MF: Mitigated Fraction

#' @importFrom methods new setClassUnion setRefClass

setClassUnion("characterORNULL", c("character", "NULL"))
setClassUnion("listORNULL", c("list", "NULL"))
setClassUnion("numericORNULL", c("numeric", "NULL"))
setClassUnion("numericORarray", c("numeric", "array"))
setClassUnion("numericORarrayORtable", c("numeric", "array", "table"))
setClassUnion("numericORinteger", c("numeric", "integer"))

#' @name mf-class
#' @title Class mf
#' @description Parent class for package MF data objects.
#' @docType class
#' @section Fields:
#' * `nboot`: numeric value specifying number of samples
#' * `alpha`: numeric value specifying complement of confidence interval
#' * `seed`: vector of integers specifying seed for pseudo-random number
#' generator used
#' * `compare`: vector of character strings naming groups compared
#' * `rng`: character string naming type of random number generator
#' @keywords documentation
#' @family mf
#' @author [MF-package]
mf <- setRefClass("mf", fields = list(nboot = "numeric",
                                      alpha = "numeric",
                                      seed = "numericORinteger",
                                      compare = "character",
                                      rng = "character"))

#' @name mfboot-class
#' @title Class mfboot
#' @description class for data objects produced by MFBoot, contains class mf
#'   with the two additional fields *stat* and *stuff*.
#' @docType class
#' @section Fields:
#' * `nboot`: numeric value specifying number of samples
#' * `alpha`: numeric value specifying complement of confidence interval
#' * `seed`: vector of integers specifying seed for pseudo-random number generator used
#' * `compare`: vector of character strings naming groups compared
#' * `rng`: character string naming type of random number generator
#' * `sample`:  what is this?
#' * `stat`: matrix of estimates
#' @section Contains: [mf-class]
#' @keywords documentation
#' @family mf
#' @seealso [MFBoot]
#' @author [MF-package]
mfboot <- setRefClass("mfboot", contains = "mf",
                      fields = list(stat = "matrix",
                                    sample = "numericORNULL"))

#' @name mfhlboot-class
#' @title Class mfhlboot
#' @description class for data objects produced by HLBoot, contains class mf
#'   with additional fields *MFstat*, *HLstat*, *QDIFstat*, *QXstat*, *QYstat*
#' @docType class
#' @section Fields:
#' * `nboot`: Numeric value specifying number of samples.
#' * `alpha`: Numeric value specifying complement of confidence interval.
#' * `seed`: Vector of integers specifying seed for pseudo-random number generator used.
#' * `compare`: Vector of character strings naming groups compared.
#' * `rng`: Character string naming type of random number generator.
#' * `sample`: The bootstrapped values.
#' * `MFstat`: Matrix with columns *observed*, *median*, *lower*, *upper* for
#' Equal Tailed and Highest Density estimates of mitigated fraction (MF).
#' * `HLstat`: Matrix with columns *observed*, *median*, *lower*, *upper* for
#' Equal Tailed and Highest Density estimates of Hodge-Lehmann estimator (HL).
#' * `QDIFstat`: Matrix with columns *observed*, *median*, *lower*, *upper* for
#' estimates of Quartile Differences.
#' * `QXstat`: Matrix with columns *observed*, *median*, *lower*, *upper* for
#' quartiles of treatments, equal tailed.
#' * `QYstat`: Matrix with columns *observed*, *median*, *lower*, *upper* for
#' quartiles of response, equal tailed.
#' @section Contains: [mf-class]
#' @keywords documentation
#' @family mf
#' @seealso [HLBoot]
#' @author [MF-package]
mfhlboot <- setRefClass("mfhlboot", contains = "mf",
                        fields = list(MFstat = "matrix",
                                      HLstat = "matrix",
                                      QDIFstat = "matrix",
                                      QXstat = "matrix",
                                      QYstat = "matrix",
                                      sample = "listORNULL"))

#' @name mfmp-class
#' @title Class mfmp
#' @description Class `mfmp` is created from output of function `MFmp`
#' @docType class
#' @section Fields:
#' * `ci`: numeric vector of point and interval estimates
#' * `x`: numeric vector of length three holding data
#' * `what`: text string describing interval type
#' * `alpha`: numeric value specifying complement of confidence interval
#' * `tdist`: Logical indicating if t distribution(TRUE) or Gaussian (FALSE)
#' * `df`: numeric value indicating degrees freedom
#' @keywords documentation
#' @family mfmp
#' @author [MF-package]
#' @seealso [MFmp]
mfmp <- setRefClass("mfmp",
                    fields = list(ci = "numeric",
                                  x = "numericORarrayORtable",
                                  what = "character",
                                  alpha = "numeric",
                                  tdist = "logical",
                                  df = "numeric"))

#' @name mfbootcluster-class
#' @title Class mfbootcluster
#' @description Class mfbootcluster is created from output of function
#'   MFClusBoot
#' @docType class
#' @section Fields:
#' * `nboot`: numeric value specifying number of samples
#' * `alpha`: numeric value specifying complement of confidence interval
#' * `seed`: vector of integers specifying seed for pseudo-random number generator used
#' * `compare`: vector of character strings naming groups compared
#' * `rng`: character string naming type of random number generator
#' * `stat`: matrix matrix with columns *observed*, *median*, *lower*, *upper*
#' for estimates
#' * `what`: character vector naming what was resampled: *clusters*, *units*,
#' *both*
#' * `excludedClusters`: character vector naming clusters excluded because of
#' missing treatment(s)
#' * `call`: the call to `MFClusBoot`
#' * `sample`: what is this?
#' * `All`: Field "All" from MFClus call.
#' @section Contains: [mf-class]
#' @keywords documentation
#' @family mf
#' @seealso [MFClusBoot]
#' @author [MF-package]
mfbootcluster <- setRefClass("mfbootcluster", contains = "mf",
                             fields = list(stat = "matrix",
                                           what = "character",
                                           excludedClusters = "character",
                                           call = "call",
                                           sample = "numericORNULL",
                                           All = "data.frame"))

#' @name mfcluster-class
#' @title Class mfcluster
#' @description Class mfcluster is created from output of function MFClus
#' @docType class
#' @section Fields:
#' * `All`: vector with elements
#'   * `w`: Wilcoxon statistic
#'   * `u`: Mann-Whitney statistic
#'   * `r`: mean ridit
#'   * `n1`: size of group 1
#'   * `n2`: size of group 2
#'   * `mf`: mitigated fraction
#' * `byCluster`: As for All, by clusters
#' * `excludedClusters`: character vector naming clusters excluded because of missing treatment
#' * `call`: the call to `MFClus`
#' * `compare`: character vector naming groups compared
#' @keywords documentation
#' @family mfcluster
#' @seealso [MFClus]
#' @author [MF-package]
mfcluster <- setRefClass("mfcluster",
                         fields = list(All = "data.frame",
                                       byCluster = "matrix",
                                       excludedClusters = "characterORNULL",
                                       call = "call",
                                       compare = "character"))

#' @name mfcomponents-class
#' @title Class mfcomponents
#' @description Class mfcomponents is created from output of function MFSubj
#' @docType class
#' @section Fields:
#' * `mf`: numeric estimator for mitigated fraction
#' * `x`: numeric vector containing responses of group 1
#' * `y`: numeric vector containing responses of group 2
#' * `subj`: matrix where `mf_j`re the subject components
#' * `compare`: character vector naming groups being compared
#' @keywords documentation
#' @family mfcomponents
#' @seealso [MFSubj]
#' @author [MF-package]
mfcomponents <- setRefClass("mfcomponents",
                            fields = list(mf = "numeric",
                                          x = "numeric",
                                          y = "numeric",
                                          subj = "matrix",
                                          compare = "character"))

#' @name mfhierdata-class
#' @title Class mfhierdata
#' @description Class mfhierdata is created from output of function MFh
#' @docType class
#' @section Fields:
#' * `coreTbl`: data.frame with one row for each unique core level showing
#' values for `nx`, `ny`, `N`, `w`, `u`, and `median` observed response.
#' * `data`: data.frame is the restructured input data used for calculations in
#' MFh and MFnest.
#' * `compare`: character vector naming groups being compared.
#' * `formula`: formula that was called by user.
#' @keywords documentation
#' @family mfhierdata
#' @seealso [MFh]
#' @author [MF-package]
mfhierdata <- setRefClass("mfhierdata",
                          fields = list(coreTbl = "tbl",
                                        data = "tbl",
                                        compare = "character",
                                        formula = "formula"))


#' @name mfclushier-class
#' @title Class mfclushier
#' @description Class mfclushier is created from output of function MFClusHier
#' @docType class
#' @section Fields:
#' * `MFh`: output from MFh. A [mfhierdata] object.
#' * `MFnest`: output from MFnest. A tibble.
#' @keywords documentation
#' @family mfclushier
#' @seealso [MFh], [MFnest]
#' @author [MF-package]
mfclushier <- setRefClass("mfclushier", fields = list(MFh = "mfhierdata",
                                                      MFnest = "tbl"))

#' @name mfclusboothier-class
#' @title Class mfclusboothier
#' @description Class mfclusboothier is created from output of function
#' MFClusBootHier.
#' @docType class
#' @section Fields:
#' * `MFhBoot` output from MFhBoot. A list.
#' * `MFnestBoot` output from MFnestBoot. A list.
#' @keywords documentation
#' @family mfclusboothier
#' @seealso [MFhBoot], [MFnestBoot]
#' @author [MF-package]
mfclusboothier <- setRefClass("mfclusboothier",
                              fields = list(MFhBoot = "list",
                                            MFnestBoot = "list"))