Revision history for Multi-entryKey
Additions:
On this page you can define the ranks that can be part of the key.
Please note that changing this setting will not detach any taxa already attached to an end-point of the key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Please note that changing this setting will not detach any taxa already attached to an end-point of the key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Deletions:
Please note that changing this setting will not detach any taxa that have already been attached to an end-point of the key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Additions:
When the Multi-access key module first opens you have to create a new matrix. When there is more than one matrix in the project you can jump to another one by clicking “select another matrix”.
Deletions:
Additions:
Character groups
Additions:
Start by giving a name for the character in both the “Internal name” and the "English name" field (or any language available in the project). Then choose a “Character type” from the pop-up list. The following types are available:
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or any language available in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (or any language available in the project). After editing click "save".
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or any language available in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (or any language available in the project). After editing click "save".
Deletions:
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or any language active in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (or any language active in the project). After editing click "save".
Additions:
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or any language active in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (or any language active in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (or any language active in the project). After editing click "save".
Deletions:
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (depending on languages available in the project). After editing click "save".
Additions:
Select a taxon which you want to relate to another taxon. After you have selected a taxon a list of other taxa appears. By clicking the + behind a name you can link taxa. This activates the "similar species" icon in the web-interface (front-end).
Deletions:
Additions:
Start by giving a name for the character in both the “Internal name” and the "English name" field (or any language active in the project). Then choose a “Character type” from the pop-up list. The following types are available:
Deletions:
Additions:
To add a state, first select the character where you want to add the new state to, then click “add new for...”
Deletions:
Additions:
On this page you can add taxa to the multi-access 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“.
On this page you can define the ranks that will be part of the key.
The taxa that are of a rank below the red line in the list are available in the key. To change the selection, move the red line up or down by clicking the ↑ and ↓ arrows. To include all ranks, move the line to the top of the list, above the first rank. As at least one rank is required to be included, the line cannot be moved below the lowest rank. When you are satisfied with your selection, click the save-button.
Please note that changing this setting will not detach any taxa that have already been attached to an end-point of the key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
On this page you can define the ranks that will be part of the key.
The taxa that are of a rank below the red line in the list are available in the key. To change the selection, move the red line up or down by clicking the ↑ and ↓ arrows. To include all ranks, move the line to the top of the list, above the first rank. As at least one rank is required to be included, the line cannot be moved below the lowest rank. When you are satisfied with your selection, click the save-button.
Please note that changing this setting will not detach any taxa that have already been attached to an end-point of the key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Deletions:
On this page you can define the ranks that will be part of your key.
The taxa that are of a rank below the red line in the list are available in your key. To change the selection, move the red line up or down by clicking the ↑ and ↓ arrows. To include all ranks, move the line to the top of the list, above the first rank. As at least one rank is required to be included, the line cannot be moved below the lowest rank. When you are satisfied with your selection, click the save-button.
Please note that changing this setting will not detach any taxa that have already been attached to an end-point of your key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Additions:
Instead, you can also use an existing character from one of the other matrices (if present). To do so, select the name from the pop-up list on the bottom of this page and click "use".
Deletions:
Additions:
When the Multi-access module first opens you have to create a new matrix. When there is more than one matrix in the project you can jump to another one by clicking “select another matrix”.
Deletions:
Additions:
Choose a taxon which you want to relate to another taxon. After you have chosen a taxon a list of other taxa appears. By clicking the + behind a name you can link taxa. This activates the "similar species" icon in the web-interface (front-end).
Deletions:
**//From here system administrator-only://**
====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====
Additions:
Available matrices: matrices present in the project
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (depending on languages available in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (depending on languages available in the project). After editing click "save".
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (depending on languages available in the project). After editing click "save".
On this page you can create a new matrix. Enter an Internal name, a Dutch name and English name (depending on languages available in the project). After editing click "save".
Deletions:
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or other languages available in the project). After editing click "save".
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".
Additions:
On this page you can examine taxon-state links in the matrix. To do so select a taxon from the list "select a taxon". You now get a list of all the characters and states which are linked to the selected taxon.
Deletions:
Additions:
• For a media-character: enter the name and upload/attach a media file for to the new state.
On this page you can change the name and data of a state or delete a state. To change the media for a media state you first have to click "delete image" to detach the current media, after that you attach a new media item. When finished click “save and return to matrix” or “save and add another state for “…”.
On this page you can change the order of the characters. Drag and drop to sort, click 'save' to store the new order.
On this page you can change the order of the states. Drag and drop to sort, click 'save' to store the new order.
You also can sort “alphabetically” or “numerically” by clicking these options. Sorted this way the new order is saved automatically.
On this page you can add taxa to your multi-access 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“.
On this page you can change the name and data of a state or delete a state. To change the media for a media state you first have to click "delete image" to detach the current media, after that you attach a new media item. When finished click “save and return to matrix” or “save and add another state for “…”.
On this page you can change the order of the characters. Drag and drop to sort, click 'save' to store the new order.
On this page you can change the order of the states. Drag and drop to sort, click 'save' to store the new order.
You also can sort “alphabetically” or “numerically” by clicking these options. Sorted this way the new order is saved automatically.
On this page you can add taxa to your multi-access 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“.
Deletions:
On this page you can change name and data of a state or delete a state. To change the media for a media state you first have to click "delete image" to detach the current media, after that you attach a new media item. When finished click “save and return to matrix” or “save and add another state for “…”.
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.
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.
On this page you can add taxa to your multi-entry 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“.
Additions:
Start by giving a name for the character in both the “Internal name” and the "English name" field (or whatever language is active in the project). Then choose a “Character type” from the pop-up list. The following types are available:
• text: a textual description.
• media: for states where an image will be attached
• 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 (if present). To do so, select the name from the pop-up list on the bottom of this page and click "use".
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 media character to a range character. And, if you change the type of a media character, its states will no longer be linked to any media files.
• text: a textual description.
• media: for states where an image will be attached
• 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 (if present). To do so, select the name from the pop-up list on the bottom of this page and click "use".
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 media character to a range character. And, if you change the type of a media character, its states will no longer be linked to any media files.
Deletions:
• Text: a textual description.
• Media: for states where an image will be attached
• 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".
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 media character to a range character. And, if you change the type of a media character, its states will no longer be linked to any media files.
Additions:
You define a taxon by linking character states to it. First select a taxon, then a character, then select the state you want to link to the selected taxon. Click “add new” at the bottom of the "taxon states" window (bottom right). The linked states of the selected character and taxon are shown in the "taxon states" window.
To delete a link from a taxon select the state in the "taxon states" window and click “delete selected”.
To delete a link from a taxon select the state in the "taxon states" window and click “delete selected”.
Deletions:
To delete a link from a taxon select the state from the linked states and click “delete selected”.
Additions:
All taxa in the current matrix file are listed. You can add taxa by clicking on “add new taxon” or remove taxa by clicking on “remove selected taxon”.
Deletions:
Additions:
When the Multi-access module first opens you have to create a new matrix. When there is more than one matrix in your project you can jump to another one by clicking “select another matrix”.
Deletions:
To add one or more states to a character, 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”.
====Editing matrix: sort characters====
Drag and drop to sort, click 'save' to store new order.
Additions:
When first using this module you have to create a new matrix. When there is more then one matrix in the project and you want to go to another matrix available in the project click "select another matrix".
When the Multi-access module first opens you first have to create a new matrix. When there is more than one matrix in your project you can jump to another one by clicking “select another matrix”.
To add one or more states to a character, 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”.
You can group some characters, like all the characters dealing with the wings, the eyes, etc. To do so, click "edit character groups", create a new group, drag the characters you want to be part of this group and click save. In the web-interface (front-end) these characters will be grouped.
When the Multi-access module first opens you first have to create a new matrix. When there is more than one matrix in your project you can jump to another one by clicking “select another matrix”.
To add one or more states to a character, 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”.
You can group some characters, like all the characters dealing with the wings, the eyes, etc. To do so, click "edit character groups", create a new group, drag the characters you want to be part of this group and click save. In the web-interface (front-end) these characters will be grouped.
Deletions:
**Before applying for your own site you can experiment with all the available functions of this module in the LNG Sandboxes: http://linnaeus.naturalis.nl/wiki/Sandboxes**
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)”.
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”.
You can group some characters, like all the characters dealing with the wings, the eyes, etc. To do so, click "edit character groups", create a new group, drag the characters you want to be part to this group and click save. In the front-end these characters will be grouped under one blue button with the name of the group stated.
Additions:
When first using this module you have to create a new matrix. When there are more then one matrices in the project and you want to go to another matrix available in the project click "select another matrix".
Deletions:
Additions:
When first using this module you have to create a new matrix. When there are more then one matrices in the project and you want to go to another matrix available in the project click "select an other matrix".
Deletions:
Additions:
======Multi-access key======
A multi-access 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.”
When first using this module you have to create a new matrix. When there are more then one matrices in the project and you want to go to an other matrix available in the project click "select an other matrix".
A multi-access 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.”
When first using this module you have to create a new matrix. When there are more then one matrices in the project and you want to go to an other matrix available in the project click "select an other matrix".
Deletions:
A multi-entry 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.”
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".
Additions:
======Multi-access Key======
Deletions:
Additions:
Available matrices: matrixes already available in the project
Create a new matrix: to create a new matrix
Taxon relations: To activate the "similar species" icon in the front end
Define ranks that can appear in key
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or other languages available in the project). After editing click "save".
====Taxon relations====
Choose a taxon which you want to relate to another taxon. After you have chosen a taxon a list of other taxa appears. By clicking the + behind a name you can link taxa. This activates the "similar species" icon in the front end.
Create a new matrix: to create a new matrix
Taxon relations: To activate the "similar species" icon in the front end
Define ranks that can appear in key
On this page you can edit the Internal name, the Dutch name and the English name of a matrix (or other languages available in the project). After editing click "save".
====Taxon relations====
Choose a taxon which you want to relate to another taxon. After you have chosen a taxon a list of other taxa appears. By clicking the + behind a name you can link taxa. This activates the "similar species" icon in the front end.
Deletions:
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".
Additions:
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 media character to a range character. And, if you change the type of a media character, its states will no longer be linked to any media files.
Deletions:
Additions:
• Media: for states where an image will be attached
Deletions:
Additions:
On this page you can change name and data of a state or delete a state. To change the media for a media state you first have to click "delete image" to detach the current media, after that you attach a new media item. When finished click “save and return to matrix” or “save and add another state for “…”.
Deletions:
Additions:
• For a media-character: enter the name and select a media file to upload/attach to the new state.
Deletions:
Deletions:
====Editing matrix "matrix"====
Additions:
Drag and drop to sort, click 'save' to store new order.
Deletions:
Additions:
You can change the order of the characters by selecting “sort characters”.
You can group some characters by clicking "edit character groups"
You can group some characters by clicking "edit character groups"
Additions:
====Editing matrix "matrix"====
You can group some characters, like all the characters dealing with the wings, the eyes, etc. To do so, click "edit character groups", create a new group, drag the characters you want to be part to this group and click save. In the front-end these characters will be grouped under one blue button with the name of the group stated.
You can group some characters, like all the characters dealing with the wings, the eyes, etc. To do so, click "edit character groups", create a new group, drag the characters you want to be part to this group and click save. In the front-end these characters will be grouped under one blue button with the name of the group stated.
Additions:
====Editing matrix: sort characters====
You can change the order of the characters by selecting “sort characters”
You can change the order of the characters by selecting “sort characters”
Deletions:
Additions:
====Editing matrix: sort characters==== You can change the order of the characters by selecting “sort characters”
Deletions:
Additions:
====sort characters==== You can change the order of the characters by selecting “sort characters”
Deletions:
Additions:
====Editing matrix: sort characters==== You can change the order of the characters by selecting “sort characters”
Deletions:
Additions:
Be aware that the setting you choose here will also apply for the Single-access key.
**//From here system administrator-only://**
**//From here system administrator-only://**
Deletions:
**//From here Sysadmin-only://**
No Differences
Additions:
====Taxon ranks in key====
On this page you can define the ranks that will be part of your key.
The taxa that are of a rank below the red line in the list are available in your key. To change the selection, move the red line up or down by clicking the ↑ and ↓ arrows. To include all ranks, move the line to the top of the list, above the first rank. As at least one rank is required to be included, the line cannot be moved below the lowest rank. When you are satisfied with your selection, click the save-button.
Please note that changing this setting will not detach any taxa that have already been attached to an end-point of your key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Be aware that the setting you choose here will also apply for the single-access key.
On this page you can define the ranks that will be part of your key.
The taxa that are of a rank below the red line in the list are available in your key. To change the selection, move the red line up or down by clicking the ↑ and ↓ arrows. To include all ranks, move the line to the top of the list, above the first rank. As at least one rank is required to be included, the line cannot be moved below the lowest rank. When you are satisfied with your selection, click the save-button.
Please note that changing this setting will not detach any taxa that have already been attached to an end-point of your key. Taxa that have a rank that is no longer part of the selection will remain connected to the key, until you manually detach them.
Be aware that the setting you choose here will also apply for the single-access key.
Additions:
**Before applying for your own site you can experiment with all the available functions of this module in the LNG Sandboxes: http://linnaeus.naturalis.nl/wiki/Sandboxes**
Additions:
**//From here Sysadmin-only://**
Deletions:
No Differences
Additions:
**//From here Sysadmin-only!://**
Deletions:
Additions:
**//From here Sysadmin-only !://**
Deletions:
Additions:
**//From here Sysamin-only!://**
Additions:
====Edit matrix====
Deletions:
Additions:
• 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.
• 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.
Deletions:
• 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.
Additions:
• 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.
• 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.
Deletions:
- 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.
Additions:
On this page you can add taxa to your multi-entry 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“.
Deletions:
Additions:
A multi-entry 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.”
Deletions:
Additions:
======Multi-entry Key======
Deletions:
Deletions:
Additions:
Edit name
Deletions:
Additions:
====Edit name====
Deletions:
Deletions:
Additions:
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.
Deletions:
Additions:
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.
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".
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”.
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:
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.
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.
- For a media-character: enter the name and select a file to upload for 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.
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.
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".
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”.
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:
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.
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.
- For a media-character: enter the name and select a file to upload for 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.
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.
Deletions:
When first using this module you have to create a new matrix. Otherwise the default matrix will be opened. To go to another matrix available in the project click "select another 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 another matrix”.
First of all, give a name tot the character in the “Characteristic name” field. Then choose a “Character type” from the pop-up. The following types of characteristics are available:
Instead, you can also use an existing character from one of your other matrices. To do so, select the name from the pop-up 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 later can change the order of the characters.
On this page you can change 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.
- For a media-character: enter the name and choose a file to upload for 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 later can change the order of the states.
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.
Additions:
When first using this module you have to create a new matrix. Otherwise the default matrix will be opened. To go to another matrix available in the project click "select another 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 another 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 another matrix”.
Deletions:
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.”
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”.
No Differences
No Differences
Additions:
To jump to a matrix already available in the project, click "Available matrices", to create a new matrix, click "Create a new matrix".
Deletions:
Additions:
To create a matrix, click "Create a new matrix", to jump to a matrix already available in the project, click "Available matrices".
Deletions:
To create a matrix, click "Create a new matrix", to jump to a matrix already available in the project, click "Available matrices".
Additions:
When first using this module you have to create a new matrix. Otherwise otherwise the default matrix will be opened. To go to another matrix available in the project click "select another matrix".
Deletions:
Management
Additions:
When first using this module you have to create a new matrix. To jump to a matrix already available in the project, otherwise the default matrix will be opened. To go to another matrix available in the project click "select another matrix".
Management
Management
Additions:
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“.
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.
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.
Additions:
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 “…”.
Additions:
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.”
To create a matrix, click "Create a new matrix", to jump to a matrix already available in the project, click "Available matrices".
First of all, give a name tot the character in the “Characteristic name” field. Then choose a “Character type” from the pop-up. 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 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 later can change the order of the characters.
On this page you can change 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.
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.
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.
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 choose 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 later can change the order of the states.
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.”
To create a matrix, click "Create a new matrix", to jump to a matrix already available in the project, click "Available matrices".
To create a matrix, click "Create a new matrix", to jump to a matrix already available in the project, click "Available matrices".
First of all, give a name tot the character in the “Characteristic name” field. Then choose a “Character type” from the pop-up. 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 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 later can change the order of the characters.
On this page you can change 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.
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.
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.
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 choose 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 later can change the order of the states.
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.”
To create a matrix, click "Create a new matrix", to jump to a matrix already available in the project, click "Available matrices".
No Differences
Deletions:
**Create a new matrix**
No Differences
Additions:
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".
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".
**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
**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".
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.
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".
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".
**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
**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".
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.
No Differences
