preparing for CRAN release

DESCRIPTION

@@ -3,8 +3,8 @@ Type: Package
 Encoding: UTF-8
 Title: A Soil Survey Toolkit
 Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
-Version: 2.2
-Date: 2024-04-03
+Version: 2.3
+Date: 2024-04-08
 Authors@R: c(
   person(given="Dylan", family="Beaudette", role = c("cre", "aut"), email = "[email protected]"), 
   person(given="Jay", family="Skovlin", role = c("aut")), 

NAMESPACE

@@ -40,7 +40,9 @@ importFrom(aqp,
            'depths<-',
            'site<-',
            slab,
-           shannonEntropy
+           shannonEntropy,
+           hzdesgnname,
+           'hzdesgnname<-'
 )
 
 importFrom(curl,

NEWS.md

@@ -1,14 +1,18 @@
-# sharpshootR 2.2 (2024-03-26)
+# sharpshootR 2.3 (2024-04-08)
+ * CRAN release
  * `prepare_SSURGO_hydro_data()` now returns more soil property data
  * major updates to `monthlyWB()`:
    - mass balance check, reporting, and messages when not closed
    - new arguments which enable / modify the distribution of PPT and PET within k-bins / month 
  * bug fix in `plotWB()`
+ * minor updates to `prepare_SSURGO_hydro_data()`
+
+# sharpshootR 2.2 (2024-08-24)
+ * CRAN release
  * added a few more soil hydraulic properties to `prepare_SSURGO_hydro_data()`
  * `plotGeomorphCrossSection()` now respects `aqp::plotSPC()` arguments via `options(.aqp.plotSPC.args = list(...))`
  * removing some hard-coded arguments passed through to `aqp::plotSPC()`
  * `SoilTaxonomyDendrogram()` gains argument to adjust taxon label font
- * minor updates to `prepare_SSURGO_hydro_data()`
 
 # sharpshootR 2.1 (2023-03-21)
  * CRAN release

R/monthlyWB.R

@@ -50,16 +50,14 @@
 #' 
 #' @return a `data.frame` with the following elements:
 #' 
-#' \itemize{
-#' \item{PPT: }{monthly PPT (mm)}
-#' \item{PET: }{monthly PET (mm)}
-#' \item{U: }{monthly surplus (mm)}
-#' \item{S: }{monthly soil moisture storage (mm)}
-#' \item{ET: }{monthly AET (mm)}
-#' \item{D: }{monthly deficit (mm)}
-#' \item{month: }{month number}
-#' \item{mo: }{month label}   
-#' }
+#'  * PPT: monthly PPT (mm)
+#'  * PET: monthly PET (mm)
+#'  * U:   monthly surplus (mm)
+#'  * S:   monthly soil moisture storage (mm)
+#'  * ET:  monthly AET (mm)
+#'  * D:   monthly deficit (mm)
+#'  * month: month number
+#'  * mo:  month label 
 #' 
 monthlyWB <- function(AWC, PPT, PET, S_init = 1, starting_month = 1, rep = 1, keep_last = FALSE, distribute = FALSE, method = c('equal', 'random', 'gaussian'), k = 10) {
 

vignettes/sharpshootR-overview.Rmd

@@ -28,26 +28,26 @@ options(width = 100, stringsAsFactors = FALSE, timeout = 600)
 ## Soil Color / Color Science
   * `aggregateColorPlot()`: unique visualization of soil color summaries generated by `aqp::aggregateColor()`
   * `colorMixtureVenn()`: simulated mixture of pigments displayed as a Venn diagram
-  * `huePositionPlot()`: 
+  * `huePositionPlot()`: visualization of Munsell hue position in CIE {A,B} coordinates, with user-specified origin, value / chroma, and more
 
 ## Spatial Data
-  * `aspect.plot()`: 
+  * `aspect.plot()`: graphical summary of aspect angle measurements
 
-  * `generateLineHash()`: 
-  * `joinAdjacency()`: 
-  * `polygonAdjacency()`: 
+  * `generateLineHash()`: create a unique ID for line segments via murmur32 hash
+  * `joinAdjacency()`: join document adjacency helper function
+  * `polygonAdjacency()`: summary of spatial adjacency from a polygon fabric
 
-  * `LL2PLSS()`:
-  * `PLSS2LL()`: 
-  * `formatPLSS()`: 
+  * `LL2PLSS()`: convert geographic coordinates into PLSS notation
+  * `PLSS2LL()`: convert PLSS notation into geographic coordinates
+  * `formatPLSS()`: properly encode PLSS notation for use by `PLSS2LL()`
 
 
 ## Regional Climate and Soil Climate
 
 ### Data Interfaces
-  * `CDEC_StationInfo()`: 
-  * `CDEC_query()`: 
-  * `CDEC_snowQuery`: 
+  * `CDEC_StationInfo()`: information on CDEC stations
+  * `CDEC_query()`: submit a generic query to CDEC web-service
+  * `CDEC_snowQuery`: submit a query to the CDEC web-service specifically for CA cooperative snow survey data
 
 ### Climate Summaries
   * `FFD()`: frost-free day estimation
@@ -56,36 +56,36 @@ options(width = 100, stringsAsFactors = FALSE, timeout = 600)
   * `PCP_plot()`: graphical depiction of "percentiles of cumulative precipitation"
 
 ### Water Balance
-  * `prepareDailyClimateData()`: 
-  * `prepare_SSURGO_hydro_data()`: 
-  * `dailyWB_SSURGO()`: 
+  * `prepareDailyClimateData()`: collect data required to run a simple water balance model at a daily time step
+  * `prepare_SSURGO_hydro_data()`: collect soil property data from SSURGO to parametrize water balance model
+  * `dailyWB_SSURGO()`: perform a daily water balance using SSURGO data 
 
-  * `simpleWB()`:
-  * `dailyWB()`: 
-  * `monthlyWB()`: 
-  * `plotWB()`: 
-  * `plotWB_lines()`: 
-  * `estimateSoilMoistureState()`: 
-  * `moistureStateProportions()`: 
-  * `moistureStateThreshold()`: 
-  * `plotAvailWater()`: 
+  * `simpleWB()`: simple interface to the hydromad `bucket.sim` (leaky bucket) model
+  * `dailyWB()`: daily water balance via hydromad `bucket.sim` (leaky bucket) model
+  * `monthlyWB()`: monthly water balance via hydromad `bucket.sim` (leaky bucket) model
+  * `plotWB()`: bar graph style visualization of water balance simulation
+  * `plotWB_lines()`: line graph style visualization of water balance simulation
+  * `estimateSoilMoistureState()`: convert volumetric water content into approximate soil moisture status
+  * `moistureStateProportions()`: summarize soil moisture state via proportions over month, week, or Julian day
+  * `moistureStateThreshold()`: convert proportions into probability of exceedance based on given threshold
+  * `plotAvailWater()`: create a simplistic diagram of various fractions of water help within the soil pore-space
 
 ## Soil Survey Data
-  * `component.adj.matrix()`: 
-  * `diagnosticPropertyPlot()`: 
-  * `plotSoilRelationGraph()`: 
-  * `plotSoilRelationChordGraph()`: 
-  * `plotTransect()`: 
+  * `component.adj.matrix()`: create an adjacency matrix from SSURGO component data
+  * `diagnosticPropertyPlot()`: multivariate summary of pedon diagnostic features
+  * `plotSoilRelationGraph()`: graphical representation of component adjacency via igraph package
+  * `plotSoilRelationChordGraph()`: graphical representation of component adjacency via circlize package
+  * `plotTransect()`: plot soil profile sketches along a cross-section
 
 ### Soil Series Summaries
-  * `vizAnnualClimate()`: 
-  * `vizFlatsPosition()`: 
-  * `vizGeomporphicComponent()`: 
-  * `vizHillslopePosition`: 
-  * `vizMountainPosition()`: 
-  * `vizSurfaceShape()`: 
-  * `vizTerracePosition()`: 
-  * `reconcileOSDGeomorph()``:
+  * `vizAnnualClimate()`: visualization method for annual climate summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `vizFlatsPosition()`: visualization method for flat geomorphic types summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `vizGeomporphicComponent()`: visualization method for 3D geomorphic description summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `vizHillslopePosition`: visualization method for 2D geomorphic description summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `vizMountainPosition()`: visualization method for mountain geomorphic description summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `vizSurfaceShape()`: visualization method for surface shape (curvature) summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `vizTerracePosition()`: visualization method for terrace geomorphic description summaries via `soilDB::fetchOSD(..., extended = TRUE)`
+  * `reconcileOSDGeomorph()`: create a subset of `SoilProfileCollection` and extended records from `soilDB::fetchOSD(..., extended = TRUE)` such that no series are missing in either
 
 ### Geomorphic Data Summaries  
   * `plotGeomorphCrossSection`: display soil profile sketches along a geomorphic cross-section