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
)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.
integer. Filter columns by their unique
identification number(s).
integer. Filter columns to those containing
section(s) as specified by their unique identification number(s).
integer. Filter columns to those containing unit(s) as
specified by their unique identification number(s).
character. Filter columns to those containing a unit
that fuzzy matches a stratigraphic name (e.g., "Hell Creek").
integer. Filter columns to those containing a
unit that matches one or more stratigraphic name(s) as specified by their
unique identification number(s).
character. Filter columns to those that overlap
with a named chronostratigraphic time interval (e.g., "Permian").
integer. Filter columns to those that overlap with
a chronostratigraphic time interval as specified by their unique
identification number(s).
numeric. Filter columns to those that overlap with the
specified numerical age, in millions of years before present.
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.
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.
numeric. Return the column at the specified decimal degree
latitude. Must also specify lng.
numeric. Return the column at the specified decimal degree
longitude. Must also specify lat.
character. Filter columns to those containing a named
lithology (e.g., "shale", "sandstone").
integer. Filter columns to those containing one or
more lithology(ies) identified by their unique identification number(s).
character. Filter columns to those containing a
named lithology type (e.g., "carbonate", "siliciclastic").
character. Filter columns to those containing a
named lithology class (e.g., "sedimentary", "igneous", "metamorphic").
character. Filter columns to those containing a
named lithology attribute (e.g., "fine", "olivine", "poorly washed").
integer. Filter columns to those containing
one or more lithology attribute(s) as specified by their unique
identification number(s).
character. Filter columns to those
containing a named category of lithology attribute (e.g., "grains",
"lithology", "bedform").
character. Filter columns to those containing a named
environment (e.g., "delta plain", "pond").
integer. Filter columns to those containing one or
more environment(s) as specified by their unique identification number(s).
character. Filter columns to those containing a
named environment type (e.g., "fluvial", "eolian", "glacial").
character. Filter columns to those containing a
named environment class (e.g., "marine", "non-marine").
integer. Filter columns to those containing
one or more Paleobiology Database collection(s) as specified by their
unique identification number(s).
character. Filter columns to those containing a named
economic attribute (e.g., "brick", "ground water", "gold").
integer. Filter columns to those containing one or more
economic attribute(s) as specified by their unique identification
number(s).
character. Filter columns to those containing a named
economic attribute type (e.g., "construction", "aquifer", "mineral").
character. Filter columns to those containing a
named economic attribute class (e.g., "material", "water", "precious
commodity").
integer. Filter columns to those contained within a
Macrostrat project as specified by its unique identification number.
logical. If column_id or lat/lng is specified,
should all columns that touch the specified column be returned? Defaults to
FALSE.
logical. Should the results be returned as an sf object?
Defaults to FALSE.
William Gearty
Christopher D. Dean
More information can be found for the inputs for this function using
the definition functions (beginning with def_).
Macrostrat data entities:
def_columns(),
get_age_model(),
get_sections(),
get_units()
# \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)
# }
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