notes, ideas

R/SoilProfileCollection-methods.R

@@ -272,7 +272,7 @@ setMethod(f = 'unique',
 
             # compute hash by profile, for selected variables
             md5 <- profileApply(x, function(i) {
-              # unlist in order to drop row names
+              # unlist() in order to drop row names
               digest::digest(unlist(as(i, 'data.frame')[, vars]))
             })
 

R/profileInformationIndex.R

@@ -324,6 +324,10 @@ profileInformationIndex <- function(x, vars, method = c('joint', 'individual'),
   x <- dice(x, fill = padNA)
 
   ## TODO: convert to data.table
+  # SPC = FALSE
+  # data.table()
+  # dt[, ]
+  # as.vector()
 
   # iterate over profiles
   # result is a vector suitable for site-level attribute

misc/sandbox/mps2-lambda-eval.R

@@ -0,0 +1,66 @@
+# install mpsline2 from CRAN
+
+library(aqp)
+library(sharpshootR)
+library(mpspline2)
+library(reshape2)
+library(lattice)
+
+# make some example data
+ids <- LETTERS[1]
+
+set.seed(10101)
+x <- lapply(ids, random_profile, n = c(6, 7, 8), n_prop = 1, method = 'LPP', SPC = TRUE, lpp.a = 5, lpp.b = 25, lpp.d = 10, lpp.e = 5, lpp.u = 25)
+x <- combine(x)
+
+# fake site data
+site(x)$fake_site_attr <- 1:length(x)
+
+# check source data
+par(mar=c(0,0,3,1))
+plotSPC(x, color='p1', col.palette = hcl.colors(10, 'viridis'))
+
+s <- seq(0, 1, by = 0.25)
+m <- lapply(s, function(i) {
+  .spc <- spc2mpspline(x, var_name = 'p1', lam = i, method = 'est_1cm')
+  profile_id(.spc) <- sprintf("%s-0%s", profile_id(.spc), i)
+  return(.spc)
+})
+
+z <- combine(m)
+z$p1 <- z$p1_spline
+
+xx <- combine(z, x)
+
+par(mar = c(0, 0, 3, 1))
+plotSPC(xx, color = 'p1', col.palette = hcl.colors(10, 'viridis'), divide.hz = FALSE, width = 0.35)
+
+
+o <- order(xx$p1_rmse)
+plotSPC(xx, color = 'p1', col.palette = hcl.colors(10, 'viridis'), divide.hz = FALSE, width = 0.35, plot.order = o)
+
+
+tps <- tactile::tactile.theme(superpose.line = list(lwd = 2))
+
+# compare depth-functions by method, no aggregation
+xyplot(cbind(top, bottom) ~ p1, id=xx$id, groups = factor(id),
+       data=as(xx, 'data.frame'),
+       par.settings=tps,
+       auto.key=list(columns=3, lines=TRUE, points=FALSE),
+       strip=strip.custom(bg=grey(0.85)),
+       ylim=c(125, -5), as.table=TRUE, panel=panel.depth_function,
+       scales = list(alternating = 1),
+       asp = 1
+)
+
+xyplot(cbind(top, bottom) ~ p1 | id, id=xx$id,
+       data=as(xx, 'data.frame'),
+       par.settings=tps,
+       auto.key=list(columns=4, lines=TRUE, points=FALSE),
+       strip=strip.custom(bg=grey(0.85)),
+       ylim=c(125, -5), as.table=TRUE, panel=panel.depth_function,
+       layout = c(6, 1),
+       scales = list(alternating = 1)
+)
+
+