Compositional analysis in archaeology
Compositional analysis in archaeology
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Klaproth was a distinguished German chemist, often acknowledged as the father of ana
lytical chemistry for establishing a systematic methodology for performing analytical
chemistry. Klaproth conducted the first known compositional analysis of ancient coins
from Greece and Rome and discovered they were made from alloys of copper. He also es
timated their composition. A report of his work was read before an audience of the Acade
mie Royale des Sciences et Belles-Lettres de Prusse in Berlin on July 9, 1795, and later
published in a volume of memoirs by the Royal Academy. Three years later, Klaproth pre
sented a second paper to the Royal Academy describing his investigation of three sam
ples of Roman glass in a mosaic recovered from the ruins of Emperor Tiberius on the is
land of Capri. The samples of glass were highly colored and opaque: one was red, one
was green, and the third was blue. He concluded the different colors were due to the
presence of copper and iron. He also produced a nearly complete analysis of the major
constituents.
Sir Humphry Davy was an English chemist best known for discovering the alkali and alka
line earth metals. His major contribution to archaeological chemistry was the characteri
zation of pigment samples from Rome and Pompeii (Davy 1815). One of Davy’s laboratory
assistants was Michael Faraday. Although Faraday is more widely recognized for his work
in the field of electromagnetism, he also studied glazed Roman pottery and discovered
the glaze was lead based.
An article by Göbel (1842), a German pharmacist and chemist, reported on his study of a
collection of brass artifacts excavated from the Russian Baltic provinces. He compared
the composition of the brass artifacts to prehistoric brass artifacts of known Greek and
Roman origins. His discovery that the Baltic artifacts were similar to those from the Ro
man Empire led Göbel to conclude the artifacts were acquired by trade instead of having
been made from local materials.
The Austrian scholar Vocel is considered the forefather of Austrian archaeology as a sci
ence. His contribution to archaeological chemistry was made in the mid-nineteenth centu
ry when he recommended that the correlations between the compositions of raw materi
als and artifacts might be used to identify the sources of raw materials.
The French mineralogist Damour (1864) proposed that the sources of stone axes might be
identified by determining the density and composition of different rock types, including
jade and obsidian. He also encouraged archaeologists to collaborate with specialists from
other disciplines such as chemistry, geology, and zoology, which he predicted would in
crease the amount of knowledge gained.
During the latter portion of the nineteenth century, compositional analyses of archaeolog
ical metals were conducted by John Percy, a metallurgist at the Royal School of Mines in
London, who contributed to several major works on the early production and use of met
als. Among the most significant of these were his analyses of metal artifacts recovered
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from the sites of Nineveh and Babylon by Austen Henry Layard (1853) and from Mycenae
by Heinrich Schliemann (1878).
The German chemist Rathgen was hired by the Royal Museums of Berlin to be its first
chemist. Later, he became the first director of its chemical laboratory. He is considered to
be the father of modern archaeological conservation for his work in developing proce
dures for the removal of corrosion from antiquities and methods for artifact preservation
(Rathgen 1898).
Until the end of the nineeteenth century, most quantitative analyses of artifacts were per
formed on metallic alloys using gravimetric methods. It was a logical method because all
determinations could be made with great precision by direct weighing of the solids pro
duced after dissolution, precipitation, filtration, and evaporation. The main disadvantage
was that measurements were limited to one element at a time.
One of the first major investigations of ceramic artifacts was a gravimetric study of
Athenian pottery from the Boston Museum of Fine Arts conducted by T. W. Richards
(1895), the first American to receive the Nobel Prize in Chemistry. Richards and his grad
uate students at Harvard University found the gravimetric method to be extremely labori
ous and not practical for application to large numbers of samples.
During the 1920s and 1930s, the development of instrumental methods of analysis, such
as optical emission spectroscopy (OES), made it possible to determine multiple trace ele
ments with greater sensitivity and to analyze more samples faster. These advances
opened the door to systematic studies of ancient metals by dedicated laboratories in
Britain, Germany, and the United States. Within a couple of decades, thousands of cop
per-based artifacts from Europe were analyzed (Otto and Witter 1952; Junghans, Sang
meister, and Schröder 1960; Caley 1964a, 1964b).
From the 1950s until the present, the number of scientific techniques grew significantly
and their application to a wider variety of archaeological materials has increased. One of
the major breakthroughs occurred in the mid-1950s when neutron activation analysis
(NAA) was first employed by Sayre and Dodson (1957) to study pottery. With NAA, sample
dissolution was no longer required, and more elements could be measured with greater
precision and accuracy. Another advantage of NAA was that many of the procedures
could be automated. In the 1960s and 1970s, dedicated NAA laboratories were estab
lished at national laboratories in the United States (Brookhaven National Laboratory and
Lawrence Berkeley National Laboratory), in museums (British Museum and Smithsonian
Institution), and at major universities (University of Michigan, University of Manchester,
Hebrew University, and University of Toronto). Almost all of the first-generation NAA lab
oratories have since been replaced by a second generation of laboratories located at the
University of Missouri, Oregon State University, University of Budapest, and so forth.
In addition to NAA, other analytical techniques were developed for bulk compositional
analysis, including X-ray fluorescence (XRF), particle-induced X-ray emission (PIXE), elec
tron probe microanalysis (EPMA), inductively coupled plasma-mass spectrometry (ICP-
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MS), and laser ablation ICP-MS (LA-ICP-MS). Most of the analytical methods are capable
of producing high-precision data, but they often require that a portion of the artifact be
destroyed to prepare the sample for analysis. However, recent developments with
portable XRF spectrometers make it possible to perform rapid, nondestructive analysis at
archaeological sites and museums for a limited suite of elements when lower precision is
acceptable.
Most of the chemical analytical methods mentioned earlier are used to determine the
compositions of inorganic archaeological materials (i.e., stone tools, pottery, metals, and
glass). Because the organic archaeological materials (i.e., human remains, food residues,
textiles, plants, etc.) are rarely preserved, measurements of bulk compositions of organic
materials are unusual. Techniques that measure isotope ratios in organic artifacts have
proven more productive.
This discussion will focus on the interpretation of data from inorganic artifacts, which can
be categorized as either natural or chemically altered. Natural materials such as obsidian,
basalt, flint, gemstones, and limestone were used to create stone tools, weapons, jewelry,
statuary, and so forth. Although these natural artifacts were modified physically, their
chemical compositions were not significantly modified. On the other hand, chemically al
tered artifacts were created from raw materials by processes such as mixing, firing, and
smelting to produce pottery, bricks, man-made glass, metals, and so forth. Matching
chemically altered artifacts to raw materials is more difficult (Neff 2000; Pernicka 2014).
Studies of the technologies used to produce chemically altered artifacts rely mainly on
data for the major elements present in the artifacts and raw materials (concentrations
>1%). On the other hand, studies to establish the sources of both natural and chemically
altered artifacts tend to rely heavily on the concentrations of the minor and trace ele
ments whose presence in most artifacts is effectively “accidental.” The latter studies are
commonly referred to as provenance investigations, and their main objective is to study
the movement of artifacts from their raw material source or place of manufacture to the
archaeological site where they were recovered.
The basic proposition underlying provenance determination was understood by the early
1970s (e.g., Perlman and Asaro 1969; Sayre 1975; Bieber et al. 1976). However, it was
Weigand et al. (1977) who first stated explicitly that linking artifacts to sources through
compositional analysis depends on satisfying the postulate “the differences in chemical
composition between different natural sources [must] exceed, in some recognizable way,
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the differences observed within a given source.” (Although Weigand’s use of the term
source might seem to imply only the location from which raw materials originated, in the
case of chemically altered artifacts, source usually refers to the workshop or production
site where the artifacts were made.)
The strategies used for provenance determination are different for certain types of arti
facts, as explained by Neff (2000). As shown in Table 1, when investigating natural arti
facts, the raw material sources should be analyzed first to establish statistically valid
compositional groups against which the chemical fingerprints of artifacts can be com
pared. For chemically altered artifacts, the artifacts should be analyzed first to establish
statistically valid compositional groups against which the chemical fingerprints of kiln
wasters, unfired sherds, and raw materials can be compared. Finally, as more chemically
altered artifacts are analyzed, the compositional groups should continue to be refined.
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The volume of compositional data generated can be substantial (e.g., >30 elements each
for hundreds of samples), usually arranged in the form of a matrix of m samples (rows) by
n elements (columns). As a result, data management, statistical analysis, and interpreta
tion can be very challenging. Large multivariate datasets necessitate the use of multivari
ate analysis (MVA) programs to discover patterns and extract knowledge from the data.
All MVA programs include data visualization routines capable of generating plots, tables,
and charts that assist in the recognition of patterns, trends, and anomalies not otherwise
apparent from numerical summaries. Visualization routines also aid the process of data
summarization and simplify explaining the interpretation of a complex dataset to the au
dience.
A range of MVA procedures for interpreting compositional data have been adapted from
the discipline of statistics (Bieber et al. 1976; Glascock 1992; Baxter 1994; Beier and
Mommsen 1994; Neff 2000; Buxeda i Garrigos and Kilikoglou 2003). No single procedure
(or combination of procedures) has been accepted as the best method for interpreting
compositional data in the field of archaeology. Every dataset has its own unique charac
teristics. A procedure that works well for one dataset may be inappropriate for another.
For a best practice, several methods should be employed and the results compared to find
the best overall solution.
Data Screening
Before investigating a compositional dataset with a series of MVA routines, the data
should be inspected to ensure it is reliable for testing. The data screening process is in
tended to detect possible errors and abnormal values that may interfere with the data
evaluation. Some of the possible errors are sample misidentification, data entry errors,
contamination, and so forth. When inconsistent values are found, they should be investi
gated for the possible need to correct, reanalyze, or reject completely.
Screening of data also includes the investigation of missing values (i.e., nondetects).
These may occur for a number of reasons: values were below the detection limit, data
were lost, or data were otherwise unavailable. Because missing values cannot be used di
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rectly by MVA routines, a number of different methods are available to supply replace
ment values (Arteaga and Ferrer 2002). When a particular element has a large number of
missing values, it may be necessary to eliminate the element from the MVA.
When the data for a single variable are arranged to display the number of instances in
which the measured variable takes each of its values, it becomes a frequency distribution.
This provides a picture of how individual data are distributed while also revealing ex
treme values (i.e., outliers). A frequency distribution is considered normal if it can be
characterized by a bell-shaped curve symmetrically centered about its mean. If the num
ber of data points is very large, the bell-shaped curve is referred to as a Gaussian distrib
ution, which takes the functional form
Here, µ is the mean of the distribution, σ is its standard deviation, and σ2 is the variance.
Geologists and statisticians have long debated over whether chemical data for archaeo
logical and geological materials are distributed normally or lognormally (Ahrens 1954;
Vistelius 1960). According to a study by Zhang et al. (2005), almost all elements show nei
ther a normal nor lognormal data distribution. However, a majority of archaeological re
searchers have found it convenient to use a logarithm transform on geochemical data be
cause it acts as a “quasi-standardization” (Sayre 1975; Neff 2000) that compensates for
the differences in absolute magnitude between the major elements, such as Al, K, and Fe
present at percent levels, and the trace elements, such as the rare earth elements (REEs)
present at parts per million and below. Thus, the transformation places the elements onto
more or less the same scale.
where σm is equal to the standard deviation of the measured mean. Ideally, the analytical
variance should be minimized in such a way that a majority of the variance is due to the
natural variance of the material. Replicate sampling and analysis of a highly homoge
neous material can be used to produce a spread of values assessing overall measurement
precision.
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The existence of correlations between many of the elements present in geological materi
als is well known. Some examples include the following: (1) Ca is usually correlated with
Sr; (2) Sc is associated with siderophile elements like Fe, Cr, and Co; (3) Hf and Zr are
correlated in mantle rocks; and (4) the rare-earth elements exhibit strong correlations
with one another.
The correlation coefficient, rjk, between two elements j and k is defined by the ratio
where σj and σk are the respective sample standard deviations and σjk is the covariance
between them. Correlation coefficients range in value from +1 to –1. A correlation of +1
indicates a perfect 1:1 relationship between the two variables; a correlation of –1 indi
cates two variables that are inversely related. The sample covariance can be calculated
from the expression
where Cij and Cik denote the respective concentrations of the jth and kth elements in sam
ple i. The mean element concentrations are given by Aj and Ak, and m represents the total
number of samples.
The main purpose for examining multivariate compositional data with MVA routines is to
identify groups from which new knowledge can be obtained. Learning from multivariate
data is often described as either supervised learning or unsupervised learning. In super
vised learning, the model or structure of the data is already known; some variables may
have more weight than others, but the structure is not modified during the learning
process. In unsupervised learning, the structure is unknown, all variables are treated
equally, and patterns within the data are sought. However, there is no certainty that the
patterns identified from unsupervised learning are correct. When the sources are already
known, the approach to assigning sources for obsidian artifacts involves supervised learn
ing through the use of discrimination or classification methods. When the sources are un
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known, as is the case with most investigations of archaeological ceramics, the MVA proce
dures involve unsupervised learning with procedures that identify patterns of composi
tional groups.
Cluster Analysis
One of the most basic unsupervised learning procedures applied to multivariate composi
tional data is hierarchical cluster analysis (HCA). HCA is a procedure that groups sam
ples according to their similarity to one another. HCA works by calculating the Euclidean
distances between pairs of samples. The HCA procedure employs a “bottoms-up” ap
proach toward building a hierarchy of clusters. Using this approach, every sample is as
sumed to be the lowest member of a cluster. As the distances between pairs of samples
are compared, those with the smallest distances between are merged together as one
moves upward in the hierarchy. Samples separated by large distances are placed in sepa
rate clusters.
HCA results are typically presented in the form a dendrogram indicating the relationships
between samples in the dataset, as shown in Figure 1 for pottery from a site in Turkey. Al
though HCA is an efficient tool for displaying the visual relationships between samples,
its major weakness is the failure to take into account the correlations between elements.
This can be a serious problem when dealing with a highly correlated data.
HCA is based on a dissimilarity matrix in which the distances between all pairs of speci
mens are calculated using one of several possible distance measures (Sayre 1975). The
most popular measure is the squared-mean Euclidean distance (SMED) by which one cal
culates a distance between specimens j and k according to the equation
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The scaling factor, n, corresponds to the number of elements actually determined. It re
moves the possible problem of missing values, since the measure averages over only
those elements for which data are included. For an assemblage containing m samples,
there are m(m−1)/2 pairs of samples, and a d2 value will be calculated for each pair. At
this stage, it is advisable to use the information on all elements having few missing values
to use the maximum amount of information possible when generating clusters.
Visual inspection of the dendrogram can be used to identify potential groups. However,
the inclination for HCA to force data into spherical groups can lead to erroneous assign
ments of samples due to the tendency for compositional groups to be elongated due to in
terelement correlation. Groups created from cluster analysis should be considered tenta
tive until validated later by a more robust evaluation that takes the effects of correlation
into account.
A clustering method known as k-means clustering is popular among some experts who
study compositional data. The k-means method differs from HCA by partitioning the
n-sample dataset into k clusters, where each sample is assigned to a cluster with the
nearest mean. A major challenge with k-means clustering is that the number of clusters
must be estimated in advance.
Using Aitchison’s procedure, the variation matrix is constructed from all possible vari
ances of the log-ratios for all n elemental concentrations. For example, the covariances
are defined by
All diagonal elements of the variation matrix are zero, and the off-diagonal elements of
the variances are defined as
As a result, the covariances can be calculated from the log-ratio variances using the equa
tion
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A large value for vt indicates greater variability and suggests the dataset is polygenic
(i.e., subgroups), whereas a small value for vt indicates less variability and suggests a
possible monogenic dataset. Aitchison (1992) also demonstrated that the total variation is
directly related to the Euclidean distances between all samples in the dataset.
In addition to total variation parameter, Buxeda i Garrigos and Kilikoglou (2003) show
that the variation matrix of the entire dataset provides other useful information. For ex
ample, sources of variability within the dataset can be revealed by examining the log-ra
tio variances, τ.t, for each element as a divisor. It provides an estimate regarding each
element’s contribution to the total variation. The information from total variation and log-
ratio variances can also be used to isolate samples suffering from various processes such
as alternation and contamination.
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Assuming the compositional data matrix has m samples and n elements, the first step in
PCA involves centering the data on the mean values for each element. This insures that
the transformed data will also be centered in the same location, but it will have no effect
on the spatial relationships between samples or the variances between elements. The first
PC is described by the linear combination of element concentrations according to the
equation
where the coefficients a11, a12, … a1n of the eigenvector represent the weighting factors
for each element, which represent the correlation coefficients between the elements and
the PCs. By definition, the weighting factors are constrained so that the sum of their
squares must equal 1.
The second PC is calculated in the same way as the first PC, with the condition that it
must be uncorrelated (i.e., perpendicular to) and it must account for the maximum
amount of remaining variance. This process is continued until the total number of PCs is
equal to the number of elements, n. Thus, PC2 and PCn can be written as:
.
The new reference axes produced by PCA represent a new coordinate system, which usu
ally offers an improved perspective for viewing the dataset. The position of every speci
men in element concentration space can be converted to its principal score in the new
PCA space.
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Ideally, a greater portion of the structure for the compositional dataset under examina
tion will be explained by the lowest PCs. The results of PCA can be studied by inspecting
in a table of weighting factors or by viewing one or more scatterplots in two or three di
mensions. Table 2 lists the weighting factors for the same Turkish pottery dataset illus
trated in Figure 1. The weighting factors contributing most strongly to each PC are high
lighted in bold. The scatterplot in Figure 2 shows the scores on PC#1 and PC#2 for the
same data. The total number of unique two-dimensional scatterplots possible for inspec
tion is n(n−1)/2; however, the scatterplots of higher ordered PC scores gradually explain
lesser amounts of the variation. Although different criteria have been proposed for deter
mining how many PCs should be investigated and how many should be ignored, one of the
most common criteria is to include all PCs until the total percent of variance explained
reaches an acceptable level. For a majority of archaeological work, this is about 90% of
the variance.
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Table 2 Weighting Factors from Principal Components Analysis for Bronze Age Pottery from Site in Turkey along
with Percent Variance Explained by Each Principal Component
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PCA can also be used to examine the basis for differences between groups. In R-mode
analysis, the weight on each PC can be used to display the scores for samples in the new
PCA space. In Q-mode analysis, the factor scores for the variables (elements) can be in
spected as vectors. As described by Neff (1994), the MVA method that performs both si
multaneously is known as RQ-mode PCA. When the RQ-mode PCA technique is used, it is
possible to display both samples and element vectors simultaneously on a single plot
known as a biplot. A biplot for the Turkish pottery is shown in Figure 3. The directions
and lengths of the element vectors can be easily interpreted in terms of explaining which
elements are responsible for differentiating compositional groups from one another and
indicating the degree of correlation between elements. Examination of the element vec
tors can also be a useful tool for identifying which element pairs have the most potential
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for use in scatterplots. In other words, scatterplots should show that the differences be
tween compositional groups are real and they are not a consequence of the PCA proce
dure. Figure 4 shows a scatterplot of Cr versus Eu for the Turkish pottery example.
Mahalanobis Distance
Compositional groups are characterized by the location of their centroids and the unique
correlations between the elements. The existence of correlations between the elements in
geological and archaeological materials mandates the use of Mahalanobis distance (MD)
measures to properly handle compositional data (Sayre 1975; Bishop and Neff 1989).
The MD is defined as the squared Euclidean distance between a sample and a group cen
troid, divided by the group variance in the direction of the sample (Sayre 1975). It is
equivalent to measuring the number of standard deviations between a sample and the
group mean along each principal component axis. Mathematically, the MD between speci
men k and the centroid of group A can be written as
Ai and Aj are the mean concentrations of elements i and j in the group, and Iij is the ijth el
ement of the inverse of the variance-covariance matrix. The MD is both unitless and scale
invariant, and it accounts for all correlations between pairs of elements as derived from
the off-diagonal terms of the variance-covariance matrix, which the simple Euclidean dis
tance does not. If all axes were rescaled such that they have unit variance, the MD dis
tance is equal to the Euclidean distance. Calculation of the probability that a particular
sample belongs to a group is based not only on its proximity to the group centroid in Eu
clidean terms but also on the rate at which the density of samples decreases away from
the centroid in the direction of the sample of interest.
where m1 and m2 are the numbers of samples in the two groups. Hotelling’s T2 statistic is
equivalent to the MD for individual data points. Therefore, the probabilities of member
ship are easily calculated after transforming the T2 statistic into the related F value by
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Variations in the procedures using MD distances have been employed by some laborato
ries to overcome some of the limitations of cluster analysis and PCA. A modified MD filter
method combined with chi-squared statistics (Beier and Mommsen 1994) establishes
groups by considering correlations, measurement uncertainties, and dilution effects. They
argue that their procedure produces improved separations between compositional groups
and reduces the effects of data shifts due to possible dilution and weathering effects.
MD distance calculations can also be used to replace missing values (Sayre 1975). When
the number of samples with missing values is modest, it is possible to calculate a replace
ment value for each sample relative to its presumed compositional group based on mini
mizing the effect on the MD distance with and without the replacement value.
Group Validation
The initial groups created from the examination of scatterplots or cluster analysis should
be validated by using the MD to calculate membership probabilities for individual sam
ples. Calculation of the MD from a sample to a group requires that number of samples in
the group exceeds the number of variables (elements or PCs) by at least one. To avoid
bias, individual samples should not be compared to a compositional group in which they
have are already a member. The solution to this problem is to use a jackknifing procedure
by which membership probability for each sample is calculated by temporarily excluding
the sample from the group to which it is being compared.
For most accurate probability calculations, theoretical studies have shown that sample-to-
element ratio, m/n, should be at least 3—5, and the larger the better (Foley 1972). Unfor
tunately, the m/n problem affects most compositional analysis projects involved in archae
ology because most archaeological sites lack the number of artifacts or more likely be
cause archaeologists lack the financial resources necessary to analyze the number of arti
facts needed to achieve the recommended sample-to-element ratio. The most common
method for circumventing the small sample-to-element ratio is to base the MD distance
measures on a reduced number of principal components rather than use the original ele
ment concentrations.
Classification and discriminant analysis are supervised learning techniques related to the
MVA methods used to create and validate compositional groups. As new archaeological
samples are analyzed, the same procedures used to validate group membership are ap
plicable to classifying (or assigning) the new samples to the existing compositional
groups. After membership to an existing group is confirmed, it may be necessary to
reevaluate the entire dataset. If the new samples do not belong to existing groups, they
may be outliers or representatives of yet-to-be-identified groups.
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lies on the assumption that the pooled variance-covariance matrix is an accurate repre
sentation of the total variance and covariance (Davis 1986). By definition, CDA also re
quires all of the samples to belong to one of the known groups.
The CDA procedure constructs a series of canonical discriminant functions (one fewer
than the number of groups), which for each group maximizes the likelihood for specimens
to belong to their assigned group and minimizes the likelihood of belonging to all other
groups. The main requirements for CDA are as follows: (1) two or more groups; (2) at
least two samples per group; and (3) the number of variables must be at least two fewer
than the number of samples. The individual discriminant functions are linear combina
tions of the original data that successively describe decreasing amounts of the separation
between the groups. Two-dimensional scatterplots of the discriminant functions are used
to illustrate the success in separating groups by CDA.
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from organizations such as the National Institute of Standards and Technology (NIST)
and the United States Geological Survey (USGS) in the United States. Most other coun
tries have similar organizations that offer standard reference materials for chemical
analysis measurements. Standards are used to develop calibration curves for the analyti
cal procedure that will be applied to the archaeological samples. Quality control samples
should be included with each batch of standards and artifacts undergoing analysis to pro
vide an independent check on data quality. Quality control of data is essential to detecting
and correcting systematic errors to ensure the long-term variability of measured data is
minimized.
Before submitting samples to an analytical laboratory for analysis, advice on the project
design would be advantageous and may avoid collection of useless data. Instructions on
how to collect, prepare, and ship samples should be provided. In exchange for collabora
tion, some laboratories will offer assistance with MVA and data interpretation. These fac
tors should be considered before undertaking a large and expensive program of analysis.
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