20: Add a hex sticker (#24)

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9013
+    rev: v0.4.0
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -13,6 +13,7 @@ repos:
           - knitr
           - testthat
           - Rdpack
+          - etm
           - openpharma/roxytypes
           - openpharma/roxylint
       - id: use-tidy-description
@@ -48,15 +49,19 @@ repos:
       - id: parsable-R
       - id: no-browser-statement
       - id: deps-in-desc
+        exclude: >
+          (?x)^(
+          data-raw/.*
+          )$
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-added-large-files
-        args: ["--maxkb=200"]
+        args: ["--maxkb=1000"]
       - id: end-of-file-fixer
         exclude: '\.Rd'
       - id: trailing-whitespace
@@ -79,6 +84,6 @@ repos:
         files: '\.Rhistory|\.RData|\.Rds|\.rds$'
         # `exclude: <regex>` to allow committing specific files.
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.35.0
+    rev: v0.39.0
     hooks:
       - id: markdownlint

data-raw/create_hex_sticker.R

@@ -0,0 +1,91 @@
+library(hexSticker)
+library(magick)
+library(rsvg)
+library(svglite)
+
+less_than_black <- "gray27"
+very_light_gray <- "gray98"
+out_path <- file.path(getwd(), "man/figures/logo-large")
+out_file <- paste(out_path, "png", sep = ".")
+
+savvyr_plot <- function() {
+  cuminc_exp <- function(t, lambda) {
+    # cumulative incidence functions for exponential distribution
+    # t: time
+    # lambda: vector of rates
+    s <- sum(lambda)
+    res <- matrix(NA, ncol = length(lambda), nrow = length(t))
+    res[, seq_along(lambda)] <- (1 - exp(-s * t)) / s
+    res[t <= 0, seq_along(lambda)] <- 0
+    res <- t(lambda * t(res))
+    rownames(res) <- t
+    colnames(res) <- lambda
+    return(res)
+  }
+
+  ts <- seq(-5, 25, by = 0.01)
+  l1 <- c(1, 1.6) / 10
+  l2 <- c(1.8, 1.2) / 10
+
+
+  # cumulative incidence
+  plot(0, 0,
+    xlim = c(0, 20), ylim = c(0, 1),
+    type = "n", xlab = "time", ylab = "cumulative AE risk",
+    main = "cumulative AE risk",
+    xaxt = "n", yaxt = "n", col.main = less_than_black, col.lab = less_than_black,
+    axes = FALSE, mgp = c(1, 1, 0), bg = very_light_gray
+  )
+  lines(ts, cuminc_exp(ts, l1)[, 1], col = "blue", lwd = 3)
+  lines(ts, cuminc_exp(ts, l2)[, 1], col = "green", lwd = 3)
+  axis(side = 2, at = c(0, 1), las = 1, col = less_than_black, col.axis = less_than_black)
+  axis(side = 1, at = c(0, 20), labels = c(0, NA), las = 1, col = less_than_black, col.axis = less_than_black)
+  text(x = 20, y = 0.53, labels = "control", col = "green", adj = c(1, 0.5), cex = 1)
+  text(x = 20, y = 0.33, labels = "experimental", col = "blue", adj = c(1, 0.5), cex = 1)
+}
+
+savvyr_plot()
+
+tmp <- tempdir()
+savvyr_fig <- file.path(tmp, "savvyr_plot.png")
+png(filename = savvyr_fig, res = 100, width = 400, height = 400, bg = "transparent")
+savvyr_plot()
+dev.off()
+
+plot(magick::image_read(savvyr_fig))
+
+x <- sticker(
+  subplot = savvyr_fig,
+  s_x = 0.9,
+  s_y = 0.95,
+  s_width = 0.8,
+  s_height = 0.8,
+  package = "savvyr",
+  url = "github.com/openpharma/savvyr",
+  u_size = 24,
+  u_color = "blue",
+  p_x = 1.0,
+  p_y = 1.3,
+  p_color = "blue",
+  p_size = 200,
+  p_family = "mono",
+  h_fill = very_light_gray,
+  h_color = less_than_black,
+  h_size = 2,
+  spotlight = FALSE,
+  l_y = 1,
+  l_x = 1,
+  l_width = 3,
+  l_height = 3,
+  l_alpha = 0.3,
+  dpi = 2000,
+  white_around_sticker = TRUE,
+  filename = out_file
+)
+# But therefore we now need to postprocess the image by transforming white
+# to transparent background.
+out_img <- magick::image_read(out_file)
+out_img <- magick::image_transparent(out_img, color = "white")
+magick::image_write(out_img, path = out_file)
+
+usethis::use_logo(out_file)

inst/WORDLIST

@@ -1,30 +1,35 @@
+Aalen
 AdVerse
+AE
+al
 Beyersmann
 BiocCheck
 Bove
 CMD
+et
+Forkers
 funder
+github
+gitleaks
 Hoffmann
+initializer
+Johansen
 Kaplan
+Kaspar
+Kuenzel
+L<U+00FC>bbert
 Pkgdown
 Pre
-Roxygen
-Sabanes
-SuperLinter
-github
-gitleaks
-initializer
 pre
 repo
-Forkers
-AE
-al
-et
-Lübbert
+Roxygen
+Rufibach
+Sabanes
+savvyr
 Schmoor
 Stegherr
+SuperLinter
 Ulm
-Universität
+Universit
+Universit<U+00E4>t
 VarYing
-Aalen
-Johansen