Sample evaluation

Source: R/BAMSAURbff.R

This function can be used to evaluate the viability of a sample for use as a reference population. It provides information on the accuracy of a sample using LOOCV, as well as details on the regression analyses performed on the sample.

BAMSAUR.bff(
  data,
  interval = "prediction",
  level = 0.68,
  varmod.method = "earth",
  nfold = n - 1,
  ncross = 3,
  ...
)

Arguments

data

Data frame containing one column for ages-at-death and a second column for the associated wear scores.
interval

Character. The type of age interval used. Can be either "prediction" or "confidence" intervals. Confidence intervals are not available for 'earth' class objects.
level

Numeric. Determines level of confidence or prediction intervals. Can be any number between 0 and 1 (not inclusive), but 0.68, 0.90, or 0.95 is recommended. To run the function without intervals, enter 0.
varmod.method

Character. Method for creating the variance model in the 'earth' function. See 'earth' package for more details.
nfold

Numeric. The number of folds to be used in the cross validation.
ncross

Numeric. Number of cross validations. Default is set at 3 to reduce computation time.
...

Additional arguments can be passed to the 'earth' function. See ?earth for more details.

Value

The function automatically returns a summary of the analysis, with the overall accuracy, the average age range (precision), the sum of squares of the predictive residuals (PRESS), the R-squared value, AIC(c), and BIC. It also includes a list containing the following items:

lin.plot

a plot of the linear regression with prediction/confidence intervals

quad.plot

a plot of the quadratic regression with prediction/confidence intervals

cub.plot

a plot of the cubic regression with prediction/confidence intervals

mars.plot

a plot of the MARS with prediction/confidence intervals

linear

class 'lm' object from the linear regression analysis.

quadratic

class 'lm' object from the quadratic regression analysis.

cubic

class 'lm' object from the cubic regression analysis.

mars

class 'earth' object from the MARS analysis.

lin.data

the data from the linear LOOCV analysis.

quad.data

the data from the quadratic LOOCV analysis.

cub.data

the data from the quadratic LOOCV analysis.

mars.data

the data from the MARS LOOCV analysis.

accuracy

A table with the percentage of estimates whose age ranges contain the actual age, the percentage of estimates within 1 year of the actual age, and within 2 years of the actual age.

Details

BAMSAUR.bff uses the "lm" and "earth" functions for the regression analyses. It automatically provides the accuracy of the sample being evaluated, based on whether the actual age of an individual falls within the estimated age range from linear and quadratic regression analyses (using the described LOOCV method). It also provides the mean of the estimated age ranges, as an indicator of method precision, as well as the predicted residual error sum of squares (PRESS), the r-squared values, Akaike information criterion (AIC; AICc for sample sizes below 80), Bayes information criterion(BIC), and generalised cross validation (GCV).

Note

If the slope of the regression is not statistically different (2 standard deviations) from 0 or 1, a warning message will appear.

See also

earth

lm

Examples

#the following expression evaluates the sample with 68% prediction intervals as age ranges
MBex <- BAMSAUR.bff(MBsimple)

#> Calculating...
#> 
#> Linear model
#> R-squared:	0.93
#> PRESS:		111.12
#> AIC:		183.63
#> BIC:		189.37
#> Accuracy:	84%
#> Average range:	+- 1.5 years
#> 	(min, max: 1.48, 1.51)
#> 
#> Quadratic model
#> R-squared:	0.95
#> PRESS:		77.22
#> AIC:		166.81
#> BIC:		173.57
#> Accuracy:	82%
#> Average range:	+- 1.25 years
#> 	(min, max: 1.24, 1.3)
#> 
#> Cubic model
#> R-squared:	0.95
#> PRESS:		77.67
#> AIC:		167.85
#> BIC:		176.04
#> Accuracy:	84%
#> Average range:	+- 1.26 years
#> 	(min, max: 1.24, 1.39)
#> 
#> MARS
#> R-squared:	0.95
#> PRESS:		89.07
#> GCV:		1.67
#> Accuracy:	78%
#> Average range	+- 1.24 years
#> 	(min, max: 0.79, 1.56)
#the following code accesses the quadratic plot
MBex$quad.plot