Retrieve Macrostrat unit data

A function to retrieve Macrostrat unit data matching a user-specified search criteria.

Usage

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
)

Arguments

unit_id: integer. Filter units by their unique identification number(s).
section_id: integer. Filter units to those contained within section(s) as specified by their unique identification number(s).
column_id: integer. Filter units to those contained within column(s) as specified by their unique identification number(s).
strat_name: character. Filter units to those containing a unit that fuzzy matches a stratigraphic name (e.g., "Hell Creek").
strat_name_id: integer. Filter units to those that match one or more stratigraphic name(s) as specified by their unique identification number(s).
interval_name: character. Filter units to those that overlap with a named chronostratigraphic time interval (e.g., "Permian").
interval_id: integer. Filter units to those that overlap with one or more chronostratigraphic time interval(s) as specified by their unique identification number(s).
age: numeric. Filter units to those that overlap with the specified numerical age, in millions of years before present.
age_top: numeric. Filter units to those that overlap with the age range between the specified numerical age and age_bottom. Should be in millions of years before present. age_bottom must also be specified, and age_top must be younger than age_bottom.
age_bottom: numeric. Filter units to those that overlap with the age range between the specified numerical age and age_top. Should be in millions of years before present. age_top must also be specified, and age_bottom must be older than age_top.
lat: numeric. Return the units at the specified decimal degree latitude. Must also specify lng.
lng: numeric. Return the units at the specified decimal degree longitude. Must also specify lat.
lithology: character. Filter units to those containing a named lithology (e.g., "shale", "sandstone").
lithology_id: integer. Filter units to those containing one or more lithology(ies) as specified by their unique identification number(s).
lithology_group: character. Filter units to those containing a named lithology group (e.g., "sandstones", "mudrocks", "unconsolidated").
lithology_type: character. Filter units to those containing a named lithology type (e.g., "carbonate", "siliciclastic").
lithology_class: character. Filter units to those containing a named lithology class (e.g., "sedimentary", "igneous", "metamorphic").
lithology_att: character. Filter units to those containing a named lithology attribute (e.g., "fine", "olivine", "poorly washed").
lithology_att_id: integer. Filter units to those containing one or more lithology attribute(s) as specified by their unique identification number(s).
lithology_att_type: character. Filter units to those containing a named category of lithology attribute (e.g., "grains", "lithology", "bedform").
environ: character. Filter units to those containing a named environment (e.g., "delta plain", "pond").
environ_id: integer. Filter units to those containing one or more environment(s) as specified by their unique identification number(s).
environ_type: character. Filter units to those containing a named environment type (e.g., "fluvial", "eolian", "glacial").
environ_class: character. Filter units to those containing a named environment class (e.g., "marine", "non-marine").
pbdb_collection_no: integer. Filter units to those containing one or more Paleobiology Database collection(s) as specified by their unique identification number(s).
econ: character. Filter units to those containing a named economic attribute (e.g., "brick", "ground water", "gold").
econ_id: integer. Filter units to those containing one or more economic attribute(s) as specified by their unique identification number(s).
econ_type: character. Filter units to those containing a named economic attribute type (e.g., "construction", "aquifer", "mineral").
econ_class: character. Filter units to those containing a named economic attribute class (e.g., "material", "water", "precious commodity").
project_id: integer. Filter units to those contained within one or more Macrostrat project(s) as specified by their unique identification number(s).
adjacents: logical. If column_id or lat/lng is specified, should all units that touch the specified column be returned? Defaults to FALSE.
sf: logical. Should the results be returned as an sf object? Defaults to FALSE.

Value

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.

Details

More information can be found for the inputs for this function using the definition functions (beginning with def_).

Developer(s)

Lewis A. Jones

Reviewer(s)

William Gearty

Examples

# \donttest{
# 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)
# }