From abe65807f07740c1de7399751b6842212a80c78e Mon Sep 17 00:00:00 2001
From: Beaudette <dylan.beaudette@usda.gov>
Date: Tue, 5 Sep 2023 09:27:41 -0700
Subject: [PATCH] new example data, archiving associated vignette for now

---
 NEWS.md                                       |   2 +-
 R/data-documentation.R                        |   8 ++
 data/SPC.with.overlap.rda                     | Bin 0 -> 1184 bytes
 man/SPC.with.overlap.Rd                       |  16 +++
 .../2020GRR014SPCdata.csv                     | 118 ++++++++++++++++++
 .../make-overlapping-SPC-data.R               |  14 +++
 misc/overlapping-horizons/notes.R             |  18 +--
 .../overlapping-horizons.Rmd                  |   0
 8 files changed, 159 insertions(+), 17 deletions(-)
 create mode 100644 data/SPC.with.overlap.rda
 create mode 100644 man/SPC.with.overlap.Rd
 create mode 100644 misc/example-data/overlapping-horizons/2020GRR014SPCdata.csv
 create mode 100644 misc/example-data/overlapping-horizons/make-overlapping-SPC-data.R
 rename {vignettes => misc/overlapping-horizons}/overlapping-horizons.Rmd (100%)

diff --git a/NEWS.md b/NEWS.md
index a9b1f0e51..ed56d1913 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# 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)
 
diff --git a/R/data-documentation.R b/R/data-documentation.R
index a5d6647b6..356bc90c2 100644
--- a/R/data-documentation.R
+++ b/R/data-documentation.R
@@ -12,6 +12,14 @@
 
 
 
+#' @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
diff --git a/data/SPC.with.overlap.rda b/data/SPC.with.overlap.rda
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diff --git a/man/SPC.with.overlap.Rd b/man/SPC.with.overlap.Rd
new file mode 100644
index 000000000..ec1649fc0
--- /dev/null
+++ b/man/SPC.with.overlap.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data-documentation.R
+\docType{data}
+\name{SPC.with.overlap}
+\alias{SPC.with.overlap}
+\title{Example SoilProfileCollection with Overlapping Horizons}
+\format{
+A \code{SoilProfileCollection}
+}
+\usage{
+data(SPC.with.overlap)
+}
+\description{
+A \code{SoilProfileCollection} with overlapping horizons, derived from a Dynamic Soil Properties project.
+}
+\keyword{datasets}
diff --git a/misc/example-data/overlapping-horizons/2020GRR014SPCdata.csv b/misc/example-data/overlapping-horizons/2020GRR014SPCdata.csv
new file mode 100644
index 000000000..e53601b75
--- /dev/null
+++ b/misc/example-data/overlapping-horizons/2020GRR014SPCdata.csv
@@ -0,0 +1,118 @@
+"","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"
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+"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"
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+"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"
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+"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"
diff --git a/misc/example-data/overlapping-horizons/make-overlapping-SPC-data.R b/misc/example-data/overlapping-horizons/make-overlapping-SPC-data.R
new file mode 100644
index 000000000..97cb55a29
--- /dev/null
+++ b/misc/example-data/overlapping-horizons/make-overlapping-SPC-data.R
@@ -0,0 +1,14 @@
+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')
diff --git a/misc/overlapping-horizons/notes.R b/misc/overlapping-horizons/notes.R
index 3f462f6b1..1fd902bd8 100644
--- a/misc/overlapping-horizons/notes.R
+++ b/misc/overlapping-horizons/notes.R
@@ -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)
diff --git a/vignettes/overlapping-horizons.Rmd b/misc/overlapping-horizons/overlapping-horizons.Rmd
similarity index 100%
rename from vignettes/overlapping-horizons.Rmd
rename to misc/overlapping-horizons/overlapping-horizons.Rmd