Closed
Description
Description
Gower function '_gower_distance_row' is normalizing the dissimilarity value that was already normalized in the main 'gower_distances' function
Steps To Reproduce
Run list_soils and then rank_soils with user data similar to the a soil that is most dissimilar (e.g., Clarion) to the top ranking soil based on the location score (e.g., Nicollet). Current code will not properly reorder soils due to this normalization problem.
For location: {"lon": -94.31005777, "lat": 42.63413723}:
list_soils return
{
"metadata":{
"location":"us",
"model":"v3",
"unit_measure":{
"distance":"m",
"depth":"cm",
"cec":"cmol(c)/kg",
"clay":"%",
"rock_fragments":"cm3/100cm3",
"sand":"%",
"ec":"ds/m"
}
},
"AWS_PIW90":2.48,
"Soil Data Value":[
"(""texture_0",
0.9202015555547535),
"(""texture_30",
0.8040345373281224),
"(""rfv_class_0",
0.2240207838259336),
"(""rfv_class_30",
0.2240207838259336)
],
"soilList":[
{
"id":{
"name":"Nicollet",
"component":"Nicollet",
"score_loc":0.85,
"rank_loc":"1"
},
"site":{
"siteData":{
"mapunitID":"797917",
"componentID":"25584956",
"componentKind":"Series",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":85,
"distance":0.0,
"minCompDistance":0.0,
"slope":2.0,
"nirrcapcl":"1",
"nirrcapscl":"None",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Aquic Hapludolls",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=nicollet",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#nicollet"
},
"siteDescription":"The Nicollet series consists of very deep, somewhat poorly drained soils that formed in calcareous loamy glacial till on till plains and moraines. Slopes range from 0 to 5 percent. Mean annual air temperature is about 9 degrees C (48 degrees F). Mean annual precipitation is about 660 mm (28 inches)."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY002MN"
],
"ecoclassname":[
"Calcareous Upland Prairies"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY002MN"
]
}
},
"bottom_depth":{
"0":25,
"1":43,
"2":91,
"3":200
},
"sand":{
"0":31,
"1":31,
"2":37,
"3":44
},
"clay":{
"0":30,
"1":30,
"2":30,
"3":21
},
"texture":{
"0":"Clay loam",
"1":"Clay loam",
"2":"Clay loam",
"3":"Loam"
},
"rock_fragments":{
"0":4,
"1":4,
"2":4,
"3":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":6.2,
"1":6.2,
"2":6.6,
"3":8.0
},
"ec":{
"0":0,
"1":0,
"2":0,
"3":0
},
"lab":{
"0":[
40.89,
1.44,
6.13
],
"1":[
51.37,
1.83,
6.76
],
"2":[
61.56,
1.08,
14.05
],
"3":[
61.56,
0.62,
14.31
]
},
"munsell":{
"0":"10YR 4/1",
"1":"10YR 5/1",
"2":"2.5Y 6/2",
"3":"2.5Y 6/2"
}
},
{
"id":{
"name":"Webster",
"component":"Webster",
"score_loc":0.679,
"rank_loc":"2"
},
"site":{
"siteData":{
"mapunitID":"797921",
"componentID":"25584964",
"componentKind":"Series",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":85,
"distance":28.0,
"minCompDistance":28.0,
"slope":1.0,
"nirrcapcl":"2",
"nirrcapscl":"w",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Typic Endoaquolls",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=webster",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#webster"
},
"siteDescription":"The Webster series consists of very deep, poorly drained, moderately permeable soils formed in glacial till or local alluvium derived from till on uplands. Slope ranges from 0 to 3 percent. Mean annual air temperature is about 48 degrees F, and mean annual precipitation is about 30 inches."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY004MN"
],
"ecoclassname":[
"Loamy Upland Prairies"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY004MN"
]
}
},
"bottom_depth":{
"0":25,
"1":51,
"2":107,
"3":200
},
"sand":{
"0":25,
"1":25,
"2":35,
"3":44
},
"clay":{
"0":33,
"1":33,
"2":28,
"3":21
},
"texture":{
"0":"Clay loam",
"1":"Clay loam",
"2":"Clay loam",
"3":"Loam"
},
"rock_fragments":{
"0":4,
"1":4,
"2":4,
"3":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":6.5,
"1":6.9,
"2":7.3,
"3":8.0
},
"ec":{
"0":0,
"1":0,
"2":0,
"3":0
},
"lab":{
"0":[
30.23,
2.2,
6.21
],
"1":[
42.28,
1.21,
7.14
],
"2":[
68.87,
-1.52,
14.95
],
"3":[
71.54,
-1.61,
15.25
]
},
"munsell":{
"0":"10YR 3/1",
"1":"10YR 4/1",
"2":"5Y 7/2",
"3":"5Y 7/2"
}
},
{
"id":{
"name":"Clarion",
"component":"Clarion",
"score_loc":0.404,
"rank_loc":"3"
},
"site":{
"siteData":{
"mapunitID":"797923",
"componentID":"25584604",
"componentKind":"Taxadjunct",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":85,
"distance":93.0,
"minCompDistance":93.0,
"slope":3.0,
"nirrcapcl":"2",
"nirrcapscl":"e",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Oxyaquic Hapludolls",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=clarion",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#clarion"
},
"siteDescription":"The Clarion series consists of very deep, moderately well drained soils on uplands. These soils formed in glacial till. Slopes range from 1 to 9 percent. Mean annual air temperature is about 8 degrees C (47 degrees F). Mean annual precipitation is about 74 centimeters (29 inches)."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY015MN"
],
"ecoclassname":[
"Depressional Marsh"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY015MN"
]
}
},
"bottom_depth":{
"0":20,
"1":40,
"2":86,
"3":200
},
"sand":{
"0":41,
"1":41,
"2":43,
"3":44
},
"clay":{
"0":25,
"1":25,
"2":23,
"3":21
},
"texture":{
"0":"Loam",
"1":"Loam",
"2":"Loam",
"3":"Loam"
},
"rock_fragments":{
"0":4,
"1":4,
"2":4,
"3":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":6.2,
"1":6.2,
"2":6.6,
"3":8.0
},
"ec":{
"0":0,
"1":0,
"2":0,
"3":0
},
"lab":{
"0":[
30.23,
2.36,
6.8
],
"1":[
35.57,
4.67,
15.88
],
"2":[
58.87,
5.65,
24.56
],
"3":[
61.56,
5.67,
25.29
]
},
"munsell":{
"0":"10YR 3/1",
"1":"10YR 3/3",
"2":"10YR 6/4",
"3":"10YR 6/4"
}
},
{
"id":{
"name":"Okoboji",
"component":"Okoboji",
"score_loc":0.05,
"rank_loc":"4"
},
"site":{
"siteData":{
"mapunitID":"797917",
"componentID":"25584952",
"componentKind":"Series",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":5,
"distance":0.0,
"minCompDistance":0.0,
"slope":0.0,
"nirrcapcl":"3",
"nirrcapscl":"w",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Cumulic Vertic Endoaquolls",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=okoboji",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#okoboji"
},
"siteDescription":"The Okoboji series consists of very deep, very poorly drained soils formed in alluvium or lacustrine sediments. These soils are in closed depressions on till plains and moraines. Slope ranges from 0 to 1 percent. Mean annual air temperature is about 8 degrees C. Mean annual precipitation is about 740 millimeters."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY004MN"
],
"ecoclassname":[
"Loamy Upland Prairies"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY004MN"
]
}
},
"bottom_depth":{
"0":20,
"1":84,
"2":97,
"3":200
},
"sand":{
"0":11,
"1":12,
"2":15,
"3":16
},
"clay":{
"0":36,
"1":36,
"2":36,
"3":31
},
"texture":{
"0":"Silty clay loam",
"1":"Silty clay loam",
"2":"Silty clay loam",
"3":"Silty clay loam"
},
"rock_fragments":{
"0":0,
"1":0,
"2":0,
"3":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":6.8,
"1":7.0,
"2":7.1,
"3":7.4
},
"ec":{
"0":0,
"1":0,
"2":0,
"3":0
},
"lab":{
"0":[
19.63,
2.11,
5.22
],
"1":[
26.31,
2.05,
5.58
],
"2":[
39.66,
-0.34,
3.81
],
"3":[
61.56,
-0.58,
9.99
]
},
"munsell":{
"0":"10YR 2/1",
"1":"10YR 3/1",
"2":"2.5GY 4/1",
"3":"5Y 6/1"
}
},
{
"id":{
"name":"Glencoe",
"component":"Glencoe",
"score_loc":0.024,
"rank_loc":"5"
},
"site":{
"siteData":{
"mapunitID":"797921",
"componentID":"25584960",
"componentKind":"Series",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":3,
"distance":28.0,
"minCompDistance":28.0,
"slope":0.0,
"nirrcapcl":"3",
"nirrcapscl":"w",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Cumulic Endoaquolls",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=glencoe",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#glencoe"
},
"siteDescription":"The Glencoe series consists of very deep, very poorly drained soils that formed in loamy sediments from till. These soils are in closed depressions on moraines. Slope ranges from 0 to 1 percent. Mean annual air temperature is about 8 degrees C. Mean annual precipitation is about 735 millimeters."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY015MN"
],
"ecoclassname":[
"Depressional Marsh"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY015MN"
]
}
},
"bottom_depth":{
"0":23,
"1":99,
"2":127,
"3":200
},
"sand":{
"0":22,
"1":26,
"2":24,
"3":35
},
"clay":{
"0":33,
"1":33,
"2":31,
"3":28
},
"texture":{
"0":"Clay loam",
"1":"Clay loam",
"2":"Clay loam",
"3":"Clay loam"
},
"rock_fragments":{
"0":1,
"1":1,
"2":4,
"3":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":7.0,
"1":7.0,
"2":7.3,
"3":8.0
},
"ec":{
"0":0,
"1":0,
"2":0,
"3":0
},
"lab":{
"0":[
2.31,
-0.02,
-0.01
],
"1":[
30.23,
2.2,
6.21
],
"2":[
61.56,
0.62,
14.31
],
"3":[
61.56,
-0.13,
14.56
]
},
"munsell":{
"0":"10Y 1/1",
"1":"10YR 3/1",
"2":"2.5Y 6/2",
"3":"2.5Y 6/2"
}
},
{
"id":{
"name":"Storden",
"component":"Storden",
"score_loc":0.024,
"rank_loc":"6"
},
"site":{
"siteData":{
"mapunitID":"797923",
"componentID":"25584602",
"componentKind":"Series",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":5,
"distance":93.0,
"minCompDistance":93.0,
"slope":8.0,
"nirrcapcl":"3",
"nirrcapscl":"e",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Typic Eutrudepts",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=storden",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#storden"
},
"siteDescription":"The Storden series consists of very deep, well drained soils that formed in calcareous loamy glacial till on glacial moraines. Slope ranges from 4 to 70 percent. Mean annual precipitation is about 660 mm (26 inches). Mean annual air temperature is about 9 degrees C (48 degrees F)."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY001MN"
],
"ecoclassname":[
"Loamy Wet Prairies"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY001MN"
]
}
},
"bottom_depth":{
"0":20,
"1":140,
"2":200
},
"sand":{
"0":46,
"1":42,
"2":44
},
"clay":{
"0":21,
"1":21,
"2":21
},
"texture":{
"0":"Loam",
"1":"Loam",
"2":"Loam"
},
"rock_fragments":{
"0":4,
"1":4,
"2":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":7.7,
"1":7.8,
"2":8.0
},
"ec":{
"0":0,
"1":0,
"2":0
},
"lab":{
"0":[
61.55,
2.96,
13.65
],
"1":[
61.56,
4.81,
21.85
],
"2":[
61.56,
5.67,
25.29
]
},
"munsell":{
"0":"10YR 6/2",
"1":"10YR 6/3",
"2":"10YR 6/4"
}
},
{
"id":{
"name":"Canisteo",
"component":"Canisteo",
"score_loc":0.016,
"rank_loc":"7"
},
"site":{
"siteData":{
"mapunitID":"797921",
"componentID":"25584962",
"componentKind":"Series",
"dataSource":"SSURGO",
"textureInfill":"No",
"rfvInfill":"No",
"componentPct":2,
"distance":28.0,
"minCompDistance":28.0,
"slope":1.0,
"nirrcapcl":"2",
"nirrcapscl":"w",
"nirrcapunit":"None",
"irrcapcl":"None",
"irrcapscl":"None",
"irrcapunit":"None",
"taxsubgrp":"Typic Endoaquolls",
"sdeURL":"https://casoilresource.lawr.ucdavis.edu/sde/?series=canisteo",
"seeURL":"https://casoilresource.lawr.ucdavis.edu/see/#canisteo"
},
"siteDescription":"The Canisteo series consists of very deep, poorly and very poorly drained soils that formed in calcareous, loamy till or in a thin mantle of loamy or silty sediments and the underlying calcareous, loamy till. These soils are on rims of depressions, depressions and flats on moraines or till plains. Slope ranges from 0 to 2 percent. Mean air annual temperature is about 9 degrees C. Mean annual precipitation is about 785 millimeters."
},
"esd":{
"ESD":{
"ecoclassid":[
"R103XY001MN"
],
"ecoclassname":[
"Loamy Wet Prairies"
],
"edit_url":[
"https://edit.jornada.nmsu.edu/catalogs/esd/103X/R103XY001MN"
]
}
},
"bottom_depth":{
"0":23,
"1":41,
"2":51,
"3":91,
"4":200
},
"sand":{
"0":30,
"1":32,
"2":32,
"3":39,
"4":44
},
"clay":{
"0":32,
"1":32,
"2":32,
"3":27,
"4":21
},
"texture":{
"0":"Clay loam",
"1":"Clay loam",
"2":"Clay loam",
"3":"Loam",
"4":"Loam"
},
"rock_fragments":{
"0":4,
"1":4,
"2":4,
"3":4,
"4":4
},
"cec":{
"0":"CEC",
"1":"CEC"
},
"ph":{
"0":7.5,
"1":7.7,
"2":7.7,
"3":8.0,
"4":8.0
},
"ec":{
"0":0,
"1":0,
"2":0,
"3":0,
"4":0
},
"lab":{
"0":[
5.01,
-0.26,
-0.08
],
"1":[
9.46,
-0.36,
-0.2
],
"2":[
35.79,
-0.89,
7.39
],
"3":[
69.04,
-1.56,
15.18
],
"4":[
71.52,
-0.77,
8.7
]
},
"munsell":{
"0":"10Y 1/1",
"1":"2.5BG 1/1",
"2":"7.5Y 3/1",
"3":"5Y 7/2",
"4":"5Y 7/1"
}
}
]
}
Expected behavior
Nicollet has the top ranking location score (clay loam surface texture). When I enter loam as the surface texture (most similar to Clarion), I expect Clarion to have the highest rank_soil score.
For location: {"lon": -94.31005777, "lat": 42.63413723}:
Example of corrected rank_soils return when user enters ' loam' surface soil
*Note that rank_data is not being correctly assigned. This is addressed in PR #257
{
"metadata":{
"location":"us",
"model":"v2"
},
"soilRank":[
{
"name":"Clarion",
"component":"Clarion",
"componentID":25584604,
"score_data_loc":0.702,
"rank_data_loc":"1",
"score_data":1.0,
"rank_data":"3",
"score_loc":0.404,
"rank_loc":3,
"componentData":"Data Complete"
},
{
"name":"Nicollet",
"component":"Nicollet",
"componentID":25584956,
"score_data_loc":0.63,
"rank_data_loc":"2",
"score_data":0.409,
"rank_data":"1",
"score_loc":0.85,
"rank_loc":1,
"componentData":"Data Complete"
},
{
"name":"Webster",
"component":"Webster",
"componentID":25584964,
"score_data_loc":0.544,
"rank_data_loc":"3",
"score_data":0.409,
"rank_data":"2",
"score_loc":0.679,
"rank_loc":2,
"componentData":"Data Complete"
},
{
"name":"Storden",
"component":"Storden",
"componentID":25584602,
"score_data_loc":0.512,
"rank_data_loc":"4",
"score_data":1.0,
"rank_data":"6",
"score_loc":0.024,
"rank_loc":6,
"componentData":"Data Complete"
},
{
"name":"Glencoe",
"component":"Glencoe",
"componentID":25584960,
"score_data_loc":0.217,
"rank_data_loc":"5",
"score_data":0.409,
"rank_data":"5",
"score_loc":0.024,
"rank_loc":5,
"componentData":"Data Complete"
},
{
"name":"Canisteo",
"component":"Canisteo",
"componentID":25584962,
"score_data_loc":0.213,
"rank_data_loc":"6",
"score_data":0.409,
"rank_data":"7",
"score_loc":0.016,
"rank_loc":7,
"componentData":"Data Complete"
},
{
"name":"Okoboji",
"component":"Okoboji",
"componentID":25584952,
"score_data_loc":0.025,
"rank_data_loc":"7",
"score_data":0.0,
"rank_data":"4",
"score_loc":0.05,
"rank_loc":4,
"componentData":"Data Complete"
}
]
}
Actual behavior
Nicollet has the top ranking location score (clay loam surface texture). When I enter loam as the surface texture (most similar to Clarion), the rank_soil order doesn't change and Nicollet is assigned the highest data score.
For location: {"lon": -94.31005777, "lat": 42.63413723},:
Example of incorrect rank_soils return when user enters 'loam' surface soil
{
"metadata":{
"location":"us",
"model":"v2"
},
"soilRank":[
{
"name":"Nicollet",
"component":"Nicollet",
"componentID":25584956,
"score_data_loc":0.914,
"rank_data_loc":"1",
"score_data":0.977,
"rank_data":"1",
"score_loc":0.85,
"rank_loc":1,
"componentData":"Data Complete"
},
{
"name":"Webster",
"component":"Webster",
"componentID":25584964,
"score_data_loc":0.826,
"rank_data_loc":"2",
"score_data":0.974,
"rank_data":"2",
"score_loc":0.679,
"rank_loc":2,
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Metadata
Metadata
Labels
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Type
Projects
Status
Done