, William Gearty [aut]
, Christopher D. Dean
[aut] , Bethany Allen
[aut] | Title: | Fetch Geologic Data from the 'Macrostrat' Platform |
|---|---|
| Description: | Work with the 'Macrostrat' (<https://macrostrat.org/>) Web Service (v.2, <https://macrostrat.org/api/v2>) to fetch geological data relevant to the spatial and temporal distribution of sedimentary, igneous, and metamorphic rocks as well as data extracted from them. |
| Authors: | Lewis A. Jones [aut, cre, cph]
, William Gearty [aut]
, Christopher D. Dean
[aut] , Bethany Allen
[aut] |
| Maintainer: | Lewis A. Jones <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.0.0 |
| Built: | 2024-10-19 03:32:44 UTC |
| Source: | CRAN |
A function to retrieve all definitions and/or metadata for a given definition set. Caution: some datasets are large and may take time to retrieve.
catalog(type = NULL)catalog(type = NULL)
type |
|
A data.frame containing an exhaustive list of the
definitions and/or metadata retrievable for the given definition set. The
variables in the data.frame will match those described in the
documentation for that definition set.
columns: Definitions of Macrostrat columns. See also
def_columns().
drilling_sites: Definitions of eODP drilling cores. See also
def_drilling_sites().
econs: Definitions of economic resources. See also def_econs().
environments: Definitions of environments. See also
def_environments().
grain_sizes: Definitions of grain sizes. See also
def_grain_sizes().
intervals: Definitions of temporal intervals. See also
def_intervals().
lithologies: Definitions of lithologies. See also
def_lithologies().
lithology_att: Definitions of lithology attributes. See also
def_lithology_att().
measurements: Definitions of measurements. See also
def_measurements().
minerals: Defintions of minerals. See also def_minerals().
plates: Definitions of tectonic plates. See also def_plates().
projects: Definitions of Macrostrat projects. See also
def_projects().
references: Definitions of references. See also def_references().
sources: Definitions of geological maps. See also def_sources().
strat_name_concepts: Definitions of stratigraphic name concepts.
See also def_strat_name_concepts().
strat_names: Definitions of stratigraphic names. See also
def_strat_names().
structures: Definitions of geological structures. See also
def_structures().
timescales: Definitions of timescales. See also def_timescales().
Bethany Allen & Lewis A. Jones
Lewis A. Jones
# Get mineral definitions ex1 <- catalog(type = "minerals") # Get grain size definitions ex2 <- catalog(type = "grain_sizes")# Get mineral definitions ex1 <- catalog(type = "minerals") # Get grain size definitions ex2 <- catalog(type = "grain_sizes")
A function to retrieve the definitions for Macrostrat columns. By default, all definitions are returned.
def_columns( column_id = NULL, column_group_id = NULL, column_name = NULL, project_id = NULL, status = NULL )def_columns( column_id = NULL, column_group_id = NULL, column_name = NULL, project_id = NULL, status = NULL )
column_id |
|
column_group_id |
|
column_name |
|
project_id |
|
status |
|
A data.frame containing the following columns:
col_id: The unique identification number for the column.
col_group_id: The unique identification number of the group to
which the column belongs.
col_name: The name of the column.
lat: Latitude of the centroid of the column.
lng: Longitude of the centroid of the column.
col_area: Area of the Macrostrat column,
in km2.
max_thick: Maximum unit thickness in meters.
ref_id: The unique identification number for the reference
associated with the column.
status: Indicates the current status of the column (values are
'active', 'in process', and 'obsolete').
t_units: Total number of Macrostrat units contained within the
column.
project_id: The unique identification number for the column's
project. Corresponds to general geographic region.
notes: Column specific notes.
William Gearty
Christopher D. Dean
Macrostrat data entities:
get_age_model(),
get_columns(),
get_sections(),
get_units()
# Return all column definitions ex1 <- def_columns() # Return subsets of column definitions ex2 <- def_columns(column_group_id = 17) ex3 <- def_columns(column_id = c(22,24)) ex4 <- def_columns(column_name = "Eastern Kentucky")# Return all column definitions ex1 <- def_columns() # Return subsets of column definitions ex2 <- def_columns(column_group_id = 17) ex3 <- def_columns(column_id = c(22,24)) ex4 <- def_columns(column_name = "Eastern Kentucky")
Obtain metadata for variables associated with the Extending Ocean Drilling Pursuits (eODP) project. By default, data for all drilling sites are returned.
def_drilling_sites(program = NULL, exp = NULL, site = NULL, sf = FALSE)def_drilling_sites(program = NULL, exp = NULL, site = NULL, sf = FALSE)
program |
|
exp |
|
site |
|
sf |
|
A data.frame object containing, for each retrieved core:
epoch: The name of the drilling program.
leg: The name of the expedition (formerly known as a 'leg').
site: The name of the drilling site.
hole: The name of the drilling hole.
lat: The decimal degree latitude of the drilling hole.
lng: The decimal degree longitude of the drilling hole.
col_id: The unique identification number of the eODP column.
col_group_id: The unique identification number of the group to
which the eODP column belongs.
penetration: The depth of the hole drilled, in meters.
cored: The amount of rock cored from the drill hole, in meters.
recovered: The amount of rock recovered from the core, in
meters.
recovery: The proportion of rock recovered from the core.
drilled_interval: The interval drilled.
drilled_intervals: The number of drilled intervals.
cores: The total number of cores drilled at the hole.
date_started: The date on which drilling commenced.
date_finished: The date on which drilling concluded.
comments: Written notes assigned to the core.
ref_id: The unique identification number of the reference.
If sf is TRUE, an sf object is returned instead, with a "geometry"
column that contains the spatial data instead of the lat/lng columns.
Bethany Allen
Christopher D. Dean
Sessa JA, Fraass AJ, LeVay LJ, Jamson KM, and Peters SE. (2023). The Extending Ocean Drilling Pursuits (eODP) Project: Synthesizing Scientific Ocean Drilling Data. Geochemistry, Geophysics, Geosystems, 24 (3) e2022GC010655. doi:10.1029/2022GC010655.
External data:
def_measurements(),
get_eodp(),
get_fossils(),
get_measurements()
# Return all core information for a specific site core_info <- def_drilling_sites(site = "U1547")# Return all core information for a specific site core_info <- def_drilling_sites(site = "U1547")
A function to retrieve the definitions for one or more economic resources in the Macrostrat database. By default, all economic definitions are returned.
def_econs(econ = NULL, econ_type = NULL, econ_class = NULL, econ_id = NULL)def_econs(econ = NULL, econ_type = NULL, econ_class = NULL, econ_id = NULL)
econ |
|
econ_type |
|
econ_class |
|
econ_id |
|
A data.frame containing the following columns:
econ_id: The unique identifier of the economic resource.
name: The name of the economic resource.
type: The type of economic resource.
class: The class of economic resource.
color: The recommended coloring for units based on the dominant
lithology.
t_units: The total number of Macrostrat units containing the
economic resource.
Bethany Allen
William Gearty
Geologic features and attributes:
def_environments(),
def_grain_sizes(),
def_lithologies(),
def_lithology_att(),
def_measurements(),
def_minerals(),
def_structures()
# Return all economic resource definitions econ_inf <- def_econs() # Return only definitions for hydrocarbon resources econ_inf <- def_econs(econ_type = "hydrocarbon")# Return all economic resource definitions econ_inf <- def_econs() # Return only definitions for hydrocarbon resources econ_inf <- def_econs(econ_type = "hydrocarbon")
A function to retrieve the definitions for one or more environments in the Macrostrat database. By default, all environment definitions are returned.
def_environments( environ = NULL, environ_type = NULL, environ_class = NULL, environ_id = NULL )def_environments( environ = NULL, environ_type = NULL, environ_class = NULL, environ_id = NULL )
environ |
|
environ_type |
|
environ_class |
|
environ_id |
|
A data.frame containing the following columns:
environ_id: The unique identification number of the
environment.
name: The name of the environment.
type: Environment type, less inclusive than class.
class: Environment class, more inclusive than type.
color: Recommended coloring for environment, based on the
dominant lithology.
t_units: The total number of Macrostrat units that are
partially, or entirely, composed of the environment.
Christopher D. Dean
Lewis A. Jones
Geologic features and attributes:
def_econs(),
def_grain_sizes(),
def_lithologies(),
def_lithology_att(),
def_measurements(),
def_minerals(),
def_structures()
# Return all environment definitions ex1 <- def_environments() # Return subsets of environment definitions ex2 <- def_environments(environ = "reef") ex3 <- def_environments(environ_type = "carbonate") ex4 <- def_environments(environ_class = "marine")# Return all environment definitions ex1 <- def_environments() # Return subsets of environment definitions ex2 <- def_environments(environ = "reef") ex3 <- def_environments(environ_type = "carbonate") ex4 <- def_environments(environ_class = "marine")
A function to return grain size definitions from the Macrostrat Database based on user-specified arguments. If no arguments are specified, all definitions are returned.
def_grain_sizes( grain_name = NULL, grain_group = NULL, soil_group = NULL, grain_id = NULL, grain_symbol = NULL, grain_classification = NULL )def_grain_sizes( grain_name = NULL, grain_group = NULL, soil_group = NULL, grain_id = NULL, grain_symbol = NULL, grain_classification = NULL )
grain_name |
|
grain_group |
|
soil_group |
|
grain_id |
|
grain_symbol |
|
grain_classification |
|
A data.frame containing the following columns:
grain_id: The unique identification number of the
grain.
grain_symbol: The grain symbol (or abbreviation) to use for
display purposes.
grain_name: The name of the grain.
grain_group: The name of the group the grain belongs to.
soil_group: The name of the soil family the grain belongs
to.
min_size: The minimum size of the size in millimeters.
max_size: The maximum size of the grain in millimeters.
classification: The classification scheme the given grain
belongs to.
Lewis A. Jones
William Gearty
Geologic features and attributes:
def_econs(),
def_environments(),
def_lithologies(),
def_lithology_att(),
def_measurements(),
def_minerals(),
def_structures()
# Return all definitions ex1 <- def_grain_sizes() # Return grain sizes by group ex2 <- def_grain_sizes(grain_group = "Gravel")# Return all definitions ex1 <- def_grain_sizes() # Return grain sizes by group ex2 <- def_grain_sizes(grain_group = "Gravel")
A function to retrieve Macrostrat time interval definitions matching a user-specific search criteria. If no arguments are specified (the default), all time interval definitions are returned.
def_intervals( timescale = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, rule = NULL, true_colors = NULL )def_intervals( timescale = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, rule = NULL, true_colors = NULL )
timescale |
|
interval_name |
|
interval_id |
|
age |
|
age_top |
|
age_bottom |
|
rule |
|
true_colors |
|
A data.frame containing the following columns:
int_id: The unique identification number of the time
interval.
name: The name of the time interval.
abbrev: The standard abbreviation for the time interval
name, if one exists.
t_age: The top age (minimum age) in millions of years
before present.
b_age: The bottom age (maximum age) in millions of years
before present.
int_type: The temporal rank of the interval (e.g., "age",
"epoch", "chron").
timescales: A data.frame containing the timescale(s)
that the interval is included in (see def_timescales() for more
details), with the following columns:
timescale_id: The unique identification number of the
timescale.
name: The name of the timescale.
color: The recommended coloring for units based on dominant
lithology.
Lewis A. Jones
William Gearty
Timescales and time intervals:
def_timescales()
# Return all intervals ex1 <- def_intervals() # Return all specific timescale intervals ex2 <- def_intervals(timescale = "international ages") # Return for specific age ex3 <- def_intervals(timescale = "international ages", age = 70)# Return all intervals ex1 <- def_intervals() # Return all specific timescale intervals ex2 <- def_intervals(timescale = "international ages") # Return for specific age ex3 <- def_intervals(timescale = "international ages", age = 70)
A function to retrieve the definitions of one or more lithologies in the Macrostrat database. If no arguments are specified (the default), all lithology definitions are returned.
def_lithologies( lithology = NULL, lithology_group = NULL, lithology_class = NULL, lithology_type = NULL, lithology_id = NULL )def_lithologies( lithology = NULL, lithology_group = NULL, lithology_class = NULL, lithology_type = NULL, lithology_id = NULL )
lithology |
|
lithology_group |
|
lithology_class |
|
lithology_type |
|
lithology_id |
|
A data.frame containing the following columns:
lith_id: The unique identification number of the lithology.
name: The name of the lithology.
type: The lithology type, less inclusive than class.
group: The lithology group, less inclusive than type.
class: The lithology class, more inclusive than type.
color: The recommended coloring for the lithology.
fill: The code for the fill pattern as established in the
Federal Geographic Data Committee's
Digital Cartographic Standard for Geologic Map Symbolization.
t_units: The total number of Macrostrat units that are
partially or entirely composed of the lithology.
William Gearty
Bethany Allen
Geologic features and attributes:
def_econs(),
def_environments(),
def_grain_sizes(),
def_lithology_att(),
def_measurements(),
def_minerals(),
def_structures()
# return all lithology definitions ex1 <- def_lithologies() # return a definition for sandstone ex2 <- def_lithologies(lithology = "sandstone") # return definitions for lithologies of a specific type ex3 <- def_lithologies(lithology_type = "sedimentary") # return definitions for lithologies using their unique ID numbers ex4 <- def_lithologies(lithology_id = c(1,5))# return all lithology definitions ex1 <- def_lithologies() # return a definition for sandstone ex2 <- def_lithologies(lithology = "sandstone") # return definitions for lithologies of a specific type ex3 <- def_lithologies(lithology_type = "sedimentary") # return definitions for lithologies using their unique ID numbers ex4 <- def_lithologies(lithology_id = c(1,5))
A function to retrieve the definitions for one or more lithology attributes in the Macrostrat database. By default, all lithology attribute definitions are returned.
def_lithology_att( lithology_att = NULL, att_type = NULL, lithology_att_id = NULL )def_lithology_att( lithology_att = NULL, att_type = NULL, lithology_att_id = NULL )
lithology_att |
|
att_type |
|
lithology_att_id |
|
A data.frame containing the following columns:
lith_att_id: The unique identifier of the lithology attribute.
name: The name of the lithology attribute.
type: The lithology attribute type.
t_units: The total number of Macrostrat units to which the
lithology attribute is attached.
Bethany Allen
Christopher D. Dean
Geologic features and attributes:
def_econs(),
def_environments(),
def_grain_sizes(),
def_lithologies(),
def_measurements(),
def_minerals(),
def_structures()
# Return all lithology attribute definitions ex1 <- def_lithology_att() # Return subsets of lithology attribute definitions ex2 <- def_lithology_att(att_type = "sed structure")# Return all lithology attribute definitions ex1 <- def_lithology_att() # Return subsets of lithology attribute definitions ex2 <- def_lithology_att(att_type = "sed structure")
A function to retrieve the definitions of different measurements that are included in the Macrostrat database. By default, all definitions are returned.
def_measurements( measure_id = NULL, measurement_type = NULL, measurement_class = NULL )def_measurements( measure_id = NULL, measurement_type = NULL, measurement_class = NULL )
measure_id |
|
measurement_type |
|
measurement_class |
|
A data.frame containing the following columns:
measure_id: The unique identification number of the
measurement.
name: The name of the measurement.
type: Measurement type, less inclusive than class
class: Measurement class, more inclusive than type.
t_units: The total number of Macrostrat units containing this
measurement.
William Gearty
Christopher D. Dean
External data:
def_drilling_sites(),
get_eodp(),
get_fossils(),
get_measurements()
Geologic features and attributes:
def_econs(),
def_environments(),
def_grain_sizes(),
def_lithologies(),
def_lithology_att(),
def_minerals(),
def_structures()
# Return all definitions ex1 <- def_measurements() # Return subsets of definitions ex2 <- def_measurements(measure_id = c(1, 2, 4)) ex3 <- def_measurements(measurement_class = "geochemical")# Return all definitions ex1 <- def_measurements() # Return subsets of definitions ex2 <- def_measurements(measure_id = c(1, 2, 4)) ex3 <- def_measurements(measurement_class = "geochemical")
A function to retrieve mineral definitions from the Macrostrat database based on user-specified arguments. If no arguments are provided, all definitions are returned.
def_minerals(mineral = NULL, mineral_type = NULL, element = NULL)def_minerals(mineral = NULL, mineral_type = NULL, element = NULL)
mineral |
|
mineral_type |
|
element |
|
A data.frame containing the following columns:
mineral_id: The unique identification number of the mineral.
mineral: The name of the mineral.
mineral_type: The name of the type of mineral.
formula: The chemical formula of the mineral.
formula_tags: The chemical formula of the mineral with
appropriate sub/superscript html tags.
url: A URL for the mineral's entry in
Mindat.
hardness_min: The minimum hardness value (Mohs Hardness
Scale) of the mineral.
hardness_max: The maximum hardness value (Mohs Hardness
Scale) of the mineral.
crystal_form: The crystal form of the mineral.
mineral_color: A description of the color of the mineral.
lustre: A description of the lustre of the mineral.
Lewis A. Jones
Bethany Allen
Geologic features and attributes:
def_econs(),
def_environments(),
def_grain_sizes(),
def_lithologies(),
def_lithology_att(),
def_measurements(),
def_structures()
# Get all mineral definitions ex1 <- def_minerals() # Get mineral definitions by type ex2 <- def_minerals(mineral_type = "element")# Get all mineral definitions ex1 <- def_minerals() # Get mineral definitions by type ex2 <- def_minerals(mineral_type = "element")
A function to retrieve tectonic plate definitions for a user-specified plate identification number, as defined by the Wright et al. (2013) Global Plate Model. If no arguments are supplied, all plates are returned.
def_plates(plate_id = NULL)def_plates(plate_id = NULL)
plate_id |
|
A data.frame containing the plate_id of the tectonic plate and
the name of the tectonic plate as defined by Wright et al. (2013).
Lewis A. Jones
Christopher D. Dean
Wright, N., Zahirovic, S., Müller, R.D., Seton, M. (2013). Towards community-driven paleogeographic reconstructions: integrating open-access paleogeographic and paleobiology data with plate tectonics. Biogeosciences, 10, 1529–1541. doi:10.5194/bg-10-1529-2013.
Paleogeography:
get_paleogeography()
# Get all tectonic plates ex1 <- def_plates() # Get name of tectonic plate by ID ex2 <- def_plates(plate_id = 604)# Get all tectonic plates ex1 <- def_plates() # Get name of tectonic plate by ID ex2 <- def_plates(plate_id = 604)
A function to obtain information concerning the different Macrostrat projects. If no arguments are specified (default), data for all projects are returned.
def_projects(project_id = NULL)def_projects(project_id = NULL)
project_id |
|
A data.frame containing:
project_id: The unique identification number of the
Macrostrat project.
project: The name of the Macrostrat project.
descrip: Description of the Macrostrat project.
timescale_id: The unique identification number of the
timescale used in the Macrostrat project.
t_cols: The total number of Macrostrat columns associated
with the project.
in_process_cols: The total number of in-progress Macrostrat
columns associated with the project.
obsolete_cols: The total number of obsolete Macrostrat
columns associated with the project.
t_units: The total number of Macrostrat units associated with
the project.
area: The area covered by the Macrostrat project in
km2.
Bethany Allen
Lewis A. Jones
Macrostrat database metadata:
def_references(),
def_sources(),
get_stats()
ex1 <- def_projects() ex2 <- def_projects(project_id = 4)ex1 <- def_projects() ex2 <- def_projects(project_id = 4)
A function to retrieve the definitions for one or more published scientific references in the Macrostrat database. By default, all reference definitions are returned.
def_references(ref_id = NULL)def_references(ref_id = NULL)
ref_id |
|
A data.frame containing the following columns:
ref_id: The unique identification number(s) for the
reference(s).
pub_year: The year of publication of the reference.
author: The author(s) of the reference.
ref: The name of the reference.
doi: The digital object identifier of the reference.
url: A URL where additional information, the source, or
contributing publication can be found.
t_units: The total number of Macrostrat units associated with
the reference.
William Gearty
Bethany Allen
Macrostrat database metadata:
def_projects(),
def_sources(),
get_stats()
# Return all references ex1 <- def_references() # Return a subset of references ex2 <- def_references(ref_id = c(1, 2, 3))# Return all references ex1 <- def_references() # Return a subset of references ex2 <- def_references(ref_id = c(1, 2, 3))
A function to retrieve the definitions for one or more geologic map sources in the Macrostrat database. By default, all source definitions are returned.
def_sources( source_id = NULL, lat = NULL, lng = NULL, shape = NULL, buffer = NULL, scale = NULL, sf = TRUE )def_sources( source_id = NULL, lat = NULL, lng = NULL, shape = NULL, buffer = NULL, scale = NULL, sf = TRUE )
source_id |
|
lat |
|
lng |
|
shape |
|
buffer |
|
scale |
|
sf |
|
A data.frame containing the following columns:
source_id: Identification number of the geologic map source.
name: Name of the geologic map source.
url: URL where additional information, the source, or
contributing publication can be found.
ref_title: Title of reference for geologic map source.
authors: Authors of geologic map source.
ref_year: Year of reference publication.
ref_source: Original publication source of the reference.
isbn_doi: The ISBN or DOI for the reference.
scale: The Macrostrat scale the geologic map source belongs
to.
features: The total number of features (i.e., outcrop shape
and point elements) associated with the geologic map source.
area: The total geographic area of the geologic map source
in km2.
If sf is TRUE (the default), an sf object is returned instead, with
the same columns plus a "geometry" column that contains the spatial data.
William Gearty
Lewis A. Jones
Geologic maps:
get_map_legends(),
get_map_outcrop(),
get_map_points()
Macrostrat database metadata:
def_projects(),
def_references(),
get_stats()
# Get all sources ex1 <- def_sources() # Get subset of sources ex2 <- def_sources(source_id = c(1,2,4)) ex3 <- def_sources(lat = 43.03, lng = -89.4, scale = "large") # Use WKT representation library(sf) line <- st_linestring(x = matrix(c(-122.3438, 37,-89.3527, 43.0582), byrow = TRUE, ncol = 2)) ex4 <- def_sources(shape = st_as_text(line), buffer = 100)# Get all sources ex1 <- def_sources() # Get subset of sources ex2 <- def_sources(source_id = c(1,2,4)) ex3 <- def_sources(lat = 43.03, lng = -89.4, scale = "large") # Use WKT representation library(sf) line <- st_linestring(x = matrix(c(-122.3438, 37,-89.3527, 43.0582), byrow = TRUE, ncol = 2)) ex4 <- def_sources(shape = st_as_text(line), buffer = 100)
A function to retrieve the definitions for stratigraphic name concepts. By default, all stratigraphic name concept definitions are returned.
def_strat_name_concepts(strat_concept_name = NULL, strat_concept_id = NULL)def_strat_name_concepts(strat_concept_name = NULL, strat_concept_id = NULL)
strat_concept_name |
|
strat_concept_id |
|
Stratigraphic name concepts consist of grouped strat_names which
represent the same geologic entity. This may be due to stratigraphic names
appearing in multiple reference maps or at multiple lithostratigraphic
ranks.
A data.frame containing the following columns:
concept_id: The unique identification number for the
stratigraphic name concept, which groups variant strat_names for same
geologic entity.
name: The name of the stratigraphic name concept.
geologic_age: The geologic age information assigned to the
stratigraphic name concept, as defined in the original reference in plain
text.
int_id: The unique identification number of the
chronostratigraphic interval associated with the stratigraphic name
concept (see def_intervals()).
b_int_id: The unique identification number of the bottom
(oldest) chronostratigraphic interval associated with the stratigraphic
name concept (see def_intervals()).
t_int_id: The unique identification number of the top
(youngest) chronostratigraphic interval associated with the stratigraphic
name concept (see def_intervals()).
usage_notes: Notes on the current validity of the
stratigraphic name concept, in plain text.
other: Other associated notes on the stratigraphic name
concept, in plain text.
province: The provinces where the stratigraphic name concept
appears, in plain text.
refs: The unique identification number of the reference from
which the stratigraphic name concept was sourced (see
def_references()).
url: The URL associated with the stratigraphic name concept,
where additional information, the source or contributing publication can
be found.
author: The authors of the source reference.
Christopher D. Dean
William Gearty
Stratigraphic names:
def_strat_names()
# Return a stratigraphic name concept based on a string ex1 <- def_strat_name_concepts(strat_concept_name = "Dakota") # Return a stratigraphic name concept based on an ID ex1 <- def_strat_name_concepts(strat_concept_id = 8212)# Return a stratigraphic name concept based on a string ex1 <- def_strat_name_concepts(strat_concept_name = "Dakota") # Return a stratigraphic name concept based on an ID ex1 <- def_strat_name_concepts(strat_concept_id = 8212)
A function to retrieve the definitions for one or more stratigraphic names in the Macrostrat database. By default, all stratigraphic name definitions are returned.
def_strat_names( strat_name = NULL, interval_name = NULL, rank = NULL, concept_id = NULL, ref_id = NULL, strat_name_id = NULL, rule = NULL )def_strat_names( strat_name = NULL, interval_name = NULL, rank = NULL, concept_id = NULL, ref_id = NULL, strat_name_id = NULL, rule = NULL )
strat_name |
|
interval_name |
|
rank |
|
concept_id |
|
ref_id |
|
strat_name_id |
|
rule |
|
A data.frame containing the following columns:
strat_name: The short-form stratigraphic name (e.g. "Hell
Creek").
strat_name_long: The long-form stratigraphic name, including
the lithostratigraphic rank of the stratigraphic name (e.g., "Hell Creek
Formation").
rank: The lithostratigraphic rank of the stratigraphic name
(e.g., "Formation"), in short form (e.g., "Fm").
strat_name_id: The unique identification number of the
stratigraphic name.
concept_id: The unique identification number of the associated
stratigraphic name concept, which groups variant strat_names for the
same geologic entity (see def_strat_name_concepts()).
bed: The stratigraphic name of the bed associated with the
specified stratigraphic name.
bed_id: The unique identification number (strat_name_id) of
the bed associated with the specified stratigraphic name associated with
the specified stratigraphic name.
mbr: The stratigraphic name of the member associated with the
specified stratigraphic name.
mbr_id: The unique identification number (strat_name_id) of
the member associated with the specified stratigraphic name.
fm: The stratigraphic name of the formation associated with
the specified stratigraphic name.
fm_id: The unique identification number (strat_name_id) of
the formation associated with the specified stratigraphic name.
subgp: The stratigraphic name of the subgroup associated with
the specified stratigraphic name.
subgp_id: The unique identification number (strat_name_id) of
the subgroup associated with the specified stratigraphic name.
gp: The stratigraphic name of the group associated with the
specified stratigraphic name.
gp_id: The unique identification number (strat_name_id) of
the group associated with the specified stratigraphic name.
sgp: The stratigraphic name of the supergroup associated with
the specified stratigraphic name.
sgp_id: The unique identification number (strat_name_id) of
the supergroup associated with the specified stratigraphic name.
b_age: The bottom age (maximum age) associated with the
stratigraphic name, in millions of years before present.
t_age: The top age (minimum age) associated with the
stratigraphic name, in millions of years before present.
b_period: The name of the oldest geologic time period
associated with the stratigraphic name (see def_intervals()).
t_period:The name of the youngest geologic time period
associated with the stratigraphic name (see def_intervals()).
c_interval: The name of the central interval associated with
the stratigraphic name (see def_intervals()).
t_units: The total number of Macrostrat units that are
associated with the stratigraphic name.
ref_id: The unique identification number of the reference from
which the stratigraphic name was sourced (see def_references()).
Christopher D. Dean
Bethany Allen
Stratigraphic names:
def_strat_name_concepts()
# Return a sample of stratigraphic names ex1 <- def_strat_names() # Return all stratigraphic names associated with a particular stratigraphic # name ex2 <- def_strat_names(strat_name = "Hell Creek") # Return all stratigraphic names that intersect with a chosen time interval ex3 <- def_strat_names(interval_name = "Campanian")# Return a sample of stratigraphic names ex1 <- def_strat_names() # Return all stratigraphic names associated with a particular stratigraphic # name ex2 <- def_strat_names(strat_name = "Hell Creek") # Return all stratigraphic names that intersect with a chosen time interval ex3 <- def_strat_names(interval_name = "Campanian")
A function to retrieve definitions for various geological structures within the Macrostrat database.
def_structures( structure = NULL, structure_class = NULL, structure_type = NULL, structure_id = NULL )def_structures( structure = NULL, structure_class = NULL, structure_type = NULL, structure_id = NULL )
structure |
|
structure_class |
|
structure_type |
|
structure_id |
|
A data.frame containing the following columns:
structure_id: The unique identification number of the
structure.
name: The name of the structure.
structure_type: Structure type, less inclusive than class.
group: Structure group, less inclusive than type.
class: Structure class, more inclusive than type.
William Gearty
Lewis A. Jones
Geologic features and attributes:
def_econs(),
def_environments(),
def_grain_sizes(),
def_lithologies(),
def_lithology_att(),
def_measurements(),
def_minerals()
# Get all structure definitions ex1 <- def_structures() # Get subset of structure definitions ex2 <- def_structures(structure_id = c(1, 3)) ex3 <- def_structures(structure_class = "igneous")# Get all structure definitions ex1 <- def_structures() # Get subset of structure definitions ex2 <- def_structures(structure_id = c(1, 3)) ex3 <- def_structures(structure_class = "igneous")
A function to retrieve all timescale definitions from the Macrostrat database. Function is called without user-specified arguments.
def_timescales()def_timescales()
A data.frame containing the following columns:
timescale_id: The unique identification number of the
timescale.
timescale: The name of the timescale.
n_intervals: The number of intervals within the timescale.
max_age: The maximum age coverage of the timescale in
millions of years before present.
min_age: The minimum age coverage of the timescale in
millions of years before present.
ref_id: The unique identification number of the associated
reference.
Lewis A. Jones
Christopher D. Dean
Timescales and time intervals:
def_intervals()
# Retrieve all timescale definitions ex1 <- def_timescales()# Retrieve all timescale definitions ex1 <- def_timescales()
A function to obtain information about the age models used for Macrostrat columns or sections. This consists of the temporal boundaries applied to the column's constituent units.
get_age_model(column_id = NULL, section_id = NULL)get_age_model(column_id = NULL, section_id = NULL)
column_id |
|
section_id |
|
The Macrostrat age models are used to determine the ages of the boundaries between units in an internally consistent manner, allowing each boundary to be dated with respect to all age information available for the column.
A data.frame containing, for each boundary between units for
each retrieved age model:
boundary_id: The unique identification number of the boundary between two units.
col_id: The unique identification number of the Macrostrat column.
section_id: The unique identification number of the Macrostrat section.
interval_id: The unique identification number of the time interval which the boundary lies within.
interval_name: The name of the time interval which the boundary lies within.
age_bottom: The numerical lower limit on the age of the boundary (maximum age), in millions of years before present.
age_top: The numerical upper limit on the age of the boundary (minimum age), in millions of years before present.
rel_position: The relative position of the boundary.
model_age: The age of the boundary, as correlated with other ages in the column, in millions of years before present.
boundary_status: The method used to determine the age of the boundary.
boundary_type: The type of boundary.
boundary_position: The position of the boundary.
unit_below: The Macrostrat unit beneath the given boundary.
unit_above: The Macrostrat unit above the given boundary.
ref_id: The unique identification number of the reference.
Bethany Allen
Lewis A. Jones
Macrostrat data entities:
def_columns(),
get_columns(),
get_sections(),
get_units()
# Get age model for specific columns by ID ex1 <- get_age_model(column_id = c(503, 504)) # Get age model for specific sections by ID ex2 <- get_age_model(section_id = c(65, 22))# Get age model for specific columns by ID ex1 <- get_age_model(column_id = c(503, 504)) # Get age model for specific sections by ID ex2 <- get_age_model(section_id = c(65, 22))
A function to retrieve independent, hexagonal, vertical columns which contain chronostratigraphically organised Macrostrat units.
get_columns( column_id = NULL, section_id = NULL, unit_id = NULL, strat_name = NULL, strat_name_id = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lat = NULL, lng = NULL, lithology = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, lithology_att = NULL, lithology_att_id = NULL, lithology_att_type = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, pbdb_collection_no = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, adjacents = FALSE, sf = FALSE )get_columns( column_id = NULL, section_id = NULL, unit_id = NULL, strat_name = NULL, strat_name_id = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lat = NULL, lng = NULL, lithology = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, lithology_att = NULL, lithology_att_id = NULL, lithology_att_type = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, pbdb_collection_no = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, adjacents = FALSE, sf = FALSE )
column_id |
|
section_id |
|
unit_id |
|
strat_name |
|
strat_name_id |
|
interval_name |
|
interval_id |
|
age |
|
age_top |
|
age_bottom |
|
lat |
|
lng |
|
lithology |
|
lithology_id |
|
lithology_type |
|
lithology_class |
|
lithology_att |
|
lithology_att_id |
|
lithology_att_type |
|
environ |
|
environ_id |
|
environ_type |
|
environ_class |
|
pbdb_collection_no |
|
econ |
|
econ_id |
|
econ_type |
|
econ_class |
|
project_id |
|
adjacents |
|
sf |
|
More information can be found for the inputs for this function using
the definition functions (beginning with def_).
A data.frame containing the following columns:
col_id: The unique identification number of the Macrostrat
column.
col_name: The name of the Macrostrat column.
col_group: Name of the group the column belongs to. Generally
corresponds to geologic provinces.
col_group_id: The unique identification number of the group to
which the column belongs.
group_col_id: The original column ID assigned to the column
(used in the original source).
lat: Decimal degree latitude of the column centroid.
lng: Decimal degree longitude of the column centroid.
col_area: The area of the Macrostrat column in
km2.
project_id: The unique identification number for project.
Corresponds to general geographic region.
col_type: The type of column.
refs: The unique identification number(s) for the reference(s)
associated with the column.
max_thick: The maximum unit thickness in meters.
max_min_thick: The maximum possible minimum thickness in
meters.
min_min_thick: The minimum possible minimum thickness in
meters.
b_age: The age of the bottom of the column, estimated using
the continuous time age model, in millions of years before present.
t_age: The age of the top of the column, estimated using the
continuous time age model, in millions of years before present.
b_int_name: The name of the time interval represented at the
bottom of the column.
t_int_name: The name of the time interval represented at the
top of the column.
pbdb_collections: The number of PBDB collections contained
within the column.
lith: a data.frame containing the lithologies present
within the column, with the following columns:
name: The named lithology (e.g., "sandstone").
type: The named lithology type (e.g., "siliciclastic").
class: The named lithology class (e.g., "sedimentary").
prop: The proportion of the lithology within the column,
calculated from the individual Macrostrat units within the column.
lith_id: The unique identification number of the lithology.
environ: a data.frame containing the environments
present within the column, with the following columns:
name: The named environment (e.g., "delta plain").
type: The named environment type (e.g., "siliciclastic").
class: The named environment class (e.g., "marine").
prop: The proportion of the environment within the column,
calculated from the individual Macrostrat units within the column.
environ_id: The unique identification number of the
environment.
econ: a data.frame containing the economic attributes
present within the column, with the following columns:
name: The named economic attribute (e.g., "gold").
type: The named economic attribute type (e.g., "mineral").
class: The named economic attribute class (e.g., "precious
commodity").
prop: The proportion of the economic attribute out of
all economic attributes contained within the column, calculated
from the individual Macrostrat units within the column.
econ_id: The unique identification number of the economic
attribute.
t_units: The total number of units contained within the
column.
t_sections: The total number of sections contained within the
column.
If sf is TRUE, an sf object is returned instead, with the same
columns plus a "geometry" column that contains the spatial data.
William Gearty
Christopher D. Dean
Macrostrat data entities:
def_columns(),
get_age_model(),
get_sections(),
get_units()
# Return columns that overlap with a named chronostratigraphic interval ex1 <- get_columns(interval_name = "Permian") # Return columns that overlap with a specified age range ex2 <- get_columns(age_top = 200, age_bottom = 250) # Return columns that contain a specific stratigraphic unit, in `sf` format ex3 <- get_columns(strat_name = "mancos", sf = TRUE) # Return the columns at a specific geographic coordinate ex4 <- get_columns(lat = 43, lng = -89, adjacents = TRUE)# Return columns that overlap with a named chronostratigraphic interval ex1 <- get_columns(interval_name = "Permian") # Return columns that overlap with a specified age range ex2 <- get_columns(age_top = 200, age_bottom = 250) # Return columns that contain a specific stratigraphic unit, in `sf` format ex3 <- get_columns(strat_name = "mancos", sf = TRUE) # Return the columns at a specific geographic coordinate ex4 <- get_columns(lat = 43, lng = -89, adjacents = TRUE)
A function to retrieve data from the
Extending Ocean Drilling Pursuits (eODP)
project, a collation of sedimentary description data
from ocean drilling cores. This currently includes cores from the Deep Sea
Drilling Project (DSDP), Integrated Ocean Drilling Program (IODP), and Ocean
Drilling Program (ODP). Note: eODP data is currently being integrated
into Macrostrat's data entities (e.g. columns and units) and should be
available via get_columns() and get_units() in the future.
get_eodp(column_id = NULL, site = NULL, leg = NULL, program = NULL, sf = FALSE)get_eodp(column_id = NULL, site = NULL, leg = NULL, program = NULL, sf = FALSE)
column_id |
|
site |
|
leg |
|
program |
|
sf |
|
More information can be found about the inputs for this function by
using def_drilling_sites().
A data.frame containing, for each retrieved core:
col_group: The name of the drilling program and
leg/expedition.
site_hole: The name of the drilling site and hole.
date_started: The date on which drilling commenced.
ref_id: The unique identifier of the reference.
col_id: The unique identifier of the Macrostrat column.
lat: Decimal degree latitude of the core.
lng: Decimal degree longitude of the core.
top_depth: A vector describing the height of the top of each
unit.
bottom_depth: A vector describing the height of the bottom of
each unit.
primary_lith: A vector giving the name of the primary
lithology of each unit.
lith_id: A vector giving the unique identifier of the primary
lithology of each unit.
minor_lith: A vector giving the name of the primary lithology
of each unit.
If sf is TRUE, an sf object is returned instead, with a "geometry"
column that contains the spatial data instead of the lat/lng columns.
Bethany Allen
William Gearty
Sessa JA, Fraass AJ, LeVay LJ, Jamson KM, and Peters SE. (2023). The Extending Ocean Drilling Pursuits (eODP) Project: Synthesizing Scientific Ocean Drilling Data. Geochemistry, Geophysics, Geosystems, 24 (3) e2022GC010655. doi:10.1029/2022GC010655.
External data:
def_drilling_sites(),
def_measurements(),
get_fossils(),
get_measurements()
# Get data for specific cores cores <- get_eodp(column_id = c(5081, 5082)) # Get data for all cores at a specific site cores <- get_eodp(site = "U1351") # Get data for all cores for a specific leg cores <- get_eodp(leg = "317") # Get data for all cores for a specific program cores <- get_eodp(program = "IODP")# Get data for specific cores cores <- get_eodp(column_id = c(5081, 5082)) # Get data for all cores at a specific site cores <- get_eodp(site = "U1351") # Get data for all cores for a specific leg cores <- get_eodp(leg = "317") # Get data for all cores for a specific program cores <- get_eodp(program = "IODP")
A function to retrieve collections from the Paleobiology Database (PBDB), matched to Macrostrat units.
get_fossils( unit_id = NULL, column_id = NULL, interval_name = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lithology = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, strat_name_id = NULL, sf = FALSE )get_fossils( unit_id = NULL, column_id = NULL, interval_name = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lithology = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, strat_name_id = NULL, sf = FALSE )
unit_id |
|
column_id |
|
interval_name |
|
age |
|
age_top |
|
age_bottom |
|
lithology |
|
lithology_id |
|
lithology_type |
|
lithology_class |
|
environ |
|
environ_id |
|
environ_type |
|
environ_class |
|
econ |
|
econ_id |
|
econ_type |
|
econ_class |
|
project_id |
|
strat_name_id |
|
sf |
|
More information can be found for the inputs for this function
using the definition functions (beginning with def_). Terminology
related to the PBDB can be found at https://paleobiodb.org/#/ or in
the suggested references below.
A dataframe containing the following columns:
collection_no: The unique identification number of the
collection, as assigned in the PBDB.
collection_name: The unique name of the collection, as
assigned in the PBDB.
t_age: The top age of the unit containing the collection,
estimated using the continuous time age model, in millions of years before
present.
b_age: The bottom age of the unit containing the collection,
estimated using the continuous time age model, in millions of years before
present.
pbdb_occs: The count of PBDB occurrences in the specified
PBDB collection.
genus_no: A vector containing the unique identification number
for each genus that appears in the collection, corresponding to the
genus_no column in the Paleobiology Database.
taxon_no: The count of unique taxa in the specified PBDB
collection.
unit_id: The unique identification number of the Macrostrat
unit containing the specified PBDB collection.
col_id: The unique identification number of the Macrostrat
column containing the specified PBDB collection.
refs: Reference for the source of the data.
strat_name_concept_id: The unique identification number of the
stratigraphic name concept containing the specified PBDB collection.
If sf = TRUE, an sf object is returned instead.
Christopher D. Dean
Lewis A. Jones
Peters, S.E. and McClennen, M. (2016). The Paleobiology Database application programming interface. Paleobiology, 42(1), pp. 1–7. doi:10.1017/pab.2015.39.
Uhen, M.D., Allen, B., Behboudi, N., Clapham, M.E., Dunne, E., Hendy, A., Holroyd, P.A., Hopkins, M., Mannion, P., Novack-Gottshall, P. and Pimiento, C. (2023). Paleobiology Database User Guide Version 1.0. PaleoBios, 40(11), pp. 1–56. doi:10.5070/P9401160531.
External data:
def_drilling_sites(),
def_measurements(),
get_eodp(),
get_measurements()
# Get fossils by Macrostrat column ID ex1 <- get_fossils(column_id = 10) # Get fossils by Macrostrat unit ID ex2 <- get_fossils(unit_id = 6279) # Get fossils by lithology and age ex3 <- get_fossils(lithology = "sandstone", age_top = 66, age_bottom = 73) # Get fossils by environment type and age ex4 <- get_fossils(environ_type = "fluvial", age = 253)# Get fossils by Macrostrat column ID ex1 <- get_fossils(column_id = 10) # Get fossils by Macrostrat unit ID ex2 <- get_fossils(unit_id = 6279) # Get fossils by lithology and age ex3 <- get_fossils(lithology = "sandstone", age_top = 66, age_bottom = 73) # Get fossils by environment type and age ex4 <- get_fossils(environ_type = "fluvial", age = 253)
A function to retrieve legend components from various geological maps.
get_map_legends( source_id = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, description = NULL, comments = NULL, scale = NULL, carto = NULL )get_map_legends( source_id = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, description = NULL, comments = NULL, scale = NULL, carto = NULL )
source_id |
|
lithology_id |
|
lithology_type |
|
lithology_class |
|
description |
|
comments |
|
scale |
|
carto |
|
Potential Macrostrat map scales are "tiny" (global), "small" (continental), "medium" (regional), or "large" (local).
A dataframe containing the following columns:
legend_id: The unique identification number of the
map legend.
source_id: The identification number of the source geologic
map (see def_sources()).
scale: The associated Macrostrat map scale for the legend.
map_unit_name:The name of the outcrop shape element as defined
in the geologic map source.
strat_name: The geologic name(s) of the outcrop shape element.
age: The chronostratigraphic bin assigned to the outcrop shape
element, as defined in the geologic map source in plain text.
lith: The lithology of the outcrop shape element as defined in
the geologic map source in plain text.
descrip: Description of the outcrop shape element in plain
text.
comments: Notes assigned to the outcrop shape element.
t_age: The estimated top age of the outcrop shape element, in
millions of years before present.
b_age: The estimated bottom age of the outcrop shape element,
in millions of years before present.
b_interval: The unique identification number of the bottom
time interval matched to the outcrop shape element.
t_interval: The unique identification number of the top time
interval matched to the outcrop shape element.
strat_name_id: A vector containing the unique identification
number(s) for known stratigraphic unit name(s) matched to the outcrop
shape element (see def_strat_names()).
unit_id: A vector containing the unique identification
number(s) for known Macrostrat unit(s) matched to the outcrop shape
element.
lith_classes: A vector containing the named lithology
class(es) (e.g., "sedimentary") matched to the outcrop shape element.
lith_types: A vector containing the named lithology type(s)
(e.g., "siliciclastic") matched to the outcrop shape element.
lith_id: A vector containing the unique identification
number(s) for known lithology(ies) represented within the outcrop shape
element (see def_lithologies()).
color: Recommended color for plotting the outcrop shape
element based on the dominant lithology.
area: The area of the outcrop shape element in
km2.
tiny_area: The area of the outcrop shape element in
km2 at "tiny" Macrostrat map
scale.
small_area: The area of the outcrop shape element in
km2 at "small" Macrostrat map
scale.
medium_area: The area of the outcrop shape element in
km2 at "medium" Macrostrat map
scale.
large_area: The area of the outcrop shape element in
km2 at "large" Macrostrat map
scale.
Christopher D. Dean
William Gearty
Geologic maps:
def_sources(),
get_map_outcrop(),
get_map_points()
# Get legend components by ID of the original source map ex1 <- get_map_legends(source_id = 1) # Get legend components for any sedimentary lithologies ex2 <- get_map_legends(lithology_type = "sedimentary") # Get any legend components that have comments with the word 'breccia' ex3 <- get_map_legends(comments = "breccia")# Get legend components by ID of the original source map ex1 <- get_map_legends(source_id = 1) # Get legend components for any sedimentary lithologies ex2 <- get_map_legends(lithology_type = "sedimentary") # Get any legend components that have comments with the word 'breccia' ex3 <- get_map_legends(comments = "breccia")
A function to retrieve data for geologic map outcrop shape elements from various sources.
get_map_outcrop( map_id = NULL, unit_id = NULL, strat_name_id = NULL, lat = NULL, lng = NULL, scale = NULL, sf = TRUE )get_map_outcrop( map_id = NULL, unit_id = NULL, strat_name_id = NULL, lat = NULL, lng = NULL, scale = NULL, sf = TRUE )
map_id |
|
unit_id |
|
strat_name_id |
|
lat |
|
lng |
|
scale |
|
sf |
|
More information can be found for the inputs for this function
using the definition functions (beginning with def_).
A data.frame containing the following columns:
map_id: The identification number of the outcrop shape
element.
source_id: The identification number of the source geologic
map.
name: The name of the outcrop shape element in the original
(or modified) source geologic map.
strat_name: The geologic name(s) of the outcrop shape
element.
lith: The lithology of the outcrop shape element as defined
in the geologic map source in plain text.
descrip: Description of the outcrop shape element in plain
text.
comments: Notes assigned to the outcrop shape element.
macro_units: A vector containing the unique identification
number(s) for known Macrostrat unit(s) matched to the outcrop shape
element.
strat_names: A vector containing the unique identification
number(s) for known stratigraphic unit name(s) matched to the outcrop
shape element (see def_strat_names()).
liths: A vector containing the unique identification
number(s) of the lithology(ies) represented within the outcrop shape
element (see def_lithologies()).
t_int_id: The identification number of the
chronostratigraphic interval containing the top boundary of the outcrop
shape element.
t_int_age: The top age of the chronostratigraphic interval
containing the top boundary of the outcrop shape element.
t_int_name: The name of the chronostratigraphic interval
containing the top boundary of the outcrop shape element.
b_int_id: The identification number of the
chronostratigraphic interval containing the bottom boundary of the
outcrop shape element.
b_int_age: The bottom age of the chronostratigraphic
interval containing the bottom boundary of the outcrop shape element.
b_int_name: The name of the chronostratigraphic interval
containing the bottom boundary of the outcrop shape element.
color: Recommended color for plotting the outcrop shape
element based on the dominant lithology.
t_age: The estimated top age (minimum age) of the outcrop
shape element, in millions of years before present.
b_age: The estimated bottom age (maximum age) of the outcrop
shape element, in millions of years before present.
best_int_name: The best/most representative interval name
for the outcrop shape element.
If sf is TRUE (the default), an sf object is returned instead, with
the same columns plus a "geometry" column that contains the spatial data.
William Gearty
Lewis A. Jones
Geologic maps:
def_sources(),
get_map_legends(),
get_map_points()
ex1 <- get_map_outcrop(lat = 43, lng = -89.3) ex2 <- get_map_outcrop(lat = 43, lng = -89.3, scale = "tiny")ex1 <- get_map_outcrop(lat = 43, lng = -89.3) ex2 <- get_map_outcrop(lat = 43, lng = -89.3, scale = "tiny")
A function to retrieve data for geologic map point shape elements from various sources.
get_map_points( point_id = NULL, point_type = NULL, min_lat = NULL, min_lng = NULL, max_lat = NULL, max_lng = NULL, source_id = NULL, sf = TRUE )get_map_points( point_id = NULL, point_type = NULL, min_lat = NULL, min_lng = NULL, max_lat = NULL, max_lng = NULL, source_id = NULL, sf = TRUE )
point_id |
|
point_type |
|
min_lat |
|
min_lng |
|
max_lat |
|
max_lng |
|
source_id |
|
sf |
|
More information can be found relating to the inputs for this
function using the definition functions (beginning with def_).
An sf object containing the following columns:
point_id: The identification number of the point element.
strike: The strike value of the point element.
dip: The dip value of the point element.
dip_dir: The dip direction of the point element.
point_type: The type of point element (e.g. "bedding").
certainty: The certainty of the point element location.
comments: Notes assigned to the point element.
source_id: The unique identification number of the source
for the point element.
geometry: The point spatial data.
If sf is TRUE (the default), an sf object is returned, with the
a "geometry" column that contains the spatial data. If sf is FALSE,
a data.frame object is returned with two additional columns (lng,
lat) containing the geographic coordinates of the point elements.
Lewis A. Jones
Bethany Allen
Geologic maps:
def_sources(),
get_map_legends(),
get_map_outcrop()
# Return a specific point ex1 <- get_map_points(point_id = 1) # Return all points within a user-specified bounding box ex2 <- get_map_points(min_lng = -80, min_lat = 40, max_lng = -70, max_lat = 50)# Return a specific point ex1 <- get_map_points(point_id = 1) # Return all points within a user-specified bounding box ex2 <- get_map_points(min_lng = -80, min_lat = 40, max_lng = -70, max_lat = 50)
Retrieve a range of measurements relevant to making geological inferences.
get_measurements( measure_id = NULL, measurement_id = NULL, measurement = NULL, measurement_type = NULL, measurement_class = NULL, measuremeta_id = NULL, measure_phase = NULL, column_id = NULL, section_id = NULL, unit_id = NULL, interval_name = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, project_id = NULL, sf = FALSE )get_measurements( measure_id = NULL, measurement_id = NULL, measurement = NULL, measurement_type = NULL, measurement_class = NULL, measuremeta_id = NULL, measure_phase = NULL, column_id = NULL, section_id = NULL, unit_id = NULL, interval_name = NULL, lithology_id = NULL, lithology_type = NULL, lithology_class = NULL, project_id = NULL, sf = FALSE )
measure_id |
|
measurement_id |
|
measurement |
|
measurement_type |
|
measurement_class |
|
measuremeta_id |
|
measure_phase |
|
column_id |
|
section_id |
|
unit_id |
|
interval_name |
|
lithology_id |
|
lithology_type |
|
lithology_class |
|
project_id |
|
sf |
|
More information can be found about the inputs and outputs for this
function by using def_measurements().
A data.frame containing the following columns:
measurement_id: The unique identification number of the
measurement.
measuremeta_id: The unique identification number of the sample.
measurement: The name of the type of measurement obtained.
measure_units: The units of the measurement.
measure_phase: The phase from which the measurement was taken.
method: The method used to generate the measurement.
n: The number of observations or measurements.
ref_id: The unique identification number of the reference
associated with the measurement.
sample_name: The name of the sample.
geo_unit: The Macrostrat unit from which the measurement was
taken.
samp_lith: A lithological description of the rock from which
the measurement was taken.
samp_lith_id: The unique identification number of the
lithological description of the rock from which the measurement was taken.
samp_desc: A description of the sample used to generate the
measurement.
samp_age: The geological time interval assigned to the
measurement.
lat: Decimal degree latitude of the measurement.
lng: Decimal degree longitude of the measurement.
unit_id: The unique identification number of the Macrostrat
unit from which the measurement was taken.
unit_rel_pos: The relative positive of the sample within the
unit.
col_id: The unique identification number of the Macrostrat
column from which the measurement was taken.
strat_name_id: The unique identification number of the
stratigraphic name attributed to the unit from which the measurement was
taken.
match_basis: A terse description of how the measuremeta data
was linked to the Macrostrat unit.
ref: The name of the reference.
measure_value: The value of the measurement.
measure_error: The reported error on the measurement value.
measure_position: The position of the measurement in the
Macrostrat column.
measure_n: The number of measurements used to generate the
measure_value; if greater than one, usually used to produce the
measure_error.
sample_no: The sample number for the measurement.
error_units: The units of the error.
If sf = TRUE, an sf object is returned instead, with the same
columns plus a "geometry" column that contains the spatial data.
Bethany Allen
Christopher D. Dean
External data:
def_drilling_sites(),
def_measurements(),
get_eodp(),
get_fossils()
# Return measurements based on their specific IDs ex1 <- get_measurements(measure_id = c(353, 354)) # Return measurements based on the ID of a specific measurement definition ex2 <- get_measurements(measurement_id = 42) # Return measurements for a specific measurement type ex3 <- get_measurements(measurement = "SiO2")# Return measurements based on their specific IDs ex1 <- get_measurements(measure_id = c(353, 354)) # Return measurements based on the ID of a specific measurement definition ex2 <- get_measurements(measurement_id = 42) # Return measurements for a specific measurement type ex3 <- get_measurements(measurement = "SiO2")
A function to retrieve paleogeographic geometries reconstructed to a given a age or interval using the Wright et al. (2013) Global Plate Model.
get_paleogeography(age = NULL, interval_name = NULL)get_paleogeography(age = NULL, interval_name = NULL)
age |
|
interval_name |
|
More information for appropriate interval inputs for this function
can be found using the def_intervals() function.
An sf object containing the geometries of the paleogeographic map.
Lewis A. Jones
Christopher D. Dean
Wright, N., Zahirovic, S., Müller, R.D., Seton, M. (2013). Towards community-driven paleogeographic reconstructions: integrating open-access paleogeographic and paleobiology data with plate tectonics. Biogeosciences, 10, 1529–1541. doi:10.5194/bg-10-1529-2013.
Paleogeography:
def_plates()
# Get paleogeographic map via age ex1 <- get_paleogeography(age = 250) # Get paleogeographic map via interval name# Get paleogeographic map via age ex1 <- get_paleogeography(age = 250) # Get paleogeographic map via interval name
A function to retrieve Macrostrat units contained within gap-bound packages (sections).
get_sections( section_id = NULL, column_id = NULL, unit_id = NULL, strat_name = NULL, strat_name_id = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lat = NULL, lng = NULL, lithology = NULL, lithology_id = NULL, lithology_group = NULL, lithology_type = NULL, lithology_class = NULL, lithology_att = NULL, lithology_att_id = NULL, lithology_att_type = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, pbdb_collection_no = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, adjacents = FALSE )get_sections( section_id = NULL, column_id = NULL, unit_id = NULL, strat_name = NULL, strat_name_id = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lat = NULL, lng = NULL, lithology = NULL, lithology_id = NULL, lithology_group = NULL, lithology_type = NULL, lithology_class = NULL, lithology_att = NULL, lithology_att_id = NULL, lithology_att_type = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, pbdb_collection_no = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, adjacents = FALSE )
section_id |
|
column_id |
|
unit_id |
|
strat_name |
|
strat_name_id |
|
interval_name |
|
interval_id |
|
age |
|
age_top |
|
age_bottom |
|
lat |
|
lng |
|
lithology |
|
lithology_id |
|
lithology_group |
|
lithology_type |
|
lithology_class |
|
lithology_att |
|
lithology_att_id |
|
lithology_att_type |
|
environ |
|
environ_id |
|
environ_type |
|
environ_class |
|
pbdb_collection_no |
|
econ |
|
econ_id |
|
econ_type |
|
econ_class |
|
project_id |
|
adjacents |
|
More information can be found for the inputs for this function
using the definition functions (beginning with defs_).
A dataframe containing the following columns:
col_id: The unique identification number of the Macrostrat
column containing the section.
col_area: The area of the associated Macrostrat column in
km2.
section_id: The unique identification number of the Macrostrat
section.
project_id: The unique identification number of the Macrostrat
project.
max_thick: The maximum thickness of the section, in meters.
min_thick: The minimum thickness of the section, in meters.
t_age: The age of the top of the section, estimated using the
continuous time age model, in millions of years before present.
b_age: The age of the bottom of the section, estimated using
the continuous time age model, in millions of years before present.
pbdb_collections: The number of PBDB collections contained
within the section.
lith: a dataframe containing the lithologies present
within the section, with the following columns:
name: The named lithology (e.g., "sandstone").
type: The named lithology type (e.g., "siliciclastic").
class: The named lithology class (e.g., "sedimentary").
prop: The proportion of the lithology within the section,
calculated from the individual Macrostrat units within the section.
lith_id: The unique identification number of the lithology.
environ: a dataframe containing the environments
present within the section, with the following columns:
name: The named environment (e.g., "delta plain").
type: The named environment type (e.g., "siliciclastic").
class: The named environment class (e.g., "marine").
prop: The proportion of the environment within the section,
calculated from the individual Macrostrat units within the section.
environ_id: The unique identification number of the
environment.
econ: a dataframe containing the economic attributes
present within the section, with the following columns:
name: The named economic attribute (e.g., "gold").
type: The named economic attribute type (e.g., "mineral").
class: The named economic attribute class (e.g., "precious
commodity").
prop: The proportion of the economic attribute out of
all economic attributes contained within the section, calculated
from the individual Macrostrat units within the section.
econ_id: The unique identification number of the economic
attribute.
Christopher D. Dean
Bethany Allen
Macrostrat data entities:
def_columns(),
get_age_model(),
get_columns(),
get_units()
# Get sections within a specified column ex1 <- get_sections(column_id = 10) # Get sections at a specific geographic coordinate ex2 <- get_sections(lng = -110.9, lat = 48.4)# Get sections within a specified column ex1 <- get_sections(column_id = 10) # Get sections at a specific geographic coordinate ex2 <- get_sections(lng = -110.9, lat = 48.4)
A function to retrieve various statistics about each Macrostrat project in the Macrostrat database. Function is called without user-specified arguments.
get_stats()get_stats()
A data.frame containing the following columns:
project_id: The unique identification number of the Macrostrat
project.
project: The name of the Macrostrat project.
columns: The number of Macrostrat columns associated with the
project.
packages: The number of Macrostrat packages/sections
associated with the project.
units: The number of Macrostrat units associated with the
project.
pbdb_collections: The number of Paleobiology Database
collections associated with the project.
measurements: The number of measurements associated with the
project.
t_polys: The number of spatial polygons associated with the
project.
William Gearty
Bethany Allen
Macrostrat database metadata:
def_projects(),
def_references(),
def_sources()
# Return all project statistics ex1 <- get_stats()# Return all project statistics ex1 <- get_stats()
A function to retrieve Macrostrat unit data matching a user-specified search criteria.
get_units( unit_id = NULL, section_id = NULL, column_id = NULL, strat_name = NULL, strat_name_id = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lat = NULL, lng = NULL, lithology = NULL, lithology_id = NULL, lithology_group = NULL, lithology_type = NULL, lithology_class = NULL, lithology_att = NULL, lithology_att_id = NULL, lithology_att_type = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, pbdb_collection_no = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, adjacents = FALSE, sf = FALSE )get_units( unit_id = NULL, section_id = NULL, column_id = NULL, strat_name = NULL, strat_name_id = NULL, interval_name = NULL, interval_id = NULL, age = NULL, age_top = NULL, age_bottom = NULL, lat = NULL, lng = NULL, lithology = NULL, lithology_id = NULL, lithology_group = NULL, lithology_type = NULL, lithology_class = NULL, lithology_att = NULL, lithology_att_id = NULL, lithology_att_type = NULL, environ = NULL, environ_id = NULL, environ_type = NULL, environ_class = NULL, pbdb_collection_no = NULL, econ = NULL, econ_id = NULL, econ_type = NULL, econ_class = NULL, project_id = NULL, adjacents = FALSE, sf = FALSE )
unit_id |
|
section_id |
|
column_id |
|
strat_name |
|
strat_name_id |
|
interval_name |
|
interval_id |
|
age |
|
age_top |
|
age_bottom |
|
lat |
|
lng |
|
lithology |
|
lithology_id |
|
lithology_group |
|
lithology_type |
|
lithology_class |
|
lithology_att |
|
lithology_att_id |
|
lithology_att_type |
|
environ |
|
environ_id |
|
environ_type |
|
environ_class |
|
pbdb_collection_no |
|
econ |
|
econ_id |
|
econ_type |
|
econ_class |
|
project_id |
|
adjacents |
|
sf |
|
More information can be found for the inputs for this function
using the definition functions (beginning with def_).
A data.frame containing the following columns:
unit_id: The unique identification number of the Macrostrat
unit.
section_id: The unique identification number of the
Macrostrat section containing the unit.
col_id: The unique identification number of the Macrostrat
column containing the unit.
project_id: The unique identification number of the
Macrostrat project.
col_area: The area of the associated Macrostrat column in
km2.
unit_name: The name of the Macrostrat unit.
strat_name_id: The unique Macrostrat stratigraphic name ID.
Mbr: The lithostratigraphic member.
Fm: The lithostratigraphic formation.
Gp: The lithostratigraphic group.
SGp: The lithostratigraphic supergroup.
t_age: The age of the top of the unit, estimated using the
continuous time age model, in millions of years before present.
b_age: The age of the bottom of the unit, estimated using the
continuous time age model, in millions of years before present.
max_thick: The maximum thickness of the unit, in meters.
min_thick: The minimum thickness of the unit, in meters.
outcrop: Type of exposure ("outcrop", "subsurface", or
"both").
pbdb_collections: The number of Paleobiology Database
collections contained within the unit.
pbdb_occurrences: The number of Paleobiology Database
occurrences contained within the unit.
lith: a dataframe containing the lithologies present
within the unit, with the following columns:
name: The named lithology (e.g., "sandstone").
prop: The proportion of the lithology within the unit,
calculated from the individual Macrostrat sub-units within the unit.
lith_id: The unique identification number of the
lithology.
type: The named lithology type (e.g., "siliciclastic").
class: The named lithology class (e.g., "sedimentary").
environ: a dataframe containing the environments
present within the unit, with the following columns:
class: The named environment class (e.g., "marine").
type: The named environment type (e.g., "siliciclastic").
name: The named environment (e.g., "delta plain").
environ_id: The unique identification number of the
environment.
econ: a dataframe containing the economic
attributes present within the unit, with the following columns:
type: The named economic attribute type (e.g.,
"mineral").
name: The named economic attribute (e.g., "gold").
econ_id: The unique identification number of the economic
attribute.
class: The named economic attribute class (e.g.,
"precious commodity").
measure: a dataframe containing the measure
attributes present within the unit, with the following columns:
measure_class: The class of measures (e.g.,
"geochemical").
measure_type: the type of measures (e.g., "minor
elements").
notes: Unit specific notes.
color: Recommended coloring for units based on dominant
lithology.
text_color: Recommended coloring for text based on color.
t_int_id: The ID of the chronostratigraphic interval
containing the top boundary of the unit.
t_int_name: The name of the time interval represented at
the top of the unit.
t_int_age: The age of the chronostratigraphic interval
containing the top boundary of the unit.
t_prop: Position of continuous time age model top boundary,
proportional to reference time interval (t_int_name).
units_above: The unit_ids of the units contacting the top
of the unit.
b_int_id: The ID of the chronostratigraphic interval
containing the bottom boundary of the unit.
b_int_name: The name of the time interval represented at
the bottom of the unit.
b_int_age: The age of the chronostratigraphic interval
containing the bottom boundary of the unit.
b_prop: Position of continuous time age model bottom
boundary, proportional to reference time interval (b_interval).
units_below: The unit_ids of the units contacting the
bottom of the unit.
strat_name_long: The stratigraphic name associated with
the unit (e.g., "Coal Valley Formation").
refs: The unique identification number(s) of the reference(s)
associated with the unit.
clat: The present day latitude of the centroid of the
column to which the unit belongs.
clng: The present day longitude of the centroid of the
column to which the unit belongs.
t_plat: The paleolatitude of the centroid of the column
which the unit belongs to at top age (clat rotated to t_age).
t_plng: The paleolongitude of the centroid of the column
which the unit belongs to at top age (clng rotated to t_age) .
b_plat: The paleolatitude of the centroid of the column
which the unit belongs to at bottom age (clat rotated to b_age).
b_plng: The paleolongitude of the the centroid of the
column which the unit belongs to at bottom age (clng rotated to
b_age).
If sf is TRUE, an sf object is returned instead, with a "geometry"
column that contains the spatial data instead of the clat/clng columns.
Lewis A. Jones
William Gearty
Macrostrat data entities:
def_columns(),
get_age_model(),
get_columns(),
get_sections()
# Get units with a specific stratigraphic name ex1 <- get_units(strat_name = "Hell Creek") # Get units at a specific geographic coordinate ex2 <- get_units(lng = -110.9, lat = 48.4)# Get units with a specific stratigraphic name ex1 <- get_units(strat_name = "Hell Creek") # Get units at a specific geographic coordinate ex2 <- get_units(lng = -110.9, lat = 48.4)