diff --git a/R/exampleGraphs.R b/R/exampleGraphs.R index e6b507e..c81c5fc 100644 --- a/R/exampleGraphs.R +++ b/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 diff --git a/R/gMCP.R b/R/gMCP.R index d61b3c3..3e2526e 100644 --- a/R/gMCP.R +++ b/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 diff --git a/R/gMCP.extended.R b/R/gMCP.extended.R index 077f69a..89ca2cc 100644 --- a/R/gMCP.extended.R +++ b/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 diff --git a/R/graphMCP.R b/R/graphMCP.R index 9860f6f..84082a3 100644 --- a/R/graphMCP.R +++ b/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\".") diff --git a/man/exampleGraphs.Rd b/man/exampleGraphs.Rd index 54a98a6..b9ab672 100644 --- a/man/exampleGraphs.Rd +++ b/man/exampleGraphs.Rd @@ -169,7 +169,7 @@ Statistics in Medicine. 22, 2387-2400. 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 diff --git a/man/gMCP.Rd b/man/gMCP.Rd index 6dba195..d547ee2 100644 --- a/man/gMCP.Rd +++ b/man/gMCP.Rd @@ -139,12 +139,13 @@ gMCP(g2, pvalues=c(0.01, 0.02, 0.04, 0.04, 0.7), upscale=TRUE) 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 diff --git a/man/gMCP.extended.Rd b/man/gMCP.extended.Rd index a56805f..19f90b1 100644 --- a/man/gMCP.extended.Rd +++ b/man/gMCP.extended.Rd @@ -87,12 +87,13 @@ gMCP(g3, pvalues=c(0.01, 0.02, 0.04, 0.04, 0.7), correlation=diag(5)) 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 diff --git a/man/parametric.test.Rd b/man/parametric.test.Rd index 4b24a07..1604884 100644 --- a/man/parametric.test.Rd +++ b/man/parametric.test.Rd @@ -81,4 +81,5 @@ 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} } diff --git a/man/rejectNode.Rd b/man/rejectNode.Rd index 771c7f7..8f001d6 100644 --- a/man/rejectNode.Rd +++ b/man/rejectNode.Rd @@ -47,7 +47,7 @@ rejectNode(graph = g, node = 4) 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} } \seealso{ \code{graphMCP} diff --git a/man/simConfint.Rd b/man/simConfint.Rd index 2b235f6..ad4bb70 100644 --- a/man/simConfint.Rd +++ b/man/simConfint.Rd @@ -78,7 +78,7 @@ ci 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} } \seealso{ \code{\link{graphMCP}}