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new example data, archiving associated vignette for now
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dylanbeaudette committed Sep 5, 2023
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2 changes: 1 addition & 1 deletion NEWS.md
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# aqp 2.01 (2023-08-29)
# aqp 2.01 (2023-09-03)
* new function `flagOverlappingHz()` for identifying horizons with perfect overlap
* `fillHzGaps()`, `dice()`, `slab()`, and several other functions now safely handle horizons with perfect overlap (#296)

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8 changes: 8 additions & 0 deletions R/data-documentation.R
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#' @title Example SoilProfileCollection with Overlapping Horizons
#' @description A `SoilProfileCollection` with overlapping horizons, derived from a Dynamic Soil Properties project.
#' @keywords datasets
#' @usage data(SPC.with.overlap)
#' @format A `SoilProfileCollection`
"SPC.with.overlap"


#' @title Example Data from Wilson et al. 2022
#' @description An example `SoilProfileCollection`, derived from Wilson et al., 2022. Select data extracted from Appendix tables.
#' @keywords datasets
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16 changes: 16 additions & 0 deletions man/SPC.with.overlap.Rd
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118 changes: 118 additions & 0 deletions misc/example-data/overlapping-horizons/2020GRR014SPCdata.csv
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"","NasisSiteName","upedonid","hzdept","hzdepb","hzname","texture","claytotest","phfield","mxhue","mxvalue","mxchroma","taxonname","dspplotid","earthcovkind1","earthcovkind2"
"1","MLRA12_Amherst","S2020MI037001",0,28,"Ap","FSL",15,6.8,"10YR",4,2,"Conover","C-CT-1","Crop cover","Close-grown crop"
"2","MLRA12_Amherst","S2020MI037001",28,37,"Bt/E (Bt)","L",20,7.2,"10YR",5,4,"Conover","C-CT-1","Crop cover","Close-grown crop"
"3","MLRA12_Amherst","S2020MI037001",28,37,"Bt/E (E)","FSL",20,7.2,"10YR",6,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"4","MLRA12_Amherst","S2020MI037001",37,55,"Bt1","L",25,7.8,"10YR",5,4,"Conover","C-CT-1","Crop cover","Close-grown crop"
"5","MLRA12_Amherst","S2020MI037001",55,76,"Bt2","CL",30,8,"10YR",5,4,"Conover","C-CT-1","Crop cover","Close-grown crop"
"6","MLRA12_Amherst","S2020MI037001",76,120,"Cd1","L",25,8.2,"10YR",5,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"7","MLRA12_Amherst","S2020MI037001",120,175,"Cd2","L",20,8.2,"10YR",5,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"8","MLRA12_Amherst","S2020MI037001A",0,25,"Ap","FSL",18,7,"10YR",4,2,"Conover","C-CT-1","Crop cover","Close-grown crop"
"9","MLRA12_Amherst","S2020MI037001A",25,36,"E/Bt (E)","L",26,7.2,"10YR",5,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"10","MLRA12_Amherst","S2020MI037001A",25,36,"E/Bt (Bt)","CL",26,7.2,"10YR",5,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"11","MLRA12_Amherst","S2020MI037001A",36,52,"Bt","CL",29,7.2,"10YR",4,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"12","MLRA12_Amherst","S2020MI037001B",0,23,"Ap","FSL",16,7.7,"10YR",4,2,"Conover","C-CT-1","Crop cover","Close-grown crop"
"13","MLRA12_Amherst","S2020MI037001B",23,33,"B/E (Bt)","L",20,7.6,"10YR",5,4,"Conover","C-CT-1","Crop cover","Close-grown crop"
"14","MLRA12_Amherst","S2020MI037001B",23,33,"B/E (E)","FSL",20,7.6,"2.5Y",6,4,"Conover","C-CT-1","Crop cover","Close-grown crop"
"15","MLRA12_Amherst","S2020MI037001B",33,55,"Bt","CL",28,7.6,"10YR",5,3,"Conover","C-CT-1","Crop cover","Close-grown crop"
"16","MLRA12_Amherst","S2020MI037002",0,22,"Ap","L",20,7.4,"10YR",3,2,"Conover","C-NT-1","Crop cover","Row crop"
"17","MLRA12_Amherst","S2020MI037002",22,37,"Bt1","CL",28,7.6,"10YR",5,4,"Conover","C-NT-1","Crop cover","Row crop"
"18","MLRA12_Amherst","S2020MI037002",37,61,"Bt2","CL",30,7.8,"10YR",5,3,"Conover","C-NT-1","Crop cover","Row crop"
"19","MLRA12_Amherst","S2020MI037002",61,98,"BCd","L",25,7.8,"10YR",5,4,"Conover","C-NT-1","Crop cover","Row crop"
"20","MLRA12_Amherst","S2020MI037002",98,145,"Cd","L",25,8.2,"10YR",5,4,"Conover","C-NT-1","Crop cover","Row crop"
"21","MLRA12_Amherst","S2020MI037002A",0,21,"Ap","L",26,7,"10YR",3,2,"Conover","C-NT-1","Crop cover","Row crop"
"22","MLRA12_Amherst","S2020MI037002A",21,53,"Bt","CL",29,7.3,"10YR",6,3,"Conover","C-NT-1","Crop cover","Row crop"
"23","MLRA12_Amherst","S2020MI037002B",0,27,"Ap","L",24,7.2,"10YR",5,2,"Conover","C-NT-1","Crop cover","Row crop"
"24","MLRA12_Amherst","S2020MI037002B",27,50,"Bt","CL",30,7.4,"10YR",5,3,"Conover","C-NT-1","Crop cover","Row crop"
"25","MLRA12_Amherst","S2020MI037003",0,14,"A","SIL",15,7.4,"10YR",2,1,"Conover","C-RF-1","Tree cover","Hardwoods"
"26","MLRA12_Amherst","S2020MI037003",14,28,"E","L",20,7.4,"10YR",6,1,"Conover","C-RF-1","Tree cover","Hardwoods"
"27","MLRA12_Amherst","S2020MI037003",28,42,"Bt1","CL",32,7.6,"10YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"28","MLRA12_Amherst","S2020MI037003",42,68,"Bt2","CL",34,7.8,"10YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"29","MLRA12_Amherst","S2020MI037003",68,87,"BCtk","CL",32,8.2,"10YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"30","MLRA12_Amherst","S2020MI037003",87,120,"Cd","L",20,8.2,"10YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"31","MLRA12_Amherst","S2020MI037003A",0,15,"A","FSL",14,6.9,"10YR",2,2,"Conover","C-RF-1","Tree cover","Hardwoods"
"32","MLRA12_Amherst","S2020MI037003A",15,28,"E","SL",17,7.1,"10YR",6,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"33","MLRA12_Amherst","S2020MI037003A",28,43,"E/B (E)","SL",19,7.2,"10YR",3,2,"Conover","C-RF-1","Tree cover","Hardwoods"
"34","MLRA12_Amherst","S2020MI037003A",28,43,"E/B (B)","CL",29,7.2,"7.5YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"35","MLRA12_Amherst","S2020MI037003A",43,55,"Bt","CL",33,7.3,"7.5YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"36","MLRA12_Amherst","S2020MI037003B",0,19,"A","L",16,7.2,"10YR",2,1,"Conover","C-RF-1","Tree cover","Hardwoods"
"37","MLRA12_Amherst","S2020MI037003B",19,29,"E","FSL",16,7.6,"10YR",6,2,"Conover","C-RF-1","Tree cover","Hardwoods"
"38","MLRA12_Amherst","S2020MI037003B",29,50,"Bt1","CL",25,7.8,"10YR",5,4,"Conover","C-RF-1","Tree cover","Hardwoods"
"39","MLRA12_Amherst","S2020MI037003B",50,62,"Bt2","CL",28,7.8,"10YR",5,3,"Conover","C-RF-1","Tree cover","Hardwoods"
"40","MLRA12_Amherst","S2020MI057001",0,20,"Ap","L",20,6.2,"10YR",3,1,"Conover","C-NT-2","Crop cover","Row crop"
"41","MLRA12_Amherst","S2020MI057001",20,35,"Bt1","L",27,6.8,"2.5Y",5,3,"Conover","C-NT-2","Crop cover","Row crop"
"42","MLRA12_Amherst","S2020MI057001",35,56,"Bt2","CL",31,7.4,"10YR",5,3,"Conover","C-NT-2","Crop cover","Row crop"
"43","MLRA12_Amherst","S2020MI057001",56,105,"BC","CL",38,7.4,"10YR",5,3,"Conover","C-NT-2","Crop cover","Row crop"
"44","MLRA12_Amherst","S2020MI057001",105,134,"C","CL",28,7.6,"10YR",5,3,"Conover","C-NT-2","Crop cover","Row crop"
"45","MLRA12_Amherst","S2020MI057001",134,173,"Cd1","L",25,8,"10YR",5,4,"Conover","C-NT-2","Crop cover","Row crop"
"46","MLRA12_Amherst","S2020MI057001",173,200,"Cd2","L",26,8,"10YR",5,3,"Conover","C-NT-2","Crop cover","Row crop"
"47","MLRA12_Amherst","S2020MI057001A",0,30,"Ap","FSL",20,7,"10YR",3,2,"Metamora","C-NT-2","Crop cover","Row crop"
"48","MLRA12_Amherst","S2020MI057001A",30,65,"Bt","SL",18,7.8,"10YR",4,4,"Metamora","C-NT-2","Crop cover","Row crop"
"49","MLRA12_Amherst","S2020MI057001A",65,74,"BC","VFSL",15,NA,NA,NA,NA,"Metamora","C-NT-2","Crop cover","Row crop"
"50","MLRA12_Amherst","S2020MI057001B",0,34,"Ap","L",25,7,"10YR",3,2,"Conover","C-NT-2","Crop cover","Row crop"
"51","MLRA12_Amherst","S2020MI057001B",34,59,"Bt","CL",29,7.7,"10YR",5,3,"Conover","C-NT-2","Crop cover","Row crop"
"52","MLRA12_Amherst","S2021MI037001",0,26,"Ap","L",20,6.4,"10YR",3,3,"Conover","C-NT-3","Crop cover","Close-grown crop"
"53","MLRA12_Amherst","S2021MI037001",26,45,"Bt1","CL",31,7.6,"10YR",5,4,"Conover","C-NT-3","Crop cover","Close-grown crop"
"54","MLRA12_Amherst","S2021MI037001",45,77,"Bt2","CL",34,7.8,"10YR",4,4,"Conover","C-NT-3","Crop cover","Close-grown crop"
"55","MLRA12_Amherst","S2021MI037001",77,102,"BCt","CL",28,8,"10YR",5,4,"Conover","C-NT-3","Crop cover","Close-grown crop"
"56","MLRA12_Amherst","S2021MI037001",102,185,"Cd","L",26,8.2,"10YR",5,3,"Conover","C-NT-3","Crop cover","Close-grown crop"
"57","MLRA12_Amherst","S2021MI037001",185,205,"2C1","SR- VFSL L",11,7.2,"10YR",5,4,"Conover","C-NT-3","Crop cover","Close-grown crop"
"58","MLRA12_Amherst","S2021MI037001",205,220,"2C2","S",1,NA,"10YR",5,4,"Conover","C-NT-3","Crop cover","Close-grown crop"
"59","MLRA12_Amherst","S2021MI037001A",0,25,"Ap","L",22,7.8,"10YR",3,3,"Conover","C-NT-3","Crop cover","Close-grown crop"
"60","MLRA12_Amherst","S2021MI037001A",25,52,"Bt","SCL",28,6.8,"10YR",5,3,"Conover","C-NT-3","Crop cover","Close-grown crop"
"61","MLRA12_Amherst","S2021MI037001B",0,24,"Ap","L",25,7.4,NA,NA,NA,"Conover","C-NT-3","Crop cover","Close-grown crop"
"62","MLRA12_Amherst","S2021MI037001B",24,39,"Bt1","CL",29,6.8,"10YR",6,3,"Conover","C-NT-3","Crop cover","Close-grown crop"
"63","MLRA12_Amherst","S2021MI037001B",39,61,"Bt2","CL",33,7.2,"10YR",5,4,"Conover","C-NT-3","Crop cover","Close-grown crop"
"64","MLRA12_Amherst","S2021MI037002",0,21,"A","L",17,6.7,"10YR",2,2,"Crosier","C-RF-2","Tree cover","Hardwoods"
"65","MLRA12_Amherst","S2021MI037002",21,40,"E","FSL",19,5.8,"10YR",5,3,"Crosier","C-RF-2","Tree cover","Hardwoods"
"66","MLRA12_Amherst","S2021MI037002",40,62,"Btg","L",25,5.8,"10YR",5,2,"Crosier","C-RF-2","Tree cover","Hardwoods"
"67","MLRA12_Amherst","S2021MI037002",62,89,"Bt","CL",29,7.6,"7.5YR",5,3,"Crosier","C-RF-2","Tree cover","Hardwoods"
"68","MLRA12_Amherst","S2021MI037002",89,140,"Cd1","CL",31,8.2,"10YR",5,3,"Crosier","C-RF-2","Tree cover","Hardwoods"
"69","MLRA12_Amherst","S2021MI037002",140,204,"Cd2","CL",34,8.3,"10YR",5,4,"Crosier","C-RF-2","Tree cover","Hardwoods"
"70","MLRA12_Amherst","S2021MI037002A",0,15,"A","L",15,6.8,"10YR",2,2,"Conover","C-RF-2","Tree cover","Hardwoods"
"71","MLRA12_Amherst","S2021MI037002A",15,23,"E","FSL",18,6.6,"10YR",5,3,"Conover","C-RF-2","Tree cover","Hardwoods"
"72","MLRA12_Amherst","S2021MI037002A",23,53,"Bt","CL",28,6.4,"10YR",4,3,"Conover","C-RF-2","Tree cover","Hardwoods"
"73","MLRA12_Amherst","S2021MI037002A",53,62,"BCtg","L",23,NA,"10YR",5,2,"Conover","C-RF-2","Tree cover","Hardwoods"
"74","MLRA12_Amherst","S2021MI037002B",0,19,"A","L",15,6.4,"10YR",3,2,"Conover","C-RF-2","Tree cover","Hardwoods"
"75","MLRA12_Amherst","S2021MI037002B",19,29,"E","FSL",15,6,"10YR",5,2,"Conover","C-RF-2","Tree cover","Hardwoods"
"76","MLRA12_Amherst","S2021MI037002B",29,55,"Bt","CL",28,6.8,"10YR",5,3,"Conover","C-RF-2","Tree cover","Hardwoods"
"77","MLRA12_Amherst","S2021MI037002B",55,62,"BCt","L",26,8,"10YR",5,3,"Conover","C-RF-2","Tree cover","Hardwoods"
"78","MLRA12_Amherst","S2021MI045001",0,20,"A","SIL",18,7.5,"10YR",2.5,2,"Conover","C-RF-3","Tree cover","Hardwoods"
"79","MLRA12_Amherst","S2021MI045001",20,37,"E/Bt","FSL L",15,7.3,"10YR",6,2,"Conover","C-RF-3","Tree cover","Hardwoods"
"80","MLRA12_Amherst","S2021MI045001",37,70,"Bt","CL",29,7.6,"10YR",5,4,"Conover","C-RF-3","Tree cover","Hardwoods"
"81","MLRA12_Amherst","S2021MI045001",70,160,"Cd1","L",23,8.2,"10YR",5,3,"Conover","C-RF-3","Tree cover","Hardwoods"
"82","MLRA12_Amherst","S2021MI045001",160,215,"Cd2","L",23,8.4,"10YR",5,4,"Conover","C-RF-3","Tree cover","Hardwoods"
"83","MLRA12_Amherst","S2021MI045001A",0,15,"A","SIL",16,7.4,"10YR",2,2,"Crosier","C-RF-3","Tree cover","Hardwoods"
"84","MLRA12_Amherst","S2021MI045001A",15,28,"E","FSL",18,7.4,"10YR",6,2,"Crosier","C-RF-3","Tree cover","Hardwoods"
"85","MLRA12_Amherst","S2021MI045001A",28,45,"Btg","CL",28,7.4,"10YR",5,2,"Crosier","C-RF-3","Tree cover","Hardwoods"
"86","MLRA12_Amherst","S2021MI045001A",45,69,"Bt","CL",29,7.6,"10YR",5,4,"Crosier","C-RF-3","Tree cover","Hardwoods"
"87","MLRA12_Amherst","S2021MI045001B",0,25,"A","SIL",16,7.6,"10YR",2,2,"Conover","C-RF-3","Tree cover","Hardwoods"
"88","MLRA12_Amherst","S2021MI045001B",25,43,"E","SL",16,7.7,"10YR",5,2,"Conover","C-RF-3","Tree cover","Hardwoods"
"89","MLRA12_Amherst","S2021MI045001B",43,66,"Bt","L",26,7.6,"10YR",5,4,"Conover","C-RF-3","Tree cover","Hardwoods"
"90","MLRA12_Amherst","S2021MI065001",0,25,"Ap1","L",18,7.8,"10YR",3,2,"Crosier","C-CT-3","Crop cover","Row crop"
"91","MLRA12_Amherst","S2021MI065001",25,40,"Ap2","L",18,7.6,"10YR",3,2,"Crosier","C-CT-3","Crop cover","Row crop"
"92","MLRA12_Amherst","S2021MI065001",40,59,"Btg","L",26,7.8,"10YR",5,2,"Crosier","C-CT-3","Crop cover","Row crop"
"93","MLRA12_Amherst","S2021MI065001",59,80,"Bt","CL",32,7.9,"10YR",4,3,"Crosier","C-CT-3","Crop cover","Row crop"
"94","MLRA12_Amherst","S2021MI065001",80,100,"Cd1","L",25,7.7,"10YR",5,3,"Crosier","C-CT-3","Crop cover","Row crop"
"95","MLRA12_Amherst","S2021MI065001",100,150,"Cd2","L",25,8.3,"10YR",5,3,"Crosier","C-CT-3","Crop cover","Row crop"
"96","MLRA12_Amherst","S2021MI065001",150,228,"Cd3","L",25,8.3,"10YR",5,3,"Crosier","C-CT-3","Crop cover","Row crop"
"97","MLRA12_Amherst","S2021MI065001A",0,22,"Ap1","L",22,7.8,"10YR",3,2,"Conover","C-CT-3","Crop cover","Row crop"
"98","MLRA12_Amherst","S2021MI065001A",22,33,"Ap2","L",24,7.8,"10YR",3,2,"Conover","C-CT-3","Crop cover","Row crop"
"99","MLRA12_Amherst","S2021MI065001A",33,55,"Bt","CL",35,8,"10YR",5,3,"Conover","C-CT-3","Crop cover","Row crop"
"100","MLRA12_Amherst","S2021MI065001A",55,60,"BCt","CL",32,NA,"10YR",4,3,"Conover","C-CT-3","Crop cover","Row crop"
"101","MLRA12_Amherst","S2021MI065001B",0,20,"Ap1","L",24,7.8,"10YR",4,2,"Conover","C-CT-3","Crop cover","Row crop"
"102","MLRA12_Amherst","S2021MI065001B",20,31,"Ap2","L",24,7.6,"10YR",4,2,"Conover","C-CT-3","Crop cover","Row crop"
"103","MLRA12_Amherst","S2021MI065001B",31,57,"Bt","CL",30,7.8,"10YR",4,4,"Conover","C-CT-3","Crop cover","Row crop"
"104","MLRA12_Amherst","S2021MI065001B",57,62,"Cd","L",24,8,"10YR",5,3,"Conover","C-CT-3","Crop cover","Row crop"
"105","MLRA12_Amherst","S2021MI155001",0,24,"Ap","L",18,6.6,"10YR",4,2,"Conover","C-CT-2","Crop cover","Row crop"
"106","MLRA12_Amherst","S2021MI155001",24,40,"Bt1","L",23,6.4,"10YR",5,4,"Conover","C-CT-2","Crop cover","Row crop"
"107","MLRA12_Amherst","S2021MI155001",40,65,"Bt2","CL",28,6.4,"10YR",5,4,"Conover","C-CT-2","Crop cover","Row crop"
"108","MLRA12_Amherst","S2021MI155001",65,110,"Bt3","CL",30,7.2,"10YR",5,3,"Conover","C-CT-2","Crop cover","Row crop"
"109","MLRA12_Amherst","S2021MI155001",110,126,"BCt","CL",28,8,"10YR",4,4,"Conover","C-CT-2","Crop cover","Row crop"
"110","MLRA12_Amherst","S2021MI155001",126,175,"Cd","L",20,8.4,"10YR",5,3,"Conover","C-CT-2","Crop cover","Row crop"
"111","MLRA12_Amherst","S2021MI155001",175,210,"C","L",20,7.8,"10YR",5,4,"Conover","C-CT-2","Crop cover","Row crop"
"112","MLRA12_Amherst","S2021MI155001A",0,28,"Ap","L",24,7.2,"10YR",4,2,"Conover","C-CT-2","Crop cover","Row crop"
"113","MLRA12_Amherst","S2021MI155001A",28,43,"Bt1","SCL",29,7.4,"10YR",5,3,"Conover","C-CT-2","Crop cover","Row crop"
"114","MLRA12_Amherst","S2021MI155001A",43,60,"Bt2","CL",32,7.6,"10YR",4,3,"Conover","C-CT-2","Crop cover","Row crop"
"115","MLRA12_Amherst","S2021MI155001B",0,20,"Ap","FSL",15,7,"10YR",3,3,"Conover","C-CT-2","Crop cover","Row crop"
"116","MLRA12_Amherst","S2021MI155001B",20,35,"Bt1","L",23,6.8,"10YR",5,3,"Conover","C-CT-2","Crop cover","Row crop"
"117","MLRA12_Amherst","S2021MI155001B",35,60,"Bt2","L",26,6.8,"10YR",4,4,"Conover","C-CT-2","Crop cover","Row crop"
14 changes: 14 additions & 0 deletions misc/example-data/overlapping-horizons/make-overlapping-SPC-data.R
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library(aqp)

x <- read.csv('misc/example-data/overlapping-horizons/2020GRR014SPCdata.csv')

depths(x) <- upedonid ~ hzdept + hzdepb
hzdesgnname(x) <- 'hzname'
site(x) <- ~ NasisSiteName + taxonname + dspplotid + earthcovkind1 + earthcovkind2

x <- x[c(1, 2, 3, 4, 8), ]


SPC.with.overlap <- x

save(SPC.with.overlap, file = 'data/SPC.with.overlap.rda', compress = 'xz')
18 changes: 2 additions & 16 deletions misc/overlapping-horizons/notes.R
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Expand Up @@ -3,23 +3,9 @@ library(aqp)
## keeping track of progress here:
# https://github.com/ncss-tech/aqp/issues/296

data("SPC.with.overlap")


## example data from Sharon

# x <- read.csv('e:/temp/2020GRR014SPCdata.csv')
#
# depths(x) <- upedonid ~ hzdept + hzdepb
# hzdesgnname(x) <- 'hzname'
# site(x) <- ~ NasisSiteName + taxonname + dspplotid + earthcovkind1 + earthcovkind2
#
# x <- x[c(1, 2, 3, 4, 8), ]
#
# saveRDS(x, file = 'misc/overlapping-horizons/example-DSP-data.rds')


# example DSP data
x <- readRDS('misc/overlapping-horizons/example-DSP-data.rds')
x <- SPC.with.overlap

# all 4 profiles have overlap
checkHzDepthLogic(x)
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0 vignettes/overlapping-horizons.Rmd → ...lapping-horizons/overlapping-horizons.Rmd
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File renamed without changes.

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