| Title: | Modeling Human Dentin Serial Sectioning |
|---|---|
| Description: | Modeling microstructures of human tooth dentin and horizontal serial-sectioning of the dentin. Corresponding age range of dentin serial sections, that is used in stable isotope analyses, can be calculated by using this package. |
| Authors: | Takumi Tsutaya [aut, cre]
|
| Maintainer: | Takumi Tsutaya <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.0-1 |
| Built: | 2025-02-11 03:10:29 UTC |
| Source: | https://github.com/cran/MDSS |
MDSS is a package to model microstructures of human tooth dentin and horizontal serial-sectioning of the dentin. The corresponding age range of dentin serial sections, that is used in stable isotope analyses, can be calculated by using this package.
| Package: | MDSS |
| Type: | Package |
| Version: | 1.0-1 |
| Date: | 2022-08-21 |
| License: | GPL (>= 3) |
Function mds models tooth dentin microstructures and horizontal sectioning patterns. The changing dentin growth rates, oblique dentin growth layers, and dentin outer shape are modeled with pre-determined parameters and user's manual adjustments in mds. Function cca calculates corresponding age ranges for each dentin serial sections set with mds. This package adopts S3 class. The detail of mathematical models is described in Tsutaya (in prep).
Takumi Tsutaya <[email protected]>
Tsutaya T 2020. Blurred time resolution of tooth dentin serial sections. American Journal of Physical Anthropology 173:748–759. DOI: 10.1002/ajpa.24113.
## See ?mds and ?cca for examples.## See ?mds and ?cca for examples.
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.
## Default S3 method: cca(x, t.start, t.end)## Default S3 method: cca(x, t.start, t.end)
x |
An object of class |
t.start |
The age at the start of tooth dentin formation. |
t.end |
The age at the end of tooth dentin formation. |
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.
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.
|
||||||||||
cca |
Matrix of assigned ages to each section. The row consists of the assigned midpoint ages to sections with equal-temporal division ( |
Takumi Tsutaya developed this model.
Tsutaya T 2020. Blurred time resolution of tooth dentin serial sections. American Journal of Physical Anthropology 173:748–759. DOI: 10.1002/ajpa.24113.
## 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$d15N[1:13], type = "o") ## Irregular sectioning for 20 mm canine. l20_C_irr.mds <- mds( tooth = "C", rt.y = 20, section.y = c(2:14, 15, 17, 19), n.GL = 100) l20_C_irr.cca <- cca( x = l20_C_irr.mds, t.start = 0.35, t.end = 13.5) # Plot corresponding age ranges. plot(l20_C_irr.cca, xlim = c(0, 14))## 18 sections for 18 mm lateral incisor l18_I2_s18.mds <- mds( tooth = "I", rt.y = 18, section.y = 0:18, n.GL = 100) l18_I2_s18.cca <- cca( x = l18_I2_s18.mds, t.start = 0.5875, t.end = 10.5) # Plot corresponding age ranges. plot(l18_I2_s18.cca) ## Example of the first molar of ST61 from the Unseiji temple. unseiji_ST61_M1.mds <- mds( tooth = "M1", rt.y = unseiji_ST61_M1$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))
Function mds models tooth dentin microstructures and horizontal sectioning patterns. The changing dentin growth rates, oblique dentin growth layers, and dentin outer shape are modeled with pre-determined parameters and user's manual adjustments.
## Default S3 method: mds(tooth, rt.y = 1, ecj = NULL, section.y, factor.GL = 1, n.GL = 500, thin = FALSE)## Default S3 method: mds(tooth, rt.y = 1, ecj = NULL, section.y, factor.GL = 1, n.GL = 500, thin = FALSE)
tooth |
Character scalar showing the target tooth type. Only |
rt.y |
A positive y-value of dentin root tip in mm. Dentin horn is set on the geometric origin, and the longitudinal central axis of dentin equals the y-axis. |
ecj |
|
section.y |
Vector of y-values for serial sections. Please sandwich by the start and end points for each section, so that the length of |
factor.GL |
Numeric vector to adjust slope of dentin growth layers (GLs). A product of |
n.GL |
Scalar indicating number of GLs. Default is 500. |
thin |
If dentin sample was sliced out into a longitudinal thin plate, put |
The mds is a function to model tooth dentin microstructures and horizontal serial-sectioning patterns for human permanent incisors, canines, and molars. The changing dentin growth rates, oblique dentin growth layers, and curved dentin outer shape are considered in this model. Users can adjust these parameters for individual tooth dentin samples. The details of this model are described in Tsutaya (in prep).
mds returns an object of class "mds".
The function plot is used to plot a figure of the results.
An object of class "mds" is a list containing at least the following components:
parea |
Matrix of weighted proportion (volume contribution) for each GL included in each section. The row and column correspond to GLs and sections, respectively. |
included |
List containing the growth line numbers that are included in each section. The crown-most section has the smallest number as a list element. |
ge.x |
Numeric vector of the standardized x-value of cross-section between growth lines and crown dentin outer shape. |
ge.y |
Numeric vector of the standardized y-value of cross-section between growth lines and crown dentin outer shape. |
gd.x |
Numeric vector of the standardized x-value of cross-section between growth lines and root dentin outer shape. |
gd.y |
Numeric vector of the standardized y-value of cross-section between growth lines and root dentin outer shape. |
ecj.x |
Scalar of the standardized x-value of ECJ. |
ecj.y |
Scalar of the standardized y-value of ECJ. |
m.y |
Numeric vector of the standardized y-value of cross-section between growth lines and longitudinal central axis of tooth (i.e., y-axis). |
n.y |
Numeric vector of the standardized y-value of cross-section between sectioning planes and longitudinal central axis of tooth (i.e., y-axis). |
EShape |
Function describing the crown dentin outer shape. |
DShape |
Function describing the root dentin outer shape. |
Gcurve |
Function describing the tooth dentin growth lines. |
call |
The matched call. |
Takumi Tsutaya developed this model.
Tsutaya T 2020. Blurred time resolution of tooth dentin serial sections. American Journal of Physical Anthropology 173:748–759. DOI: 10.1002/ajpa.24113.
## 18 sections for 18 mm lateral incisor l18_I2_s18.mds <- mds( tooth = "I", rt.y = 18, section.y = 0:18, n.GL = 100) # Plot tooth dentin anatomy. plot(l18_I2_s18.mds) ## 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$section.y, n.GL = 100) # Plot tooth dentin anatomy. plot(unseiji_ST61_M1.mds) ## Irregular sectioning for 20 mm canine. l20_C_irr.mds <- mds( tooth = "C", rt.y = 20, section.y = c(2:14, 15, 17, 19), n.GL = 100) # Plot tooth dentin anatomy. plot(l20_C_irr.mds)## 18 sections for 18 mm lateral incisor l18_I2_s18.mds <- mds( tooth = "I", rt.y = 18, section.y = 0:18, n.GL = 100) # Plot tooth dentin anatomy. plot(l18_I2_s18.mds) ## Example of the first molar of ST61 from the Unseiji temple. unseiji_ST61_M1.mds <- mds( tooth = "M1", rt.y = unseiji_ST61_M1$rt.y, ecj = unseiji_ST61_M1$ecj, section.y = unseiji_ST61_M1$section.y, n.GL = 100) # Plot tooth dentin anatomy. plot(unseiji_ST61_M1.mds) ## 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) # Plot tooth dentin anatomy. plot(l20_C_irr.mds)
plot.cca is a plotting utile for quick visualization of the modeled age range of tooth dentin serial sections under an object of class "cca". The modeled age ranges are plotted for each section.
## S3 method for class 'cca' plot(x, age = NULL, delta = NULL, error = 0.1, ...)## S3 method for class 'cca' plot(x, age = NULL, delta = NULL, error = 0.1, ...)
x |
An object of class |
age |
Numeric vector of originally assigned ages for each section. If omitted, midpoint ages calculated with equal temporal division according to the relative height of sections are used. |
delta |
Numeric vector of stable isotope ratios for each section. If omitted, corresponding age ranges are plotted without information on stable isotope ratios. |
error |
Analytical error of stable isotope ratios. Default is 0.1. |
... |
Additional arguments passed to |
If the argument delta is omitted, the corresponding age ranges for each serial section are plotted with its positions in the standardized y-axis. If the argument delta is specified, the originally-assigned ages and the modeled age ranges for each section are plotted with its stable isotope ratios.
Takumi Tsutaya developed this model.
Tsutaya T 2020. Blurred time resolution of tooth dentin serial sections. American Journal of Physical Anthropology 173:748–759. DOI: 10.1002/ajpa.24113.
## See ?cca for examples.## See ?cca for examples.
plot.mds is a plotting utile for quick visualization of the modeled the tooth dentin microstructures under an object of class "mds". The modeled dentin growth layers and outer shape are plotted on a geometric plane.
## S3 method for class 'mds' plot(x, ...)## S3 method for class 'mds' plot(x, ...)
x |
An object of class |
... |
Additional arguments passed to |
The modeled tooth dentin is plotted on a geometric plane. Dentin horn and root tip equal the geometric origin and the coordinate (0, 1), respectively. Growth lines are shown with oblique colored lines inside the longitudinal half of tooth dentin outer shape. Horizontal sections are shown with horizontal solid black lines.
Takumi Tsutaya developed this model.
Tsutaya T 2020. Blurred time resolution of tooth dentin serial sections. American Journal of Physical Anthropology 173:748–759. DOI: 10.1002/ajpa.24113.
## See ?mds for examples.## See ?mds for examples.
PlotSections plots the corresponding age range for horizontal dentin serial sections with multiple class "cca" objects.
PlotSections(age, delta, obj, error = 0.1, col = "black", pch = 21, ...)PlotSections(age, delta, obj, error = 0.1, col = "black", pch = 21, ...)
age |
List of user-assigned ages for each sections. |
delta |
List of vector observed delta values for each sections. |
obj |
List of class |
error |
Vector of analytical error. Used for the height of "beans". |
col |
Vector of |
pch |
Vector of |
... |
Additional arguments passed to |
Function PlotSections plots corresponding age range with its measured delta values and equally assigned ages for a series of serial sections. Multiple trajectories can be plotted together into a single figure.
A plot of multiple trajectories of dentin serial sections.
Takumi Tsutaya developed this model.
Tsutaya T 2020. Blurred time resolution of tooth dentin serial sections. American Journal of Physical Anthropology 173:748–759. DOI: 10.1002/ajpa.24113.
## 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$t.end) unseiji_ST61_C.mds <- mds( tooth = "C", rt.y = unseiji_ST61_C$rt.y, ecj = unseiji_ST61_C$ecj, section.y = unseiji_ST61_C$section.y, n.GL = 100) unseiji_ST61_C.cca <- cca( x = unseiji_ST61_C.mds, t.start = unseiji_ST61_C$t.start, t.end = unseiji_ST61_C$t.end) # Plot C and M1 modeled age ranges with stable nitrogen isotope ratios. PlotSections( age = list( unseiji_ST61_C$section$age, unseiji_ST61_M1$section$age), delta = list( unseiji_ST61_C$section$d15N, unseiji_ST61_M1$section$d15N), obj = list( C = unseiji_ST61_C.cca, M1 = unseiji_ST61_M1.cca)) # Plot the same data with different colors. PlotSections( age = list( unseiji_ST61_C$section$age, unseiji_ST61_M1$section$age), delta = list( unseiji_ST61_C$section$d15N, unseiji_ST61_M1$section$d15N), obj = list( C = unseiji_ST61_C.cca, M1 = unseiji_ST61_M1.cca), col = c("red", "blue"), pch = c(1, 2))## 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$t.end) unseiji_ST61_C.mds <- mds( tooth = "C", rt.y = unseiji_ST61_C$rt.y, ecj = unseiji_ST61_C$ecj, section.y = unseiji_ST61_C$section.y, n.GL = 100) unseiji_ST61_C.cca <- cca( x = unseiji_ST61_C.mds, t.start = unseiji_ST61_C$t.start, t.end = unseiji_ST61_C$t.end) # Plot C and M1 modeled age ranges with stable nitrogen isotope ratios. PlotSections( age = list( unseiji_ST61_C$section$age, unseiji_ST61_M1$section$age), delta = list( unseiji_ST61_C$section$d15N, unseiji_ST61_M1$section$d15N), obj = list( C = unseiji_ST61_C.cca, M1 = unseiji_ST61_M1.cca)) # Plot the same data with different colors. PlotSections( age = list( unseiji_ST61_C$section$age, unseiji_ST61_M1$section$age), delta = list( unseiji_ST61_C$section$d15N, unseiji_ST61_M1$section$d15N), obj = list( C = unseiji_ST61_C.cca, M1 = unseiji_ST61_M1.cca), col = c("red", "blue"), pch = c(1, 2))
This data set gives the stable carbons and nitrogen isotope ratios of dentin serial sections obtained from a human mandibular canine tooth of an individual ST61 (AD 1655–1732) from the Unseiji temple, Japan, reported in Tsutaya et al. (2016).
unseiji_ST61_Cunseiji_ST61_C
unseiji_ST61_C is a list containing 6 elements.
rt.y |
y-value for the root tip (i.e., length [mm] of the dentin). |
ecj |
x- and y-coordinates of enamel-cement junction. Dentin horn is placed on the geometric origin, and root tip is placed on the y-axis with a positive value. |
section.y |
y-values for the horizontal sections. |
t.start and t.end |
The age at the start and end of dentin formation, respectively. |
section |
Data frame with 18 dentin serial sections (rows) and 3 variables (columns) of assigned midpoint age with equal temporal division, carbon, and nitrogen isotope ratios, named age, d13C, and d15N, respectively.
|
See detail for Tsutaya et al. (2016).
Tsutaya T, Miyamoto H, Uno H, Omori T, Gakuhari T, Inahara A, Nagaoka T, Abe M, Yoneda M. 2016. From cradle to grave: multi-isotopic investigations on the life history of a higher-status female in the Edo period Japan. Anthropological Science 124:185–197. DOI: 10.1537/ase.161029.
This data set gives the stable carbons and nitrogen isotope ratios of dentin serial sections obtained from a human maxillary first molar tooth of an individual ST61 (AD 1655–1732) from the Unseiji temple, Japan, reported in Tsutaya et al. (2016).
unseiji_ST61_M1unseiji_ST61_M1
unseiji_ST61_C is a list containing 6 elements.
rt.y |
y-value for the root tip (i.e., length [mm] of the dentin). |
ecj |
x- and y-coordinates of enamel-cement junction. Dentin horn is placed on the geometric origin, and root tip is placed on the y-axis with a positive value. |
section.y |
y-values for the horizontal sections. |
t.start and t.end |
The age at the start and end of dentin formation, respectively. |
section |
Data frame with 16 dentin serial sections (rows) and 3 variables (columns) of assigned midpoint age with equal temporal division, carbon, and nitrogen isotope ratios, named age, d13C, and d15N, respectively. Stable isotope ratios of the last 3 sections (i.e., row number 14-16) should be excluded because of the porous structure of inner dentin.
|
See detail for Tsutaya et al. (2016).
Tsutaya T, Miyamoto H, Uno H, Omori T, Gakuhari T, Inahara A, Nagaoka T, Abe M, Yoneda M. 2016. From cradle to grave: multi-isotopic investigations on the life history of a higher-status female in the Edo period Japan. Anthropological Science 124:185–197. DOI: 10.1537/ase.161029.