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Merge 66a2a18 into 8720775
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@brownag
brownag authored Oct 25, 2023
2 parents 8720775 + 66a2a18 commit 32aff17
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40 changes: 14 additions & 26 deletions R/parseOSD_functions.R
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Expand Up @@ -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)
}
Expand Down Expand Up @@ -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("^.*[;,]? \\b([a-z]+ ?effervescen[tce]+ to [a-z]+ ?effervescen[tce]+).*$|^.*[;,] \\b(very [a-z]+ effervescen[tce]+).*$|^.*[;,] \\b([a-z]+ ?effervescen[tce]+).*$|^.*[;,]? \\b(very [a-z]+ effervescen[tce]+).*$|^.*[;,]? \\b([a-z]+ ?effervescen[tce]+).*$|.*",
"\\1\\2\\3\\4\\5", 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) {
Expand All @@ -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)
Expand Down Expand Up @@ -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)"

Expand Down Expand Up @@ -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
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4 changes: 2 additions & 2 deletions inst/extdata/OSD/A/AAZDAHL.json
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Expand Up @@ -135,7 +135,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "gradual",
"topography": "wavy",
"narrative": "Bk--20 to 36 inches; grayish brown (2.5Y 5/2) clay loam; weak medium subangular blocky structure; friable; about 5 percent coarse fragments; violent effervescence; moderately alkaline; gradual wavy boundary. (0 to 20 inches thick)"
Expand All @@ -158,7 +158,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "NA",
"topography": "NA",
"narrative": "C--36 to 60 inches; light olive brown (2.5Y 5/4) clay loam; common fine faint yellowish brown (10YR 5/6) and few fine prominent gray (5Y 5/1) mottles; massive; friable; about 5 percent coarse fragments; strong effervescence; moderately alkaline."
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8 changes: 4 additions & 4 deletions inst/extdata/OSD/A/ABERDEEN.json
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Expand Up @@ -181,7 +181,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "slightly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "clear",
"topography": "wavy",
"narrative": "Bkyz1--26 to 31 inches; light gray (2.5Y 7/2) silty clay loam, grayish brown (2.5Y 5/2) moist; weak medium prismatic structure parting to weak medium subangular blocky; hard, firm, sticky and plastic; common fine nests of gypsum and other salts; common very fine accumulations of carbonate; strong effervescence; slightly alkaline; clear wavy boundary."
Expand All @@ -204,7 +204,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "slightly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "gradual",
"topography": "wavy",
"narrative": "Bkyz2--31 to 38 inches; light brownish gray (2.5Y 6/2) silty clay loam, dark grayish brown (2.5Y 4/2) moist; weak medium prismatic structure parting to weak medium subangular blocky; hard, firm, sticky and plastic; common fine nests of gypsum and other salts; common very fine accumulations of carbonate; strong effervescence; slightly alkaline; gradual wavy boundary. (Combined Bkyz horizons 0 to 20 inches thick)"
Expand All @@ -227,7 +227,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "slightly alkaline",
"eff_class": "NA",
"eff_class": "slight effervescence",
"distinctness": "gradual",
"topography": "wavy",
"narrative": "C1--38 to 51 inches; light gray (2.5Y 7/2) silt loam, grayish brown (2.5Y 5/2) moist; few fine prominent of yellowish brown (10YR 5/6) redoximorphic concentrations and few fine distinct gray (10YR 5/1) moist redoximorphic depletions; massive; hard, friable, slightly sticky and slightly plastic; few fine threads and nests of gypsum and other salts; slight effervescence; slightly alkaline; gradual wavy boundary."
Expand All @@ -250,7 +250,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "slightly alkaline",
"eff_class": "NA",
"eff_class": "slight effervescence",
"distinctness": "NA",
"topography": "NA",
"narrative": "C2--51 to 60 inches; pale yellow (2.5Y 7/4) silt loam, laminated with thin layers of silty clay and very fine sandy loam, light olive brown (2.5Y 5/4) moist; common fine prominent yellowish brown (10YR 5/6) and strong brown (7.5YR 5/6) redoximorphic concentrations, and gray (10YR 5/1) moist redoximorphic depletions; massive; laminations 1 to 3 mm thick; slightly hard, friable, slightly sticky and slightly plastic; slight effervescence; slightly alkaline."
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8 changes: 4 additions & 4 deletions inst/extdata/OSD/A/ACKETT.json
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Expand Up @@ -158,7 +158,7 @@
"cf_class": "extremely cobbly",
"pH": 8.4,
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "abrupt",
"topography": "smooth",
"narrative": "2Btkq--15 to 20 cm; light gray (10YR 7/2) extremely cobbly clay, very pale brown (10YR 7/3) moist; massive; extremely hard, extremely firm, moderately sticky and moderately plastic; common distinct clay films on faces of peds and in pores; many continuous silica cemented laminations throughout; fractures are 0.6 cm wide and are 20 cm apart; few very fine roots in fractures; few very fine tubular pores; 70 percent cobbles, 10 percent gravel; violent effervescence; moderately alkaline (pH 8.4); abrupt smooth boundary. (0 to 8 cm thick)"
Expand All @@ -181,7 +181,7 @@
"cf_class": "very gravelly",
"pH": 8.4,
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "abrupt",
"topography": "smooth",
"narrative": "2Btk--20 to 36 cm; very pale brown (10YR 7/3) very gravelly clay loam, pale brown (10YR 6/3) moist; weak medium subangular blocky structure; hard, firm, moderately sticky and moderately plastic; few very fine and fine roots; few very fine tubular pores; common distinct clay films on faces of peds and in pores; 40 percent gravel size duripan fragments; violent effervescence (25 percent calcium carbonate); moderately alkaline (pH 8.4); abrupt smooth boundary. (8 to 18 cm thick)"
Expand All @@ -204,7 +204,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "NA",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "abrupt",
"topography": "smooth",
"narrative": "2Bkqm--36 to 71 cm; white (10YR 8/1) fractured indurated duripan; very pale brown (10YR 7/3) moist; massive; many continuous silica cemented laminations throughout the duripan; fractures are 0.6 cm wide and are 50 cm apart; few very fine roots in fractures of the duripan; violent effervescence; abrupt smooth boundary. (20 to 38 cm thick)"
Expand All @@ -227,7 +227,7 @@
"cf_class": "extremely gravelly",
"pH": 8.2,
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "abrupt",
"topography": "smooth",
"narrative": "3Bkq--71 to 127 cm; multi-colored extremely gravelly sand; single grain; loose in places; 80 percent gravel; weak carbonate-silica cementation with carbonate pendants on undersides of gravel; violent effervescence; moderately alkaline (pH 8.2); abrupt smooth boundary. (25 to 60 cm)"
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2 changes: 1 addition & 1 deletion inst/extdata/OSD/A/ADE.json
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Expand Up @@ -181,7 +181,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "NA",
"topography": "NA",
"narrative": "C--60 to 70 inches; brownish yellow (10YR 6/6) fine sand; single grain; loose; strong effervescence; moderately alkaline."
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8 changes: 4 additions & 4 deletions inst/extdata/OSD/A/AGAR.json
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Expand Up @@ -158,7 +158,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "slightly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "clear",
"topography": "wavy",
"narrative": "Bk1--18 to 22 inches; grayish brown (10YR 5/2) silty clay loam, dark grayish brown (10YR 4/2) moist; weak coarse prismatic structure parting to moderate medium and fine subangular blocky; hard, friable; few fine accumulations of carbonate; strong effervescence; slightly alkaline; clear wavy boundary."
Expand All @@ -181,7 +181,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "gradual",
"topography": "wavy",
"narrative": "Bk2--22 to 34 inches; light brownish gray (2.5Y 6/2) silty clay loam, dark grayish brown (2.5Y 4/2) moist; weak coarse prismatic structure parting to weak medium subangular blocky; hard, friable; common medium accumulations of carbonate; strong effervescence; moderately alkaline; gradual wavy boundary."
Expand All @@ -204,7 +204,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "gradual",
"topography": "wavy",
"narrative": "Bk3--34 to 40 inches; light brownish gray (2.5Y 6/2) silt loam, grayish brown (2.5Y 5/2) moist; weak medium subangular blocky structure; hard, friable; common medium accumulations of carbonate; strong effervescence; moderately alkaline; gradual wavy boundary. (Combined Bk horizon is 10 to 25 inches.)"
Expand All @@ -227,7 +227,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "NA",
"topography": "NA",
"narrative": "C3--40 to 61 inches; light brownish gray (2.5Y 6/2) silt loam, dark grayish brown (2.5Y 4/2) moist; massive; slightly hard, friable; few fine and medium accumulations of carbonate; strong effervescence; moderately alkaline."
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2 changes: 1 addition & 1 deletion inst/extdata/OSD/A/AGENCY.json
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Expand Up @@ -204,7 +204,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "NA",
"eff_class": "NA",
"eff_class": "moderately effervescent",
"distinctness": "NA",
"topography": "NA",
"narrative": "2Crkq--29 to 33 inches; paralithic tuff with silica and calcium carbonate coatings along fractures; moderately effervescent. ( 0 to 6 inches thick )"
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10 changes: 5 additions & 5 deletions inst/extdata/OSD/A/AGUILAR.json
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Expand Up @@ -135,7 +135,7 @@
"cf_class": "NA",
"pH": 8.8,
"pH_class": "strongly alkaline",
"eff_class": "NA",
"eff_class": "slight effervescence",
"distinctness": "clear",
"topography": "smooth",
"narrative": "Btn2--10 to 14 inches (25 to 36 cm); brown (10YR 5/3), silty clay, brown (10YR 4/3) moist; moderate coarse columnar structure parting to strong medium subangular blocks; extremely hard, very firm, very sticky and very plastic; few very fine and fine roots; common continuous distinct clay films on faces of peds; common fine salt threads; slight effervescence, 21 percent sodium absorption ratio; strongly alkaline (pH 8.8); clear smooth boundary. (combined thickness of the Btn horizons is 8 to 14 inches)"
Expand All @@ -158,7 +158,7 @@
"cf_class": "NA",
"pH": 8.8,
"pH_class": "strongly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "clear",
"topography": "smooth",
"narrative": "Btny--14 to 23 inches (36 to 58 cm); brown (10YR 5/3) clay, brown (10YR 4/3) moist; moderate medium columnar structure parting to strong medium angular blocks; extremely hard, very firm, very sticky and very plastic; few very fine roots; common continuous distinct clay films on faces of peds; common medium salt and gypsum threads; strong effervescence, 21 percent sodium absorption ratio; strongly alkaline (pH 8.8); clear smooth boundary. (7 to 14 inches thick)"
Expand All @@ -181,7 +181,7 @@
"cf_class": "NA",
"pH": 8.6,
"pH_class": "strongly alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "clear",
"topography": "smooth",
"narrative": "Btkny--23 to 29 inches (58 to 74 cm); brown (10YR 5/3) clay loam, brown (10YR 4/3) moist; strong medium subangular blocky structure; extremely hard, very firm, moderately sticky and moderately plastic; few patchy distinct clay films on faces of peds; common coarse carbonate threads and common coarse salt and gypsum masses; violent effervescence, 22 percent sodium absorption ratio; strongly alkaline (pH 8.6); clear smooth boundary. (2 to 10 inches thick)"
Expand All @@ -204,7 +204,7 @@
"cf_class": "NA",
"pH": 8.4,
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "gradual",
"topography": "smooth",
"narrative": "Bkny--29 to 45 inches (74 to 114 cm); grayish brown (10YR 5/2) silty clay loam, brown (10YR 5/3) moist; 18 percent sand; moderate medium subangular blocky structure; very hard, firm, moderately sticky and moderately plastic; common medium salt and gypsum threads; common medium distinct carbonate threads; violent effervescence (3 percent calcium carbonate equivalent), 22 percent sodium absorption ratio; moderately alkaline (pH 8.4); gradual smooth boundary. (10 to 20 inches thick)"
Expand All @@ -227,7 +227,7 @@
"cf_class": "NA",
"pH": 8.2,
"pH_class": "moderately alkaline",
"eff_class": "NA",
"eff_class": "violent effervescence",
"distinctness": "NA",
"topography": "NA",
"narrative": "Bny--45 to 65 inches (114 to 165 cm); grayish brown (10YR 5/2) silty clay loam, brown (10YR 5/3) moist; weak medium subangular blocky structure; very hard, firm, moderately sticky and moderately plastic; common medium salt and gypsum threads; common medium carbonate threads; violent effervescence (2 percent calcium carbonate equivalent); 21 percent sodium absorption ratio; moderately alkaline (pH 8.2)."
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12 changes: 6 additions & 6 deletions inst/extdata/OSD/A/AHOLT.json
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Expand Up @@ -89,7 +89,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "neutral",
"eff_class": "NA",
"eff_class": "slight effervescence",
"distinctness": "clear",
"topography": "smooth",
"narrative": "Ap--0 to 6 inches; black (10YR 2/1) clay, very dark gray (10YR 3/1) dry; strong fine and very fine granular structure; very sticky, very hard; many fine roots; slight effervescence; neutral; clear smooth boundary. (4 to 10 inches thick)"
Expand All @@ -112,7 +112,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "mildly alkaline",
"eff_class": "NA",
"eff_class": "slight effervescence",
"distinctness": "NA",
"topography": "NA",
"narrative": "Bg1--6 to 14 inches; black (10YR 2/1) clay, dark gray (N 4/0) dry; few fine distinct brown (10YR 4/3) mottles; strong very fine angular and subangular blocky structure; very sticky, very hard; common fine roots; shiny pressure faces; slight effervescence, mildly alkaline; smooth gradual boundary."
Expand All @@ -135,7 +135,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "mildly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "gradual",
"topography": "smooth",
"narrative": "Bg2--14 to 22 inches; very dark gray (10YR 3/1) clay, dark gray (N 4/0) dry; few fine distinct dark grayish brown (2.5Y 4/2) and brown (10YR 4/3) mottles; moderate medium angular and subangular blocky structure; very sticky, very hard; few fine roots; few very fine calcium carbonate concretions; shiny pressure faces; strong effervescence; mildly alkaline; gradual smooth boundary."
Expand All @@ -158,7 +158,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "mildly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "gradual",
"topography": "smooth",
"narrative": "Bg3--22 to 34 inches; gray (5Y 5/1) clay, common fine distinct dark grayish brown (2.5Y 4/2) and common fine prominent olive brown (2.5Y 4/4) mottles; moderate medium angular and subangular blocky structure; very sticky, very hard; few fine calcium carbonate concretions; shiny pressure faces; strong effervescence; mildly alkaline; gradual smooth boundary."
Expand All @@ -181,7 +181,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "mildly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "clear",
"topography": "smooth",
"narrative": "Bg4--34 to 46 inches; mixed gray (5Y 5/1) and dark gray (5Y 4/1) clay; common fine prominent olive brown (2.5Y 4/4) mottles; weak coarse subangular blocky structure; very sticky, very hard; few fine calcium carbonate concretions; shiny pressure faces; strong effervescence; mildly alkaline; clear smooth boundary. (Combined thickness of the Bg horizon is 34 to more than 70 inches.)"
Expand All @@ -204,7 +204,7 @@
"cf_class": "NA",
"pH": "NA",
"pH_class": "mildly alkaline",
"eff_class": "NA",
"eff_class": "strong effervescence",
"distinctness": "gradual",
"topography": "smooth",
"narrative": "Cg1--46 to 58 inches; gray (5Y 5/1) and (5Y 6/1) silty clay loam; common medium prominent light olive brown (2.5Y 5/4) mottles; massive; sticky, hard; strong effervescence; mildly alkaline; gradual smooth boundary. Cg2--58 to 66 inches; mottled gray (10YR 5/1) and yellowish brown (10YR 5/6) silty clay loam; massive; sticky, hard; strong effervescence; mildly alkaline."
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