Merge pull request #5 from rwoldford/master

Getting to the release

.travis.yml

@@ -14,13 +14,13 @@ sudo: false
 
 language: r
 before_install:
-  - cd R
   - export DISPLAY=':99.0'
   - Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
+  - R -q -e 'install.packages(c("PairViz","testthat","knitr","rmarkdown"))'
+  - R -q -e 'install.packages("BiocManager"); BiocManager::install(c("graph","RDRToolbox","Rgraphviz"), update = FALSE, ask=FALSE)'
 
 cache: packages
 
 r:
  - release
- - devel
 

DESCRIPTION

@@ -4,28 +4,29 @@ Title: Direct interactive visual exploration in R
 Version: 0.1.0
 Authors@R: c(person(given = "R. Wayne", family = "Oldford",
                     email = "[email protected]", 
-                    role = c("aut", "cre")),
-             person(given = "Adrian", family = "Waddell", 
-                    email = "[email protected]", 
-                    role = c("aut"))
+                    role = c("aut", "cre"))
                     )
-Description: 'diveR' is a set of `loon` related packages (`diver` is another name for `loon`)
+Description: 'diveR' is a set of `loon` related packages 
+     (the great northern `diver` being the  name for the Common `loon` -- Gavia immer).
     The packages work together to provide a more complete Direct manipulation Interactive Visualization Environment
     in `R`.  It is designed for exploratory data analysis, particularly for data having many
     dimensions but also provides the tools for the user to develop experimental interactive
     displays of their own.
     The package exists primarily to gather the related packages together and
     to make it easy to install and load these multiple 'diveR' packages in a single step. 
 License: GPL-2 
-URL: https://github.com/great-northern-diver
-BugReports: https://github.com/great-northern-diver/loon/issues
+URL: https://github.com/great-northern-diver/diver/
+BugReports: https://github.com/great-northern-diver/diver/issues
 Depends: 
     R (>= 3.4)
 Imports: 
     cli (>= 1.1.0),
     crayon (>= 1.3.4),
     rstudioapi (>= 0.10),
     loon (>= 1.2.2),
+    loon.data,
+    ggmulti,
+    loon.ggplot (>= 1.1.0),
     zenplots
 Suggests: 
     knitr,
@@ -35,4 +36,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1

R/attach.R

@@ -1,10 +1,17 @@
 ## Copied from file of the same name in tidyverse and modified for diveR
 
-diveRcore <- c("loon", "zenplots")
+diveRcore <- function() {
+  c("loon", "ggmulti", "loon.ggplot", "zenplots")
+  } #, "loon.tourr")
+
+presentationPackages  <- function() {
+  c("cli", "crayon", "rstudioapi")
+}
 
 core_unloaded <- function() {
-  search <- paste0("package:", diveRcore)
-  diveRcore[!search %in% search()]
+  diveRpkgs <- diveRcore()
+  search <- paste0("package:", diveRpkgs)
+  diveRpkgs[!search %in% search()]
 }
 
 # Attach the package from the same package library it was
@@ -17,6 +24,19 @@ same_library <- function(pkg) {
   )
 }
 
+diveR_message <- function(pkgs = diveRcore()) {
+  l_web_msg <- "To learn more about any diveR package, see l_web()."
+  if (length(pkgs) > 0) {
+    eg_msg <- paste0("\n", "E.g.")
+    pkg_egs <- paste0("\t",
+                      "l_web(package = \"",
+                      pkgs,
+                      "\")",
+                      collapse = "\n")
+    l_web_msg <- paste0(l_web_msg, eg_msg, pkg_egs, "\n")
+  }
+}
+
 diveR_attach <- function() {
   to_load <- core_unloaded()
   if (length(to_load) == 0)
@@ -44,6 +64,8 @@ diveR_attach <- function() {
 
   msg(paste(info, collapse = "\n"), startup = TRUE)
 
+  msg(diveR_message(), startup = TRUE)
+
   suppressPackageStartupMessages(
     lapply(to_load, same_library)
   )

R/diveR_packages.R

@@ -9,14 +9,16 @@ diveR_packages <- function(include_self = TRUE) {
     imports <- strsplit(raw, ",")[[1]]
     parsed <- gsub("^\\s+|\\s+$", "", imports)
     names <- vapply(strsplit(parsed, "\\s+"), "[[", 1, FUN.VALUE = character(1))
-
+    names <- setdiff(names, presentationPackages())
     if (include_self) {
         names <- c(names, "diveR")
     }
 
     names
 }
 
+#
+# all modified from tidyverse
 msg <- function(..., startup = FALSE) {
     if (startup) {
         if (!isTRUE(getOption("diveR.quiet"))) {

R/ns-hooks.R

@@ -1,5 +1,6 @@
 .onAttach <- function(...) {
-  needed <- diveRcore[!is_attached(diveRcore)]
+  diveRpkgs <- diveRcore()
+  needed <- diveRpkgs[!is_attached(diveRpkgs)]
   if (length(needed) == 0)
     return()
 

README.md

@@ -12,7 +12,6 @@ It is designed for exploratory data analysis, particularly for data having many
 
 The package exists primarily to gather the related packages together and to make it easy to install and load these multiple 'diveR' packages in a single step. 
 
-The package manual appears [here](http://great-northern-diver.github.io/diveR/).
-- an introduction to  `loon` is available [here](http://great-northern-diver.github.io/loon/articles/introduction.html).
+An introduction to  `loon` is available [here](http://great-northern-diver.github.io/loon/articles/introduction.html).
 
 

_pkgdown.yml

@@ -9,14 +9,21 @@ navbar:
       menu:
       - text: loon
         href: https://great-northern-diver.github.io/loon/
+      - text: loon.data
+        href: https://great-northern-diver.github.io/loon.data/
+      - text: loon.ggplot
+        href: https://great-northern-diver.github.io/loon.ggplot/
+      - text: ggmulti
+        href: https://great-northern-diver.github.io/ggmulti/
       - text: zenplots
-        href: https://cran.r-project.org/web/packages/zenplots/index.html
-    - text: Other packages
+        href: https://great-northern-diver.github.io/zenplots/
+
+    - text: related packages
       menu:
-      - text: cli
-        href: https://cran.r-project.org/web/packages/cli/index.html
-      - text: crayon
-        href: https://cran.r-project.org/web/packages/crayon/index.html
+      - text: eikosograms
+        href: https://rwoldford.github.io/eikosograms/
+      - text: qqtest
+        href: https://rwoldford.github.io/qqtest/
 
   right:
   - icon: fa-github fa-lg
@@ -29,7 +36,8 @@ destination: docs/
 
 
 reference:
-  - title: Packages
-    desc: Information about packages defining diveR
+
+  - title: DiveR only functions
+    desc: Functions peculiar to diveR package
     contents:
     - diveR_packages