touchups for examples

NAMESPACE

@@ -41,6 +41,7 @@ export(SimFunctions)
 export(SimResults)
 export(SimShiny)
 export(SimSolve)
+export(addMissing)
 export(add_missing)
 export(aggregate_simulations)
 export(bias)

R/SFA.R

@@ -87,7 +87,7 @@
 #'
 #' sim <- runSimulation(design=Design, replications=10,
 #'                      generate=Generate, analyse=Analyse,
-#'                      summarise=Summarise, store_results=TRUE,
+#'                      summarise=Summarise, store_results=TRUE, save=FALSE,
 #'                      progress=FALSE, control=list(print_RAM=FALSE))
 #' sim
 #'
@@ -128,7 +128,7 @@
 #'
 #' sim2 <- runSimulation(design=Design, replications=100,
 #'                      generate=Generate, analyse=Analyse,
-#'                      summarise=Summarise, store_results=TRUE,
+#'                      summarise=Summarise, store_results=TRUE, save=FALSE,
 #'                      progress=FALSE, control=list(print_RAM=FALSE))
 #' sim2
 #' sum(sim2$REPLICATIONS) # more replications in total
@@ -168,7 +168,7 @@
 #'
 #' sim3 <- runSimulation(design=Design, replications=50,
 #'                       generate=Generate, analyse=Analyse,
-#'                       summarise=Summarise, store_results=TRUE,
+#'                       summarise=Summarise, store_results=TRUE, save=FALSE,
 #'                       progress=FALSE, control=list(print_RAM=FALSE))
 #' sim3
 #' sum(sim3$REPLICATIONS)

R/addMissing.R

@@ -48,7 +48,7 @@
 #' Carlo simulation. \code{Journal of Statistics Education, 24}(3), 136-156.
 #' \doi{10.1080/10691898.2016.1246953}
 #'
-#' @export add_missing
+#' @export
 #'
 #' @author Phil Chalmers \email{rphilip.chalmers@@gmail.com}
 #'

R/bootPredict.R

@@ -69,8 +69,8 @@
 #' }
 #'
 #' Summarise <- function(condition, results, fixed_objects) {
-#'     ret <- c(mu_bias = bias(results[,1], 0),
-#'              mu_coverage = ECR(results[,2:3], parameter = 0))
+#'     ret <- c(mu_bias = bias(results[,"mean"], 0),
+#'              mu_coverage = ECR(results[,c("lower", "upper")], parameter = 0))
 #'     ret
 #' }
 #'
@@ -103,7 +103,7 @@
 #' (beta / .001)^2
 #' }
 #'
-bootPredict <- function(condition, generate, analyse, summarise, fixed_objects, ...,
+bootPredict <- function(condition, generate, analyse, summarise, fixed_objects=NULL, ...,
                         Rstar = seq(100, 500, by=100), boot_draws = 1000){
     replications <- max(Rstar)
     results <- runSimulation(design=condition, generate=generate, analyse=analyse,

R/reSummarise.R

@@ -97,7 +97,7 @@
 #' res2 <- reSummarise(Summarise2, dir = 'simresults/')
 #' res2
 #'
-#' SimClean('simresults/')
+#' SimClean(dir='simresults/')
 #'
 #' }
 #'

R/summary_functions.R

@@ -1028,10 +1028,8 @@ ECR <- function(CIs, parameter, tails = FALSE, CI_width = FALSE,
     if(is.data.frame(parameter)) parameter <- unlist(parameter)
     stopifnot(is.vector(parameter))
     if(length(parameter) != 1L) stopifnot(length(parameter) == nrow(CIs))
-    if(CIs[1,1] > CIs[1,2]){
-        warning('First column not less than second. Temporarily switching')
-        CIs <- cbind(CIs[,2L], CIs[,1L])
-    }
+    if(any(CIs[,1] > CIs[,2]))
+        stop('lower CIs higher than upper CIs. Please inspect')
     if(CI_width){
         ret <- mean(CIs[,2L] - CIs[,1L])
         if(!is.null(names))