title: "Exported Data" output: html_document: theme: cosmo toc: true toc_float: collapsed: false
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sneer
return valueHaving run an embedding:
iris_tsne <- sneer(iris)
what exactly does iris_tsne
give you? It's a list with something like the
following:
coords
- a matrix of all-important coordinates. It's dimensions are n
x
ndim
where n
is the number of observations that were embedded and ndim
is the number of output dimensions. That will normally be 2.method
- a string containing the embedding method name.cost
- the final cost associated with the output configuration in coords
.
See the Reporting section for more on this.norm_cost
- the normalized version of cost
. Again, see the
Reporting section for more.iter
- the iteration number at which the embedding stopped.nf
- the number of cost function evaluations.ng
- the number of cost gradient evaluations.nf
and ng
only count the function and gradient values with respect to the
error in the coordinates. Extra function and gradient evaluations made as part
of optimizing "dynamic" parameters, if they were optimized separately from the
coordinates (i.e. you set alt_opt = TRUE
), are not included here. See the
Embedding Methods section for details on which
methods are (or can be made) dynamic in this way. See the section on the dyn
return value below to get these separate function and gradient counts.
ret
You can also ask for some other data. Some of it might be useful for
diagnostics, debugging, visualization or as input to another algorithm. To
get access to it, pass a vector of names to the ret
parameter.
The names you can ask for are:
pcost
- The final cost
, decomposed into the sum of n values, with n
being the number of points. Be aware that these individual components don't
have to be positive, e.g. if the cost function is a divergence. For the pca
method, the mmds
cost function is used.x
- input coordinates after Preprocessing and column
filtering.dx
- input distance matrix. Calculated if not present. Note that this of
class matrix
, not dist
.dy
- output distance matrix. Calculated if not present. Note that this of
class matrix
, not dist
.p
- input probability matrix. Only available if using a probability-based
embedding.q
- output probability matrix. Only available if using a probability-based
embedding.prec
- vector of input kernel precisions. Corresponds to the
values summarized as prec
in the console log after input initialization.
Only available if using a probability-based embedding. See the
Input Initialization section for more on the
exact definition of the precision.dim
- vector of intrinsic dimensionalities for each observation, calculated
according to the method given in the
multiscale JSE paper.
These are meaningless if not using the default exponential
\code{perp_kernel_fun}. See the
Input Initialization section for more.deg
Vector of degree centrality of the input observations as used in
ws-SNE.
Calculated if not present. A summary of this vector appears in the console
log after input initialization if carrying out ws-SNE (by setting
method = "wssne"
).dyn
Dynamically optimized non-coordinate parameters. A list containing
sublists, with names corresponding to the names of the parameters optimized.
This is available if using you used the dyn
input variable to make an
embedding method "dynamic", or if you selected
Inhomogeneous t-SNE
(method = "itsne"
), or DHSSNE (method = "dhssne"
). For it-SNE, dyn
will
contain a list of dof
, which contains the optimized degrees of freedom
parameter for each output coordinate. If using method = "dhssne"
method, dyn
contains a list called alpha
, which contains the optimized global alpha
value. See the Embedding Methods for more. If the
parameters were optimized separately from the coordinates, then this list will
also contain the number of function and gradient evaluations used for
parameter optimization under nf
and ng
, respectively.costs
All the costs which were logged to screen during the optimization, as
a matrix, with the iteration number in the first column.For every name you provide, the list returned by sneer
will contain an extra
item in the list with the same name. If you ask for an item that doesn't make
sense, e.g. a probability matrix from an embedding method that never calculated
one, the request is silently ignored. Otherwise, the value will be calculated
if possible, e.g. even though degree centrality is only used in ws-SNE, you can
ask for it to be returned from any probability-based embedding, because it's
related to the input probabilities, so it can be calculated.
# return the point-wise cost function, output distance matrix and the degree centrality
# in tsne_iris$dy and tsne_iris$deg, respectively
tsne_iris <- sneer(iris, ret = c("pcost", "dy", "deg"))
# returns the output distance matrix in sammon_iris$dy, but no
# sammon_iris$deg, because that would require the presence of data that
# Sammon Mapping doesn't create
sammon_iris <- sneer(iris, ret = c("dy", "deg"))
Although sneer
requires input distance matrix data to be of class dist
,
internally, it uses objects of class matrix
for all matrices, even distance
matrices. So dy
and dx
will be of class matrix
. If you want to pass dy
or dx
back into sneer
for some crazy scheme or other, you will need to cast
them into dist
objects via as.dist
:
s1k_tsne <- sneer(s1k, ret = c("dy"))
# ... work some unseen magic on s1k_tsne$dy ...
# return it to sneer for more processing
s1k_mmds <- sneer(as.dist(s1k_tsne$dy), method = "mmds", labels = s1k$Label)
You may find some use for the numerical vectors that can be returned with ret
by coloring the embedding plot based on their magnitude. The
Visualization section can tell you more.
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