Annals of Human Biology

ISSN: 0301-4460 (Print) 1464-5033 (Online) Journal homepage: http://www.tandfonline.com/loi/iahb20

Multivariate cumulative probit for age estimation

using ordinal categorical data
Lyle W. Konigsberg
To cite this article: Lyle W. Konigsberg (2015) Multivariate cumulative probit for age
estimation using ordinal categorical data, Annals of Human Biology, 42:4, 368-378, DOI:
10.3109/03014460.2015.1045430
To link to this article: http://dx.doi.org/10.3109/03014460.2015.1045430

Published online: 20 Jul 2015.

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http://informahealthcare.com/ahb
ISSN: 0301-4460 (print), 1464-5033 (electronic)
Ann Hum Biol, 2015; 42(4): 368378
! 2015 Informa UK Ltd. DOI: 10.3109/03014460.2015.1045430

RESEARCH PAPER

Multivariate cumulative probit for age estimation using ordinal

categorical data
Lyle W. Konigsberg

Downloaded by [109.175.205.64] at 15:30 03 December 2015

Department of Anthropology, University of Illinois, Urbana, IL, USA

Abstract

Keywords

Background: Multivariate ordinal categorical data have figured prominently in the age
estimation literature. Unfortunately, the osteological and dental age estimation literature is
often disconnected from the statistical literature that provides the underpinnings for rationale
analyses.
Aim: The aim of the study is to provide an analytical basis for age estimation using multiple
ordinal categorical traits.
Subjects and methods: Data on ectocranial suture closure from 1152 individuals are analysed in a
multivariate cumulative probit model fit using a Markov Chain Monte Carlo (MCMC) method.
Results: Twenty-six parameters in a five variable analysis are estimated, including the 10 unique
elements of the five  five correlation matrix. The correlation matrix differs substantially from
the identity matrix one would assume under conditional independence among the sutures.
Conclusion: While the assumption of conditional independence between traits greatly simplifies
the use of parametric models in age estimation, this assumption is not a necessary step.
Further, in the analysis discussed here there are considerable residual correlations between
ectocranial suture closure scores even after regressing out the effect of age.

Forensic anthropology, Markov chain Monte

Carlo, paleodemography

Introduction
Following the publication of the Rostock Volume on
paleodemography (Hoppa & Vaupel, 2002) and particularly
the contained chapter on transition analysis (Boldsen
et al., 2002), there has been considerable interest in applying
parametric models to ordinal categorical data (Cardoso et al.,
2010; DiGangi et al., 2009; Franklin & Flavel, 2015; Godde
& Hens, 2012, 2015; Gregersen et al., 2006; Kimmerle et al.,
2008; Konigsberg et al., 2008; Langley-Shirley & Jantz,
2010; Milner & Boldsen, 2012; Passalacqua, 2013; Prince
et al., 2008; Ros et al., 2008; Shirley & Jantz, 2011;
Thevissen et al., 2010). There had certainly been considerable historical precedent for such age estimation models
(Fanning, 1961; Holman and Jones, 1998; Konigsberg &
Holman, 1999; Kuykendall et al., 1992; Moorrees et al.,
1963a,b), but the new millennium brought with it the
realisation that the analysis of ordinal categorical age
indicators could become routine. Now that transition
analysis has become more common it will be useful to
review the method with a particular eye to applications
involving multiple indicators.
The following makes extensive use of ectocranial suture
closure data to demonstrate some of the properties of age

Correspondence: Dr Lyle W. Konigsberg, PhD,

Department of
Anthropology, MC-148, 109 Davenport Hall, 607 S. Mathews Ave.,
University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
E-mail: lylek@illinois.edu

History
Received 22 April 2015
Accepted 23 April 2015
Published online 20 July 2015

estimation from multiple ordinal categorical data. Ectocranial

suture closure was selected not because this is a particularly
useful aspect of morphology for estimating ages, but rather
because it is rather uninformative regarding the age of the
individual. When the correlation between age and one or more
indicators of age is high, then there is little practical
difference in estimated ages from different methods. From a
Bayesian standpoint, when the correlation between age and the
indicators is high, the likelihood (the information about age
from the indicators) will dominate the prior distribution for
age. Thus, for continuous indicators such as long bone lengths,
inverse calibration (regression of age on long bone length in
juveniles) and classical calibration (regression of long bone
length on age followed by solving for age) will provide very
similar results. However, for indicators that are only loosely
related to age there can be a considerable difference between
Bayesian methods (such as inverse calibration) and maximum
likelihood methods (such as classical calibration).

The sample
The following analysis makes use of ectocranial suture
closure data from 1152 individuals. Of these individuals,
363 are males from McKern & Stewarts (1957) Korean War
dead study and the data consist of observations extracted from
Keysort Card No. 1. The remaining 789 individuals are
males and females from the Robert J. Terry Anatomical
Collection (Hunt & Albanese, 2005). For the McKern and
Stewart data ages-at-death were obtained by converting the

Age estimation using ordinal categorical data

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DOI: 10.3109/03014460.2015.1045430

birth and death dates to decimal years (Pearl & Miner, 1932;
McVarish, 1962; Toops, 1922) and subtracting the birth from
the death date. For the Terry Collection the recorded
chronological age in years was used as the age-at-death.
Assuming a Gompertz mortality model (Finch & Pike, 1996;
Pletcher, 1999; Wilson, 1993) starting at age 15 years, the a3
and b3 parameters for the combined Korean War dead and
Terry samples are 0.025 and 0.018, respectively. The
numbering of the two parameters is in reference to the third
(senescent) component of the Siler mortality model (Gage,
1991; Gage & Dyke, 1986; Siler, 1979; Wood et al., 2002).
The analyses in this paper make use of five suture sites,
these being the mid-lambdoid suture, the sagittal/lambdoid
suture at lambda, the anterior part of the sagittal suture, the
coronal/sagittal suture at bregma and the sphenofrontal
suture. The McKern and Stewart data was originally coded
by them as 0 for open, 1 for one-quarter closed, 2 for
half closed, 3 for three-quarters closed and 4 for closed.
The Terry sample data were collected using Meindl and
Lovejoys (1985) scale of open, minimal, significant
and closed. Given the definitions of stages in McKern and
Stewart and in Meindl and Lovejoy, the latters open
corresponds to McKern and Stewarts 0, minimal corresponds to McKern and Stewarts 1 and 2, significant
corresponds to McKern and Stewarts 3 and closed
corresponds to their 4. For the first four sutures a further
reduction was made so that these sutures were scored as
open, minimal and significant through closed. The
fifth suture was maintained as four separate stages. The
collapsed scoring for the first four sutures was based on
goodness-of-fit tests for the cumulative probit model
(described below in the section on Does the cumulative
probit model fit?).

Methods using sums of scores

A common approach to examining multivariate age indicator data uses the sum of scores for the individual traits under
study. The simplest of these methods simply sums the ordinal
scores represented as integers across the traits (Buckberry &
Chamberlain, 2002; Falys & Prangle, 2015; Gilbert &
McKern, 1973; McKern & Stewart, 1957; Meindl &
Lovejoy, 1985). This approach is problematic on a number
of grounds, not least of which is that the scaling of each trait
with respect to the remaining traits is not considered. The
more complicated method does use optimal scaling to find the
best set of scores that can be summed across traits (Demirjian
et al., 1973; Tanner et al., 1975). Although this latter
approach has been used to study maturation, it has not
previously been applied to study senescence.
However, the optimal scaling approach is also not wellsuited to age estimation applications because: (1) optimal
scaling cannot be applied to single traits, (2) missing data are
not allowed, (3) probabilities of being in particular stages at
given ages cannot be calculated and (4) the relationship
among traits is not modelled. Because of these problems, the
following analysis only considers parametric models for
ordinal categorical data.
Before turning to these parametric models, it will be useful
to examine the typical osteological approach of summing
across ordinal scores and then giving the distribution of ages

369

across these composite scores. As mentioned previously, this

method has been in use since at least the 1950s (McKern &
Stewart, 1957) and it continues to be used today (Falys &
Prangle, 2015). In the dental age estimation literature it is not
unusual to find studies that give the distributions of age (or
summary statistics for these distributions) conditioned on
stage (Mitchell et al., 2009; Peiris et al., 2009; Roberts
et al., 2008). As pointed out in various publications
(Bocquet-Appel & Masset, 1982, 1985, 1996; Konigsberg &
Frankenberg, 1992; Konigsberg et al., 2008), the approach of
conditioning age on stage carries with it the problem that it
produces an age estimation method that is in part dependent
on the age structure of the reference sample. This dependency
can be removed by having a reference sample with a uniform
age distribution. The problem is much less of a concern when
there is a strong relationship between age and the indicators. Neither of these conditions is true for the cranial suture
example examined here.
A simulation approach can be used to demonstrate the
problems inherent with conditioning age on stage. Consider a
simulated second sample which ages in the same way as the
actual sample of 1152 individuals, but which has a very
different age structure. Specifically, this second sample can be
simulated using a3 and b3 Gompertz parameter values of 0.01
and 0.06. The section near the end of this paper (Using
multivariate cumulative probit to estimate age) explains the
simulation procedure. Table 1 contains a comparison of
summary statistics for age across composite scores from the
actual sample of 1152 and from the simulated sample. The
median ages within composite scores show particularly
clearly that the distribution of age within stages is influenced
by the overall age structure of the sample. Consequently, the
conditioning needs to be reversed so that stages are made
conditional on age. From a biological standpoint, such an
approach makes much more sense as it makes the age
indicators dependent on age.

The cumulative probit model as transition analysis

The cumulative probit model has been used very extensively
in applications to ordinal categorical data (Aitchison &
Silvey, 1957; Becker & Kennedy, 1992; Daykin & Moffatt,
Table 1. Count of number of cases in composite scores, mean age,
standard deviation of age, median age and age range within composite
scores. The table shows both the actual data and simulated data under a
Gompertz model (see text for Gompertz parameter values).
Composite
Actual data
56
78
910
1112
1314
1516
Simulated data
56
78
910
1112
1314
1516

Count

Mean

SD

Median

Range

313
150
116
162
169
242

26.5
33.7
41.1
47.0
49.0
56.8

12.1
15.7
17.3
19.7
18.2
17.6

22.0
28.0
36.0
45.0
48.0
55.5

1495
17.786
19102
17101
17.695
21.795

277
151
125
160
166
273

33.3
37.9
41.4
43.4
46.3
50.0

12.5
11.8
12.7
12.3
12.6
11.1

31.1
37.8
41.2
43.3
45.8
50.7

15.173.6
16.368.7
15.673.7
15.475.5
16.382.5
19.377

L. W. Konigsberg

Ann Hum Biol, 2015; 42(4): 368378

1.0
0.8
0.6

Probability

0.4
0.2
0.0
50

50

100

150

Age

Figure 1. Cumulative probit curves for closure of the mid-lambdoid

suture. The braces show the probabilities that a 50 year-old would be in
each of the three states for this suture.

0.012

Normal transition distributions

0.010

12
23

0.008

where y is the ordinal scoring of 1 (for open), 2 (for

minimal) and 3 (for significant through closed), x is
age and  is the standard normal integral for the lower
tail. Figure 1 shows these equations plotted from age 50
to 150 years. Also shown in Figure 1 is an example of using the
probit analysis to find the probability that a 50 year old would
be in each of the three states. The probability of being in
the first state comes directly from 1:037
0:031  50 0:513 0:304, the probability of being
in
the
second
state
comes
from
1:754
 0:031  50  0:304 0:277 and the probability of
being in the third state is 1  1:754  0:031
50 0:419. Note that the probability that a 50 year old is
in any of the closure states is 0:304 0:277 0:419 1:0.
In the transition analysis paradigm, the regression parameters from the probit analysis are converted to the means and
common standard deviation for moving (transitioning)
between adjacent stages. The means are equal to the
intercepts divided by the slope, or 1:037=0:031 33:45
and 1:754=0:031 56:58, while the common standard
deviation is the inverse of the slope, or 1=0:031 32:26.

0.581 0.304 = 0.277

(1.037 0.031 Age)

0.006

(1.754 0.031 Age)

0.304

Density

Py 1j x 1:037  0:031  x

1.0 0.581 = 0.419

0.004

Py  2j x 1:754  0:031  x

These transition distributions are graphed in Figure 2.

Figure 2 shows some of the apparent problems of using
cumulative ordinal probit analysis with a single slope
(or equivalently a common standard deviation). First, the
model is not constrained in any way so as to exclude the
possibility of transitions to higher stages before birth. For
example, in the current example,  15% of the sample is
predicted to have moved out of the open stage and into the
minimal closure stage before birth. The model is also
unrealistic in that it assumes a constant standard deviation for
transitions between all adjacent categories. Boldsen et al.
(2002) dealt with this latter problem by using a continuation
ratio approach, while Konigsberg & Herrmann (2002)
suggested using unrestricted cumulative probit. Neither of

0.002

2002; Fanning, 1961; Johnson & Albert, 1999; Konigsberg &

Hens, 1998; Konigsberg & Herrmann, 2002; Konigsberg &
Holman, 1999; Konigsberg et al., 2008; McKelvey &
Zavoina, 1975; Moorrees et al., 1963a,b; Terza, 1985).
Although the cumulative logit model has also been used for
age estimation (Acharya et al., 2014; Boldsen et al., 2002;
Hillewig et al., 2013; Thevissen et al., 2010), it is not
considered here because logit and probit give very similar
results. Logit was previously often favoured over probit,
because the latter required numerical integration of the
standard normal while logit required no such integration. In
the modern era of statistical computing, the necessity for
unidimensional numerical integration is no longer a rational
basis for selecting one method over the other. Importantly,
cumulative probit can be easily extended to the multivariate
case using the multivariate normal distribution. Although
cumulative logit can also be extended to the multivariate case
using the multivariate logistic distribution, this is a much
more difficult enterprise.
To present the model, first consider only closure of the
mid-lambdoid suture with closure scored as open, minimal and significant or closed. The cumulative probit
model can be fit in R (R Core Team, 2014) using polr
from the package MASS (Venables & Ripley, 2002),
clm from the package ordinal (Christensen, 2014) or
vglm from the package VGAM (Yee, 2010). The model
can also be fit using Markov Chain Monte Carlo (MCMC)
estimation with MCMCoprobit from the package
MCMCpack (Martin et al., 2011) or using the script
from page 222 of Lynchs (2007) text. MCMC will be covered
for multiple traits in a following section, so for now the focus
is on direct estimation of the cumulative probit by maximum
likelihood estimation. Using any of the three R packages
will lead to estimating the slope and two intercepts that can be
used in the following equations:

0.000

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370

50

50

100

150

Age

Figure 2. Re-drawing of Figure 1 using transition distributions with a

common standard deviation.

Age estimation using ordinal categorical data

DOI: 10.3109/03014460.2015.1045430

Table 2. Goodness-of-fit p values for the four- and three-stage scorings

of suture closure in cumulative (log) age probit models and pseudo R2
values between (log) age and the indicator. For the pseudo R2 values the
first four sutures were scored using three stages and the last suture was
scored using the full four stages.

0.020

Log normal transition distributions

0.010
0.005

Density

0.015

12
23

0.000
0

4-stages

3-stages

pseudo R2

mid-lambdoid
Lambda
anterior sagittal
Bregma
sphenofrontal

50.0001
50.0001
50.0001
0.0006
0.4394

0.5618
0.2190
0.1088
0.8213

0.290
0.294
0.218
0.327
0.346

35.0

20

40

60

80

100

Age

Downloaded by [109.175.205.64] at 15:30 03 December 2015

Suture

Does the cumulative probit model fit and how strong

is the relationship of the age indicator to age?

19.2
10.5

371

Figure 3. A re-drawing of the model depicted in Figure 2 but using lognormal transitions rather than normal transitions. The modal age for the
first transition (19.2) is indicated, as are the left and right boundaries for
the 50% highest posterior density region.

these approaches deals directly with the problem of restricting

the transition distributions so that transitions cannot have
occurred before birth. The simplest solution is to assume that
the transitions have a log-normal distribution, as was done in
Fanning (1961) and Moorrees et al. (1963a,b). In their case
they also added 0.75 years as a conception correction to age
because some early dental transitions could occur before birth.
In the example here, log-normal transitions can be fit by
doing the cumulative probit regression on the natural
logarithm of age. This produces intercepts of 4.908 and
5.649 and a slope of 1.423, which give log means of
4:908=1:423 3:449 and 5:649=1:423 3:970 and a log
standard deviation of 1=1:423 0:703. Figure 3 plots these
two log-normal distributions along with the modal age of
transition (19.2 years) and the 50% highest density region
(from 10.535.0 years) for the first transition. These parameters are included with the first transition to emphasise that
the log mean and log standard deviation provide all of the
relevant information to characterise the log-normal distribution. Authors often choose to exponentiate the log-means
(Konigsberg et al., 2008; Langley-Shirley & Jantz, 2010;
Shirley & Jantz, 2011; Godde & Hens, 2012; Lottering et al.,
2013), which produces the median transition age, but the log
mean and log standard deviation can also be used to find the
mode (as in Figure 3) and the mean on the raw scale
(Shackelford et al., 2012). The log mean  and log
standard deviation  can also be used to find the (raw
scale) standard deviation
around the mean as exp2 2
1
2 2
 exp2   . This is not a particularly useful measure
as it is the average squared deviation around a point to the
right of the mode. A very few authors (Godde & Hens, 2012)
have apparently erroneously taken the anti-log of the log-scale
common standard deviation for transitions or listed the logscale standard deviation with the (raw-scale) median (Godde
& Hens, 2015). This number has no meaning in the raw (antilog) scale.

One question that often arises in analyses of age indicators

is whether the selected parametric model is appropriate for
the data. In a number of instances researchers have abandoned
parametric approaches in favour of non-parametric methods
for age estimation, specifically using the Sugeno fuzzy
integral (Anderson et al., 2010) and kernel densities (Love
& Muller, 2002; Lucy et al., 2002; Muller et al., 2002;
Roksandic & Armstrong, 2011). Because there is a specification test for the cumulative probit and logit (Glewwe, 1997;
Johnson, 1996; Weiss, 1997), it is possible to directly test
whether the logit and/or the probit give an adequate fit to the
data. Table 2 contains the p values from this goodness-of-fit
test using log-age cumulative probit. The first column
contains p values for the four-stage scoring of open,
minimal, significant and closed, while the next
column contains p values for the reduced scoring where
significant and closed are combined. The table shows
that only for the sphenofrontal suture can the four-stage
scoring be retained. Importantly, the results from this table
show that there is no reason to abandon the parametric model
in analysing the closure of these particular sutures.
An additional question that often arises is about the
strength of the relationship between the age indicator and
age. To answer this, Table 2 also contains pseudo R2
values calculated following Cragg and Uhler (1970). These
values were obtained using Jackmans (2014) pscl package. These pseudo R2 values have the same interpretation as
in linear regression, save for the fact that they are scaled
against the maximum possible value. The highest pseudo R2
value from Tables 3 and 4 is only 0.346, meaning that only
 35% of the variation in this particular suture (the
sphenofrontal) can be explained by (log) age. It is clear that
ectocranial suture closure is relatively uninformative with
regard to age, a point made in the introduction to this paper
and extensively in the existing literature.

Multivariate cumulative probit as latent trait

analysis
While the transition analysis paradigm is useful for
understanding univariate parametric models for ordinal categorical data, a latent trait approach is more useful for
understanding multivariate forms. The univariate cumulative
probit can be easily understood as a latent trait analysis, so
this section first re-examines mid-lambdoid suture closure

372

L. W. Konigsberg

Ann Hum Biol, 2015; 42(4): 368378

Table 3. Slopes (zero-intercept model) and thresholds for the multivariate cumulative probit model using five sutures. T1 is the threshold
value between open and minimal, T2 is the threshold value between
minimal and significant and T3 is the threshold value between
significant and closed. For the first four sutures T2 and T3 are
shown as equal because significant and closed were not distinguished.
Suture

Slope

T1

T2

T3

mid-lambdoid (S1)
lambda (S2)
anterior sagittal (S3)
bregma (S4)
sphenofrontal (S5)

1.457
1.414
1.142
1.556
1.734

5.045
4.721
3.555
5.442
6.369

5.775
5.325
4.086
6.117
6.713

5.775
5.325
4.086
6.117
7.191

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Table 4. Residual correlations between the five sutures

after accounting for log-age in the cumulative probit
regression.

S2
S3
S4
S5

S1

S2

S3

S4

0.837
0.699
0.656
0.466

0.785
0.708
0.441

0.825
0.506

0.564

from the latent trait perspective before extending the analysis

to include multiple suture sites. In latent trait analysis the
ordinal categorical trait is assumed to be produced by an
unobserved underlying continuous trait that is discretised by
thresholds. As such, this model is very similar to the multiple
threshold model used to study ordered categorical nonmetric osteological or dental traits. The latent trait model is
related to the cumulative probit model in that the probit
regression determines the mean for the normally distributed
latent trait. As a consequence, the distribution for the latent
trait is assumed to be a normal with the mean from the probit
regression on age (or log age) and a variance of 1.0. The
probit regression intercepts then form the thresholds. This is
shown in Figure 4(a) with the latent trait distributions shown
at ages of 20, 40 and 60 years. Note that the thresholds are
drawn at 4.908 and 5.649, these being the intercepts from the
cumulative probit analysis. The curve for the mean latent
score regressed on age has a slope of 1.423 when plotted on
the logarithm of age scale (again, from the cumulative probit
regression) and has an intercept of zero on the log scale (i.e.
an age of 1 year on the raw scale of age). Figure 4(b) shows an
alternative parameterisation where the first threshold is
subtracted so that the first threshold is at 0.0 and the probit
regression line has an intercept of 4.908 at age 0 on the log
scale (again, an age of 1 year on the raw scale of age). This
latter parameterisation is common in some of the statistical
literature (Albert & Chib, 1993; Johnson & Albert, 1999;
Lynch, 2007), but it is by no means universal.
To extend the cumulative probit to the multivariate case all
that needs be done is to include estimation of the (Pearson)
correlations between the latent traits. First consider just the
bivariate extension using the mid-lambdoid suture and
the sphenofrontal suture. The likelihood can be written
across the two (marginal) regressions of the latent traits on
age with the inclusion of the correlation coefficient. The
likelihood, therefore, involves calculation of bivariate normal

integrals and the optimisation must be constrained so that the

thresholds are ordered and so that the correlation coefficient
is between 1 and 1. This optimisation can be done in R
using the package alabama (Varadhan, 2012). This leads to
thresholds for the mid-lambdoid suture of 4.918 and 5.655
with a slope on the log scale of 1.425, thresholds for the
sphenofrontal suture of 6.205, 6.551 and 7.031, with a slope
on the log scale of 1.694 and a correlation coefficient of
0.458. Figure 5 shows a plot of the 10%, 20%, 30%, 40% and
50% isodensity ellipses for the two latent traits at ages 20 and
60 years as well as the thresholds for the two traits. Extension
beyond the bivariate case becomes numerically difficult
because a multivariate normal density must be integrated
numerous times between thresholds that are moving during
the optimisation process. Instead of using numerical integration and optimisation for the multivariate case, a Markov
Chain Monte Carlo (MCM) method given in Lynch (2007)
can be used. To circumvent a potentially long burn-in
phase univariate cumulative probit analysis can be used to
find good starting values for thresholds and slopes. Similarly,
each bivariate correlation can be found holding the two
marginal cumulative probit parameters at their estimated
values and these can then be used as starting values for the
five  five correlation matrix. Fifty thousand iterations of the
MCMC were run, retaining every 50th iteration for a total of
1000 retained iterations. Tables 3 and 4 contain the mean
MCMC values from these 1000 retained iterations.

A comment on the maximum likelihood point

estimate of age under an assumption of
conditional independence
Before more generally showing how the parameters from
Tables 3 and 4 can be used to estimate ages, it will be useful
to examine the effect on the maximum likelihood estimate of
age when there is a lack of conditional independence. As
Lucy et al. (2002) note, conditional independence in the
age estimation context refers to the case where all of the
correlations between age indicators are due to their
correlations with age. Were this true, then the residual
correlations (after accounting for age) between sutures in
Table 4 would be zero. As this is clearly not the case, it is
important to understand the effect of assuming conditional
independence when the assumption is unwarranted. Milner
and Boldsen (2012: 100) have written that: Point estimates
of age at death are not affected by the lack of conditional
independence, but that is not true of confidence limits. This
statement, which is not referenced to the literature, appears to
be based on large sample asymptotics. Here large sample
refers to the number of age indicators and not to the sample
size of the known-age collection. As the number of indicators
in osteological studies is typically fairly small, one can find
examples where both point estimates and confidence intervals
are affected by a lack of conditional independence. Figure 6
shows posterior densities of age under a uniform prior from
ages 15120 years. The example shown in Figure 6 is for an
individual with their mid-lambdoid suture, sagittal/lambdoid
suture at lambda, anterior part of the sagittal suture and
coronal/sagittal suture at bregma all closed, but their
sphenofrontal suture open. The labelled dashed lines show

Age estimation using ordinal categorical data

DOI: 10.3109/03014460.2015.1045430

Zero Intercept Parameterisation

(b)

Zero First Threshold Parameterisation

4

(a)

373

significant
minimal
open

Latent trait

Latent trait

significant
minimal
open

10

20

30

40

50

60

10

20

Age

30

40

50

60

Age

Figure 4. (a) Latent trait representation of the model from Figure 3. The curved line represents the regression of the mean latent trait value on the
logarithm of age. This line has an intercept of 0 on the log scale (1 year on the raw scale). (b) A re-drawing of (a) that uses zero for the first threshold
and consequently has a non-zero intercept for the regression line.

0.020

closed

S1 = 3, S2 = 3, S3 = 3, S4 = 3, S5 = 1

independent

S5

dependent

Density

S4

0.005

open

0.010

0.015

S
M

6
5
4

Sphenofrontal suture

Isodensity ellipses for 20 and 60 yearolds

S2

S1

open

significant

minimal

0.000

S3

Downloaded by [109.175.205.64] at 15:30 03 December 2015

Midlambdoid suture

Figure 5. Latent trait representation for the cumulative probit analysis of

the mid-lambdoid and sphenofrontal sutures. Isodensity ellipses are
shown at ages 20 and 60 years for the 10%, 20%, 30%, 40% and 50%
levels.

the posterior densities from the individual sutures, while the

heavy dashed line and the heavy solid line give the posterior
densities where conditional independence is assumed and
where it is not. When conditional independence is assumed
the point estimate for age (rounding to the nearest integer) is
70 years, while it is 46 years when the residual correlations
are taken into consideration. It is important to note that,
while this pattern of suture closure is uncommon in
the reference sample, it is found in 34 out of the 1152
individuals.

20

40

60

80

100

120

Age

Figure 6. Posterior densities of age under a uniform prior from 15120

years. The first four sutures are closed while the last (sphenofrontal) is
open. Labelled dashed lines give the individual sutures, the heavy dashed
line gives the posterior under the assumption of conditional independence and the heavy solid line gives the posterior accounting for residual
correlations between the sutures.

Using multivariate cumulative probit to estimate age

With the estimated parameters now in hand, it will be useful
to examine how these parameters can be applied to estimate
individual ages. Although the problem is still small enough
that it can be handled using numerical integration (with five
dimensions for the sutures and one for age, as was done for
Figure 6), it is useful to continue using an MCMC method.

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374

L. W. Konigsberg

Ann Hum Biol, 2015; 42(4): 368378

The reason for doing so is that ultimately this approach allows

for broader applications. For example, one could combine the
estimation of the cumulative probit parameters in the
reference sample with the estimation of hazard parameters
in a target sample and ultimately with the estimation of
individual posterior densities of age in the target sample. This
addresses one of the problems raised by Bocquet-Appel &
Masset (1996) that oftentimes estimated parameters from a
reference sample are treated as if they were known with
complete certainty.
The following uses a random walk Metropolis-Hastings
sampler to sample from the posterior age distribution for 500
simulated individuals. This approach of using simulated data
is quite different from many previous studies which have
attempted comparisons between a sample with known ages
and the ages estimated from that sample using the indicator
data and a reference sample or a published method (Bedford
et al., 1993; Falys et al., 2006; Godde & Hens, 2012; Hens &
Belcastro, 2012; Hens et al., 2008; Martrille et al., 2007;
Mulhern & Jones, 2005). These types of studies ultimately
become either an indirect test of different rates of senescence
across samples or populations or they reveal flaws in the
assumptions made in particular methods. By using simulated
data it is possible to show the basic properties of multivariate
cumulative probit in a Bayesian setting where prior information is available about the age distribution. Some comment is
necessary here regarding this prior information. There are
essentially two contexts that can provide prior information
about the age distribution. In the forensic setting this prior
information may be obtained from previous casework, from
the age distribution of missing persons or from a passenger
manifest in the case of a closed population mass disaster.
In the paleodemographic setting, the prior age-at-death
distribution ultimately comes as one of the steps in estimating
individual ages (Hoppa & Vaupel, 2002). The term prior is
used here for the age distribution in the paleodemographic
setting only in the sense that this is the presumed age
distribution for an individual skeleton from a target sample
prior to receiving information about age indicators for that
particular skeleton. This prior is actually Seguy et al.s
(2013) posterior for the age-at-death distribution. Their
prior is a weak (Dirichlet) prior for the proportion of
individuals in age classes.
To simulate 500 ages-at-death, a Gompertz mortality
function is used starting at age 15 years with a3 and b3 equal
to 0.001 and 0.1, respectively. By inverting the survivorship
function, one can simulate ages-at-death from a random
uniform deviate U (between zero and one) as:
log1  b3  logU =a3 =b3 15:

With the simulated ages in hand, rmvnorm from the

package mvtnorm (Genz et al., 2014) can be used to
simulate the correlated latent traits given the predicted latent
trait means (conditional on the simulated age). The simulated
latent traits are then compared to the thresholds to determine
suture closure states.
The random walk Metropolis-Hastings sampler uses the
following steps. First, each of the 500 simulated cases was
given a starting value of 50 years for their age. The sampler

was run with a thinning interval of five iterations and the

first 200 of the iterations that would have been saved were
discarded. This means that every case had a burn-in of
1000 iterations, so the starting value that was used should
have virtually no effect on the simulated chains. Second,
latent traits were simulated using predicted means for the
latent traits given the current age and with truncations at the
thresholds given the observed suture closure states. These
truncated multivariate random normal deviates were simulated using rtmvnorm from the package mvtnorm.
Third, the current density value was then found by multiplying the probability density for the simulated latent trait values
(given the current age) with the probability density value for
the current age given the Gompertz parameters. These
Gompertz parameters were assumed to be known at
a3 0:001 and b3 0:1. Fourth, a candidate age was
simulated by drawing from a truncated normal distribution
with the current age as the mean, with a standard deviation of
30 years and with truncation at ages 15 and 120 years. Fifth,
the density value calculated in the third step was also
calculated, but this time using the candidate age value.
Finally, the Metropolis-Hastings step was completed by
forming an acceptance ratio based on the densities from the
third and fifth steps as well as the asymmetry of the jumping
distribution. This asymmetry comes from the boundaries (at
ages 15 and 120) for the jumping distribution. The
probabilities of a forward jump from the current age
value to the candidate value and a backward jump from the
candidate to the current age value were found from truncated
normal densities. The truncated normal density is implemented in dtruncnorm from the package truncnorm
(Trautmann et al., 2014). After the burn-in the sampler was
run for 5000 iterations, taking every fifth iteration for a
retained 1000 iterations. This was done for each of the 500
individuals.
Table 5 contains the realised coverages at the 10th
through 90th percentage highest posterior densities (HPD) in
intervals of 10%. The highest posterior densities were found
for each case by taking the 1000 iterations and evaluating
them using the emp.hpd function from the package
TeachingDemos (Snow, 2013) after making a slight
modification so that the HPDs could be evaluated at less
than 50%. Table 5 also gives p values from the exact binomial
test (Clopper & Pearson, 1934) for the realised coverage vs
the expected. The realised coverages are not significantly
different from the expected coverages, except for the 10%
coverage where the HPDs are too narrow. In other words, its
coverage is lower than it should be, including only 7.2% of the
cases vs the 10% it should include. These results can be
contrasted with the case where a uniform prior is assumed for
age. Table 5 shows results from two different uniform priors,
the first being from ages 15120 years and the second being
from ages 1585 years. The first prior, from 15120 years, is
clearly unreasonable. Under the Gompertz model used to
simulate the data, only  1% of the sample would be expected
to survive past the age of 76 years. The uniform prior that
includes ages up to 120 years performs poorly on all HPDs
except for the 90% HPD. While lowering the maximum
possible age to 85 years causes the 60%, 70% and 80% HPD
coverages to not differ significantly from their nominal levels,

Age estimation using ordinal categorical data

DOI: 10.3109/03014460.2015.1045430

375

Table 5. Realised coverage under an informative (Gompertz) prior and two uniform priors for age (15120 years and 1585 years). The p
values are from the exact binomial test.
Informative prior
Expected count

Realised count

p Value

Realised count

p Value

Realised count

p Value

50
100
150
200
250
300
350
400
450

36
85
146
205
251
303
345
382
437

0.037
0.105
0.773
0.648
0.964
0.820
0.626
0.050
0.062

38
70
120
168
207
253
301
376
460

0.074
0.001
0.003
0.003
50.001
50.001
50.001
0.009
0.156

35
71
99
167
210
284
252
408
464

0.025
0.001
50.001
0.003
50.001
0.144
0.884
0.402
0.037

Discussion
This paper has shown that it is indeed feasible to analyse
multivariate ordinal categorical age indicator data while
accounting for the potentially non-zero residual correlations
between indicators. Although direct optimisation of the
likelihood in this setting is a perilous and slow process, the
optimisation can be replaced using Markov Chain Monte
Carlo methods. In the current example, the first principal

50

Age

60

70

80

Gompertz Prior (50% HPD, 50.2% realised)

40

it does cause the 90% HPDs to be too wide. In other words,

that interval contains too many cases (92.5% rather than the
expected 90%).
Aside from comparing the nominal to the actual coverage,
it will be useful to examine the pattern of HPDs against the
actual ages. The style of plots used in Figures 26 from
Milner & Boldsen (2012) are useful for making this
examination. Figure 7 shows such a plot using the
Gompertz prior for the 50% HPD. As there are approximately
twice the number of cases in this simulation study relative to
Milner and Boldsens study, the HPDs are plotted only for
every other case. In the plot the vertical lines represent HPDs
that include the actual age, while the dotted lines are for
HPDs that do not include the actual age. Because there is an
informative prior in this analysis, the HPDs for younger
individuals are typically higher than the actual age, while the
HPDs are typically lower than the actual age for older
individuals. This is in contrast to Figure 8, which summarises
the results for the 50% HPD from the analysis using a uniform
prior from ages 1585 years. Because there is a noninformative prior the HPDs have the appearance of a lack of
bias in the sense that HPDs overlap actual ages throughout the
age range from 1585. However, this apparent lack of bias
does come at the high price of producing HPDs that include
fewer cases than they should. Figure 9 shows a plot similar to
that from Figure 7 in that an informative Gompertz prior is
assumed. However, to draw Figure 9 it was also assumed that
the suture closure sites were conditionally independent. In
other words, the correlation matrix in Table 4 was replaced
with an identity matrix when running the Metropolis-Hastings
sampler. Figure 9 shows the dire consequences of assuming
conditional independence when the assumption is unwarranted. The stated 50% HPDs include only 37.8% of the cases
because the intervals are too narrow and because some of the
estimates are biased (as in Figure 6).

30

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10%
20%
30%
40%
50%
60%
70%
80%
90%

Uniform prior (1585 years)

20

Coverage

Uniform prior (15120 years)

100

200

300

400

500

Index

Figure 7. Fifty per cent highest posterior densities (HPD) of age for the
500 cases in the simulation sample. The heavy line shows the (sorted)
ages for the 500 individuals. The vertical dotted lines are instances where
the 50% HPDs do not include the age while the solid lines are instances
where the age is included. Vertical lines are shown only for every other
case. This figure uses an informative Gompertz prior for age.

component of the residual correlation matrix (after partialling

out the effect of age) among the five ectocranial sutures
contained 72% of the variation. If the sutures were indeed
independent after regressing out age then the first principal
component would contain only a fifth (20%) of the total
variation. While it may well be possible to find traits with low
residual correlations (i.e. ones that are conditionally independent), it is unlikely that structures that belong to functional
anatomical units would mature or senesce independently of
one another. For example, it is unlikely that individual teeth
would be conditionally independent, such that if, say, the first
molar was accelerated in its development within an individual
the second molar would not also be accelerated. Similarly,
systems that attempt to atomise phases into individual
components, such as McKern & Stewarts (1957) approach to
the pubic symphysis or Buckberry & Chamberlains (2002)
approach to the auricular surface, are highly unlikely to
produce conditionally independent traits.

376

L. W. Konigsberg

Ann Hum Biol, 2015; 42(4): 368378

50
20

30

40

Age

60

70

80

Uniform Prior (50% HPD, 42% realised)

100

200

300

400

500

Figure 8. As in Figure 7, but with a uniform prior (from 1585 years)

for age.

Acknowledgements
I thank the co-editors of this issue for their invitation to participate and
the anonymous reviewers for their helpful comments on a previous draft.

80

Gompertz Prior, Conditional Independence Assumed

(50% HPD, 37.8% realised)

Declaration of interest

50

References

30

40

Age

60

70

The author reports no conflicts of interest.

The data analysed in this paper were collected under funding from
the National Science Foundation (BCS97-27386).

20

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Index

As an example of the former, we can consider any publications that use a reference sample with a non-uniform age
distribution to provide summary statistics for age distributions
within stages. Unless the relationship between age and the
indicators is strong, such studies will contain an inherent
bias from the reference sample age distribution as BocquetAppel & Masset (1982) previously showed. As an example of
the latter problem of providing programs without access to
raw data, we can consider the ADBOU program. Although the
ADBOU software (Milner & Boldsen, 2012) is now readily
available (it can be downloaded from http://math.mercyhurst.edu/~sousley/Software/), the reference sample data is not
available with the software. This is unfortunate as there are
alternative methods of analysis that researchers may want to
consider in the future. Ultimately, to be of greatest utility,
researchers need to have access to source code for compiled
programs or scripts for interpreted languages. They also need
to have access to the raw reference sample data. It is for this
reason that all of the code and data used in this paper are
available for download from tinyurl.com/n7eagfp.

100

200

300

400

500

Index

Figure 9. As in Figure 7, but assuming conditional independence among

traits.

Much effort has been devoted in the past to collecting reference sample information and in defining new
scoring systems and methods for age estimation.
Unfortunately, considerably less effort has been expended in
developing the statistical and probabilistic basis for estimation
of individual ages and estimation of hazard parameters for
osteological or dental samples. Equally unfortunate is that
there has been a general disconnect between the studies
that focus on osteological or dental scoring methods and those
that focus on the appropriate methods for analysing the
resultant data. This disconnect is also apparent in the
publication of summary statistics that cannot be appropriately
applied in actual analyses and in the production of software
that does not allow access to the raw reference sample data.

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