.. KDXplore Trial and Nursery Design

.. include:: imagerefs.txt

=======================
Trial Design - Overview
=======================



.. Note:: This Module Is In Alpha. There is significant work underway on the Trial Design module. Check back here or contact us at kdxplore@diversityarrays.com for more information. 


Aims
====

The KDXplore **Trial Design Plug-in** assists users with designing the physical layout and placement of germplasm within a field or nursery.

It was specifically designed to cater for multiplicity between site, trial and trial replicates.

The outcome of using **Trial Design** will be the creation of designs that encompass multiple experiments, with multiple replicates and each or all of which can be at multiple locations.


Advantages
==========

.. KEY POINT: is that we understand the multiplicity between Site *-* Experiment -* Replicate

Trial/Nursery Design functionality within KDXplore has the following main design features:

- An easy to use single interface for the placement of multiple experiments, with N replicates at multiple, different Sites
- Agnostic to Organism type
- Germplasm lists can be imported and combined from file or KDDart. They can then be edited allowing better visibility and control over what will be planted in what experiments
- The Trial Design module in KDXplore offers two ways of designing your trial;
  1. Algorithmic Driven design or
  2. Manual design
- Algorithmic driven design, allows the user to select from range of experimental design methods (Randomised Complete Block, Latin Square etc.) and process the design with one click, using the provided list of germplasm
- Algorithms presented are of a plugin format, easily replicated and the list presented by KDXplore is designed to be appended or edited by users
- Manual design allows the user to have more control over a field, built for breeders and scientists that have non-generic layouts designs in mind or are unable to apply a standard algorithmic design.
- Can be used to allocate plots around field obstructions according to the users wishes.
- Customisable placememt of spatial variation checks.
- Overlays for easy visualisation of Trial components, e.g. the different replicates
- Customisable randomisation option.
- Easily user extendable plot types allowing easy distinction between what is planted (Field Variation Check, Genetic check, Filler plot, Do-not-plant etc.)


.. figure:: images/TrialDesign1.png
   :scale: 50 %
   :alt: Algorithmic Driven Design

   Algorithmic Driven Design

.. figure:: images/TrialDesign2.png
   :scale: 50 %
   :alt: Manual Control Design

   Manual Control Design

.. figure:: images/TrialDesign3.png
   :scale: 50 %
   :alt: Building the Field Layout

   Building the Field Layout


General Workflow
================

Manual Design
-------------



.. list-table:: Manual Design
   :widths: 1 60
   :header-rows: 1
   :stub-columns: 1

   * - Step
     - Description
   * - 1.
     - Defining Trial Size layout parameters (e.g. plot length, Alley length...) so calculate available plots inside of available fields.
   * - 2.
     - Importing from file and KDDart germplasm lists and defining them as individual experiments.
   * - 3.
     - Selecting the number of replicates for each experiment. |br| For the selected Sites or all at once (Fields where the experiments will be placed):
   * - 4.
     - Place spatial variation checks (optional).
   * - 5.
     - Customise block options.
   * - 6.
     - Customise randomisation options.
   * - 7.
     - Place filler or do-not-plant plots (optional).
   * - 8.
     - Allocate germplasm with single click according to parameters.
   * - 9.
     - Edit the resultant Trial layout (optional).
   * - 10.
     - Save the Trial and export to CSV for planting.


Algorithmic Driven Design
-------------------------


.. list-table:: Algorithmic Driven Design
   :widths: 1 60
   :header-rows: 1
   :stub-columns: 1

   * - Step
     - Description
   * - 1.
     - Importing from file and KDDart germplasm lists and defining them as individual experiments.
   * - 2.
     - Select algorithm from list in KDXplore, potentially reading the also availabel documentation (in KDXplore).
   * - 3.
     - Install any depencies (instructions given through KDXplore - only if using for the first time)
   * - 4.
     - Enter parameters for the algortihm.
   * - 5.
     - Save the resultant layout or export to CSV for planting.