Nothing
R/minimize.R
In QCA: Qualitative Comparative Analysis
Defines functions
`eqmcc`
`minimizeLoop`
`minimize`
# Copyright (c) 2016 - 2020, Adrian Dusa
# All rights reserved.
#
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# modification, in whole or in part, are permitted provided that the
# following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * The names of its contributors may NOT be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL ADRIAN DUSA BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
`minimize` <-
function(input, include = "", dir.exp = NULL, details = FALSE, all.sol = FALSE,
row.dom = FALSE, min.pin = FALSE, max.comb = 0, first.min = FALSE,
method = "CCubes", ...) {
metacall <- match.call()
dots <- substitute(list(...))
if (is.element("data", names(dots))) {
input <- eval.parent(dots$data)
dots$data <- NULL
}
enter <- if (is.element("enter", names(dots))) "" else "\n"
if (missing(input)) {
cat(enter)
stop(simpleError(paste0("The input (a truth table or a dataset) is missing.", enter, enter)))
}
else {
if (is.matrix(input)) {
if (is.null(colnames(input))) {
cat(enter)
stop(simpleError(paste0("The data should have column names.", enter, enter)))
}
if (any(duplicated(rownames(input)))) {
rownames(input) <- seq(nrow(input))
}
input <- as.data.frame(input)
for (i in seq(ncol(input))) {
if (admisc::possibleNumeric(input[, i])) {
input[, i] <- admisc::asNumeric(input[, i])
}
}
}
if(!(is.data.frame(input) | methods::is(input, "QCA_tt"))) {
cat(enter)
stop(simpleError(paste0("The input should be a truth table or a dataset.", enter, enter)))
}
}
ttinput <- methods::is(input, "QCA_tt")
print.truth.table <- details & !ttinput
if (ttinput) {
nms <- colnames(input$recoded.data)[seq(length(input$noflevels))]
}
else {
nms <- colnames(input)
}
if (length(dots) > 1) {
for (i in seq(2, length(dots))) {
dots[[i]] <- admisc::recreate(dots[[i]], nms)
}
}
dots <- eval(dots)
back.args <- c("outcome", "conditions", "n.cut", "incl.cut", "complete", "show.cases", sort.by = "", "use.letters", "inf.test",
"rowdom", "direxp", "neg.out", "data", "relation", "explain", "omit", "exclude")
check.args <- pmatch(names(dots), back.args)
names(dots)[!is.na(check.args)] <- back.args[check.args[!is.na(check.args)]]
explain <- if (is.element("explain", names(dots))) dots$explain else "1"
outcome <- if (is.element("outcome", names(dots))) dots$outcome else ""
conditions <- if (is.element("conditions", names(dots))) dots$conditions else ""
incl.cut <- if (is.element("incl.cut", names(dots))) dots$incl.cut else 1
n.cut <- if (is.element("n.cut", names(dots))) dots$n.cut else 1
complete <- if (is.element("complete", names(dots))) dots$complete else FALSE
show.cases <- if (is.element("show.cases", names(dots))) dots$show.cases else FALSE
dcc <- if (is.element("dcc", names(dots))) dots$dcc else FALSE
sort.by <- if (is.element("sort.by", names(dots))) dots$sort.by else ""
use.letters <- if (is.element("use.letters", names(dots))) dots$use.letters else FALSE
inf.test <- if (is.element("inf.test", names(dots))) dots$inf.test else ""
relation <- if (is.element("relation", names(dots))) dots$relation else "sufficiency"
neg.out <- if (is.element("neg.out", names(dots))) dots$neg.out else FALSE
pi.cons <- if (is.element("pi.cons", names(dots))) dots$pi.cons else 0
pi.depth <- if (is.element("pi.depth", names(dots))) dots$pi.depth else 0
sol.cons <- if (is.element("sol.cons", names(dots))) dots$sol.cons else 0
sol.cov <- if (is.element("sol.cov", names(dots))) dots$sol.cov else 1
sol.depth <- if (is.element("sol.depth", names(dots))) dots$sol.depth else 0
exclude <- if (is.element("exclude", names(dots))) dots$exclude else NULL
keep.trying <- if (is.element("keep.trying", names(dots))) dots$keep.trying else FALSE
if (is.null(exclude)) {
if (is.element("omit", names(dots))) {
exclude <- dots$omit
}
}
if (is.null(include)) {
cat(enter)
stop(simpleError(paste0("The \"include\" argument cannot be NULL.", enter, enter)))
}
dir.exp <- admisc::recreate(substitute(dir.exp))
row.dom <- if (is.element("rowdom", names(dots))) dots$rowdom else row.dom
dir.exp <- if (is.element("direxp", names(dots))) dots$direxp else dir.exp
if (identical(dir.exp, character(0))) {
dir.exp <- NULL
}
else if (!is.null(dir.exp)) {
if (length(dir.exp) == 1) {
if (grepl(":", dir.exp)) {
des <- unlist(strsplit(dir.exp, split = ":"))
if (!all(is.element(des, nms))) {
cat(enter)
stop(simpleError(paste0("Inexisting condition(s) in the sequence of directional expectations.", enter, enter)))
}
dir.exp <- nms[seq(which(nms == des[1]), which(nms == des[2]))]
}
else {
dir.exp <- admisc::splitstr(dir.exp)
}
}
}
if (identical(include, "")) {
if (!is.null(dir.exp)) {
cat(enter)
stop(simpleError(paste0("Directional expectations cannot be specified without including the remainders.", enter, enter)))
}
}
if (is.character(explain) & !identical(explain, "1")) {
explain <- admisc::splitstr(explain)
}
if (is.character(include) & !identical(include, "")) {
include <- admisc::splitstr(include)
}
if (is.character(outcome) & !identical(outcome, "")) {
outcome <- admisc::splitstr(outcome)
}
if (ttinput) {
tt <- input
curly <- grepl("\\{", tt$options$outcome)
if (is.null(tt$options$exclude) & !is.null(exclude)) {
callist <- as.list(tt$call)
dataname <- callist$data
callist$data <- tt$initial.data
callist$exclude <- exclude
tt <- do.call("truthTable", callist[-1])
callist$data <- dataname
tt$call <- as.call(callist)
}
recdata <- tt$recoded.data
conditions <- colnames(recdata)[seq(length(tt$noflevels))]
outcome <- colnames(recdata)[ncol(recdata)]
indata <- tt$initial.data[, match(colnames(recdata), colnames(tt$initial.data)), drop = FALSE]
}
else {
if (identical(outcome, "")) {
cat(enter)
stop(simpleError(paste0("Consider creating a truth table first, or formally specify the argument \"outcome\".", enter, enter)))
}
if (any(c(pi.cons, sol.cons) > 0) & incl.cut[1] == 1) {
incl.cut[1] <- min(c(pi.cons, sol.cons))
}
if (length(outcome) > 1) {
return(do.call("minimizeLoop", as.list(metacall)[-1], envir = parent.frame()))
}
outcome.copy <- outcome
indata <- input
curly <- grepl("\\{", outcome)
testoutcome <- ifelse(curly,
admisc::curlyBrackets(admisc::notilde(outcome), outside = TRUE),
admisc::squareBrackets(admisc::notilde(outcome), outside = TRUE))
if (!is.element(testoutcome, colnames(input))) {
cat(enter)
stop(simpleError(paste0("Outcome not found in the data.", enter, enter)))
}
outcome.name <- testoutcome
if (identical(conditions, "")) {
conditions <- names(input)[-which(names(input) == outcome.name)]
}
else {
conditions <- admisc::splitstr(conditions)
}
verify.data(input, outcome.name, conditions)
if (length(conditions) == 1) {
if (grepl(":", conditions)) {
nms <- colnames(data)
cs <- unlist(strsplit(conditions, split = ":"))
conditions <- nms[seq(which(nms == cs[1]), which(nms == cs[2]))]
}
}
input <- input[, c(conditions, outcome.name)]
verify.minimize(input, outcome.name, conditions, explain, include, use.letters)
if (!is.element("incl.cut", names(dots))) {
dots$incl.cut <- incl.cut
}
tt <- do.call("truthTable", c(list(data = input), dots))
tt$initial.data <- indata
indata <- input
recdata <- tt$recoded.data
outcome <- outcome.name
names(indata) <- c(conditions, outcome)
}
use.letters <- tt$options$use.letters
show.cases <- show.cases | tt$options$show.cases
neg.out <- tt$options$neg.out
output <- list()
output$tt <- tt
output$options$print.truth.table <- print.truth.table
rowsNotMissing <- which(tt$tt$OUT != "?")
if (any(tt$tt$OUT == "?")) {
missings <- which(tt$tt$OUT == "?")
tt$tt <- tt$tt[-missings, , drop = FALSE]
}
ttrownms <- admisc::asNumeric(rownames(tt$tt))
noflevels <- tt$noflevels
mbase <- as.integer(rev(c(1, cumprod(rev(noflevels))))[-1])
mbaseplus <- rev(c(1, cumprod(rev(noflevels + 1))))[-1]
alreadyletters <- sum(nchar(colnames(recdata)[-ncol(recdata)])) == ncol(recdata) - 1
tt$tt[seq(length(conditions))] <- as.data.frame(lapply(tt$tt[seq(length(conditions))], function(x) {
x[is.element(x, c("-", "dc"))] <- -1
return(admisc::asNumeric(x))
}))
pos.incl <- unique(c(explain, include))
subset.tt <- ttrownms[is.element(tt$tt[, "OUT"], explain)]
subset.pos <- is.element(tt$tt[, "OUT"], pos.incl)
pos.matrix <- as.matrix(tt$tt[subset.pos, seq(length(noflevels))])
rownames(pos.matrix) <- drop(pos.matrix %*% mbase) + 1
pos.matrix <- pos.matrix + 1
neg.matrix <- as.matrix(tt$tt[!is.element(tt$tt[, "OUT"], pos.incl), seq(length(noflevels))])
neg.matrix <- matrix(as.numeric(neg.matrix), ncol = length(noflevels)) + 1
rownames(neg.matrix) <- drop((neg.matrix - 1) %*% mbase) + 1
if (sum(subset.pos) == 0) {
cat(enter)
stop(simpleError(paste0("None of the values in OUT is explained. Please check the truth table.", enter, enter)))
}
inputt <- as.matrix(tt$tt[is.element(ttrownms, subset.tt), seq(length(noflevels)), drop = FALSE])
rownames(inputt) <- drop(inputt %*% mbase) + 1
inputt <- inputt + 1
inputcases <- tt$cases[is.element(tt$indexes, subset.tt)]
nofcases1 <- sum(tt$tt$n[tt$tt$OUT == 1])
nofcases0 <- sum(tt$tt$n[tt$tt$OUT == 0])
nofcasesC <- sum(tt$tt$n[tt$tt$OUT == "C"])
excl.matrix <- matrix(nrow = 0, ncol = length(conditions))
output$negatives <- sort(drop((neg.matrix - 1) %*% mbase) + 1)
rownms <- rownames(inputt)
if (nrow(pos.matrix) == 0) {
cat(enter)
stop(simpleError(paste0("Nothing to explain. Please check the truth table.", enter, enter)))
}
incl.rem <- is.element("?", include)
if (nrow(neg.matrix) == 0 & incl.rem & !is.element("causalChain", names(dots))) {
cat(enter)
stop(simpleError(paste0("All truth table configurations are used, all conditions are minimized.\n",
" Please check the truth table.", enter, enter)))
}
expressions <- pos.matrix
recdata[, conditions] <- as.data.frame(lapply(recdata[, conditions, drop = FALSE], function(x) {
x[is.element(x, c("-", "?", "dc"))] <- -1
return(as.numeric(x))
}))
mv <- any(recdata[, seq(ncol(recdata) - 1)] > 1)
collapse <- "*"
changed <- FALSE
if (use.letters & !alreadyletters) {
colnms <- LETTERS[seq(ncol(inputt))]
changed <- TRUE
}
else {
colnms <- colnames(recdata[, seq(ncol(inputt)), drop = FALSE])
}
setColnames(expressions, colnms)
setColnames(inputt, colnms)
setColnames(pos.matrix, colnms)
setColnames(neg.matrix, colnms)
rownames(neg.matrix) <- (neg.matrix - 1) %*% mbase + 1
output$initials <- admisc::writePrimeimp(inputt, mv = mv, collapse = collapse)
if (any(c(pi.cons, sol.cons) > 0)) {
incl.rem <- TRUE
method <- "CCubes"
}
expressions <- .Call("C_QMC", expressions, noflevels, PACKAGE = "QCA")
if (is.element("simplify", names(dots))) {
expressions <- admisc::sortExpressions(expressions)
}
callist <- list(expressions=expressions, mv=mv, collapse=collapse, inputt=inputt, row.dom=row.dom,
initial=rownms, all.sol=all.sol, indata=indata, curly=curly)
callist <- c(callist, dots)
if (!incl.rem || (!is.null(dir.exp) & !identical(include, ""))) {
c.sol <- p.sol <- do.call("getSolution", callist)
}
if (incl.rem) {
pos.matrix <- inputt
if (method == "QMC") {
expressions <- .Call("C_QMC", createMatrix(noflevels)[-output$negatives, , drop = FALSE] + 1, noflevels, PACKAGE = "QCA")
setColnames(expressions, colnames(inputt))
}
else if (method == "eQMC") {
if (nrow(neg.matrix) > 0) {
expressions <- sort.int(setdiff(findSupersets(pos.matrix, noflevels + 1), findSupersets(neg.matrix, noflevels + 1)))
}
else {
expressions <- sort.int(findSupersets(pos.matrix, noflevels + 1))
}
expressions <- .Call("C_removeRedundants", expressions, noflevels, mbaseplus, PACKAGE = "QCA")
expressions <- admisc::sortExpressions(getRow(expressions, noflevels + 1))
setColnames(expressions, colnames(inputt))
}
else {
extended.data <- as.matrix(tt$recoded.data)
if (nrow(excl.matrix) > 0) {
extended.data <- rbind(extended.data, cbind(excl.matrix, 0))
}
if (sol.cons > 0 & all.sol & sol.depth == 0) {
sol.depth <- 7
}
expressions <- .Call("C_Cubes", list(
tt = cbind(rbind(pos.matrix, neg.matrix) - 1, rep(c(1, 0), c(nrow(pos.matrix), nrow(neg.matrix)))),
data = extended.data,
all.sol = all.sol,
row.dom = row.dom,
min.pin = min.pin,
pi.cons = pi.cons,
depth = as.integer(c(pi.depth, sol.depth)),
sol.cons = sol.cons,
sol.cov = sol.cov,
fs = tt$fs,
max.comb = max.comb,
first.min = first.min,
keep.trying = keep.trying),
PACKAGE = "QCA")
}
callist$expressions <- expressions
p.sol <- do.call("getSolution", callist)
}
output$PIchart <- p.sol$mtrx
class(output$PIchart) <- c("matrix", "QCA_pic")
attr(output$PIchart, "PI") <- p.sol$expressions
output$primes <- p.sol$reduced$expressions
output$solution <- p.sol$solution.list[[1]]
output$essential <- p.sol$solution.list[[2]]
output$options$explain <- explain
output$options$neg.out <- neg.out
output$options$details <- details
output$options$sol.cons <- sol.cons
output$options$sol.cov <- sol.cov
output$options$relation <- relation
output$options$show.cases <- show.cases
output$options$use.letters <- use.letters
output$options$collapse <- collapse
output$options$curly <- curly
expr.cases <- rep(NA, nrow(p.sol$reduced$expressions))
tt.rows <- admisc::writePrimeimp(inputt, mv = mv, collapse = collapse)
if (any(grepl("[*]", rownames(p.sol$reduced$expressions)))) {
if (use.letters) {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), snames = LETTERS[seq(length(conditions))], configs = tt.rows, mv = mv, noflevels = noflevels)
}
else {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), snames = conditions, configs = tt.rows, mv = mv, noflevels = noflevels)
}
}
else {
if (use.letters) {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), configs = tt.rows, snames = LETTERS[seq(length(conditions))], mv = mv, noflevels = noflevels)
}
else {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), configs = tt.rows, snames = conditions, mv = mv, noflevels = noflevels)
}
}
colnames(mtrxlines) <- colnames(p.sol$reduced$mtrx) <- rownms
for (l in seq(length(expr.cases))) {
expr.cases[l] <- paste(inputcases[mtrxlines[l, ]], collapse="; ")
}
output$inputcases <- inputcases
conds <- conditions
if (all(is.element(colnames(p.sol$reduced$expressions), conditions))) {
conds <- colnames(p.sol$reduced$expressions)
}
else {
if (all(is.element(colnames(p.sol$reduced$expressions), LETTERS))) {
conds <- conditions[match(colnames(p.sol$reduced$expressions), LETTERS)]
}
}
poflist <- list(setms = paste(rownames(p.sol$reduced$expressions), collapse = "+"),
outcome = tt$options$outcome, data = indata, neg.out = neg.out,
use.letters = tt$options$use.letters, show.cases = TRUE, cases = expr.cases,
conditions = conds, relation = "sufficiency", minimize = TRUE)
if (length(output$solution) > 1) {
poflist$solution.list <- output$solution
poflist$essential <- output$essential
}
if (!is.element("simplify", names(dots))) {
listIC <- do.call("pof", poflist)
listIC$options$show.cases <- show.cases
output$pims <- listIC$pims
attr(output$pims, "conditions") <- conditions
output$IC <- listIC
}
output$numbers <- c(OUT1 = nofcases1, OUT0 = nofcases0, OUTC = nofcasesC, Total = nofcases1 + nofcases0 + nofcasesC)
mtrx <- p.sol$mtrx[p.sol$all.PIs, , drop = FALSE]
SA <- TRUE
if (is.element("SA", names(dots))) {
SA <- dots$SA
}
if (SA & 3^length(noflevels) < 2^31) {
conds <- conditions
if (tt$options$use.letters) {
conds <- LETTERS[seq(length(conditions))]
}
mbaseexpr <- rev(c(1, cumprod(rev(noflevels[is.element(conds, colnames(p.sol$reduced$expressions))] + 1))))[-1]
output$SA <- lapply(p.sol$solution.list[[1]], function(x) {
p.expressions <- p.sol$reduced$expressions[x, , drop = FALSE]
temp <- apply(p.expressions, 1, function(pr) {
indices <- rev(which(pr == 0))
tempr <- NULL
for (k in indices) {
if (is.null(tempr)) {
tempr <- drop(mbaseexpr %*% pr) + sum(mbaseexpr[pr == 0])
temp2 <- tempr
}
for (lev in seq(noflevels[k] - 1)) {
temp2 <- c(temp2, tempr + mbaseexpr[k]*lev)
}
tempr <- temp2
}
return(tempr)
})
if (all(is.null(temp))) {
SAx <- matrix(nrow = 0, ncol = ncol(inputt))
}
else {
temp <- sort(unique(as.vector(unlist(temp))))
temp <- temp[!is.element(temp, drop(inputt %*% mbaseplus))]
if (length(temp) == 0) {
SAx <- matrix(nrow = 0, ncol = ncol(inputt))
}
else {
SAx <- getRow(temp + 1, noflevels + 1) - 1L
rownames(SAx) <- drop(SAx %*% mbase) + 1
}
}
colnames(SAx) <- colnames(inputt)
return(SAx)
})
prettyNums <- formatC(seq(length(p.sol$solution.list[[1]])), digits = nchar(length(p.sol$solution.list[[1]])) - 1, flag = 0)
if (!is.null(dir.exp) & !identical(include, "")) {
if (!identical(c.sol$solution.list, NA)) {
dir.exp <- verify.dir.exp(recdata, outcome, conditions, noflevels, dir.exp, enter)
isoliscsol <- identical(dir.exp, matrix(0L, ncol = length(conditions)))
if (all(unlist(lapply(output$SA, is.null))) | isoliscsol) {
ECmat <- as.data.frame(matrix(ncol = length(conditions), nrow = 0))
colnames(ECmat) <- colnames(inputt)
}
else {
result <- .Call("C_getEC", dir.exp,
c.sol$expressions, c.sol$sol.matrix,
p.sol$expressions, p.sol$sol.matrix,
output$SA, as.integer(noflevels),
PACKAGE = "QCA")
EClist <- result[[1]]
isols <- result[[2]]
intsel <- result[[3]]
}
tt.rows <- admisc::writePrimeimp(inputt, mv = mv, collapse = collapse)
i.sol <- vector("list", ncol(c.sol$sol.matrix)*ncol(p.sol$sol.matrix))
index <- 1
for (c.s in seq(ncol(c.sol$sol.matrix))) {
for (p.s in seq(ncol(p.sol$sol.matrix))) {
names(i.sol)[index] <- paste("C", c.s, "P", p.s, sep = "")
if (all(unlist(lapply(output$SA, is.null))) | isoliscsol) {
i.sol[[index]]$EC <- ECmat
i.sol[[index]]$DC <- ECmat
i.sol.index <- c.sol
i.sol.index$solution.list[[1]] <- c.sol$solution.list[[1]][[c.s]]
}
else {
i.sol[[index]]$EC <- EClist[[index]]
i.sol[[index]]$DC <- output$SA[[p.s]][setdiff(rownames(output$SA[[p.s]]), rownames(EClist[[index]])), , drop = FALSE]
pos.matrix.i.sol <- unique(as.matrix(rbind(pos.matrix, EClist[[index]] + 1L)))
expressions <- .Call("C_QMC", pos.matrix.i.sol, noflevels, PACKAGE = "QCA")
callist$expressions <- expressions
i.sol.index <- do.call("getSolution", callist)
i.sol.index$expressions <- i.sol.index$expressions[rowSums(i.sol.index$mtrx) > 0, , drop = FALSE]
}
i.sol[[index]]$solution <- i.sol.index$solution.list[[1]]
i.sol[[index]]$essential <- i.sol.index$solution.list[[2]]
i.sol[[index]]$primes <- i.sol.index$reduced$expressions
i.sol[[index]]$PIchart <- i.sol.index$mtrx
class(i.sol[[index]]$PIchart) <- c("matrix", "QCA_pic")
i.sol[[index]]$c.sol <- c.sol$solution.list[[1]][[c.s]]
i.sol[[index]]$p.sol <- p.sol$solution.list[[1]][[p.s]]
expr.cases <- rep(NA, nrow(i.sol.index$reduced$expressions))
if (use.letters) {
mtrxlines <- makeChart(primes = rownames(i.sol.index$reduced$expressions), configs = tt.rows, snames = LETTERS[seq(length(conditions))], mv = mv, noflevels = noflevels)
}
else {
mtrxlines <- makeChart(primes = rownames(i.sol.index$reduced$expressions), configs = tt.rows, snames = conditions, mv = mv, noflevels = noflevels)
}
for (l in seq(length(expr.cases))) {
expr.cases[l] <- paste(inputcases[which(mtrxlines[l, ])], collapse="; ")
}
poflist <- list(setms = paste(rownames(i.sol.index$reduced$expressions), collapse = "+"),
outcome = tt$options$outcome, data = indata, neg.out = neg.out,
use.letters = tt$options$use.letters, show.cases = TRUE, cases = expr.cases,
conditions = conditions, relation = "sufficiency", minimize = TRUE)
if (length(i.sol.index$solution.list[[1]]) > 1) {
poflist$solution.list <- i.sol.index$solution.list[[1]]
poflist$essential <- i.sol.index$solution.list[[2]]
}
i.sol[[index]]$IC <- do.call("pof", poflist)
i.sol[[index]]$IC$options$show.cases <- show.cases
i.sol[[index]]$pims <- i.sol[[index]]$IC$pims
attr(i.sol[[index]]$pims, "conditions") <- conditions
i.sol[[index]]$IC$pims <- NULL
index <- index + 1
}
}
output$i.sol <- i.sol
}}
names(output$SA) <- paste("M", prettyNums, sep = "")
output$SA <- lapply(output$SA, as.data.frame)
}
if (any(names(output) == "i.sol")) {
for (i in seq(length(output$i.sol))) {
output$i.sol[[i]]$EC <- as.data.frame(output$i.sol[[i]]$EC)
}
}
if (!methods::is(input, "QCA_tt")) {
output$tt$options$outcome <- outcome.copy
}
output$complex <- p.sol$complex
output$call <- metacall
if (is.element("via.web", names(dots))) {
output$via.web <- TRUE
}
if (mv & !grepl(mvregexp, output$tt$options$outcome)) {
output$tt$options$outcome <- paste(output$tt$options$outcome, "[1]", sep = "")
}
return(structure(output, class = "QCA_min"))
}
`minimizeLoop` <-
function(...) {
allargs <- list(...)
verify.mqca(allargs)
outcome <- admisc::splitstr(allargs$outcome)
minimize.list <- lapply(outcome, function(x) {
allargs[["outcome"]] <- x
return(do.call("minimize", allargs))
})
names(minimize.list) <- outcome
return(structure(minimize.list, class = "QCA_loopmin"))
}
`eqmcc` <- function(...) {
.Deprecated(msg = "Function eqmcc() is deprecated, and has been renamed to minimize()\n")
minimize(...)
}
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Defines functions `eqmcc` `minimizeLoop` `minimize`
# Copyright (c) 2016 - 2020, Adrian Dusa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, in whole or in part, are permitted provided that the
# following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * The names of its contributors may NOT be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL ADRIAN DUSA BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
`minimize` <-
function(input, include = "", dir.exp = NULL, details = FALSE, all.sol = FALSE,
row.dom = FALSE, min.pin = FALSE, max.comb = 0, first.min = FALSE,
method = "CCubes", ...) {
metacall <- match.call()
dots <- substitute(list(...))
if (is.element("data", names(dots))) {
input <- eval.parent(dots$data)
dots$data <- NULL
}
enter <- if (is.element("enter", names(dots))) "" else "\n"
if (missing(input)) {
cat(enter)
stop(simpleError(paste0("The input (a truth table or a dataset) is missing.", enter, enter)))
}
else {
if (is.matrix(input)) {
if (is.null(colnames(input))) {
cat(enter)
stop(simpleError(paste0("The data should have column names.", enter, enter)))
}
if (any(duplicated(rownames(input)))) {
rownames(input) <- seq(nrow(input))
}
input <- as.data.frame(input)
for (i in seq(ncol(input))) {
if (admisc::possibleNumeric(input[, i])) {
input[, i] <- admisc::asNumeric(input[, i])
}
}
}
if(!(is.data.frame(input) | methods::is(input, "QCA_tt"))) {
cat(enter)
stop(simpleError(paste0("The input should be a truth table or a dataset.", enter, enter)))
}
}
ttinput <- methods::is(input, "QCA_tt")
print.truth.table <- details & !ttinput
if (ttinput) {
nms <- colnames(input$recoded.data)[seq(length(input$noflevels))]
}
else {
nms <- colnames(input)
}
if (length(dots) > 1) {
for (i in seq(2, length(dots))) {
dots[[i]] <- admisc::recreate(dots[[i]], nms)
}
}
dots <- eval(dots)
back.args <- c("outcome", "conditions", "n.cut", "incl.cut", "complete", "show.cases", sort.by = "", "use.letters", "inf.test",
"rowdom", "direxp", "neg.out", "data", "relation", "explain", "omit", "exclude")
check.args <- pmatch(names(dots), back.args)
names(dots)[!is.na(check.args)] <- back.args[check.args[!is.na(check.args)]]
explain <- if (is.element("explain", names(dots))) dots$explain else "1"
outcome <- if (is.element("outcome", names(dots))) dots$outcome else ""
conditions <- if (is.element("conditions", names(dots))) dots$conditions else ""
incl.cut <- if (is.element("incl.cut", names(dots))) dots$incl.cut else 1
n.cut <- if (is.element("n.cut", names(dots))) dots$n.cut else 1
complete <- if (is.element("complete", names(dots))) dots$complete else FALSE
show.cases <- if (is.element("show.cases", names(dots))) dots$show.cases else FALSE
dcc <- if (is.element("dcc", names(dots))) dots$dcc else FALSE
sort.by <- if (is.element("sort.by", names(dots))) dots$sort.by else ""
use.letters <- if (is.element("use.letters", names(dots))) dots$use.letters else FALSE
inf.test <- if (is.element("inf.test", names(dots))) dots$inf.test else ""
relation <- if (is.element("relation", names(dots))) dots$relation else "sufficiency"
neg.out <- if (is.element("neg.out", names(dots))) dots$neg.out else FALSE
pi.cons <- if (is.element("pi.cons", names(dots))) dots$pi.cons else 0
pi.depth <- if (is.element("pi.depth", names(dots))) dots$pi.depth else 0
sol.cons <- if (is.element("sol.cons", names(dots))) dots$sol.cons else 0
sol.cov <- if (is.element("sol.cov", names(dots))) dots$sol.cov else 1
sol.depth <- if (is.element("sol.depth", names(dots))) dots$sol.depth else 0
exclude <- if (is.element("exclude", names(dots))) dots$exclude else NULL
keep.trying <- if (is.element("keep.trying", names(dots))) dots$keep.trying else FALSE
if (is.null(exclude)) {
if (is.element("omit", names(dots))) {
exclude <- dots$omit
}
}
if (is.null(include)) {
cat(enter)
stop(simpleError(paste0("The \"include\" argument cannot be NULL.", enter, enter)))
}
dir.exp <- admisc::recreate(substitute(dir.exp))
row.dom <- if (is.element("rowdom", names(dots))) dots$rowdom else row.dom
dir.exp <- if (is.element("direxp", names(dots))) dots$direxp else dir.exp
if (identical(dir.exp, character(0))) {
dir.exp <- NULL
}
else if (!is.null(dir.exp)) {
if (length(dir.exp) == 1) {
if (grepl(":", dir.exp)) {
des <- unlist(strsplit(dir.exp, split = ":"))
if (!all(is.element(des, nms))) {
cat(enter)
stop(simpleError(paste0("Inexisting condition(s) in the sequence of directional expectations.", enter, enter)))
}
dir.exp <- nms[seq(which(nms == des[1]), which(nms == des[2]))]
}
else {
dir.exp <- admisc::splitstr(dir.exp)
}
}
}
if (identical(include, "")) {
if (!is.null(dir.exp)) {
cat(enter)
stop(simpleError(paste0("Directional expectations cannot be specified without including the remainders.", enter, enter)))
}
}
if (is.character(explain) & !identical(explain, "1")) {
explain <- admisc::splitstr(explain)
}
if (is.character(include) & !identical(include, "")) {
include <- admisc::splitstr(include)
}
if (is.character(outcome) & !identical(outcome, "")) {
outcome <- admisc::splitstr(outcome)
}
if (ttinput) {
tt <- input
curly <- grepl("\\{", tt$options$outcome)
if (is.null(tt$options$exclude) & !is.null(exclude)) {
callist <- as.list(tt$call)
dataname <- callist$data
callist$data <- tt$initial.data
callist$exclude <- exclude
tt <- do.call("truthTable", callist[-1])
callist$data <- dataname
tt$call <- as.call(callist)
}
recdata <- tt$recoded.data
conditions <- colnames(recdata)[seq(length(tt$noflevels))]
outcome <- colnames(recdata)[ncol(recdata)]
indata <- tt$initial.data[, match(colnames(recdata), colnames(tt$initial.data)), drop = FALSE]
}
else {
if (identical(outcome, "")) {
cat(enter)
stop(simpleError(paste0("Consider creating a truth table first, or formally specify the argument \"outcome\".", enter, enter)))
}
if (any(c(pi.cons, sol.cons) > 0) & incl.cut[1] == 1) {
incl.cut[1] <- min(c(pi.cons, sol.cons))
}
if (length(outcome) > 1) {
return(do.call("minimizeLoop", as.list(metacall)[-1], envir = parent.frame()))
}
outcome.copy <- outcome
indata <- input
curly <- grepl("\\{", outcome)
testoutcome <- ifelse(curly,
admisc::curlyBrackets(admisc::notilde(outcome), outside = TRUE),
admisc::squareBrackets(admisc::notilde(outcome), outside = TRUE))
if (!is.element(testoutcome, colnames(input))) {
cat(enter)
stop(simpleError(paste0("Outcome not found in the data.", enter, enter)))
}
outcome.name <- testoutcome
if (identical(conditions, "")) {
conditions <- names(input)[-which(names(input) == outcome.name)]
}
else {
conditions <- admisc::splitstr(conditions)
}
verify.data(input, outcome.name, conditions)
if (length(conditions) == 1) {
if (grepl(":", conditions)) {
nms <- colnames(data)
cs <- unlist(strsplit(conditions, split = ":"))
conditions <- nms[seq(which(nms == cs[1]), which(nms == cs[2]))]
}
}
input <- input[, c(conditions, outcome.name)]
verify.minimize(input, outcome.name, conditions, explain, include, use.letters)
if (!is.element("incl.cut", names(dots))) {
dots$incl.cut <- incl.cut
}
tt <- do.call("truthTable", c(list(data = input), dots))
tt$initial.data <- indata
indata <- input
recdata <- tt$recoded.data
outcome <- outcome.name
names(indata) <- c(conditions, outcome)
}
use.letters <- tt$options$use.letters
show.cases <- show.cases | tt$options$show.cases
neg.out <- tt$options$neg.out
output <- list()
output$tt <- tt
output$options$print.truth.table <- print.truth.table
rowsNotMissing <- which(tt$tt$OUT != "?")
if (any(tt$tt$OUT == "?")) {
missings <- which(tt$tt$OUT == "?")
tt$tt <- tt$tt[-missings, , drop = FALSE]
}
ttrownms <- admisc::asNumeric(rownames(tt$tt))
noflevels <- tt$noflevels
mbase <- as.integer(rev(c(1, cumprod(rev(noflevels))))[-1])
mbaseplus <- rev(c(1, cumprod(rev(noflevels + 1))))[-1]
alreadyletters <- sum(nchar(colnames(recdata)[-ncol(recdata)])) == ncol(recdata) - 1
tt$tt[seq(length(conditions))] <- as.data.frame(lapply(tt$tt[seq(length(conditions))], function(x) {
x[is.element(x, c("-", "dc"))] <- -1
return(admisc::asNumeric(x))
}))
pos.incl <- unique(c(explain, include))
subset.tt <- ttrownms[is.element(tt$tt[, "OUT"], explain)]
subset.pos <- is.element(tt$tt[, "OUT"], pos.incl)
pos.matrix <- as.matrix(tt$tt[subset.pos, seq(length(noflevels))])
rownames(pos.matrix) <- drop(pos.matrix %*% mbase) + 1
pos.matrix <- pos.matrix + 1
neg.matrix <- as.matrix(tt$tt[!is.element(tt$tt[, "OUT"], pos.incl), seq(length(noflevels))])
neg.matrix <- matrix(as.numeric(neg.matrix), ncol = length(noflevels)) + 1
rownames(neg.matrix) <- drop((neg.matrix - 1) %*% mbase) + 1
if (sum(subset.pos) == 0) {
cat(enter)
stop(simpleError(paste0("None of the values in OUT is explained. Please check the truth table.", enter, enter)))
}
inputt <- as.matrix(tt$tt[is.element(ttrownms, subset.tt), seq(length(noflevels)), drop = FALSE])
rownames(inputt) <- drop(inputt %*% mbase) + 1
inputt <- inputt + 1
inputcases <- tt$cases[is.element(tt$indexes, subset.tt)]
nofcases1 <- sum(tt$tt$n[tt$tt$OUT == 1])
nofcases0 <- sum(tt$tt$n[tt$tt$OUT == 0])
nofcasesC <- sum(tt$tt$n[tt$tt$OUT == "C"])
excl.matrix <- matrix(nrow = 0, ncol = length(conditions))
output$negatives <- sort(drop((neg.matrix - 1) %*% mbase) + 1)
rownms <- rownames(inputt)
if (nrow(pos.matrix) == 0) {
cat(enter)
stop(simpleError(paste0("Nothing to explain. Please check the truth table.", enter, enter)))
}
incl.rem <- is.element("?", include)
if (nrow(neg.matrix) == 0 & incl.rem & !is.element("causalChain", names(dots))) {
cat(enter)
stop(simpleError(paste0("All truth table configurations are used, all conditions are minimized.\n",
" Please check the truth table.", enter, enter)))
}
expressions <- pos.matrix
recdata[, conditions] <- as.data.frame(lapply(recdata[, conditions, drop = FALSE], function(x) {
x[is.element(x, c("-", "?", "dc"))] <- -1
return(as.numeric(x))
}))
mv <- any(recdata[, seq(ncol(recdata) - 1)] > 1)
collapse <- "*"
changed <- FALSE
if (use.letters & !alreadyletters) {
colnms <- LETTERS[seq(ncol(inputt))]
changed <- TRUE
}
else {
colnms <- colnames(recdata[, seq(ncol(inputt)), drop = FALSE])
}
setColnames(expressions, colnms)
setColnames(inputt, colnms)
setColnames(pos.matrix, colnms)
setColnames(neg.matrix, colnms)
rownames(neg.matrix) <- (neg.matrix - 1) %*% mbase + 1
output$initials <- admisc::writePrimeimp(inputt, mv = mv, collapse = collapse)
if (any(c(pi.cons, sol.cons) > 0)) {
incl.rem <- TRUE
method <- "CCubes"
}
expressions <- .Call("C_QMC", expressions, noflevels, PACKAGE = "QCA")
if (is.element("simplify", names(dots))) {
expressions <- admisc::sortExpressions(expressions)
}
callist <- list(expressions=expressions, mv=mv, collapse=collapse, inputt=inputt, row.dom=row.dom,
initial=rownms, all.sol=all.sol, indata=indata, curly=curly)
callist <- c(callist, dots)
if (!incl.rem || (!is.null(dir.exp) & !identical(include, ""))) {
c.sol <- p.sol <- do.call("getSolution", callist)
}
if (incl.rem) {
pos.matrix <- inputt
if (method == "QMC") {
expressions <- .Call("C_QMC", createMatrix(noflevels)[-output$negatives, , drop = FALSE] + 1, noflevels, PACKAGE = "QCA")
setColnames(expressions, colnames(inputt))
}
else if (method == "eQMC") {
if (nrow(neg.matrix) > 0) {
expressions <- sort.int(setdiff(findSupersets(pos.matrix, noflevels + 1), findSupersets(neg.matrix, noflevels + 1)))
}
else {
expressions <- sort.int(findSupersets(pos.matrix, noflevels + 1))
}
expressions <- .Call("C_removeRedundants", expressions, noflevels, mbaseplus, PACKAGE = "QCA")
expressions <- admisc::sortExpressions(getRow(expressions, noflevels + 1))
setColnames(expressions, colnames(inputt))
}
else {
extended.data <- as.matrix(tt$recoded.data)
if (nrow(excl.matrix) > 0) {
extended.data <- rbind(extended.data, cbind(excl.matrix, 0))
}
if (sol.cons > 0 & all.sol & sol.depth == 0) {
sol.depth <- 7
}
expressions <- .Call("C_Cubes", list(
tt = cbind(rbind(pos.matrix, neg.matrix) - 1, rep(c(1, 0), c(nrow(pos.matrix), nrow(neg.matrix)))),
data = extended.data,
all.sol = all.sol,
row.dom = row.dom,
min.pin = min.pin,
pi.cons = pi.cons,
depth = as.integer(c(pi.depth, sol.depth)),
sol.cons = sol.cons,
sol.cov = sol.cov,
fs = tt$fs,
max.comb = max.comb,
first.min = first.min,
keep.trying = keep.trying),
PACKAGE = "QCA")
}
callist$expressions <- expressions
p.sol <- do.call("getSolution", callist)
}
output$PIchart <- p.sol$mtrx
class(output$PIchart) <- c("matrix", "QCA_pic")
attr(output$PIchart, "PI") <- p.sol$expressions
output$primes <- p.sol$reduced$expressions
output$solution <- p.sol$solution.list[[1]]
output$essential <- p.sol$solution.list[[2]]
output$options$explain <- explain
output$options$neg.out <- neg.out
output$options$details <- details
output$options$sol.cons <- sol.cons
output$options$sol.cov <- sol.cov
output$options$relation <- relation
output$options$show.cases <- show.cases
output$options$use.letters <- use.letters
output$options$collapse <- collapse
output$options$curly <- curly
expr.cases <- rep(NA, nrow(p.sol$reduced$expressions))
tt.rows <- admisc::writePrimeimp(inputt, mv = mv, collapse = collapse)
if (any(grepl("[*]", rownames(p.sol$reduced$expressions)))) {
if (use.letters) {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), snames = LETTERS[seq(length(conditions))], configs = tt.rows, mv = mv, noflevels = noflevels)
}
else {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), snames = conditions, configs = tt.rows, mv = mv, noflevels = noflevels)
}
}
else {
if (use.letters) {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), configs = tt.rows, snames = LETTERS[seq(length(conditions))], mv = mv, noflevels = noflevels)
}
else {
mtrxlines <- makeChart(primes = rownames(p.sol$reduced$expressions), configs = tt.rows, snames = conditions, mv = mv, noflevels = noflevels)
}
}
colnames(mtrxlines) <- colnames(p.sol$reduced$mtrx) <- rownms
for (l in seq(length(expr.cases))) {
expr.cases[l] <- paste(inputcases[mtrxlines[l, ]], collapse="; ")
}
output$inputcases <- inputcases
conds <- conditions
if (all(is.element(colnames(p.sol$reduced$expressions), conditions))) {
conds <- colnames(p.sol$reduced$expressions)
}
else {
if (all(is.element(colnames(p.sol$reduced$expressions), LETTERS))) {
conds <- conditions[match(colnames(p.sol$reduced$expressions), LETTERS)]
}
}
poflist <- list(setms = paste(rownames(p.sol$reduced$expressions), collapse = "+"),
outcome = tt$options$outcome, data = indata, neg.out = neg.out,
use.letters = tt$options$use.letters, show.cases = TRUE, cases = expr.cases,
conditions = conds, relation = "sufficiency", minimize = TRUE)
if (length(output$solution) > 1) {
poflist$solution.list <- output$solution
poflist$essential <- output$essential
}
if (!is.element("simplify", names(dots))) {
listIC <- do.call("pof", poflist)
listIC$options$show.cases <- show.cases
output$pims <- listIC$pims
attr(output$pims, "conditions") <- conditions
output$IC <- listIC
}
output$numbers <- c(OUT1 = nofcases1, OUT0 = nofcases0, OUTC = nofcasesC, Total = nofcases1 + nofcases0 + nofcasesC)
mtrx <- p.sol$mtrx[p.sol$all.PIs, , drop = FALSE]
SA <- TRUE
if (is.element("SA", names(dots))) {
SA <- dots$SA
}
if (SA & 3^length(noflevels) < 2^31) {
conds <- conditions
if (tt$options$use.letters) {
conds <- LETTERS[seq(length(conditions))]
}
mbaseexpr <- rev(c(1, cumprod(rev(noflevels[is.element(conds, colnames(p.sol$reduced$expressions))] + 1))))[-1]
output$SA <- lapply(p.sol$solution.list[[1]], function(x) {
p.expressions <- p.sol$reduced$expressions[x, , drop = FALSE]
temp <- apply(p.expressions, 1, function(pr) {
indices <- rev(which(pr == 0))
tempr <- NULL
for (k in indices) {
if (is.null(tempr)) {
tempr <- drop(mbaseexpr %*% pr) + sum(mbaseexpr[pr == 0])
temp2 <- tempr
}
for (lev in seq(noflevels[k] - 1)) {
temp2 <- c(temp2, tempr + mbaseexpr[k]*lev)
}
tempr <- temp2
}
return(tempr)
})
if (all(is.null(temp))) {
SAx <- matrix(nrow = 0, ncol = ncol(inputt))
}
else {
temp <- sort(unique(as.vector(unlist(temp))))
temp <- temp[!is.element(temp, drop(inputt %*% mbaseplus))]
if (length(temp) == 0) {
SAx <- matrix(nrow = 0, ncol = ncol(inputt))
}
else {
SAx <- getRow(temp + 1, noflevels + 1) - 1L
rownames(SAx) <- drop(SAx %*% mbase) + 1
}
}
colnames(SAx) <- colnames(inputt)
return(SAx)
})
prettyNums <- formatC(seq(length(p.sol$solution.list[[1]])), digits = nchar(length(p.sol$solution.list[[1]])) - 1, flag = 0)
if (!is.null(dir.exp) & !identical(include, "")) {
if (!identical(c.sol$solution.list, NA)) {
dir.exp <- verify.dir.exp(recdata, outcome, conditions, noflevels, dir.exp, enter)
isoliscsol <- identical(dir.exp, matrix(0L, ncol = length(conditions)))
if (all(unlist(lapply(output$SA, is.null))) | isoliscsol) {
ECmat <- as.data.frame(matrix(ncol = length(conditions), nrow = 0))
colnames(ECmat) <- colnames(inputt)
}
else {
result <- .Call("C_getEC", dir.exp,
c.sol$expressions, c.sol$sol.matrix,
p.sol$expressions, p.sol$sol.matrix,
output$SA, as.integer(noflevels),
PACKAGE = "QCA")
EClist <- result[[1]]
isols <- result[[2]]
intsel <- result[[3]]
}
tt.rows <- admisc::writePrimeimp(inputt, mv = mv, collapse = collapse)
i.sol <- vector("list", ncol(c.sol$sol.matrix)*ncol(p.sol$sol.matrix))
index <- 1
for (c.s in seq(ncol(c.sol$sol.matrix))) {
for (p.s in seq(ncol(p.sol$sol.matrix))) {
names(i.sol)[index] <- paste("C", c.s, "P", p.s, sep = "")
if (all(unlist(lapply(output$SA, is.null))) | isoliscsol) {
i.sol[[index]]$EC <- ECmat
i.sol[[index]]$DC <- ECmat
i.sol.index <- c.sol
i.sol.index$solution.list[[1]] <- c.sol$solution.list[[1]][[c.s]]
}
else {
i.sol[[index]]$EC <- EClist[[index]]
i.sol[[index]]$DC <- output$SA[[p.s]][setdiff(rownames(output$SA[[p.s]]), rownames(EClist[[index]])), , drop = FALSE]
pos.matrix.i.sol <- unique(as.matrix(rbind(pos.matrix, EClist[[index]] + 1L)))
expressions <- .Call("C_QMC", pos.matrix.i.sol, noflevels, PACKAGE = "QCA")
callist$expressions <- expressions
i.sol.index <- do.call("getSolution", callist)
i.sol.index$expressions <- i.sol.index$expressions[rowSums(i.sol.index$mtrx) > 0, , drop = FALSE]
}
i.sol[[index]]$solution <- i.sol.index$solution.list[[1]]
i.sol[[index]]$essential <- i.sol.index$solution.list[[2]]
i.sol[[index]]$primes <- i.sol.index$reduced$expressions
i.sol[[index]]$PIchart <- i.sol.index$mtrx
class(i.sol[[index]]$PIchart) <- c("matrix", "QCA_pic")
i.sol[[index]]$c.sol <- c.sol$solution.list[[1]][[c.s]]
i.sol[[index]]$p.sol <- p.sol$solution.list[[1]][[p.s]]
expr.cases <- rep(NA, nrow(i.sol.index$reduced$expressions))
if (use.letters) {
mtrxlines <- makeChart(primes = rownames(i.sol.index$reduced$expressions), configs = tt.rows, snames = LETTERS[seq(length(conditions))], mv = mv, noflevels = noflevels)
}
else {
mtrxlines <- makeChart(primes = rownames(i.sol.index$reduced$expressions), configs = tt.rows, snames = conditions, mv = mv, noflevels = noflevels)
}
for (l in seq(length(expr.cases))) {
expr.cases[l] <- paste(inputcases[which(mtrxlines[l, ])], collapse="; ")
}
poflist <- list(setms = paste(rownames(i.sol.index$reduced$expressions), collapse = "+"),
outcome = tt$options$outcome, data = indata, neg.out = neg.out,
use.letters = tt$options$use.letters, show.cases = TRUE, cases = expr.cases,
conditions = conditions, relation = "sufficiency", minimize = TRUE)
if (length(i.sol.index$solution.list[[1]]) > 1) {
poflist$solution.list <- i.sol.index$solution.list[[1]]
poflist$essential <- i.sol.index$solution.list[[2]]
}
i.sol[[index]]$IC <- do.call("pof", poflist)
i.sol[[index]]$IC$options$show.cases <- show.cases
i.sol[[index]]$pims <- i.sol[[index]]$IC$pims
attr(i.sol[[index]]$pims, "conditions") <- conditions
i.sol[[index]]$IC$pims <- NULL
index <- index + 1
}
}
output$i.sol <- i.sol
}}
names(output$SA) <- paste("M", prettyNums, sep = "")
output$SA <- lapply(output$SA, as.data.frame)
}
if (any(names(output) == "i.sol")) {
for (i in seq(length(output$i.sol))) {
output$i.sol[[i]]$EC <- as.data.frame(output$i.sol[[i]]$EC)
}
}
if (!methods::is(input, "QCA_tt")) {
output$tt$options$outcome <- outcome.copy
}
output$complex <- p.sol$complex
output$call <- metacall
if (is.element("via.web", names(dots))) {
output$via.web <- TRUE
}
if (mv & !grepl(mvregexp, output$tt$options$outcome)) {
output$tt$options$outcome <- paste(output$tt$options$outcome, "[1]", sep = "")
}
return(structure(output, class = "QCA_min"))
}
`minimizeLoop` <-
function(...) {
allargs <- list(...)
verify.mqca(allargs)
outcome <- admisc::splitstr(allargs$outcome)
minimize.list <- lapply(outcome, function(x) {
allargs[["outcome"]] <- x
return(do.call("minimize", allargs))
})
names(minimize.list) <- outcome
return(structure(minimize.list, class = "QCA_loopmin"))
}
`eqmcc` <- function(...) {
.Deprecated(msg = "Function eqmcc() is deprecated, and has been renamed to minimize()\n")
minimize(...)
}
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