Matrix Key

On this page you can set up or edit a 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 multiple identify 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 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 another 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".

Matrices

Available matrices
On this page you see a list of matrices that are currently defined. In order to edit a matrix' name, click "edit name". In order 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".
Acquire state image dimensions

New matrix

Create a 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".

Editing matrix

New character

Editing character

Editing state

Editing matrix: sort characters

Editing matrix: sort states

Adding taxa

Taxon-state links

New state

Management

Nexus import

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 either, 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 [204]