R/change_family.R

In mi: Missing Data Imputation and Model Checking

# Part of the mi package for multiple imputation of missing data
# Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015 Trustees of Columbia University
# 
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

## these change the parametric family used in the imputation process

setMethod("change_family", signature(data = "missing", y = "missing_variable", to = "family"), def = 
  function(y, to) {
    y@family <- to
    validObject(y, complete = TRUE)
    return(y)
  })

setMethod("change_family", signature(data = "missing", y = "missing_variable", to = "missing"), def = 
  function(y, to) {
    cat("Likely families include:", y@known_families, sep = "\n")
    return(invisible(NULL))
  })

setMethod("change_family", signature(data = "missing", y = "proportion", to = "family"), def = 
  function(y, to) {
    y@family <- to
    if(y@family$family == "gaussian") {
      y@transformation <- qnorm
      y@inverse_transformation <- pnorm
    }
    else if(y@family$family == "binomial") {
      y@transformation <- .identity_transform
      y@transformation <- .identity_transform
    }
    y@data <- y@transformation(y@data)
    validObject(y, complete = TRUE)
    return(y)
  })

setMethod("change_family", signature(data = "missing", y = "unordered-categorical", to = "family"), def = 
  function(y, to) {
    y@family <- to
    y@estimator <- if(y@family$family == "binomial") "RNL" else "MNL"
    return(y)
  }
)

setMethod("change_family", signature(data = "missing_data.frame", y = "character", to = "character"), def =
  function(data, y, to) {
    if(length(to) == 1) to <- rep(to, length(y))
    else if(length(to) != length(y)) stop("'y' and 'to' must have the same length")
    if(all(y %in% names(getClass("missing_variable")@subclasses))) {
      classes <- sapply(data@variables, class)
      y <- c(sapply(y, FUN = function(x) {
        names(classes[which(classes == x)])
      }))
      if(is.list(y)) stop(paste("no variables of class", names(y)[1]))
#       else y <- y[1]
    }
    y <- match.arg(y, data@DIMNAMES[[2]], several.ok = TRUE)
    for(i in 1:length(y)) {
      #     link <- data@variables[[y[i]]]@family$link
      if(i <= length(to)) fam <- do.call(to[i], args = list())
      data@variables[[y[i]]] <- change_family(y = data@variables[[y[i]]], to = fam)
    }
    return(invisible(data))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "character", to = "list"), def =
  function(data, y, to) {
    if(length(to) == 1) to <- rep(to, length(y))
    else if(length(to) != length(y)) stop("'y' and 'to' must have the same length")
    if(all(y %in% names(getClass("missing_variable")@subclasses))) {
      classes <- sapply(data@variables, class)
      y <- c(sapply(y, FUN = function(x) {
        names(classes[which(classes == x)])
      }))
      if(is.list(y)) stop(paste("no variables of class", names(y)[1]))
#       else y <- y[1]
    }
    y <- match.arg(y, data@DIMNAMES[[2]], several.ok = TRUE)
    for(i in 1:length(y)) {
      data@variables[[y[i]]] <- change_family(y = data@variables[[y[i]]], to = to[[i]])
    }
    return(invisible(data))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "character", to = "family"), def =
  function(data, y, to) {
    if(all(y %in% names(getClass("missing_variable")@subclasses))) {
      classes <- sapply(data@variables, class)
      y <- c(sapply(y, FUN = function(x) {
        names(classes[which(classes == x)])
      }))
    }
    y <- match.arg(y, data@DIMNAMES[[2]], several.ok = TRUE)
    for(i in 1:length(y)) {
      data@variables[[y[i]]] <- change_family(y = data@variables[[y[i]]], to = to)
    }
    return(invisible(data))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "numeric", to = "character"), def =
  function(data, y, to, ...) {
    if(length(to) == 1) to <- rep(to, length(y))
    else if(length(to) != length(y)) stop("'y' and 'to' must have the same length")
    for(i in 1:length(y)) {
      data@variables[[y]] <- change_family(y = data@variables[[y]], to = do.call(to[i], args = list(...)))
    }
    return(invisible(data))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "numeric", to = "list"), def =
  function(data, y, to) {
    if(length(to) == 1) to <- rep(to, length(y))
    else if(length(to) != length(y)) stop("'y' and 'to' must have the same length")
    for(i in 1:length(y)) {
      data@variables[[y]] <- change_family(y = data@variables[[y]], to = to[[i]])
    }
    return(invisible(data))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "numeric", to = "family"), def =
  function(data, y, to) {
    for(i in 1:length(y)) {
      data@variables[[y]] <- change_family(y = data@variables[[y]], to = to)
    }
    return(invisible(data))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "logical", to = "character"), def =
  function(data, y, to) {
    if(length(y) != data@DIM[2]) {
      stop("the length of 'y' must equal the number of variables in 'data'")
    }
    return(change_family(data, which(y), to))
  })

setMethod("change_family", signature(data = "missing_data.frame", y = "logical", to = "family"), def =
  function(data, y, to) {
    if(length(y) != data@DIM[2]) {
      stop("the length of 'y' must equal the number of variables in 'data'")
    }
    return(change_family(data, which(y), to))
  })