Fixing merge conflicts

Merge branch 'master' into devel

# Conflicts:
#	.Rbuildignore
#	DESCRIPTION
#	NEWS.md
#	R/Tabu_shortform.R
#	R/simulated_annealing.R
#	R/simulated_annealing_internals.R
#	README-ACO example-1.png
#	README-ACO example-2.png
#	README-ACO example-3.png
#	README-Simulated Annealing example-1.png
#	README-Tabu short form-1.png
#	README.Rmd
#	README.md
#	man/tabuShortForm.Rd

.Rbuildignore

@@ -12,3 +12,4 @@ cran-comments.md
 README-*
 ^CRAN-RELEASE$
 ^ignore$
+NEWS.Rmd

NEWS

@@ -0,0 +1,180 @@
+ShortForm
+=========
+
+*News*
+======
+
+ShortForm v0.5.0
+================
+
+Introduction of S4 Function Classes
+-----------------------------------
+
+-   This version (re-)introduces classes to each of the main function outputs 
+    using S4 methods (instead of the S3 methods present in the prior version)
+
+-   Each method has a `show` (print), `summary`, and `plot` method that provides 
+    revamped, concise information about the algorithm
+
+-   Functions have been updated to accomodate these changes
+
+Parallelized Short Form Functions
+---------------------------------
+
+-   Some short form functions have been modified to work with parallel 
+    processors, resulting in noticeably faster results particularly when the
+    solution space is larger (e.g., more starting items) or with more complex
+    models
+
+    -   This has resulted in some function argument changes. Please check any 
+        code that was written with older versions!
+
+ShortForm 0.4.6
+===============
+
+Updated argument check
+----------------------
+
+-   The argument check for fit statistics (ACO, SA) were updated to
+    include fit statistics related to the “WLSMV” estimator (i.e, for
+    ordered data).
+
+Bugfixes
+--------
+
+-   A bug in the SA function that sometimes resulted in improper items
+    has been fixed.
+
+-   A bug in the Tabu short form function that caused the Tabu list to
+    be erased if the best criterion value was reached has been fixed.
+
+ShortForm 0.4.5
+===============
+
+Extra arugment checks
+---------------------
+
+-   There are now additional checks for the function arguments related
+    to the fit statistics (ACO, SA) and the fit statistic tests (ACO)
+    with informative warnings for when the function arguments are not
+    valid.
+
+ShortForm 0.4.2
+===============
+
+Introduction of Function Classes
+--------------------------------
+
+-   This version introduces classes to each of the main function outputs
+    (`antcolony.lavaan` == “antcolony”, `simulatedAnnealing` ==
+    “simulatedAnnealing”, `tabuShortForm` == “tabu”)
+
+-   This will allow for `plot` and `print` methods for each of these
+    functions
+
+Broken functionality: antcolony\_plot
+-------------------------------------
+
+-   The function `antcolony_plot` was replaced with `plot.antcolony`
+    (aka, a plot method)
+
+New functionality: S3 method for plotting
+-----------------------------------------
+
+-   With the addition of classes, a plot method and accompanying
+    documentation has been added.
+
+-   Future updates will expand S3 methods for `print()` and `summary()`
+
+Bugfixes
+--------
+
+-   Bugfixes to the main functions when using them to create shortforms
+    of bifactor models.
+-   They should now produce actual bifactor shortforms (in 0.4.1,
+    sometimes the item names would be cut off in later iterations
+    \[FIXED\] and the relationship between latent variables would be
+    changed when they should have been kept constant \[FIXED\]).
+
+Added a package loading message
+-------------------------------
+
+-   Now, when using an interactive R session, a package message is
+    printed out (with a little Penguin holding it all up)!
+
+ShortForm 0.4.1
+===============
+
+New functionality: Simulated Annealing
+--------------------------------------
+
+-   The Simulated Annealing (SA) algorithm has been added to the
+    package, with a single user-facing function `simulatedAnnealing()`.
+-   SA can be used on anything lavaan can run, though the current
+    implementation focuses on traditional confirmatory models using
+    `lavaan::cfa()`. However, there are plans for more user control in
+    the modelling process to allow for other model defaults.
+
+New functionality: Tabu Search (Short Form)
+-------------------------------------------
+
+-   An adaptation of the Tabu search to short form creation has been
+    added.
+
+New functionality: ACO Plots
+----------------------------
+
+-   The `antcolony_lavaan()` function has been modified so that it no
+    longer will print a `summaryfile.txt`. Rather, the function
+    maintains the old summary file as an internal object and returns it
+    after completion,
+-   The new function `antcolony_plot()` takes the results from
+    `antcolony_lavaan()` and creates three graphs: (a) a plot showing
+    how pheremone levels change as the algorithm progresses, (b) a plot
+    showing how the mean value of the regression coefficients changes as
+    the algorithm progresses, and (c) a plot showing how the mean
+    variance explained changes as the algorithm progresses.
+
+New functionality: Bifactor Models
+----------------------------------
+
+-   Each of the short form functions utilizing lavaan
+    (`antcolony.lavaan()`, `simulatedAnnealing()`, `tabuShortForm()`)
+    are capable of handling bifactor models.
+-   In theory, this means relatively arbitrary models can be specified
+    as well, but the functions utilize the “~” and “~~” operators for
+    the additional functionality as well as the `bifactor` logical
+    option. No guarantee that an arbitrary model will work beyond those
+    currently tested.
+
+### Minor revisions
+
+-   The lavaan-based functions all have more controlled output to the R
+    console. This is most noticeable with the `antcolony.lavaan()`
+    function.
+
+ShortForm 0.4.0
+===============
+
+New functionality: Tabu Search
+------------------------------
+
+-   The Tabu search has been added to the package, with user-facing
+    functions `tabu.sem()` and `search.prep()` for most of the heavy
+    lifting and various helper and internal functions. The code was
+    taken primarily from Carl Falk and Katerina Marcoulides (see
+    Marcoulides, K. M., & Falk, C. F. (2018). Model Specification
+    Searches in Structural Equation Modeling with R. Structural Equation
+    Modeling: A Multidisciplinary Journal, 1-8.). These have been tested
+    in limited circumstances, so please report any bugs as you find
+    them!
+
+Minor changes
+-------------
+
+-   NEWS.md created.
+-   Description file updated.
+-   Authorship has been updated and URLs have been added to the ant
+    colony functions.
+-   No bugs have been found in the package thus far, but just a reminder
+    for any users that bug reports are helpful and welcome.

NEWS.Rmd

@@ -0,0 +1,94 @@
+---
+output:
+  github_document:
+    html_preview: FALSE
+  md_document:
+    pandoc_args: ["--output", "NEWS",]
+# rmarkdown::render("NEWS.Rmd", output_format = "all")
+---
+
+# ShortForm
+
+# *News* 
+
+# ShortForm 0.4.6
+
+## Updated argument check
+* The argument check for fit statistics (ACO, SA) were updated to include fit statistics related to the "WLSMV" estimator (i.e, for ordered data).
+
+## Bugfixes
+
+* A bug in the SA function that sometimes resulted in improper items has been fixed.
+
+* A bug in the Tabu short form function that caused the Tabu list to be erased if the best criterion value was reached has been fixed.
+
+# ShortForm 0.4.5
+
+## Extra arugment checks
+
+* There are now additional checks for the function arguments related to the fit statistics (ACO, SA) and the fit statistic tests (ACO) with informative warnings for when the function arguments are not valid.
+
+# ShortForm 0.4.2
+
+## Introduction of Function Classes
+
+* This version introduces classes to each of the main function outputs (`antcolony.lavaan` == "antcolony", `simulatedAnnealing` == "simulatedAnnealing", `tabuShortForm` == "tabu")
+
+* This will allow for `plot` and `print` methods for each of these functions
+
+## Broken functionality: antcolony_plot
+
+* The function `antcolony_plot` was replaced with `plot.antcolony` (aka, a plot method)
+
+## New functionality: S3 method for plotting
+
+* With the addition of classes, a plot method and accompanying documentation has been added.
+
+* Future updates will expand S3 methods for `print()` and `summary()`
+
+## Bugfixes
+
+* Bugfixes to the main functions when using them to create shortforms of bifactor models.
+* They should now produce actual bifactor shortforms (in 0.4.1, sometimes the item names would be cut off in later iterations [FIXED] and the relationship between latent variables would be changed when they should have been kept constant [FIXED]).
+
+## Added a package loading message
+
+* Now, when using an interactive R session, a package message is printed out (with a little Penguin holding it all up)!
+
+# ShortForm 0.4.1
+
+## New functionality: Simulated Annealing
+
+* The Simulated Annealing (SA) algorithm has been added to the package, with a single user-facing function `simulatedAnnealing()`. 
+* SA can be used on anything lavaan can run, though the current implementation focuses on traditional confirmatory models using `lavaan::cfa()`. However, there are plans for more user control in the modelling process to allow for other model defaults.
+
+## New functionality: Tabu Search (Short Form)
+
+* An adaptation of the Tabu search to short form creation has been added.
+
+## New functionality: ACO Plots
+
+* The `antcolony_lavaan()` function has been modified so that it no longer will print a `summaryfile.txt`. Rather, the function maintains the old summary file as an internal object and returns it after completion,
+* The new function `antcolony_plot()` takes the results from `antcolony_lavaan()` and creates three graphs: (a) a plot showing how pheremone levels change as the algorithm progresses, (b) a plot showing how the mean value of the regression coefficients changes as the algorithm progresses, and (c) a plot showing how the mean variance explained changes as the algorithm progresses.
+
+## New functionality: Bifactor Models
+
+* Each of the short form functions utilizing lavaan (`antcolony.lavaan()`, `simulatedAnnealing()`, `tabuShortForm()`) are capable of handling bifactor models.
+* In theory, this means relatively arbitrary models can be specified as well, but the functions utilize the "~" and "~~" operators for the additional functionality as well as the `bifactor` logical option. No guarantee that an arbitrary model will work beyond those currently tested.
+
+### Minor revisions
+
+* The lavaan-based functions all have more controlled output to the R console. This is most noticeable with the `antcolony.lavaan()` function.
+
+# ShortForm 0.4.0
+
+## New functionality: Tabu Search
+
+* The Tabu search has been added to the package, with user-facing functions `tabu.sem()` and `search.prep()` for most of the heavy lifting and various helper and internal functions. The code was taken primarily from Carl Falk and Katerina Marcoulides (see Marcoulides, K. M., & Falk, C. F. (2018). Model Specification Searches in Structural Equation Modeling with R. Structural Equation Modeling: A Multidisciplinary Journal, 1-8.). These have been tested in limited circumstances, so please report any bugs as you find them!
+
+## Minor changes
+
+* NEWS.md created.
+* Description file updated.
+* Authorship has been updated and URLs have been added to the ant colony functions.
+* No bugs have been found in the package thus far, but just a reminder for any users that bug reports are helpful and welcome.