R/DistatisR-package.R

In HerveAbdi/DistatisR: DiSTATIS Three Way Metric Multidimensional Scaling

#'  implements three way metric multidimensional scaling:
#' DISTATIS and COVSTATIS.
#'
#' \code{DistatisR}: package implements three way 
#' metric multidimensional scaling:
#' DISTATIS and COVSTATIS.
#'
#' Analyzes sets of distance (or covariance)
#'  matrices collected on the same set
#' of observations and find common and specific metric spaces.
#'
#' \tabular{ll}{ Package: \tab DistatisR\cr 
#' Type: \tab Package\cr Version: \tab
#' 1.1.0\cr Date: \tab 2022-09-28\cr 
#' License: \tab GPL-2\cr Depends: \tab
#' prettyGraphs (>= 2.0.0), car} 
#' The example shown here comes from Abdi
#' \emph{et al.} (2007), \code{distatis} 
#' paper on the sorting task.
#'
#' @name DistatisR-package
#' @aliases DistatisR-package DistatisR DiSTATISR
#' @docType package
#' @author Derek Beaton [aut, com, ctb], & Herve Abdi
#' [aut, cre]
#'
#' Maintainer: Herve Abdi <herve@@utdallas.edu>
#' @seealso % Optional links to other man pages, e.g.  % \code{\link{}}
#' \code{\link{distatis}} \code{\link{BootFactorScores}}
#' \code{\link{BootFromCompromise}} \code{\link{DistanceFromSort}}
#' \code{\link{distatis}} \code{\link{GraphDistatisAll}}
#' \code{\link{GraphDistatisBoot}} \code{\link{GraphDistatisCompromise}}
#' \code{\link{GraphDistatisPartial}} \code{\link{GraphDistatisRv}}
#' \code{\link{mmds}}
#' \code{\link{prettyGraphs}}
#' @references % Note: these papers are available from
#'  \url{https://personal.utdallas.edu/~herve/}
#'
#' Abdi, H., Valentin, D., O'Toole, A.J., & Edelman, B. (2005). 
#' DISTATIS: The
#' analysis of multiple distance matrices. 
#'  \emph{Proceedings of the IEEE
#' Computer Society: International Conference 
#' on Computer Vision and Pattern
#' Recognition.} (San Diego, CA, USA). pp. 42-47.
#'
#' Abdi, H., Valentin, D., Chollet, S., & Chrea, C. (2007).  
#' Analyzing
#' assessors and products in sorting tasks: 
#' DISTATIS, theory and applications.
#' \emph{Food Quality and Preference}, \bold{18}, 627--640.
#'
#' Abdi, H., & Valentin, D., (2007).  
#' Some new and easy ways to describe,
#' compare, and evaluate products and assessors.  
#' In D., Valentin, D.Z. Nguyen,
#' L. Pelletier (Eds): 
#' \emph{New trends in sensory evaluation of food and
#' non-food products}. 
#'  Ho Chi Minh (Vietnam): Vietnam National University & Ho
#' Chi Minh City Publishing House. pp. 5--18.
#'
#' Abdi, H., Dunlop, J.P., & Williams, L.J. (2009).  
#' How to compute reliability
#' estimates and display confidence and tolerance 
#' intervals for pattern
#' classiffers using the Bootstrap 
#' and 3-way multidimensional scaling
#' (DISTATIS).  \emph{NeuroImage}, \bold{45}, 89--95.
#'
#' Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. 
#' (2012).  STATIS
#' and DISTATIS: Optimum multi-table principal component 
#' analysis and three way
#' metric multidimensional scaling.  
#' \emph{Wiley Interdisciplinary Reviews:
#' Computational Statistics}, \bold{4}, 124--167.
#'
#' Chollet, S., Valentin, D., & Abdi, H. (2014). 
#' The free sorting
#' task.  In. P.V. Tomasco & G. Ares (Eds), 
#' \emph{Novel Techniques in Sensory
#' Characterization and Consumer Profiling.} 
#' Boca Raton: Taylor and Francis.
#'
#' Valentin, D., Chollet, S., Nestrud, M., & Abdi, H. (2018).
#' Sorting and similarity methodologies.  
#' In. S. Kemp, S., J. Hort, & T.
#' Hollowood (Eds.), 
#' \emph{Descriptive Analysis in Sensory Evaluation}.
#' London: Wiley-Blackwell.
#' @keywords package
#' @examples
#'
#' # Here we use the sorting task from Abdi et al.' (2007) paper.
#' # where 10 Assessors sorted 8 beers.
#'
#' #-----------------------------------------------------------------------------
#' #  1. Get the data from the 2007 sorting example
#' #      this is the way they look from Table 1 of
#' #      Abdi et al. (2007).
#' #                       Assessors
#' #                  1 2 3 4 5 6 7 8 9 10
#' # Beer        Sex  f m f f m m m m f m
#' #            -----------------------------
#' #Affligen          1 4 3 4 1 1 2 2 1 3
#' #Budweiser         4 5 2 5 2 3 1 1 4 3
#' #Buckler_Blonde    3 1 2 3 2 4 3 1 1 2
#' #Killian           4 2 3 3 1 1 1 2 1 4
#' #St. Landelin      1 5 3 5 2 1 1 2 1 3
#' #Buckler_Highland  2 3 1 1 3 5 4 4 3 1
#' #Fruit Defendu     1 4 3 4 1 1 2 2 2 4
#' #EKU28             5 2 4 2 4 2 5 3 4 5
#'
#'
#' # 1.1. Create the
#' #     Name of the Beers
#' BeerName <- c('Affligen', 'Budweiser','Buckler Blonde',
#'               'Killian','St.Landelin','Buckler Highland',
#'               'Fruit Defendu','EKU28')
#' # 1.2. Create the name of the Assessors
#' #      (F are females, M are males)
#' Juges <- c('F1','M2', 'F3', 'F4', 'M5', 'M6', 'M7', 'M8', 'F9', 'M10')
#'
#' # 1.3. Get the sorting data
#' SortData <- c(1, 4, 3, 4, 1, 1, 2, 2, 1, 3,
#'               4, 5, 2, 5, 2, 3, 1, 1, 4, 3,
#'               3, 1, 2, 3, 2, 4, 3, 1, 1, 2,
#'               4, 2, 3, 3, 1, 1, 1, 2, 1, 4,
#'               1, 5, 3, 5, 2, 1, 1, 2, 1, 3,
#'               2, 3, 1, 1, 3, 5, 4, 4, 3, 1,
#'               1, 4, 3, 4, 1, 1, 2, 2, 2, 4,
#'               5, 2, 4, 2, 4, 2, 5, 3, 4, 5)
#' # 1.4 Create a data frame
#' Sort <- matrix(SortData,ncol = 10, byrow= TRUE, dimnames = list(BeerName, Juges))
#' #     (alternatively we could have read a csv file)
#' # 1.5 Example of how to read a csv filw
#' # Sort <- read.table("BeeerSortingTask.csv", header=TRUE,
#' #   sep=",", na.strings="NA", dec=".", row.names=1, strip.white=TRUE)
#'
#' #------------------------------------------------------------------
#' # 2. Create the set of distance matrices 
#' #  (one distance matrix per assessor)
#' #    (uses the function DistanceFromSort)
#' DistanceCube <- DistanceFromSort(Sort)
#' #------------------------------------------------------------------
#' # 3. Call the DISTATIS routine with the cube of distance as parameter
#' testDistatis <- distatis(DistanceCube)
#' # The factor scores for the beers are in
#' # testDistatis$res4Splus$F
#' # the factor scores for the assessors are in (RV matrice)
#' #  testDistatis$res4Cmat$G
#'
#' #------------------------------------------------------------------
#' # 4. Inferences on the beers obtained via bootstrap
#' #    here we use two different bootstraps:
#' #    1. Bootstrap on factors (very fast but could be too liberal
#' #         when the number of assessors is very large)
#' #    2. Complete bootstrap obtained by computing sets of compromises
#' #       and projecting them (could be significantly longer because a lot
#' #       of computations is required)
#' #
#' # 4.1 Get the bootstrap factor scores (with default 1000 iterations)
#' BootF <- BootFactorScores(testDistatis$res4Splus$PartialF)
#' #
#' # 4.2 Get the boostrap from full bootstrap (default niter = 1000)
#'  F_fullBoot <- BootFromCompromise(DistanceCube,niter=1000)
#'
#'
#' #------------------------------------------------------------------
#' # 5. Create the Graphics
#' # 5.1 an Rv map
#'  rv.graph.out <- GraphDistatisRv(testDistatis$res4Cmat$G)
#' # 5.2 a compromise plot
#'  compromise.graph.out <- GraphDistatisCompromise(testDistatis$res4Splus$F)
#' # 5.3 a partial factor score plot
#'  partial.scores.graph.out <-
#'  	GraphDistatisPartial(testDistatis$res4Splus$F,testDistatis$res4Splus$PartialF)
#' # 5.4 a bootstrap confidence interval plot
#'  #5.4.1 with ellipses
#'  boot.graph.out.ell <- GraphDistatisBoot(testDistatis$res4Splus$F,BootF)
#'  #or
#'  # boot.graph.out <- GraphDistatisBoot(testDistatis$res4Splus$F,F_fullBoot)
#'  #5.4.2 with hulls
#'  boot.graph.out.hull <- GraphDistatisBoot(testDistatis$res4Splus$F,BootF,ellipses=FALSE)
#'  #or
#'  # boot.graph.out <- GraphDistatisBoot(testDistatis$res4Splus$F,F_fullBoot,ellipses=FALSE)
#' #5.5 all the plots at once
#' all.plots.out <-
#' 	GraphDistatisAll(testDistatis$res4Splus$F,testDistatis$res4Splus$PartialF,
#' 		BootF,testDistatis$res4Cmat$G)
#'
#'
#'
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