问题
I want to do hierarchical clustering by using cosine similarity with the R programming language for corpus of documents, but I got the following error:
Error in if (is.na(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") : missing value where TRUE/FALSE needed
What should I do?
To reproduce it, here's an example:
library(tm)
doc <- c( "The sky is blue.", "The sun is bright today.", "The sun in the sky is bright.", "We can see the shining sun, the bright sun." )
doc_corpus <- Corpus( VectorSource(doc) )
control_list <- list(removePunctuation = TRUE, stopwords = TRUE, tolower = TRUE)
tdm <- TermDocumentMatrix(doc_corpus, control = control_list)
tf <- as.matrix(tdm)
( idf <- log( ncol(tf) / ( 1 + rowSums(tf != 0) ) ) )
( idf <- diag(idf) )
tf_idf <- crossprod(tf, idf)
colnames(tf_idf) <- rownames(tf)
tf_idf
cosine_dist = 1-crossprod(tf_idf) /(sqrt(colSums(tf_idf^2)%*%t(colSums(tf_idf^2))))
cluster1 <- hclust(cosine_dist, method = "ward.D")
Then I get the error:
Error in if (is.na(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") : missing value where TRUE/FALSE needed
回答1:
There are 2 issues:
1: cosine_dist = 1-crossprod(tf_idf) /(sqrt(colSums(tf_idf^2)%*%t(colSums(tf_idf^2))))
creates NaN's because you divide by 0.
2: hclust
needs a dist object, not just a matrix. See ?hclust
for more details
Both can be solved with the following code:
.....
cosine_dist = 1-crossprod(tf_idf) /(sqrt(colSums(tf_idf^2)%*%t(colSums(tf_idf^2))))
# remove NaN's by 0
cosine_dist[is.na(cosine_dist)] <- 0
# create dist object
cosine_dist <- as.dist(cosine_dist)
cluster1 <- hclust(cosine_dist, method = "ward.D")
plot(cluster1)
来源:https://stackoverflow.com/questions/52391558/hierarchical-clustering-using-cosine-distance-in-r