Merge pull request #17 from inbo/plotly

ThierryO · web-flow · commit a7aa52cd9b37 · 2024-06-04T10:19:42.000+02:00
Plotly
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,6 +14,7 @@
 ^data-raw$
 ^docs$
 ^man-roxygen$
+^organisation.yml$
 ^pkgdown$
 appveyor.yml
 tic.R
diff --git a/.zenodo.json b/.zenodo.json
@@ -1,9 +1,9 @@
 {
   "title": "effectclass: Classification and Visualisation of Effects",
-  "version": "0.1.4",
+  "version": "0.1.5",
   "license": "GPL-3.0",
   "upload_type": "software",
-  "description": "<p>Classify effects by comparing the confidence intervals with\nthresholds.<\/p>",
+  "description": "<p>Classify effects by comparing the confidence intervals with thresholds.<\/p>",
   "keywords": [
     "classification",
     "effect size",
@@ -17,11 +17,11 @@
       "name": "Onkelinx, Thierry",
       "affiliation": "Research Institute for Nature and Forest (INBO)",
       "orcid": "0000-0001-8804-4216",
-      "type": "ContactPerson"
+      "type": "contactperson"
     },
     {
       "name": "Research Institute for Nature and Forest (INBO)",
-      "type": "RightsHolder"
+      "type": "rightsholder"
     }
   ],
   "creators": [
diff --git a/CITATION.cff b/CITATION.cff
@@ -24,4 +24,4 @@ abstract: "Classify effects by comparing the confidence intervals with threshold
 identifiers:
 - type: url
   value: https://inbo.github.io/effectclass/
-version: 0.1.4
+version: 0.1.5
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: effectclass
 Title: Classification and Visualisation of Effects
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: c(
     person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -31,4 +31,4 @@ Config/checklist/keywords: classification; effect size; uncertainty;
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# effectclass 0.1.5
+
+* `add_fan()` groups the traces when setting `name`.
+
 # effectclass 0.1.4
 
 * `add_fan()`, `add_classification()`, `reference_shape()` and
diff --git a/R/add_fan.R b/R/add_fan.R
@@ -53,8 +53,11 @@ add_fan <- function(
   if (is.null(text)) {
     text <- ~hoverinfo
   }
+  if (!missing(name)) {
+    dots$legendgroup <- name
+  }
   for (prob in seq(max_prob, 1e-6, by = -step)) {
-    dots$hoverinfo <- ifelse(prob < max_prob, "none", hoverinfo)
+    dots$hoverinfo <- hoverinfo
     dots$x <- x
     dots$text <- text
     dots$ymin <- ~lcl
@@ -64,6 +67,7 @@ add_fan <- function(
     dots$inherit <- TRUE
     dots$line <- list(width = 0)
     dots$fillcolor <- fillcolor
+    dots$color <- I(fillcolor)
     dots$p <- p
     dots$data <- error_ribbon(
       data = data, y = y, sd = sd, prob = prob, link = link
@@ -76,7 +80,8 @@ add_fan <- function(
   p |>
     add_ribbons(
       data = data, x = x, ymin = y, ymax = y, opacity = 1, showlegend = TRUE,
-      line = list(width = 0), fillcolor = fillcolor, name = name
+      line = list(width = 0), fillcolor = fillcolor, name = name,
+      legendgroup = name
     )
 }
 
diff --git a/R/change_breaks.R b/R/change_breaks.R
@@ -2,17 +2,23 @@
 #'
 #' Breaks a set of pretty breaks for changes.
 #' @param n the number of breaks on either side of the reference
+#' @param extra An optional vector of additional breaks.
+#' The function always appends these breaks.
+#' Use this option when you want to force this values to be a part of the
+#' breaks.
 #' @export
 #' @importFrom assertthat assert_that is.count
 #' @importFrom utils head tail
 #' @family utils
-change_breaks <- function(n = 2) {
+change_breaks <- function(n = 2, extra = NULL) {
   assert_that(is.count(n))
   n_default <- n
-  function(x, n = n_default) {
+  extra_default <- extra
+  function(x, n = n_default, extra = extra_default) {
     if (length(x) == 0) {
       return(numeric(0))
     }
+    stopifnot(is.numeric(x))
     abs(x) |>
       max() |>
       exp() -> extreme
@@ -32,11 +38,22 @@ change_breaks <- function(n = 2) {
     rel_position <- log(candidate) / max(log(candidate))
     seq(0, 1, length = n + 1) |>
       outer(rel_position, "-") -> delta
-    selected <- candidate[apply(delta ^ 2, 1, which.min)]
+    selected <- candidate[unique(apply(delta ^ 2, 1, which.min))]
     rev(1 / selected) |>
       head(-1) |>
       c(selected) |>
-      log()
+      log() -> breaks
+    if (is.null(extra)) {
+      return(breaks)
+    }
+    stopifnot(is.numeric(extra))
+    outer(breaks, extra, "-") |>
+      abs() -> delta
+    to_replace <- which(delta < min(diff(breaks)) / 5, arr.ind = TRUE)
+    breaks[to_replace[, "row"]] <- extra[to_replace[, "col"]]
+    c(breaks, extra) |>
+      sort() |>
+      unique()
   }
 }
 
diff --git a/inst/CITATION b/inst/CITATION
@@ -2,12 +2,12 @@ citHeader("To cite `effectclass` in publications please use:")
 # begin checklist entry
 bibentry(
   bibtype = "Manual",
-  title = "effectclass: Classification and Visualisation of Effects. Version 0.1.4",
+  title = "effectclass: Classification and Visualisation of Effects. Version 0.1.5",
   author = c( author = c(person(given = "Thierry", family = "Onkelinx"))),
-  year = 2023,
+  year = 2024,
   url = "https://inbo.github.io/effectclass/",
   abstract = "Classify effects by comparing the confidence intervals with thresholds.",
-  textVersion = "Onkelinx, Thierry (2023) effectclass: Classification and Visualisation of Effects. Version 0.1.4. https://inbo.github.io/effectclass/",
+  textVersion = "Onkelinx, Thierry (2024) effectclass: Classification and Visualisation of Effects. Version 0.1.5. https://inbo.github.io/effectclass/",
   keywords = "classification; effect size; uncertainty; visualisation",
 )
 # end checklist entry
diff --git a/man/change_breaks.Rd b/man/change_breaks.Rd
diff --git a/man/stat_effect.Rd b/man/stat_effect.Rd
diff --git a/man/stat_fan.Rd b/man/stat_fan.Rd
diff --git a/organisation.yml b/organisation.yml
@@ -0,0 +1,13 @@
+community: inbo
+email: info@inbo.be
+github: inbo
+funder: Research Institute for Nature and Forest (INBO)
+rightsholder: Research Institute for Nature and Forest (INBO)
+organisation:
+  inbo.be:
+    affiliation:
+    - Research Institute for Nature and Forest (INBO)
+    - Instituut voor Natuur- en Bosonderzoek (INBO)
+    - Institut de Recherche sur la Nature et les Forêts (INBO)
+    - Institut für Natur- und Waldforschung (INBO)
+    orcid: yes
