From e4b64475865d885639ef0b049705b2576ed7c3a6 Mon Sep 17 00:00:00 2001
From: sbuis <samuel.buis@inra.fr>
Date: Thu, 26 Feb 2026 11:06:47 +0100
Subject: [PATCH 1/2] feat(dominance): compute Dominance levels from input data
 instead of hard coded

- Levels of the 'Dominance' column are now derived from the input data frames `sim` and `obs`.
- If 'Dominance' is absent or contains NA values, these are replaced by the hard-coded value "Single Crop".
---
 R/cropr_formatting.R   | 6 +++---
 R/generic_formatting.R | 6 ++++--
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/cropr_formatting.R b/R/cropr_formatting.R
index 3ac9493..9a383fd 100644
--- a/R/cropr_formatting.R
+++ b/R/cropr_formatting.R
@@ -104,7 +104,7 @@ format_cropr <- function(sim, obs = NULL, obs_sd = NULL,
   if (is_mixture_sim) {
     sim$Dominance <- factor(
       sim$Dominance,
-      levels = c("Principal", "Associated")
+      levels = unique(sim$Dominance)
     )
   }
 
@@ -174,11 +174,11 @@ format_cropr <- function(sim, obs = NULL, obs_sd = NULL,
       }
     } else {
       obs$Dominance <- factor(obs$Dominance,
-        levels = c("Principal", "Associated")
+        levels = unique(obs$Dominance)
       )
       if (is_obs_sd) {
         obs_sd$Dominance <- factor(obs_sd$Dominance,
-          levels = c("Principal", "Associated")
+          levels = unique(obs_sd$Dominance)
         )
       }
     }
diff --git a/R/generic_formatting.R b/R/generic_formatting.R
index 7b5b1ee..2f9c7c1 100644
--- a/R/generic_formatting.R
+++ b/R/generic_formatting.R
@@ -37,8 +37,10 @@ generic_formatting <- function(
   # Replace NAs with "Single-crop" in Dominance in order to make
   # the legend understandable
   if ("Dominance" %in% colnames(df)) {
-    levels(df$Dominance) <- c("Principal", "Associated", "Single crop")
-    df$Dominance[which(is.na(df$Dominance))] <- "Single crop"
+    if ((!"Single crop" %in% levels(df$Dominance)) & any(is.na(df$Dominance))) {
+      levels(df$Dominance) <- c(levels(df$Dominance), "Single crop")
+      df$Dominance[is.na(df$Dominance)] <- "Single crop"
+    }
   }
 
   # Add group_var column to data frame if overlap != null

From 228e8533ef9a1b3fa16d02f23c38522ab91271fb Mon Sep 17 00:00:00 2001
From: sbuis <samuel.buis@inra.fr>
Date: Thu, 26 Feb 2026 13:35:55 +0100
Subject: [PATCH 2/2] fix: preserve factor levels when converting Dominance
 columns

Add conditional checks in `format_cropr` so `sim$Dominance`, `obs$Dominance`, and `obs_sd$Dominance` are only converted to factors if not already. This ensures existing factor levels and their order are preserved, preventing unnecessary warnings and unintended changes.
---
 R/cropr_formatting.R | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/R/cropr_formatting.R b/R/cropr_formatting.R
index 9a383fd..aaa3025 100644
--- a/R/cropr_formatting.R
+++ b/R/cropr_formatting.R
@@ -102,10 +102,12 @@ format_cropr <- function(sim, obs = NULL, obs_sd = NULL,
 
   # Treating Dominance as a factor if any (for plotting reasons):
   if (is_mixture_sim) {
-    sim$Dominance <- factor(
-      sim$Dominance,
-      levels = unique(sim$Dominance)
-    )
+    if (!is.factor(sim$Dominance)) {
+      sim$Dominance <- factor(
+        sim$Dominance,
+        levels = unique(sim$Dominance)
+      )
+    }
   }
 
   # Check variable names:
@@ -173,10 +175,12 @@ format_cropr <- function(sim, obs = NULL, obs_sd = NULL,
         obs_sd <- dplyr::full_join(obs_sd, corresp_table, by = "Plant")
       }
     } else {
-      obs$Dominance <- factor(obs$Dominance,
-        levels = unique(obs$Dominance)
-      )
-      if (is_obs_sd) {
+      if (!is.factor(obs$Dominance)) {
+        obs$Dominance <- factor(obs$Dominance,
+          levels = unique(obs$Dominance)
+        )
+      }
+      if (is_obs_sd & !is.factor(obs_sd$Dominance)) {
         obs_sd$Dominance <- factor(obs_sd$Dominance,
           levels = unique(obs_sd$Dominance)
         )