,
Kelly Bodwin [aut],
Posit Software, PBC [cph, fnd]| Title: | A Common API to Clustering |
|---|---|
| Description: | A common interface to specifying clustering models, in the same style as 'parsnip'. Creates unified interface across different functions and computational engines. |
| Authors: | Emil Hvitfeldt [aut, cre] ,
Kelly Bodwin [aut],
Posit Software, PBC [cph, fnd] |
| Maintainer: | Emil Hvitfeldt <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.2.3.9000 |
| Built: | 2024-09-30 05:22:05 UTC |
| Source: | https://github.com/tidymodels/tidyclust |
augment() will add column(s) for predictions to the given data.
## S3 method for class 'cluster_fit' augment(x, new_data, ...)## S3 method for class 'cluster_fit' augment(x, new_data, ...)
x |
A |
new_data |
A data frame or matrix. |
... |
Not currently used. |
For partition models, a .pred_cluster column is added.
A tibble::tibble() with containing new_data with columns added
depending on the mode of the model.
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% augment(new_data = mtcars)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% augment(new_data = mtcars)
An object with class "cluster_fit" is a container for information about a model that has been fit to the data.
The following model types are implemented in tidyclust:
K-Means in k_means()
Hierarchical (Agglomerative) Clustering in hier_clust()
The main elements of the object are:
spec: A cluster_spec object.
fit: The object produced by the fitting function.
preproc: This contains any data-specific information required to
process new a sample point for prediction. For example, if the underlying
model function requires arguments x and the user passed a formula to
fit, the preproc object would contain items such as the terms object
and so on. When no information is required, this is NA.
As discussed in the documentation for cluster_spec, the original
arguments to the specification are saved as quosures. These are evaluated for
the cluster_fit object prior to fitting. If the resulting model object
prints its call, any user-defined options are shown in the call preceded by a
tilde (see the example below). This is a result of the use of quosures in the
specification.
This class and structure is the basis for how tidyclust stores model objects after seeing the data and applying a model.
cluster_metric_set() allows you to combine multiple metric functions
together into a new function that calculates all of them at once.
cluster_metric_set(...)cluster_metric_set(...)
... |
The bare names of the functions to be included in the metric set.
These functions must be cluster metrics such as |
All functions must be:
Only cluster metrics
A cluster_metric_set() object, combining the use of all input
metrics.
An object with class "cluster_spec" is a container for information about a model that will be fit.
The following model types are implemented in tidyclust:
K-Means in k_means()
Hierarchical (Agglomerative) Clustering in hier_clust()
The main elements of the object are:
args: A vector of the main arguments for the model. The
names of these arguments may be different from their counterparts n the
underlying model function. For example, for a k_means() model, the argument
name for the number of clusters are called "num_clusters" instead of "k" to
make it more general and usable across different types of models (and to not
be specific to a particular model function). The elements of args can
tune() with the use in tune_cluster().
For more information see https://www.tidymodels.org/start/tuning/. If left
to their defaults (NULL), the arguments will use the underlying model
functions default value. As discussed below, the arguments in args are
captured as quosures and are not immediately executed.
...: Optional model-function-specific parameters. As with args, these
will be quosures and can be tune().
mode: The type of model, such as "partition". Other modes will be added
once the package adds more functionality.
method: This is a slot that is filled in later by the model's constructor
function. It generally contains lists of information that are used to
create the fit and prediction code as well as required packages and similar
data.
engine: This character string declares exactly what software will be
used. It can be a package name or a technology type.
This class and structure is the basis for how tidyclust stores model objects prior to seeing the data.
An important detail to understand when creating model specifications is that they are intended to be functionally independent of the data. While it is true that some tuning parameters are data dependent, the model specification does not interact with the data at all.
For example, most R functions immediately evaluate their arguments. For
example, when calling mean(dat_vec), the object dat_vec is immediately
evaluated inside of the function.
tidyclust model functions do not do this. For example, using
k_means(num_clusters = ncol(mtcars) / 5)
does not execute ncol(mtcars) / 5 when creating the specification.
This can be seen in the output:
> k_means(num_clusters = ncol(mtcars) / 5)
K Means Cluster Specification (partition)
Main Arguments:
num_clusters = ncol(mtcars)/5
Computational engine: stats
The model functions save the argument expressions and their associated
environments (a.k.a. a quosure) to be evaluated later when either
fit.cluster_spec() or fit_xy.cluster_spec() are called with the actual
data.
The consequence of this strategy is that any data required to get the parameter values must be available when the model is fit. The two main ways that this can fail is if:
The data have been modified between the creation of the model specification and when the model fit function is invoked.
If the model specification is saved and loaded into a new session where those same data objects do not exist.
The best way to avoid these issues is to not reference any data objects in
the global environment but to use data descriptors such as .cols(). Another
way of writing the previous specification is
k_means(num_clusters = .cols() / 5)
This is not dependent on any specific data object and is evaluated immediately before the model fitting process begins.
One less advantageous approach to solving this issue is to use quasiquotation. This would insert the actual R object into the model specification and might be the best idea when the data object is small. For example, using
k_means(num_clusters = ncol(!!mtcars) - 1)
would work (and be reproducible between sessions) but embeds the entire
mtcars data set into the num_clusters expression:
> k_means(num_clusters = ncol(!!mtcars) / 5) K Means Cluster Specification (partition) Main Arguments: num_clusters = ncol(structure(list(mpg = c(21, 21, 22.8, 21.4, 18.7,<snip> Computational engine: stats
However, if there were an object with the number of columns in it, this wouldn't be too bad:
> num_clusters_val <- ncol(mtcars) / 5 > num_clusters_val [1] 10 > k_means(num_clusters = !!num_clusters_val) K Means Cluster Specification (partition) Main Arguments: num_clusters = 2.2
More information on quosures and quasiquotation can be found at https://adv-r.hadley.nz/quasiquotation.html.
Options can be passed to the fit.cluster_spec() function that control the
output and computations.
control_cluster(verbosity = 1L, catch = FALSE)control_cluster(verbosity = 1L, catch = FALSE)
verbosity |
An integer where a value of zero indicates that no messages
or output should be shown when packages are loaded or when the model is
fit. A value of 1 means that package loading is quiet but model fits can
produce output to the screen (depending on if they contain their own
|
catch |
A logical where a value of |
An S3 object with class "control_cluster" that is a named list with the results of the function call
control_cluster() control_cluster(catch = TRUE)control_cluster() control_cluster(catch = TRUE)
Used in most tidyclust::hier_clust() models.
cut_height(range = c(0, dials::unknown()), trans = NULL)cut_height(range = c(0, dials::unknown()), trans = NULL)
range |
A two-element vector holding the defaults for the smallest and largest possible values, respectively. If a transformation is specified, these values should be in the transformed units. |
trans |
A |
cut_height()cut_height()
When applied to a fitted cluster specification, returns a tibble with cluster location. When such locations doesn't make sense for the model, a mean location is used.
extract_centroids(object, ...)extract_centroids(object, ...)
object |
An fitted |
... |
Other arguments passed to methods. Using the |
Some model types such as K-means as seen in k_means() stores the centroid
in the object itself. leading the use of this function to act as an simple
extract. Other model types such as Hierarchical (Agglomerative) Clustering as
seen in hier_clust(), are fit in such a way that the number of clusters can
be determined at any time after the fit. Setting the num_clusters or
cut_height in this function will be used to determine the clustering when
reported.
Further more, some models like hier_clust(), doesn't have a notion of
"centroids". The mean of the observation within each cluster assignment is
returned as the centroid.
The ordering of the clusters is such that the first observation in the training data set will be in cluster 1, the next observation that doesn't belong to cluster 1 will be in cluster 2, and so on and forth. As the ordering of clustering doesn't matter, this is done to avoid identical sets of clustering having different labels if fit multiple times.
extract_centroids() is a part of a trio of functions doing similar things:
extract_cluster_assignment() returns the cluster assignments of the
training observations
extract_centroids() returns the location of the centroids
predict() returns the cluster a new
observation belongs to
A tibble::tibble() with 1 row for each centroid and their position.
.cluster denotes the cluster name for the centroid. The remaining
variables match variables passed into model.
extract_cluster_assignment() predict.cluster_fit()
set.seed(1234) kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% extract_centroids() # Some models such as `hier_clust()` fits in such a way that you can specify # the number of clusters after the model is fit. # A Hierarchical (Agglomerative) Clustering method doesn't technically have # clusters, so the center of the observation within each cluster is returned # instead. hclust_spec <- hier_clust() %>% set_engine("stats") hclust_fit <- fit(hclust_spec, ~., mtcars) hclust_fit %>% extract_centroids(num_clusters = 2) hclust_fit %>% extract_centroids(cut_height = 250)set.seed(1234) kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% extract_centroids() # Some models such as `hier_clust()` fits in such a way that you can specify # the number of clusters after the model is fit. # A Hierarchical (Agglomerative) Clustering method doesn't technically have # clusters, so the center of the observation within each cluster is returned # instead. hclust_spec <- hier_clust() %>% set_engine("stats") hclust_fit <- fit(hclust_spec, ~., mtcars) hclust_fit %>% extract_centroids(num_clusters = 2) hclust_fit %>% extract_centroids(cut_height = 250)
When applied to a fitted cluster specification, returns a tibble with cluster assignments of the data used to train the model.
extract_cluster_assignment(object, ...)extract_cluster_assignment(object, ...)
object |
An fitted |
... |
Other arguments passed to methods. Using the |
Some model types such as K-means as seen in k_means() stores the
cluster assignments in the object itself. leading the use of this function to
act as an simple extract. Other model types such as Hierarchical
(Agglomerative) Clustering as seen in hier_clust(), are fit in such a way
that the number of clusters can be determined at any time after the fit.
Setting the num_clusters or cut_height in this function will be used to
determine the clustering when reported.
The ordering of the clusters is such that the first observation in the training data set will be in cluster 1, the next observation that doesn't belong to cluster 1 will be in cluster 2, and so on and forth. As the ordering of clustering doesn't matter, this is done to avoid identical sets of clustering having different labels if fit multiple times.
extract_cluster_assignment() is a part of a trio of functions doing
similar things:
extract_cluster_assignment() returns the cluster assignments of the
training observations
extract_centroids() returns the location of the centroids
predict() returns the cluster a new
observation belongs to
A tibble::tibble() with 1 column named .cluster. This tibble will
correspond the the training data set.
extract_centroids() predict.cluster_fit()
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% extract_cluster_assignment() kmeans_fit %>% extract_cluster_assignment(prefix = "C_") # Some models such as `hier_clust()` fits in such a way that you can specify # the number of clusters after the model is fit hclust_spec <- hier_clust() %>% set_engine("stats") hclust_fit <- fit(hclust_spec, ~., mtcars) hclust_fit %>% extract_cluster_assignment(num_clusters = 2) hclust_fit %>% extract_cluster_assignment(cut_height = 250)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% extract_cluster_assignment() kmeans_fit %>% extract_cluster_assignment(prefix = "C_") # Some models such as `hier_clust()` fits in such a way that you can specify # the number of clusters after the model is fit hclust_spec <- hier_clust() %>% set_engine("stats") hclust_fit <- fit(hclust_spec, ~., mtcars) hclust_fit %>% extract_cluster_assignment(num_clusters = 2) hclust_fit %>% extract_cluster_assignment(cut_height = 250)
S3 method to get fitted model summary info depending on engine
extract_fit_summary(object, ...)extract_fit_summary(object, ...)
object |
a fitted |
... |
other arguments passed to methods |
The elements cluster_names and cluster_assignments will be factors.
A list with various summary elements
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% extract_fit_summary()kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% extract_fit_summary()
These functions extract various elements from a clustering object. If they do not exist yet, an error is thrown.
extract_fit_engine() returns the engine specific fit embedded within
a tidyclust model fit. For example, when using k_means()
with the "lm" engine, this returns the underlying kmeans object.
extract_parameter_set_dials() returns a set of dials parameter objects.
## S3 method for class 'cluster_fit' extract_fit_engine(x, ...) ## S3 method for class 'cluster_spec' extract_parameter_set_dials(x, ...)## S3 method for class 'cluster_fit' extract_fit_engine(x, ...) ## S3 method for class 'cluster_spec' extract_parameter_set_dials(x, ...)
x |
A |
... |
Not currently used. |
Extracting the underlying engine fit can be helpful for describing the
model (via print(), summary(), plot(), etc.) or for variable
importance/explainers.
However, users should not invoke the
predict() method on an extracted model.
There may be preprocessing operations that tidyclust has executed on the
data prior to giving it to the model. Bypassing these can lead to errors or
silently generating incorrect predictions.
Good:
tidyclust_fit %>% predict(new_data)
Bad:
tidyclust_fit %>% extract_fit_engine() %>% predict(new_data)
The extracted value from the tidyclust object, x, as described in the
description section.
kmeans_spec <- k_means(num_clusters = 2) kmeans_fit <- fit(kmeans_spec, ~., data = mtcars) extract_fit_engine(kmeans_fit)kmeans_spec <- k_means(num_clusters = 2) kmeans_fit <- fit(kmeans_spec, ~., data = mtcars) extract_fit_engine(kmeans_fit)
The finalize_* functions take a list or tibble of tuning parameter values
and update objects with those values.
finalize_model_tidyclust(x, parameters) finalize_workflow_tidyclust(x, parameters)finalize_model_tidyclust(x, parameters) finalize_workflow_tidyclust(x, parameters)
x |
A recipe, |
parameters |
A list or 1-row tibble of parameter values. Note that the
column names of the tibble should be the |
An updated version of x.
kmeans_spec <- k_means(num_clusters = tune()) kmeans_spec best_params <- data.frame(num_clusters = 5) best_params finalize_model_tidyclust(kmeans_spec, best_params)kmeans_spec <- k_means(num_clusters = tune()) kmeans_spec best_params <- data.frame(num_clusters = 5) best_params finalize_model_tidyclust(kmeans_spec, best_params)
fit() and fit_xy() take a model specification, translate_tidyclust the
required code by substituting arguments, and execute the model fit routine.
## S3 method for class 'cluster_spec' fit(object, formula, data, control = control_cluster(), ...) ## S3 method for class 'cluster_spec' fit_xy(object, x, case_weights = NULL, control = control_cluster(), ...)## S3 method for class 'cluster_spec' fit(object, formula, data, control = control_cluster(), ...) ## S3 method for class 'cluster_spec' fit_xy(object, x, case_weights = NULL, control = control_cluster(), ...)
object |
An object of class |
formula |
An object of class |
data |
Optional, depending on the interface (see Details below). A data frame containing all relevant variables (e.g. predictors, case weights, etc). Note: when needed, a named argument should be used. |
control |
A named list with elements |
... |
Not currently used; values passed here will be ignored. Other
options required to fit the model should be passed using |
x |
A matrix, sparse matrix, or data frame of predictors. Only some
models have support for sparse matrix input. See |
case_weights |
An optional classed vector of numeric case weights. This
must return |
fit() and fit_xy() substitute the current arguments in the
model specification into the computational engine's code, check them for
validity, then fit the model using the data and the engine-specific code.
Different model functions have different interfaces (e.g. formula or
x/y) and these functions translate_tidyclust between the interface used
when fit() or fit_xy() was invoked and the one required by the
underlying model.
When possible, these functions attempt to avoid making copies of the data.
For example, if the underlying model uses a formula and fit() is invoked,
the original data are references when the model is fit. However, if the
underlying model uses something else, such as x/y, the formula is
evaluated and the data are converted to the required format. In this case,
any calls in the resulting model objects reference the temporary objects
used to fit the model.
If the model engine has not been set, the model's default engine will be
used (as discussed on each model page). If the verbosity option of
control_cluster() is greater than zero, a warning will be produced.
If you would like to use an alternative method for generating contrasts
when supplying a formula to fit(), set the global option contrasts to
your preferred method. For example, you might set it to: options(contrasts = c(unordered = "contr.helmert", ordered = "contr.poly")). See the help
page for stats::contr.treatment() for more possible contrast types.
A cluster_fit object that contains several elements:
spec: The model specification object (object in the
call to fit)
fit: when the model is executed without error, this is the
model object. Otherwise, it is a try-error
object with the error message.
preproc: any objects needed to convert between a formula and
non-formula interface
(such as the terms object)
The return value will also have a class related to the fitted model (e.g.
"_kmeans") before the base class of "cluster_fit".
A fitted cluster_fit object.
set_engine(), control_cluster(), cluster_spec,
cluster_fit
library(dplyr) kmeans_mod <- k_means(num_clusters = 5) using_formula <- kmeans_mod %>% set_engine("stats") %>% fit(~., data = mtcars) using_x <- kmeans_mod %>% set_engine("stats") %>% fit_xy(x = mtcars) using_formula using_xlibrary(dplyr) kmeans_mod <- k_means(num_clusters = 5) using_formula <- kmeans_mod %>% set_engine("stats") %>% fit(~., data = mtcars) using_x <- kmeans_mod %>% set_engine("stats") %>% fit_xy(x = mtcars) using_formula using_x
Computes distance from observations to centroids
get_centroid_dists(new_data, centroids, dist_fun = Rfast::dista)get_centroid_dists(new_data, centroids, dist_fun = Rfast::dista)
new_data |
A data frame |
centroids |
A data frame where each row is a centroid. |
dist_fun |
A function for computing matrix-to-matrix distances. Defaults
to |
This method glances the model in a tidyclust model object, if it exists.
## S3 method for class 'cluster_fit' glance(x, ...)## S3 method for class 'cluster_fit' glance(x, ...)
x |
model or other R object to convert to single-row data frame |
... |
other arguments passed to methods |
a tibble
hier_clust() defines a model that fits clusters based on a distance-based
dendrogram
There are different ways to fit this model, and the method of estimation is chosen by setting the model engine. The engine-specific pages for this model are listed below.
hier_clust( mode = "partition", engine = "stats", num_clusters = NULL, cut_height = NULL, linkage_method = "complete" )hier_clust( mode = "partition", engine = "stats", num_clusters = NULL, cut_height = NULL, linkage_method = "complete" )
mode |
A single character string for the type of model. The only possible value for this model is "partition". |
engine |
A single character string specifying what computational engine
to use for fitting. Possible engines are listed below. The default for this
model is |
num_clusters |
Positive integer, number of clusters in model (optional). |
cut_height |
Positive double, height at which to cut dendrogram to
obtain cluster assignments (only used if |
linkage_method |
the agglomeration method to be used. This should be (an
unambiguous abbreviation of) one of |
To predict the cluster assignment for a new observation, we find the closest cluster. How we measure “closeness” is dependent on the specified type of linkage in the model:
single linkage: The new observation is assigned to the same cluster as its nearest observation from the training data.
complete linkage: The new observation is assigned to the cluster with the smallest maximum distances between training observations and the new observation.
average linkage: The new observation is assigned to the cluster with the smallest average distances between training observations and the new observation.
centroid method: The new observation is assigned to the cluster with the closest centroid, as in prediction for k_means.
Ward’s method: The new observation is assigned to the cluster with the smallest increase in error sum of squares (ESS) due to the new addition. The ESS is computed as the sum of squared distances between observations in a cluster, and the centroid of the cluster.
A hier_clust cluster specification.
# Show all engines modelenv::get_from_env("hier_clust") hier_clust()# Show all engines modelenv::get_from_env("hier_clust") hier_clust()
k_means() defines a model that fits clusters based on distances to a number
of centers. This definition doesn't just include K-means, but includes
models like K-prototypes.
There are different ways to fit this model, and the method of estimation is chosen by setting the model engine. The engine-specific pages for this model are listed below.
stats: Classical K-means
ClusterR: Classical K-means
klaR: K-Modes
clustMixType: K-prototypes
k_means(mode = "partition", engine = "stats", num_clusters = NULL)k_means(mode = "partition", engine = "stats", num_clusters = NULL)
mode |
A single character string for the type of model. The only possible value for this model is "partition". |
engine |
A single character string specifying what computational engine
to use for fitting. Possible engines are listed below. The default for this
model is |
num_clusters |
Positive integer, number of clusters in model. |
For a K-means model, each cluster is defined by a location in the predictor space. Therefore, prediction in tidyclust is defined by calculating which cluster centroid an observation is closest too.
A k_means cluster specification.
# Show all engines modelenv::get_from_env("k_means") k_means()# Show all engines modelenv::get_from_env("k_means") k_means()
The agglomeration Linkage method
linkage_method(values = values_linkage_method) values_linkage_methodlinkage_method(values = values_linkage_method) values_linkage_method
values |
A character string of possible values. See |
An object of class character of length 8.
This parameter is used in tidyclust models for hier_clust().
values_linkage_method linkage_method()values_linkage_method linkage_method()
Determine the minimum set of model fits
## S3 method for class 'cluster_spec' min_grid(x, grid, ...)## S3 method for class 'cluster_spec' min_grid(x, grid, ...)
x |
A cluster specification. |
grid |
A tibble with tuning parameter combinations. |
... |
Not currently used. |
A tibble with the minimum tuning parameters to fit and an additional list column with the parameter combinations used for prediction.
These functions provide convenient wrappers to create the one
type of metric functions in celrry: clustering metrics. They add a
metric-specific class to fn. These features are used by
cluster_metric_set() and by tune_cluster() when tuning.
new_cluster_metric(fn, direction)new_cluster_metric(fn, direction)
fn |
A function. |
direction |
A string. One of:
|
A cluster_metric object.
Apply to a model to create different types of predictions. predict() can be
used for all types of models and uses the "type" argument for more
specificity.
## S3 method for class 'cluster_fit' predict(object, new_data, type = NULL, opts = list(), ...) ## S3 method for class 'cluster_fit' predict_raw(object, new_data, opts = list(), ...)## S3 method for class 'cluster_fit' predict(object, new_data, type = NULL, opts = list(), ...) ## S3 method for class 'cluster_fit' predict_raw(object, new_data, opts = list(), ...)
object |
An object of class |
new_data |
A rectangular data object, such as a data frame. |
type |
A single character value or |
opts |
A list of optional arguments to the underlying predict function
that will be used when |
... |
Arguments to the underlying model's prediction function cannot be
passed here (see |
If "type" is not supplied to predict(), then a choice is made:
type = "cluster" for clustering models
predict() is designed to provide a tidy result (see "Value" section below)
in a tibble output format.
The ordering of the clusters is such that the first observation in the training data set will be in cluster 1, the next observation that doesn't belong to cluster 1 will be in cluster 2, and so on and forth. As the ordering of clustering doesn't matter, this is done to avoid identical sets of clustering having different labels if fit multiple times.
Prediction is not always formally defined for clustering models. Therefore,
each cluster_spec method will have their own section on how "prediction"
is interpreted, and done if implemented.
predict() when used with tidyclust objects is a part of a trio of functions
doing similar things:
extract_cluster_assignment() returns the cluster assignments of the
training observations
extract_centroids() returns the location of the centroids
predict() returns the cluster a new
observation belongs to
With the exception of type = "raw", the results of
predict.cluster_fit() will be a tibble as many rows in the output as
there are rows in new_data and the column names will be predictable.
For clustering results the tibble will have a .pred_cluster column.
Using type = "raw" with predict.cluster_fit() will return the
unadulterated results of the prediction function.
When the model fit failed and the error was captured, the predict()
function will return the same structure as above but filled with missing
values. This does not currently work for multivariate models.
extract_cluster_assignment() extract_centroids()
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% predict(new_data = mtcars) # Some models such as `hier_clust()` fits in such a way that you can specify # the number of clusters after the model is fit hclust_spec <- hier_clust() %>% set_engine("stats") hclust_fit <- fit(hclust_spec, ~., mtcars) hclust_fit %>% predict(new_data = mtcars[4:6, ], num_clusters = 2) hclust_fit %>% predict(new_data = mtcars[4:6, ], cut_height = 250)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) kmeans_fit %>% predict(new_data = mtcars) # Some models such as `hier_clust()` fits in such a way that you can specify # the number of clusters after the model is fit hclust_spec <- hier_clust() %>% set_engine("stats") hclust_fit <- fit(hclust_spec, ~., mtcars) hclust_fit %>% predict(new_data = mtcars[4:6, ], num_clusters = 2) hclust_fit %>% predict(new_data = mtcars[4:6, ], cut_height = 250)
Prepares data and distance matrices for metric calculation
prep_data_dist(object, new_data = NULL, dists = NULL, dist_fun = Rfast::Dist)prep_data_dist(object, new_data = NULL, dists = NULL, dist_fun = Rfast::Dist)
object |
A fitted |
new_data |
A dataset to calculate predictions on. If |
dists |
A distance matrix for the data. If |
dist_fun |
A custom distance functions. |
A list
When forcing one-to-one, the user needs to decide what to prioritize:
"accuracy": optimize raw count of all observations with the same label across the two assignments
"precision": optimize the average percent of each alt cluster that matches the corresponding primary cluster
reconcile_clusterings_mapping( primary, alternative, one_to_one = TRUE, optimize = "accuracy" )reconcile_clusterings_mapping( primary, alternative, one_to_one = TRUE, optimize = "accuracy" )
primary |
A vector containing cluster labels, to be matched |
alternative |
Another vector containing cluster labels, to be changed |
one_to_one |
Boolean; should each alt cluster match only one primary cluster? |
optimize |
One of "accuracy" or "precision"; see description. |
Retains the cluster labels of the primary assignment, and relabel the alternate assignment to match as closely as possible. The user must decide whether clusters are forced to be "one-to-one"; that is, are we allowed to assign multiple labels from the alternate assignment to the same primary label?
A tibble with 3 columns; primary, alt, alt_recoded
factor1 <- c("Apple", "Apple", "Carrot", "Carrot", "Banana", "Banana") factor2 <- c("Dog", "Dog", "Cat", "Dog", "Fish", "Fish") reconcile_clusterings_mapping(factor1, factor2) factor1 <- c("Apple", "Apple", "Carrot", "Carrot", "Banana", "Banana") factor2 <- c("Dog", "Dog", "Cat", "Dog", "Fish", "Parrot") reconcile_clusterings_mapping(factor1, factor2, one_to_one = FALSE)factor1 <- c("Apple", "Apple", "Carrot", "Carrot", "Banana", "Banana") factor2 <- c("Dog", "Dog", "Cat", "Dog", "Fish", "Fish") reconcile_clusterings_mapping(factor1, factor2) factor1 <- c("Apple", "Apple", "Carrot", "Carrot", "Banana", "Banana") factor2 <- c("Dog", "Dog", "Cat", "Dog", "Fish", "Parrot") reconcile_clusterings_mapping(factor1, factor2, one_to_one = FALSE)
Change arguments of a cluster specification
## S3 method for class 'cluster_spec' set_args(object, ...)## S3 method for class 'cluster_spec' set_args(object, ...)
object |
A model specification. |
... |
One or more named model arguments. |
An updated cluster_spec object.
Change engine of a cluster specification
## S3 method for class 'cluster_spec' set_engine(object, engine, ...)## S3 method for class 'cluster_spec' set_engine(object, engine, ...)
object |
A model specification. |
engine |
A character string for the software that should be used to fit the model. This is highly dependent on the type of model (e.g. linear regression, random forest, etc.). |
... |
Any optional arguments associated with the chosen computational
engine. These are captured as quosures and can be tuned with |
An updated cluster_spec object.
Change mode of a cluster specification
## S3 method for class 'cluster_spec' set_mode(object, mode)## S3 method for class 'cluster_spec' set_mode(object, mode)
object |
A model specification. |
mode |
A character string for the model type (e.g. "classification" or "regression") |
An updated cluster_spec object.
Measures silhouette between clusters
silhouette(object, new_data = NULL, dists = NULL, dist_fun = Rfast::Dist)silhouette(object, new_data = NULL, dists = NULL, dist_fun = Rfast::Dist)
object |
A fitted tidyclust model |
new_data |
A dataset to predict on. If |
dists |
A distance matrix. Used if |
dist_fun |
A function for calculating distances between observations. Defaults to Euclidean distance on processed data. |
silhouette_avg() is the corresponding cluster metric function that
returns the average of the values given by silhouette().
A tibble giving the silhouette for each observation.
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) dists <- mtcars %>% as.matrix() %>% dist() silhouette(kmeans_fit, dists = dists)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) dists <- mtcars %>% as.matrix() %>% dist() silhouette(kmeans_fit, dists = dists)
Measures average silhouette across all observations
silhouette_avg(object, ...) ## S3 method for class 'cluster_spec' silhouette_avg(object, ...) ## S3 method for class 'cluster_fit' silhouette_avg(object, new_data = NULL, dists = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' silhouette_avg(object, new_data = NULL, dists = NULL, dist_fun = NULL, ...) silhouette_avg_vec( object, new_data = NULL, dists = NULL, dist_fun = Rfast::Dist, ... )silhouette_avg(object, ...) ## S3 method for class 'cluster_spec' silhouette_avg(object, ...) ## S3 method for class 'cluster_fit' silhouette_avg(object, new_data = NULL, dists = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' silhouette_avg(object, new_data = NULL, dists = NULL, dist_fun = NULL, ...) silhouette_avg_vec( object, new_data = NULL, dists = NULL, dist_fun = Rfast::Dist, ... )
object |
A fitted kmeans tidyclust model |
... |
Other arguments passed to methods. |
new_data |
A dataset to predict on. If |
dists |
A distance matrix. Used if |
dist_fun |
A function for calculating distances between observations. Defaults to Euclidean distance on processed data. |
Not to be confused with silhouette() that returns a tibble
with silhouette for each observation.
A double; the average silhouette.
Other cluster metric:
sse_ratio(),
sse_total(),
sse_within_total()
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) dists <- mtcars %>% as.matrix() %>% dist() silhouette_avg(kmeans_fit, dists = dists) silhouette_avg_vec(kmeans_fit, dists = dists)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) dists <- mtcars %>% as.matrix() %>% dist() silhouette_avg(kmeans_fit, dists = dists) silhouette_avg_vec(kmeans_fit, dists = dists)
Compute the ratio of the WSS to the total SSE
sse_ratio(object, ...) ## S3 method for class 'cluster_spec' sse_ratio(object, ...) ## S3 method for class 'cluster_fit' sse_ratio(object, new_data = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' sse_ratio(object, new_data = NULL, dist_fun = NULL, ...) sse_ratio_vec(object, new_data = NULL, dist_fun = Rfast::dista, ...)sse_ratio(object, ...) ## S3 method for class 'cluster_spec' sse_ratio(object, ...) ## S3 method for class 'cluster_fit' sse_ratio(object, new_data = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' sse_ratio(object, new_data = NULL, dist_fun = NULL, ...) sse_ratio_vec(object, new_data = NULL, dist_fun = Rfast::dista, ...)
object |
A fitted kmeans tidyclust model |
... |
Other arguments passed to methods. |
new_data |
A dataset to predict on. If |
dist_fun |
A function for calculating distances to centroids. Defaults to Euclidean distance on processed data. |
A tibble with 3 columns; .metric, .estimator, and .estimate.
Other cluster metric:
silhouette_avg(),
sse_total(),
sse_within_total()
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_ratio(kmeans_fit) sse_ratio_vec(kmeans_fit)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_ratio(kmeans_fit) sse_ratio_vec(kmeans_fit)
Compute the total sum of squares
sse_total(object, ...) ## S3 method for class 'cluster_spec' sse_total(object, ...) ## S3 method for class 'cluster_fit' sse_total(object, new_data = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' sse_total(object, new_data = NULL, dist_fun = NULL, ...) sse_total_vec(object, new_data = NULL, dist_fun = Rfast::dista, ...)sse_total(object, ...) ## S3 method for class 'cluster_spec' sse_total(object, ...) ## S3 method for class 'cluster_fit' sse_total(object, new_data = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' sse_total(object, new_data = NULL, dist_fun = NULL, ...) sse_total_vec(object, new_data = NULL, dist_fun = Rfast::dista, ...)
object |
A fitted kmeans tidyclust model |
... |
Other arguments passed to methods. |
new_data |
A dataset to predict on. If |
dist_fun |
A function for calculating distances to centroids. Defaults to Euclidean distance on processed data. |
A tibble with 3 columns; .metric, .estimator, and .estimate.
Other cluster metric:
silhouette_avg(),
sse_ratio(),
sse_within_total()
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_total(kmeans_fit) sse_total_vec(kmeans_fit)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_total(kmeans_fit) sse_total_vec(kmeans_fit)
Calculates Sum of Squared Error in each cluster
sse_within(object, new_data = NULL, dist_fun = Rfast::dista)sse_within(object, new_data = NULL, dist_fun = Rfast::dista)
object |
A fitted kmeans tidyclust model |
new_data |
A dataset to predict on. If |
dist_fun |
A function for calculating distances to centroids. Defaults to Euclidean distance on processed data. |
sse_within_total() is the corresponding cluster metric function
that returns the sum of the values given by sse_within().
A tibble with two columns, the cluster name and the SSE within that cluster.
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_within(kmeans_fit)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_within(kmeans_fit)
Compute the sum of within-cluster SSE
sse_within_total(object, ...) ## S3 method for class 'cluster_spec' sse_within_total(object, ...) ## S3 method for class 'cluster_fit' sse_within_total(object, new_data = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' sse_within_total(object, new_data = NULL, dist_fun = NULL, ...) sse_within_total_vec(object, new_data = NULL, dist_fun = Rfast::dista, ...)sse_within_total(object, ...) ## S3 method for class 'cluster_spec' sse_within_total(object, ...) ## S3 method for class 'cluster_fit' sse_within_total(object, new_data = NULL, dist_fun = NULL, ...) ## S3 method for class 'workflow' sse_within_total(object, new_data = NULL, dist_fun = NULL, ...) sse_within_total_vec(object, new_data = NULL, dist_fun = Rfast::dista, ...)
object |
A fitted kmeans tidyclust model |
... |
Other arguments passed to methods. |
new_data |
A dataset to predict on. If |
dist_fun |
A function for calculating distances to centroids. Defaults to Euclidean distance on processed data. |
Not to be confused with sse_within() that returns a tibble
with within-cluster SSE, one row for each cluster.
A tibble with 3 columns; .metric, .estimator, and .estimate.
Other cluster metric:
silhouette_avg(),
sse_ratio(),
sse_total()
kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_within_total(kmeans_fit) sse_within_total_vec(kmeans_fit)kmeans_spec <- k_means(num_clusters = 5) %>% set_engine("stats") kmeans_fit <- fit(kmeans_spec, ~., mtcars) sse_within_total(kmeans_fit) sse_within_total_vec(kmeans_fit)
This method tidies the model in a tidyclust model object, if it exists.
## S3 method for class 'cluster_fit' tidy(x, ...)## S3 method for class 'cluster_fit' tidy(x, ...)
x |
An object to be converted into a tidy |
... |
Additional arguments to tidying method. |
a tibble
translate_tidyclust() will translate_tidyclust a model specification into a
code object that is specific to a particular engine (e.g. R package). It
translate tidyclust generic parameters to their counterparts.
translate_tidyclust(x, ...) ## Default S3 method: translate_tidyclust(x, engine = x$engine, ...)translate_tidyclust(x, ...) ## Default S3 method: translate_tidyclust(x, engine = x$engine, ...)
x |
A model specification. |
... |
Not currently used. |
engine |
The computational engine for the model (see |
translate_tidyclust() produces a template call that lacks the
specific argument values (such as data, etc). These are filled in once
fit() is called with the specifics of the data for the model. The call
may also include tune() arguments if these are in the specification. To
handle the tune() arguments, you need to use the tune package. For more information see
https://www.tidymodels.org/start/tuning/
It does contain the resolved argument names that are specific to the model fitting function/engine.
This function can be useful when you need to understand how tidyclust
goes from a generic model specific to a model fitting function.
Note: this function is used internally and users should only use it to understand what the underlying syntax would be. It should not be used to modify the cluster specification.
Prints translated code.
tune_cluster() computes a set of performance metrics (e.g. accuracy or
RMSE) for a pre-defined set of tuning parameters that correspond to a model
or recipe across one or more resamples of the data.
tune_cluster(object, ...) ## S3 method for class 'cluster_spec' tune_cluster( object, preprocessor, resamples, ..., param_info = NULL, grid = 10, metrics = NULL, control = tune::control_grid() ) ## S3 method for class 'workflow' tune_cluster( object, resamples, ..., param_info = NULL, grid = 10, metrics = NULL, control = tune::control_grid() )tune_cluster(object, ...) ## S3 method for class 'cluster_spec' tune_cluster( object, preprocessor, resamples, ..., param_info = NULL, grid = 10, metrics = NULL, control = tune::control_grid() ) ## S3 method for class 'workflow' tune_cluster( object, resamples, ..., param_info = NULL, grid = 10, metrics = NULL, control = tune::control_grid() )
object |
A |
... |
Not currently used. |
preprocessor |
A traditional model formula or a recipe created using
|
resamples |
An |
param_info |
A |
grid |
A data frame of tuning combinations or a positive integer. The data frame should have columns for each parameter being tuned and rows for tuning parameter candidates. An integer denotes the number of candidate parameter sets to be created automatically. |
metrics |
A |
control |
An object used to modify the tuning process. Defaults to
|
An updated version of resamples with extra list columns for
.metrics and .notes (optional columns are .predictions and
.extracts). .notes contains warnings and errors that occur during
execution.
library(recipes) library(rsample) library(workflows) library(tune) rec_spec <- recipe(~., data = mtcars) %>% step_normalize(all_numeric_predictors()) %>% step_pca(all_numeric_predictors()) kmeans_spec <- k_means(num_clusters = tune()) wflow <- workflow() %>% add_recipe(rec_spec) %>% add_model(kmeans_spec) grid <- tibble(num_clusters = 1:3) set.seed(4400) folds <- vfold_cv(mtcars, v = 2) res <- tune_cluster( wflow, resamples = folds, grid = grid ) res collect_metrics(res)library(recipes) library(rsample) library(workflows) library(tune) rec_spec <- recipe(~., data = mtcars) %>% step_normalize(all_numeric_predictors()) %>% step_pca(all_numeric_predictors()) kmeans_spec <- k_means(num_clusters = tune()) wflow <- workflow() %>% add_recipe(rec_spec) %>% add_model(kmeans_spec) grid <- tibble(num_clusters = 1:3) set.seed(4400) folds <- vfold_cv(mtcars, v = 2) res <- tune_cluster( wflow, resamples = folds, grid = grid ) res collect_metrics(res)
If parameters of a cluster specification need to be modified,
update() can be used in lieu of recreating the object from scratch.
## S3 method for class 'hier_clust' update( object, parameters = NULL, num_clusters = NULL, cut_height = NULL, linkage_method = NULL, fresh = FALSE, ... ) ## S3 method for class 'k_means' update(object, parameters = NULL, num_clusters = NULL, fresh = FALSE, ...)## S3 method for class 'hier_clust' update( object, parameters = NULL, num_clusters = NULL, cut_height = NULL, linkage_method = NULL, fresh = FALSE, ... ) ## S3 method for class 'k_means' update(object, parameters = NULL, num_clusters = NULL, fresh = FALSE, ...)
object |
A cluster specification. |
parameters |
A 1-row tibble or named list with main parameters to
update. Use either |
num_clusters |
Positive integer, number of clusters in model. |
cut_height |
Positive double, height at which to cut dendrogram to
obtain cluster assignments (only used if |
linkage_method |
the agglomeration method to be used. This should be (an
unambiguous abbreviation of) one of |
fresh |
A logical for whether the arguments should be modified in-place or replaced wholesale. |
... |
Not used for |
An updated cluster specification.
kmeans_spec <- k_means(num_clusters = 5) kmeans_spec update(kmeans_spec, num_clusters = 1) update(kmeans_spec, num_clusters = 1, fresh = TRUE) param_values <- tibble::tibble(num_clusters = 10) kmeans_spec %>% update(param_values)kmeans_spec <- k_means(num_clusters = 5) kmeans_spec update(kmeans_spec, num_clusters = 1) update(kmeans_spec, num_clusters = 1, fresh = TRUE) param_values <- tibble::tibble(num_clusters = 10) kmeans_spec %>% update(param_values)