Merge pull request #28 from Merck/ported-patch

Port essential upstream changes in gMCP 0.8-16

R/exampleGraphs.R

@@ -83,7 +83,7 @@
 #' Bretz, F., Maurer, W., Brannath, W., Posch, M.: A graphical approach to
 #' sequentially rejective multiple test procedures. Statistics in Medicine 2009
 #' vol. 28 issue 4 page 586-604.
-#' \url{http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
+#' \url{https://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
 #'
 #' Bretz, F., Maurer, W. and Hommel, G. (2011), Test and power considerations
 #' for multiple endpoint analyses using sequentially rejective graphical
@@ -448,7 +448,7 @@ improvedParallelGatekeeping <- function() {
 	edgeAttr(graph, "H4", "H2", "labelY") <- 200
 	attr(graph, "description") <- paste("Graph representing an improved parallel gatekeeping procedure",
 			"",
-			"Literature: Bretz, F., Maurer, W., Brannath, W., Posch, M.: A graphical approach to sequentially rejective multiple test procedures. Statistics in Medicine 2009 vol. 28 issue 4 page 586-604. URL: http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf .", sep="\n")
+			"Literature: Bretz, F., Maurer, W., Brannath, W., Posch, M.: A graphical approach to sequentially rejective multiple test procedures. Statistics in Medicine 2009 vol. 28 issue 4 page 586-604. URL: https://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf .", sep="\n")
 	return(graph)
 }
 
@@ -1022,7 +1022,7 @@ WangTing2014 <- function(nu, tau) {
                                       "with \\nu=\\epsilon, \\tau=\\epsilon graph from figure 5.",
                                       "",
                                       "Literature: Wang, B., Ting, N. (2014). An Application of Graphical Approach to Construct Multiple Testing Procedures in a Hypothetical Phase III Design. Frontiers in public health, 1 (75).",
-                                      "URL: http://journal.frontiersin.org/Journal/10.3389/fpubh.2013.00075/full", sep="\n")
+                                      "URL: https://www.frontiersin.org/articles/10.3389/fpubh.2013.00075/full", sep="\n")
 
   variables <- list()
   if (!missing(nu)) variables[["nu"]] <- nu

R/gMCP.R

@@ -108,12 +108,13 @@
 #' @references Frank Bretz, Willi Maurer, Werner Brannath, Martin Posch: A
 #' graphical approach to sequentially rejective multiple test procedures.
 #' Statistics in Medicine 2009 vol. 28 issue 4 page 586-604.
-#' \url{http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
+#' \url{https://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
 #'
 #' Bretz F., Posch M., Glimm E., Klinglmueller F., Maurer W., Rohmeyer K.
 #' (2011): Graphical approaches for multiple endpoint problems using weighted
 #' Bonferroni, Simes or parametric tests. Biometrical Journal 53 (6),
 #' pages 894-913, Wiley.
+#' \doi{10.1002/bimj.201000239}
 #'
 #' Strassburger K., Bretz F.: Compatible simultaneous lower confidence bounds
 #' for the Holm procedure and other Bonferroni based closed tests. Statistics
@@ -437,7 +438,7 @@ adjPValues <- function(graph, pvalues, upscale=FALSE, verbose=FALSE) {
 #' @references Frank Bretz, Willi Maurer, Werner Brannath, Martin Posch: A
 #' graphical approach to sequentially rejective multiple test procedures.
 #' Statistics in Medicine 2009 vol. 28 issue 4 page 586-604.
-#' \url{http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
+#' \url{https://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
 #' @keywords htest graphs
 #'
 #' @export rejectNode

R/gMCP.extended.R

@@ -155,6 +155,7 @@ bonferroni.test <- function(pvalues, weights, alpha=0.05, adjPValues=TRUE, verbo
 #' (2011): Graphical approaches for multiple endpoint problems using weighted
 #' Bonferroni, Simes or parametric tests. Biometrical Journal 53 (6),
 #' pages 894-913, Wiley.
+#' \doi{10.1002/bimj.201000239}
 #'
 #' @export
 parametric.test <- function(pvalues, weights, alpha=0.05, adjPValues=TRUE, verbose=FALSE, correlation, ...) {
@@ -361,12 +362,13 @@ simes.test <- function(pvalues, weights, alpha=0.05, adjPValues=TRUE, verbose=FA
 #' @references Frank Bretz, Willi Maurer, Werner Brannath, Martin Posch: A
 #' graphical approach to sequentially rejective multiple test procedures.
 #' Statistics in Medicine 2009 vol. 28 issue 4 page 586-604.
-#' \url{http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
+#' \url{https://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
 #'
 #' Bretz F., Posch M., Glimm E., Klinglmueller F., Maurer W., Rohmeyer K.
 #' (2011): Graphical approaches for multiple endpoint problems using weighted
 #' Bonferroni, Simes or parametric tests. Biometrical Journal 53 (6),
 #' pages 894-913, Wiley.
+#' \doi{10.1002/bimj.201000239}
 #'
 #' Strassburger K., Bretz F.: Compatible simultaneous lower confidence bounds
 #' for the Holm procedure and other Bonferroni based closed tests. Statistics

R/graphMCP.R

@@ -449,7 +449,7 @@ getWeightStr <- function(graph, from, to, LaTeX=FALSE) {
 			return(getLaTeXFraction(weight))
 		} else {
       asNr <- try(eval(parse(text=weight), envir=NULL, enclos=NULL), silent=TRUE)
-		  if (!is.na(asNr) && !("try-error"%in%class(asNr))) {
+		  if (!is.na(asNr) && !(inherits(asNr, "try-error"))) {
 		    return(getLaTeXFraction(asNr))
 		  }
 		}
@@ -514,7 +514,7 @@ setMethod("plot", "graphMCP",
 #' @references Frank Bretz, Willi Maurer, Werner Brannath, Martin Posch: A
 #' graphical approach to sequentially rejective multiple test procedures.
 #' Statistics in Medicine 2009 vol. 28 issue 4 page 586-604.
-#' \url{http://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
+#' \url{https://www.meduniwien.ac.at/fwf_adaptive/papers/bretz_2009_22.pdf}
 #'
 #' @keywords htest graphs
 #'
@@ -568,12 +568,12 @@ setMethod("simConfint", c("graphMCP"), function(object, pvalues, confint, altern
 			if (alternative=="greater") {
 				stderr <- abs(estimates/dist(1-pvalues))
 				lb <- estimates+dist(alpha)*stderr
-				lb <- ifelse(getRejected(result), max(0,lb), lb)
+				lb <- ifelse(getRejected(result), pmax(mu, lb), lb)
 				ub <- rep(Inf,length(lb))
 			} else if (alternative=="less") {
 				stderr <- abs(estimates/dist(pvalues))
 				ub <- estimates+dist(1-alpha)*stderr
-				ub <- ifelse(getRejected(result), min(0,ub), ub)
+				ub <- ifelse(getRejected(result), pmin(mu, ub), ub)
 				lb <- rep(-Inf,length(ub))
 			} else {
 				stop("Specify alternative as \"less\" or \"greater\".")