testing eff class, will keep for a little while, until happy with res…

…ults and soilweb import code updated

misc/OSD-error-reporting/test-effervescance-class.R

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+
+library(aqp)
+library(soilDB)
+library(purrr)
+library(furrr)
+
+# series names to iterate over
+sc <- get_soilseries_from_NASIS()
+
+# # subset of series names for testing
+# s <- sample(sc$soilseriesname, size = 1000)
+
+# all established soil series names
+s <- sc$soilseriesname[which(sc$soilseriesstatus == 'established')]
+
+# test effervescence class
+# singe parsed OSD at a time
+testEffClass <- function(i) {
+
+  # there may be no data for a given series
+  # return NULL
+  # these series are ignored / no result
+  if(length(i$HORIZONS) < 1) {
+    return(NULL)
+  }
+
+  # extract eff class data for all horizons
+  .e <- i$HORIZONS[[1]]$eff_class
+
+  # remove NA, may result in length 0
+  .e <- na.omit(.e)
+
+  # no non-NA matches, likely no carbonates
+  if(length(.e) < 1) {
+    # all NA
+    .res <- FALSE
+  } else {
+
+    # possibly more criteria here, such as effervescence class > threshold
+    # or in B horizons
+
+    # simplest possible test: 
+    # exclude when all, non-NA, horizons are noneffervescent
+    if(all(.e == 'noneffervescent')) {
+      .res <- FALSE
+    } else {
+      # some effervescence in profile
+      .res <- TRUE
+    }
+
+  }
+
+  # TODO: maybe list reason for TRUE/FALSE
+
+  # pack into a data.frame for simple use later
+  .d <- data.frame(series = i$SERIES[1], eff = .res)
+  return(.d)
+}
+
+
+
+# setup parallel processing
+plan(multisession, workers = 8)
+
+
+# load selected OSDs from local JSON
+# ~ 1 minutes for all established soil series
+# adjust local URL to SKB working copy
+system.time(
+  osds <- future_map(
+    s,
+    .progress = TRUE,
+    .f = get_OSD, 
+    base_url = 'E:/working_copies/SoilKnowledgeBase/inst/extdata/OSD/'
+  )
+)
+
+
+## tests
+# all noneffervescent
+testEffClass(osds[[which(s == 'TOADTOWN')]])
+testEffClass(osds[[which(s == 'FRAZWELL')]])
+
+# no eff class included in typical pedon narrative
+# all NA
+testEffClass(osds[[which(s == 'AMADOR')]])
+testEffClass(osds[[which(s == 'CECIL')]])
+
+# some horizons with eff class > noneffervescent
+testEffClass(osds[[which(s == 'PIERRE')]])
+
+
+## shutdown parallel back-ends
+plan(sequential)
+
+# apply test / criteria to all parsed soil series
+# single-threaded
+# result is a data.frame
+x <- map_df(osds, .f = testEffClass, .progress = TRUE)
+
+# check: ok
+head(x)
+table(x$eff)
+
+## interpretation notes:
+# 1. NA -> FALSE could mean 
+#  - "unable to parse due to poorly formatted text"
+#  - "eff class not given"
+# 
+# 2. number / thickness of effervescent horizons not part of criteria
+# 
+
+## save
+saveRDS(x, file = 'e:/temp/osd-eff-class-interpretation.rds')
+
+
+
+