Improve mixed crop detection (remove Dominance) and allow flexible plot aesthetics

[sbuis]

Description

Currently, the detection of intercropping (mixed crops) in CroPlotR relies solely on the Dominance column. Graphical outputs also automatically distinguish intercropping results by both species and crop role (main vs. associated), which can lead to unnecessary complexity in the figures.

There are two points to address:

1. Detection of mixed crops

   • The current approach uses the Dominance column.
   • A more robust method would be to detect mixed crops based on the Plant column, or Plant combined with Genotype when available, by checking for different plants or genotypes simulated on the same date.
   • In such cases, a new column Stand_type could be added to the data frame with values like Mixed or Monovarietal.

2. Graphical representation

   • Currently, intercropping is automatically represented in a predefined way.
   • Users may want to distinguish treatments and intercrops differently (e.g., one with colors, the other with symbols), which is difficult with the current approach.
   • It would be helpful to allow the user to define colors and symbols based on the content (total or partial, e.g., if the situation name contains the treatment name) of one or several columns in sim and obs (e.g., Plant, Genotype, or their combination).

Proposed changes

• Implement mixed crop detection based on Plant (and optionally Genotype) and store the result in a Stand_type column.
• Modify plotting functions to allow users to map aesthetics (color, symbol) from arbitrary columns or combinations of columns, providing flexibility to distinguish treatments and intercrops.
• For intercropping plots, consider simplifying default aesthetics by focusing on species/genotypes and Stand_type rather than main/associated crop roles, while still allowing user customization.