MDSS: cca – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

cca

Calculate corresponding age range for dentin serial sections

Description

cca calculates corresponding age range for horizontal dentin serial sections under a given class "mds" object and given ages at the start and end of tooth dentin formation.

Usage

## Default S3 method:
cca(x, t.start, t.end)

Arguments

`x`	An object of class `"mds"`.
`t.start`	The age at the start of tooth dentin formation.
`t.end`	The age at the end of tooth dentin formation.

Details

Function cca calculates corresponding age range for each serial section. Each GL has its formation age, and serial sections consist of several GLs that were formed in different ages. Relative volume assigned to each GL in a section is used to weigh the contribution from the GL. Modeled age ranges for the stable isotopic trajectory of dentin serial sections can be obtained by using this function.

Value

cca returns an object of class "cca".
The function plot is used to show figures of the results.
An object of class "cca" has following list components in addition to those succeeded from "mds":

t.all

List including 5 elements.

`t.g`	Numeric vector of assigned age to each growth lines with the equal temporal division.
`t.n`	Numeric vector of assigned age to each sectioning plane with the equal temporal division.
`t.g.mid`	Numeric vector of midpoint age of each GL.
`t.n.ref`	Numeric vector of calculated midpoint of the modeled age range of each section with the consideration of changing dentin growth rates and oblique growth layers.
`t.n.obs`	Numeric vector of assigned midpoint age to each section with the equal temporal division.

cca

Matrix of assigned ages to each section. The row consists of the assigned midpoint ages to sections with equal-temporal division (equally), the modeled midpoint age calculated from the weighted contribution from GLs (weighted), the duration of modeled age range (duration), and lower and upper ages of the modeled age range (lower and upper). The column corresponds to each section, and the smallest column number represents the crown-most section.

Author(s)

Takumi Tsutaya developed this model.

References

Tsutaya T. in prep. Blurred time resolution of tooth dentin serial sections.

Examples

## 18 sections for 18 mm lateral incisor
l18_I2_s18.mds <- mds(
  tooth = "I",
  rt.y = 18,
  section.y = 0:18,
  n.GL = 100)
l18_I2_s18.cca <- cca(
  x = l18_I2_s18.mds,
  t.start = 0.5875,
  t.end = 10.5)

# Plot corresponding age ranges.
plot(l18_I2_s18.cca)

## Example of the first molar of ST61 from the Unseiji temple.
unseiji_ST61_M1.mds <- mds(
  tooth = "M1",
  rt.y = unseiji_ST61_M1$rt.y,
  ecj = unseiji_ST61_M1$ecj,
  section.y = unseiji_ST61_M1$section.y,
  n.GL = 100)
unseiji_ST61_M1.cca <- cca(
  x = unseiji_ST61_M1.mds,
  t.start = unseiji_ST61_M1$t.start,
  t.end = unseiji_ST61_M1$t.end)

# Plot modeled age ranges with stable nitrogen isotope ratios.
plot(unseiji_ST61_M1.cca,
  age = unseiji_ST61_M1$section$age,
  delta = unseiji_ST61_M1$section$d15N,
  type = "o")

# Plot without excluded sections with the porous dentin structure.
plot(unseiji_ST61_M1.cca,
  age = unseiji_ST61_M1$section$age[1:13],
  delta = unseiji_ST61_M1$section$d15N[1:13],
  type = "o")

## Irregular sectioning for 20 mm canine.
l20_C_irr.mds <- mds(
  tooth = "C",
  rt.y = 20,
  section.y = c(2:14, 15, 17, 19),
  n.GL = 100)
l20_C_irr.cca <- cca(
  x = l20_C_irr.mds,
  t.start = 0.35,
  t.end = 13.5)

# Plot corresponding age ranges.
plot(l20_C_irr.cca, xlim = c(0, 14))

MDSS

Modeling Human Dentin Serial Sectioning

v1.0-0

GPL (>= 3)

Authors

Takumi Tsutaya [aut, cre] (<https://orcid.org/0000-0001-5104-5223>)

Initial release

2020-02-20

cca