtm":

• "flat" - always flat for QUIC-Fire

• "dtm" - uses the topo.dat file created based on the DTM; potentially for FIRETEC

cbd_method

character. one of "landfire" or "cruz":

• Tree crown biomass method:

  • "landfire" - based on LANDFIRE's Forest Canopy Bulk Density (CBD) data (trees_biomass_landfire())

  • "cruz" - based on Cruz et al. (2003) canopy fuel stratum equations (trees_biomass_cruz())

output_dir

parent directory where new folder lanl_trees_delivery will be written for exports

fuel_litter

list. a list() or numeric vector c(). see default.

• must have parameters in order:

  • "ilitter" : 0 = no litter, 1 = litter

  • "lrho" : litter bulk density (kg/m3)

  • "lmoisture : litter moisture (percent on 0-1 scale)

  • "lss" : litter sizescale (m)

  • "ldepth" : litter depth (m)

fuel_grass

list. a list() or numeric vector c(). see default.

• must have parameters in order:

  • "igrass" : 0 = no grass, 1 = grass

  • "grho" : grass bulk density (kg/m3)

  • "gmoisture" : grass moisture (percent on 0-1 scale)

  • "gss" : grass sizescale (m)

  • "gdepth" : grass depth (m)

Value

Returns a list of objects:

• "tree_list" = the cropped tree list based on the study area extent with customized settings

• "aoi" = the study area extent with customized settings

• "dtm" = the cropped DTM based on the study area extent with customized settings

• "domain_path" = the path to the "Lidar_Bounds.geojson" file

• "topofile_path" = the path to the "topo.dat" file

• "fuellist_path" = the path to the TREES program "fuellist" file

• "treelist_path" = the path to the "Cloud2Trees_TreeList.txt" file

References

• https://github.com/lanl/Trees/

• Quic-Fire

Examples

 if (FALSE) { # \dontrun{
 # test las file but this could also be a directory path with >1 .las|.laz files
 i <- system.file("extdata", "MixedConifer.laz", package="lidR")
 # set the dir to write the output
 my_dir <- tempdir()
 # run it
 cloud2trees_ans <- cloud2trees::cloud2trees(
   output_dir = my_dir
   , input_las_dir = i
   # turn on all of the attribute estimations
   , estimate_tree_dbh = T
   , estimate_tree_type = T
   , estimate_tree_hmd = T
   , hmd_tree_sample_prop = 0.5
   , hmd_estimate_missing_hmd = T
   , estimate_biomass_method = "landfire"
   , estimate_tree_cbh = T
   , cbh_tree_sample_prop = 0.3
   , cbh_estimate_missing_cbh = T
 )
 # generate a fake study_boundary we know overlaps the tree list
 my_aoi <- cloud2trees_ans$treetops_sf %>%
   sf::st_bbox() %>%
   sf::st_as_sfc() %>%
   sf::st_buffer(-10) %>%
   sf::st_as_sf()
 # plot it
 ggplot2::ggplot() +
   ggplot2::geom_sf(data = cloud2trees_ans$treetops_sf) +
   ggplot2::geom_sf(data = my_aoi, fill = NA, color = "blue")
 # cloud2trees::cloud2trees() wrote the `point_cloud_processing_delivery` folder
 cloud2trees_output_dir <- file.path(my_dir,"point_cloud_processing_delivery")
 list.files(cloud2trees_output_dir)
 list.dirs(cloud2trees_output_dir, recursive = F)
 # now cloud2trees_to_lanl_trees()
 cloud2trees_to_lanl_trees_ans <- cloud2trees_to_lanl_trees(
   input_dir = cloud2trees_output_dir
   , study_boundary = my_aoi
   , bbox_aoi = F
   , buffer = 0
   , topofile = "flat"
   , cbd_method = "landfire"
   , output_dir = cloud2trees_output_dir
 )
 cloud2trees_to_lanl_trees_ans %>% names()
 list.dirs(cloud2trees_output_dir, recursive = F)
 lanl_trees_output_dir <- file.path(cloud2trees_output_dir,"lanl_trees_delivery")
 list.files(lanl_trees_output_dir)
 } # }