Merge pull request #303 from ncss-tech/suggest-sp

Move {sp} to suggests

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: aqp
-Version: 2.0.4
+Version: 2.1.0
 Title: Algorithms for Quantitative Pedology
 Authors@R: c(person(given="Dylan", family="Beaudette", role = c("aut", "cre"), email = "dylan.beaudette@usda.gov"), person(given="Pierre", family="Roudier", email="roudierp@landcareresearch.co.nz", role = c("aut", "ctb")), person(given="Andrew", family="Brown", email="andrew.g.brown@usda.gov", role = c("aut", "ctb")))
 Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
 Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
 Depends: R (>= 3.5.0)
-Imports: grDevices, graphics, stats, utils, methods, grid, lattice, cluster, sp, stringr, data.table, farver
-Suggests: mvtnorm, colorspace, ape, soilDB, sf, latticeExtra, tactile, compositions, sharpshootR, markovchain, xtable, testthat, Gmedian, Hmisc, tibble, RColorBrewer, scales, digest, MASS, mpspline2, soiltexture, gower, knitr, rmarkdown, plyr
+Imports: grDevices, graphics, stats, utils, methods, grid, lattice, cluster, stringr, data.table, farver
+Suggests: mvtnorm, colorspace, ape, soilDB, sp, sf, latticeExtra, tactile, compositions, sharpshootR, markovchain, xtable, testthat, Gmedian, Hmisc, tibble, RColorBrewer, scales, digest, MASS, mpspline2, soiltexture, gower, knitr, rmarkdown, plyr
 Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
 License: GPL (>= 3)
 LazyLoad: yes

NAMESPACE

@@ -242,8 +242,6 @@ exportMethods(trunc)
 exportMethods(unique)
 exportMethods(validSpatialData)
 import(data.table)
-importClassesFrom(sp,SpatialPoints)
-importClassesFrom(sp,SpatialPointsDataFrame)
 importFrom(cluster,daisy)
 importFrom(cluster,pam)
 importFrom(cluster,silhouette)
@@ -307,11 +305,6 @@ importFrom(methods,setOldClass)
 importFrom(methods,setReplaceMethod)
 importFrom(methods,slot)
 importFrom(methods,slotNames)
-importFrom(sp,"coordinates<-")
-importFrom(sp,"proj4string<-")
-importFrom(sp,SpatialPoints)
-importFrom(sp,coordinates)
-importFrom(sp,proj4string)
 importFrom(stats,TukeyHSD)
 importFrom(stats,aggregate)
 importFrom(stats,aov)

NEWS.md

@@ -1,10 +1,14 @@
-# aqp 2.0.4 (2024-10-10)
+# aqp 2.1.0 (2024-10-10)
+ * added Munsell values of 8.5 and 9.5 to Munsell look up table and (interpolated) reference spectra (#318)
+ * `munsell2rgb()` now safely selects the closest Munsell value and chroma to those available in the package LUT 
+ * new function `soilTextureColorPal()` for suggesting a color palette suitable for soil texture class
+ * **Breaking Change**: `@sp` slot of the SoilProfileCollection object, and dependency on sp package, has been removed. 
+  * Any SoilProfileCollection objects previously written to file (.rda, .rds) with aqp <2.1.x will need to be rebuilt using `rebuildSPC()` due to changes to S4 object structure
+
+# aqp 2.0.4 (2024-07-30)
  * CRAN release
  * ragged bottom lines in `plotSPC()` now adjusted as function of number of profiles and device width
  * additional metadata from `plotSPC()` saved to `last_spc_plot` in `aqp.env`
- * added Munsell values of 8.5 and 9.5 to Munsell LUT and (interpolated) reference spectra (#318)
- * `munsell2rgb()` now safely selects the closest Munsell value and chroma to those available in the package LUT 
- * new function `soilTextureColorPal()` for suggesting a color palette suitable for soil texture class
 
 # aqp 2.0.3 (2024-04-18)
  * CRAN release

R/AAAA.R

@@ -5,7 +5,6 @@ aqp.env <- new.env(hash = TRUE, parent = parent.frame())
 # register options for later use
 .onLoad <- function(libname, pkgname) {
   options(.aqp.show.n.cols = 10)
-
 }
 
 # no longer needed since it is imported

R/Class-SoilProfileCollection.R

@@ -9,28 +9,24 @@
 #' @slot metadata list.
 #' @slot horizons data.frame.
 #' @slot site data.frame.
-#' @slot sp SpatialPoints.
 #' @slot diagnostic data.frame.
 #' @slot restrictions data.frame.
+#' 
+#' @details
+#' After aqp 2.0.2, the `@sp` slot was removed from the SoilProfileCollection object. If you run into errors related to old object definitions, use `rebuildSPC()` on the problematic object.
+#' 
 #' @aliases SoilProfileCollection-class
 #' @rdname SoilProfileCollection-class
-#' @importFrom sp SpatialPoints proj4string coordinates proj4string<- coordinates<-
-#' @importClassesFrom sp SpatialPoints SpatialPointsDataFrame
 setClass(
   Class = 'SoilProfileCollection',
   representation = representation(
     idcol = 'character', # column name containing IDs
     hzidcol = 'character', # column name containing unique horizon IDs
     depthcols = 'character', # 2 element vector with column names for hz top, bottom
-
     metadata = 'list', # list with key-value mapping
-
     horizons = 'data.frame', # all horizons sorted by ID & top depth
-
     site = 'data.frame', # data about the sampling sites
-
-    sp = 'SpatialPoints', # spatial data stored here, initialized as 'empty' sp object
-
+    # sp = 'NULL', # no longer used, formerly 'empty' sp object
     diagnostic = 'data.frame',# (optional) diagnostic horizons are stored here
     restrictions = 'data.frame' # (optional) restrictions are stored here
   ),
@@ -47,7 +43,7 @@ setClass(
                           top = numeric(0), bottom = numeric(0),
                           stringsAsFactors = FALSE),
     site = data.frame(id = character(0), stringsAsFactors = FALSE),
-    sp = sp::SpatialPoints(data.frame(x = 0, y = 0))[-1, ],
+    # sp = NULL, 
     diagnostic = data.frame(stringsAsFactors = FALSE),
     restrictions = data.frame(stringsAsFactors = FALSE)
   ),
@@ -61,18 +57,18 @@ setClass(
 # c/o: https://gis.stackexchange.com/questions/291069/creating-empty-spatialpoints-or-spatialpointsdataframe-in-r
 # old: new('SpatialPoints')
 # new: SpatialPoints(data.frame(x = 0, y = 0))[-1,]
+# new new: NULL
 
 #' Constructor for the SoilProfileCollection object
 #'
-#' @param idcol character Profile ID Column Name
-#' @param hzidcol character Horizon ID Column Name
-#' @param depthcols character, length 2 Top and Bottom Depth Column Names
-#' @param metadata list, metadata including data.frame class in use and depth units
-#' @param horizons data.frame An object inheriting from data.frame containing Horizon data.
-#' @param site data.frame An object inheriting from data.frame containing Site data.
-#' @param sp SpatialPoints A SpatialPoints object. No longer used in aqp 2+, see `?initSpatial`
-#' @param diagnostic data.frame An object inheriting from data.frame containing diagnostic feature data. Must contain profile ID. See \code{diagnostic_hz()}
-#' @param restrictions data.frame An object inheriting from data.frame containing restrictive feature data. Must contain profile ID. See \code{restrictions()}
+#' @param idcol character. Profile ID Column Name
+#' @param hzidcol character. Horizon ID Column Name
+#' @param depthcols character. length 2 Top and Bottom Depth Column Names
+#' @param metadata list. metadata including data.frame class in use and depth units
+#' @param horizons data.frame. An object inheriting from data.frame containing Horizon data.
+#' @param site data.frame. An object inheriting from data.frame containing Site data.
+#' @param diagnostic data.frame. An object inheriting from data.frame containing diagnostic feature data. Must contain profile ID. See \code{diagnostic_hz()}
+#' @param restrictions data.frame. An object inheriting from data.frame containing restrictive feature data. Must contain profile ID. See \code{restrictions()}
 #'
 #' @description In general, one should use \code{depths()} to initiate a SoilProfileCollection object from data. However, sometimes there are instances where either an empty, or very specific, object is needed. If that is the case, the general constructor \code{SoilProfileCollection} is available.
 #'
@@ -184,7 +180,7 @@ setClass(
              stringsAsFactors = FALSE
            ),
            site = data.frame(id = character(0), stringsAsFactors = FALSE),
-           sp = new('SpatialPoints'),
+           # sp = NULL, 
            diagnostic = data.frame(stringsAsFactors = FALSE),
            restrictions = data.frame(stringsAsFactors = FALSE)) {
 
@@ -227,7 +223,7 @@ setClass(
       metadata = metadata,
       horizons = .as.data.frame.aqp(horizons, hzclass),
       site = .as.data.frame.aqp(site, hzclass),
-      sp = sp,
+      # sp = sp,
       diagnostic = .as.data.frame.aqp(diagnostic, hzclass),
       restrictions = .as.data.frame.aqp(restrictions, hzclass)
     )

R/SoilProfileCollection-coercion.R

@@ -12,7 +12,7 @@
 #' @docType methods
 #' @rdname coercion-methods
 #'
-#' @examples 
+#' @examples
 #' # load example data stored as SoilProfileCollection
 #' data(sp5)
 #' 
@@ -30,11 +30,19 @@
 #' sp5$x <- sp5$y <- rnorm(length(sp5))
 #' initSpatial(sp5, crs = "OGC:CRS84") <- ~ x + y
 #' 
-#' # SpatialPointsDataFrame output
-#' str(as(sp5, 'SpatialPointsDataFrame'))
+#' if (requireNamespace("sf")) {
+#' 
+#'   # sf output
+#'   str(as(sp5, 'sf'))
+#' 
+#'   # SpatialPointsDataFrame output
+#'   str(as(sp5, 'SpatialPointsDataFrame'))
+#' 
+#'   # SpatialPoints output
+#'   str(as(sp5, 'SpatialPoints'))
+#'   
+#' }
 #' 
-#' # SpatialPoints output
-#' str(as(sp5, 'SpatialPoints'))
 setAs("SoilProfileCollection", "list", function(from) {
 
   # get slot names from prototype

R/SoilProfileCollection-metadata.R

@@ -70,7 +70,7 @@
 
   # transfer attributes https://github.com/ncss-tech/aqp/issues/204
   customattr <- attributes(src)
-  customattr <- customattr[!names(customattr) %in% names(attributes(SoilProfileCollection()))]
+  customattr <- customattr[!names(customattr) %in% c("sp", names(attributes(SoilProfileCollection())))]
   attributes(dest)[names(customattr)] <- attributes(src)[names(customattr)]
 
   # original.order metadata no longer created, not transferred

R/SoilProfileCollection-operators.R

@@ -164,7 +164,7 @@ setMethod("[", signature(x = "SoilProfileCollection"),
                              s <- s.all[s.i, , drop = FALSE]
 
                              # copy empty SpatialPoints object
-                             sp <- x@sp
+                             # sp <- x@sp
 
                              # subset diagnostic data
                              d <- diagnostic_hz(x)
@@ -307,7 +307,7 @@ setMethod("[", signature(x = "SoilProfileCollection"),
                              metadata = aqp::metadata(x),
                              horizons = .as.data.frame.aqp(h, aqp_df_class(x)),
                              site = .as.data.frame.aqp(s, aqp_df_class(x)),
-                             sp = sp,
+                             # sp = sp,
                              diagnostic = .as.data.frame.aqp(d, aqp_df_class(x)),
                              restrictions = .as.data.frame.aqp(r, aqp_df_class(x))
                            )
@@ -409,9 +409,7 @@ setMethod("[", signature(x = "SoilProfileCollection"),
 #   which is an error caused by RStudio? when doing tab completion
 #   with %>% operator on a SPC
 
-setMethod("[[", signature(x = "SoilProfileCollection",
-                          i = "ANY",
-                          j = "ANY"),
+setMethod("[[", signature(x = "SoilProfileCollection"),
           function(x, i, j) {
             if (length(i) == 1) {
               # site names take precedence for those
@@ -446,9 +444,7 @@ setMethod("[[", signature(x = "SoilProfileCollection",
 #' @aliases [[<-,SoilProfileCollection-method [[<-,SoilProfileCollection,ANY,ANY-method 
 #' @docType methods
 #' @rdname doublebracket-set
-setReplaceMethod("[[", signature(x = "SoilProfileCollection",
-                                 i = "ANY",
-                                 value = "ANY"),
+setReplaceMethod("[[", signature(x = "SoilProfileCollection"),
                  function(x, i, value) {
                    lv <- length(value)
                    lx <- length(x)

R/SoilProfileCollection-spatial.R

@@ -11,7 +11,7 @@ setGeneric("prj", function(object, ...)
 #' @export
 #' @seealso [initSpatial<-()]
 #' @rdname SoilProfileCollection-crs
-#' @aliases prj
+#' @aliases prj proj4string
 setMethod("prj", 'SoilProfileCollection',
           function(object, ...) {
             value <- metadata(object)$crs
@@ -26,7 +26,7 @@ setGeneric("prj<-", function(object, ..., value)
   standardGeneric("prj<-"))
 
 #' @description `prj()<-`: Set Coordinate Reference System metadata for the SoilProfileCollection
-#' @aliases prj<-
+#' @aliases prj<- proj4string<-
 #' @rdname SoilProfileCollection-crs
 #' @export
 setReplaceMethod("prj", 'SoilProfileCollection',
@@ -65,6 +65,9 @@ setReplaceMethod("prj", 'SoilProfileCollection',
                  }
 )
 
+setGeneric("proj4string", function(obj)
+  standardGeneric("proj4string"))
+
 #' @description `proj4string()`: (Deprecated) Get Coordinate Reference System as PROJ4 String
 #' @rdname SoilProfileCollection-crs
 #' @export
@@ -76,10 +79,14 @@ setMethod("proj4string", signature(obj = 'SoilProfileCollection'),
           }
 )
 
+setGeneric("proj4string<-", function(obj, value)
+  standardGeneric("proj4string<-"))
+
 #' @description `proj4string()<-`: (Deprecated) Set Coordinate Reference System metadata for the SoilProfileCollection
 #' @rdname SoilProfileCollection-crs
 #' @export
-setReplaceMethod("proj4string", signature(obj = 'SoilProfileCollection'),
+setReplaceMethod("proj4string", signature(obj = "SoilProfileCollection",
+                                          value = "ANY"),
                  function(obj, value) {
                    .Deprecated("prj<-", package = "aqp", 
                                msg = "Methods based on sp class definitions have been deprecated and will be removed by October 1, 2023. See ?`prj<-`")
@@ -181,6 +188,9 @@ setMethod("getSpatial", signature(object = "SoilProfileCollection"),
             return(as.matrix(sapply(cn, function(x) object[[x]])))
           })
 
+setGeneric("coordinates", function(obj)
+  standardGeneric("coordinates"))
+
 #' @param obj A SoilProfileCollection
 #' @export
 #' @rdname initSpatial
@@ -193,6 +203,9 @@ setMethod("coordinates", signature(obj = "SoilProfileCollection"),
             getSpatial(obj)
           })
 
+setGeneric("coordinates<-", function(object, value)
+  standardGeneric("coordinates<-"))
+
 #' @rdname initSpatial
 #' @export
 #' @aliases coordinates<-

R/combine.R

@@ -348,7 +348,7 @@ pbindlist <- function(l, new.idname = NULL, verbose = TRUE) {
   o.s <- lapply(spc.list, '[[', 'site')
   o.d <- lapply(spc.list, '[[', 'diagnostic')
   o.r <- lapply(spc.list, '[[', 'restrictions')
-  o.sp <- lapply(spc.list, '[[', 'sp')
+  # o.sp <- lapply(spc.list, '[[', 'sp')
 
   # generate new SPC components
   # https://github.com/ncss-tech/aqp/issues/71
@@ -379,8 +379,8 @@ pbindlist <- function(l, new.idname = NULL, verbose = TRUE) {
   }
 
   # sp slot is deprecated; always empty/uninitialized now
-  o.sp <- new('SpatialPoints')
-
+  o.sp <- NULL
+  
   ## sanity check: profile IDs should be unique
   if (length(o.s[[new.pID]]) != length(unique(o.s[[new.pID]]))) {
     stop('non-unique profile IDs detected')

R/plotSPC.R

@@ -1742,6 +1742,5 @@ plotSPC <- function(
 #' @aliases plot,SoilProfileCollection-method plot,SoilProfileCollection,ANY-method
 #' @rdname SoilProfileCollection-plotting-methods
 #' @export
-setMethod("plot", signature(x = "SoilProfileCollection",
-                            y = "ANY"),
+setMethod("plot", signature(x = "SoilProfileCollection"),
           definition = {function(x, y, ...) plotSPC(x, ...)})

R/rebuildSPC.R

@@ -27,10 +27,13 @@
 #' @seealso \code{\link{checkSPC}}
 #' @export
 rebuildSPC <- function(x) {
-
   # break into pieces as list
   x.list <- suppressWarnings(as(x, 'list'))
 
+  if (.hasSlot(x, "sp")) {
+    x.list <- x.list[!names(x.list) %in% "sp"]
+  }
+
   # seed object for new SPC
   res <- .as.data.frame.aqp(x.list$horizons, aqp_df_class(x))
 
@@ -103,7 +106,7 @@ rebuildSPC <- function(x) {
 
       site(res) <- newsp
       initSpatial(res) <- colnames(newsp)[2:3]
-      try(prj(res) <- x.list$sp@proj4string)
+      try(prj(res) <- x.list$sp@proj4string, silent = TRUE)
     }
   }
   return(res)