how to create and edit a map using gbif data in modestr

Step by step tutorial: How to create and edit a map downloading data from GBIF

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What do you need for this tutorial:

1. ModestR software installed (this

tutorial is done with Modestr V.2 beta) 2. Internet connection 3. A ModestR database (see first step by

step tutorial “How to create a database”) 4. About 20 minutes

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ModestR software can be freely downloaded from http://www.ipez.es/ModestR

We’ll describe how to create a new map downloading data from GBIF, how to

edit it, and how to store it in a ModestR database. Follow the next steps!

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1. Run ModestR MapMaker and select an existing database using the File/Select database menu option.

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Select the database MapMaker will work with. In this example we’ll assume you’re

using the “MyModestRDatabase” created in the step by step tutorial “How to

create a ModestR database”)

2. Let’s suppose you want to download occurrence records from GBIF. Then select File/Import/Samples from online GBIF database

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Other options already exist such as importing occurrence data from a CSV file, from KML files,

shapefiles, etc. All those options are

explained in the ModestR Tutorial

available in the ModestR website.

3. In the dialog box that will appear we will select the species from the database.

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Other options already exist to select which

kind of records to download from GBIF, and to use synonyms. All those options are

explained in the ModestR Tutorial available in the

ModestR website.

Click on the Select from database

button to select the species to be downloaded.

You can also directly type the species

name in the textbox.

4. The taxonomy tree of the database will be displayed. Now you can select the species to be downloaded from GBIF.

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Click on the Enable/Disable

search button to show the search

options. You can also directly

select the species from the tree.

3.Click on the Select button to select the

species and close this dialog box.

2.Select the species “Carcharhinus

acarenatus” in the search results.

5. You can easily search for the species and select it to continue download process.

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1.Type the first letters of the species: “Carcharhinus”

6. Now you are ready to start downloading by clicking on the Accept button.

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Just click on the Accept button.

Selected species name appears on the text

box

7. The first step will download all synonyms of the species found in the GBIF online database. For this example, you just accept to download data for all of them and continue.

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Click on the Continue button to accept

downloading occurrence data

including all synonyms of the species.

This list shows all synonyms of the

species found in the GBIF online database.

You can eventually select which

synonyms to include when downloading occurrence data. By

default, all are included.

8. The next step will query GBIF database how many occurrence records there are for the selected species. It will display this information and ask you to confirm you want to continue downloading.

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Just click on the Accept button to

continue downloading occurrence data from

GBIF.

9. Downloading of occurrence records will be done. Wait a few minutes. When download finished, click on accept and continue.

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10. Select the valid habitats for the species. In this case, it is the Sea habitat. This information will be used by MapMaker to automatically check samples validity.

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Check the Sea habitat and the Accept button

to continue

There are other options to clean imported data. Now we’ll just use the default

settings. But all those options are

explained in the ModestR Tutorial available in the

ModestR website.

By default samples will autochecked. That is, ModestR will automatically check samples validity regarding the habitat.

11. Once imported, MapMaker will display a brief summary of the imported, valid and invalid samples.

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12. You can also save a CSV file with all downloaded data, including GBIF information about data sources, rights and citation information.

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13. Now imported data are shown on the map. By default samples are automatically checked regarding species valid habitats, and displayed using different colors. Let’s zoom on a zone where the species is present.

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1. Select the Zoom tool on the left toolbar

2. Click on one corner of the wanted zone

and drag to the opposite corner to

select the zone.

3. Click with the right button of the mouse

and select Zoom

14. Repeat the last action until you see samples with more precision.

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Zoom on the area several times if

needed.

15. Now we are seeing samples with more precision. Let’s suppose that you have found several samples that are clearly out of the valid habitats of the species and you want to delete them.

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Let’s suppose you want to delete those

samples.

By default, samples are automatically checked regarding species valid habitats, and displayed using different colors.

16. You can simply delete any samples selecting an area in the map and using the Freehand tool to select them and next the Delete samples feature.

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1. Select the Freehand tool

2. Select an area that contains the

samples to be deleted

3. Right-click with the mouse and select Selected

samples and next Delete samples.

Alternatively you can

use the Delete Sample button.

1. Samples have been deleted

17. The selected samples will be deleted from the map. But let’s suppose you made a mistake. Then, you will undo last modifications using the Undo button or the Edit/Undo menu.

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2. Undo last modifications using the Undo button or

the Edit/Undo menu.

1. Samples have been restored

18. Samples will be restored. In fact, you decided that you’d rather relocate the samples in turn of deleting them. To do that, you can use the Edit sample tool.

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2. Select Edit sample tool.

3. Click on the sample to be moved and drag it to its new positon. Then release the mouse button. While you drag the sample you can immediately see, by its color, if it is located in a valid habitat (only if it is an habitat autovalidated samples)

19. The Edit sample tool can also be used to delete a single sample. Just select the sample and press the Delete key.

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1. Select Edit sample tool.

You can also right-click on the sample to be

deleted and select the Delete sample option

in the contextual menu.

2. Select the sample and press the Delete key. The sample is removed.

20. But remember that you can also just let stay the invalid samples in the map if you want. ModestR will store them but will always left them out when doing any map processing or calculation. So you are not obliged to delete them.

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Moreover, ModestR will always recheck samples validity if

there are modifications in the world map used as

reference. If, for example, a new lake is added to the

ModestR world map, all samples will be

automatically rechecked.

21. Another possibility is to manually validate a sample. Let’s suppose that you want to consider that all the samples shown as invalid near Australia are in fact valid. In this case you can validate them manually. ModestR will always consider them as valid regardless of where they are located.

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1. Select the Freehand tool

2. Select an area that contains the

samples to be validated

3. Right-click with the mouse and select Selected

samples and next Manually validate

samples, and finally Only not valid.

22. Now the samples that were invalid have been manually validated. If you zoom on the area, you will see that those samples have a different color that the automatically validated samples.

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Here automatically validated samples

are light green, while manually

validated samples are brown.

Even if less usual, the opposite operation can also be done: you can

manually invalidate samples. Those samples

will be stored in the map, but they will not be took

into account for any calculation or processing.

ModestR will always consider them as valid

regardless of where they are located.

23. To make easier to distinguish them, you can modify samples color and transparency going to Options/Preferences.

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1. Just click on the color rectangles to modify the color of the different types of samples in the

map.

2. By default new settings will be

saved for the next time you run MapMaker.

24. You can also manually add samples if you want. If you use habitat autovalidated samples, you can drag the sample and immediately see if it is located in a valid habitat before placing it in the map.

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1. Select the Add sample tool

3. Click on the position where you want to add a new sample. You can drag the sample and

immediately see, by its color, if it is located in a valid habitat before placing it in the map

(only if you use habitat autovalidated samples).

2. Select the valid habitats. In this case,

just Sea.

25. Once the map edited, you can store it in the database. Just click on the corresponding button!

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Click on the button of the toolbar to save the current

map in the database

You can also go to menu File/Save/To

ModestR Maps Database

The map will be saved in the current working

database, replacing the existing map, if any.

Remember that you can easily change the working

database going to the menu File/Select

database.

It was the Step by step tutorial:

How to create and edit a map downloading data from GBIF

Thank you for your interest.

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You can find this one and other tutorials in PDF in http://www.ipez.es/ModestR (see Documentation section)