R/concept_lattice.R

#' @title
#' R6 class for a concept lattice
#'
#' @description
#' This class implements the data structure and methods for concept lattices.
#'
#' @examples
#' # Build a formal context
#' fc_planets <- FormalContext$new(planets)
#'
#' # Find the concepts
#' fc_planets$find_concepts()
#'
#' # Find join- and meet- irreducible elements
#' fc_planets$concepts$join_irreducibles()
#' fc_planets$concepts$meet_irreducibles()
#'
#' # Get concept support
#' fc_planets$concepts$support()
#'
#' @export
#' @import R6
#'
ConceptLattice <- R6::R6Class(

  classname = "ConceptLattice",

  inherit = ConceptSet,

  public = list(

    #' @description
    #' Create a new \code{ConceptLattice} object.
    #'
    #' @param extents (\code{dgCMatrix}) The extents of all concepts
    #' @param intents (\code{dgCMatrix}) The intents of all concepts
    #' @param objects (character vector) Names of the objects in the formal context
    #' @param attributes (character vector) Names of the attributes in the formal context
    #' @param I (\code{dgCMatrix}) The matrix of the formal context
    #'
    #' @return
    #' A new \code{ConceptLattice} object.
    #'
    #' @export
    initialize = function(extents, intents,
                          objects, attributes,
                          I = NULL) {

      private$objects <- objects
      private$attributes <- attributes
      private$pr_extents <- extents
      private$pr_intents <- intents

      if (!capabilities()["long.double"] & getRversion() < "4.1.0") {

        private$can_plot <- FALSE

      }

      super$initialize(extents, intents,
                       objects, attributes,
                       I)

    },

    #' @description
    #' Plot the concept lattice
    #'
    #' @param object_names  (logical) If \code{TRUE}, plot object names, otherwise omit them from the diagram.
    #' @param to_latex      (logical) If \code{TRUE}, export the plot as a \code{tikzpicture} environment that can be included in a \code{LaTeX} file.
    #' @param ...          Other parameters to be passed to the \code{tikzDevice} that renders the lattice in \code{LaTeX}, or for the figure caption. See \code{Details}.
    #'
    #' @details
    #' Particular parameters that control the size of the \code{tikz} output are: \code{width}, \code{height} (both in inches), and \code{pointsize} (in points), that should be set to the font size used in the \code{documentclass} header in the \code{LaTeX} file where the code is to be inserted.
    #'
    #' If a \code{caption} is provided, the whole \code{tikz} picture will be wrapped by a \code{figure} environment and the caption set.
    #'
    #' @return If \code{to_latex} is \code{FALSE}, it returns nothing, just plots the graph of the concept lattice. Otherwise, this function returns the \code{LaTeX} code to reproduce the concept lattice.
    #' @export
    #'
    plot = function(object_names = TRUE,
                    to_latex = FALSE,
                    ...) {

      if (self$size() == 0) {

        warning("No concepts.", call. = FALSE)
        return(invisible(NULL))

      }

      if (!private$can_plot) {

        warning("The R system has not the needed capabilities to plot.",
                call. = FALSE)
        return(invisible(FALSE))

      }

      if (!requireNamespace("hasseDiagram", quietly = TRUE)) {

        warning("You have not installed the 'hasseDiagram' package, which is needed to plot the lattice.",
                call. = FALSE)

        return(invisible(FALSE))

      }

      if ((super$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      lattice_plot(extents = private$pr_extents,
                   intents = private$pr_intents,
                   subconcept_matrix = private$subconcept_matrix,
                   objects = private$objects,
                   attributes = private$attributes,
                   object_names = object_names,
                   to_latex = to_latex,
                   ...)


    },

    #' @description
    #' Sublattice
    #'
    #' @param ... See Details.
    #'
    #' @details
    #' As argument, one can provide both integer indices or \code{Concepts}, separated by commas. The corresponding concepts are used to generate a sublattice.
    #'
    #' @return
    #' The generated sublattice as a new \code{ConceptLattice} object.
    #'
    #' @export
    sublattice = function(...) {

      idx <- private$to_indices(...)

      if (length(idx) > 0) {

        if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

          private$subconcept_matrix <- .subset(private$pr_extents)

        }

        idx <- .get_sublattice(private$subconcept_matrix,
                               starting_idx = idx)

        if (length(idx) > 1) {

          my_intents <- private$pr_intents[, idx]
          my_extents <- private$pr_extents[, idx]

        } else {

          my_intents <- .extract_column(private$pr_intents, idx)
          my_extents <- .extract_column(private$pr_extents, idx)

        }

        cl <- ConceptLattice$new(extents = my_extents,
                                 intents = my_intents,
                                 objects = private$objects,
                                 attributes = private$attributes,
                                 I = private$I)

        return(cl)

      }

    },

    #' @description Top of a Lattice
    #'
    #' @return The top of the Concept Lattice
    #' @export
    #'
    #' @examples
    #' fc <- FormalContext$new(planets)
    #' fc$find_concepts()
    #' fc$concepts$top()
    #'
    top = function() {

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      idx <- which(Matrix::colSums(private$subconcept_matrix) == self$size())

      self[idx]$to_list()[[1]]

    },

    #' @description Bottom of a Lattice
    #'
    #' @return The bottom of the Concept Lattice
    #' @export
    #'
    #' @examples
    #' fc <- FormalContext$new(planets)
    #' fc$find_concepts()
    #' fc$concepts$bottom()
    #'
    bottom = function() {

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      idx <- which(Matrix::colSums(private$subconcept_matrix) == 1)

      self[idx]$to_list()[[1]]

    },


    #' @description
    #' Join-irreducible Elements
    #'
    #' @return
    #' The join-irreducible elements in the concept lattice.
    #'
    #' @export
    #'
    join_irreducibles = function() {

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      if (is.null(private$reduced_matrix)) {

        private$reduced_matrix <- .reduce_transitivity(private$subconcept_matrix)

      }

      idx <- which(Matrix::colSums(private$reduced_matrix) == 1)
      self[idx]

    },

    #' @description
    #' Meet-irreducible Elements
    #'
    #' @return
    #' The meet-irreducible elements in the concept lattice.
    #'
    #' @export
    #'
    meet_irreducibles = function() {

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      M <- .reduce_transitivity(Matrix::t(private$subconcept_matrix))

      idx <- which(Matrix::colSums(M) == 1)
      self[idx]

    },

    #' @description
    #' Decompose a concept as the supremum of meet-irreducible concepts
    #'
    #' @param C A list of \code{Concept}s
    #' @return
    #' A list, each field is the set of meet-irreducible elements whose supremum is the corresponding element in \code{C}.
    #'
    #' @export
    #'
    decompose = function(C) {

      irreducible <- self$meet_irreducibles()

      irr_intents <- irreducible$intents()

      C_intents <- C$intents()

      ss <- lapply(seq(C$size()),
                   function(i) {

                     r <- Matrix::Matrix(C_intents[, i],
                                         sparse = TRUE)

                     if (sum(r) == 0) return(C[i])

                     id <- Matrix::which(.subset(irr_intents,
                                                 r))

                     if (length(id) > 1) {

                       MM <- .subset(irr_intents[, id])
                       id <- id[Matrix::rowSums(MM) == 1]

                     }
                     decomposition <- irreducible[id]

                     return(decomposition)

                   })


      return(ss)

    },

    #' @description
    #' Supremum of Concepts
    #'
    #' @param ... See Details.
    #'
    #' @details
    #' As argument, one can provide both integer indices or \code{Concepts}, separated by commas. The corresponding concepts are used to compute their supremum in the lattice.
    #'
    #' @return
    #' The supremum of the list of concepts.
    #'
    #' @export
    supremum = function(...) {

      idx <- private$to_indices(...)

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      return(self[join(private$subconcept_matrix, idx)]$to_list()[[1]])

    },

    #' @description
    #' Infimum of Concepts
    #'
    #' @param ... See Details.
    #'
    #' @details
    #' As argument, one can provide both integer indices or \code{Concepts}, separated by commas. The corresponding concepts are used to compute their infimum in the lattice.
    #'
    #' @return
    #' The infimum of the list of concepts.
    #'
    #' @export
    infimum = function(...) {

      idx <- private$to_indices(...)

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      return(self[meet(private$subconcept_matrix, idx)]$to_list()[[1]])

    },

    #' @description
    #' Subconcepts of a Concept
    #'
    #' @param C (numeric or \code{SparseConcept}) The concept to which determine all its subconcepts.
    #'
    #' @return
    #' A list with the subconcepts.
    #' @export
    subconcepts = function(C) {

      idx <- private$to_indices(C)

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      # Get the index of all subconcepts
      M <- Matrix::t(private$subconcept_matrix)[idx, ]
      candidates <- Matrix::which(M > 0)

      self[candidates]

    },

    #' @description
    #' Superconcepts of a Concept
    #'
    #' @param C (numeric or \code{SparseConcept}) The concept to which determine all its superconcepts.
    #'
    #' @return
    #' A list with the superconcepts.
    #' @export
    superconcepts = function(C) {

      idx <- private$to_indices(C)

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      # Get the index of all superconcepts
      M <- private$subconcept_matrix[idx, ]
      candidates <- which(M > 0)

      self[candidates]

    },

    #' @description
    #' Lower Neighbours of a Concept
    #'
    #' @param C (\code{SparseConcept}) The concept to which find its lower neighbours
    #'
    #' @return
    #' A list with the lower neighbours of \code{C}.
    #'
    #' @export
    lower_neighbours = function(C) {

      idx <- private$to_indices(C)

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      if (is.null(private$reduced_matrix)) {

        private$reduced_matrix <- .reduce_transitivity(private$subconcept_matrix)

      }

      self[which(private$reduced_matrix[, idx] > 0)]

    },

    #' @description
    #' Upper Neighbours of a Concept
    #'
    #' @param C (\code{SparseConcept}) The concept to which find its upper neighbours
    #'
    #' @return
    #' A list with the upper neighbours of \code{C}.
    #'
    #' @export
    upper_neighbours = function(C) {

      idx <- private$to_indices(C)

      if ((self$size() > 0) & (is.null(private$subconcept_matrix))) {

        private$subconcept_matrix <- .subset(private$pr_extents)

      }

      if (is.null(private$reduced_matrix)) {

        private$reduced_matrix <- .reduce_transitivity(private$subconcept_matrix)

      }

      self[which(private$reduced_matrix[idx, ] > 0)]

    }

  ),

  private = list(

    subconcept_matrix = NULL,
    reduced_matrix = NULL,

    can_plot = TRUE,

    concept_list_to_indices = function(concept_list) {

      extents <- lapply(concept_list,
                        function(l) l$get_extent()$get_vector())

      extents <- Reduce(cbind, extents)

      indices <- .equal_sets(x = extents,
                             y = private$pr_extents)

      indices <- arrayInd(Matrix::which(indices),
                          .dim = dim(indices))[, 2]

      return(indices)

    },

    to_indices = function(...) {

      dots <- list(...)
      if (is.list(dots[[1]])) {

        dots <- unlist(dots)

      }

      if (is.logical(dots[[1]])) {

        return(which(dots[[1]]))

      }

      csets_idx <- sapply(dots,
                          function(l) inherits(l, "ConceptSet"))
      if (length(csets_idx) > 0) {

        csets <- sapply(dots[csets_idx],
                        function(l) l$to_list()) %>%
          unlist()

      } else {

        csets <- c()

      }

      sets <- sapply(dots,
                     function(l)
                       inherits(l, "Concept"))
      sets <- c(csets, dots[which(sets)])

      indices <- sapply(dots, is.numeric)
      idx <- c()

      if (length(indices) > 0) {

        idx <- c(idx, Reduce(c, dots[indices]))

      }

      if (length(sets) > 0) {

        idx <- c(idx,
                 private$concept_list_to_indices(sets))

      }

      return(idx)

    }

  )

)

Try the fcaR package in your browser

Any scripts or data that you put into this service are public.

fcaR documentation built on June 29, 2021, 1:06 a.m.