Merge pull request #323 from ncss-tech/vignette-images

Lower DPI for vignette images to fix CRAN errors and notes

Author: dylanbeaudette

DESCRIPTION

@@ -6,7 +6,7 @@ Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut
 Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
 Depends: R (>= 3.5.0)
 Imports: grDevices, graphics, stats, utils, methods, grid, lattice, cluster, stringr, data.table, farver, digest, colorspace, ape
-Suggests: mvtnorm, soilDB, sp, sf, latticeExtra, tactile, compositions, markovchain, xtable,testthat, Gmedian, Hmisc, tibble, RColorBrewer, scales, MASS, mpspline2, soiltexture, gower, knitr, rmarkdown, dendextend
+Suggests: mvtnorm, soilDB, sp, sf, latticeExtra, tactile, compositions, markovchain, xtable,testthat, Gmedian, Hmisc, tibble, RColorBrewer, scales, mpspline2, soiltexture, gower, knitr, rmarkdown, dendextend
 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

NEWS.md

@@ -1,5 +1,6 @@
 # aqp 2.2 (2025-02-14)
  * CRAN release
+ * `evanGenHz()` now uses `stats::cmdscale()` instead of `MASS:isoMDS()`
  * migrating a few functions from sharpshootR to aqp:
   - `plotProfileDendrogram()`
   - `aggregateColorPlot()`

R/aqp-package.R

@@ -59,6 +59,7 @@
 #' 
 #' @importFrom ape as.phylo plot.phylo tiplabels
 #' 
+#' 
 "_PACKAGE"
 
 #' @export aqp.env

R/evalGenHz.R

@@ -4,7 +4,7 @@
 #' Data-driven evaluation of generalized horizon labels using nMDS and
 #' silhouette width.
 #'
-#' Non-metric multidimensional scaling is performed via [MASS::isoMDS()].
+#' Classic multidimensional scaling is performed via [stats::cmdscale()].
 #' The input distance matrix is generated by [cluster::daisy()] using
 #' (complete cases of) horizon-level attributes from `obj` as named in
 #' `vars`.
@@ -25,14 +25,12 @@
 #' 
 #' @param stand standardize variables before computing distance matrix, passed to [cluster::daisy()]
 #' 
-#' @param trace verbose output from passed to [MASS::isoMDS()]
-#' 
 #' @param metric distance metric, passed to [cluster::daisy()]
 #' 
 #' @return a list is returned containing: 
 #'   * horizons: `c('mds.1', mds.2', 'sil.width', 'neighbor')` 
 #'   * stats: mean and standard deviation `vars`, computed by generalized horizon label
-#'   * dist: the distance matrix as passed to [MASS::isoMDS()]
+#'   * dist: the distance matrix as passed to [stats::cmdscale()]
 #'   
 #' @author D.E. Beaudette
 #' 
@@ -41,9 +39,7 @@
 #' @keywords manip
 #' 
 #' @export
-evalGenHZ <- function(obj, genhz = GHL(obj, required = TRUE), vars, non.matching.code='not-used', stand=TRUE, trace=FALSE, metric='euclidean') {
-  if(!requireNamespace("MASS", quietly = TRUE))
-    stop("package `MASS` is required", call.=FALSE)
+evalGenHZ <- function(obj, genhz = GHL(obj, required = TRUE), vars, non.matching.code = 'not-used', stand = TRUE, metric = 'euclidean') {
 
   # hack to make R CMD check happy
   value <- summarize <- NULL
@@ -81,8 +77,9 @@ evalGenHZ <- function(obj, genhz = GHL(obj, required = TRUE), vars, non.matching
     d[dupe.idx] <- fudge
   }
 
-  # perform non-metric MDS of dissimilarity matrix
-  mds <- MASS::isoMDS(d, trace = trace)
+  ## TODO: allow user-defined ordination function
+  # perform metric MDS of dissimilarity matrix
+  mds <- stats::cmdscale(d, k = 2)
 
   # compute silhouette widths after removing not-used genhz class
   sil.idx <-  which(complete.cases(h[, vars, drop = FALSE]) & h[[genhz]] != non.matching.code)
@@ -95,9 +92,10 @@ evalGenHZ <- function(obj, genhz = GHL(obj, required = TRUE), vars, non.matching
   h$sil.width <- NA
   h$neighbor <- NA
 
+  ## TODO: access results from user-defined ordination function
   # copy values
-  h$mds.1[no.na.idx] <- mds$points[, 1]
-  h$mds.2[no.na.idx] <- mds$points[, 2]
+  h$mds.1[no.na.idx] <- mds[, 1]
+  h$mds.2[no.na.idx] <- mds[, 2]
   h$sil.width[sil.idx] <- sil[, 3]
   h$neighbor[sil.idx] <- levels(h[[genhz]])[sil[, 2]]
 

R/previewColors.R

@@ -32,9 +32,8 @@
 #' 
 #' @author D.E. Beaudette
 #' 
-#' 
 #'
-#' @return When \code{method = "grid" or "manual"} a vector of color order is returned. When \code{method = "MDS"}, the output from \code{MASS::cmdscale}.
+#' @return When `method` = "grid" or "manual", a vector of color order is returned. When `method = "MDS"`, the output from [stats::cmdscale()].
 #' @export
 #'
 #' @examples

README.md

@@ -59,7 +59,7 @@ Install suggested packages:
 p <- c("colorspace", "ape", "soilDB", "latticeExtra", "tactile", "compositions", 
 "sharpshootR", "markovchain", "xtable", "testthat", "Gmedian", 
 "farver", "Hmisc", "tibble", "RColorBrewer", "scales", "digest", 
-"MASS", "mpspline2", "soiltexture", "knitr", "rmarkdown", "mvtnorm")
+ "mpspline2", "soiltexture", "knitr", "rmarkdown", "mvtnorm")
 
 install.packages(p)
 ```

man/evalGenHZ.Rd

@@ -152,3 +152,4 @@ test_that("generalizeHz SPC method", {
 
   expect_equal(GHL(sp4), "mylabel")
 })
+

man/previewColors.Rd

@@ -9,12 +9,14 @@ vignette: >
 
 ```{r setup, echo=FALSE, results='hide', warning=FALSE}
 knitr::opts_chunk$set(
-message = FALSE,
-warning = FALSE,
-background = '#F7F7F7',
-fig.align = 'center',
-dev = 'png',
-comment = "#>"
+  message = FALSE,
+  warning = FALSE,
+  background = '#F7F7F7',
+  fig.align = 'center',
+  dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
+  comment = "#>"
 )
 options(width = 100, stringsAsFactors = FALSE, timeout = 600)
 

tests/testthat/test-genhz.R

@@ -14,6 +14,8 @@ knitr::opts_chunk$set(
   background = '#F7F7F7',
   fig.align = 'center',
   dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
   comment = "#>"
 )
 

vignettes/Introduction-to-SoilProfileCollection-Objects.Rmd

@@ -14,6 +14,8 @@ knitr::opts_chunk$set(
   background = '#F7F7F7',
   fig.align = 'center',
   dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
   comment = "#>"
 )
 

vignettes/Munsell-color-conversion.Rmd

@@ -14,6 +14,8 @@ knitr::opts_chunk$set(
   background = '#F7F7F7',
   fig.align = 'center',
   dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
   comment = "#>"
 )
 

vignettes/NCSP.Rmd

@@ -14,6 +14,8 @@ knitr::opts_chunk$set(
   background = '#F7F7F7',
   fig.align = 'center',
   dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
   comment = "#>"
 )
 options(width = 100, stringsAsFactors = FALSE, timeout = 600)

vignettes/aqp-overview.Rmd

@@ -14,6 +14,8 @@ knitr::opts_chunk$set(
   background = '#F7F7F7',
   fig.align = 'center',
   dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
   comment = "#>"
 )
 
@@ -148,4 +150,4 @@ plotSPC(x, color = 'hz.not.missing', width = 0.33, name.style = 'center-center',
 text(x = 1:length(x), y = .b[o], labels = x$abs.not.missing[o], cex = 0.85, pos = 1)
 mtext('Absolute Non-Missing (cm)', side = 1, line = -0.5)
 
-```
+```

vignettes/label-placement.Rmd

@@ -14,6 +14,8 @@ knitr::opts_chunk$set(
   background = '#F7F7F7',
   fig.align = 'center',
   dev = 'png',
+  dpi = as.integer(Sys.getenv("R_AQP_VIGNETTE_IMAGE_DPI", unset = 32)),
+  optipng = knitr::hook_optipng,
   comment = "#>"
 )