diff --git a/.travis.yml b/.travis.yml index 8a2c43e..cd7e688 100644 --- a/.travis.yml +++ b/.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 diff --git a/DESCRIPTION b/DESCRIPTION index 54531c2..ec3f08a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,12 +4,10 @@ Title: Direct interactive visual exploration in R Version: 0.1.0 Authors@R: c(person(given = "R. Wayne", family = "Oldford", email = "rwoldford@uwaterloo.ca", - role = c("aut", "cre")), - person(given = "Adrian", family = "Waddell", - email = "adrian@waddell.ch", - 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 @@ -17,8 +15,8 @@ Description: 'diveR' is a set of `loon` related packages (`diver` is another nam 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: @@ -26,6 +24,9 @@ Imports: 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 diff --git a/R/attach.R b/R/attach.R index dc0a96f..2179b9a 100644 --- a/R/attach.R +++ b/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) ) diff --git a/R/diveR_packages.R b/R/diveR_packages.R index cbabd48..e26e123 100644 --- a/R/diveR_packages.R +++ b/R/diveR_packages.R @@ -9,7 +9,7 @@ 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") } @@ -17,6 +17,8 @@ diveR_packages <- function(include_self = TRUE) { names } +# +# all modified from tidyverse msg <- function(..., startup = FALSE) { if (startup) { if (!isTRUE(getOption("diveR.quiet"))) { diff --git a/R/ns-hooks.R b/R/ns-hooks.R index 2edeb8b..6f9b115 100644 --- a/R/ns-hooks.R +++ b/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() diff --git a/README.md b/README.md index a18a6ef..1996a1a 100644 --- a/README.md +++ b/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). diff --git a/_pkgdown.yml b/_pkgdown.yml index f990c0f..59b4c2f 100644 --- a/_pkgdown.yml +++ b/_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 diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..4515514 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,183 @@ + + + + + + + + +Page not found (404) • diveR + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+ + +Content not found. Please use links in the navbar. + +
+ + + +
+ + + + +
+ + + + + + + + diff --git a/docs/apple-touch-icon-120x120.png b/docs/apple-touch-icon-120x120.png new file mode 100644 index 0000000..3c0ca23 Binary files /dev/null and b/docs/apple-touch-icon-120x120.png differ diff --git a/docs/apple-touch-icon-152x152.png b/docs/apple-touch-icon-152x152.png new file mode 100644 index 0000000..41510f2 Binary files /dev/null and b/docs/apple-touch-icon-152x152.png differ diff --git a/docs/apple-touch-icon-180x180.png b/docs/apple-touch-icon-180x180.png new file mode 100644 index 0000000..c39ee7a Binary files /dev/null and b/docs/apple-touch-icon-180x180.png differ diff --git a/docs/apple-touch-icon-60x60.png b/docs/apple-touch-icon-60x60.png new file mode 100644 index 0000000..ac6ca79 Binary files /dev/null and b/docs/apple-touch-icon-60x60.png differ diff --git a/docs/apple-touch-icon-76x76.png b/docs/apple-touch-icon-76x76.png new file mode 100644 index 0000000..f68425e Binary files /dev/null and b/docs/apple-touch-icon-76x76.png differ diff --git a/docs/apple-touch-icon.png b/docs/apple-touch-icon.png new file mode 100644 index 0000000..99cb358 Binary files /dev/null and b/docs/apple-touch-icon.png differ diff --git a/docs/authors.html b/docs/authors.html index 03d9ac6..ef512cd 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -8,21 +8,36 @@ Authors • diveR + + + + + + + + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +45,10 @@ - + - + @@ -47,9 +62,10 @@ + - +
+
@@ -140,10 +153,6 @@

Authors

R. Wayne Oldford. Author, maintainer.

-
  • -

    Adrian Waddell. Author. -

    -
  • @@ -151,19 +160,23 @@

    Authors

    + + + diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $(''); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
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    -
    +

    -diveR +diveR

    ‘diveR’ is a set of loon related packages (diver is another name for loon).

    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.

    -

    The package manual appears here.

    -
      -
    • an introduction to loon is available here.
    • -
    +

    An introduction to loon is available here.

    -
    +
    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.5.1.

    +
    + diff --git a/docs/logo.png b/docs/logo.png index 2fa73d5..7979c60 100644 Binary files a/docs/logo.png and b/docs/logo.png differ diff --git a/docs/news/index.html b/docs/news/index.html index c0020bd..fe820d2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -8,21 +8,36 @@ Changelog • diveR + + + + + + + + - + - - + + + + + + + - + + - + - - + + + @@ -30,10 +45,10 @@ - + - + @@ -47,9 +62,10 @@ + - +
    +
    -
    -

    -diveR 0.1.0

    +
    +

    +diveR 0.1.0

    • just getting started
    - +
    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.5.1.

    +
    + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c03fb08..c01e592 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -17,12 +17,14 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; flex-direction: column; - - padding-top: 60px; } body > .container .row { @@ -69,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -102,37 +108,135 @@ a.anchor { margin-top: -40px; } -/* Static header placement on mobile devices */ -@media (max-width: 767px) { - .navbar-fixed-top { - position: absolute; - } - .navbar { - padding: 0; - } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; } +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} /* Sidebar --------------------------*/ -#sidebar { +#pkgdown-sidebar { margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; } -#sidebar h2 { + +#pkgdown-sidebar h2 { font-size: 1.5em; margin-top: 1em; } -#sidebar h2:first-child { +#pkgdown-sidebar h2:first-child { margin-top: 0; } -#sidebar .list-unstyled li { +#pkgdown-sidebar .list-unstyled li { margin-bottom: 0.5em; } +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { - height: 16px; + font-size: 16px; + color: #A6CE39; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; vertical-align: middle; } @@ -222,6 +326,19 @@ a.sourceLine:hover { visibility: visible; } +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + /* mark.js ----------------------------*/ mark { @@ -234,3 +351,17 @@ mark { .html-widget { margin-bottom: 10px; } + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index eb7e83d..7e7048f 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,18 +2,11 @@ (function($) { $(function() { - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); - }); + $('.navbar-fixed-top').headroom(); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); }); $('[data-toggle="tooltip"]').tooltip(); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4a4f52a..9bc57c7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,6 @@ -pandoc: 1.19.2.1 -pkgdown: 1.3.0 +pandoc: 2.7.3 +pkgdown: 1.5.1 pkgdown_sha: ~ articles: [] +last_built: 2021-05-06T19:58Z diff --git a/docs/reference/diveR_packages.html b/docs/reference/diveR_packages.html index b4b6fdc..1f93e75 100644 --- a/docs/reference/diveR_packages.html +++ b/docs/reference/diveR_packages.html @@ -8,21 +8,36 @@ List all packages in diveR — diveR_packages • diveR + + + + + + + + - + - - + + + + + + + - + + - + - - + + + @@ -30,12 +45,11 @@ - + - - + @@ -49,9 +63,10 @@ + - +
    +
    -

    List all packages in diveR

    -
    diveR_packages(include_self = TRUE)
    - +

    Arguments

    @@ -155,36 +165,36 @@

    Arg

    Include diveR in the list?

    - +

    Examples

    -
    diveR_packages()
    #> [1] "cli" "crayon" "rstudioapi" "loon" "zenplots" -#> [6] "diveR"
    +
    diveR_packages()
    #> [1] "loon" "loon.data" "ggmulti" "loon.ggplot" "zenplots" +#> [6] "diveR"
    - +
    -

    Site built with pkgdown 1.3.0.

    +

    Site built with pkgdown 1.5.1.

    +
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    Reference

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    Packages

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    Information about packages defining diveR

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    DiveR only functions

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    Functions peculiar to diveR package

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    Contents

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