Merge pull request #9 from AnthonyRaborn/bugfix

Bugfix

Author: AnthonyRaborn

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ShortForm
 Type: Package
 Title: Automatic Short Form Creation
-Version: 0.4.4
-Date: 2019-10-9
+Version: 0.4.5
+Date: 2020-02-24
 Authors@R: c(person("Anthony", "Raborn", email = "anthony.w.raborn@gmail.com", role = c("aut", "cre")), person("Walter", "Leite", email = "Walter.Leite@coe.ufl.edu", role = "aut"))
 Description: Performs automatic creation of short forms of scales with an 
     ant colony optimization algorithm and a Tabu search. As implemented in the 
@@ -19,7 +19,7 @@ Description: Performs automatic creation of short forms of scales with an
     <doi:10.1080/10705511.2017.1409074> for an applied example of the Tabu search.
 License: LGPL (>= 2.0, < 3) | Mozilla Public License
 LazyData: TRUE
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Suggests:
     knitr,
     MplusAutomation (>= 0.7),
@@ -31,7 +31,6 @@ Imports:
     stringr
 Depends:
     R (>= 3.0.0)
-Roxygen: list(wrap = FALSE)
 URL: https://github.com/AnthonyRaborn/ShortForm
 BugReports: https://github.com/AnthonyRaborn/ShortForm/issues
 Encoding: UTF-8

NEWS.md

@@ -1,3 +1,7 @@
+# Package v0.4.5
+## 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.
+
 # Package v0.4.2
 ## Introduction of Function Classes
 * This version introduces classes to each of the main function outputs (`antcolony.lavaan` == "antcolony", `simulatedAnnealing` == "simulatedAnnealing", `tabuShortForm` == "tabu")

R/ACO_lavaan.R

@@ -213,7 +213,8 @@ antcolony.lavaan = function(data = NULL, sample.cov = NULL, sample.nobs = NULL,
   if(!requireNamespace("lavaan", quietly = TRUE)){
     stop("The `lavaan` package is required to use this function. Please install `lavaan`, then try to use this function again.")
   }
-
+  fitmeasuresCheck(fit.indices)
+  fitStatTestCheck(fit.indices, fit.statistics.test)
   antcolony.lavaan.env <- new.env(parent = baseenv())
 
   if(pheromone.calculation %in% c("gamma", "beta", "regression", "variance") == FALSE) {
@@ -264,6 +265,7 @@ antcolony.lavaan = function(data = NULL, sample.cov = NULL, sample.nobs = NULL,
   step = 1
 
   # creates objects in the global environment that are fed into the lavaan function in order to fine-tune the model to user specifications
+  checkModelSpecs(lavaan.model.specs)
   mapply(assign, names(lavaan.model.specs), lavaan.model.specs, MoreArgs=list(envir = antcolony.lavaan.env))
 
   # create the function to check for and save error/warning messages within the lavaan output, as well as saving the fit indices

R/Tabu_shortform.R

@@ -60,6 +60,7 @@ tabuShortForm <-
              estimator = "default"
            ),
            bifactor = FALSE) {
+    checkModelSpecs(lavaan.model.specs)
     mapply(
       assign,
       names(lavaan.model.specs),

R/simulated_annealing.R

@@ -93,15 +93,15 @@ simulatedAnnealing <-
     currentStep = 0
     consecutive = 0
     allFit = c()
-    
+    fitmeasuresCheck(fitStatistic)
     # creates objects in the function environment that are fed into the lavaan function in order to fine-tune the model to user specifications
     # solution from: https://stackoverflow.com/questions/6375790/r-creating-an-environment-in-the-globalenv-from-inside-a-function
     # makeCache <- function() {
     #   # list(get = function(key) cache[[key]],
     #   #      set = function(key, value) cache[[key]] <- value
     #   #      )
     # }
-    
+    checkModelSpecs(lavaan.model.specs)
     mapply(
       assign,
       names(lavaan.model.specs),

R/simulated_annealing_internals.R

@@ -197,3 +197,104 @@ fitWarningCheck <- function(expr, maximize) {
   )
   return(value)
 }
+
+
+checkModelSpecs <- 
+  function(
+    x
+  ) {
+    
+    requiredElements <-
+      c('model.type',
+        'auto.var',
+        'estimator',
+        'ordered',
+        'int.ov.free',
+        'int.lv.free',
+        'auto.fix.first',
+        'auto.fix.single',
+        'auto.cov.lv.x',
+        'auto.th',
+        'auto.delta',
+        'auto.cov.y',
+        'std.lv')
+    
+    missingSpecs <-
+      requiredElements[
+        which(
+          !requiredElements %in% names(x)
+        )
+        ]
+    
+    if (length(missingSpecs) > 0) {
+      errorMessage <-
+        paste0("The following elements of lavaan.model.specs have not been specified:\n\n",
+               paste(missingSpecs, collapse = "\n"),
+               "\n\nPlease include the proper specifications for these elements, or use the default values provided.")
+      stop(errorMessage)
+    }
+  }
+
+fitmeasuresCheck <-
+  function(
+    x
+  ) {
+    validMeasures <-
+      c(
+        "npar", "fmin",
+        "chisq", "df", "pvalue", 
+        "baseline.chisq", "baseline.df", "baseline.pvalue",    
+        "cfi", "tli", "nnfi",
+        "rfi", "nfi", "pnfi",
+        "ifi", "rni",                
+        "logl", "unrestricted.logl",
+        "aic", "bic", "ntotal", "bic2",
+        "rmsea", "rmsea.ci.lower", "rmsea.ci.upper", "rmsea.pvalue",
+        "rmr", "rmr_nomean", 
+        "srmr", "srmr_bentler", "srmr_bentler_nomean", 
+        "crmr", "crmr_nomean", "srmr_mplus", "srmr_mplus_nomean",
+        "cn_05", "cn_01", 
+        "gfi", "agfi", "pgfi", "mfi", "ecvi"
+      )
+    
+    invalidMeasures <-
+      x[
+        which(
+          !x %in% validMeasures
+        )
+        ]
+    
+    if (length(invalidMeasures) > 0) {
+      errorMessage <-
+        paste0("The following elements of fit.indices or fitStatistics are not valid fit measures provided by the lavaan::fitmeasures function:\n\n",
+               paste(invalidMeasures, collapse = "\n"),
+               "\n\nPlease check the output of this function for proper spelling and capitalization of the fit measure(s) you are interested in.")
+      stop(errorMessage)
+    }
+
+  }
+
+fitStatTestCheck <-
+  function(measures, test) {
+    tempEnv <-
+      new.env()
+    mapply(
+      assign, 
+      measures, 
+      0, 
+      MoreArgs=list(envir = tempEnv))
+    
+    checkIfEval <-
+      tryCatch(
+        expr = eval(parse(text=test), 
+                    envir = tempEnv), 
+        error = function(e) {
+          stop("There was a problem with the fit.statistics.test provided. It cannot be evaluated properly. Please read the function documentation to see how to properly specify a test.")
+        }
+      )
+    
+    if (!is.character(test)) {
+          stop("There is a problem with the fit.statistics.test provided. The fit.statistics.test was given as a logical, not a character. Please read the function documentation to see how to properly specify a test. ")
+        }
+      
+  }

cran-comments.md

@@ -1,12 +1,14 @@
 ## Resubmission
-This is a resubmission. In this version I have fixed a bug that caused the lavaan-based functions to improperly use the initial model syntax instead of building the intermediate model syntax when the initial model syntax was specified in an untested manner.
+This is a resubmission. In this version I have included three checks to function arguments that will give informative errors if the user misspecifies the arguments.
 
 ## Test Environments
 
-* local Windows 10 Enterprise install, R 3.6.1
+* local Windows 10 Home install, R 3.6.2
 
 * Ubuntu 16.04.5 LTS xenial (travis ci), R 3.6.1
 
+* r-hub and win_check
+
 ## R CMD check results
 0 errors | 0 warnings | 0 notes