diff --git a/R/DPMGibbsN.R b/R/DPMGibbsN.R index d9073b1..fe6e026 100644 --- a/R/DPMGibbsN.R +++ b/R/DPMGibbsN.R @@ -37,7 +37,6 @@ #' is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -58,7 +57,6 @@ #' \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"gaussian"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsN_SeqPrior.R b/R/DPMGibbsN_SeqPrior.R index 75eb0ee..880748a 100644 --- a/R/DPMGibbsN_SeqPrior.R +++ b/R/DPMGibbsN_SeqPrior.R @@ -37,7 +37,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -57,7 +56,6 @@ #' \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} #' \item{\code{clust_distrib}:}{ the parametric distribution of the mixture component - \code{"gaussian"}} #' \item{\code{hyperG0}:}{ the prior on the cluster location} -#' } #' #'@author Boris Hejblum, Chariff Alkhassim #' diff --git a/R/DPMGibbsN_parallel.R b/R/DPMGibbsN_parallel.R index e9edf3f..c23b896 100644 --- a/R/DPMGibbsN_parallel.R +++ b/R/DPMGibbsN_parallel.R @@ -50,7 +50,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -71,7 +70,6 @@ #' \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"gaussian"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsSkewN.R b/R/DPMGibbsSkewN.R index ba4cd4c..27256c0 100644 --- a/R/DPMGibbsSkewN.R +++ b/R/DPMGibbsSkewN.R @@ -37,7 +37,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -53,7 +52,6 @@ #' \item{\code{nb_mcmcit}:}{the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewnorm"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsSkewN_parallel.R b/R/DPMGibbsSkewN_parallel.R index bc2c534..8438141 100644 --- a/R/DPMGibbsSkewN_parallel.R +++ b/R/DPMGibbsSkewN_parallel.R @@ -53,7 +53,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -69,7 +68,6 @@ #' \item{\code{nb_mcmcit}:}{the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewnorm"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsSkewT.R b/R/DPMGibbsSkewT.R index 85194af..a66b5a1 100644 --- a/R/DPMGibbsSkewT.R +++ b/R/DPMGibbsSkewT.R @@ -60,7 +60,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}: }{ a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -77,7 +76,6 @@ #' \item{\code{nb_mcmcit}: }{the number of MCMC iterations} #' \item{\code{clust_distrib}: }{the parametric distribution of the mixture component - \code{"skewt"}} #' \item{\code{hyperG0}: }{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsSkewT_SeqPrior.R b/R/DPMGibbsSkewT_SeqPrior.R index 9d96ac8..c2eb4c4 100644 --- a/R/DPMGibbsSkewT_SeqPrior.R +++ b/R/DPMGibbsSkewT_SeqPrior.R @@ -35,7 +35,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -52,7 +51,6 @@ #' \item{\code{nb_mcmcit}:}{the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewt"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsSkewT_SeqPrior_parallel.R b/R/DPMGibbsSkewT_SeqPrior_parallel.R index 6e2d7de..01a5e95 100644 --- a/R/DPMGibbsSkewT_SeqPrior_parallel.R +++ b/R/DPMGibbsSkewT_SeqPrior_parallel.R @@ -46,7 +46,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -63,7 +62,6 @@ #' \item{\code{nb_mcmcit}:}{the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewt"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMGibbsSkewT_parallel.R b/R/DPMGibbsSkewT_parallel.R index 4a9d202..198a1d9 100644 --- a/R/DPMGibbsSkewT_parallel.R +++ b/R/DPMGibbsSkewT_parallel.R @@ -49,7 +49,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -66,7 +65,6 @@ #' \item{\code{nb_mcmcit}:}{the number of MCMC iterations} #' \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewt"}} #' \item{\code{hyperG0}:}{the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/DPMpost.R b/R/DPMpost.R index 8fa1583..a577236 100644 --- a/R/DPMpost.R +++ b/R/DPMpost.R @@ -57,7 +57,6 @@ #'Only used if \code{doPlot} is \code{TRUE}. #' #'@return a object of class \code{DPMclust} with the following attributes: -#' \itemize{ #' \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each #' element \code{mcmc_partitions[n]} is a vector of length #' \code{n} giving the partition of the \code{n} observations.} @@ -74,7 +73,6 @@ #' \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} #' \item{\code{clust_distrib}:}{ the parametric distribution of the mixture component} #' \item{\code{hyperG0}:}{ the prior on the cluster location} -#' } #' #'@author Boris Hejblum #' diff --git a/R/RcppExports.R b/R/RcppExports.R index 851b0d8..f4a1c6e 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -49,9 +49,8 @@ FmeasureC_no0 <- function(pred, ref) { #'@param c a matrix where each column is one MCMC partition #' #'@return a list with the following elements: -#'\itemize{ #' \item{\code{Fmeas:}}{ TODO} -#'} +#' \item{\code{cost:}}{ TODO} #'@export #' #'@examples @@ -382,11 +381,9 @@ mmvtpdfC <- function(x, mean, varcovM, df, Log = TRUE) { #'@param loglik logical flag or returning the log-likelihood instead of the likelihood. #'Default is \code{TRUE}. #'@return a list: -#'\itemize{ #'\item{\code{"indiv"}:}{ vector of likelihood of length n;} #'\item{\code{"clust"}:}{ vector of likelihood of length K;} #'\item{\code{"total"}:}{ total (log)-likelihood;} -#'} #' #'@author Boris Hejblum #' @@ -447,11 +444,9 @@ mvnpdfC <- function(x, mean, varcovM, Log = TRUE) { #'@param loglik logical flag or returning the log-likelihood instead of the likelihood. #'Default is \code{TRUE}. #'@return a list: -#'\itemize{ #'\item{\code{"indiv"}:}{ vector of likelihood of length n;} #'\item{\code{"clust"}:}{ vector of likelihood of length K;} #'\item{\code{"total"}:}{ total (log)-likelihood;} -#'} #' #'@author Boris Hejblum #' @@ -475,11 +470,9 @@ mvsnlikC <- function(x, c, clustval, xi, psi, sigma, loglik = TRUE) { #'@param loglik logical flag or returning the log-likelihood instead of the likelihood. #'Default is \code{TRUE}. #'@return a list: -#'\itemize{ #'\item{\code{"indiv"}:}{ vector of likelihood of length n;} #'\item{\code{"clust"}:}{ vector of likelihood of length K;} #'\item{\code{"total"}:}{ total (log)-likelihood;} -#'} #' #'@author Boris Hejblum #' diff --git a/R/cluster_est_Fmeasure.R b/R/cluster_est_Fmeasure.R index a196886..40c7d5d 100644 --- a/R/cluster_est_Fmeasure.R +++ b/R/cluster_est_Fmeasure.R @@ -10,7 +10,6 @@ #'partition from \code{c} used to break ties when minimizing the cost function #' #'@return a \code{list}: -#' \itemize{ #' \item{\code{c_est}:}{ a vector of length \code{n}. Point estimate of the partition} #' \item{\code{cost}:}{ a vector of length \code{N}. \code{cost[j]} is the cost #' associated to partition \code{c[[j]]}} @@ -18,7 +17,6 @@ #' (see \code{\link{similarityMat}})} #' \item{\code{opt_ind}:}{ the index of the optimal partition #' among the MCMC iterations.} -#' } #' #' #'@author Francois Caron, Boris Hejblum diff --git a/R/cluster_est_Mbinder_norm.R b/R/cluster_est_Mbinder_norm.R index 88eaa76..e19facb 100644 --- a/R/cluster_est_Mbinder_norm.R +++ b/R/cluster_est_Mbinder_norm.R @@ -31,7 +31,6 @@ #'partition from \code{c} used to break ties when minimizing the cost function #' #'@return a \code{list}: -#' \itemize{ #' \item{\code{c_est}:}{ a vector of length \code{n}. Point estimate of the partition} #' \item{\code{cost}:}{ a vector of length \code{N}. \code{cost[j]} is the cost #' associated to partition \code{c[[j]]}} @@ -39,7 +38,6 @@ #' (see \code{\link{similarityMat}})} #' \item{\code{opt_ind}:}{ the index of the optimal partition #' among the MCMC iterations.} -#' } #' #' #'@author Chariff Alkhassim diff --git a/R/cluster_est_pear.R b/R/cluster_est_pear.R index 6796e9e..2d12e45 100644 --- a/R/cluster_est_pear.R +++ b/R/cluster_est_pear.R @@ -7,7 +7,6 @@ #' #' #'@return a \code{list}: -#' \itemize{ #' \item{\code{c_est}:}{ a vector of length \code{n}. Point estimate of the partition} #' \item{\code{pear}:}{ a vector of length \code{N}. \code{pear[j]} is the #' posterior expected adjusted Rand index associated to partition \code{c[[j]]}} @@ -15,7 +14,6 @@ #' (see \code{\link{similarityMat}})} #' \item{\code{opt_ind}:}{ the index of the optimal partition #' among the MCMC iterations.} -#' } #' #' #'@author Chariff Alkhassim diff --git a/R/evalClustLoss.R b/R/evalClustLoss.R index 60342b3..1a3601b 100644 --- a/R/evalClustLoss.R +++ b/R/evalClustLoss.R @@ -12,10 +12,10 @@ #'Either "F-measure" or "Binder" (see Details). Default is "F-measure". #' #'@param a only relevant if \code{lossFn} is "Binder". Penalty for wrong -#'co-clustering in \code{c} compared to code{gs}. Defaults is 1. +#'co-clustering in \code{c} compared to \code{gs}. Defaults is 1. #' #'@param b only relevant if \code{lossFn} is "Binder". Penalty for missed -#'co-clustering in \code{c} compared to code{gs}. Defaults is 1. +#'co-clustering in \code{c} compared to \code{gs}. Defaults is 1. #' #'@return the cost of the point estimate \code{c} in regard of the #'gold standard \code{gs} for a given loss function. diff --git a/R/postProcess.DPMMclust.R b/R/postProcess.DPMMclust.R index 9f972b3..b656606 100644 --- a/R/postProcess.DPMMclust.R +++ b/R/postProcess.DPMMclust.R @@ -19,14 +19,12 @@ #'@param ... further arguments passed to or from other methods #' #'@return a \code{list}: -#' \itemize{ #' \item{\code{burnin}:}{an integer passing along the \code{burnin} argument} #' \item{\code{thin}:}{an integer passing along the \code{thin} argument} #' \item{\code{lossFn}:}{a character string passing along the \code{lossFn} argument} #' \item{\code{point_estim}:}{} #' \item{\code{loss}:}{} #' \item{\code{index_estim}:}{} -#' } #' #'@details The cost of a point estimate partition is calculated using either a pairwise #' coincidence loss function (Binder), or 1-Fmeasure (F-measure). diff --git a/R/summary.DPMMclust.R b/R/summary.DPMMclust.R index fef8275..1925aa7 100644 --- a/R/summary.DPMMclust.R +++ b/R/summary.DPMMclust.R @@ -21,7 +21,6 @@ #'@param ... further arguments passed to or from other methods #' #'@return a \code{list} containing the following elements: -#' \itemize{ #' \item{\code{nb_mcmcit}:}{ an integer giving the value of \code{m}, the number of retained #' sampled partitions, i.e. \code{(N - burnin)/thin}} #' \item{\code{burnin}:}{ an integer passing along the \code{burnin} argument} @@ -45,7 +44,6 @@ #' \item{\code{U_SS_list}:}{ a list of length \code{m} containing the containing the lists of sufficient statistics for all the mixture components, #' for each sampled partition} #' \item{\code{data}: a \code{d x n} matrix containing the clustered data} -#' } #' #' #'@details The cost of a point estimate partition is calculated using either a pairwise diff --git a/cran-comments.md b/cran-comments.md index 6dfdb0a..2fbcd7e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,7 +2,7 @@ ## Test environments * local R installation, R 4.3.2 on macOS 13.5.2 - * Linux (Ubuntu 20.04), macOS (11.6) and Windows (Server 2019 10.0), R devel and release (through GitHub Actions) + * Linux (Ubuntu 22.04), macOS (12.7) and Windows (Server 2022 10.0), R devel and release (through GitHub Actions) ## R CMD check results 0 errors | 0 warnings | 0 note diff --git a/man/DPMGibbsN.Rd b/man/DPMGibbsN.Rd index ea70356..4376f15 100644 --- a/man/DPMGibbsN.Rd +++ b/man/DPMGibbsN.Rd @@ -57,7 +57,6 @@ is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -78,7 +77,6 @@ and \code{n} observations in columns.} \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"gaussian"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ Slice Sampling of the Dirichlet Process Mixture Model with a prior on alpha diff --git a/man/DPMGibbsN_SeqPrior.Rd b/man/DPMGibbsN_SeqPrior.Rd index 2aa27c2..30c2b55 100644 --- a/man/DPMGibbsN_SeqPrior.Rd +++ b/man/DPMGibbsN_SeqPrior.Rd @@ -57,7 +57,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -77,7 +76,6 @@ and \code{n} observations in columns.} \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} \item{\code{clust_distrib}:}{ the parametric distribution of the mixture component - \code{"gaussian"}} \item{\code{hyperG0}:}{ the prior on the cluster location} - } } \description{ Slice Sampling of Dirichlet Process Mixture of Gaussian distributions diff --git a/man/DPMGibbsN_parallel.Rd b/man/DPMGibbsN_parallel.Rd index ceb528e..e4f8d30 100644 --- a/man/DPMGibbsN_parallel.Rd +++ b/man/DPMGibbsN_parallel.Rd @@ -73,7 +73,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -94,7 +93,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"gaussian"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ Slice Sampling of the Dirichlet Process Mixture Model diff --git a/man/DPMGibbsSkewN.Rd b/man/DPMGibbsSkewN.Rd index 2f1631e..fd3b3ff 100644 --- a/man/DPMGibbsSkewN.Rd +++ b/man/DPMGibbsSkewN.Rd @@ -58,7 +58,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -74,7 +73,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewnorm"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ Slice Sampling of Dirichlet Process Mixture of skew normal distributions diff --git a/man/DPMGibbsSkewN_parallel.Rd b/man/DPMGibbsSkewN_parallel.Rd index 3ee744d..ac9a250 100644 --- a/man/DPMGibbsSkewN_parallel.Rd +++ b/man/DPMGibbsSkewN_parallel.Rd @@ -72,7 +72,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -88,7 +87,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewnorm"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ If the \code{monitorfile} argument is a character string naming a file to diff --git a/man/DPMGibbsSkewT.Rd b/man/DPMGibbsSkewT.Rd index 626c268..dd1b9d9 100644 --- a/man/DPMGibbsSkewT.Rd +++ b/man/DPMGibbsSkewT.Rd @@ -81,7 +81,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}: }{ a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -98,7 +97,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}: }{the number of MCMC iterations} \item{\code{clust_distrib}: }{the parametric distribution of the mixture component - \code{"skewt"}} \item{\code{hyperG0}: }{the prior on the cluster location} - } } \description{ Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions diff --git a/man/DPMGibbsSkewT_SeqPrior.Rd b/man/DPMGibbsSkewT_SeqPrior.Rd index 6d5a75d..d4e50a9 100644 --- a/man/DPMGibbsSkewT_SeqPrior.Rd +++ b/man/DPMGibbsSkewT_SeqPrior.Rd @@ -56,7 +56,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -73,7 +72,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewt"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions diff --git a/man/DPMGibbsSkewT_SeqPrior_parallel.Rd b/man/DPMGibbsSkewT_SeqPrior_parallel.Rd index 8080d75..84963af 100644 --- a/man/DPMGibbsSkewT_SeqPrior_parallel.Rd +++ b/man/DPMGibbsSkewT_SeqPrior_parallel.Rd @@ -69,7 +69,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -86,7 +85,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewt"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions diff --git a/man/DPMGibbsSkewT_parallel.Rd b/man/DPMGibbsSkewT_parallel.Rd index 861d607..58bc6c8 100644 --- a/man/DPMGibbsSkewT_parallel.Rd +++ b/man/DPMGibbsSkewT_parallel.Rd @@ -72,7 +72,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -89,7 +88,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{the number of MCMC iterations} \item{\code{clust_distrib}:}{the parametric distribution of the mixture component - \code{"skewt"}} \item{\code{hyperG0}:}{the prior on the cluster location} - } } \description{ Slice Sampling of Dirichlet Process Mixture of skew Student's t-distributions diff --git a/man/DPMpost.Rd b/man/DPMpost.Rd index 0b19986..21abf15 100644 --- a/man/DPMpost.Rd +++ b/man/DPMpost.Rd @@ -70,7 +70,6 @@ Only used if \code{doPlot} is \code{TRUE}.} } \value{ a object of class \code{DPMclust} with the following attributes: - \itemize{ \item{\code{mcmc_partitions}:}{ a list of length \code{N}. Each element \code{mcmc_partitions[n]} is a vector of length \code{n} giving the partition of the \code{n} observations.} @@ -87,7 +86,6 @@ and \code{n} observations in columns} \item{\code{nb_mcmcit}:}{ the number of MCMC iterations} \item{\code{clust_distrib}:}{ the parametric distribution of the mixture component} \item{\code{hyperG0}:}{ the prior on the cluster location} - } } \description{ Partially collapse slice Gibbs sampling for Dirichlet process mixture of multivariate diff --git a/man/Fmeasure_costC.Rd b/man/Fmeasure_costC.Rd index 068e54c..22d8392 100644 --- a/man/Fmeasure_costC.Rd +++ b/man/Fmeasure_costC.Rd @@ -11,9 +11,8 @@ Fmeasure_costC(c) } \value{ a list with the following elements: -\itemize{ \item{\code{Fmeas:}}{ TODO} -} + \item{\code{cost:}}{ TODO} } \description{ C++ implementation of multiple cost computations with the F-measure as the loss diff --git a/man/cluster_est_Fmeasure.Rd b/man/cluster_est_Fmeasure.Rd index f5ee34b..f860946 100644 --- a/man/cluster_est_Fmeasure.Rd +++ b/man/cluster_est_Fmeasure.Rd @@ -16,7 +16,6 @@ partition from \code{c} used to break ties when minimizing the cost function} } \value{ a \code{list}: - \itemize{ \item{\code{c_est}:}{ a vector of length \code{n}. Point estimate of the partition} \item{\code{cost}:}{ a vector of length \code{N}. \code{cost[j]} is the cost associated to partition \code{c[[j]]}} @@ -24,7 +23,6 @@ a \code{list}: (see \code{\link{similarityMat}})} \item{\code{opt_ind}:}{ the index of the optimal partition among the MCMC iterations.} - } } \description{ Get a point estimate of the partition using the F-measure as the cost function. diff --git a/man/cluster_est_Mbinder_norm.Rd b/man/cluster_est_Mbinder_norm.Rd index 552c45d..f15a321 100644 --- a/man/cluster_est_Mbinder_norm.Rd +++ b/man/cluster_est_Mbinder_norm.Rd @@ -30,7 +30,6 @@ partition from \code{c} used to break ties when minimizing the cost function} } \value{ a \code{list}: - \itemize{ \item{\code{c_est}:}{ a vector of length \code{n}. Point estimate of the partition} \item{\code{cost}:}{ a vector of length \code{N}. \code{cost[j]} is the cost associated to partition \code{c[[j]]}} @@ -38,7 +37,6 @@ a \code{list}: (see \code{\link{similarityMat}})} \item{\code{opt_ind}:}{ the index of the optimal partition among the MCMC iterations.} - } } \description{ Get a point estimate of the partition using a modified Binder loss function diff --git a/man/cluster_est_pear.Rd b/man/cluster_est_pear.Rd index b8220cf..1ebb3bc 100644 --- a/man/cluster_est_pear.Rd +++ b/man/cluster_est_pear.Rd @@ -14,7 +14,6 @@ the cluster allocation of observation \code{i=1...n} at iteration } \value{ a \code{list}: - \itemize{ \item{\code{c_est}:}{ a vector of length \code{n}. Point estimate of the partition} \item{\code{pear}:}{ a vector of length \code{N}. \code{pear[j]} is the posterior expected adjusted Rand index associated to partition \code{c[[j]]}} @@ -22,7 +21,6 @@ a \code{list}: (see \code{\link{similarityMat}})} \item{\code{opt_ind}:}{ the index of the optimal partition among the MCMC iterations.} - } } \description{ Gets a point estimate of the partition using posterior expected adjusted diff --git a/man/evalClustLoss.Rd b/man/evalClustLoss.Rd index 91ee94c..40cfc16 100644 --- a/man/evalClustLoss.Rd +++ b/man/evalClustLoss.Rd @@ -17,10 +17,10 @@ partition of the \code{n} observations.} Either "F-measure" or "Binder" (see Details). Default is "F-measure".} \item{a}{only relevant if \code{lossFn} is "Binder". Penalty for wrong -co-clustering in \code{c} compared to code{gs}. Defaults is 1.} +co-clustering in \code{c} compared to \code{gs}. Defaults is 1.} \item{b}{only relevant if \code{lossFn} is "Binder". Penalty for missed -co-clustering in \code{c} compared to code{gs}. Defaults is 1.} +co-clustering in \code{c} compared to \code{gs}. Defaults is 1.} } \value{ the cost of the point estimate \code{c} in regard of the diff --git a/man/mvnlikC.Rd b/man/mvnlikC.Rd index aced241..1348847 100644 --- a/man/mvnlikC.Rd +++ b/man/mvnlikC.Rd @@ -26,12 +26,10 @@ Default is \code{TRUE}.} } \value{ a list: -\itemize{ \item{\code{"indiv"}:}{ vector of likelihood of length n;} \item{\code{"clust"}:}{ vector of likelihood of length K;} \item{\code{"total"}:}{ total (log)-likelihood;} } -} \description{ C++ implementation of multivariate Normal probability density function for multiple inputs } diff --git a/man/mvsnlikC.Rd b/man/mvsnlikC.Rd index 7d3ea62..226fb4f 100644 --- a/man/mvsnlikC.Rd +++ b/man/mvsnlikC.Rd @@ -28,12 +28,10 @@ Default is \code{TRUE}.} } \value{ a list: -\itemize{ \item{\code{"indiv"}:}{ vector of likelihood of length n;} \item{\code{"clust"}:}{ vector of likelihood of length K;} \item{\code{"total"}:}{ total (log)-likelihood;} } -} \description{ C++ implementation of multivariate skew normal likelihood function for multiple inputs } diff --git a/man/mvstlikC.Rd b/man/mvstlikC.Rd index 899ed31..449d9ca 100644 --- a/man/mvstlikC.Rd +++ b/man/mvstlikC.Rd @@ -30,12 +30,10 @@ Default is \code{TRUE}.} } \value{ a list: -\itemize{ \item{\code{"indiv"}:}{ vector of likelihood of length n;} \item{\code{"clust"}:}{ vector of likelihood of length K;} \item{\code{"total"}:}{ total (log)-likelihood;} } -} \description{ C++ implementation of multivariate skew t likelihood function for multiple inputs } diff --git a/man/postProcess.DPMMclust.Rd b/man/postProcess.DPMMclust.Rd index 215e9ec..1e9e2e1 100644 --- a/man/postProcess.DPMMclust.Rd +++ b/man/postProcess.DPMMclust.Rd @@ -35,14 +35,12 @@ Either "F-measure" or "Binder" (see Details). Default is "F-measure".} } \value{ a \code{list}: - \itemize{ \item{\code{burnin}:}{an integer passing along the \code{burnin} argument} \item{\code{thin}:}{an integer passing along the \code{thin} argument} \item{\code{lossFn}:}{a character string passing along the \code{lossFn} argument} \item{\code{point_estim}:}{} \item{\code{loss}:}{} \item{\code{index_estim}:}{} - } } \description{ Post-processing Dirichlet Process Mixture Models results to get diff --git a/man/summary.DPMMclust.Rd b/man/summary.DPMMclust.Rd index 0c24ee0..c4ce0b6 100644 --- a/man/summary.DPMMclust.Rd +++ b/man/summary.DPMMclust.Rd @@ -35,7 +35,6 @@ computed. Default is \code{FALSE}} } \value{ a \code{list} containing the following elements: - \itemize{ \item{\code{nb_mcmcit}:}{ an integer giving the value of \code{m}, the number of retained sampled partitions, i.e. \code{(N - burnin)/thin}} \item{\code{burnin}:}{ an integer passing along the \code{burnin} argument} @@ -59,7 +58,6 @@ a \code{list} containing the following elements: \item{\code{U_SS_list}:}{ a list of length \code{m} containing the containing the lists of sufficient statistics for all the mixture components, for each sampled partition} \item{\code{data}: a \code{d x n} matrix containing the clustered data} - } } \description{ Summary methods for \code{DPMMclust} objects. diff --git a/src/FmeasureC.cpp b/src/FmeasureC.cpp index c2f268f..888cea9 100644 --- a/src/FmeasureC.cpp +++ b/src/FmeasureC.cpp @@ -143,9 +143,8 @@ double FmeasureC_no0(const NumericVector & pred, const NumericVector & ref){ //'@param c a matrix where each column is one MCMC partition //' //'@return a list with the following elements: -//'\itemize{ //' \item{\code{Fmeas:}}{ TODO} -//'} +//' \item{\code{cost:}}{ TODO} //'@export //' //'@examples diff --git a/src/mvnlikC.cpp b/src/mvnlikC.cpp index a89a761..5f0fc65 100644 --- a/src/mvnlikC.cpp +++ b/src/mvnlikC.cpp @@ -19,11 +19,9 @@ const double log2pi2 = log(2.0 * M_PI)/2.0; //'@param loglik logical flag or returning the log-likelihood instead of the likelihood. //'Default is \code{TRUE}. //'@return a list: -//'\itemize{ //'\item{\code{"indiv"}:}{ vector of likelihood of length n;} //'\item{\code{"clust"}:}{ vector of likelihood of length K;} //'\item{\code{"total"}:}{ total (log)-likelihood;} -//'} //' //'@author Boris Hejblum //' diff --git a/src/mvsnlikC.cpp b/src/mvsnlikC.cpp index 06d3aff..582aeff 100644 --- a/src/mvsnlikC.cpp +++ b/src/mvsnlikC.cpp @@ -20,11 +20,9 @@ const double log2pi2 = log(2.0 * M_PI)/2.0; //'@param loglik logical flag or returning the log-likelihood instead of the likelihood. //'Default is \code{TRUE}. //'@return a list: -//'\itemize{ //'\item{\code{"indiv"}:}{ vector of likelihood of length n;} //'\item{\code{"clust"}:}{ vector of likelihood of length K;} //'\item{\code{"total"}:}{ total (log)-likelihood;} -//'} //' //'@author Boris Hejblum //' diff --git a/src/mvstlikC.cpp b/src/mvstlikC.cpp index c6e459c..8cf9e7d 100644 --- a/src/mvstlikC.cpp +++ b/src/mvstlikC.cpp @@ -20,11 +20,9 @@ using namespace arma; //'@param loglik logical flag or returning the log-likelihood instead of the likelihood. //'Default is \code{TRUE}. //'@return a list: -//'\itemize{ //'\item{\code{"indiv"}:}{ vector of likelihood of length n;} //'\item{\code{"clust"}:}{ vector of likelihood of length K;} //'\item{\code{"total"}:}{ total (log)-likelihood;} -//'} //' //'@author Boris Hejblum //'