SDAR data model

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SDAR data model

John Ortiz ^1,2,3, Carlos Jaramillo ^1,2

¹ Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama, ² Corporación Geológica ARES, Bogotá, Colombia. ³ Servicio Geológico Colombiano, Bogotá, Colombia.

SDAR is a fast and consistent tool for plotting and facilitating the analysis of stratigraphic and sedimentological data, designed to plot detailed stratigraphic sections and to perform quantitative stratigraphic analyses.

This document presents the specific types of data required by SDAR package. The representation schemes and standard formats that should be satisfied by the input data set to be integrated on SDAR are mentioned.

Data model

Many of the sedimentological, stratigraphical and paleontological features share common properties. For example, lithology, bioturbation, and lithostratigraphic and chronostratigraphic units are all defined over a stratigraphic range (i.e., each of them has to be defined by a base and a top). Moreover, features as structural data, and geochemical and geochronological analysis, are usually collected, or correspond to a specific stratigraphic position (i.e., each of them represents a unique depth into the well log). On the other hand, other features as fossil occurrences, samples, and sedimentary structures, could be described by both, stratigraphic range, or a specific stratigraphic position (e.g., a fossil occurrence could be presented in a specific depth, throughout a bed, or throughout a set of beds). Therefore, a flexible data model able to store and to integrate all the previous descriptions was implemented. SDAR allows users to provide stratigraphic information in these three main types: beds, intervals and punctual features. A description and an example of each data type are provided below.

NOTE: The SDAR project includes the development of a graphic user interface to connect this R package with a database management system; for this reason the structure of the data and headers (column names) should be followed in order to match the database structure.

beds (data format to integrate rock layers)

A layer of rock is the fundamental unit in an Stratigraphic Columns (SC) representation. It describes the thickness, composition, and texture of a rock. In order to integrate a stratigraphic layer in SDAR, the information required for each layer is bed number, thickness (i.e, it is defined by a base and a top), rock type, primary lithology, and grain size. To improve communication between geoscientists, some conventions, defined by sedimentologists to draw lithology patterns, and to describe grain size and color, are implemented. Details on the information required to define a layer and the sources for the conventions implemented are provided below.

bed_number: numeric; It is often useful to give to each bed, or rock unit, a number so as to facilitate later reference; begins at the stratigraphically lowest bed (tucker2011).
base and top: numeric; They define the bed thickness of each layer. Overlapping is not allowed between layers.
rock_type: string; This field must include only the values listed in Table 1.

Table 1: Rock type

id	Rock Type
1	sedimentary
2	volcaniclastic
3	covered

prim_litho: string; This field must include only the values listed in Table 2. Primary lithology (To draw lithologic patterns, conventions suggested by the Federal Geographic Data Committee FGDC (fgdc2006) are implemented).

Table 2: Primary lithology

id	Lithology
1	claystone	13	coal
2	mudstone	14	gypsum
3	shale	15	halite
4	siltstone	16	chert
5	sandstone	17	glauconite
6	conglomerate	18	limonite
7	breccia	19	siderite
8	limestone	20	phosphorite
9	dolostone	21	tuff
10	marl	22	lapillistone
11	chalk	23	agglomerate
12	diatomite	24	bentonite

grain_size: string; This field must include only the values listed in Table 3. The conventions are based on the Wentworth classification system for siliciclastic rocks (wentworth 1922), for pyroclastic rocks (wentworth 1932), and for classification of carbonate rocks (dunham 1962) are implemented.

Table 3: Grain size table

id	Grain Size
1	clay	22	mudstone
2	clay / silt	23	wackestone
3	silt	24	packstone
4	silt / very fine sand	25	grainstone
5	very fine sand	26	floatstone
6	very fine / fine sand	27	rudstone
7	fine sand	28	boundstone
8	fine / medium sand	29	framestone
9	medium sand	30	bindstone
10	medium / coarse sand	31	bafflestone
11	coarse sand	32	crystalline
12	coarse / very coarse sand	33	fine ash
13	very coarse sand	34	medium ash
14	very coarse / granule	35	coarse ash
15	granule	36	very coarse ash
16	granule / pebble	37	fine lapilli
17	pebble	38	medium lapilli
18	pebble / cobble	39	coarse lapilli
19	cobble	40	fine blocks and bombs
20	cobble / boulder	41	coarse blocks and bombs
21	boulder

In summary, a table with the structure presented in table 4 must be provided. Each row in this data array describes a stratigraphic bed/layer. This example is from a borehole core where depths are measured down from the surface, therefore “base” is greather than “top”.

Table 4: Example of beds/layers table.

bed_number	base	top	rock_type	prim_litho	grain_size
1	671	670.2	sedimentary	claystone	clay
2	670.2	669.4	covered
3	669.4	669.18	sedimentary	sandstone	medium sand
4	669.18	667.6	sedimentary	limestone	wackestone
5	667.6	667.2	sedimentary	conglomerate	boulder
6	667.2	666.2	sedimentary	shale	silt

We have provided on the SDAR repositoy a template of the data format used by SDAR as a Microsoft Excel spreadsheet, SDAR_v0.95_beds_template.xlsx. This is the suggested format by SDAR to store thickness, and texture description of rock layers (beds).

The fields “bed_number”, “base”, “top”, “rock_type”, prim_litho" and “grain_size” must be provided to draw a stratigraphic column on SDAR.
The fields “grading”, “grain_size_base”, “grain_size_top”, “munsell_color” and “Rcolor” are optional fields, if any of these optional fields are provided, SDAR will incorporate it on the graphical output.
The fields “base_contact” and “notes” are included on the template, but the current version is not able to display it on the graphical output, we are working on making it available in the next version.
The fields “prim_litho_percent”, “sec_litho”, “grain_size_sec_litho”, “sec_litho_percent” are included on the template in order to store information for mixed rocks, current version of SDAR is not able to display patterns for mixed rocks yet, but we encourage user to store it.
The fields “sorting”, “roundness”, “matrix”, “cement” and “fabric” are included on the template to store texture description of rock layers, this information is not display on the graphical output.

Optional fields

grading: string; This field must include only the values listed in Table 5. Grading commonly consists of an upward decrease in grain size (normal grading), however, certain sedimentary process result in an upward increase in grain size (inverse grading).

Table 5: Grading

id	Grading
1	normal
2	inverse

grain_size_base and grain_size_top: string; These fields must include only the values listed in Table 3. When grading is normal or inverse, the grain size of the base and top must be provided.
munsell_color: string; This field must include only the values listed in Table 6. It uses color description based on the Munsell chart codes from the Geological Society of America Rock Color Chart (Committee 1991).

Table 6: Munsell Colors

id	Munsell Color
1	5R 8/2	30	10YR 8/6	59	10GY 3/2	88	5B 9/1
2	5R 7/4	31	10YR 7/4	60	5G 7/2	89	5G 8/1
3	5R 6/2	32	10YR 6/2	61	5G 7/4	90	5GY 8/1
4	5R 6/6	33	10YR 6/6	62	5G 6/6	91	5Y 8/1
5	5R 5/4	34	10YR 5/4	63	5G 5/2	92	5YR 8/1
6	5R 4/2	35	10YR 4/2	64	5G 5/6	93	5B 7/1
7	5R 4/6	36	10YR 2/2	65	5G 3/2	94	5YR 6/1
8	5R ¾	37	5Y 8/4	66	10G 8/2	95	5Y 6/1
9	5R 2/2	38	5Y 7/2	67	10G 6/2	96	5G 6/1
10	5R 2/6	39	5Y 7/6	68	10G 4/2	97	5GY 6/1
11	10R 8/2	40	5Y 6/4	69	5BG 7/2	98	5B 5/1
12	10R 7/4	41	5Y 5/2	70	5BG 6/6	99	5G 4/1
13	10R 6/2	42	5Y 5/6	71	5BG 5/2	100	5GY 4/1
14	10R 6/6	43	5Y 4/4	72	5BG 4/6	101	5Y 4/1
15	10R 5/4	44	5Y 3/2	73	5BG 3/2	102	5YR 4/1
16	10R 4/2	45	10Y 8/2	74	5B 8/2	103	5G 2/1
17	10R 4/6	46	10Y 7/4	75	5B 7/6	104	5GY 2/1
18	10R ¾	47	10Y 6/2	76	5B 6/2	105	5Y 2/1
19	10R 2/2	48	10Y 6/6	77	5B 5/6	106	5YR 2/1
20	5YR 8/4	49	10Y 5/4	78	5PB 7/2	107	N9
21	5YR 7/2	50	10Y 4/2	79	5PB 5/2	108	N8
22	5YR 6/4	51	5GY 7/2	80	5PB 3/2	109	N7
23	5YR 5/2	52	5GY 7/4	81	5P 6/2	110	N6
24	5YR 5/6	53	5GY 5/2	82	5P 4/2	111	N5
25	5YR 4/4	54	5GY 3/2	83	5P 2/2	112	N4
26	5YR 3/2	55	10GY 7/2	84	5RP 8/2	113	N3
27	5YR ¾	56	10GY 6/4	85	5RP 6/2	114	N2
28	5YR 2/2	57	10GY 5/2	86	5RP 4/2	115	N1
29	10YR 8/2	58	10GY 4/4	87	5RP 2/2

Rcolor: string; Any color name valid in R format (colors function from grDevices package provide a complete list of colors available in R). Instead of using a color name, color can also be defined with a hexadecimal value. Examples are provided on Table 7

Table 7: Examples of R colors

id	Rcolor	example
1	goldenrod
2	seagreen
3	deepskyblue
4	#8968CD
5	#E9967A

base_contact: string; This field must include only the values listed in Table 8. The nature of the boundary at the base of the layer. Base contact is included on the template, but the current version is not able to display it on the graphical output, we are working on making it available in the next version.

Table 8: Base contact

id	Base contact
1	sharp planar
2	gradational
3	faulted
4	covered

notes: string; Additional description in a free text format, maximum 200 characters by bed (’Comments/Remarks’). Notes is included on the template, but the current version is not able to display it on the graphical output, we are working on making it available in the next version.

Mixed rocks

sec_litho: string; Secondary lithology, this field must include only the values listed in Table 2.
grain_size_sec_litho: string; Grain size of secondary lithology, this field must include only the values listed in Table 3.
prim_litho_percent and sec_litho_percent: numeric; Percent composition of primary and secondary lithology.
Note: The fields “prim_litho_percent”, “sec_litho”, “grain_size_sec_litho”, “sec_litho_percent”* are included on the template in order to store information for mixed rocks, current version of SDAR is not able to display patterns for mixed rocks yet, but we encourage user to store it.

Texture description

sorting: string; This field must include only the values listed in Table 9. Description of the degree of uniformity of grain size.

Table 9: Sorting

id	Sorting
1	very well sorted
2	well sorted
3	moderately sorted
4	poorly sorted
5	very poorly sorted

roundness: string; This field must include only the values listed in Table 10. Measurement of roundness of sedimentary particles (Krumbein 1941).

Table 10: Roundness

id	Roudness
1	very angular
2	angular
3	sub angular
4	sub rounded
5	rounded
6	well rounded

matrix: string; This field must include only the values listed in Table 11. Composition of material wherein larger grains, crystals or clasts are embedded.

Table 11: Matrix

id	Matrix
1	muddy
2	sandy
3	ashy
4	micrite
5	not recognizable

cement: string; This field must include only the values listed in Table 12. Composition of the crystalline material precipitated around the edges of grains.

Table 12: Cement

id	Cement
1	siliceous
2	ferruginous
3	calcite
4	dolomite
5	kaolinitic
6	sparite
7	not recognizable

fabric: string; This field must include only the values listed in Table 13. Grain fabric (packing).

Table 13: Fabric

id	Fabric
1	clast supported
2	matrix supported

Note: The fields “sorting”, “roundness”, “matrix”, “cement” and “fabric”* are included on the template to store texture description of rock layers, this information is not display on the graphical output.

Interval features

An interval is defined over a stratigraphic range; it has to be defined by a base and a top. The main requirement to set an interval is that the recorded geological feature (e.g., sedimentary structures, bioturbation, unit name, fossil content) is presented throughout the defined stratigraphic range. Furthermore, users can define an interval by the stratigraphic thickness contained into a given bed. For example; if bioturbation is present just in the top of the bed, users could define the base and top of the bioturbed interval and store it in this format. Following this approach users can store in this format the following features:

core number
samples
visual oil stain
bioturbation
sedimentary structures
fossils
other symbols
lithostratigraphic frame
chronostratigraphic frame

In the data structure to define intervals, the user must define a stratigraphical base, top, and the recorded feature of each interval as is presented in Table 14. Each row in this data array describes a stratigraphic interval with the geological feature described on it. In some interval features overlapping is allowed (e.g., fossils, samples).

Table 14: Example of intervals table (sedimentary structures).

base	top	sed_structure
671	670.2	cross bedding
671.5	671.5	climbing ripples
669.4	669.18	lenticular lamination
668.2	667.6	normal grading
667.2	666.2	wavy lamination

We have provided on the SDAR repositoy a template of intervals data format used by SDAR as a Microsoft Excel spreadsheet, SDAR_v0.95_intervals_template.xlsx. This is the suggested format by SDAR to store fossils, sedimentary structures, bioturbation, etc. (intervals).

In summary, a table with the structure presented in table 14 must be provided for each recorder feature. The possible values admitted by each geological feature are presented in tables 15-22. The names of the columns must to be called as is presented in each reference table.

samples: string; This field must include only the values listed in Table 15.

Table 15: Samples

id	Sample Type	Default symbol - pch
1	rock sample	15
2	fossil sample	16
3	foraminifera	17
4	geochemistry	18
5	palynology	8
6	petrography	9
7	petrophysics	7
8	XRD	11

oil.stain: string; This field must include only the values listed in Table 16.

Table 16: Visual Oil Stain

id	Intensity	color
1	weak
2	moderate weak
3	moderate
4	moderate strong
5	strong

bioturbation: string; This field must include only the values listed in Table 17.

Table 17: Bioturbation

id	Index
1	sparse
2	low
3	moderate
4	high
5	intense
6	complete

sed.structures: string; This field must include only the values listed in Table 18.

Table 18: Sedimentary Structures

id	Sedimentary Structures
1	masive	21	ball and pillow
2	planar lamination	22	convolute bedding
3	horizontal bedding	23	dish and pillar
4	normal grading	24	evaporite molds
5	inverse grading	25	flame structures
6	cross bedding	26	flute casts
7	festoon cross bedding	27	groove cast
8	herringbone cross bedding	28	hardground
9	hummocky cross bedding	29	load cast
10	planar cross bedding	30	mudcrack
11	through cross bedding	31	pseudo nodules
12	swaley cross bedding	32	tool marks
13	ripple lamination	33	rain prints
14	climbing ripples	34	slump structures
15	current ripple cross lamination	35	syneresis cracks
16	wave ripple cross lamination	36	mottling
17	flaser lamination	37	peds
18	heterolithic lamination	38	rooting
19	lenticular lamination	39	slickensides
20	wavy lamination

fossils: string; This field must include only the values listed in Table 19.

Table 19: Fossils

id	Fossils
1	macrofossils	30	reptiles
2	invertebrates	31	plants
3	annelids	32	leaves
4	arthropods	33	roots
5	arachnids	34	wood
6	crustaceans	35	algae
7	insects	36	conifers
8	trilobites	37	ferns
9	brachiopods	38	flowering plants
10	bryozoans	39	stromatolites
11	cnidarians	40	fungi
12	corals	41	microfossils
13	stromatoporoids	42	conodontss
14	echinoderms	43	diatoms
15	crinoids	44	foraminifera
16	echinoids	45	larger foraminifera
17	graptolites	46	benthonic foraminifera
18	mollusks	47	planktonic foraminifera
19	cephalopods	48	nannofossils
20	ammonoids	49	ostracodes
21	belemnoids	50	palynomorphs
22	nautiloid	51	acritarchs
23	gastropods	52	chitinozoans
24	bivalves	53	dinoflagellates
25	sponges	54	pollen spores
26	vertebrates	55	radiolarians
27	amphibians	56	silicoflagellates
28	fish	57	spicules
29	mammals

other.sym: string; This field must include only the values listed in Table 20.

Table 20: other symbols

id	Other Symbols
1	concretions	9	kaolinite
2	nodules	10	mica
3	intraclasts	11	olivine
4	stylolites	12	organic matter
5	calcite	13	pyrite
6	feldspar	14	pyroxene
7	glauconite	15	siderite
8	gypsum	16	sulphur

lithostrat: string; This field must include only the values listed in Table 21.

Table 21: Lithostratigraphic Ranks

id	Litho Unit Rank
1	group
2	formation
3	member

chronostrat: string; This field must include only the values listed in Table 22.

Table 22: Chronostratigraphic Units

id	Chrono Unit
1	super_eonothem
2	eonothem
3	erathem
4	system
5	series
6	series_subseries
7	stage

Acknowledgments

This project has been sponsored by Carlos Jaramillo (Smithsonian Tropical Research Institute), financial support of this research was provided by COLCIENCIAS (partly funding the master studies of the main author) fundación para la Investigación de la Ciencia y la Tecnológia del Banco de la República, (Colombia), Corporación Geológica ARES (Colombia), and the Smithsonian Tropical Research Institute, the Anders Foundation, 1923 Fund and Gregory D. and Jennifer Walston Johnson.

The Saltarin 1A well dataset for this analysis, was provided by Alejandro Mora of HOCOL S.A.

Bibliography

Committee, F. G. D. (2006). Fgdc digital cartographic standard for geologic map symbolization.
Committee, R.-C. C. (1991). The Geological Society of America Rock Color Chart with Genuine Munsell Color Chips. Geological Society of America.
Dunham, R. (1962). American association of petroleum geologists memoir. Classification of carbonate rocks according to depositional texture. In Ham, W.E. Classification of carbonate rocks, 1:108-121.
Johnson, M. R. (1992). A proposed format for general-purpose comprehensive graphic logs. Sedimentary Geology, 81(3-4):289-298.
Krumbein, W. C. 1941.The effects of abrasion on the size, shape and roundness of rock fragments. The Journal of Geology 49(5), 482-520.
Miall, A. D. (1990). Principles of Sedimentary Basin Analysis. Springer-Verlag.
R Core Team (2014). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
Tucker, M. E. (2011). Sedimentary Rocks in the Field: A Practical Guide. Geological Field Guide. Wiley.
Wentworth, C. K. (1922). A scale of grade and class terms for clastic sediments. Journal of Geology, 30:377-392.
Wentworth, C. K. and Williams, H. (1932). Classification and terminology of pyroclastic rocks. National Research Council Bulletin, 89:19-53.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.

SDAR data model

John Ortiz 1,2,3, Carlos Jaramillo 1,2

Data model

beds (data format to integrate rock layers)

Table 1: Rock type

Table 2: Primary lithology

Table 3: Grain size table

Table 4: Example of beds/layers table.

Optional fields

Table 5: Grading

Table 6: Munsell Colors

Table 7: Examples of R colors

Table 8: Base contact

Mixed rocks

Texture description

Table 9: Sorting

Table 10: Roundness

Table 11: Matrix

Table 12: Cement

Table 13: Fabric

Interval features

Table 14: Example of intervals table (sedimentary structures).

Table 15: Samples

Table 16: Visual Oil Stain

Table 17: Bioturbation

Table 18: Sedimentary Structures

Table 19: Fossils

Table 20: other symbols

Table 21: Lithostratigraphic Ranks

Table 22: Chronostratigraphic Units

Acknowledgments

Bibliography

John Ortiz ^1,2,3, Carlos Jaramillo ^1,2