Trial Manager - Traits

Traits are used in KDSmart to record (score) traits for trials and nurseries. Traits are usually phenotypic information although this arbitrary.

It is best to manage these traits from Trial Manager in KDXPlore because it serves as a central point of management, however, traits can also be managed in KDSmart.

Traits can be defined with validation rules to facilitate strict data capture rules to assist in preventing recording errors. These rules can also be utilised to also make scoring more efficient by minimising the required keystrokes.

The Traits Tab (pictured below) provides a list of all available traits and options for management of traits including importing and exporting.


Traits Tab
Traits Tab (select to zoom)


What is a Trait?

Traits are the quality or characteristic being inspected, measured and recorded for the organism. Within KDSmart, traits have the following characteristics and features:

  • User definable;
  • Defined by six different data types;
  • Optionally lockable once scored to prevent accidental change;
  • Importable and exportable;
  • Can be grouped into bundles for easier management; and
  • Are either plot level or sub-plot level.

A measurement is stored for each trait instance in each plot or sub-plot includes the:

  • Date and time when the measurement was taken;
  • GPS coordinates (if this is enabled); and
  • Value of the measurement.

Some examples of traits include the height of a plant (this might be called Plant_Height) or the date that a plot was irrigated (which could be called Irrigated).


Trait Attributes

Each trait contains a set of attributes that define its characteristics. The following table lists the attributes of a trait:

Trait Attributes
Attribute Description
Trait Name Must be unique and short for display in the Scoring Screen where space is limited on smaller devices (i.e. phones).
Alias An alternative trait name, useful when the trait name is too long for the screen.
Description This is an optional longer explanation of the trait to assist in data entry.
Data Type

Constrains permitted values of traits. Types available are:

  • CATEGORICAL,
  • DATE,
  • ELAPSED_DAYS,
  • INTEGER,
  • DECIMAL; or
  • TEXT;

For details refer to Trait Data Types

Unit An arbitrary term for the unit of the trait to assist with what value to enter when scoring (e.g. measurement in millimetres or centimetres).
Validation Rule The validation rule optionally restricts the values being entered. The nature of the rule is dependent upon the selection of a data type.

Note

Unless specified in the CSV, traits loaded to KDSmart from CSV default to the TEXT data type. If the trait already exists and is not yet scored unless they have previously been loaded or defined. Once loaded you may edit the trait definition to define its data type etc.

Trait Data Types

The following table describes the available data types for traits:

Trait Data Types
Data Type Description Data Entry Style Example Validation Rule
TEXT No constraint on what may be entered. A text input field with a full keyboard. No rule required.
CATEGORICAL Value is constrained to be one from a list of allowed values.
Translations to other languages are supported.
A list of the allowed values is presented and the user touches the value desired. Example:
CHOICE(BLUE|YELLOW|RED)
There must be at least two values provided in the pipe separated list (such as in the example above).
In a later release, the format will support providing a description for each value. This will likely be of the form
value:description
To prevent future problems you should not use the colon (:) character in any current value.
DATE Value is a date. A calendar is presented from which to choose a date. May be left blank or specified as date.
ELAPSED_DAYS Value is the number of days since the trial’s planting date.
The range in the calendar is constrained by the start date and an optional upper limit.
KDSmart stores the values as a date but presents the value as a number when required.
A list of days around the current date are presented and the user selects the desired value or chooses ‘Other’ to use a calendar to pick a date outside this range.
The choices in the list (-3d, -2d, -1d, Today, +1d, +2d, +3d) may be presented in different languages depending on locale support.
May be left blank or specified as
elapsed_days.
To enforce a maximum value, use:
elapsed_days_max=NNN.
INTEGER Integer numeric values in a range specified.
The range is specified as a lower and upper bound and whether or not the bounds are included in the range.
If the number of values is ‘small’ then the entry is similar to the categorical data type. Otherwise, a numeric keypad is presented (excluding a decimal point key).
The changeover from categorical style to numeric keypad may be altered in the Settings Screen.
For Example: RERANGE(1..5) presents as a list of choices: 1,2,3,4 but RANGE(1..500) presents a keypad.
Specify the range of values as:
RANGE(min..max)
or use LERANGE, RERANGE, BERANGE to exclude the left, right or both limits respectively.

Example: RERANGE(-1..5)
means the accepted values are
-1, 0, 1, 2, 3, 4

Note: If you use a custom keyboard, this may affect the appearance of the numeric keypad.
DECIMAL Specify a lower and upper bound and whether or not the bounds are included in the range and the number of digits of precision that will be recorded. Entry is done using a numeric keypad that includes the decimal point.
NOTE: If you use a custom keyboard, this may affect the appearance of the numeric keypad.
RANGE(min..max)
or use LERANGE, RERANGE, BERANGE
However, min and max must now contain a decimal point and at least one digit following the point.
So: BERANGE(1.0..2.99)
means accept values for x where 1.00 < x < 2.99
(the greater number of digits after the “.” for min/max is the “precision” desired).
CALC Calculated or Derived Trait.

See Calculated or Derived Traits below for further description.
Data entry is not permitted for this type.

Traits with this data type cannot be scored during data collection.
A simple calculated or derived trait is:
CALC( max(PH_CM/5,1) )
This calculation references a trait named PH_CM, dividing the value by 5 and returning the maximum of the division or 1, whichever is the greater. So a value of 17 for PH_CM gives a result of 3.
Alternatively,
CALC( max(PH_CM/5,1) , 1 )
will retain the result with one decimal place.
In this case the value of 17 for PH_CM results in 3.4.


Calculated or Derived Traits

The validation rule has either one or two components (with a comma separating them if required):

  • The first component provides a formula that may reference other traits (by the trait name), using the operators and functions listed below.
  • If present, the second component indicates the number of decimal digits to retain in the computed result.

The functions available are in a table below. Arithmetic operators are:

* / % (the last is the modulo operation)
+ - (unary minus is also supported)
^ ** (for exponentiation).

Note

The comparison operators: < <= = != > >= and the logical operators: && || evaluate to either 1 or 0 representing true or false respectively. This is relevant for the if(cond,a,b) function.


Functions Available For CALC Data Type

The following table describes the functions available for the CALC data type.

Functions Available For CALC Data Type
Function Name(s) Description Example
sin cos tan asin acos atan Trigonometric functions  
sinh cosh tanh Hyperbolic functions  
abs round floor ceil sqrt exp ln log sign Unary mathematical functions:
ROUND, FLOOR and CEIL return an integral portion of the input.
LN is the natural logarithm
LOG is the logarithm to base 10
round(1.5) returns 2.0
round(1.4) returns 1.0
floor(1.5) returns 1.0
ceil(1.5) returns 2.0
pow min max Binary mathematical functions pow(2,3) returns 8.0
pow(3,2) returns 9.0
rnd deg(radians) rad(degrees) Other functions:
rnd(a) returns the value of a multiplied by a random number satisfying the constraint RERANGE(0..1.0) i.e. a value x where: 0.0 <= x < 1.0
deg and rad convert between degrees and radians.
rnd(10) will return a value y satisfying:
0 <= y < 10
if(expr , a , b) Conditional expression:
If the value of expr is 1, the result is the expression a otherwise the result is expression b
if(PH_CM <= 5 , 1 , 2)
evaluates to 1 if the value of the trait PH_CM is 5 or less otherwise to 2

Tip

Why can’t I import my CALC trait?!

  • Ensure validation rules using comma’s (e.g. CALC( max(PH_CM/5,1) , 1 )) are wrapped by double quotes (e.g. “CALC( max(PH_CM/5,1) , 1 )”). Excel handles this automatically.
  • Ensure the number of opening and closing brackets match (It’s an easy thing to miss at a glance).
  • Trait names that use white spaces in their names cannot be used for derived CALC traits.


Categorical Traits

At times during scoring, the precision level required can vary. This may be dictated by a number of factors, e.g. sheer volume of specimens, time frame for data collection, reduced/limited people to perform the scoring, etc. In these instances, the Categorical Data Type may prove useful.

Typically Categorical is used for constraining the data entered to a predefined list of values, such as the following definitions:

  • CHOICE(BLUE | YELLOW | RED); and
  • CHOICE(White | Yellow | Purple | Variegated | Brown | Orange yellow | Mottled | White top | Red | Sun red | Blue | Other).

A categorical other trait is one where an other field can be used as a text field.

Note

In these examples, the pipe character ‘|’ is shown with a space character either side to improve legibility.


Using Categorical Traits

In some situations using a categorical data type may be more beneficial as this facilitates the use of selection ranges instead of data entry.

The following table illustrates the collection of plant height using both methods:

Comparison Scoring Integer VS Categorical Trait Type - Required Precision 5cm
  Trait Defined as Integer Trait Defined as Categorical
Entry Method Plant height entered by selecting a value buttons.
Plant height entered by selecting a value range from a list.
Conditions Trait validation with a minimum of 5 and maximum of 50 Trait validation with six ranges defined (e.g. The unit of measure may be 5 centimetres).
Validation Rule 5 <= x <= 50 CHOICE(5-10 | 10-15 | 15-20 | 20-25 | 25-30 | 30++).
Key Presses Minimum 2 button press per sub-plot (single digit) then Accept Button. Minimum 1 button press per sub-plot, unless a long condition list requires scrolling.

Note

For a categorical trait, the number of choices may be limited to suit the circumstances of the trial stage.


Trait Management

Traits in Trial Manager are managed from the Traits Tab which is outlined in the Trial Manager - Overview page. The following actions can be performed in the Traits Tab.

  • Create new traits;
  • Edit traits;
  • Delete traits;
  • Bundle traits;
  • Import traits from a CSV file; and
  • Export selected traits to a CSV file.


Creating Traits

Traits can either be created in Trial Manager or imported. Follow the instructions below to create a new trait.


Creating Traits
Creating Traits (select to zoom)


Creating Tags
Step Action
1. From the Traits Tab, select the add_btn Add Button and then the Add Trait option to open the Edit Trait Properties Window (as pictured in the above image).
2. Enter all trait attributes for the new trait including its name, datatype, and validation rules. The above example demonstrates creating a trait called Plant_height that is measured in centimetres. See the Trait Attributes section above for more information.
3. Use the checkboxes in the Add Trait to Bundle Panel to add the new trait to any existing trait bundles. All new traits will automatically be added to the All Traits bundle.
4. Select the Save Button to save the new trait.

Note

Traits can also be created in KDSmart so it is not always necessary to organise traits before exporting trials to be scored. However, a trait created on a KDSmart device will then need to be imported into Trial Manager so that other KDSmart devices can utilise the trait.


Editing Traits

Any trait in Trial Manager can also be edited. By default, trait editing is locked to ensure data integrity. Trait editing is locked if the lock_btn Lock Button appears locked. Double+click the button See the below information for instruction on editing traits:


Editing Traits
Editing Traits (select to zoom)


Editing Traits
Step Action
1. From the Traits Panel, ensure that trait editing is not locked. If it is, select the lock_btn Lock Button and to unlock editing.
1. Double+click a trait to be edited. This will open the Edit Trait Properties Window.
2. The Edit Trait Properties Window will be the same as when creating a trait except the trait name will be disabled as it is not possible to change a trait name. Any other trait attributes can be edited.
3. After editing all required fields, select the Save Button. The trait will now be updated.

Note

Be careful with editing traits that are currently being used to score trials.


Deleting Traits

Traits that are not needed can be deleted. One or more traits can also be deleted at once. See the instructions below for more information:


Deleting Traits
Deleting Traits (select to zoom)


Deleting Traits
Step Action
1. From the Traits Panel, select one or more traits to be deleted and select the delete_btn Delete Button (as in the above image).
2. Select the Delete Traits option.
3. There will be a confirmation dialogue which will ask for confirmation to delete the selected trait/s Either select the Yes Button to confirm the deletion or the No Button to cancel deletion of the traits.


Trait Bundle Management

Traits can be grouped into bundles to assist with management. Trait bundles can be created in Trial Manager and imported/exported from other devices as well. There will always be a bundle that is automatically created called All Traits. The image of the Traits Panel below contains trait bundles such as Grapes and Plant dimensions.


Trait Bundle Example
Trait Bundle Example (select to zoom)


See the sections below for trait bundle management.


Creating Trait Bundles

The steps below are an example of how to create a new trait bundle:


Creating Trait Bundles
Creating Trait Bundles (select to zoom)


Creating Trait Bundles
Step Action
1. Select the add_btn Add Button from the Traits Panel and choose the Add Trait Bundle option to open the Add/Edit Trait Bundle Window as pictured above.
2. To add a trait to the new bundle, either double-click a trait or select it with a single-click then select the arrow_right_btn Add To Bundle Button. Click+drag, shift+click, or ctrl+click to select multiple traits.
3. Enter a name for the bundle in the field at circle1.
4. Ensure that all necessary traits have been added and then select the Save Button.


Editing Trait Bundles

Trait bundles can also be edited to change the bundle name and add or remove traits from the bundle.


Editing Trait Bundles
Editing Trait Bundles (select to zoom)


Editing Trait Bundles
Step Action
1. From the Traits Panel, select a trait bundle to be edited and then select the edit_btn Edit Button. This will open the Add/Edit Trait Bundle Window
2. To remove traits from a bundle, select one or more traits from the bundle (listed in the Traits In Bundle Panel) to be deleted and select the backspace_btn Remove Button to confirm the edit.
3. More traits can also be added to the bundle. To add traits, select one or more traits from the Traits From Bundle Panel and then the arrow_right_btn Add To Bundle Button to confirm the edit.


Deleting Trait Bundles

Trait bundles that are not needed can be deleted from Trial Manager in a similar way to deleting individual traits.


Deleting Trait Bundles
Deleting Trait Bundles (select to zoom)


Deleting Trait Bundles
Step Action
1. From the Traits Panel, select a trait bundle to be deleted and select the delete_btn Delete Button (as in the above image).
2. Select the Delete Trait Bundles option.
3. There will be a confirmation dialogue which will ask for confirmation to delete the selected trait/s Either select the Yes Button to confirm the deletion or the No Button to cancel deletion of the traits.