updates to pass CRAN and GitHub checks

R/dynEGA.ind.pop.R

@@ -144,7 +144,8 @@
 #' # Obtain data
 #' sim.dynEGA <- sim.dynEGA # bypasses CRAN checks
 #'
-#' \donttest{# Dynamic EGA individual and population structure
+#' \dontrun{
+#' # Dynamic EGA individual and population structure
 #' dyn.ega1 <- dynEGA.ind.pop(
 #'   data = sim.dynEGA, n.embed = 5, tau = 1,
 #'   delta = 1, id = 25, use.derivatives = 1,

R/methods.section.R

@@ -44,48 +44,50 @@
 #' @return Automated HTML Methods section in your default browser
 #' 
 #' @examples
-#' \donttest{# Estimate EGA
-#' ## plot.type = "qqraph" used for CRAN checks
-#' ## plot.type = "GGally" is the default
-#' ega.wmt <- EGA(data = wmt2[,7:24], plot.type = "qgraph")
-#' }
+#' # Load data
+#' wmt <- wmt2[,7:24]
+#' 
+#' \dontrun{
+#' # Estimate EGA
+#' ega.wmt <- EGA(data = wmt)
+#' 
 #' # EGA Methods section
-#' if(interactive()){
 #' methods.section(ega.wmt)
-#' }
 #' 
-#' \donttest{# Estimate standardized network loadings
+#' # Estimate standardized network loadings
 #' wmt.loads <- net.loads(ega.wmt)$std
-#' }
+#' 
 #' # EGA Methods section with network loadings
-#' if(interactive()){
 #' methods.section(ega.wmt, stats = "net.loads")
-#' }
 #' 
-#' \dontrun{# bootEGA example
+#' # bootEGA example
 #' ## plot.type = "qqraph" used for CRAN checks
 #' ## plot.type = "GGally" is the default
-#' boot.wmt <- bootEGA(data = wmt2[,7:24], iter = 500, plot.type = "qgraph",
-#' type = "parametric", ncores = 2)
-#' }
+#' boot.wmt <- bootEGA(
+#'   data = wmt, iter = 500,
+#'   type = "parametric", ncores = 2
+#' )
+#' 
 #' # EGA and bootEGA Methods section
-#' if(interactive()){
 #' methods.section(ega.wmt, boot.wmt)
-#' }
 #' 
-#' \donttest{# Estimate structural consistency
+#' # Estimate structural consistency
 #' sc.wmt <- dimensionStability(boot.wmt)
-#' }
+#'
 #' # EGA and bootEGA Methods section with structural consistency and item stability
-#' if(interactive()){
 #' methods.section(boot.wmt, stats = c("dimensionStability", "itemStability"))
-#' }
 #' 
 #' # EGA with network loadings and
 #' # bootEGA Methods section with structural consistency and item stability
-#' if(interactive()){
-#' methods.section(ega.wmt, boot.wmt, stats = c("net.loads", "dimensionStability", "itemStability"))
-#' }
+#' methods.section(
+#'   ega.wmt,
+#'   boot.wmt, 
+#'   stats = c(
+#'     "net.loads",
+#'     "dimensionStability",
+#'     "itemStability"
+#'   )
+#' )}
 #' 
 #' @importFrom utils packageVersion browseURL
 #'

R/net.loads.R

@@ -55,7 +55,8 @@
 #' # Load data
 #' wmt <- wmt2[,7:24]
 #'
-#' \donttest{# Estimate EGA
+#' \dontrun{
+#' # Estimate EGA
 #' ega.wmt <- EGA(
 #'   data = wmt,
 #'   plot.EGA = FALSE # No plot for CRAN checks
@@ -64,7 +65,8 @@
 #' # Network loadings
 #' net.loads(ega.wmt)
 #' 
-#' \donttest{# Produce Methods section
+#' \dontrun{
+#' # Produce Methods section
 #' methods.section(
 #'   ega.wmt,
 #'   stats = "net.loads"

R/net.scores.R

@@ -69,7 +69,8 @@
 #' # Load data
 #' wmt <- wmt2[,7:24]
 #'
-#' \donttest{# Estimate EGA
+#' \dontrun{
+#' # Estimate EGA
 #' ega.wmt <- EGA(
 #'   data = wmt,
 #'   plot.EGA = FALSE # No plot for CRAN checks
@@ -78,7 +79,8 @@
 #' # Network scores
 #' net.scores(data = wmt, A = ega.wmt)
 #' 
-#' \donttest{# Produce Methods section
+#' \dontrun{
+#' # Produce Methods section
 #' methods.section(
 #'   ega.wmt,
 #'   stats = "net.scores"

R/residualEGA.R

@@ -36,17 +36,16 @@
 #' @author Hudson F. Golino <hfg9s at virginia.edu> and Robert Moulder <rgm4fd@virginia.edu>
 #'
 #' @examples
-#' 
+#' # Load data
 #' data <- optimism
 #' 
 #' \dontrun{
-#' # resEGA example
+#' # Residual EGA example
 #' opt.res <- residualEGA(data = data, manifests = colnames(optimism),
 #' lat = 1, negative.items = c(3,7,9))
 #'
 #' # Fit:
-#' opt.res$Fit
-#' }
+#' opt.res$Fit}
 #'
 #' @seealso \code{\link[EGAnet]{EGA}} to estimate the number of dimensions of an instrument using EGA
 #' and \code{\link[EGAnet]{CFA}} to verify the fit of the structure suggested by EGA using confirmatory factor analysis.

R/simDFM.R

@@ -45,17 +45,12 @@
 #' Set to \code{TRUE} to add slight variation to all parameters
 #'
 #' @examples
-#'
-#'
 #' \dontrun{
-#' \donttest{
 #' # Estimate EGA network
 #' data1 <- simDFM(variab = 5, timep = 50, nfact = 3, error = 0.05,
 #' dfm = "DAFS", loadings = 0.7, autoreg = 0.8,
 #' crossreg = 0.1, var.shock = 0.18,
-#' cov.shock = 0.36, burnin = 1000)
-#'  }
-#'}
+#' cov.shock = 0.36, burnin = 1000)}
 #'
 #' @references
 #' Engle, R., & Watson, M. (1981).

R/utils-EGAnet.R

@@ -7029,7 +7029,7 @@ parallel_process <- function(
     count_computations <- 0
 
     # Create data splits (necessary for progress bar)
-    if(iter <= 100 | os != "windows"){
+    if(total_computations <= 100 | os != "windows"){
 
       # Split computations
       split_computations <- ncores
@@ -7077,7 +7077,7 @@ parallel_process <- function(
       )
 
       # Batch splits
-      batch_computations <- round(iter / 100)
+      batch_computations <- round(total_computations / 100)
 
       # Set start and end points of data batches
       batch_start <- seq(1, length(split_end), batch_computations)