Nothing
R/ACO_MPlus.R
In ShortForm: Automatic Short Form Creation
Defines functions
antcolony.mplus
Documented in
antcolony.mplus
#' A function to implement the ant colony optimization algorithm for short form
#' specification searches, either using MPlus directly via
#' \code{\link[base]{system}} calls or using Mplus indirectly with the package
#' \link[MplusAutomation]{MplusAutomation}.
#'
#' @description The Ant Colony Optimization (ACO) algorithm (Dorigo & Stutzle,
#' 2004) can produce short forms of scales that are optimized with respect to
#' characteristics selected by the developer, such as model fit and predictive
#' relationships with other variables. The algorithm is based on the foraging
#' behavior of a group of ants, which start searching for food in a variety of
#' directions and then eventually all ants converge to the shortest distance to
#' the food source. This behavior occurs because ants leave a pheromone trail
#' behind as they search for food and ants in shorter paths leave stronger
#' pheromone trails, which are detected by other ants and that will lead them to
#' follow the shortest trail.
#'
#' @details This function sends a specified number of ants
#' per iteration, which randomly select items to build a model, then evaluates
#' the model based on pheromone levels. The pheromone levels are updated after
#' each iteration according to the best-fitting model of that iteration. The
#' algorithm's stopping rule is to end the search when a certain solution is the
#' same for a given number of ants in a row. When constructing the mplus dataset
#' and when \code{Mplus.Automation=FALSE}, make sure that items in 'categorical
#' are' and 'usevariables' are specifications that take the same number of lines
#' per short form.
#'
#' PREPARATORY STEPS: For the ACO algorithm implementation for short
#' for selection, the following decisions are needed:
#'
#' 1. Determine the target size for the short form.
#'
#' 2. Determine which characteristics should be optimized.
#'
#' 3. Define how the pheromone level will be computed: This is a function of the
#' characteristics of the short form that will be optimized. In Leite, Huang and
#' Marcoulides (2008), the pheromone level was zero if model fit indices did
#' not meet Hu and Bentler's (1999) suggested thresholds, and equal to the sum of
#' path coefficients of a predictor variable if model fit indices met thresholds.
#' Currently, the package only implements pheromone calculation based on
#' regression coefficients or variance explained, with user-selected model fit
#' index thresholds.
#'
#' 4. Define how many short forms should be evaluated before the best-so-far
#' pheromone level is examined. Leite, Huang and Marcoulides (2008) used 10 short
#' forms.
#'
#' 5. Define the percentage of pheromone evaporation, if any. Leite, Huang and
#' Marcoulides (2008) used 5\%.
#'
#' 6. Define convergence criterion. Leite, Huang and Marcoulides (2008) set the
#' algorithm to converge if the short form did not improve in 100 x number of
#' short forms in step 4.
#'
#' IMPLEMENTATION: Once these decisions are made, the ACO algorithm
#' selects short forms with the following steps:
#'
#' Step 1. All items are assigned an initial weight of 1.
#'
#' Step 2. A set of n short forms is selected by sampling with probability
#' proportional to the items' weights.
#'
#' Step 3. Fit latent variable model to the n short forms.
#'
#' Step 4. Calculate the pheromone levels for the n short forms. Define the
#' best-so-far pheromone level (if iteration 1) or compare the current best
#' pheromone from the set of n short forms to the best-so-far pheromone.
#'
#' Step 5. If the pheromone level of the best short form from step 4 exceeds the
#' best-so-far pheromone level, update the best-so-far pheromone level and add it
#' to the current weight of the items of the best short form.
#'
#' Step 6. Return to step 2 until convergence criterion is reached.
#'
#' @param ants A numeric value indicating the number of ants to send send (short
#' forms to evaluate) per iteration. Default value is 20.
#' @param evaporation A numeric value which sets the percentage of the pheremone
#' that is retained after evaporation between steps of the algorithm. Default
#' value is 0.9, indicating 10% evaporation. Should be within the range of
#' (0,1), exclusive.
#' @param mplus When \code{Mplus.Automation=FALSE}, this is a character value
#' indicating the name of the MPlus input file without the file extension
#' ".inp". If not in the current working directory, include the full file path
#' where it is located. This file will be changed during the ant colony search,
#' so it's suggested to make a backup of the original file before running the
#' function. When \code{Mplus.Automation=TRUE}, this is an object of class
#' \link[MplusAutomation]{mplusObject} created by
#' \link[MplusAutomation]{MplusAutomation} and containing the initial model.
#' @param list.items A list containing one or more character vectors of item
#' names for each factor, where each factor is a separate element of the list.
#' The items should be input in the order in which the factors are input in
#' \code{i.per.f} and \code{factors}.
#' @param full A numeric value indicating the total number of unique items in the
#' test or scale.
#' @param i.per.f A vector with number of items per factor (e.g. target number),
#' in the same order of \code{list.items} and \code{factors}.
#' @param factors A character vector with the names of the factors in the same
#' order of \code{list.items} and \code{i.per.f}.
#' @param steps A numeric value that sets the stopping rule, which is the number
#' of ants in a row for which the model does not change.
#' @param max.run The maximum number of ants to run before the algorithm stops.
#' This includes failed iterations as well. Default is 1000.
#' @param resultfile A character vector containing the file path where the MPlus
#' results for the current ant model is saved. If the file is not in the
#' current working directery, the full path must be specified. Not used when
#' \code{Mplus.Automation=FALSE}.
#' @param min.CFI A numeric value indicating the minimum CFI for "acceptable"
#' model fit. Models with CFI less than this value are automatically rejected.
#' Default is 0.95.
#' @param min.TLI A numeric value indicating the minimum TLI for "acceptable"
#' model fit. Models with TLI less than this value are automatically rejected.
#' Default is 0.95.
#' @param max.RMSEA A numeric value indicating the maximum RMSEA for "acceptable"
#' model fit. Models with RMSEA greater than this value are automatically
#' rejected. Default is 0.06
#' @param summaryfile A character vector containing the name of the summary file
#' generated. A .txt file is suggested. Default is "summary.txt" and writes
#' into the current working directory. This file writes a line for each ant
#' within each step and includes (a) a vector of a 0/1 value for each item
#' indicating whether the item was selected by that ant, (b) the run number,
#' (c) the count number, (d) the ant number, and (e) the current pheromone
#' level.
#' @param feedbackfile A character vector containing the name of the feedback
#' file generated. An .html file is suggested. Default is "iteration.html" and
#' writes into the current working directory. This file saves the result of
#' each run, which includes (a) the run number, (b) the count number, (c) the
#' ant number, (d) the step number (if the current run is successful) or
#' "Failure" (if the current run is unsuccessful), and for successful runs (f)
#' the value of CFI, TLI, and RMSEA fit indices, the average of the gammas
#' (standardized regression coefficients), and the overall variance explained
#' of the current run.
#' @param loc.gammas A numeric vector with the line numbers where the regression
#' coefficients of the MIMIC model start and end (locations). Not used with
#' \code{Mplus.Automation=TRUE}
#' @param loc.variances A numeric vector with the line numbers of the residual
#' variances of the latent factors. Not used with \code{Mplus.Automation=TRUE}
#' @param predictors Character vector with names of predictor variables, if any.
#' @param var.predictors A numeric vector with variances of the predictor(s), if
#' any. Not used with \code{Mplus.Automation=TRUE}
#' @param Mplus.Automation Logical. If \code{TRUE}, uses the
#' \code{MplusAutomation} package to modify the model as the algorithm
#' procedes. The "mplus" option will then be used as Defaults to \code{FALSE}
#' as it is in the process of being built.
#' @param dataOut A character vector specifying the location and name of the data
#' file generated by \code{MplusAutomation} for each iteration of the
#' algorithm. Default is "tempData.dat" and saves to the current working
#' directory. When specifying the name, be sure to use a data format that Mplus
#' can read. You must change the working directory to the location in which
#' this file will be saved. Only used when \code{Mplus.Automation=TRUE}.
#' @param modelOut A character vector specifying the location and name of the
#' Mplus model file generated by \code{MplusAutomation} for each iteration of
#' the algorithm. Default is "tempModel.inp" and saves to the current working
#' directory. When specifying the name of the model file, it must be a ".inp"
#' extension. You must change the working directory to the location in which
#' this file will be saved. Only used when \code{Mplus.Automation=TRUE}.
#' @return A named matrix containing final model's best RMSEA, CFI, and TLI
#' values, the final pheromone level (the mean of the standardized regression
#' coefficients (gammas)), and a series of 0/1 values indicating the items
#' selected in the final solution.
#' @family Ant Colony Algorithms
#' @seealso \code{\link{antcolony.lavaan}}
#' @examples
#' \dontrun{
#' # use MplusAutomation to find a 15-item short form of a simulated 56-item unidimensional test
#' # first, create the list of the items by the factors
#' # in this case, all items load onto the general 'Ability' factor
#' list.items <- list(c(
#' "Item1", "Item2", "Item3", "Item4", "Item5",
#' "Item6", "Item7", "Item8", "Item9", "Item10",
#' "Item11", "Item12", "Item13", "Item14", "Item15",
#' "Item16", "Item17", "Item18", "Item19", "Item20",
#' "Item21", "Item22", "Item23", "Item24", "Item25",
#' "Item26", "Item27", "Item28", "Item29", "Item30",
#' "Item31", "Item32", "Item33", "Item34", "Item35",
#' "Item36", "Item37", "Item38", "Item39", "Item40",
#' "Item41", "Item42", "Item43", "Item44", "Item45",
#' "Item46", "Item47", "Item48", "Item49", "Item50",
#' "Item51", "Item52", "Item53", "Item54", "Item55",
#' "Item56"
#' ))
#' # then, load the data
#' data(simulated_test_data)
#'
#' # Create the mplusObject with MplusAutomation
#' # notice the explicit call of each item, instead of the shorthand "Item1-Item56"
#' initial.MplusAutomation.model <- MplusAutomation::mplusObject(
#' TITLE = "Trial ACO MpluAutomation with FERA 2016 Data;",
#' MODEL = "Ability BY Item1 Item2 Item3 Item4 Item5
#' Item6 Item7 Item8 Item9 Item10 Item11 Item12
#' Item13 Item14 Item15 Item16 Item17 Item18
#' Item19 Item20 Item21 Item22 Item23 Item24
#' Item25 Item26 Item27 Item28 Item29 Item30
#' Item31 Item32 Item33 Item34 Item35 Item36
#' Item37 Item38 Item39 Item40 Item41 Item42
#' Item43 Item44 Item45 Item46 Item47 Item48
#' Item49 Item50 Item51 Item52 Item53 Item54
#' Item55 Item56;",
#' ANALYSIS = "ESTIMATOR = WLSMV;",
#' VARIABLE = "CATEGORICAL = Item1 Item2 Item3 Item4 Item5
#' Item6 Item7 Item8 Item9 Item10 Item11 Item12
#' Item13 Item14 Item15 Item16 Item17 Item18
#' Item19 Item20 Item21 Item22 Item23 Item24
#' Item25 Item26 Item27 Item28 Item29 Item30
#' Item31 Item32 Item33 Item34 Item35 Item36
#' Item37 Item38 Item39 Item40 Item41 Item42
#' Item43 Item44 Item45 Item46 Item47 Item48
#' Item49 Item50 Item51 Item52 Item53 Item54
#' Item55 Item56;",
#' OUTPUT = "stdyx;",
#' rdata = simulated_test_data
#' )
#'
#' # finally, call the function with some minor changes to the default values.
#' abilityShortForm <- antcolony.mplus(
#' ants = 3, evaporation = 0.7,
#' mplus = initial.MplusAutomation.model, list.items = list.items, full = 56,
#' i.per.f = 15, factors = "Ability", steps = 3, max.run = 50, resultfile = NULL,
#' summaryfile = "C:/Users/lordmaxwell/Desktop/summary.txt",
#' min.CFI = 0.95, min.TLI = 0.95, max.RMSEA = 0.06,
#' feedbackfile = "C:/Users/lordmaxwell/Desktop/iteration.html", Mplus.Automation = TRUE,
#' dataOut = "exampleModel.dat",
#' modelOut = "exampleModel.inp"
#' )
#' }
#' @export
#' @author Walter Leite; Anthony W Raborn, \email{anthony.w.raborn@@gmail.com}
#' @references \doi{10.1080/00273170802285743}
antcolony.mplus <- function(ants = 20, evaporation = 0.95, mplus = NULL, list.items = NULL, full = NULL,
i.per.f = NULL, factors = NULL, steps = 50, max.run = 1000,
resultfile = NULL, summaryfile = "summary.txt",
min.CFI = 0.95, min.TLI = 0.95, max.RMSEA = 0.06,
feedbackfile = "iteration.html", loc.gammas,
loc.variances, predictors, var.predictors,
Mplus.Automation = FALSE, dataOut = "tempModel.dat", modelOut = "tempModel.inp") {
# create initial, empty summaryfile to be used
write(x = "", file = summaryfile)
# creates the table of initial pheromone levels.
include <- rep(2, full)
# puts initial best solution (all items selected).
best.so.far.solution <- include
# starts counting the iterations
count <- 1
# starts counting continuous runs regardless of result.
run <- 1
# creates a vector with all items.
item.vector <- unlist(list.items, use.names = F)
# defines initial best so far (overall) pheromone
best.so.far.pheromone <- 0
# defines initial best pheromone for the current trial of n ants.
best.pheromone <- 0
# defines initial solutions.
previous.solution <- include
step <- 0
# creates selected.items list
selected.items <- list()
# check whether to use MplusAutomation or to call Mplus directly through R
if (Mplus.Automation == FALSE) {
# reads mplus syntax.
# setwd("C:/Program Files/Mplus")
input <- scan(file = paste(mplus, ".inp", sep = ""), what = "character", sep = "\n", quote = NULL)
# creates a list to store factors.
selected.items <- list.items
# starts loop through iterations.
while (count <= steps) {
if (run <= max.run) {
# sends a number of ants per time.
ant <- 1
while (ant <= ants) {
print(paste0("Count Number ", count, " and Ant Number", ant, " and Run Number ", run, "."))
# selects items for all factors.
for (factor in 1:length(list.items)) {
# selects the items for a short form for the factor
positions <- is.element(item.vector, list.items[[factor]])
prob <- include[positions] / sum(include[positions])
items <- sample(list.items[[factor]], size = i.per.f[factor], replace = F, prob)
# stores selected items.
selected.items[[factor]] <- items
# replaces the mplus syntax for factor specification.
# make sure the factor name provided is the same as the one in the MPLUS file.
factor.position <- grep(paste(factors[factor], "BY"), input, ignore.case = T)
input[factor.position] <- paste(c(factors[factor], "BY", items, ";"), collapse = " ")
# finishes loop
}
selected.items <- lapply(selected.items, sort)
selected.vector <- unlist(selected.items, use.names = F)
select.indicator <- is.element(item.vector, selected.vector)
notselect.indicator <- (select.indicator == FALSE)
# MODIFY MPLUS SYNTAX.
# when constructing mplus file, leave two lines blank after the usevariables command.
# make sure there are at least three lines of space between them.
# defines variables to be used.
position1 <- grep("usevariables", input, ignore.case = T)
input[position1] <- paste("usevariables are ", predictors)
input[position1 + 1] <- paste(c(selected.vector[1:round(sum(i.per.f) / 2, 0)]),
collapse = " "
)
input[position1 + 2] <- paste(c(selected.vector[(round(sum(i.per.f) / 2, 0) + 1):sum(i.per.f)], ";"),
collapse = " "
)
position2 <- grep("categorical", input, ignore.case = T)
input[position2 + 1] <- paste(c(selected.vector[1:round(sum(i.per.f) / 2, 0)]),
collapse = " "
)
input[position2 + 2] <- paste(c(selected.vector[(round(sum(i.per.f) / 2, 0) + 1):sum(i.per.f)], ";"),
collapse = " "
)
# writes the mplus syntax for fitting the short form.
write.table(input,
file = paste(mplus, ".inp", sep = ""), quote = F,
col.names = F, row.names = F
)
# Run MPLUS with the syntax file specified.
system(paste("mplus.exe ", mplus, ".inp", sep = ""), wait = TRUE)
outfile <- c(paste(mplus, ".out", sep = ""))
# read the output file to verify the outcome of the analysis.
output <- scan(file = outfile, what = character(), sep = "\n")
# check if the outcome was a non-positive definite matrix.
outcome1 <- grep("WARNING", output, ignore.case = T)
# check if there was non-convergence.
outcome0 <- grep("EXCEEDED", output, ignore.case = T)
outcome2 <- grep("Model estimation did not terminate normally. No results were saved", output, ignore.case = T)
# set pheromone to zero if the there was non-convergence or a non-positive definite solution.
if ((length(outcome1) == 1) || (length(outcome0) == 1) || (length(outcome2) == 1)) {
pheromone <- 0
# writes summary about non-convergence and non-positive definite.
fit.info <- matrix(c(select.indicator, run, count, ant, 999, 999, round((include), 5)), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste("<h1>", run, "-", count, "-", ant, "-", step, "- Failure", "</h1>"))
write(feedback, file = feedbackfile)
# finishes if for non-convergent cases.
} else {
# The SAVE command at the MPLUS syntax specifies that results should be
# saved to results.txt.
# scans all results.
results <- scan(resultfile)
# read the CFI,TLI and RMSEA.
CFI.row <- output[grep("CFI[ ]{1,}", output)]
CFI <- as.numeric(regmatches(CFI.row, regexpr("[0-9\\.]{5}", CFI.row)))
TLI.row <- output[grep("TLI[ ]{1,}", output)]
TLI <- as.numeric(regmatches(TLI.row, regexpr("[0-9\\.]{5}", TLI.row)))
RMSEA.row <- output[grep("RMSEA", output) + 1]
RMSEA <- as.numeric(regmatches(RMSEA.row, regexpr("[0-9\\.]{5}", RMSEA.row)))
# reads the regression coefficients (gammas)
gammas <- results[loc.gammas]
# reads the residual variances of the latent variables.
res.variances <- results[loc.variances]
# obtains the variance explained by the predictors using path tracing
var.explained <- t(t(gammas)^2 * var.predictors)
var.explained <- apply(var.explained, 1, sum)
# obtains the total variance of the latent variable
# residual variance + variance explained
variances <- res.variances + var.explained
# standardizes the gammas.
std.gammas <- gammas / sqrt(variances)
# saves summary information about the selected items and the RMSEA they generated.
fit.info <- matrix(c(
select.indicator, run, count, ant, CFI, TLI, RMSEA, mean(std.gammas),
round(include, 2)
), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste(
"<h1>", "run:", run, "count:", count, "ant:", ant, "step:", step, "<br>",
"CFI:", CFI, "TLI:", TLI, "RMSEA:", RMSEA, "<br>",
"GAMMA:", mean(std.gammas), "</h1>"
))
write(feedback, file = feedbackfile)
print(feedback)
# implements fit requirement.
if ((CFI < min.CFI) | (TLI < min.TLI) | (RMSEA > max.RMSEA)) {
pheromone <- 0
} else {
# calculate pheromone (mean of standardized gammas).
pheromone <- mean(std.gammas)
}
# adjusts count based on outcomes and selects best solution.
if (pheromone >= best.pheromone) {
# updates solution.
best.solution <- select.indicator
# updates best fit indices
best.RMSEA <- RMSEA
best.CFI <- CFI
best.TLI <- TLI
# updates best pheromone
best.pheromone <- pheromone
}
# Move to next ant.
ant <- ant + 1
# end else clause for converged solutions
}
# ends loop through ants.
run <- run + 1
}
# adjusts pheromone only if the current pheromone is best than the previous.
if (best.pheromone > best.so.far.pheromone) {
# implements pheromone evaporation.
include <- include * evaporation
# Adjusts the pheromone levels.
include.pheromone <- best.solution * best.pheromone * (0.1 * run)
# updates pheromone.
include <- include + include.pheromone
# updates best so far solution and pheromone, with corresponding RMSEA.
best.so.far.solution <- best.solution
best.so.far.pheromone <- best.pheromone
best.so.far.RMSEA <- best.RMSEA
best.so.far.CFI <- best.CFI
best.so.far.TLI <- best.TLI
# re-starts count.
count <- 1
# end if clause for pheromone adjustment.
} else {
# advances count.
count <- count + 1
# adds more pheromone to the best so far solution.
# include.pheromone = best.so.far.solution * best.so.far.pheromone
# updates pheromone.
# include = include + include.pheromone
# finish else clause.
}
# ends loop.
} else {
stop("Maximum number of runs reached.")
}
}
} else if (Mplus.Automation == TRUE) {
if (!requireNamespace("MplusAutomation", quietly = TRUE)) {
stop("The `MplusAutomation` package is required to use this function. Please install `MplusAutomation`, then try to use this function again.")
}
# starts loop through iterations.
while (count <= steps) {
if (run <= max.run) {
# sends a number of ants per time.
ant <- 1
while (ant <= ants) {
print(paste0("Count Number ", count, " and Ant Number ", ant, " and Run Number ", run, "."))
# selects items for all factors.
for (factor in 1:length(list.items)) {
# selects the items for a short form for the factor
positions <- is.element(item.vector, list.items[[factor]])
prob <- include[positions] / sum(include[positions])
items <- sample(list.items[[factor]], size = i.per.f[factor], replace = F, prob)
# stores selected items.
selected.items[[factor]] <- items
# finishes loop
}
# replaces the mplus syntax for factor specification.
# make sure the factor name provided is the same as the one in the mplusObject!
measurement.pattern <- c()
for (i in 1:length(factors)) measurement.pattern[i] <- paste0("(", factors[i], " BY)[ A-z0-9]*")
updated.model <- gsub("\\n", " ", mplus$MODEL)
for (i in 1:length(factors)) updated.model <- gsub(measurement.pattern[i], paste(c(factors[i], "BY", selected.items[[i]]), collapse = " "), updated.model)
updated.model <- gsub("(;)(\\s|$)", "\\1\n", updated.model)
updated.model <- gsub("(.{1,80})(\\s|$)", "\\1\n", updated.model)
updated.model <- gsub(";", ";\n", updated.model)
# writes the mplus syntax for fitting the short form.
new.input <- mplus
new.input$MODEL <- updated.model
factor.patterns <- c()
for (i in 1:length(factors)) factor.patterns[i] <- paste0("(", factors[i], " BY|", factors[i], " ON| ON ", factors[i], ")", collapse = "")
new.usevariables <- updated.model
for (i in 1:length(factors)) new.usevariables <- gsub(factor.patterns[i], "", new.usevariables)
new.usevariables <- gsub(";\\n", "", new.usevariables)
new.usevariables <- gsub("\\n", " ", new.usevariables)
new.usevariables <- unlist(lapply(strsplit(new.usevariables, " "), unique))
new.usevariables <- new.usevariables[new.usevariables != ""]
new.usevariables <- new.usevariables[new.usevariables != "ON"]
new.usevariables <- new.usevariables[!(new.usevariables %in% factors)]
new.input$usevariables <- new.usevariables
outcome.vars <- unlist(regmatches(updated.model, gregexpr("[A-z0-9 ]{1,} (ON) [A-z0-9 ]{1,}", updated.model)))
for (i in 1:length(factors)) outcome.vars <- gsub(factors[i], "", outcome.vars)
outcome.vars <- gsub("( ON){1,}", "", outcome.vars)
outcome.vars <- unique(gsub(" ", "", outcome.vars))
if (length(outcome.vars) == 0) outcome.vars <- "none"
dependent.vars <- new.usevariables[new.usevariables != outcome.vars]
if (grepl(outcome.vars, mplus$VARIABLE)) {
new.input$VARIABLE <- gsub("(.{1,80})(\\s|$)", "\\1\n", gsub("(?<= ){1}[A-z0-9 - \\n]{1,}", paste(c(outcome.vars, dependent.vars), collapse = " "), new.input$VARIABLE, perl = TRUE))
} else {
new.input$VARIABLE <- gsub("(.{1,80})(\\s|$)", "\\1\n", gsub("(?<= ){1}[A-z0-9 - \\n]{1,}", paste(dependent.vars, collapse = " "), new.input$VARIABLE, perl = TRUE))
}
selected.items <- lapply(selected.items, sort)
selected.vector <- unlist(selected.items, use.names = F)
select.indicator <- is.element(item.vector, selected.vector)
notselect.indicator <- (select.indicator == FALSE)
# Run MPLUS with the updated model just specified.
current.ant.model <- MplusAutomation::mplusModeler(new.input, dataout = dataOut, modelout = modelOut, run = 1, writeData = "always", hashfile = FALSE)
# check if the outcome was a non-positive definite matrix.
output <- paste(c(unlist(current.ant.model$results$warnings), unlist(current.ant.model$results$errors)), collapse = " ")
outcome1 <- grep("WARNING", output, ignore.case = T)
# check if there was non-convergence.
outcome0 <- grep("EXCEEDED", output, ignore.case = T)
outcome2 <- grep("Model estimation did not terminate normally. No results were saved", output, ignore.case = T)
# set pheromone to zero if the there was non-convergence or a non-positive definite solution.
if ((length(outcome1) == 1) || (length(outcome0) == 1) || (length(outcome2) == 1)) {
pheromone <- 0
# writes feedback about non-convergence and non-positive definite.
fit.info <- matrix(c(select.indicator, run, count, ant, 999, 999, round((include), 5)), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste("<h1> Run", run, "- Count", count, "- Ant", ant, "- Step", step, "- Failure", "</h1>"))
write(feedback, file = feedbackfile)
# finishes if for non-convergent cases.
} else {
# read the CFI,TLI and RMSEA.
CFI <- current.ant.model$results$summaries$CFI
TLI <- current.ant.model$results$summaries$TLI
RMSEA <- current.ant.model$results$summaries$RMSEA_Estimate
# extract the standardized regression coefficients
std.gammas <- current.ant.model$results$parameters$std[grep(".ON", current.ant.model$results$parameters$unstandardized$paramHeader), "est"]
if (length(std.gammas) == 0) {
std.gammas <- current.ant.model$results$parameters$r2$est
}
# saves information about the selected items and the RMSEA they generated.
fit.info <- matrix(c(
select.indicator, run, count, ant, CFI, TLI, RMSEA, mean(std.gammas),
round(include, 2)
), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste(
"<h1>", "run:", run, "count:", count, "ant:", ant, "step:", step, "<br>",
"CFI:", CFI, "TLI:", TLI, "RMSEA:", RMSEA, "<br>",
"GAMMA:", mean(std.gammas), "</h1>"
))
write(feedback, file = feedbackfile)
print(feedback)
# implements fit requirement.
if ((CFI < min.CFI) | (TLI < min.TLI) | (RMSEA > max.RMSEA)) {
pheromone <- 0
} else {
# calculate pheromone (mean of standardized gammas).
pheromone <- mean(std.gammas)
}
# adjusts count based on outcomes and selects best solution.
if (pheromone >= best.pheromone) {
# updates solution.
best.solution <- select.indicator
# updates best RMSEA.
best.RMSEA <- RMSEA
best.CFI <- CFI
best.TLI <- TLI
# updates best pheromone
best.pheromone <- pheromone
}
# Move to next ant.
ant <- ant + 1
# end else clause for converged solutions
}
# ends loop through ants.
run <- run + 1
}
# adjusts pheromone only if the current pheromone is best than the previous.
if (best.pheromone > best.so.far.pheromone) {
# implements pheromone evaporation.
include <- include * evaporation
# Adjusts the pheromone levels.
include.pheromone <- best.solution * best.pheromone * (0.1 * run)
# updates pheromone.
include <- include + include.pheromone
# updates best so far solution and pheromone, with corresponding RMSEA.
best.so.far.solution <- best.solution
best.so.far.pheromone <- best.pheromone
best.so.far.RMSEA <- best.RMSEA
best.so.far.CFI <- best.CFI
best.so.far.TLI <- best.TLI
# re-starts count.
count <- 1
# end if clause for pheromone adjustment.
} else {
# advances count.
count <- count + 1
# adds more pheromone to the best so far solution.
include.pheromone <- best.so.far.solution * best.so.far.pheromone
# updates pheromone.
include <- include + include.pheromone
}
} else {
stop("Maximum number of runs reached.")
}
# ends loop.
}
}
final.solution <- matrix(c(best.so.far.RMSEA, best.so.far.CFI, best.so.far.TLI, best.so.far.pheromone, best.so.far.solution), 1, dimnames = list(NULL, c("RMSEA", "CFI", "TLI", "mean_gamma", item.vector)))
# FINISH FUNCTION.
return(final.solution)
}
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Defines functions antcolony.mplus
Documented in antcolony.mplus
#' A function to implement the ant colony optimization algorithm for short form
#' specification searches, either using MPlus directly via
#' \code{\link[base]{system}} calls or using Mplus indirectly with the package
#' \link[MplusAutomation]{MplusAutomation}.
#'
#' @description The Ant Colony Optimization (ACO) algorithm (Dorigo & Stutzle,
#' 2004) can produce short forms of scales that are optimized with respect to
#' characteristics selected by the developer, such as model fit and predictive
#' relationships with other variables. The algorithm is based on the foraging
#' behavior of a group of ants, which start searching for food in a variety of
#' directions and then eventually all ants converge to the shortest distance to
#' the food source. This behavior occurs because ants leave a pheromone trail
#' behind as they search for food and ants in shorter paths leave stronger
#' pheromone trails, which are detected by other ants and that will lead them to
#' follow the shortest trail.
#'
#' @details This function sends a specified number of ants
#' per iteration, which randomly select items to build a model, then evaluates
#' the model based on pheromone levels. The pheromone levels are updated after
#' each iteration according to the best-fitting model of that iteration. The
#' algorithm's stopping rule is to end the search when a certain solution is the
#' same for a given number of ants in a row. When constructing the mplus dataset
#' and when \code{Mplus.Automation=FALSE}, make sure that items in 'categorical
#' are' and 'usevariables' are specifications that take the same number of lines
#' per short form.
#'
#' PREPARATORY STEPS: For the ACO algorithm implementation for short
#' for selection, the following decisions are needed:
#'
#' 1. Determine the target size for the short form.
#'
#' 2. Determine which characteristics should be optimized.
#'
#' 3. Define how the pheromone level will be computed: This is a function of the
#' characteristics of the short form that will be optimized. In Leite, Huang and
#' Marcoulides (2008), the pheromone level was zero if model fit indices did
#' not meet Hu and Bentler's (1999) suggested thresholds, and equal to the sum of
#' path coefficients of a predictor variable if model fit indices met thresholds.
#' Currently, the package only implements pheromone calculation based on
#' regression coefficients or variance explained, with user-selected model fit
#' index thresholds.
#'
#' 4. Define how many short forms should be evaluated before the best-so-far
#' pheromone level is examined. Leite, Huang and Marcoulides (2008) used 10 short
#' forms.
#'
#' 5. Define the percentage of pheromone evaporation, if any. Leite, Huang and
#' Marcoulides (2008) used 5\%.
#'
#' 6. Define convergence criterion. Leite, Huang and Marcoulides (2008) set the
#' algorithm to converge if the short form did not improve in 100 x number of
#' short forms in step 4.
#'
#' IMPLEMENTATION: Once these decisions are made, the ACO algorithm
#' selects short forms with the following steps:
#'
#' Step 1. All items are assigned an initial weight of 1.
#'
#' Step 2. A set of n short forms is selected by sampling with probability
#' proportional to the items' weights.
#'
#' Step 3. Fit latent variable model to the n short forms.
#'
#' Step 4. Calculate the pheromone levels for the n short forms. Define the
#' best-so-far pheromone level (if iteration 1) or compare the current best
#' pheromone from the set of n short forms to the best-so-far pheromone.
#'
#' Step 5. If the pheromone level of the best short form from step 4 exceeds the
#' best-so-far pheromone level, update the best-so-far pheromone level and add it
#' to the current weight of the items of the best short form.
#'
#' Step 6. Return to step 2 until convergence criterion is reached.
#'
#' @param ants A numeric value indicating the number of ants to send send (short
#' forms to evaluate) per iteration. Default value is 20.
#' @param evaporation A numeric value which sets the percentage of the pheremone
#' that is retained after evaporation between steps of the algorithm. Default
#' value is 0.9, indicating 10% evaporation. Should be within the range of
#' (0,1), exclusive.
#' @param mplus When \code{Mplus.Automation=FALSE}, this is a character value
#' indicating the name of the MPlus input file without the file extension
#' ".inp". If not in the current working directory, include the full file path
#' where it is located. This file will be changed during the ant colony search,
#' so it's suggested to make a backup of the original file before running the
#' function. When \code{Mplus.Automation=TRUE}, this is an object of class
#' \link[MplusAutomation]{mplusObject} created by
#' \link[MplusAutomation]{MplusAutomation} and containing the initial model.
#' @param list.items A list containing one or more character vectors of item
#' names for each factor, where each factor is a separate element of the list.
#' The items should be input in the order in which the factors are input in
#' \code{i.per.f} and \code{factors}.
#' @param full A numeric value indicating the total number of unique items in the
#' test or scale.
#' @param i.per.f A vector with number of items per factor (e.g. target number),
#' in the same order of \code{list.items} and \code{factors}.
#' @param factors A character vector with the names of the factors in the same
#' order of \code{list.items} and \code{i.per.f}.
#' @param steps A numeric value that sets the stopping rule, which is the number
#' of ants in a row for which the model does not change.
#' @param max.run The maximum number of ants to run before the algorithm stops.
#' This includes failed iterations as well. Default is 1000.
#' @param resultfile A character vector containing the file path where the MPlus
#' results for the current ant model is saved. If the file is not in the
#' current working directery, the full path must be specified. Not used when
#' \code{Mplus.Automation=FALSE}.
#' @param min.CFI A numeric value indicating the minimum CFI for "acceptable"
#' model fit. Models with CFI less than this value are automatically rejected.
#' Default is 0.95.
#' @param min.TLI A numeric value indicating the minimum TLI for "acceptable"
#' model fit. Models with TLI less than this value are automatically rejected.
#' Default is 0.95.
#' @param max.RMSEA A numeric value indicating the maximum RMSEA for "acceptable"
#' model fit. Models with RMSEA greater than this value are automatically
#' rejected. Default is 0.06
#' @param summaryfile A character vector containing the name of the summary file
#' generated. A .txt file is suggested. Default is "summary.txt" and writes
#' into the current working directory. This file writes a line for each ant
#' within each step and includes (a) a vector of a 0/1 value for each item
#' indicating whether the item was selected by that ant, (b) the run number,
#' (c) the count number, (d) the ant number, and (e) the current pheromone
#' level.
#' @param feedbackfile A character vector containing the name of the feedback
#' file generated. An .html file is suggested. Default is "iteration.html" and
#' writes into the current working directory. This file saves the result of
#' each run, which includes (a) the run number, (b) the count number, (c) the
#' ant number, (d) the step number (if the current run is successful) or
#' "Failure" (if the current run is unsuccessful), and for successful runs (f)
#' the value of CFI, TLI, and RMSEA fit indices, the average of the gammas
#' (standardized regression coefficients), and the overall variance explained
#' of the current run.
#' @param loc.gammas A numeric vector with the line numbers where the regression
#' coefficients of the MIMIC model start and end (locations). Not used with
#' \code{Mplus.Automation=TRUE}
#' @param loc.variances A numeric vector with the line numbers of the residual
#' variances of the latent factors. Not used with \code{Mplus.Automation=TRUE}
#' @param predictors Character vector with names of predictor variables, if any.
#' @param var.predictors A numeric vector with variances of the predictor(s), if
#' any. Not used with \code{Mplus.Automation=TRUE}
#' @param Mplus.Automation Logical. If \code{TRUE}, uses the
#' \code{MplusAutomation} package to modify the model as the algorithm
#' procedes. The "mplus" option will then be used as Defaults to \code{FALSE}
#' as it is in the process of being built.
#' @param dataOut A character vector specifying the location and name of the data
#' file generated by \code{MplusAutomation} for each iteration of the
#' algorithm. Default is "tempData.dat" and saves to the current working
#' directory. When specifying the name, be sure to use a data format that Mplus
#' can read. You must change the working directory to the location in which
#' this file will be saved. Only used when \code{Mplus.Automation=TRUE}.
#' @param modelOut A character vector specifying the location and name of the
#' Mplus model file generated by \code{MplusAutomation} for each iteration of
#' the algorithm. Default is "tempModel.inp" and saves to the current working
#' directory. When specifying the name of the model file, it must be a ".inp"
#' extension. You must change the working directory to the location in which
#' this file will be saved. Only used when \code{Mplus.Automation=TRUE}.
#' @return A named matrix containing final model's best RMSEA, CFI, and TLI
#' values, the final pheromone level (the mean of the standardized regression
#' coefficients (gammas)), and a series of 0/1 values indicating the items
#' selected in the final solution.
#' @family Ant Colony Algorithms
#' @seealso \code{\link{antcolony.lavaan}}
#' @examples
#' \dontrun{
#' # use MplusAutomation to find a 15-item short form of a simulated 56-item unidimensional test
#' # first, create the list of the items by the factors
#' # in this case, all items load onto the general 'Ability' factor
#' list.items <- list(c(
#' "Item1", "Item2", "Item3", "Item4", "Item5",
#' "Item6", "Item7", "Item8", "Item9", "Item10",
#' "Item11", "Item12", "Item13", "Item14", "Item15",
#' "Item16", "Item17", "Item18", "Item19", "Item20",
#' "Item21", "Item22", "Item23", "Item24", "Item25",
#' "Item26", "Item27", "Item28", "Item29", "Item30",
#' "Item31", "Item32", "Item33", "Item34", "Item35",
#' "Item36", "Item37", "Item38", "Item39", "Item40",
#' "Item41", "Item42", "Item43", "Item44", "Item45",
#' "Item46", "Item47", "Item48", "Item49", "Item50",
#' "Item51", "Item52", "Item53", "Item54", "Item55",
#' "Item56"
#' ))
#' # then, load the data
#' data(simulated_test_data)
#'
#' # Create the mplusObject with MplusAutomation
#' # notice the explicit call of each item, instead of the shorthand "Item1-Item56"
#' initial.MplusAutomation.model <- MplusAutomation::mplusObject(
#' TITLE = "Trial ACO MpluAutomation with FERA 2016 Data;",
#' MODEL = "Ability BY Item1 Item2 Item3 Item4 Item5
#' Item6 Item7 Item8 Item9 Item10 Item11 Item12
#' Item13 Item14 Item15 Item16 Item17 Item18
#' Item19 Item20 Item21 Item22 Item23 Item24
#' Item25 Item26 Item27 Item28 Item29 Item30
#' Item31 Item32 Item33 Item34 Item35 Item36
#' Item37 Item38 Item39 Item40 Item41 Item42
#' Item43 Item44 Item45 Item46 Item47 Item48
#' Item49 Item50 Item51 Item52 Item53 Item54
#' Item55 Item56;",
#' ANALYSIS = "ESTIMATOR = WLSMV;",
#' VARIABLE = "CATEGORICAL = Item1 Item2 Item3 Item4 Item5
#' Item6 Item7 Item8 Item9 Item10 Item11 Item12
#' Item13 Item14 Item15 Item16 Item17 Item18
#' Item19 Item20 Item21 Item22 Item23 Item24
#' Item25 Item26 Item27 Item28 Item29 Item30
#' Item31 Item32 Item33 Item34 Item35 Item36
#' Item37 Item38 Item39 Item40 Item41 Item42
#' Item43 Item44 Item45 Item46 Item47 Item48
#' Item49 Item50 Item51 Item52 Item53 Item54
#' Item55 Item56;",
#' OUTPUT = "stdyx;",
#' rdata = simulated_test_data
#' )
#'
#' # finally, call the function with some minor changes to the default values.
#' abilityShortForm <- antcolony.mplus(
#' ants = 3, evaporation = 0.7,
#' mplus = initial.MplusAutomation.model, list.items = list.items, full = 56,
#' i.per.f = 15, factors = "Ability", steps = 3, max.run = 50, resultfile = NULL,
#' summaryfile = "C:/Users/lordmaxwell/Desktop/summary.txt",
#' min.CFI = 0.95, min.TLI = 0.95, max.RMSEA = 0.06,
#' feedbackfile = "C:/Users/lordmaxwell/Desktop/iteration.html", Mplus.Automation = TRUE,
#' dataOut = "exampleModel.dat",
#' modelOut = "exampleModel.inp"
#' )
#' }
#' @export
#' @author Walter Leite; Anthony W Raborn, \email{anthony.w.raborn@@gmail.com}
#' @references \doi{10.1080/00273170802285743}
antcolony.mplus <- function(ants = 20, evaporation = 0.95, mplus = NULL, list.items = NULL, full = NULL,
i.per.f = NULL, factors = NULL, steps = 50, max.run = 1000,
resultfile = NULL, summaryfile = "summary.txt",
min.CFI = 0.95, min.TLI = 0.95, max.RMSEA = 0.06,
feedbackfile = "iteration.html", loc.gammas,
loc.variances, predictors, var.predictors,
Mplus.Automation = FALSE, dataOut = "tempModel.dat", modelOut = "tempModel.inp") {
# create initial, empty summaryfile to be used
write(x = "", file = summaryfile)
# creates the table of initial pheromone levels.
include <- rep(2, full)
# puts initial best solution (all items selected).
best.so.far.solution <- include
# starts counting the iterations
count <- 1
# starts counting continuous runs regardless of result.
run <- 1
# creates a vector with all items.
item.vector <- unlist(list.items, use.names = F)
# defines initial best so far (overall) pheromone
best.so.far.pheromone <- 0
# defines initial best pheromone for the current trial of n ants.
best.pheromone <- 0
# defines initial solutions.
previous.solution <- include
step <- 0
# creates selected.items list
selected.items <- list()
# check whether to use MplusAutomation or to call Mplus directly through R
if (Mplus.Automation == FALSE) {
# reads mplus syntax.
# setwd("C:/Program Files/Mplus")
input <- scan(file = paste(mplus, ".inp", sep = ""), what = "character", sep = "\n", quote = NULL)
# creates a list to store factors.
selected.items <- list.items
# starts loop through iterations.
while (count <= steps) {
if (run <= max.run) {
# sends a number of ants per time.
ant <- 1
while (ant <= ants) {
print(paste0("Count Number ", count, " and Ant Number", ant, " and Run Number ", run, "."))
# selects items for all factors.
for (factor in 1:length(list.items)) {
# selects the items for a short form for the factor
positions <- is.element(item.vector, list.items[[factor]])
prob <- include[positions] / sum(include[positions])
items <- sample(list.items[[factor]], size = i.per.f[factor], replace = F, prob)
# stores selected items.
selected.items[[factor]] <- items
# replaces the mplus syntax for factor specification.
# make sure the factor name provided is the same as the one in the MPLUS file.
factor.position <- grep(paste(factors[factor], "BY"), input, ignore.case = T)
input[factor.position] <- paste(c(factors[factor], "BY", items, ";"), collapse = " ")
# finishes loop
}
selected.items <- lapply(selected.items, sort)
selected.vector <- unlist(selected.items, use.names = F)
select.indicator <- is.element(item.vector, selected.vector)
notselect.indicator <- (select.indicator == FALSE)
# MODIFY MPLUS SYNTAX.
# when constructing mplus file, leave two lines blank after the usevariables command.
# make sure there are at least three lines of space between them.
# defines variables to be used.
position1 <- grep("usevariables", input, ignore.case = T)
input[position1] <- paste("usevariables are ", predictors)
input[position1 + 1] <- paste(c(selected.vector[1:round(sum(i.per.f) / 2, 0)]),
collapse = " "
)
input[position1 + 2] <- paste(c(selected.vector[(round(sum(i.per.f) / 2, 0) + 1):sum(i.per.f)], ";"),
collapse = " "
)
position2 <- grep("categorical", input, ignore.case = T)
input[position2 + 1] <- paste(c(selected.vector[1:round(sum(i.per.f) / 2, 0)]),
collapse = " "
)
input[position2 + 2] <- paste(c(selected.vector[(round(sum(i.per.f) / 2, 0) + 1):sum(i.per.f)], ";"),
collapse = " "
)
# writes the mplus syntax for fitting the short form.
write.table(input,
file = paste(mplus, ".inp", sep = ""), quote = F,
col.names = F, row.names = F
)
# Run MPLUS with the syntax file specified.
system(paste("mplus.exe ", mplus, ".inp", sep = ""), wait = TRUE)
outfile <- c(paste(mplus, ".out", sep = ""))
# read the output file to verify the outcome of the analysis.
output <- scan(file = outfile, what = character(), sep = "\n")
# check if the outcome was a non-positive definite matrix.
outcome1 <- grep("WARNING", output, ignore.case = T)
# check if there was non-convergence.
outcome0 <- grep("EXCEEDED", output, ignore.case = T)
outcome2 <- grep("Model estimation did not terminate normally. No results were saved", output, ignore.case = T)
# set pheromone to zero if the there was non-convergence or a non-positive definite solution.
if ((length(outcome1) == 1) || (length(outcome0) == 1) || (length(outcome2) == 1)) {
pheromone <- 0
# writes summary about non-convergence and non-positive definite.
fit.info <- matrix(c(select.indicator, run, count, ant, 999, 999, round((include), 5)), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste("<h1>", run, "-", count, "-", ant, "-", step, "- Failure", "</h1>"))
write(feedback, file = feedbackfile)
# finishes if for non-convergent cases.
} else {
# The SAVE command at the MPLUS syntax specifies that results should be
# saved to results.txt.
# scans all results.
results <- scan(resultfile)
# read the CFI,TLI and RMSEA.
CFI.row <- output[grep("CFI[ ]{1,}", output)]
CFI <- as.numeric(regmatches(CFI.row, regexpr("[0-9\\.]{5}", CFI.row)))
TLI.row <- output[grep("TLI[ ]{1,}", output)]
TLI <- as.numeric(regmatches(TLI.row, regexpr("[0-9\\.]{5}", TLI.row)))
RMSEA.row <- output[grep("RMSEA", output) + 1]
RMSEA <- as.numeric(regmatches(RMSEA.row, regexpr("[0-9\\.]{5}", RMSEA.row)))
# reads the regression coefficients (gammas)
gammas <- results[loc.gammas]
# reads the residual variances of the latent variables.
res.variances <- results[loc.variances]
# obtains the variance explained by the predictors using path tracing
var.explained <- t(t(gammas)^2 * var.predictors)
var.explained <- apply(var.explained, 1, sum)
# obtains the total variance of the latent variable
# residual variance + variance explained
variances <- res.variances + var.explained
# standardizes the gammas.
std.gammas <- gammas / sqrt(variances)
# saves summary information about the selected items and the RMSEA they generated.
fit.info <- matrix(c(
select.indicator, run, count, ant, CFI, TLI, RMSEA, mean(std.gammas),
round(include, 2)
), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste(
"<h1>", "run:", run, "count:", count, "ant:", ant, "step:", step, "<br>",
"CFI:", CFI, "TLI:", TLI, "RMSEA:", RMSEA, "<br>",
"GAMMA:", mean(std.gammas), "</h1>"
))
write(feedback, file = feedbackfile)
print(feedback)
# implements fit requirement.
if ((CFI < min.CFI) | (TLI < min.TLI) | (RMSEA > max.RMSEA)) {
pheromone <- 0
} else {
# calculate pheromone (mean of standardized gammas).
pheromone <- mean(std.gammas)
}
# adjusts count based on outcomes and selects best solution.
if (pheromone >= best.pheromone) {
# updates solution.
best.solution <- select.indicator
# updates best fit indices
best.RMSEA <- RMSEA
best.CFI <- CFI
best.TLI <- TLI
# updates best pheromone
best.pheromone <- pheromone
}
# Move to next ant.
ant <- ant + 1
# end else clause for converged solutions
}
# ends loop through ants.
run <- run + 1
}
# adjusts pheromone only if the current pheromone is best than the previous.
if (best.pheromone > best.so.far.pheromone) {
# implements pheromone evaporation.
include <- include * evaporation
# Adjusts the pheromone levels.
include.pheromone <- best.solution * best.pheromone * (0.1 * run)
# updates pheromone.
include <- include + include.pheromone
# updates best so far solution and pheromone, with corresponding RMSEA.
best.so.far.solution <- best.solution
best.so.far.pheromone <- best.pheromone
best.so.far.RMSEA <- best.RMSEA
best.so.far.CFI <- best.CFI
best.so.far.TLI <- best.TLI
# re-starts count.
count <- 1
# end if clause for pheromone adjustment.
} else {
# advances count.
count <- count + 1
# adds more pheromone to the best so far solution.
# include.pheromone = best.so.far.solution * best.so.far.pheromone
# updates pheromone.
# include = include + include.pheromone
# finish else clause.
}
# ends loop.
} else {
stop("Maximum number of runs reached.")
}
}
} else if (Mplus.Automation == TRUE) {
if (!requireNamespace("MplusAutomation", quietly = TRUE)) {
stop("The `MplusAutomation` package is required to use this function. Please install `MplusAutomation`, then try to use this function again.")
}
# starts loop through iterations.
while (count <= steps) {
if (run <= max.run) {
# sends a number of ants per time.
ant <- 1
while (ant <= ants) {
print(paste0("Count Number ", count, " and Ant Number ", ant, " and Run Number ", run, "."))
# selects items for all factors.
for (factor in 1:length(list.items)) {
# selects the items for a short form for the factor
positions <- is.element(item.vector, list.items[[factor]])
prob <- include[positions] / sum(include[positions])
items <- sample(list.items[[factor]], size = i.per.f[factor], replace = F, prob)
# stores selected items.
selected.items[[factor]] <- items
# finishes loop
}
# replaces the mplus syntax for factor specification.
# make sure the factor name provided is the same as the one in the mplusObject!
measurement.pattern <- c()
for (i in 1:length(factors)) measurement.pattern[i] <- paste0("(", factors[i], " BY)[ A-z0-9]*")
updated.model <- gsub("\\n", " ", mplus$MODEL)
for (i in 1:length(factors)) updated.model <- gsub(measurement.pattern[i], paste(c(factors[i], "BY", selected.items[[i]]), collapse = " "), updated.model)
updated.model <- gsub("(;)(\\s|$)", "\\1\n", updated.model)
updated.model <- gsub("(.{1,80})(\\s|$)", "\\1\n", updated.model)
updated.model <- gsub(";", ";\n", updated.model)
# writes the mplus syntax for fitting the short form.
new.input <- mplus
new.input$MODEL <- updated.model
factor.patterns <- c()
for (i in 1:length(factors)) factor.patterns[i] <- paste0("(", factors[i], " BY|", factors[i], " ON| ON ", factors[i], ")", collapse = "")
new.usevariables <- updated.model
for (i in 1:length(factors)) new.usevariables <- gsub(factor.patterns[i], "", new.usevariables)
new.usevariables <- gsub(";\\n", "", new.usevariables)
new.usevariables <- gsub("\\n", " ", new.usevariables)
new.usevariables <- unlist(lapply(strsplit(new.usevariables, " "), unique))
new.usevariables <- new.usevariables[new.usevariables != ""]
new.usevariables <- new.usevariables[new.usevariables != "ON"]
new.usevariables <- new.usevariables[!(new.usevariables %in% factors)]
new.input$usevariables <- new.usevariables
outcome.vars <- unlist(regmatches(updated.model, gregexpr("[A-z0-9 ]{1,} (ON) [A-z0-9 ]{1,}", updated.model)))
for (i in 1:length(factors)) outcome.vars <- gsub(factors[i], "", outcome.vars)
outcome.vars <- gsub("( ON){1,}", "", outcome.vars)
outcome.vars <- unique(gsub(" ", "", outcome.vars))
if (length(outcome.vars) == 0) outcome.vars <- "none"
dependent.vars <- new.usevariables[new.usevariables != outcome.vars]
if (grepl(outcome.vars, mplus$VARIABLE)) {
new.input$VARIABLE <- gsub("(.{1,80})(\\s|$)", "\\1\n", gsub("(?<= ){1}[A-z0-9 - \\n]{1,}", paste(c(outcome.vars, dependent.vars), collapse = " "), new.input$VARIABLE, perl = TRUE))
} else {
new.input$VARIABLE <- gsub("(.{1,80})(\\s|$)", "\\1\n", gsub("(?<= ){1}[A-z0-9 - \\n]{1,}", paste(dependent.vars, collapse = " "), new.input$VARIABLE, perl = TRUE))
}
selected.items <- lapply(selected.items, sort)
selected.vector <- unlist(selected.items, use.names = F)
select.indicator <- is.element(item.vector, selected.vector)
notselect.indicator <- (select.indicator == FALSE)
# Run MPLUS with the updated model just specified.
current.ant.model <- MplusAutomation::mplusModeler(new.input, dataout = dataOut, modelout = modelOut, run = 1, writeData = "always", hashfile = FALSE)
# check if the outcome was a non-positive definite matrix.
output <- paste(c(unlist(current.ant.model$results$warnings), unlist(current.ant.model$results$errors)), collapse = " ")
outcome1 <- grep("WARNING", output, ignore.case = T)
# check if there was non-convergence.
outcome0 <- grep("EXCEEDED", output, ignore.case = T)
outcome2 <- grep("Model estimation did not terminate normally. No results were saved", output, ignore.case = T)
# set pheromone to zero if the there was non-convergence or a non-positive definite solution.
if ((length(outcome1) == 1) || (length(outcome0) == 1) || (length(outcome2) == 1)) {
pheromone <- 0
# writes feedback about non-convergence and non-positive definite.
fit.info <- matrix(c(select.indicator, run, count, ant, 999, 999, round((include), 5)), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste("<h1> Run", run, "- Count", count, "- Ant", ant, "- Step", step, "- Failure", "</h1>"))
write(feedback, file = feedbackfile)
# finishes if for non-convergent cases.
} else {
# read the CFI,TLI and RMSEA.
CFI <- current.ant.model$results$summaries$CFI
TLI <- current.ant.model$results$summaries$TLI
RMSEA <- current.ant.model$results$summaries$RMSEA_Estimate
# extract the standardized regression coefficients
std.gammas <- current.ant.model$results$parameters$std[grep(".ON", current.ant.model$results$parameters$unstandardized$paramHeader), "est"]
if (length(std.gammas) == 0) {
std.gammas <- current.ant.model$results$parameters$r2$est
}
# saves information about the selected items and the RMSEA they generated.
fit.info <- matrix(c(
select.indicator, run, count, ant, CFI, TLI, RMSEA, mean(std.gammas),
round(include, 2)
), 1, )
write.table(fit.info,
file = summaryfile, append = T,
quote = F, sep = " ", row.names = F, col.names = F
)
# provide feedback about search.
feedback <- c(paste(
"<h1>", "run:", run, "count:", count, "ant:", ant, "step:", step, "<br>",
"CFI:", CFI, "TLI:", TLI, "RMSEA:", RMSEA, "<br>",
"GAMMA:", mean(std.gammas), "</h1>"
))
write(feedback, file = feedbackfile)
print(feedback)
# implements fit requirement.
if ((CFI < min.CFI) | (TLI < min.TLI) | (RMSEA > max.RMSEA)) {
pheromone <- 0
} else {
# calculate pheromone (mean of standardized gammas).
pheromone <- mean(std.gammas)
}
# adjusts count based on outcomes and selects best solution.
if (pheromone >= best.pheromone) {
# updates solution.
best.solution <- select.indicator
# updates best RMSEA.
best.RMSEA <- RMSEA
best.CFI <- CFI
best.TLI <- TLI
# updates best pheromone
best.pheromone <- pheromone
}
# Move to next ant.
ant <- ant + 1
# end else clause for converged solutions
}
# ends loop through ants.
run <- run + 1
}
# adjusts pheromone only if the current pheromone is best than the previous.
if (best.pheromone > best.so.far.pheromone) {
# implements pheromone evaporation.
include <- include * evaporation
# Adjusts the pheromone levels.
include.pheromone <- best.solution * best.pheromone * (0.1 * run)
# updates pheromone.
include <- include + include.pheromone
# updates best so far solution and pheromone, with corresponding RMSEA.
best.so.far.solution <- best.solution
best.so.far.pheromone <- best.pheromone
best.so.far.RMSEA <- best.RMSEA
best.so.far.CFI <- best.CFI
best.so.far.TLI <- best.TLI
# re-starts count.
count <- 1
# end if clause for pheromone adjustment.
} else {
# advances count.
count <- count + 1
# adds more pheromone to the best so far solution.
include.pheromone <- best.so.far.solution * best.so.far.pheromone
# updates pheromone.
include <- include + include.pheromone
}
} else {
stop("Maximum number of runs reached.")
}
# ends loop.
}
}
final.solution <- matrix(c(best.so.far.RMSEA, best.so.far.CFI, best.so.far.TLI, best.so.far.pheromone, best.so.far.solution), 1, dimnames = list(NULL, c("RMSEA", "CFI", "TLI", "mean_gamma", item.vector)))
# FINISH FUNCTION.
return(final.solution)
}
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