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Look up geological intervals and assign geological stages

Source: R/look_up.R
look_up.Rd

A function that uses interval names to assign either international geological stages and numeric ages from the International Commission on Stratigraphy (ICS), or user-defined intervals, to fossil occurrences.

Usage

look_up(
  occdf,
  early_interval = "early_interval",
  late_interval = "late_interval",
  int_key = FALSE,
  assign_with_GTS = "GTS2020",
  return_unassigned = FALSE
)

Arguments

occdf

data.frame. A dataframe of fossil occurrences or other geological data, with columns of class character specifying the earliest and the latest possible interval associated with each occurrence.

early_interval

character. Name of the column in occdf that contains the earliest interval from which the occurrences are from. Defaults to "early_interval".

late_interval

character. Name of the column in occdf that contains the latest interval from which the occurrences are from. Defaults to "late_interval".

int_key

data.frame. A dataframe linking interval names to international geological stage names from the ICS, or other, user-defined intervals. This dataframe should contain the following named columns containing character values:

  • interval_name contains the names to be matched from occdf

  • early_stage contains the names of the earliest stages corresponding to the intervals

  • late_stage contains the latest stage corresponding to the intervals

Optionally, named numeric columns provide maximum and minimum ages for the intervals:

  • max_ma

  • min_ma

If set to FALSE (default), stages and numerical ages can be assigned based on one of the GTS tables (see below).

assign_with_GTS

character or FALSE. Allows intervals to be searched in the GTS2020 (default) or the GTS2012 table. Set to FALSE to disable.

return_unassigned

logical. Return interval names which could not be assigned, instead of the dataframe with assignments. Defaults to FALSE.

Value

A dataframe of the original input data with the following appended columns is returned: early_stage and late_stage, corresponding to the earliest and latest international geological stage which could be assigned to the occurrences based on the given interval names. interval_max_ma and interval_min_ma return maximum and minimum interval ages if provided in the interval key, or if they can be fetched from GTS2012 or GTS2020. A column interval_mid_ma is appended to provide the midpoint ages of the intervals.

Details

If int_key is set to FALSE (default), this function can be used to assign numerical ages solely based on stages from a GTS table, and to assign stages based on GTS interval names.

Instead of geological stages, the user can supply any names in the early_stage and late_stage column of int_key. assign_with_GTS should then be set to FALSE.

An exemplary int_key has been included within this package (interval_key). This key works well for assigning geological stages to many of the intervals from the Paleobiology Database and the PaleoReefs Database. palaeoverse cannot guarantee that all of the stage assignments with the exemplary key are accurate. The table corresponding to this key can be loaded with palaeoverse::interval_key.

Developer(s)

Kilian Eichenseer & William Gearty

Reviewer(s)

Lewis A. Jones & Christopher D. Dean

Examples

## Just use GTS2020 (default):
# create exemplary dataframe
taxdf <- data.frame(name = c("A", "B", "C"),
early_interval = c("Maastrichtian", "Campanian", "Sinemurian"),
late_interval = c("Maastrichtian", "Campanian", "Bartonian"))
# assign stages and numerical ages
taxdf <- look_up(taxdf)

## Use exemplary int_key
# Get internal reef data
occdf <- reefs
 # assign stages and numerical ages
occdf <- look_up(occdf,
                early_interval = "interval",
                late_interval = "interval",
                int_key = interval_key)

## Use exemplary int_key and return unassigned
# Get internal tetrapod data
occdf <- tetrapods
# assign stages and numerical ages
occdf <- look_up(occdf, int_key = palaeoverse::interval_key)
#> Warning: `NA`, `""` or `" "` entries from `late_interval` have been
#>             filled in with the corresponding `early_interval` entries
#> Warning: The following intervals could not be matched with intervals from int_key
#>       or GTS: Early Triassic, Late Pennsylvanian, Vokhmian
# return unassigned intervals
unassigned <- look_up(occdf, int_key = palaeoverse::interval_key,
                      return_unassigned = TRUE)
#> Warning: `NA`, `""` or `" "` entries from `late_interval` have been
#>             filled in with the corresponding `early_interval` entries

## Use own key and GTS2012:
# create example data
occdf <- data.frame(
  stage = c("any Permian", "first Permian stage",
            "any Permian", "Roadian"))
# create example key
interval_key <- data.frame(
  interval_name = c("any Permian", "first Permian stage"),
  early_stage = c("Asselian", "Asselian"),
  late_stage = c("Changhsingian", "Asselian"))
# assign stages and numerical ages:
occdf <- look_up(occdf,
                 early_interval = "stage", late_interval = "stage",
                 int_key = interval_key, assign_with_GTS = "GTS2012")