Traits¶

Traits are used in KDSmart to record (score) traits for trials and nurseries. Traits are usually phenotypic information, although they are used to score other data too.

It is best to manage these traits from Trial Manager in KDXplore because it serves as a central management point. However, you can also manage traits in KDSmart.

Traits are defined with validation rules to facilitate strict data capture rules to help with preventing recording errors. You can also use these rules to make scoring more efficient by minimising the required keystrokes.

The Traits tab (pictured below) lists all available traits and options for managing traits, including importing and exporting.

What is a Trait?¶

Traits are the quality or characteristic being inspected, measured and recorded for the organism. Within KDSmart, traits have the following attributes 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
Either plot-level or subplot-level.

Measurements for each trait instance in each plot or subplot include the:

Date and time user took the measurement;
GPS coordinates (if this is enabled); and
Value of the measurement.

Examples of traits include the height of a plant (this might be called Plant_Height) or the date 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 that is helpful when the trait name is too long for the screen.
Description	An optional longer explanation of the trait to help with data entry.
Data Type	Constrains permitted values of traits. The types available are: CATEGORICAL; DATE; ELAPSED_DAYS; INTEGER; DECIMAL; TEXT; and CALC. For details, refer to Trait Data Types.
Unit	The unit of the value to enter when scoring (e.g. measurement in millimetres or centimetres).
Validation Rule	A validation rule can protect against misentered data. The nature of the rule is dependent on the selection of a data type.

Note

Unless specified in the CSV, traits loaded to KDSmart from CSV default to the TEXT data type. 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 you can enter.	A text input field with a full keyboard.	No rule is required.
CATEGORICAL	Value is constrained to be one from a list of allowed values. Translations to other languages are supported.	The user selects from a list of allowed values.	Example: CHOICE(BLUE\|YELLOW\|RED) You must provide at least two values in the pipe separated list (such as in the example above). To prevent future problems, you should not use the colon (:) character in any current value.
DATE	Value is a date.	A calendar where you can choose a date.	May be left blank or specified as a 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 needed.	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 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.	Enter data 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 depends on a few 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 be helpful.

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 on 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 button.	Plant height entered by selecting a value range from a list.
Conditions	Trait validation with a minimum of 5 and a 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 subplot (single digit) then Accept button.	Minimum 1 button press per subplot, 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 on the Trial Manager Overview page. You can perform the following actions 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 Tags¶
Step	Action
1.	From the Traits tab, select the Add button and then the Add Trait option to open the Edit Trait Properties window (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

You can also create traits 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 need to be imported into Trial Manager so that other KDSmart devices can use the trait.

Editing Traits¶

Any trait in Trial Manager can also be edited. By default, trait editing is locked to ensure data integrity. In this case the Lock button appears locked. Double+click the button to unlock it if you want to edit traits. See the below information for instructions on editing:

Editing Traits¶
Step	Action
1.	From the Traits panel, ensure that trait editing is not locked. If it is, select the Lock button to unlock editing.
1.	Double+click the 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’s 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¶
Step	Action
1.	From the Traits panel, select one or more traits to be deleted and select the Delete button (as in the above image).
2.	Select the Delete Traits option.
3.	There will be a confirmation dialogue that 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 the deletion of the traits.

Trait Bundle Management¶

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

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¶
Step	Action
1.	Select the 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 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 .
4.	Ensure that all necessary traits have been added, and then select the Save button.

Editing Trait Bundles¶

You can also edit trait bundles to change the bundle name and add or remove traits from the bundle.

Editing Trait Bundles¶
Step	Action
1.	From the Traits panel, select a trait bundle to be edited and then select the 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 Remove button to confirm the edit.
3.	You can also add more traits to the bundle. To add traits, select one or more traits from the Traits From Bundle panel and then the Add To Bundle button to confirm the edit.

Deleting Trait Bundles¶

Trait bundles that aren’t needed are deletable from Trial Manager. Deleting trait bundles is done in the same way as deleting individual traits.

Deleting Trait Bundles¶
Step	Action
1.	From the Traits panel, select a trait bundle to be deleted and select the Delete button (as in the above image).
2.	Select the Delete Trait Bundles option.
3.	There will be a confirmation dialogue which that 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 the deletion of the traits.