knitr::opts_chunk$set(echo = TRUE)
For a description of the Reinert clustering method and its implementation in rainette
, please see the algorithms description vignette.
As it doesn't take into account terms frequencies but only there presence / absence, and as it assigns each document to only one cluster, the Reinert method must be applied to short and "homogeneous" documents. It could be ok if you work on tweets or short answers to a specific question, but with longer documents they must first be split into short textual segments.
You can use the split_segments()
function for that, and it can be applied directly on a tm
or
quanteda
corpus. In this article we will apply it to the sample data_corpus_inaugural
corpus provided by quanteda
.
library(quanteda) library(rainette) ## Split documents into segments corpus <- split_segments(data_corpus_inaugural, segment_size = 40)
split_segments
will split the original texts into smaller chunks, attempting to
respect sentences and punctuation when possible. The function takes two
arguments :
segment_size
: the preferred segment size, in wordssegment_size_window
: the "window" into which looking for the best segment
split, in words. If NULL
, it is set to 0.4 * segment_size
.The result of the function is a quanteda
corpus, which keeps the
original corpus metadata and adds an additional segment_source
variable, which keeps track of which segment belongs to which document.
corpus
head(docvars(corpus))
The next step is to compute the document-feature matrix. As our corpus
object is
a quanteda
corpus, we can tokenize it and then use the dfm()
function.
tok <- tokens(corpus, remove_punct = TRUE) tok <- tokens_tolower(tok) tok <- tokens_remove(tok, stopwords("en")) dtm <- dfm(tok)
We also filter out terms that appear in less than 10 segments by using dfm_trim
.
dtm <- dfm_trim(dtm, min_docfreq = 10)
We are now ready to compute a simple Reinert clustering by using the
rainette()
function. Its main arguments are :
k
: the number of clusters to compute.min_segment_size
: the minimum number of terms in each segment.
If a segment contains less than this number of terms, it will be merged
with the following or previous one if they come from the same source document.
The default value is 0, ie no merging is done.min_split_members
: if a cluster is smaller than this value, it won't be
split afterwards (default : 5).Here we will compute 5 clusters with a min_segment_size
of 15 :
res <- rainette(dtm, k = 5, min_segment_size = 15)
To help exploring the clustering results, rainette
provides an interactive interface which can be launched with rainette_explor()
:
rainette_explor(res, dtm, corpus)
The interface allows to change the number of clusters, the displayed statistic, etc., and see the result in real time. By default the most specific terms are displayed with a blue bar or a red one for those with a negative keyness (if Show negative values has been checked).
You can also click on the Get R code button to get the R code to reproduce the current plot and to compute cluster membership.
The Cluster documents tab allows to browse the documents from a given cluster. You can filter them by giving a term or a regular expression in the Filter by term field :
You can use cutree
to get each document cluster at
level k
:
cluster <- cutree(res, k = 5)
This vector can be used, for example, as a new corpus metadata variable :
corpus$cluster <- cutree(res, k = 5) head(docvars(corpus))
Here, the clusters have been assigned to the segments, not to the original documents as a whole. The clusters_by_doc_table
allows to display, for each original document, the number of segment belonging to each cluster :
clusters_by_doc_table(corpus, clust_var = "cluster")
By adding prop = TRUE
, the same table is displayed with row percentages :
clusters_by_doc_table(corpus, clust_var = "cluster", prop = TRUE)
Conversely, the docs_by_cluster_table
allows to display, for each cluster, the number and proportion of original document including at least one segment of this cluster :
docs_by_cluster_table(corpus, clust_var = "cluster")
rainette
also provides a "double clustering" algorithm, as described in the algorithms description vignette : two simple clusterings are computed with different min_segment_size
values, and then crossed together to get more robust clusters.
This can be done with the rainette2()
function, which can be applied to two already
computed simple clusterings. Here, we compute them with min_segment_size
at 10 and 15.
res1 <- rainette(dtm, k = 5, min_segment_size = 10) res2 <- rainette(dtm, k = 5, min_segment_size = 15)
We then use rainette2()
to combine them. The max_k
argument is used to specify the maximum number of clusters.
res <- rainette2(res1, res2, max_k = 5)
One important argument of rainette2()
is the full
argument :
full = TRUE
(the default), the best crossed clusters partition selection is made by keeping all non empty crossed clusters. This allows an exhaustive search and to identify the partition either with the highest sum of association χ², or the one with the highest total size. However, computation times can rise rapidly with the number of clusters.full = FALSE
, only the crossed clusters whose clusters are the most mutually associated are kept. Computations are much faster, but the highest k level with available partitions may be lower, and only the partitions with the highest association χ² values can be identified.To be noted : with full = TRUE
, if runtime is too high you can add the parallel = TRUE
argument to paralellise some computations (won't work on Windows, though, and may use much more RAM).
In both cases, the resulting object is a tibble with, for each level k, the optimal
partitions and their characteristics. Another interactive interface is
available to explore the results. It is launched with rainette2_explor()
.
rainette2_explor(res, dtm, corpus)
The interface is very similar to the previous one, except there is no
dendrogram anymore, but a single barplot of cluster sizes instead. Be
careful of the number of NA
(not assigned segments), as it can be quite
high.
If some points are not assigned to any cluster, you can use
rainette2_complete_groups()
to assign them to the nearest one by using a
k-nearest-neighbors algorithm (with k=1). However this may not be recommended as you would then loose the "robustness" of the new clusters computed by rainette2()
.
clusters <- cutree(res, k = 5) clusters_completed <- rainette2_complete_groups(dtm, clusters)
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