version 0.96-3

cran · Jul 7, 2015 · e09c9cf · e09c9cf
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,16 +1,17 @@
 Package: gsbDesign
 Type: Package
 Title: Group Sequential Bayes Design
-Version: 0.96-2
-Date: 2013-04-21
+Version: 0.96-3
+Date: 2015-07-07
 Author: Florian Gerber, Thomas Gsponer
 Depends: gsDesign, lattice, grid,
+Imports: stats, graphics, grDevices, utils
 Maintainer: Florian Gerber <flora.fauna.gerber@gmail.com>
 Description: Group Sequential Operating Characteristics for Clinical,
         Bayesian two-arm Trials with known Sigma and Normal Endpoints.
 License: GPL-3
 LazyLoad: yes
-Packaged: 2013-04-21 15:51:07 UTC; flow
-Repository: CRAN
-Date/Publication: 2013-05-04 16:17:50
 NeedsCompilation: no
+Packaged: 2015-07-08 08:36:50 UTC; flo
+Repository: CRAN
+Date/Publication: 2015-07-08 11:16:27
diff --git a/MD5 b/MD5
@@ -1,11 +1,11 @@
-0dd924a895740842fe7fc8b4f12b28f1 *DESCRIPTION
-e020eb7a5e24a2ea69d651f93c27f87a *NAMESPACE
-67cfe2da8ac40477549eff3afd80d5fd *R/package.r
-e7dea97a21431d703e7ba94be0548e95 *changeLog
-b912c3220abb02462af4d0f01df3bada *man/gsb-internal.Rd
-294ad25fa46b25e41a36e06fd505166c *man/gsb-package.Rd
-60567b16c57399ee4a64154dbd8039d0 *man/gsb.Rd
+20c96793ee3ad2f01c7d138a9eaaa731 *ChangeLog
+3da903d30fa70b0a93ad347bdc79ac9c *DESCRIPTION
+59bc54cdb8022bce7066181d4795f5d7 *NAMESPACE
+c3912ece9e08b821c759c3f2360e8fcd *R/package.r
+7398a8c28d9e9ccafc5f907b41e79f4b *inst/CITATION
+dfea06b08bc691957afa4682f9b8a2da *man/gsb-package.Rd
+7cc5d9b6bca931ccaf0e403b4601d6d8 *man/gsb.Rd
 bd086cbe6586d32ee06d45a4baec457c *man/gsbBayesUpdate.Rd
 6c96bf5f53cb8cb28cf91e7b4bbdd2cd *man/gsbCriteria.Rd
-b23671619e43f4f541deed9864177a4c *man/plot.gsbMainOut.Rd
+fe6cfa11671802033d8ca4467aa8b88d *man/plot.gsbMainOut.Rd
 c80a48e280b144d30a606a1156369308 *man/tab.Rd
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,10 +1,12 @@
-## imports
+import(grid, lattice, gsDesign)
+importFrom(stats, approx, na.omit, predict, qnorm, rnorm, runif)
+importFrom(graphics, barplot, plot)
+importFrom(grDevices, colorRampPalette, dev.off, png)
+importFrom(utils, write.table)
 
-## exports
 export(gsb, gsbDesign, gsbSimulation, tab, gsbBayesUpdate, gsbCriteria)
 
 ## not exported functions (access with ::: operator)
-
 ## integer2numeric
 ## rmvnorm
 ## gsbCgrid
@@ -24,13 +26,10 @@ export(gsb, gsbDesign, gsbSimulation, tab, gsbBayesUpdate, gsbCriteria)
 
 ## S3methods
 S3method(summary,gsbMainOut)
-
 S3method(as.data.frame,gsbCriteria)
-
 S3method(print,gsbDesign)
 S3method(print,gsbSimulation)
 S3method(print,gsbMainOut)
-
 S3method(plot,gsbSimulation)
 S3method(plot,gsbMainOut)
 S3method(plot,gsbDesign)

diff --git a/R/package.r b/R/package.r
@@ -946,7 +946,7 @@ gsbSimArm <- function(design,
     Pfut <- array(data=NA,dim=c(i,length(delta.p)))
 
 
-    # index für warnings
+    # index for warnings
     warning.index <- rep(0,times=ld.p)
 
 

diff --git a/changeLog b/changeLog
@@ -2,6 +2,11 @@
 -- ChangeLog - gsbDesign --
 ---------------------------
 
+2015-07-07 Florian Gerber (version 0.96-3)
+	* minor modifications to pass the CRAN check without notes.
+	* citations updated
+	* no modifications in the code
+
 2013-04-21 Florian Gerber (version 0.96-2)
 	* Bug "wrong stage labels" corrected (comment Heinz).
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,39 @@
+citHeader("To cite `gsbDesign` in publications use:")
+
+citEntry(entry = "Article",
+  title        = "gsbDesign: An R Package for Evaluating the Operating Characteristics of a Group Sequential Bayesian Design",
+  author       = personList(as.person("Florian Gerber"),
+                            as.person("Thomas Gsponer")),
+  journal      = "Journal of Statistical Software, accepted",
+  year         = "2015",
+
+  textVersion  =
+  paste("Florian Gerber, Thomas Gsponer.",
+        "gsbDesign: An R Package for Evaluating the Operating Characteristics of a Group Sequential Bayesian Design.",
+        "Journal of Statistical Software, accepted."),
+)
+
+citEntry(entry = "Article",
+  title        = "A practical guide to Bayesian group sequential designs",
+  author       = personList(as.person("Thomas Gsponer"),
+                            as.person("Florian Gerber"),
+                            as.person("Bjorn Bornkamp"),
+                            as.person("David Ohlssen"),
+                            as.person("Marc Vandemeulebroecke"),
+                            as.person("Heinz Schmidli")),
+  journal      = "Pharmaceutical Statistics",
+  year         = "2014",
+  volume       = "13",
+  number       = "1",
+  pages        = "71--80",
+  url          = "http://dx.doi.org/10.1002/pst.1593",
+  doi          = "10.1002/pst.1593",
+  issn         = "1539-1612",
+
+  textVersion  =
+  paste("Thomas Gsponer, Florian Gerber, Bjorn Bornkamp, David Ohlssen, Marc Vandemeulebroecke, Heinz Schmidli (2014).",
+        "A practical guide to Bayesian group sequential designs.",
+        "Pharmaceutical Statistics, 13(1), 71-80.",
+        "DOI:10.1002/pst.1593"),
+)
+
diff --git a/man/gsb-internal.Rd b/man/gsb-internal.Rd
diff --git a/man/gsb-package.Rd b/man/gsb-package.Rd
@@ -36,15 +36,14 @@ Maintainer: <flora.fauna.gerber at gmail.com>
 }
 \references{
   \itemize{
-    \item Gerber F, Bornkamp B, Ohlssen D, Schmidli H, Gsponer T (2012). 
+    \item Gerber F, Gsponer T (2015). 
     An R Package for evaluating operating characteristics for a group
     sequential Bayesian design.
-    Journal of Statistical Software, submitted.
+    Journal of Statistical Software, accepted.
     \item Gsponer T, Gerber F, Bornkamp B, Ohlssen D, Vandemeulebroecke
-    M, Schmidli H (2012).
-    Bayesian group sequential designs for clinical trials and their
-    operating characteristics.
-    Pharmaceutical Statistics, submitted.
+    M, Schmidli H (2014).
+    A practical guide to Bayesian group sequential designs.
+    Pharmaceutical Statistics, 13(1) 71-80, DOI: 10.1002/pst.1593
     \item Berry SM, Carlin BP, Lee JJ, and Mueller P
     (2010). Bayesian Adaptive Methods for Clinical
     Trials. Chapman&Hall/CRC, London.

diff --git a/man/gsb.Rd b/man/gsb.Rd
@@ -208,15 +208,14 @@ See Gerber et al. (2012) for more details.
 }
 \references{
   \itemize{
-    \item Gerber F, Bornkamp B, Ohlssen D, Schmidli H, Gsponer T (2012). 
+    \item Gerber F, Gsponer T (2015). 
     An R Package for evaluating operating characteristics for a group
     sequential Bayesian design.
-    Journal of Statistical Software, submitted.
+    Journal of Statistical Software, accepted.
     \item Gsponer T, Gerber F, Bornkamp B, Ohlssen D, Vandemeulebroecke
-    M, Schmidli H (2012).
-    Bayesian group sequential designs for clinical trials and their
-    operating characteristics.
-    Pharmaceutical Statistics, submitted.
+    M, Schmidli H (2014).
+    A practical guide to Bayesian group sequential designs.
+    Pharmaceutical Statistics, 13(1) 71-80, DOI: 10.1002/pst.1593
     \item Berry SM, Carlin BP, Lee JJ, and Mueller P
     (2010). Bayesian Adaptive Methods for Clinical
     Trials. Chapman&Hall/CRC, London.

diff --git a/man/plot.gsbMainOut.Rd b/man/plot.gsbMainOut.Rd
@@ -147,7 +147,8 @@ datgraph2 <- datgraph2[order(datgraph2$delta),]
 
 
 ## plots
-p1 <- qplot(delta,value,geom="blank",color=type,facets=.~stage,data=datgraph2, xlab=expression(delta))
+p1 <- qplot(delta,value,geom="blank",color=type,facets=.~stage,data=datgraph2,
+xlab=expression(delta))
 
 p1+geom_line(size=1.5)+scale_color_manual(values = c("cumulative futility" = "dark red",
 "indeterminate" = "orange", "cumulative success" = "dark green"))