AIT.dist                Returns the distance between two compositional
                        vectors using Aitchison's distance measure.
AIT.more                Used to provide additional information on
                        various model components evaluated at the
                        optimal solution, i.e., using the QFASA diet
                        estimates and Aitchison distance measure.
AIT.obj                 Used in 'solnp()' as the objective function to
                        be minimized when Aitchison distance measure is
                        chosen.
CC                      Fatty acid calibration coefficients.
CS.more                 Used to provide additional information on
                        various model components evaluated at the
                        optimal solution, i.e., using the QFASA diet
                        estimates and chi-square distance measure.
CS.obj                  Used in 'solnp()' as the objective function to
                        be minimized when chi-square distance measure
                        is chosen. Unlike 'AIT.obj()' and 'KL.obj()',
                        does not require modifying zeros.
FAset                   List of fatty acids used in sample prey and
                        predator data sets, 'preyFAs' and 'predatorFAs'
                        respectively.
KL.dist                 Returns the distance between two compositional
                        vectors using Kullback-Leibler distance
                        measure.
KL.more                 Used to provide additional information on
                        various model components evaluated at the
                        optimal solution, i.e., using the QFASA diet
                        estimates and Kullback-Leibler distance
                        measure.
KL.obj                  Used in 'solnp()' as the objective function to
                        be minimized when Kullback-Leibler distance
                        measure is chosen.
MEANmeth                Returns the multivariate mean FA signature of
                        each prey group entered into the QFASA model.
                        Result can be passed to prey.mat in
                        'p.QFASA()'.
QFASA                   QFASA: A package for Quantitative Fatty Acid
                        Signature Analysis
QFASA.const.eqn         Returns 'sum(alpha)' and used in 'solnp()'.
beta.meths.CI           Returns individual confidence intervals and
                        simultaneous confidence intervals based on the
                        zero-inflated beta distribution (not bias
                        corrected - see note below).
bias.all                Calculate bias correction for confidence
                        intervals from 'beta.meths.CI'.
chisq.CA                Called by 'create.d.mat()' to compute the
                        chi-square distance.
chisq.dist              Returns the distance between two compositional
                        vectors using the chi-square distance.
create.d.mat            Called by 'testfordiff.ind.boot.fun()' to
                        create a matrix of distances.
mean.geometric          Returns the geometric mean of a compositional
                        vector
p.QFASA                 Computes the diet estimate for each predator in
                        seal.mat using either the Kullback-Leibler
                        Distance (KL), the Aitchison Distance (AIT) or
                        the Chi-Square Distance (CS).
predatorFAs             Predator fatty acid signatures. Each predator
                        signature is a row with fatty acid proportions
                        in columns.
prey.cluster            This function performs a hierarchical cluster
                        analysis of prey fatty acid signatures using a
                        matrix of dissimilarities for the n objects
                        being clustered.  Initially, each object is
                        assigned as its own cluster and then the
                        algorithm proceeds iteratively, at each stage
                        joining the two most similar clusters, until
                        there is just a single cluster.
prey.on.prey            Each prey fatty acid signature is
                        systematically removed from the supplied prey
                        database and its QFASA diet estimate is
                        obtained by treating the individual as a
                        predator.
preyFAs                 Prey fatty acid signatures. Each prey signature
                        is a row with fatty acid proportions in
                        columns.
pseudo.pred             Generate a pseudo predator by sampling with
                        replacement from prey database.
pseudo.seal             Generate a single pseudo predator FA signature
split.prey              Splits prey database into a simulation set
                        (1/3) and a modelling set (2/3). Returns a
                        list:
testfordiff.ind.boot    Called by 'testfordiff.ind.pval()'.
testfordiff.ind.boot.fun
                        Called by 'testfordiff.ind.boot()'.
testfordiff.ind.pval    Test for a difference between two independent
                        samples of compositional data. Zeros of any
                        type are allowed.
