Updating cross_section_pts() function to remove and reevaluate "flat" Z value cross sections

.Rbuildignore

@@ -9,3 +9,17 @@ workspace
 ^docs$
 ^pkgdown$
 ^vignettes/articles$
+^\\runners$
+^runners/.*$
+
+^hydrofabric3D\.Rproj$
+^\.github$
+^\\.urs_cookies$
+^\\.dodsrc$
+^[.].*$
+^.*/[.].*$
+^general_visuals\.R$
+^scraps\.R$
+^scraps2\.R$
+^scraps3\.R$
+

.gitignore

@@ -2,4 +2,21 @@
 .Rhistory
 .RData
 .Ruserdata
-R/scraps.R
+
+.DS_Store
+*.DS_Store
+**/.DS_Store
+
+.urs_cookies
+*.urs_cookies
+**/.urs_cookies
+
+R/scraps.R
+
+runners/cs_runner/
+tmp_plots.R
+
+scraps.R
+scraps2.R
+scraps3.R
+general_visuals.R

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hydrofabric3D
 Title: hydrofabric3D
-Version: 0.0.1
+Version: 0.0.96
 Authors@R: c(person("Mike", "Johnson", role = c("aut", "cre"), email = "[email protected]"),
              person("Angus", "Watters",  role = "aut"),
              person("Arash", "Modaresi",  role = "ctb"),
@@ -16,19 +16,27 @@ Imports:
   wk,
   terra,
   dplyr,
-  terra,
   tidyr,
   vctrs,
   sf,
   smoothr,
   zoo,
   nhdplusTools,
-  fastmap
+  fastmap,
+  ggplot2,
+  rlang,
+  lwgeom,
+  rmapshaper,
+  AHGestimation
+Remotes:
+  mikejohnson51/AHGestimation
 Depends: 
     R (>= 2.10)
 LazyData: true
 Config/Needs/website: rmarkdown
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 hydrofabric3D authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,36 +1,83 @@
 # Generated by roxygen2: do not edit by hand
 
+export(add_angle_at_point_type)
+export(add_cs_bathymetry)
+export(add_middle_index_by_point_type)
+export(add_point_type_counts)
+export(add_relief)
+export(add_tmp_id)
+export(align_banks_and_bottoms)
+export(angle_at_index)
 export(classify_points)
 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(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(geos_extend_line)
 export(get_braid_list)
+export(get_coords_around_parabola)
+export(get_cs_bottom_length)
+export(get_extensions_by_id)
+export(get_point_type_counts)
+export(get_relief)
+export(get_transect_extension_distances_to_polygons)
 export(get_transects)
+export(get_unique_tmp_ids)
+export(improve_invalid_cs)
 export(is_braided)
+export(make_progress_bar)
+export(pct_pts_near_bottom)
+export(pick_extension_pts)
+export(plot_cs_pts)
+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)
+importFrom(AHGestimation,cross_section)
 importFrom(dplyr,`%>%`)
 importFrom(dplyr,add_count)
 importFrom(dplyr,all_of)
+importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,between)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,case_when)
+importFrom(dplyr,count)
+importFrom(dplyr,ends_with)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,lag)
+importFrom(dplyr,last_col)
 importFrom(dplyr,lead)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
+importFrom(dplyr,n_distinct)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
+importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
+importFrom(dplyr,slice_max)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
+importFrom(dplyr,sym)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(fastmap,fastmap)
@@ -42,19 +89,32 @@ importFrom(geos,geos_interpolate_normalized)
 importFrom(geos,geos_intersection)
 importFrom(geos,geos_intersects)
 importFrom(geos,geos_intersects_any)
+importFrom(geos,geos_intersects_matrix)
 importFrom(geos,geos_is_empty)
 importFrom(geos,geos_length)
 importFrom(geos,geos_make_linestring)
 importFrom(geos,geos_point_end)
+importFrom(geos,geos_point_start)
+importFrom(geos,geos_simplify_preserve_topology)
 importFrom(geos,geos_type)
+importFrom(geos,geos_within_matrix)
 importFrom(geos,geos_x)
 importFrom(geos,geos_y)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
+importFrom(lwgeom,st_linesubstring)
 importFrom(nhdplusTools,get_UT)
 importFrom(nhdplusTools,get_node)
 importFrom(nhdplusTools,get_sorted)
 importFrom(nhdplusTools,get_tocomid)
 importFrom(nhdplusTools,make_node_topology)
 importFrom(nhdplusTools,rename_geometry)
+importFrom(rlang,as_name)
+importFrom(rlang,enquo)
+importFrom(rmapshaper,ms_simplify)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_cast)
 importFrom(sf,st_centroid)
@@ -65,10 +125,12 @@ importFrom(sf,st_geometry)
 importFrom(sf,st_intersects)
 importFrom(sf,st_length)
 importFrom(sf,st_line_sample)
+importFrom(sf,st_segmentize)
 importFrom(sf,st_set_geometry)
 importFrom(sf,st_transform)
 importFrom(smoothr,densify)
 importFrom(smoothr,smooth)
+importFrom(stats,median)
 importFrom(stats,setNames)
 importFrom(terra,crs)
 importFrom(terra,extract)
@@ -77,7 +139,11 @@ importFrom(terra,project)
 importFrom(terra,rast)
 importFrom(terra,res)
 importFrom(terra,vect)
+importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)
 importFrom(tidyr,unnest)
+importFrom(utils,str)
+importFrom(utils,txtProgressBar)
 importFrom(vctrs,vec_c)
 importFrom(wk,wk_affine_compose)
 importFrom(wk,wk_affine_rotate)