moves stuff to supplements

deps.R

@@ -3,6 +3,7 @@
 # =============================================================================
 # This file contains necessary variables that will be used in the whole process
 # and all necessary library imports.
+# See the configuration section for theming, debug mode and so on.
 # =============================================================================
 
 # ---- Helper functions -------------------------------------------------------
@@ -64,7 +65,7 @@ if (length(missing)) {
 install_if_missing(pkgs)
 invisible(lapply(pkgs, library, character.only = TRUE))
 
-# ---- GitHub packages --------------------------------------------------------
+# ---- GitHub packages ---------------------------------------------------
 
 # Serosurvey
 install_github_if_missing("serosurvey", "avallecam/serosurvey")
@@ -74,6 +75,49 @@ library(serosurvey)
 install_github_if_missing("ggthemr", "Mikata-Project/ggthemr")
 library(ggthemr)
 
+# =============================================================================
+# Configuration
+# =============================================================================
+
+# ---- Output format ----------------------------------------------------------
+# it is important to set the correct pandoc/quarto output format as knitr tables don't work in docx.
+# possible formats:
+# - docx
+# - pdf/tex
+
+# Read OUTPUT_FORMAT from env; default to "pdf/tex"
+output_format <- Sys.getenv("OUTPUT_FORMAT", "pdf/tex")
+# Background: some tables needs special treatment for docx rendering.
+
+# ---- Debug Mode -------------------------------------------------------------
+debug_mode <- TRUE
+if (isTRUE(debug_mode)) debug_info <- list()
+
+# ---- Theme & Colors ---------------------------------------------------------
+# Theme
+ggthemr('fresh')
+
+# consitent colors for open science practices among plots
+osp_cols <- c(
+  "Preregistration" = "#ee5927",
+  "Open Data" = "#321c3d",
+  "Open Materials" = "#005c5c",
+  "Open Access" = "#bf1869",
+  "Statistical Inference" = "#f2a900"
+)
+
+name_mapping <- c(
+  "Preregistration" = "is_prereg",
+  "Open Data" = "is_open_data", 
+  "Open Materials" = "is_open_materials",
+  "Open Access" = "is_open_access",
+  "Statistical Inference" = "is_statistical_inference"
+)
+
+# map names & colors
+osp_cols2 <- osp_cols
+names(osp_cols2) <- name_mapping[names(osp_cols)]
+
 # =============================================================================
 # DIRECTORY PATHS
 # =============================================================================