| Title: | Estimating the Age using Auricular Surface by DNE |
| Version: | 4.5 |
| Maintainer: | Jisun Jang <jisun.jang.19@ucl.ac.uk> |
| Description: | The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), and principal component logistic regression analysis (PCLR) methods, principal component regression analysis with Southeast Asian (A_PCR), and principal component regression analysis with multipopulation (M_PCR). The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan, and the skeletal collection at Khon Kaen University (KKU) Human Skeletal Research Centre (HSRC), housed in the Department of Anatomy in the Faculty of Medicine at KKU in Khon Kaen. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Depends: | R (≥ 2.10) |
| LazyData: | true |
| Imports: | dplyr, MASS, molaR, nnet, Rvcg |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2025-05-03 14:23:43 UTC; jangj |
| Author: | Jisun Jang [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2025-05-03 22:30:05 UTC |
JSDNE: Estimating the Age using Auricular Surface by DNE
Description
The age is estimated by calculating the Dirichlet Normal Energy (DNE) on the whole auricular surface and the apex of the auricular surface. It involves three estimation methods: principal component discriminant analysis (PCQDA), and principal component logistic regression analysis (PCLR) methods, principal component regression analysis with Southeast Asian (A_PCR), and principal component regression analysis with multipopulation (M_PCR). The package is created with the data from the Louis Lopes Collection in Lisbon, the 21st Century Identified Human Remains Collection in Coimbra, and the CAL Milano Cemetery Skeletal Collection in Milan, and the skeletal collection at Khon Kaen University (KKU) Human Skeletal Research Centre (HSRC), housed in the Department of Anatomy in the Faculty of Medicine at KKU in Khon Kaen.
Author(s)
Maintainer: Jisun Jang jisun.jang.19@ucl.ac.uk
A_PCR_Test
Description
A_PCR_Test is the test set of the A_PCR model. It consists of Age, MeanDNE.Apex, Proportion.DNEunder0.0001, Proportion.DNEover0.6, IQRDNE.Whole. The number of rows is 66.
Usage
A_PCR_Test
Format
An object of class data.frame with 66 rows and 5 columns.
A_PCR_Train
Description
A_PCR_Train is the train set of the A_PCR model. It consists of Age, MeanDNE.Apex, Proportion.DNEunder0.0001, Proportion.DNEover0.6, IQRDNE.Whole. The number of rows is 269.
Usage
A_PCR_Train
Format
An object of class data.frame with 269 rows and 5 columns.
Estimating the age using A_PCR method
Description
A_PCR method is the principal component linear regression analysis with Southeast Asian (A_PCR) method using the Dirichlet Normal Energy (DNE). The function automatically calculates the DNE on the auricular surface It provides the estimated age and standard errors (SE, 9.0yrs).
Usage
A_PCR_result(x, y)
Arguments
x |
the name of inputted ply file of the whole auricular surface |
y |
the name of inputted ply file of the apex of the auricular surface |
Value
estimated result gets printed to the console
Surface mesh of apex of auricular surface.
Description
Surface mesh of apex of auricular surface.
Usage
data(Apex)
Format
An object of class mesh3d of length 4.
Examples
PCQDA_output <- PCQDA_result(WholeSurface,Apex)
PCR_output <- PCR_result(WholeSurface,Apex)
PCLR_output <- PCLR_result(WholeSurface,Apex)
M_PCR_Train
Description
M_PCR_Train is the test set of the M_PCR model. It consists of Age,MeanDNE.Apex,MedianDNE.Apex,MeanDNE.Convex,MeanDNE.Concave,Proportion.DNEunder0.0001,Population. The number of rows is 272.
Usage
M_PCR_Test
Format
An object of class data.frame with 272 rows and 7 columns.
M_PCR_Train
Description
M_PCR_Train is the train set of the M_PCR model. It consists of Age, MeanDNE.Apex, MedianDNE.Apex, MeanDNE.Convex, MeanDNE.Concave, Proportion.DNEunder0.0001, Population. The number of rows is 953.
Usage
M_PCR_Train
Format
An object of class data.frame with 953 rows and 7 columns.
Estimating the age using M_PCR method
Description
M_PCR method is the principal component linear regression analysis with multi-population (M_PCR) method using the Dirichlet Normal Energy (DNE). The function automatically calculates the DNE on the auricular surface It provides the estimated age and standard errors (SE, 10.2yrs).
Usage
M_PCR_result(x, y)
Arguments
x |
the name of inputted ply file of the whole auricular surface |
y |
the name of inputted ply file of the apex of the auricular surface |
Value
estimated result gets printed to the console
PCLR_Test
Description
PCR_Train is the test set of the PCR model. It consists of Age, Cluster1, MeanDNE.Apex, TotalDNE.TotalPolygonFaces, MedianDNE.Whole, IQRDNE.Whole and MeanDNE.Convex. The number of rows is 191.
Usage
PCLR_Test
Format
An object of class data.frame with 191 rows and 7 columns.
PCLR_Train
Description
PCLR_Train is the train set of the PCR model. It consists of Age, Cluster1, MeanDNE.Apex, TotalDNE.TotalPolygonFaces, MedianDNE.Whole, IQRDNE.Whole and MeanDNE.Convex. The number of rows is 699.
Usage
PCLR_Train
Format
An object of class data.frame with 699 rows and 7 columns.
Estimating the age using DNE_PCLR method
Description
DNE_PCLR method is the principal component logistic regression analysis (PCLR) method using the Dirichlet Normal Energy (DNE). This method involves 2 age groups to distinguish if the specimen is over 63 or under 67. The function automatically calculates the DNE on the auricular surface. It provides the estimated age group and age range of the estimated age group.
Usage
PCLR_result(x, y)
Arguments
x |
the name of inputted ply file of the whole auricular surface |
y |
the name of inputted ply file of the apex of the auricular surface |
Value
estimated result gets printed to the console
PCQDA_Test
Description
PCQDA_Test is the test set of the PCQDA model. It consists of Cluster2, Age, MeanDNE.Apex, TotalDNE.TotalPolygonFaces, Proportion.DNEunder0.0001, and Proportion.DNEover0.6. The number of rows is 186.
Usage
PCQDA_Test
Format
An object of class data.frame with 186 rows and 6 columns.
PCQDA_Train
Description
PCQDA_Train is the train set of the PCQDA model. It consists of Cluster2, Age, MeanDNE.Apex, TotalDNE.TotalPolygonFaces, Proportion.DNEunder0.0001, and Proportion.DNEover0.6. The number of rows is 704.
Usage
PCQDA_Train
Format
An object of class data.frame with 704 rows and 6 columns.
Estimating the age using DNE_PCQDA method
Description
DNE_PCQDA method is the principal component quadratic discriminant analysis (PCQDA) method using the Dirichlet Normal Energy (DNE). This method involves 4 age groups. The function automatically calculates the DNE on the auricular surface. It provides the estimated age group and age range of the estimated age group.
Usage
PCQDA_result(x, y)
Arguments
x |
the name of inputted ply file of the whole auricular surface |
y |
the name of inputted ply file of the apex of the auricular surface |
Value
estimated result gets printed to the console
PCR_Test
Description
PCR_Train is the test set of the PCR model. It consists of Age, MeanDNE.Apex, IQRDNE.Apex, TotalDNE.TotalPolygonFaces, MeanDNE.Convex and Proportion.DNEunder0.0001. The number of rows is 188.
Usage
PCR_Test
Format
An object of class data.frame with 188 rows and 6 columns.
PCR_Train
Description
PCR_Train is the train set of the PCR model. It consists of Age, MeanDNE.Apex, IQRDNE.Apex, TotalDNE.TotalPolygonFaces, MeanDNE.Convex and Proportion.DNEunder0.0001. The number of rows is 702.
Usage
PCR_Train
Format
An object of class data.frame with 702 rows and 6 columns.
Estimating the age using PCR method
Description
DNE_PCR method is the principal component linear regression analysis (PCR) method using the Dirichlet Normal Energy (DNE). The function automatically calculates the DNE on the auricular surface It provides the estimated age and standard errors (SE).
Usage
PCR_result(x, y)
Arguments
x |
the name of inputted ply file of the whole auricular surface |
y |
the name of inputted ply file of the apex of the auricular surface |
Value
estimated result gets printed to the console
Surface mesh of whole auricular surface.
Description
Surface mesh of whole auricular surface.
Usage
data(WholeSurface)
Format
An object of class mesh3d of length 4.
Examples
PCQDA_output <- PCQDA_result(WholeSurface,Apex)
PCR_output <- PCR_result(WholeSurface,Apex)
PCLR_output <- PCLR_result(WholeSurface,Apex)