version 1.0-2

ChangeLog

@@ -1,6 +1,10 @@
 ---------------------------
 -- ChangeLog - gsbDesign --
 ---------------------------
+2021-10-02 Bjoern Bornkamp (version 1.0-1)
+	* Changes to bring gsbDesign back to CRAN (was archived due
+	temporary archival of package dependency gsDesign)
+
 2019-12-07 Bjoern Bornkamp (version 1.0-1)
 	* Fix errors on CRAN (class(.) == * issue)
 

DESCRIPTION

@@ -1,17 +1,25 @@
 Package: gsbDesign
 Type: Package
+Version: 1.0-2
+Date: 2021-10-02
 Title: Group Sequential Bayes Design
-Version: 1.0-1
-Date: 2019-12-07
-Author: Florian Gerber, Thomas Gsponer
+Authors@R: c(person("Florian", "Gerber", role = c("aut")),
+             person("Thomas", "Gsponer", role = "aut"),	 
+             person("Bjoern", "Bornkamp", role = "cre",
+                    email = "bbnkmp@mail.de",
+		    comment = "maintainer"))
 Depends: gsDesign, lattice, grid,
 Imports: stats, graphics, grDevices, utils
-Maintainer: Bjoern Bornkamp <bbnkmp@mail.de>
 Description: Group Sequential Operating Characteristics for Clinical,
-        Bayesian two-arm Trials with known Sigma and Normal Endpoints.
+        Bayesian two-arm Trials with known Sigma and Normal Endpoints,
+	as described in Gerber and Gsponer (2016) <doi: 10.18637/jss.v069.i11>.
 License: GPL-3
 LazyLoad: yes
 NeedsCompilation: no
-Packaged: 2019-12-07 05:03:30 UTC; bjoern
+Packaged: 2021-10-02 12:17:47 UTC; bjoern
 Repository: CRAN
-Date/Publication: 2019-12-09 10:30:02 UTC
+Date/Publication: 2021-10-04 08:20:05 UTC
+Author: Florian Gerber [aut],
+  Thomas Gsponer [aut],
+  Bjoern Bornkamp [cre] (maintainer)
+Maintainer: Bjoern Bornkamp <bbnkmp@mail.de>

MD5

@@ -1,20 +1,20 @@
-83b07c2340986d4bb1f8d3296f90c54b *ChangeLog
-018ac65952be3fdecd935fffdb569c2c *DESCRIPTION
+f7d2bfb99e06729963b06d6ede268aa4 *ChangeLog
+2c6584a1c61f03b53a64f90fd476a310 *DESCRIPTION
 59bc54cdb8022bce7066181d4795f5d7 *NAMESPACE
-2f6afb2c3e5f8c839b5fdadf3282cb0f *R/package.r
-3f872b1783452147e04931a686e5799e *build/vignette.rds
+818844f329335d7415633fba91f5fedf *R/package.r
+bcc9ded8b0103362bcebf4a65017ab8d *build/vignette.rds
 30415f885d01651d302cf22a474987ee *demo/00Index
 a45e4ca4555b2749663abb6f3f1feb82 *demo/JSS-poc.R
 4e8b7e2c2f3f83c9d25239c2c7268b53 *demo/JSS-usage.R
 9fb4ce5055467e82017dcdb1f9c74b15 *inst/CITATION
-65a189b143bb8cd152b49fc4fd2e683d *inst/doc/JSS-gsbDesign.R
-bd26590f00f3af2259d4fcff465c9cfd *inst/doc/JSS-gsbDesign.Rnw
-676a1e974bc3ca7caf26e6087802359b *inst/doc/JSS-gsbDesign.pdf
-875e041b75b2fd8aa3375331232a41d3 *man/gsb-package.Rd
-7f6ee2c9625ac30d94f8f5d0e7a228ff *man/gsb.Rd
+dc9ae46fc3c85cd920f2e848fa119ad2 *inst/doc/JSS-gsbDesign.R
+897a7f4a3594beb94ad9ef585c48063d *inst/doc/JSS-gsbDesign.Rnw
+39818b7d70c88446857660519b6f42c1 *inst/doc/JSS-gsbDesign.pdf
+eca216a85a1aafa34fc6fea7fa925982 *man/gsb-package.Rd
+bcdbb198cc6c87e56a62263d80175140 *man/gsb.Rd
 7c9030aaafc021120759b5947bebf983 *man/gsbBayesUpdate.Rd
 188463742b9e4f47404cf00d3d022875 *man/gsbCriteria.Rd
-5667a6bc73cc3de6a73543cca1b6fef4 *man/plot.gsbMainOut.Rd
-fa21316d9eb2dfcd216ffa7f01ff5898 *man/tab.Rd
-bd26590f00f3af2259d4fcff465c9cfd *vignettes/JSS-gsbDesign.Rnw
+a3e6d7dbcc2b1c44973a0a912bd7d6d4 *man/plot.gsbMainOut.Rd
+9f2f15e78ecfc0e2b6b33ffa64b2887f *man/tab.Rd
+897a7f4a3594beb94ad9ef585c48063d *vignettes/JSS-gsbDesign.Rnw
 b35192e5421e0b038f55ac5a9ddeaa71 *vignettes/JSS-gsbDesign.bib

R/package.r

@@ -1359,11 +1359,11 @@ gsbDesign <- function(nr.stages=NULL,
   if(is.null(patients))
     stop("Please specify the argument \"patients\".")
 
-
-  if(class(patients)!="numeric" & class(patients)!="matrix")
+  
+  if(!(inherits(patients, "numeric") | inherits(patients, "matrix")))
     stop("Argument \"patients\" has to be of class \"numeric\" or \"matrix\".\n")
 
-  if(class(patients)=="numeric"){
+  if(inherits(patients, "numeric")){
 
     if(length(patients)>2)
       stop("Argument \"patients\" has to be a vector of length 1 or 2 or a matrix of size \"nr.stages x 2\"  or size \"nr.stages x 1\".")
@@ -1887,7 +1887,7 @@ plot.gsbMainOut <- function(x,
                             smooth=100,
                             contour=TRUE,
                             export=FALSE,
-                            path=getwd(),
+                            path=tempdir(),
                             sliced=FALSE,
                             range.control="default",
                             ...){
@@ -2253,7 +2253,7 @@ tab <- function(x,
                 digits = 3,
                 export = FALSE, 
                 sep = ",",
-                path = getwd()) 
+                path = tempdir()) 
 {
 
   ## control / prepare arguments

inst/doc/JSS-gsbDesign.R

@@ -3,11 +3,10 @@
 ###################################################
 ### code chunk number 1: preliminaries
 ###################################################
-remove(list=ls())
 set.seed(144)
-options(prompt = "R> ", continue = "+  ", width = 70, useFancyQuotes = FALSE)
-if(!file.exists("./Figures/"))
-    dir.create("./Figures/",recursive=TRUE)
+old <- options(prompt = "R> ", continue = "+  ", width = 70, useFancyQuotes = FALSE)
+##if(!file.exists("./Figures/"))
+##    dir.create("./Figures/",recursive=TRUE)
 
 
 ###################################################
@@ -154,7 +153,6 @@ print(p12)
 ###################################################
 ### code chunk number 22: preliminaries
 ###################################################
-remove(list=ls())
 set.seed(155)
 
 
@@ -232,5 +230,6 @@ print(xtable(tSum,caption="Operating characteristics of the two stage design.",
  label = "tab1", align=rep("c",7),digits=c(0,0,3,3,3,3,0)),
      stype="latex",sanitize.colnames.function=function(x){x},
      include.rownames=FALSE)
+options(old)
 
 

inst/doc/JSS-gsbDesign.Rnw

@@ -57,7 +57,7 @@ We illustrate the use of \pkg{gsbDesign} with a detailed case study.
 \usepackage{amssymb}
 \usepackage{booktabs}
 
-\graphicspath{{Figures/}}
+%\graphicspath{{Figures/}}
 
 
 \begin{document}
@@ -481,15 +481,14 @@ stopping for futility and stopping for success are available, the
 expected sample size is straightforward to compute.
 
 \SweaveOpts{engine=R,eps=FALSE,pdf=TRUE}
-\SweaveOpts{prefix=TRUE,prefix.string=Figures/Application,include=TRUE,keep.source=TRUE}
+%\SweaveOpts{prefix=TRUE,prefix.string=Figures/Application,include=TRUE,keep.source=TRUE}
 \setkeys{Gin}{width=\textwidth}
 
 <<preliminaries,echo=FALSE,results=hide>>=
-remove(list=ls())
 set.seed(144)
-options(prompt = "R> ", continue = "+  ", width = 70, useFancyQuotes = FALSE)
-if(!file.exists("./Figures/"))
-    dir.create("./Figures/",recursive=TRUE)
+old <- options(prompt = "R> ", continue = "+  ", width = 70, useFancyQuotes = FALSE)
+##if(!file.exists("./Figures/"))
+##    dir.create("./Figures/",recursive=TRUE)
 @
 
 % ----------------------------------------------------------------------
@@ -929,7 +928,6 @@ frame \code{oc2$OC}.
 
 
 <<preliminaries,echo=FALSE,results=hide>>=
-remove(list=ls())
 set.seed(155)
 @
 
@@ -1154,6 +1152,7 @@ print(xtable(tSum,caption="Operating characteristics of the two stage design.",
  label = "tab1", align=rep("c",7),digits=c(0,0,3,3,3,3,0)),
      stype="latex",sanitize.colnames.function=function(x){x},
      include.rownames=FALSE)
+options(old)
 @
 
 

man/gsb-package.Rd

@@ -24,8 +24,8 @@ The main function of the package is \code{gsb()}. More detailed information can
   \tabular{ll}{
     Package: \tab gsbDesign\cr
     Type: \tab Package\cr
-    Version: \tab 1.00\cr
-    Date: \tab 2016-03-27\cr
+    Version: \tab 1.0-2\cr
+    Date: \tab 2021-10-02\cr
     License: \tab GNU General Public License >=3\cr
     LazyLoad: \tab yes\cr
   }

man/gsb.Rd

@@ -396,7 +396,7 @@ plot(x2b, what="std.boundary")
 
 
 
-\dontrun{
+\donttest{
 ## E X A M P L E 3: Update on treatment effect, informative prior
 ##
 ## A. Trial Design

man/plot.gsbMainOut.Rd

@@ -24,7 +24,7 @@ Methods for plotting the results of \code{gsb()}.}
      smooth = 100,
      contour = TRUE, 
      export = FALSE,
-     path = getwd(),
+     path = tempdir(),
      sliced = FALSE,
      range.control="default", ...)
 
@@ -81,7 +81,7 @@ Methods for plotting the results of \code{gsb()}.}
   }
   \item{path}{
     \code{character}. to specify the location to which to table should
-    be exported. the default 'getwd()' exports the table to the working
+    be exported. the default 'tempdir()' exports the table to a temporary
     directory.
   }
   \item{sliced}{
@@ -95,7 +95,9 @@ Methods for plotting the results of \code{gsb()}.}
   }
   \item{...}{further arguments passed to or from other methods.}
 }
-
+\value{
+  Returns an object of class \code{"trellis"}
+}
 \references{
 uses the R-package 'lattice'. 
 }
@@ -116,7 +118,7 @@ Florian Gerber <florian.gerber@math.uzh.ch>, Thomas Gsponer
 ## --------------------------------------
 ## alternative plots can be created for example
 ## with package 'ggplot2'.
-\dontrun{
+\donttest{
 des <- gsbDesign(nr.stages=2,
                      patients=10,
                      sigma=10,
@@ -135,7 +137,7 @@ datgraph <- x$OC
 
 
 ## prepare for plot
-sub <- levels(datgraph$type)[1:3]
+sub <- c("success", "futility", "success or futility")
 datgraph2 <- subset(datgraph,datgraph$type \%in\% sub)
 datgraph2$type <- as.factor(paste(datgraph2$type))
 datgraph2$value[datgraph2$type=="cumulative success or futility"] <-

man/tab.Rd

@@ -20,7 +20,7 @@ tab(x,
     digits = 3,
     export = FALSE,
     sep = ",",
-    path = getwd())
+    path = tempdir())
 }
 
 \arguments{
@@ -56,11 +56,15 @@ tab(x,
  }
   \item{path}{
     \code{character}. to specify the location to which to table should
-  be exported. the default 'getwd()' exports the table to the working
+  be exported. the default 'tempdir()' exports the table to a temporary
   directory.
   }
 
 }
+\value{
+  Returns a matrix with the results from the output of function
+  \code{gsb()}. 
+}
 
 \author{
 Florian Gerber <florian.gerber@math.uzh.ch>

vignettes/JSS-gsbDesign.Rnw

@@ -57,7 +57,7 @@ We illustrate the use of \pkg{gsbDesign} with a detailed case study.
 \usepackage{amssymb}
 \usepackage{booktabs}
 
-\graphicspath{{Figures/}}
+%\graphicspath{{Figures/}}
 
 
 \begin{document}
@@ -481,15 +481,14 @@ stopping for futility and stopping for success are available, the
 expected sample size is straightforward to compute.
 
 \SweaveOpts{engine=R,eps=FALSE,pdf=TRUE}
-\SweaveOpts{prefix=TRUE,prefix.string=Figures/Application,include=TRUE,keep.source=TRUE}
+%\SweaveOpts{prefix=TRUE,prefix.string=Figures/Application,include=TRUE,keep.source=TRUE}
 \setkeys{Gin}{width=\textwidth}
 
 <<preliminaries,echo=FALSE,results=hide>>=
-remove(list=ls())
 set.seed(144)
-options(prompt = "R> ", continue = "+  ", width = 70, useFancyQuotes = FALSE)
-if(!file.exists("./Figures/"))
-    dir.create("./Figures/",recursive=TRUE)
+old <- options(prompt = "R> ", continue = "+  ", width = 70, useFancyQuotes = FALSE)
+##if(!file.exists("./Figures/"))
+##    dir.create("./Figures/",recursive=TRUE)
 @
 
 % ----------------------------------------------------------------------
@@ -929,7 +928,6 @@ frame \code{oc2$OC}.
 
 
 <<preliminaries,echo=FALSE,results=hide>>=
-remove(list=ls())
 set.seed(155)
 @
 
@@ -1154,6 +1152,7 @@ print(xtable(tSum,caption="Operating characteristics of the two stage design.",
  label = "tab1", align=rep("c",7),digits=c(0,0,3,3,3,3,0)),
      stype="latex",sanitize.colnames.function=function(x){x},
      include.rownames=FALSE)
+options(old)
 @