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Structure and classes of the stratcols package

Source: vignettes/stratcols_doc.Rmd
stratcols_doc.Rmd

Introduction

This vignette provides an overview of the structure of the stratcols package and the classes used therein.

S3 classes

S3 class stratcol

Description

The S3 class stratcol represents a simple stratigraphic column. Structurally, they are lists with 3 fields:

  • bdry : numeric vector, boundary of beds or units in the stratigraphic column

  • fa : vector, facies names of the beds

  • L_unit : NULL or a string, length unit of the bed thickness

The fields have the following constraints: fa must have exactly one element less than bdry. bdry must have at least 2 elements.

Construction

The following functions construct stratcol objects:

  • as_stratcol : standard constructor

Logic

The following functions examine the logic of stratcol objects:

  • is_stratcol : is an object a valid stratcol object?

Representation

  • plot.stratcol for basic plotting. Wraps the StratigrapheR package.
  • print.stratcol for printing stratigraphic columns to the console
  • summary.stratcol for printing a summary of a stratigraphic column to the console

Modification

The following functions modify existing stratcol objects:

  • set_L_unit to set length unit

Extracting information

The following functions extract information from stratcol objects:

  • bed_thickness

  • facies_names : get facies names of all beds

  • facies_repetitions : are there successive beds with identical facies?

  • get_base : position of lowest bed boundary

  • get_L_unit : extract length unit

  • merge_beds : combine beds in stratigraphic column

  • no_beds : number of beds in column

  • no_facies: number of distinct facies in column

  • total_thickness : total thickness of column

  • unique_facies_names : get unique names of facies

Transformation

The following functions transform stratcol objects:

  • rename_facies : change facies names

fa_tran_mat_c

Description

fa_tran_mant_p is a facies transition matrix with raw transition counts. it is square with the number of unique facies as column and row size, and the dim names are “from” and “to”. All entries are nonnegative integers, and the column/row names are the facies names.

Construction

via trans_count_matrix

fa_tran_mat_p

Description

fa_tran_mat_p is a facies transition matrix with transition probabilities. It is a matrix with dimension names “from” and “to”, and the facies names as column names. It specifies the transition probability/frequency between the facies.

Construction

Via transition_matrix.

Further reading

See also

vignette("stratcols")

for an overview of the available functionalit of the stratcols package, including how to create stratigraphic columns, plot them and modify them.

See

vignette("stratorder")

for available methods to estimate stratigraphic order metrics, such as the runs order metric (ROM) and the Markov order metric (MOM).