Difference between revisions of "London Atlas: Materials and methods II: data visualisation"

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Ferreira, A, Johnson, C C, Appleton, J D, Flight, D M A, Lister, T R, Knights, K V, Ander, L, Scheib, C, Scheib, A, Cave, M, Wragg, J, Fordyce, F and Lawley, R. 2017. London Region Atlas of Topsoil Geochemistry. British Geological Survey.


The dataset described here, the London Region Topsoil Dataset (LRD), was initially created to investigate how the geochemical baseline of the London region is influenced by the underlying parent material. The data are a combination of the G-BASE[1] urban data released as part of the London Earth[2] project in 2011 (Johnson, 2011[3]) plus other available rural or urban G-BASE[1] topsoil results falling within the rectangular area shown in Figure 2. This includes samples collected over several summer field campaigns from 2005 to 2009, which in practice can be grouped into two main subsets, SEEN and LOND, as previously described. The area selected was designed to give insight in to how geochemical signatures may change over the same parent materials passing from central London to more rural areas on the periphery. As such, the rectangular areas of the LRA include, whenever possible, a representative number of rural SEEN samples over the same parent material (PM, simplified geology) classes that underlie the urban LOND. The number of topsoil samples in LOND and in SEEN subsets collected on each PM are shown in Table 7. The simplified geological classes are ordered from the most to the least represented in LOND, and the font is coloured grey for the simplified geological class not represented (or poorly represented) in one of the subsets (LOND and SEEN) at least. The background colour of the first column is according to the geological time period.

Thirteen (out of the 21) PMs observed in the LRA are able to be compared as they are fairly well represented in both subset areas (LOND and SEEN). Only one of the PM classes represented in the urban LOND, Thames Group (sand-gravel), is poorly represented (one sample only) in the surrounding rural SEEN. Seven PM classes are represented in SEEN subset only, including two on which topsoil was casually not collected, due to small spatial extension relative to the sampling density (Table 7). The parent material (PM) mapping method described by Appleton and Adlam (2012)[4] was used to create geochemical images in ESRI® ArcGIS and their geogenic signatures are described in Appleton et al. (2013)[5]. Using PM polygons as soil chemistry mapping units, it is possible to estimate element concentrations based on local averages, without significant errors at PM boundaries (Appleton et al., 2008[6]; Appleton and Adlam, 2012[4]). In case of a large positive skewness distribution, the geometric mean (GM) should be used for mapping the spatial variation in element concentrations, in order to minimise the bias associated with that type of distribution. The PM methodology is generally appropriate in situations and for elements where PM explains a relatively high proportion of the variance, but less so for elements where the proportion of variance explained by PM is low, for example where point or non-point source anthropogenic contamination is a major factor, such as Pb. Previously published London Earth[2] geochemical images were based on standard inverse distance weighted squared (IDW2) maps created in ArcGIS with an 80 m cell size and an isotropic search radius of 750 m. By contrast, the parent material mapping method uses parent material (simplified geology) polygons subdivided into separate 200 m square cells (subdivisions of the BNG). These store non-topological geometry and attribute information for the spatial features that form the basis for the production of the geochemical maps.

Parent material (PM) codes for each 200 m grid square were attached to the locations of all soil samples. Parent material geochemical mapping was executed using an ArcGIS tool written in Vb.Net (Appleton and Adlam, 2012[4]) to calculate the geometric mean (GM) element concentration for each 200 m-PM polygon. The optimum number of samples for calculating the GMs was between four and seven for topsoil data (Appleton et al. 2008[7]). For the maps generated here, GMs were calculated using data for the nearest four samples on the same PM apart from (a) four very minor PM units (calcrete, peat, the Upper Greensand and the Wealden Group), which comprise about 0.2% of the study area and which have no soil samples located on them and (b) polygons for which the average distance to the four samples required to calculate the GM was greater than 7000 m, which comprise about 4% of the study area. This largely affects sinuous polygon features, such as narrow alluvium areas along the upper reaches of tributaries to the River Thames. This approach was adopted to prevent excessive extrapolation of high element concentrations related to anthropogenic contamination, such as Pb. For both these sets of polygons (a and b), the GM was calculated from soil chemistry data for the nearest four samples, irrespective of PM.

The colour coding of the geochemical maps of the London Region follow the standard G-BASE[1] geochemical map classification applied in past geochemical atlases (e.g., BGS, 2000[8]). The percentiles 5, 10, 15, 25, 50, 75, 90, 95 and 99 of the data distribution are used as class boundaries for a ramp of colours (Table 8).


Table 7 The number of topsoil samples (out of 8400) observed in LOND and in SEEN subsets over each simplified geology class.

----Geological time period----

----Simplified geology class----

----LOND----

----SEEN----

----LRD----

Palaeogene

Thames Gp. (clay)

2328

274

2602

Quaternary

River terrace deposits

1677

147

1824

Quaternary

Alluvium

618

72

690

Cretaceous

White Chalk SubGp.

449

258

707

Quaternary

Brickearth

370

20

390

Quaternary

Head (clay-silt)

326

100

426

Palaeogene

Thames Gp. (sand-gravel)

306

1

307

Palaeogene

Lambeth Group

178

35

213

Quaternary

Clay-with-flints

159

153

312

Quaternary

Plateau gravels

152

109

261

Palaeogene

Thanet Sand Fm.

136

26

159

Quaternary

Glacial till

68

224

292

Palaeogene

Bagshot Fm.

25

63

88

Quaternary

Head (gravel-sand)

9

14

23

Cretaceous

Lower Greensand Gp.

0

46

46

Palaeogene

Bracklesham Gp. (sand-silt)

0

20

20

Cretaceous

Grey Chalk SubGp.

0

15

15

Cretaceous

Gault Fm.

0

13

13

Palaeogene

Bracklesham Gp. (sand)

0

12

12

Cretaceous

Upper Greensand

0

0

0

Cretaceous

Wealden Gp. (mudstone)

0

0

0


Table 8 Percentiles of topsoil element concentrations (N = 8400) plus LOI (N = 7928) and pH (N = 7929). Concentrations are in wt% for the 10 most abundant elements (shown as oxides) and for LOI; the remaining 34 elements are in mg/kg and pH is in log[H+] mol/L.

Colour

Percentile

Al2O3

CaO

Fe2O3

K2O

MgO

MnO

Na2O

P2O5

SiO2

TiO2

Ag

As

Ba

Bi

Br

Cd

Ce

Co

Cr

Cs

Cu

Ga

Ge

Min

0.8

<0.05

0.13

0.12

<0.3

<0.005

<0.3

<0.05

4.6

0.17

<0.5

<2.4

139

<0.3

1.1

<0.5

16

<1.5

9

1

3

1.0

<0.5

5

3.9

0.37

2.09

0.74

0.4

0.022

<0.3

0.15

48.0

0.37

<0.5

8.6

257

<0.3

6.4

<0.5

33

5.3

46

2

13

7.2

0.5

10

4.7

0.50

2.48

0.88

0.4

0.030

0.3

0.18

54.2

0.41

<0.5

10.0

283

<0.3

7.4

<0.5

37

6.7

52

2

17

7.9

0.7

15

5.2

0.59

2.71

0.97

0.5

0.035

0.3

0.19

56.8

0.44

0.5

10.9

300

<0.3

8.1

<0.5

39

7.7

56

2

20

8.4

0.8

20

5.6

0.67

2.93

1.03

0.5

0.039

0.3

0.218

58.7

0.46

0.5

11.6

313

<0.3

8.7

<0.5

41

8.4

59

2

22

8.7

0.9

25

5.9

0.74

3.10

1.08

0.6

0.043

0.3

0.22

60.2

0.47

0.5

12.2

324

<0.3

9.2

<0.5

43

9.0

61

2

24

9.1

1.0

30

6.2

0.81

3.24

1.13

0.6

0.046

0.3

0.24

61.6

0.49

0.5

12.8

334

<0.3

9.7

0.5

44

9.6

63

2

26

9.4

1.1

35

6.5

0.89

3.38

1.18

0.7

0.048

0.4

0.25

62.9

0.51

0.5

13.3

344

<0.3

10.1

0.5

45

10.0

65

2

29

9.7

1.2

40

6.9

0.96

3.52

1.23

0.7

0.051

0.4

0.27

64.1

0.53

0.5

13.8

353

<0.3

10.5

0.5

47

10.5

67

3

32

9.9

1.2

45

7.2

1.06

3.67

1.27

0.7

0.054

0.4

0.28

65.4

0.55

0.5

14.3

362

<0.3

11.0

0.5

49

11.0

70

3

35

10.3

1.3

50

7.6

1.18

3.80

1.32

0.8

0.056

0.4

0.31

66.6

0.57

0.5

14.8

371

<0.3

11.4

0.6

50

11.4

73

3

38

10.6

1.4

55

8.0

1.32

3.96

1.38

0.8

0.060

0.4

0.31

68.0

0.59

0.5

15.4

379

0.3

11.9

0.6

52

11.9

75

3

43

11.0

1.5

60

8.4

1.48

4.13

1.45

0.9

0.062

0.4

0.33

69.3

0.61

0.5

16.0

387

0.3

12.4

0.7

54

12.5

78

3

47

11.3

1.6

65

8.8

1.68

4.31

1.52

0.9

0.066

0.5

0.35

70.5

0.64

0.5

16.6

396

0.4

13.0

0.7

56

13.0

81

3

52

11.8

1.7

70

9.4

1.92

4.49

1.61

1.0

0.070

0.5

0.37

72.0

0.67

0.5

17.3

405

0.5

13.7

0.7

57

13.7

84

4

59

12.3

1.9

75

10.0

2.23

4.70

1.71

1.2

0.075

0.5

0.40

73.3

0.70

0.5

18.2

417

0.6

14.5

0.8

59

14.4

88

4

67

12.9

2.1

80

10.6

2.65

4.92

1.82

1.1

0.081

0.5

0.43

75.0

0.74

0.5

19.2

432

0.7

15.4

0.9

61

15.2

93

4

77

13.6

2.3

85

11.3

3.28

5.20

1.94

1.2

0.092

0.6

0.47

76.9

0.78

0.6

20.5

455

0.9

16.6

1.0

64

16.4

98

5

91

14.3

2.6

90

12.0

4.31

5.52

2.07

1.4

0.108

0.6

0.54

79.2

0.82

1.0

22.9

490

1.2

18.5

1.3

68

18.0

104

5

114

15.1

3.1

95

13.2

6.95

6.09

2.28

1.6

0.147

0.7

0.66

82.7

0.88

2.2

27.5

577

2.2

22.1

1.9

74

20.8

116

6

167

16.3

4.1

99

15.3

23.26

7.14

2.58

2.2

0.264

0.9

1.09

89.1

0.97

11.5

46.5

885

7.5

33.6

6.8

101

31.6

172

7

433

18.9

7.6

Max

25.5

48.97

15.59

3.47

4.6

0.697

10.0

4.49

100.0

1.10

268.8

160.9

3475

70.5

241.1

165.2

238

85.2

2094

11

5326

44.1

38.7

Colour

Percentile

Hf

I

La

Mo

Nb

Nd

Ni

Pb

Rb

Sb

Sc

Se

Sn

Sr

Th

U

V

W

Y

Zn

Zr

LOI

pH

Min

1.1

<0.5

3

<0.2

4.7

<4

<1.3

10

6.5

<0.5

<3

<0.2

0.9

11

<0.7

<0.5

9

<0.6

3

<1.3

35

0.7

2.8

5

4.5

1.5

14

0.6

9.3

10.4

11.3

38

33.1

0.7

3.0

0.2

3.1

38

3.8

1.4

44

0.8

12

44

182

3.9

4.0

10

5.2

1.8

16

0.7

9.9

12.9

13.9

46

38.4

0.9

4.0

0.3

3.7

45

4.4

1.6

50

1.1

14

58

204

4.5

4.6

15

5.5

2.1

18

0.8

10.3

14.6

15.9

54

41.3

1.0

4.8

0.3

4.3

50

4.8

1.7

54

1.3

15

66

218

5.0

5.0

20

5.9

2.2

19

0.9

10.7

15.9

17.3

62

43.7

1.2

5.4

0.4

4.9

54

5.1

1.8

58

1.4

16

74

230

5.3

5.2

25

6.2

2.4

20

1.0

11.0

17.0

18.7

70

45.9

1.3

5.8

0.4

5.6

57

5.4

1.9

61

1.6

17

81

240

5.7

5.5

30

6.4

2.5

21

1.1

11.3

18.0

19.8

80

48.0

1.5

6.2

0.4

6.5

61

5.7

1.9

63

1.7

18

88

250

6.0

5.8

35

6.6

2.7

22

1.1

11.6

19.0

21.0

92

50.1

1.7

6.6

0.5

7.4

64

6.0

2.0

66

1.8

19

97

259

6.3

6.0

40

6.9

2.8

23

1.2

11.9

19.9

22.2

105

52.2

1.9

7.0

0.5

8.4

67

6.2

2.1

69

1.9

19

107

269

6.6

6.2

45

7.2

3.0

24

1.3

12.3

20.8

23.4

121

54.3

2.1

7.4

0.5

9.6

70

6.5

2.2

72

2.0

20

118

278

6.9

6.4

50

7.4

3.1

25

1.4

12.6

21.8

24.6

138

56.5

2.4

7.8

0.5

10.9

73

6.8

2.2

75

2.1

21

130

288

7.1

6.5

55

7.7

3.3

26

1.5

13.0

22.7

25.9

159

59.1

2.7

8.2

0.6

12.6

77

7.1

2.3

79

2.2

21

144

299

7.4

6.7

60

8.0

3.5

27

1.6

13.4

23.6

27.2

182

62.0

3.0

8.6

0.6

14.5

80

7.4

2.4

83

2.3

22

159

309

7.8

6.8

65

8.4

3.7

28

1.7

13.9

24.5

28.6

209

65.1

3.4

9.1

0.6

16.7

83

7.7

2.4

87

2.4

23

178

322

8.1

6.9

70

8.7

3.9

29

1.8

14.5

25.6

30.2

243

68.6

3.9

9.6

0.7

19.4

87

8.1

2.5

92

2.5

24

199

334

8.5

6.9

75

9.1

4.2

30

2.0

15.1

26.9

32.2

284

72.5

4.5

10.2

0.7

22.6

93

8.4

2.6

98

2.6

25

225

350

8.9

7.0

80

9.6

4.6

32

2.1

15.7

28.3

34.5

340

77.1

5.3

10.9

0.8

26.4

100

8.7

2.7

105

2.8

26

256

368

9.4

7.1

85

10.3

5.4

33

2.4

16.2

30.1

37.3

415

82.9

6.4

11.7

0.9

32.8

111

9.1

2.8

113

3.0

27

301

391

10.0

7.2

90

11.3

6.6

36

2.8

16.9

32.5

41.3

531

89.5

8.2

12.6

1.0

44.2

125

9.5

2.9

122

3.3

29

371

424

10.9

7.3

95

12.8

8.8

40

3.6

17.8

36.7

49.6

775

98.0

12.7

14.0

1.2

67.2

153

10.1

3.1

135

3.9

32

521

478

12.5

7.4

99

15.8

16.7

59

7.5

19.0

54.8

78.3

1668

113.5

33.1

16.9

2.3

169.1

272

11.0

3.6

163

8.4

50

1120

580

18.3

7.6

Max

40.7

79.9

134

561.2

146.7

172.7

505.6

25206

157.2

612.3

35.6

19.6

1041.5

601

456.5

11.5

531

316.8

158

10095

1488

72.1

8.4

References

  1. 1.0 1.1 1.2 Geochemical Baseline Survey of the Environment (G-BASE) http://www.bgs.ac.uk/gbase/home.html
  2. 2.0 2.1 London Earth http://www.bgs.ac.uk/gbase/londonearth.html
  3. Johnson, C C. 2011 Understanding the quality of chemical data from the urban environment. Part 1, quality control procedures. 61–76 In: Johnson, C C et al., (eds.) Mapping the chemical environment of urban areas. Wiley.
  4. 4.0 4.1 4.2 Appleton, J D, and Adlam, K A M. 2012. Geogenic control on soil chemistry in urban areas: a novel method for urban geochemical mapping using parent material classified data. Applied Geochemistry, Vol. 27, 161–170. 10.1016/j.apgeochem.2011.10.001
  5. Appleton, J D, Johnson, C C, Ander, E L, and Flight, D M A. 2013. Geogenic signatures detectable in topsoils of urban and rural domains in the London region, UK, using parent material classified data. Applied Geochemistry, Vol. 39, 169–180. DOI 10.1016/j.apgeochem.2013.07.010
  6. Appleton, J D, Rawlins, B G, and Thornton, I. 2008. National-scale estimation of potentially harmful element ambient background concentrations in topsoil using parent material classified soil:stream–sediment relationships. Applied Geochemistry, Vol. 23, 2596–2611. DOI 10.1016/j.apgeochem.2008.05.010
  7. Appleton, J D, Rawlins, B G, and Thornton I. 2008. National-scale estimation of potentially harmful element ambient background concentrations in topsoil using parent material classified soil:stream–sediment relationships. Applied Geochemistry, Vol. 23, 2596–2611. DOI 10.1016/j.apgeochem.2008.05.010
  8. BGS (British Geological Survey), 2000. Regional geochemistry of Wales and part of west-central England: stream sediment and soil. Keyworth, Nottingham: British Geological Survey.