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Spearman correlations between the dissimilarities and the
approximating distances for each object.
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c. {cmd:estat} {cmd:pairwise} reports a set of statistics
for each pairwise comparison; it reports the dissimilarities, the
approximating distances, and the raw residuals.
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d. {cmd:estat} {cmd:quantiles} reports the quantiles of
the residuals for each observation (after {cmd:mds}) or object (after
{cmd:mdslong} or {cmd:mdsmat}).
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e. {cmd:estat} {cmd:stress} reports the Kruskal stress
(loss) measure between the transformed dissimilarities and fitted
distances per object.
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See {help mds postestimation:{bf:[MV] mds postestimation}}
for more information.
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In addition, there are two new commands for graphing results from a
multidimensional scaling:
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a. {cmd:mdsconfig} plots the approximating Euclidean configuration of the
first two dimensions; see
{help mds postestimation##mdsconfig:{bf:[MV] mds postestimation}}.
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b. {cmd:mdsshepard} produces a Shepard diagram of the dissimilarities
against the approximating Euclidean distances; see
{help mds postestimation##mdsshepard:{bf:[MV] mds postestimation}}.
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{cmd:predict} after any multidimensional-scaling command will
produce
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a. variables containing the approximating configuration
({cmd:predict} {it:newvarlist}{cmd:,} {cmd:config});
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b. variables containing the dissimilarity, distance, and raw residuals
({cmd:predict} {it:newvarlist}{cmd:,} {cmd:pairwise})
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See {help mds postestimation##predict:{bf:[MV] mds postestimation}}
for more information.
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2. New commands {cmd:ca} and {cmd:camat} perform two-way correspondence
analysis using any of several available forms of normalization.
{cmd:ca} performs the analysis on the cross-tabulation of two categorical
variables; {cmd:camat} performs the analysis on a matrix of
counts; see {help ca:{bf:[MV] ca}} for more information on both.
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The following new {cmd:estat} commands work after {cmd:ca} and {cmd:camat}
and provide additional statistics and results
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a. {cmd:estat} {cmd:coordinates} reports the coordinates in both the row
space and the column space.
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b. {cmd:estat} {cmd:distances} reports the chi-squared distances between
the row profiles and between the column profiles, including the
distances to the marginal distributions (commonly called centers).
Both observed or fitted profiles are available.
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c. {cmd:estat} {cmd:inertia} reports the inertia contributions of the
individual cells.
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d. {cmd:estat} {cmd:profiles} reports the row profiles and column
profiles -- the conditional distributions, given the other dimension.
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e. {cmd:estat} {cmd:summarize} reports summary information of the row
and column variables over the estimation sample.
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f. {cmd:estat} {cmd:table} reports the fitted correspondence table,
the observed "correspondence" table, or the expected table under
the assumption of independence.
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See {help ca postestimation:{bf:[MV] ca postestimation}}
for more information.
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In addition, there are two new commands for graphing results from a
correspondence analysis:
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a. {cmd:cabiplot} produces a biplot of each row category and
each column category;
see {help ca postestimation##cabiplot:{bf:[MV] ca postestimation}}.
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b. {cmd:caprojection} produces a graph that shows the ordering of row
categories
and column categories on each principal dimension of the analysis.
Each principal dimension is represented by a vertical line; markers
are plotted on the lines where the row categories and column
categories project
onto the dimensions; see
{help ca postestimation##caprojection:{bf:[MV] ca postestimation}}.
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{cmd:predict} after {cmd:ca} and {cmd:camat} computes fitted values and
row or column scores for any dimension; see
{help ca postestimation##predict:{bf:[MV] ca postestimation}}.
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3. The new command {cmd:procrustes} performs Procrustean analysis for
comparing and measuring the similarity between two sets of variables:
source and target. Two datasets can also be compared if the datasets
are first merged by record.
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The following new {cmd:estat} commands work after {cmd:procrustes} and
provide additional statistics and results:
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a. {cmd:estat} {cmd:compare} reports fit statistics of the three
transformations available in Procrustean analysis: orthogonal,
oblique, and unrestricted.
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b. {cmd:estat} {cmd:mvreg} reports the multivariate regression that is
related to the current Procrustean analysis.
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c. {cmd:estat} {cmd:summarize} reports summary information of the two
sets of variables over the estimation sample.
{p 9 9 2}
See
{help procrustes postestimation:{bf:[MV] procrustes postestimation}}
for more information.
{p 9 9 2}
New command {cmd:procoverlay} after {cmd:procrustes} creates an
overlay graph comparing the target variables to the fitted values derived
from the source variables; see
{help procrustes postestimation##procoverlay:{bf:[MV] procrustes postestimation}}.
{p 9 9 2}
{cmd:predict} after {cmd:procrustes} produces fitted values for all
variables, residuals for all variables, or residual sums of squares for a
specified target variable; see
{help procrustes postestimation##predict:{bf:[MV] procrustes postestimation}}.
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4. New command {cmd:biplot} performs a biplot analysis of a dataset and
produces a two-dimensional biplot of the results. A biplot simultaneously
displays the observations (rows) and the relative positions of the
variables (columns). Observations are projected to two dimensions such
that the distance between the observations is approximately preserved.
The variables are plotted as arrows, with the cosine of the angle between
arrows approximating the correlation between the variables.
See {helpb biplot:[MV] biplot}.
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5. New command {cmd:tetrachoric} computes a tetrachoric correlation
matrix for a set of binary variables. {cmd:tetrachoric} is
documented in {bf:[R]} but will often be used in multivariate analyses;
see {help tetrachoric:{bf:[R] tetrachoric}}.
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{cmd:tetrachoric} results can be used in subsequent factor
analyses or principal component analyses using the new
{cmd:factormat} and {cmd:pcamat} commands. See
{helpb factor:[MV] factor} and {helpb pca:[MV] pca}.
{p 5 9 2}
6. Existing command {cmd:canon} now allows analysis and presentation of
more than one linear combination and has new options for reporting the raw
or standardized coefficients and for reporting significance tests of the
canonical correlations; see {help canon:{bf:[MV] canon}}.
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The following new {cmd:estat} commands work after {cmd:canon} and
provide additional statistics and results:
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a. {cmd:estat} {cmd:correlations} reports the correlations among all
variables.
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b. {cmd:estat} {cmd:loadings} reports the matrices of canonical loadings.
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See
{help canon postestimation:{bf:[MV] canon postestimation}}
for more information.
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7. Existing command {cmd:cluster dendrogram} has many new features,
including horizontal dendrograms and the ability to label branch counts.
The look of the graph can now be changed (titles, axes, colors, etc.);
see {help cluster dendrogram:{bf:[MV] cluster dendrogram}}.
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8. The existing hierarchical cluster commands have new option
{cmd:measure()} that specifies the proximity measure to use in
computing dissimilarities between observations. Any of 33
measures
may be specified; see
{help measure_option:{bf:[MV]} {it:measure_option}}. Previously
most of the measures were available under other option names; those
options continue to work but are undocumented. See
{help cluster:{bf:[MV] cluster}}.
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9. Existing command {cmd:cluster stop} has new option {cmd:varlist()}
that specifies alternative variables to use when computing the
stopping rules; see {help cluster stop:{bf:[MV] cluster stop}}.
{title:What's new: Analysis of proximity matrices}
{pstd}
All of Stata's multivariate analysis facilities that rely on pairwise
comparisons of distance, similarity, dissimilarity, covariance, correlation,
or other proximity measures can now work directly with
proximity matrices that you compute or obtain from other sources.
{pstd}
Previously, all these facilities worked only with raw datasets. The new
commands implement analyses on matrices. They share the common ability to
accept either full matrices or vectors representing the lower or upper
triangle of a symmetric proximity matrix.
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10. New command {cmd:clustermat} extends all of Stata's hierarchical
clustering facilities to the analysis of matrices of a dissimilarity
measure (sometimes called a distance or proximity measure). This
includes all seven linkage methods and the ability to create dendrograms
of the results; see {help clustermat:{bf:[MV] clustermat}}.
{p 4 9 2}
11. New command {cmd:factormat} performs factor analysis on a matrix of
correlations, extending all the new and previously available
capabilities of the existing command {helpb factor:[MV] factor}
to precomputed
matrices of correlations; see {help factor:{bf:[MV] factor}}.
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12. New command {cmd:pcamat} performs principal component analysis on an
existing correlation or covariance matrix; see
{help pca:{bf:[MV] pca}}.
{p 4 9 2}
13. New {cmd:matrix} subcommand {cmd:dissimilarity} computes similarity,
dissimilarity, or distance matrices using any of 19
proximity measures for continuous data
and 14 measures for binary data; see
{help measure_option:{bf:[MV]} {it:measure_option}}
and see
{help matrix dissimilarity:{bf:[MV] matrix dissimilarity}}.
{title:What's new: Factor and principal component analysis additions}
{p 5 5 2}
In addition to allowing direct analysis of correlation and covariance matrices
using {helpb factormat} and {helpb pcamat}, Stata's factor analysis and
principal components analysis (PCA) methods have been expanded,
particularly through the addition of postestimation commands for reporting and
graphing results.
{p 4 9 2}
14. Command {cmd:factor} has new reporting option
{cmd:altdivisor}, that specifies
the trace of the correlation matrix be used as the divisor for
proportions, rather than the default (the sum of all eigenvalues).
{p 4 9 2}
15.
New {cmd:estat} commands for use after {cmd:factor} and
{cmd:factormat} provide additional statistics and
results:
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a. {cmd:estat} {cmd:common} reports the correlation matrix of the common
factors and is more of interest after oblique rotations.
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b. {cmd:estat} {cmd:factors} reports model-selection criteria (AIC and
BIC) over all the factors retained in an analysis.
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c. {cmd:estat} {cmd:rotatecompare} reports the unrotated factor loadings
next to the most-recent rotated loadings.
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d. {cmd:estat} {cmd:structure} reports the factor structure -- the
correlations between the variables and the common factors.
{p 9 9 2}
See {help factor postestimation:{bf:[MV] factor postestimation}}
for more information.
{p 4 9 2}
16. Existing command {cmd:pca} allows several new options:
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a. Option {cmd:vce(normal)} computes the VCE of the eigenvalues and
eigenvectors, assuming multivariate normality.
{p 13 13 2}
This gives you access to many of Stata's postestimation facilities
for analyzing estimation results, including tests of eigenvalue and
eigenvector significance, tests of linear and nonlinear
combinations ({helpb test:[R] test} and {helpb testnl:[R] testnl}),
linear and
nonlinear combinations with confidence intervals
({helpb lincom:[R] lincom}
and {helpb nlcom:[R] nlcom}),
and nonlinear predictions with confidence
intervals ({helpb predictnl:[R] predictnl}).
{p 13 13 2}
{cmd:vce(normal)} also produces the ingredients for
adding confidence intervals to screeplots;
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