Cleanups and moving old code out

.Rbuildignore

@@ -19,7 +19,13 @@ workspace
 ^[.].*$
 ^.*/[.].*$
 ^general_visuals\.R$
-^scraps\.R$
+
+^scrap\.r$ 
+^scraps\.r$
 ^scraps2\.R$
 ^scraps3\.R$
+^braids_tmp\.R$
+^braids2\.R$
+^braids3\.R$
+
 

.gitignore

@@ -19,4 +19,21 @@ tmp_plots.R
 scraps.R
 scraps2.R
 scraps3.R
-general_visuals.R
+
+# TODO: remove paper related scripts
+general_visuals.R
+visual_utils.R
+paper.R
+validity_scoring.R
+transect_extensions_viz.R
+ras_comp.R
+cs_area2.R
+cs_based_extensions_viz.R
+paper/
+
+
+scrap.R
+braids_tmp.R
+braids2.R
+braids3.R
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hydrofabric3D
 Title: hydrofabric3D
-Version: 0.0.96
+Version: 0.1.51
 Authors@R: c(person("Mike", "Johnson", role = c("aut", "cre"), email = "[email protected]"),
              person("Angus", "Watters",  role = "aut"),
              person("Arash", "Modaresi",  role = "ctb"),
@@ -22,12 +22,16 @@ Imports:
   smoothr,
   zoo,
   nhdplusTools,
+  hydroloom,
   fastmap,
+  DescTools,
+  purrr,
   ggplot2,
   rlang,
   lwgeom,
   rmapshaper,
-  AHGestimation
+  AHGestimation,
+  methods
 Remotes:
   mikejohnson51/AHGestimation
 Depends: 

NAMESPACE

@@ -1,55 +1,61 @@
 # Generated by roxygen2: do not edit by hand
 
-export(add_angle_at_point_type)
+export(add_braid_ids)
+export(add_cs_area)
+export(add_cs_area2)
 export(add_cs_bathymetry)
-export(add_middle_index_by_point_type)
+export(add_hydrofabric_id)
+export(add_is_outlet_flag)
+export(add_length_col)
 export(add_point_type_counts)
+export(add_powerlaw_bankful_width)
 export(add_relief)
 export(add_tmp_id)
+export(adjust_flagged_transects)
+export(adjust_transect_lengths)
 export(align_banks_and_bottoms)
-export(angle_at_index)
 export(classify_points)
+export(compare_cs_validity)
 export(cross_section_pts)
-export(cross_section_pts_v2)
-export(cross_section_pts_v3)
 export(cut_cross_sections)
 export(cut_transect)
-export(extend_invalid_transects)
-export(extend_transects)
-export(extend_transects_by_distances)
-export(extend_transects_by_length)
+export(drop_incomplete_cs_pts)
+export(extend_by_length)
+export(extend_by_percent)
+export(extend_transects_by_cs_attributes)
+export(extend_transects_sides)
 export(extend_transects_to_polygons)
 export(extend_transects_to_polygons2)
-export(fill_missing_ahg_coords)
 export(find_braids)
-export(find_connected_components)
-export(fix_braid_transects)
+export(find_cs_area2)
+export(fix_braided_transects)
+export(flag_transects_for_change)
 export(geos_extend_line)
+export(get_bank_attributes)
 export(get_braid_list)
-export(get_coords_around_parabola)
 export(get_cs_bottom_length)
 export(get_extensions_by_id)
+export(get_improved_cs_pts)
 export(get_point_type_counts)
 export(get_relief)
-export(get_transect_extension_distances_to_polygons)
+export(get_start_node)
 export(get_transects)
 export(get_unique_tmp_ids)
-export(improve_invalid_cs)
+export(get_validity_tally)
 export(is_braided)
-export(make_progress_bar)
 export(pct_pts_near_bottom)
-export(pick_extension_pts)
 export(plot_cs_pts)
+export(pts_to_XY)
 export(pts_to_reevaluate)
-export(rectify_cs)
 export(rectify_flat_cs)
 export(rectify_summary)
-export(subset_polygons_in_transects)
-export(subset_transects_in_polygons)
-export(unique_braids)
-export(unnpack_braids)
+export(unpack_braids)
+export(validate_transects)
+export(validate_transects_against_flowlines)
 importFrom(AHGestimation,cross_section)
+importFrom(DescTools,AUC)
 importFrom(dplyr,`%>%`)
+importFrom(dplyr,across)
 importFrom(dplyr,add_count)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
@@ -58,6 +64,7 @@ importFrom(dplyr,between)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,count)
+importFrom(dplyr,distinct)
 importFrom(dplyr,ends_with)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
@@ -71,6 +78,7 @@ importFrom(dplyr,n)
 importFrom(dplyr,n_distinct)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
+importFrom(dplyr,row_number)
 importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
@@ -105,19 +113,24 @@ importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
+importFrom(hydroloom,add_toids)
+importFrom(hydroloom,align_names)
+importFrom(hydroloom,hy)
+importFrom(hydroloom,make_attribute_topology)
+importFrom(hydroloom,make_node_topology)
+importFrom(hydroloom,rename_geometry)
 importFrom(lwgeom,st_linesubstring)
-importFrom(nhdplusTools,get_UT)
+importFrom(methods,is)
 importFrom(nhdplusTools,get_node)
-importFrom(nhdplusTools,get_sorted)
-importFrom(nhdplusTools,get_tocomid)
-importFrom(nhdplusTools,make_node_topology)
 importFrom(nhdplusTools,rename_geometry)
+importFrom(purrr,map_dbl)
 importFrom(rlang,as_name)
 importFrom(rlang,enquo)
 importFrom(rmapshaper,ms_simplify)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_cast)
 importFrom(sf,st_centroid)
+importFrom(sf,st_coordinates)
 importFrom(sf,st_crs)
 importFrom(sf,st_distance)
 importFrom(sf,st_drop_geometry)
@@ -141,6 +154,7 @@ importFrom(terra,res)
 importFrom(terra,vect)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate_rows)
 importFrom(tidyr,unnest)
 importFrom(utils,str)
 importFrom(utils,txtProgressBar)