gagolews / genie

Genie: A Fast and Robust Hierarchical Clustering Algorithm (this R package has now been superseded by genieclust)

Prof. Marek Gagolewski

My research interests include data science, machine learning, data aggregation and clustering, computational and applied statistics, and mathematical modelling (the science of science, sport, economics, social sciences, psychometrics, bibliometrics, etc.). In my spare time, I write books for my students and develop open-source data analysis software.

Open-access textbooks

• Deep R Programming (HTML) (PDF) (paper copy) (GitHub)

• Minimalist Data Wrangling in Python (HTML) (PDF) (paper copy) (GitHub)

Software

Python packages

• genieclust – Fast and robust hierarchical clustering with noise point detection (GitHub) (PyPI) (paper)
• clustering-benchmarks – A framework for benchmarking clustering algorithms (GitHub) (PyPI) (paper)

R packages

• stringi – Fast and portable character string processing in R (one of the most often downloaded packages for R) (GitHub) (CRAN) (paper)
• genieclust – Fast and robust hierarchical clustering with noise point detection (GitHub) (CRAN) (paper)
• stringx – Drop-in replacements for base R string functions powered by stringi (GitHub) (CRAN)
• realtest – Where expectations meet reality: Realistic unit testing in R (GitHub) (CRAN)
• TurtleGraphics – Learn computer programming in R while having a jolly time! (GitHub) (CRAN)

Data

• Clustering benchmarks (framework, datasets, results)
• Datasets for teaching

genie's Issues

installation of genie

I am trying to install the genie package (R 3.4.0, Linux 64 Mint) and get the message below. From the message I can't see what the problem is, can you help me out?

> install.packages("genie", dep = T)
Installing package into '/home/henk/R/x86_64-pc-linux-gnu-library/3.4'
(as 'lib' is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/genie_1.0.4.tar.gz'
Content type 'application/x-gzip' length 30845 bytes (30 KB)
==================================================
downloaded 30 KB

* installing *source* package ‘genie’ ...
** package ‘genie’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG  -I"/home/henk/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"   -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
In file included from /home/henk/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/Rcpp.h:34:0,
                 from RcppExports.cpp:4:
/home/henk/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/Rcpp/grow.h:73:47: fatal error: Rcpp/generated/grow__pairlist.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'RcppExports.o' failed
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘genie’
* removing ‘/home/henk/R/x86_64-pc-linux-gnu-library/3.4/genie’
Warning in install.packages :
  installation of package 'genie' had non-zero exit status

The downloaded source packages are in
	'/tmp/RtmpCiD3pB/downloaded_packages'

how to find best thresholdgini ??

hi @gagolews ,
what's threshlodgini meaning in hclust2? a deadline, over which belongs to group a ,else belongs to group b ? or sm other interesting things ?
how to find the best thresholegini in hclust2 ?

This package has been superseded by `genieclust`

see https://genieclust.gagolewski.com/

OWA-based linkages

Add support for the "smoothed" single linkage (OWAs over few nearest neighbours) as described in our manuscript submitted for publication in Information Sciences.