update effervescence, drop ordered factors

R/parseOSD_functions.R

@@ -94,7 +94,10 @@
   m <- tolower(m)
 
   # convert to ordered factor
-  m <- factor(m, levels = textures, ordered = TRUE)
+  #
+  # m <- factor(m, levels = textures, ordered = TRUE)
+  #
+  # factors cannot be preserved in JSON output, and wont work for multiple classes/ranges of classes
 
   return(m)
 }
@@ -196,33 +199,19 @@
   m <- tolower(m)
 
   # return as an ordered factor acidic -> basic
-  m <- factor(m, levels = pH_classes, ordered = TRUE)
+  # m <- factor(m, levels = pH_classes, ordered = TRUE)
+  # factors cannot be preserved in JSON output, and wont work for multiple classes/ranges of classes
 
   return(m)
 }
 
-
-
 # vectorized parsing of effervescence class
-#' @importFrom stringi stri_match
-.parse_eff_class <- function(text) {
-
-  # mineral texture classes
-  .classes <- c('noneffervescent', 'very slightly effervescent', 'slightly effervescent', 'strongly effervescent', 'violently effervescent')
-
-  ## 2019-05-29: generalized for all non-greedy, exact matching
-  m <- .findClass(needle = .classes, haystack = text)
-  m <- tolower(m)
-
-  # return as an ordered factor acidic -> basic
-  m <- factor(m, levels = .classes, ordered = TRUE)
-
-  return(m)
-
+.parse_eff_class <- function(x) {
+  SoilKnowledgeBase:::.zerochar_to_na(gsub("^.*(very [a-z]+ effervescen[tce]+).*$|^.*\\b([a-z]+ ?effervescen[tce]+).*$|.*",
+                                           "\\1\\2", x, ignore.case = TRUE))
+  # factors cannot be preserved in JSON output, and wont work for multiple classes/ranges of classes
 }
 
-
-
 # vectorized parsing of drainage class
 #' @importFrom stringi stri_match
 .parse_drainage_class <- function(text) {
@@ -248,7 +237,6 @@
 
   # return as an ordered factor
   # m <- factor(m, levels = classes, ordered = TRUE)
-
   # factors cannot be preserved in JSON output, and wont work for multiple classes/ranges of classes
 
   return(m)
@@ -324,11 +312,11 @@
   #       "O" = "0"
   #       "l" = "1"
   ## ideas: http://stackoverflow.com/questions/15474741/python-regex-optional-capture-group
-  
-  ## TODO: it isn't clear if the new files will be in 
+
+  ## TODO: it isn't clear if the new files will be in
   # expect em dashes (\u2014) used after horizon designation as of May 2023
   # https://github.com/ncss-tech/SoilKnowledgeBase/issues/64
-  
+
   # detect horizons with both top and bottom depths
   hz.rule <-            "([\\^\\'\\/a-zA-Z0-9]+)\\s*[-=\u2014]+\\s*([Ol0-9.]+)\\s*?(to|-)?\\s+?([Ol0-9.]+)\\s*?(in|inches|cm|centimeters)"
 
@@ -494,7 +482,7 @@
   res$pH <- .parse_pH(narrative.data$narrative)
   res$pH_class <- .parse_pH_class(narrative.data$narrative)
   res$eff_class <- .parse_eff_class(narrative.data$narrative)
-  
+
   bdy <- .parse_hz_boundary(narrative.data$narrative)
   res$distinctness <- bdy$distinctness
   res$topography <- bdy$topography

misc/OSD-error-reporting/typical-pedon.R

@@ -1,4 +1,5 @@
 library(aqp)
+library(soilDB)
 library(data.table)
 
 source("https://raw.githubusercontent.com/ncss-tech/soilDB/master/R/get_OSD.R")