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# 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 are convience functions that implicitly change something else by changing the model buzzword
setMethod("change_model", signature(data = "missing", y = "missing_variable", to = "character"), def =
function(y, to) {
switch(to,
"logit" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = binomial(link = "logit")),
"probit" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = binomial(link = "probit")),
"cauchit" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = binomial(link = "cauchit")),
"cloglog" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = binomial(link = "cloglog")),
"qlogit" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = quasibinomial(link = "logit")),
"qprobit" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = quasibinomial(link = "probit")),
"qcauchit" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = quasibinomial(link = "cauchit")),
"qcloglog" = new("binary", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = quasibinomial(link = "cloglog")),
"ologit" = new("ordered-categorical", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = multinomial(link = "logit")),
"oprobit" = new("ordered-categorical", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = multinomial(link = "probit")),
"ocauchit" = new("ordered-categorical", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = multinomial(link = "cauchit")),
"ocloglog" = new("ordered-categorical", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = multinomial(link = "cloglog")),
"mlogit" = new("unordered-categorical", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = multinomial(link = "logit")),
"RNL" = new("unordered-categorical", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = binomial(link = "logit")),
"qpoisson" = new("count", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = quasipoisson(link = "log")),
"poisson" = new("count", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = poisson(link = "log")),
"linear" = new("continuous", variable_name = y@variable_name, raw_data = y@raw_data,
imputation_method = y@imputation_method, family = gaussian(link = "identity")),
stop("model not recognized")
)
})
setMethod("change_model", 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]))
to <- rep(to[1], length(y))
}
y <- match.arg(y, data@DIMNAMES[[2]], several.ok = TRUE)
check <- FALSE
for(i in 1:length(y)) {
categorical <- is(data@variables[[y[i]]], "categorical")
data@variables[[y[i]]] <- change_model(y = data@variables[[y[i]]], to = to[i])
if(categorical & !is(data@variables[[y[i]]], "categorical")) check <- TRUE
if(!categorical & is(data@variables[[y[i]]], "categorical")) check <- TRUE
}
if(check) return(new(class(data), variables = data@variables))
else return(data)
})
setMethod("change_model", 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)) {
categorical <- is(data@variables[[y[i]]], "categorical")
data@variables[[y[i]]] <- change_model(y = data@variables[[y[i]]], to = to[[i]])
if(categorical & !is(data@variables[[y[i]]], "categorical")) check <- TRUE
if(!categorical & is(data@variables[[y[i]]], "categorical")) check <- TRUE
}
if(check) return(new(class(data), variables = data@variables))
else return(data)
})
setMethod("change_model", 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_model(data, which(y), to))
})
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