From b2bd8172dd1fbe259e117297f336eace339d73a7 Mon Sep 17 00:00:00 2001 From: Beaudette Date: Thu, 4 Jan 2024 15:43:02 -0800 Subject: [PATCH] Update aqp-overview.Rmd --- vignettes/aqp-overview.Rmd | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/vignettes/aqp-overview.Rmd b/vignettes/aqp-overview.Rmd index 2fee8e67b..c10753ea6 100644 --- a/vignettes/aqp-overview.Rmd +++ b/vignettes/aqp-overview.Rmd @@ -102,7 +102,7 @@ Soil morphology, observed properties, and geomorphic context represent a complex * `horizonNames()`: horizon-level column names ### Subset - * `glom()`: extract horizons based on single depth or depth interval + * `glom()`: extract horizons based on overlap criteria defined by point or interval * `trunc()`: truncate SPC to given depth interval * `subset()`: subset profiles based on logical expressions * `subsetHz()`: subset horizons based on logical expressions @@ -139,16 +139,14 @@ Soil morphology, observed properties, and geomorphic context represent a complex ### Iteration * `profileApply()`: apply a function to each profile within an SPC (slow but simple interface) - * `glomApply()`: - * `mutate_profiles()`: - * `summarizeSPC()`: - * `transform()`: + * `summarizeSPC()`: perform group-wise summaries over profiles within an SPC + * `transform()`: modify a SPC using expressions that operation on site or horizon-level data ### Change of Support * `dice()`: convert SPC to 1 depth-unit intervals by replication * `slab()`: apply an aggregate function over groups within a "dice()-ed" SPC * `spc2mpspline()`: interface to equal-area spline fitting from mpspline2 package - * `segment()`: generate segment lables for depth-weighted aggregation + * `segment()`: generate segment labels for depth-weighted aggregation * `L1_profiles()`: create representative profiles via multivariate median (L1 estimator) * `slicedHSD()`: apply Tukey's HSD over groups within a "dice()-ed" SPC @@ -157,7 +155,7 @@ Soil morphology, observed properties, and geomorphic context represent a complex * `fillHzGaps()`: fill topological gaps in horizon depth * `repairMissingHzDepths()`: attempt fixing missing or duplicated horizon bottom depths * `flagOverlappingHz()`: flag horizons with perfect overlap - * `checkHzDepthLogic()`: apply battery of horizon depth toplogical tests + * `checkHzDepthLogic()`: apply battery of horizon depth topological tests * `splitLogicErrors()`: split an SPC according to variety of possibly horizon depth errors * `HzDepthLogicSubset()`: remove profiles from an SPC if any depth logic errors are present @@ -173,9 +171,9 @@ Soil morphology, observed properties, and geomorphic context represent a complex * `as(SPC, 'sf')`: convert site and spatial data to sf object ### Spatial Data - * `prj()` - * `initSpatial()` - * `getSpatial()` + * `prj()`: get/set coordinate reference system (CRS) metadata + * `initSpatial()`: set (site-level) column names containing coordinates + * `getSpatial()`: get spatial data (site + coordinates) from an SPC ### Internal Consistency * `checkSPC()`: check SPC for internal consistency @@ -253,14 +251,14 @@ Soil morphology, observed properties, and geomorphic context represent a complex ### Coarse Fragments * `fragmentSieve()`: classify coarse fragments by fragment diameter - * `texmod_to_fragvoltot()`: - * `texture_to_texmod()`: - * `fragvol_to_texmod()`: + * `texmod_to_fragvoltot()`: estimate ranges in coarse fragment volume based on a soil texture modifier + * `texture_to_texmod()` + * `fragvol_to_texmod()` * `fragmentClasses()`: coarse fragment diameter thresholds used by USDA-NRCS ### Soil Taxonomy - * `getArgillicBounds()` - * `getCambicBounds()` + * `getArgillicBounds()`: estimate the upper and lower boundaries of an argillic horizon + * `getCambicBounds()`: estimate the upper and lower boundaries of a cambic horizon * `getSurfaceHorizonDepth()` * `getMineralSoilSurfaceDepth()` * `getPlowLayerDepth()`