diff --git a/DESCRIPTION b/DESCRIPTION index 84f60f5..c79aae0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: aricode Type: Package Title: Efficient Computations of Standard Clustering Comparison Measures -Version: 1.0.2 +Version: 1.0.3 Authors@R: c( person("Julien", "Chiquet", role = c("aut", "cre"), email = "julien.chiquet@inrae.fr", comment = c(ORCID = "0000-0002-3629-3429")), diff --git a/NEWS.md b/NEWS.md index 5dcfe9f..60e0eb1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +## aricode 1.0-3 (2023-10-19) + +- minor fix in package documentation due to evolution of roxygen2 7.0.0 . + ## aricode 1.0-2 (2022-12-14) - fix a serious bug in the AMI function pointed by Florent Bersani diff --git a/R/aricode-package.R b/R/aricode-package.R index 9295a73..73a9109 100644 --- a/R/aricode-package.R +++ b/R/aricode-package.R @@ -1,3 +1,6 @@ +#' @keywords internal +"_PACKAGE" + #' aricode #' #' A package for efficient computations of standard clustering comparison measures. Most of the available measures are described in the paper of Vinh et al, JMLR, 2009 (see reference below). @@ -24,8 +27,12 @@ #' @author Martina Sundqvist \email{martina.sundqvist@@agroparistech.fr} #' @references Nguyen Xuan Vinh, Julien Epps, and James Bailey. "Information theoretic measures for clusterings comparison: Variants, properties, normalization and correction for chance." Journal of Machine Learning Research 11.Oct (2010): 2837-2854. as described in Vinh et al (2009) #' @seealso \code{\link{ARI}}, \code{\link{RI}}, \code{\link{NID}}, \code{\link{NVI}}, \code{\link{AMI}}, \code{\link{NMI}}, \code{\link{entropy}}, \code{\link{clustComp}} -#' @docType package -#' @name aricode +#' @name aricode-package + +# The following block is used by usethis to automatically manage +# roxygen namespace tags. Modify with care! +## usethis namespace: start #' @useDynLib aricode #' @importFrom Rcpp sourceCpp +## usethis namespace: end NULL diff --git a/inst/WORDLIST b/inst/WORDLIST index 35d9ab8..b0e9731 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,20 +1,23 @@ -al AMI ARI -clustComp -doi -EMI -entropies +CMD Epps -et JMLR Lifecycle MARIraw -mclust NID NMI NVI -sortPairs +ORCID SortPairs Vinh Xuan +al +clustComp +doi +entropies +et +mclust +radix +roxygen +sortPairs diff --git a/man/aricode.Rd b/man/aricode-package.Rd similarity index 60% rename from man/aricode.Rd rename to man/aricode-package.Rd index 3c789b2..62c5c99 100644 --- a/man/aricode.Rd +++ b/man/aricode-package.Rd @@ -1,10 +1,13 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/aricode-package.R \docType{package} -\name{aricode} +\name{aricode-package} \alias{aricode} -\title{aricode} +\alias{aricode-package} +\title{aricode: Efficient Computations of Standard Clustering Comparison Measures} \description{ +Implements an efficient O(n) algorithm based on bucket-sorting for fast computation of standard clustering comparison measures. Available measures include adjusted Rand index (ARI), normalized information distance (NID), normalized mutual information (NMI), adjusted mutual information (AMI), normalized variation information (NVI) and entropy, as described in Vinh et al (2009) \doi{10.1145/1553374.1553511}. Include AMI (Adjusted Mutual Information) since version 0.1.2, a modified version of ARI (MARI), as described in Sundqvist et al. \doi{10.1007/s00180-022-01230-7} and simple Chi-square distance since version 1.0.0. + A package for efficient computations of standard clustering comparison measures. Most of the available measures are described in the paper of Vinh et al, JMLR, 2009 (see reference below). } \details{ @@ -32,12 +35,35 @@ The functions included in aricode are: Nguyen Xuan Vinh, Julien Epps, and James Bailey. "Information theoretic measures for clusterings comparison: Variants, properties, normalization and correction for chance." Journal of Machine Learning Research 11.Oct (2010): 2837-2854. as described in Vinh et al (2009) } \seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/jchiquet/aricode (dev version)} + \item Report bugs at \url{https://github.com/jchiquet/aricode/issues} +} + + \code{\link{ARI}}, \code{\link{RI}}, \code{\link{NID}}, \code{\link{NVI}}, \code{\link{AMI}}, \code{\link{NMI}}, \code{\link{entropy}}, \code{\link{clustComp}} } \author{ +\strong{Maintainer}: Julien Chiquet \email{julien.chiquet@inrae.fr} (\href{https://orcid.org/0000-0002-3629-3429}{ORCID}) + +Authors: +\itemize{ + \item Guillem Rigaill \email{guillem.rigaill@inrae.fr} + \item Martina Sundqvist \email{martina.sundqvist@agroparistech.fr} +} + +Other contributors: +\itemize{ + \item Valentin Dervieux \email{valentin.dervieux@gmail.com} [contributor] + \item Florent Bersani \email{florent@bersani.org} [contributor] +} + + Julien Chiquet \email{julien.chiquet@inrae.fr} Guillem Rigaill \email{guillem.rigaill@inrae.fr} Martina Sundqvist \email{martina.sundqvist@agroparistech.fr} } +\keyword{internal}