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Retrieve Macrostrat column data

Source: R/get_columns.R
get_columns.Rd

A function to retrieve independent, hexagonal, vertical columns which contain chronostratigraphically organised Macrostrat units.

Usage

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
)

Arguments

column_id

integer. Filter columns by their unique identification number(s).

section_id

integer. Filter columns to those containing section(s) as specified by their unique identification number(s).

unit_id

integer. Filter columns to those containing unit(s) as specified by their unique identification number(s).

strat_name

character. Filter columns to those containing a unit that fuzzy matches a stratigraphic name (e.g., "Hell Creek").

strat_name_id

integer. Filter columns to those containing a unit that matches one or more stratigraphic name(s) as specified by their unique identification number(s).

interval_name

character. Filter columns to those that overlap with a named chronostratigraphic time interval (e.g., "Permian").

interval_id

integer. Filter columns to those that overlap with a chronostratigraphic time interval as specified by their unique identification number(s).

age

numeric. Filter columns to those that overlap with the specified numerical age, in millions of years before present.

age_top

numeric. Filter columns 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 this must be younger than age_bottom.

age_bottom

numeric. Filter columns 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 this must be older than age_top.

lat

numeric. Return the column at the specified decimal degree latitude. Must also specify lng.

lng

numeric. Return the column at the specified decimal degree longitude. Must also specify lat.

lithology

character. Filter columns to those containing a named lithology (e.g., "shale", "sandstone").

lithology_id

integer. Filter columns to those containing one or more lithology(ies) identified by their unique identification number(s).

lithology_type

character. Filter columns to those containing a named lithology type (e.g., "carbonate", "siliciclastic").

lithology_class

character. Filter columns to those containing a named lithology class (e.g., "sedimentary", "igneous", "metamorphic").

lithology_att

character. Filter columns to those containing a named lithology attribute (e.g., "fine", "olivine", "poorly washed").

lithology_att_id

integer. Filter columns to those containing one or more lithology attribute(s) as specified by their unique identification number(s).

lithology_att_type

character. Filter columns to those containing a named category of lithology attribute (e.g., "grains", "lithology", "bedform").

environ

character. Filter columns to those containing a named environment (e.g., "delta plain", "pond").

environ_id

integer. Filter columns to those containing one or more environment(s) as specified by their unique identification number(s).

environ_type

character. Filter columns to those containing a named environment type (e.g., "fluvial", "eolian", "glacial").

environ_class

character. Filter columns to those containing a named environment class (e.g., "marine", "non-marine").

pbdb_collection_no

integer. Filter columns to those containing one or more Paleobiology Database collection(s) as specified by their unique identification number(s).

econ

character. Filter columns to those containing a named economic attribute (e.g., "brick", "ground water", "gold").

econ_id

integer. Filter columns to those containing one or more economic attribute(s) as specified by their unique identification number(s).

econ_type

character. Filter columns to those containing a named economic attribute type (e.g., "construction", "aquifer", "mineral").

econ_class

character. Filter columns to those containing a named economic attribute class (e.g., "material", "water", "precious commodity").

project_id

integer. Filter columns to those contained within a Macrostrat project as specified by its unique identification number.

adjacents

logical. If column_id or lat/lng is specified, should all columns 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:

  • 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.

Details

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

Developer(s)

William Gearty

Reviewer(s)

Christopher D. Dean

See also

Macrostrat data entities: def_columns(), get_age_model(), get_sections(), get_units()

Examples

# \donttest{
# 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)
# }