help mds postestimation dialogs: predict estat
mdsconfig mdsshepard
also see: mds, mdslong, mdsmat
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Title
[MV] mds postestimation -- Postestimation tools for mds, mdsmat, and
mdslong
Description
The following postestimation commands are of special interest after mds,
mdsmat, and mdslong:
command description
-------------------------------------------------------------------------
estat config coordinates of the approximating configuration
estat correlations correlations between disparities and distances
estat pairwise pairwise disparities, distances, and residuals
estat quantiles quantiles of the residuals per object
estat stress Kruskal stress (loss) measure (only after
classical MDS)
+ estat summarize estimation sample summary
mdsconfig plot of approximating configuration
mdsshepard Shepard diagram
screeplot plot eigenvalues (only after classical MDS)
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+ estat summarize is not available after mdsmat.
The following standard postestimation commands are also available:
command description
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* estimates cataloging estimation results
predict approximating configuration, disparities,
dissimilarities, distances, and residuals
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* All estimates subcommands except table and stats are available.
Special-interest postestimation commands
estat config lists the coordinates of the approximating configuration.
estat correlations lists the Pearson and Spearman correlations between
the disparities or dissimilarities and the Euclidean distances for each
object.
estat pairwise lists the pairwise statistics: the disparities, the
distances, and the residuals.
estat quantiles lists the quantiles of the residuals per object.
estat stress displays the Kruskal stress (loss) measure between the
(transformed) dissimilarities and fitted distances per object (only after
classical MDS).
estat summarize summarizes the variables in the MDS over the estimation
sample. After mds, estat summarize also reports whether and how
variables were transformed before computing similarities or
dissimilarities.
mdsconfig produces a plot of the approximating Euclidean configuration.
By default, dimensions 1 and 2 are plotted.
mdsshepard produces a Shepard diagram of the disparities against the
Euclidean distances. Ideally, the points in the plot should be close to
the y=x line. Optionally, separate plots are generated for each "row"
(value of id()).
Syntax for predict
predict [type] {stub*|newvarlist} [if] [in] [, statistic options]
statistic description
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Main
config approximating configuration; specify
dimension() or fewer variables
pairwise(pstats) selected pairwise statistics; specify
same number of variables
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pstats description
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disparities disparities =
transformed(dissimilarities)
dissimilarities dissimilarities
distances Euclidean distances between configuration
points
rresiduals raw residual = dissimilarity - distance
tresiduals transformed residual = disparity -
distance
weights weights
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options description
-------------------------------------------------------------------------
Main
* saving(filename[, replace]) save results to filename; use replace to
overwrite existing filename
full create predictions for all pairs of
object; pairwise() only
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* saving() is required after mdsmat, after mds if pairwise is selected,
and after mdslong if config is selected.
Menu
Statistics > Postestimation > Predictions, residuals, etc.
Options for predict
+------+
----+ Main +-------------------------------------------------------------
config generates variables containing the approximating configuration in
Euclidean space. Specify as many new variables as approximating
dimensions (as determined by the dimension() option of mds, mdsmat,
or mdslong), though you may specify fewer. estat config displays the
same information but does not store the information in variables.
After mdsmat and mdslong, you must also specify the saving() option.
pairwise(pstats) generates new variables containing pairwise statistics.
The number of new variables should be the same as the number of
specified statistics. The following statistics are allowed
disparities generates the disparities, i.e., the transformed
dissimilarities. If no transformation is applied (modern MDS
with transform(identity)), disparities are the same as
dissimilarities.
dissimilarities generates the dissimilarities used in MDS. If
mds, mdslong, or mdsmat was invoked on similarity data, the
associated dissimilarities are returned.
distances generates the (unsquared) Euclidean distances between
the fitted configuration points.
rresiduals generates the raw residuals: dissimilarities -
distances.
tresiduals generates the transformed residuals: disparities -
distances.
weights generates the weights. Missing proximities are
represented by zero weights.
estat pairwise displays some of the same information but does not
store the information in variables.
After mds and mdsmat, you must also specify the saving() option.
With n objects, the pairwise dataset has n(n-1)/2 observations. In
addition to the three requested variables, predict produces variables
id1 and id2, which identify pairs of objects. With mds, id is the
name of the identification variable (id() option) and with mdsmat it
is "Category".
saving(filename[, replace]) is required after mdsmat, after mds if
pairwise() is selected, and after mdslong if config is selected.
saving() indicates that the generated variables are to be created in
a new Stata dataset and saved in the file named filename. Unless
saving() is specified, the variables are generated in the current
dataset.
replace indicates that filename specified in saving() may be
overwritten.
full creates predictions for all pairs of objects (j1,j2). The default
is to generate predictions only for pairs (j1,j2) where j1>j2. full
may be specified only with pairwise().
Syntax for estat
List the coordinates of the approximating configuration
estat config [, maxlength(#) format(%fmt)]
List the Pearson and Spearman correlations
estat correlations [, maxlength(#) format(%fmt) notransform nototal]
List the pairwise statistics: disparities, distances, and residuals
estat pairwise [, maxlength(#) notransform full separator]
List the quantiles of the residuals
estat quantiles [, maxlength(#) format(%fmt) nototal notransform]
Display the Kruskal stress (loss) measure per point (only after classical
MDS)
estat stress [, maxlength(#) format(%fmt) nototal notransform]
Summarize the variables in MDS
estat summarize [, labels]
options description
-------------------------------------------------------------------------
maxlength(#) maximum number of characters for displaying object
names; default is 12
format(%fmt) display format
nototal suppress display of overall summary statistics
notransform suppress the linear transformation of the
dissimilarities
full display all pairs (j1,j2); default is (j1>j2) only
separator draw separating lines
labels display variable labels
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Menu
Statistics > Postestimation > Reports and statistics
Options for estat
maxlength(#), an option used with all but estat summarize, specifies the
maximum number of characters of the object names to be displayed; the
default is maxlength(12).
format(%fmt), an option used with estat config, estat correlations, estat
quantiles, and estat stress, specifies the display format; the
default differs between the subcommands.
nototal, an option used with estat correlations, estat quantiles, and
estat stress, suppresses the overall summary statistics.
notransform, an option used with estat correlations, estat pairwise,
estat quantiles, and estat stress, specifies that the untransformed
dissimilarities be used instead of the transformed dissimilarities
(disparities).
full, an option used with estat pairwise, displays a row for all pairs
(j1,j2). The default is to display rows only for pairs where j1>j2.
separator, an option used with estat pairwise, draws separating lines
between blocks of rows corresponding to changes in the first of the
pair of objects.
labels, an option used with estat summarize, displays variable labels.
Syntax for mdsconfig
mdsconfig [, options]
options description
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Main
dimensions(# #) two dimensions to be displayed;
default is dimensions(2 1)
xnegate negate data relative to the x axis
ynegate negate data relative to the y axis
autoaspect adjust aspect ratio on the basis of the data;
default aspect ratio is 1
maxlength(#) maximum number of characters used in marker
labels
cline_options affect rendition of the lines connecting points
marker_options change look of markers (color, size, etc.)
marker_label_options change look or position of marker labels
Y axis, X axis, Titles, Legend, Overall
twoway_options any options other than by() documented in
[G] twoway_options
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Menu
Statistics > Multivariate analysis > Multidimensional scaling (MDS) >
Postestimation > Approximating configuration plot
Options for mdsconfig
+------+
----+ Main +-------------------------------------------------------------
dimensions(# #) identifies the dimensions to be displayed. For instance,
dimensions(3 2) plots the third dimension (vertically) versus the
second dimension (horizontally). The dimension number cannot exceed
the number of extracted dimensions. The default is dimensions(2 1).
xnegate specifies that the data be negated relative to the x axis.
ynegate specifies that the data be negated relative to the y axis.
autoaspect specifies that the aspect ratio be automatically adjusted
based on the range of the data to be plotted. This option can make
some plots more readable. By default, mdsconfig uses an aspect ratio
of one, producing a square plot. Some plots will have little
variation in the y-axis direction, and use of the autoaspect option
will better fill the available graph space while preserving the
equivalence of distance in the x and y axes.
As an alternative to autoaspect, the twoway_option aspectratio() can
be used to override the default aspect ratio. mdsconfig accepts the
aspectratio() option as a suggestion only and will override it when
necessary to produce plots with balanced axes; i.e., distance on the
x axis equals distance on the y axis.
twoway_options, such as xlabel(), xscale(), ylabel(), and yscale(),
should be used with caution. These options are accepted but may have
unintended side effects on the aspect ratio.
maxlength(#) specifies the maximum number of characters for object names
used to mark the points; the default is maxlength(12).
cline_options affect the rendition of the lines connecting the plotted
points; see [G] cline_options. If you are drawing connected lines,
the appearance of the plot depends on the sort order of the data.
marker_options affect the rendition of the markers drawn at the plotted
points, including their shape, size, color, and outline; see [G]
marker_options.
marker_label_options specify if and how the markers are to be labeled;
see [G] marker_label_options.
+-----------------------------------------+
----+ Y axis, X axis, Titles, Legend, Overall +--------------------------
twoway_options are any of the options documented in [G] twoway_options,
excluding by(). These include options for titling the graph (see [G]
title_options) and for saving the graph to disk (see [G]
saving_option). See autoaspect above for a warning against using
options such as xlabel(), xscale(), ylabel(), and yscale().
Syntax for mdsshepard
mdsshepard [, options]
options description
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Main
notransform use dissimilarities instead of disparities
autoaspect adjust aspect ratio on the basis of the data;
default aspect ratio is 1
separate draw separate Shepard diagrams for each object
marker_options change look of markers (color, size, etc.)
Y axis, X axis, Titles, Legend, Overall
twoway_options any options other than by() documented in
[G] twoway_options
byopts(by_option) affect the rendition of combined graphs; separate
only
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Menu
Statistics > Multivariate analysis > Multidimensional scaling (MDS) >
Postestimation > Shepard diagram
Options for mdsshepard
+------+
----+ Main +-------------------------------------------------------------
notransform uses dissimilarities instead of disparities, i.e., suppresses
the transformation of the dissimilarities.
autoaspect specifies that the aspect ratio is to be automatically
adjusted based on the range of the data to be plotted. By default,
mdsshepard uses an aspect ratio of one, producing a square plot.
See the description of the autoaspect option of mdsconfig for more
details.
separate displays separate plots of each value of the id variable. This
may be time consuming if the number of distinct id values is not
small.
marker_options affect the rendition of the markers drawn at the plotted
points, including their shape, size, color, and outline; see [G]
marker_options.
+-----------------------------------------+
----+ Y axis, X axis, Titles, Legend, Overall +--------------------------
twoway_options are any of the options documented in [G] twoway_options,
excluding by(). These include options for titling the graph (see [G]
title_options) and for saving the graph to disk (see [G]
saving_option). See the autoaspect option of mdsconfig for a warning
against using options such as xlabel(), xscale(), ylabel(), and
yscale().
byopts(by_option) is documented in [G] by_option. This option affect the
appearance of the combined graph and only allowed with the separate
option.
Examples
. sysuse auto
. mds price-gear, id(make) dim(2) std
. estat config
. estat correlations
. estat quantiles
. estat pairwise
. estat stress
. estat summarize
. mdsconfig
. mdsshepard
. predict d1 d2, config
. predict disp diss dist, pairwise(disp diss dist) saving(gd3)
Saved results
estat correlations saves the following in r():
Matrices
r(R) statistics per object; columns with # of obs., Pearson
corr., and Spearman corr.
r(T) overall statistics; # of obs., Pearson corr., and
Spearman corr.
estat quantiles saves the following in r():
Macros
r(dtype) adjusted or raw; dissimilarity transformation
Matrices
r(Q) statistics per object; columns with # of obs., min.,
p25, p50, p75, and max.
r(T) overall statistics; # of obs., min., p25, p50, p75, and
max.
estat stress saves the following in r():
Macros
r(dtype) adjusted or raw; dissimilarity transformation
Matrices
r(S) Kruskal's stress/loss measure per object
r(T) 1 x 1 matrix with the overall Kruskal stress/loss
measure
Also see
Manual: [MV] mds postestimation
Help: [MV] mds;
[MV] mdslong, [MV] mdsmat [MV] screeplot
