fixing errors in the sampling chapter

Part1/05-sampling.Rmd

@@ -182,10 +182,11 @@ library(ggplot2)
 set.seed(4)
 
 # Create a sixteen square polygon
-bb <- st_make_grid(st_bbox(c(xmin = 0, xmax = 6, ymin = 0, ymax = 6)), n = 6)
+n = 4
+bb <- st_make_grid(st_bbox(c(xmin = 0, xmax = n, ymin = 0, ymax = n)), n = n)
 grd <- st_as_sf(bb)
 grd$ID <- 1:length(bb)
-
+grd <- rmapshaper::ms_explode(grd)
 ```
 
 
@@ -273,13 +274,14 @@ In stratified random sampling, the sampling region is spatially subset into diff
 
 
 ```{r stratified, fig.width=4, fig.height=4, eval=TRUE}
-grd2 <- st_cast(grd, "MULTIPOLYGON")
-st_crs(grd2) <- 5070
-
-test <- st_sample(grd2, size = 16, type = "random", by_polygon = TRUE)
+idx <- 1:nrow(grd)
+test <- sapply(idx, function(x) st_sample(grd[x, ], size = 1))
+test <- do.call("rbind", test) |>
+  as.data.frame() |> 
+  st_as_sf(coords = 1:2)
 
 ggplot() + 
-  geom_sf(data = grd2) + 
+  geom_sf(data = grd) + 
   geom_sf(data = test) + 
   ggtitle("Stratified")
 ```
@@ -310,11 +312,12 @@ In multistage random sampling, the region is separated into different subsets th
 ```{r two_stage, fig.width=4, fig.height=4, eval=TRUE}
 # Select 8 samples from each square
 idx <- sample(1:nrow(grd), size = 2, replace = FALSE)
-grd_sub <- grd[idx, ]
-test <- sapply(1:2, function(i) {
-  st_coordinates(st_sample(grd_sub[i, ], size = 8, type = "random"))
+test <- sapply(idx, function(i) {
+  st_sample(grd[i, ], size = 8, type = "random")
 })
-test <- st_as_sf(as.data.frame(test), coords = 1:2)
+test <- do.call("rbind", test) |> 
+  as.data.frame() |> 
+  st_as_sf(coords = 1:2)
 
 ggplot() + 
   geom_sf(data = grd) + 
@@ -384,7 +387,7 @@ Covariate space coverage sampling is a stratified sampling technique to obtain r
 ```{r, eval=TRUE}
 library(sf)
 library(terra)
-source("https://raw.githubusercontent.com/ncss-tech/stats_for_soil_survey/master/exercises/fcsc.R")
+library(sgsR)
 
 # import volcano DEM, details at http://geomorphometry.org/content/volcano-maungawhau
 data("volcano")
@@ -407,14 +410,13 @@ slope_r <- terrain(volcano_r, v = "slope", unit = "degrees")
 rs  <- c(volcano_r, slope_r)
 
 # Covariate Space Coverage Sampling
-source("https://raw.githubusercontent.com/ncss-tech/stats_for_soil_survey/master/exercises/fcsc.R")
-fs <- cscs(rs, vars = c("elev", "slope"), n = 20)
-
-fs_sf <- st_as_sf(fs, coords = c("x", "y"), crs = crs(rs))
+n = 20
+fs_strata <- strat_kmeans(rs, nStrata = n, iter = 10000)
+fs_samp   <- sample_nc(rs, nSamp = n, iter = 10000)
 
 # Plot CSCS Samples
-plot(volcano_r, axes=FALSE)
-points(fs_sf)
+plot(fs_strata, col = map.pal("random", n))
+plot(fs_samp, col = "black", cex = 1, pch = 19, add = TRUE)
 ```
 
 ### Conditioned Latin Hypercube (cLHS)
@@ -502,7 +504,7 @@ sys <- spatSample(rs, size = 20, method = "regular", as.points = TRUE)
 cs <- clhs(rs2, size = 20, progress = FALSE, simple = FALSE)
 
 # take a CSCS sample
-fs <- cscs(rs, vars = c("elev", "slope"), n = 20)
+fs <- sample_nc(rs, nSamp = 20) |> extract(rs, y = _) |> select(elev, slope)
 
 # Combind and Extract Samples
 s <- rbind(
@@ -534,7 +536,7 @@ plot(volcano_r, main = "cLHS", cex.main = 2, axes=FALSE)
 points(cs$sampled_data, pch = 3, cex = 1.2)
 
 plot(volcano_r, main = "CSCS", cex.main = 2, axes=FALSE)
-points(fs_sf, pch = 3, cex = 1.2)
+points(fs_samp, pch = 3, cex = 1.2)
 ```
 
 The overlapping density plots above illustrate the differences between large and small sets of samples using several sampling designs. 

Part1/book.bib

@@ -62,7 +62,7 @@ @book{brus2022
 	edition = {1},
 	title = {Spatial {Sampling} with {R}},
 	isbn = {978-1-00-325894-0},
-	url = {https://www.taylorfrancis.com/books/9781003258940},
+	url = {https://dickbrus.github.io/SpatialSamplingwithR/},
 	language = {en},
 	urldate = {2023-04-01},
 	publisher = {Chapman and Hall/CRC},
@@ -126,7 +126,7 @@ @incollection{gelman2020
 	edition = {1},
 	title = {16 - {Design} and sample size decisions},
 	isbn = {9781139161879 9781107023987 9781107676510},
-	url = {https://www.cambridge.org/highereducation/product/9781139161879/book},
+	url = {https://avehtari.github.io/ROS-Examples/},
 	urldate = {2022-01-31},
 	booktitle = {Regression and {Other} {Stories}},
 	publisher = {Cambridge University Press},

Part1/packages.bib

@@ -1,7 +1,7 @@
 @Manual{R-aqp,
   title = {aqp: Algorithms for Quantitative Pedology},
   author = {Dylan Beaudette and Pierre Roudier and Andrew Brown},
-  note = {R package version 2.1.1},
+  note = {R package version 2.1.0},
   url = {https://github.com/ncss-tech/aqp},
   year = {2025},
 }
@@ -128,6 +128,14 @@ @Manual{R-sf
   url = {https://r-spatial.github.io/sf/},
 }
 
+@Manual{R-sgsR,
+  title = {sgsR: Structurally Guided Sampling},
+  author = {Tristan RH Goodbody and Nicholas C Coops and Martin Queinnec},
+  year = {2024},
+  note = {R package version 1.4.5},
+  url = {https://github.com/tgoodbody/sgsR},
+}
+
 @Manual{R-shape,
   title = {shape: Functions for Plotting Graphical Shapes, Colors},
   author = {Karline Soetaert},
@@ -307,6 +315,14 @@ @Article{sf2018
   number = {1},
 }
 
+@Manual{sgsR2023,
+  title = {sgsR: a structurally guided sampling toolbox for LiDAR-based forest inventories.},
+  author = {Tristan R.H. Goodbody and Nicholas C. Coops and Martin Queinnec and Joanne C. White and Piotr Tompalski and Andrew T. Hudak and David Auty and Ruben Valbuena and Antoine LeBoeuf and Ian Sinclair and Grant McCartney and Jean-Francois Prieur and Murray E. Woods},
+  journal = {Forestry: An International Journal of Forest Research},
+  year = {2023},
+  doi = {10.1093/forestry/cpac055},
+}
+
 @Article{sp2005,
   author = {Edzer J. Pebesma and Roger Bivand},
   title = {Classes and methods for spatial data in {R}},

book/404.html

@@ -23,7 +23,7 @@
 <meta name="author" content="Soil Survey Staff" />
 
 
-<meta name="date" content="2025-01-28" />
+<meta name="date" content="2025-01-30" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -73,7 +73,7 @@
 
 <style type="text/css">
 pre > code.sourceCode { white-space: pre; position: relative; }
-pre > code.sourceCode > span { line-height: 1.25; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
@@ -145,7 +145,6 @@
 div.csl-bib-body { }
 div.csl-entry {
   clear: both;
-  margin-bottom: 0em;
 }
 .hanging div.csl-entry {
   margin-left:2em;