typos, cleanup, fresh HTML documentation

ncss-tech · Oct 21, 2020 · b9e6bd6 · b9e6bd6
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diff --git a/R/data-documentation.R b/R/data-documentation.R
@@ -101,7 +101,7 @@
 
 #'
 #' @title US State Soils
-#' @description A listing of the 52 US state soils, including Puerto Rico and Virgin Islands.
+#' @description A listing of the 50 US state soils, along with Puerto Rico and Virgin Islands.
 #' @keywords datasets
 #' @usage data(us.state.soils)
 #' @format 

diff --git a/R/duplicate.R b/R/duplicate.R
@@ -1,7 +1,7 @@
 
 
-#' @title Duplicte Profiles of a SoilProfileColection
-#' @description A simple function to duplicate the contents of a \code{SoilProfileColection} object. Old profile IDs are saved as a site-level attribute (\code{oldID}) and new IDs are generated using a numeric serial number.
+#' @title Duplicte Profiles of a SoilProfileCollection
+#' @description A simple function to duplicate the contents of a \code{SoilProfileCollection} object. Old profile IDs are saved as a site-level attribute (\code{oldID}) and new IDs are generated using a numeric serial number.
 #' 
 #' @author D.E. Beaudette
 #' 

diff --git a/R/glomApply.R b/R/glomApply.R
@@ -6,7 +6,7 @@
 #'
 #' \code{glomApply} works by accepting a function \code{.fun} as argument. This function is used on each profile to process a multi-profile SPC for input to \code{glom} (via \code{profileApply}). For each profile, \code{.fun} returns a 2-length numeric vector of top and bottom boundaries \code{glom} arguments: \code{z1}, \code{z2}.
 #'
-#' \code{glomApply} essentially provides the option to programattically generate profile-specfic glom depths for a large SPC and handles iteration and rebuilding of a subset SPC object. Optional argument sinclude: \code{truncate} to cut the boundaries to specified \code{[z1, z2]}; \code{invert} to the portion outside \code{[z1, z2]}, \code{modality} to either \code{"all"} horizons or \code{"thickest"} horizon in the \code{glom} interval. \code{...} are various expressions you can run on the individual profiles using NSE, similar to \code{mutate}.
+#' \code{glomApply} essentially provides the option to programattically generate profile-specfic glom depths for a large SPC and handles iteration and rebuilding of a subset SPC object. Optional arguments include: \code{truncate} to cut the boundaries to specified \code{[z1, z2]}; \code{invert} to the portion outside \code{[z1, z2]}, \code{modality} to either \code{"all"} horizons or \code{"thickest"} horizon in the \code{glom} interval. \code{...} are various expressions you can run on the individual profiles using NSE, similar to \code{mutate}.
 #'
 #' @param object A SoilProfileCollection
 #'

diff --git a/R/hzBoundary.R b/R/hzBoundary.R
@@ -14,7 +14,7 @@
 #' 
 #' @return vector of offsets with same length as \code{x}
 #' 
-#' @details The default offests are based on the high-end of ranges presented in "transitional zone thickness criteria" from the Field Book version 3.0 (page 2-6). Offsets are returned as 1/2 of the transitional zone thickness so that horizon boundaries can be adjusted up/down from horizon depths. See \code{\link{plotSPC}}, specifically the \code{hz.distinctness.offset} argument for vizualization ideas. Missing data in \code{x} (NA) or codes that are not defined in \code{codes} are returned as 0 offsets.
+#' @details The default offests are based on the high-end of ranges presented in "transitional zone thickness criteria" from the Field Book version 3.0 (page 2-6). Offsets are returned as 1/2 of the transitional zone thickness so that horizon boundaries can be adjusted up/down from horizon depths. See \code{\link{plotSPC}}, specifically the \code{hz.distinctness.offset} argument for visualization ideas. Missing data in \code{x} (NA) or codes that are not defined in \code{codes} are returned as 0 offsets.
 #' 
 #' @seealso \code{\link{plotSPC}}
 #' 

diff --git a/R/permute_profile.R b/R/permute_profile.R
@@ -13,7 +13,7 @@
 #'
 #' So, a standard deviation of 1-2cm would yield a "boundary thickness" in the 3-5cm range ("clear" distinctness class).
 #'
-#' Of course, boundaries are not symmetrical and this is at best an approximation for properties like organic matter, nutrients or salts that can have strong depth-dependence within horizons. Also, boundary topography is non-uniform. There are definitely ways to implement other distributions, but invokes more detailed assumptions about field data that are generally only semi-quantiative or are not available.
+#' Of course, boundaries are not symmetrical and this is at best an approximation for properties like organic matter, nutrients or salts that can have strong depth-dependence within horizons. Also, boundary topography is non-uniform. There are definitely ways to implement other distributions, but invokes more detailed assumptions about field data that are generally only semi-quantitative or are not available.
 #'
 #' Future implementations may use boundary topography as a second hierarchical level (e.g. trig-based random functions), but think that distinctness captures the "uncertainty" about horizon separation at a specific "point" on the ground (or line in the profile quite well, and the extra variation may be hard to interpret, in general.
 #'

diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.7.2
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2020-10-13T20:51Z
+last_built: 2020-10-21T17:28Z
 
diff --git a/docs/reference/argillic.clay.increase.depth.html b/docs/reference/argillic.clay.increase.depth.html
diff --git a/docs/reference/barron.torrent.redness.LAB.html b/docs/reference/barron.torrent.redness.LAB.html
diff --git a/docs/reference/buntley.westin.index.html b/docs/reference/buntley.westin.index.html
diff --git a/docs/reference/duplicate.html b/docs/reference/duplicate.html
diff --git a/docs/reference/estimateSoilDepth-1.png b/docs/reference/estimateSoilDepth-1.png
diff --git a/docs/reference/estimateSoilDepth-2.png b/docs/reference/estimateSoilDepth-2.png
diff --git a/docs/reference/estimateSoilDepth.html b/docs/reference/estimateSoilDepth.html
diff --git a/docs/reference/get.ml.hz.html b/docs/reference/get.ml.hz.html
diff --git a/docs/reference/glomApply.html b/docs/reference/glomApply.html