Merge pull request #10 from rpahl/dev

Dev

Author: rpahl

.Rbuildignore

@@ -1,6 +1,7 @@
 .git
 .gitignore
 TODO
+.Rprofile
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
@@ -10,7 +11,6 @@ tags
 ^docs$
 ^doc$
 ^README\.Rmd$
-^doc$
 ^Meta$
 
 ^images$

.gitignore

@@ -1,6 +1,7 @@
 .Rproj.user
 .Rhistory
 .RData
+.Rprofile
 *.Rproj
 
 vignettes/*.html

DESCRIPTION

@@ -13,10 +13,10 @@ Imports:
     tcltk2,
     mvtnorm,
     container (>= 1.0.0)
-Suggests: knitr, tinytest, rmarkdown
+Suggests: knitr, tinytest, rmarkdown, ggplot2, gridExtra
 VignetteBuilder: knitr
 License: GPL-3
-URL: https://github.com/rpahl/GroupSeq
+URL: https://rpahl.github.io/GroupSeq/
 BugReports: https://github.com/rpahl/GroupSeq/issues
 NeedsCompilation: no
 Author: Roman Pahl [aut, cre]

NAMESPACE

@@ -1,7 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(seqDesign)
-export(seqProb)
 export(start_gui)
 import(mvtnorm)
 import(tcltk)

NEWS.md

@@ -1,6 +1,7 @@
 # GroupSeq 1.4.0
 
 * Create package site
+* Set new GroupSeq logo in GUI
 
 
 # GroupSeq 1.3.3

R/groupseq.R

@@ -65,13 +65,13 @@ update_changed_parameters <- function()
 
 
 #' @title Start GroupSeq
-#' @description Starts the graphical user interface, optionally the legacy
-#'  version of GroupSeq prior to version 2.
-#' @param legacy `logical` if `TRUE`, starts legacy GroupSeq version < 2.
+#' @description Starts the graphical user interface.
 #' @export
-start_gui <- function(legacy = FALSE)
+start_gui <- function()
 {
+    legacy = TRUE
     init_env(legacy)
+
     if (legacy) {
         guiMode()
     } else {
@@ -85,7 +85,7 @@ start_gui <- function(legacy = FALSE)
 {
     .env <<- container::dict()
 
-    doStart <- getOption("AutostartGroupSeq", default = FALSE)
+    doStart <- getOption("AutostartGroupSeq", default = TRUE)
     if (interactive() && doStart) {
         start_gui()
     } else {

R/gui.R

@@ -23,10 +23,10 @@ gui <- function(root, tabs = c("Test parameters", "Boundaries"))
     # Make sure cleanup takes place also when user closes window via "X" button
     tkwm.protocol(root, "WM_DELETE_WINDOW", onQuit)
     tkwm.title(root, paste0("[New] - GroupSeq"))
-    if (.Platform$OS.type == "windows") {
-        iconfile <- system.file("icons", "gs-logo.ico", package = "GroupSeq")
-        tkwm.iconbitmap(root, iconfile)
-    }
+
+    logofile <- system.file("img", "logo32.gif", package = "GroupSeq")
+    tkimage.create("photo", "::image::logoIcon", file = logofile)
+    tcl("wm", "iconphoto", root, "-default", "::image::logoIcon")
 
     # Menu
     menu <- tkmenu(root)

R/sequential.R

@@ -39,7 +39,7 @@
 #' p <- seqProb(c(2, 1), mean=0)
 #' seqProb(c(2, 1), mean=0, tau=c(.25, 0.5)) == p         # TRUE
 #' seqProb(c(2, 1), mean=0, tau=c(.25, 1)) == p           # FALSE
-#' @export
+#' @noRd
 seqProb <- function(up,
                     lo = rep(-Inf, length(up)),
                     tau = seq_along(up) / length(up),
@@ -148,6 +148,7 @@ seqProb <- function(up,
 #'   provide the total expected sample size.
 #'
 #' @examples
+#' library(GroupSeq)
 #' # 1-stage
 #' # #######
 #' alpha <- 0.05
@@ -184,7 +185,7 @@ seqProb <- function(up,
 #' # Increasing max sample size to 98, yields expected n = 69 and power 87.8%
 #' res <- seqDesign(pocock, mu=.3, n=98)
 #' lapply(unlist(res, recursive=FALSE)[c("n.nkExp", "p.exit")], sum)
-#' @export
+#' @noRd
 seqDesign <- function(crit,
                       mu = 0, sd = 1,
                       tau = seq_along(crit) / length(crit),

R/zzz-groupseq-legacy.R

@@ -6428,6 +6428,10 @@ guiMode <- function()
   pkg.env$taskWindow <- tcltk::tktoplevel()
   taskWindow <- pkg.env$taskWindow
 
+  logofile <- system.file("img", "logo32.gif", package = "GroupSeq")
+  tkimage.create("photo", "::image::logoIcon", file = logofile)
+  tcl("wm", "iconphoto", taskWindow, "-default", "::image::logoIcon")
+
   tkwm.title(taskWindow,"Choose a Task")
   listBoxTasks<-tklistbox(taskWindow,height=4,width=40,selectmode="single",background="white")
   tkgrid(tklabel(taskWindow,text="Select a Task!"))

README.Rmd

@@ -1,17 +1,23 @@
 ---
 output: github_document
+
+bibliography: vignettes/references.bib
+link-citations: yes
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 ```{r, include = FALSE}
+library(knitr)
+
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#",
   prompt = F,
   fig.path = "images/README-",
   tidy = FALSE,
   cache = FALSE,
+  dpi = 300,
   out.width = "100%"
 )
 
@@ -34,19 +40,12 @@ options(width = 100L)
 
 GroupSeq computes probabilities related to group sequential designs for normally
 distributed test statistics. It enables to derive critical boundaries, power,
-drift, and confidence intervals of such designs and supports the alpha
-spending approach by Lan-DeMets.
-
-
-### Installation
-
-```{r, eval = FALSE}
-# Install release version from CRAN
-install.packages("GroupSeq")
+drift, and confidence intervals of such designs, mostly using the
+alpha spending approach of @pmid7973215.
 
-# Install development version from GitHub
-devtools::install_github("rpahl/GroupSeq")
-```
+The main motivation for the development of this package was to make this area
+of statistics freely available for a broad audience, which is one of the
+reasons why all functionality is provided by a graphical user interface.
 
 
 ### Installation
@@ -67,5 +66,40 @@ Load the library to start the graphical user interface.
 library("GroupSeq")
 ```
 
-<img src="man/figures/menu-after-load.png" align="left"/>
+```{r, out.width = "30%", echo = FALSE}
+include_graphics("man/figures/menu-after-load.png")
+```
+
+<br>
+
+To get started see the
+[General Introduction](https://rpahl.github.io/GroupSeq/articles/GroupSeq.html)
+page.
+
+
+### Alternative tools
+
+Since the package was written back in 2005, the
+graphical user interface may appear a bit outdated. Still, it does it's job and
+at least has stood the test of time[$^1$](#refs).
+Luckily in recent years others have started to
+develop R-based tools with graphical user interface and similar (and more)
+statistical functionality:
+
+* [gsDesign](https://CRAN.R-project.org/package=gsDesign) with a free
+    [shiny web interface](https://gsdesign.shinyapps.io/prod/) including tutorials.
+* [rpact](https://CRAN.R-project.org/package=rpact) also with a free
+    [shiny web interface](https://rpact.shinyapps.io/public) and lots of
+    [vignettes](https://www.rpact.com/vignettes).
+
+
+### References {#refs}
+
+<div id="refs"></div>
+
+---
 
+1. The package author is considering to
+work on a second version with more functionality and a revised user interface
+in the near future. Feel free to request new features
+[here](https://github.com/rpahl/GroupSeq/issues).

README.md

@@ -16,18 +16,14 @@
 
 GroupSeq computes probabilities related to group sequential designs for
 normally distributed test statistics. It enables to derive critical
-boundaries, power, drift, and confidence intervals of such designs and
-supports the alpha spending approach by Lan-DeMets.
+boundaries, power, drift, and confidence intervals of such designs,
+mostly using the alpha spending approach of [DeMets and
+Lan](#ref-pmid7973215) ([1994](#ref-pmid7973215)).
 
-### Installation
-
-``` r
-# Install release version from CRAN
-install.packages("GroupSeq")
-
-# Install development version from GitHub
-devtools::install_github("rpahl/GroupSeq")
-```
+The main motivation for the development of this package was to make this
+area of statistics freely available for a broad audience, which is one
+of the reasons why all functionality is provided by a graphical user
+interface.
 
 ### Installation
 
@@ -47,4 +43,46 @@ Load the library to start the graphical user interface.
 library("GroupSeq")
 ```
 
-<img src="man/figures/menu-after-load.png" align="left"/>
+<img src="man/figures/menu-after-load.png" width="30%" />
+
+<br>
+
+To get started see the [General
+Introduction](https://rpahl.github.io/GroupSeq/articles/GroupSeq.html)
+page.
+
+### Alternative tools
+
+Since the package was written back in 2005, the graphical user interface
+may appear a bit outdated. Still, it does it’s job and at least has
+stood the test of time[<sup>1</sup>](#refs). Luckily in recent years
+others have started to develop R-based tools with graphical user
+interface and similar (and more) statistical functionality:
+
+-   [gsDesign](https://CRAN.R-project.org/package=gsDesign) with a free
+    [shiny web interface](https://gsdesign.shinyapps.io/prod/) including
+    tutorials.
+-   [rpact](https://CRAN.R-project.org/package=rpact) also with a free
+    [shiny web interface](https://rpact.shinyapps.io/public) and lots of
+    [vignettes](https://www.rpact.com/vignettes).
+
+### References
+
+<div id="refs" class="references csl-bib-body hanging-indent">
+
+<div id="ref-pmid7973215" class="csl-entry">
+
+DeMets, D. L., and K. K. Lan. 1994. “<span class="nocase">Interim
+analysis: the alpha spending function approach</span>.” *Stat Med* 13
+(13-14): 1341–52. <https://doi.org/10.1002/sim.4780131308>.
+
+</div>
+
+</div>
+
+------------------------------------------------------------------------
+
+1.  The package author is considering to work on a second version with
+    more functionality and a revised user interface in the near future.
+    Feel free to request new features
+    [here](https://github.com/rpahl/GroupSeq/issues).

_pkgdown.yml

@@ -10,6 +10,21 @@ authors:
     href: https://rpahl.github.io/r-some-blog/about.html
 
 
+articles:
+  - title: "Overview"
+    contents:
+    - "understanding-gs-designs"
+    - "GroupSeq"
+    - "task-1-compute-bounds-H0"
+    - "task-2-compute-drift"
+    - "task-3-compute-bounds-H1"
+    - "task-4-compute-CI"
+
+home:
+  links:
+  - text: Visit my R blog
+    href: https://rpahl.github.io/r-some-blog/
+
 navbar:
   title: "GroupSeq"
   left:
@@ -21,7 +36,29 @@ navbar:
       href: reference/index.html
     - text: "Changelog"
       href: news/index.html
-    - text: "All Packages"
+    - text: "Articles"
+      menu:
+        - title: "Overview"
+        - text: "Overview"
+          href: articles/index.html
+        - text: "---"
+        - text: "Understanding group sequential designs"
+          href: articles/understanding-gs-designs.html
+        - text: "Introduction to GroupSeq"
+          href: articles/GroupSeq.html
+        - text: "-1- Compute Bounds"
+          href: articles/task-1-compute-bounds-H0.html
+        - text: "-2- Compute Drift given Power and Bounds"
+          href: articles/task-2-compute-drift.html
+        - text: "-3- Compute Probabilities given Bounds and Drift"
+          href: articles/task-3-compute-bounds-H1.html
+        - text: "-4- Compute Confidence Interval"
+          href: articles/task-4-compute-CI.html
+        - text: "---"
+        - text: "Other"
+        - text: "GroupSeq article in R News 2006"
+          href: "https://www.r-project.org/doc/Rnews/Rnews_2006-2.pdf#page=21"
+    - text: "My Packages"
       menu:
         - text: "container"
           href: https://rpahl.github.io/container/
@@ -36,3 +73,4 @@ navbar:
       href: https://twitter.com/romanpahl
     - icon: fas fa-blog
       href: https://rpahl.github.io/r-some-blog/
+