iNaturalist Species Mapping

iNaturalist data, Google Tile Set, and QGIS mapping of Asimina species observations of the viewed part of the United States.

4/23/2018 Been a while since a post, here is a good one for mapping.

iNaturalist is a site, a movement to map the organisms of the world. I think through an app on smart phones, you can take pictures and record GPS coordinates, then upload what you find to the web. Others review your post and can help identify what you found. Then people can see what and where you found the organism.

So for example, if you want to see all the locations of zebras, species Equus zebra, you can search and it will give you a map. This is an screen shot part of the iNaturalist site looking at Equus zebra.

Map generated through iNaturalist for Equus zebra. iNaturalist.org web application at http://www.inaturalist.org. Accessed 23 April 2018. https://www.inaturalist.org/taxa/43330-Equus-zebra.

This can be done for all kinds of organisms, animals, plants, etc. I think this is very neat. Even neater than an anteater is you can download the data! That is right you can download the points of any species and map them!

Since I am all about plants, I will focus on the Paw-Paw, Asimina species. No I am not talking about the 1985-1986 cartoon with native American bears fighting off the Dark Paw, I am talking about a plant. There are a few species of Paw-Paw. People eat the fruit of the most widespread species, Asimina triloba. But let us practice with an example:

Go to https://www.gbif.org/occurrence/search.
 On the left side, begin to open the taxonomic tree by clicking:
Scientific Name
Plantae
Tracheophyta
Magnoliopsida
Magnoliales
Annona
Asimina
Then you can click the number of observation beside the text "Asimina." yesterday it was 4,513. Today it is 4,530. So more observations are being added all the time, even for this plant.

Example from gbif.org part of the iNaturalist stuff showing observations for Asimina, Paw-Paw.

To get the data, I had to have a registered account with the website. Then I navigated back to the asimina page.
From here I clicked download.
Click the button for the download of the csv file. Click Understood.
Then I waited for an email. A minute or two, I received the email. I clicked the link provided in the email for the download of the data and saved it.
The saved file was a zip file, I just right clicked and unzipped it.

I then opened Excel. In Excel I clicked the "Data" tab. Then I clicked the "From Text" option. I navigated to the unzipped file and selected the csv file. Within the "Text Import Wizard" for file origin I selected Unicode (UTF-9). I clicked next, next, finish. This imported the information into the Excel spreadsheet. I then saved the file as a .csv (comma deliminated). I closed Excel.

I opened QGIS:
From the top, I selected "Layer."
Then I clicked "Add Layer"
Then "Add Deliminated Text Layer."
I browsed to the csv file I had just saved from Excel and doubled clicked it. The QGIS program loaded the information and auto filled the X and Y fields. The Encoding was automatically selected to UTF-8. I then clicked the button to Add the layer. This added points, the location of Asimina plants.

Within the QGIS Brower, I selected the XYZ Tiles option, then doubled clicked Google. I discussed setting this up in a previous post. The instruction listed again:
1.Within the "Browser" section, scroll down to "XYZ Tiles."
2.Right click "XYZ Tiles" and select new connection.
3.In the pop-up window, for Name you can type Google. in the URL enter: http://www.google.cn/maps/vt?lyrs=s@189&gl=cn&x={x}&y={y}&z={z}. Set Max. Zoom Level to 19. Click ok.
4.Might have to expand the "XYZ Tiles" menus to see what is in it. Then double click the new Google option to add it to the map.
I then added the picture of the world and refreshed to that the points would go to the correct place.

iNatural data and Google tiles within QGIS showing locations of Asimina plants observed and recorded throughout the world.

 Now I thought this was cool. This is an Eastern North American genus. But it is neat to see it has been taken and observed in Europe, South America, Africa, Australia, and Japan. All continents besides the Iceberg in the south.

I zoomed into Eastern North America. Ont he left side of QGIS, I double clicked the symbol of the points, I changed the symbol from Single to Categorized. For Column I selected Species. I clicked apply, then I clicked Classify and unchecked the very bottom symbol.

iNaturalist data, Google Tile Set, and QGIS mapping of Asimina species observations of Eastern North America.

This shows all the species colored in different points. Most of the points are of Asimina triloba. Asimina diversity, different species, are mostly found in the southeastern United States.

iNaturalist data, Google Tile Set, and QGIS mapping of Asimina species observations of the viewed part of the United States.

Using the key at the left, you can look at the map to view where different species are located.

The Paw-Paw, Asimina, is one of my favorite plants! Everyone should "get a hit of" the smell of leaves of plants of this genus.

It is nice to see the work of many people to obtain these points and the work of others to make this data available! This could be done for countless other species. The website has statistics on how many species and observations, and it is growing every day. I hope this material will be around for a long time as this has the potential to be powerful information. This type of data goes beyond government, scientists, and industry. This is open and free for anyone!

I don't personally contribute to iNaturalist, but it could be cool for others.

Thanks for reading!
Comment if you would like!
Ask questions if you have any.
If you made a map using QGIS and iNaturalist, take a picture and contact me and I will post it on a future blog!
Thank you and have a Great day!

QGIS - Free Powerful Home Mapping Program

Today I plan to obtain and use QGIS so that I can work at home. If you are familiar with ArcGIS, QGIS is supposedly a good alternative, if not better. 
Objectives:
1. Obtain the program and get it functional
2. Add files such as:
-Add points
-Aerial Imagery

Obtaining the Program and Get it Functional
Download the program at https://www.qgis.org/en/site/. I selected the QGIS standalone installer. OSGeo4W is for more advance stuff that I haven't investigated fully.

This is about a 450 megabyte file, so it took a few moments to download. Once finished I doubled clicked it and installed the program. Installation took a few moments. Once complete I opened the program.

Adding Points
This is the program without any data added to it. I have some point data I collected (I plan to make a post to show how to collect data later). At the top I selected Layer, Add Data, Add Vector Layer as shown.

I then browsed to the file that contained my point shapefile, and I just double clicked that .shp file, then clicked add. A pop-up then comes up about Coordinate reference systems stuff. From my experience, most GPS units use WGS 84. That seems to be the standard, the program already had it selected for me, and I used that by clicking OK.Success! There isn't any real references, just points.
Adding Aerial Imagery
I tested a few ways to add aerial imagery. I would like to download the file, then add it to the map, but these files are large. I also had trouble finding them.

Instead I am using the built in XYZ Tiles option with instruction I found at another blog called GEODOSE. They do show pictures. I won't repeat their work, but I will list the instructions:
1.Within the "Browser" section, scroll down to "XYZ Tiles."
2.Right click "XYZ Tiles" and select new connection.
3.In the pop-up window, for Name you can type Google. in the URL enter: http://www.google.cn/maps/vt?lyrs=s@189&gl=cn&x={x}&y={y}&z={z}. Set Max. Zoom Level to 19. Click ok.
4.Might have to expand the "XYZ Tiles" menus to see what is in it. Then double click the new Google option to add it to the map.
The map may look a little funky based on projection or something. Zoom in and out a few times.
Here is my result for the points I had previously:


At this stage I completed my objectives to point you in the direction to get you going making your own maps at home. 

Saving Imagery Files
I mentioned it earlier, so I now go into getting the aerial imagery files onto your computer. Here is a government site available to all by the USDA.

Click either NAIP Download or Direct Download - I think they go to the same place.


Next look up the FIPs code of the area you wan the image of, by clicking #1 pictured. Click the drop down and select the state you would like. I used Georgia as an example.
Once the state is selected, a list will appear with numbers for each county.
I wanted Wayne County, so I noted the numbers GA, 13,305,H1.

Then I returned to the Geospatial Data Gateway and selected #2.

A list of folders with dates are shown. The most recent date may be 2017, but not all 50 states are available. I found and clicked 2013.

Another list of folders with state abbreviations were shown, I didn't take a picture. I clicked "ga" for Georgia. Then a list of files are shown. I clicked name to sort the files. I then looked for the ga305:

I clicked that file, click download, then save the file. These files are large, many over hundreds of megabytes, so it might take a few moments to download the file. Once completed, exact the zip file to a folder you put all your map layers. In QGIS go to "Layer" found at the top, Add Layer, Add Raster Layer... Then navigate to the file and select the .sid file of the file set. Add it to the map.
When zoomed in I compared the USDA imagery:
To the Google imagery:The Google imagery is of sharper quality, and is more up to date. On the other side, if you lose the internet, I think you lose these capabilities. The USDA site allows you to save the file on your computer.

Thank you for viewing!
Comment if you would like!
Have a Great day!