Matrix Key

A matrix key is a multiple-entry key based on a matrix of “objects” (species and other taxa) and character states. The matrix defines each object as a series of character states. For example, the definition for an object with green eyes and four legs would contain the state “green” for the character “eyes,” and the state 4 for the character “number of legs.”

This module has been designed to allow for multiple identification files for each taxonomic group. Thus, you could create one matrix file for basic taxonomic descriptions, one for ecological characteristics, and one for morphologic or structural information. Or it could be useful to create one matrix file for characters as seen in preserved specimens, and another for fresh specimens.
You can also create a tree-shaped hierarchy of matrix files – a “master” file with a general key for your group, leading to several other files with more detailed keys of subgroups.

When first using this module you have to create a new matrix. Otherwise the default matrix will be opened. To go to an other matrix available in the project click "select an other matrix".

Editing matrix

When the Matrix module first opens, a new “untitled” file is automatically created. When there is more than one matrix in your project you can jump to another one by clicking “select an other matrix”.
To get a list of matrices that are currently defined click “Get and save state image dimensions (for newly imported matrices)”.

Characters
The characters are shown in the upper left field.
To add one or more characters to the matrix, click “add new”.
To edit or delete a character select the character you want to edit and click “edit/ delete selected”.
To add one or more character states to the matrix, click “add new” in the “states” section. To edit or delete a state select the state you want to edit and click “edit/ delete selected”.
A character’s type is shown between brackets () to the right of its name.
You can change the order of the characters by selecting “sort characters”

States
The states of the selected character are shown in the bottom left field.
To add a state, click on “add new for...”
To edit or delete a state select the state you want to edit and click “edit/ delete selected”.
You can change the order of the states by selecting “sort states”

Taxa
The taxa are shown in the upper right field.
Lists all taxa in the current matrix file. You can add taxa by clicking on “add new taxon” or remove taxa by clicking on “remove selected taxon”.

Links
You define a taxon by linking character states to it. First click in the list of character states (in the top left corner of the window) to select a character, and then click in the list of states (in the bottom left corner) to choose the state that you want to link to the selected taxon. Then click “add new”. The linked states of the selected character and taxon are shown in the bottom right field.
To delete a link from a taxon select the state from the linked states and click “delete selected”.
To see an overview of all character states linked to the selected taxon click "display current links per taxon & other matrices".

New character

Start by giving a name to the character in the “Internal name” field. Then choose a “Character type” from the pop-up list. The following types of characteristics are available:
• text: a textual description.
• media: an image, video or sound file.
• range: a value range, defined by a lowest and a highest value.
• distribution: a value distribution, defined by a mean and values for one and two standard deviations.

Instead, you can also use an existing character from one of your other matrices. To do so, select the name from the pop-up list on the bottom of this page and click "use".

Click “save” before leaving this page. The character is added to the bottom of the list of characters (sorted in entry order). You can later change the order of the characters.

Editing character

On this page you can change the name and the type of a character or delete a character. However, you cannot change the character type of a range character, and you cannot change a “text” or multimedia character to a range character. And, if you change the type of a multimedia character, its states will no longer be linked to any multimedia files.

New state

On this page you can add a new state to a character.

- For a text-character: enter the name and text of the new state.
- For a media-character: enter the name and select a file to upload for the new state.
- For a range-character: enter the name and lower and upper limit (inclusive) of the new state.
- For a distribution-character: enter the name, mean and standard deviation of the new state.

When finished click “save and return to matrix” or “save and add another state for “…”. The new state will now be added to the bottom of the list. You can later change the order of the states.

Editing state

On this page you can change name and data of a state or delete a state. When finished click “save and return to matrix” or “save and add another state for “…”.

Editing matrix: sort characters

On this page you can change the order of the characters. To change the order click on the ↑ and ↓ arrows. The new order is saved automatically.

Editing matrix: sort states

On this page you can change the order of the states. To sort all at once click on “alphabetically” or “numerically”. Sorted this way the new order is saved automatically.
You also can drag and drop to sort, click 'save' to store new order. Sorted this way the new order is NOT saved automatically. Click “save” to save this new order.

Adding taxa

On this page you can add taxa to your matrix key. Select the taxa you want to add from the list "Taxon to add". With shift you can select more than one taxon at a time. After selecting click “save and return to matrix” or “save and add another taxon“.

Taxon-state links

On this page you can examine taxon-state links in the matrix. To do so select a taxon from the list "Choose a taxon". You now get a list of all the characters and states which are linked to the selected taxon.

Management

To jump to a matrix already available in the project, click "Available matrices", to create a new matrix, click "Create a new matrix".

Matrices

On this page you see a list of matrices that are currently defined. To edit a matrix' name, click "edit name". To edit the actual matrix, click its name. To set as default, click "set as default". In the list the default matrix has an * behind its name.

Edit name
On this page you can edit the Internal name, the Dutch name and the English name (or other languages available in the project). After editing click "save".

New matrix

On this page you can create a new matrix. You can enter an Internal name, a Dutch name and the English name (or other languages available in the project). After editing click "save".

Nexus import

This importer allows you to import Nexus-files exported from Linnaeus 2. It has not been tested with Nexus-files from other sources. When exporting from Linnaeus 2, make sure to choose the version with tabs, not the "standard" version.

Import creates a new matrix with the name of the .NEX file minus its extension. You can later change this. The importer does not check whether another matrix with the same name already exists, but simply creates another one when there is.

The importer checks the taxon names in the matrix against the list of taxa already present in the species module of the project. If that fails, it attempts to clean up the taxon name by stripping out any ranks that might be present in the taxon name (for instance reducing "Genus Flickingeria" to "Flickingeria"), as LNG stores all taxa without the rank. While cleaning up, the importer only attempts to remove English names from the taxon names. If the ranks in your file are in another language, you will have to remove the ranks' names manually from the matrix in the file.
If the cleansed name cannot be found, it is assumed that it does not exist in the species module. The user is notified and the taxon, as well as its states, are discarded. The importer does not create new taxa.

The file contains some meta-information on the matrix, which is only partly used:

• DIMENSIONS NTAX=x NCHAR=y: importer checks whether the actual number of taxa and characters match these numbers. If they do not, a warning is generated, but import continues.

• FORMAT MISSING=? GAP=- SYMBOLS= " 0 1 2 3 4";: the importer does not match the actual values against these standards. The use of '?' for missing values is hardcoded in the code, the symbol for GAP has never been encountered (or noticed), the valid values for SYMBOLS are simply ignored.

Multiple states for one combination of taxon and character are specified as "19" (for 0,2 & 3). It is unclear what notation is used when the index becomes larger than 9; the importer will always split the string into single digits.

SDD Import

SDD Import Results

LinnaeusAdminPages

Linnaeus NG Wiki : Multi-entryKey

Revision [348]