Shelf Planting and Light Intensity

Shelf Planting and Light Intensity
5/26/2018
Looking at the cups of plants of my 2018 planting, I again question the intensity of light on the different areas of the shelf.

2018 planting seed cups.

 

The cups of plants in the middle are getting more of a dose of light.

The cups of plants on the edge aren't getting light from the reflective curve portion of the light apparatus.

I had these thoughts for last year's 2017 Planting. It seems the plants on the edge of the shelf are green and grow tall. They may be taller because they are reaching for light. They may be green in order to process as much light that does hit them.

Sarracenia flava var rugelii x Sarracenia flava var atropurpurea variety Waccamaw seedling positioned to get less of the light from the grow lights.

The plants in the middle, under more light, seem to remain dwarf, are more red rather than green, and don't grow as tall. Maybe not having to reach for light, no need to grow tall. Maybe since they are getting a lot of light, no need to produce as much chlorophyll (green) to process as much light that does hit the plant.

Sarracenia flava var rugelii x Sarracenia flava var atropurpurea variety Waccamaw seedling positioned to get a lot of light from the grow lights.

 Although smaller, the plants in the middle seemed to have more pitchers.

Removing the affect of positioning of the 2017 not pictured here: Cups of plants the 2017 Planting were placed randomly on the shelf, a system that required a random number generator (this is different from me just hap haphazardly picking a cup and putting it where I felt like). The random placement was chosen to remove differences that could be caused by positioning. For the Portulaca Planting, I randomly moved plants every week in order to prevent any affects of their area on the shelf. I did not remove the affect of position in reference to the light in this 2018 planting, light I believe has an influence.

Different species: Last year I had so many different species. Different species will grow differently. This time I have the same type of seeds in all cups being tested.

Last year (2017) I cross pollinated one of my most vigorous plants, a Sarracenia flava var rugelii (purchased from Meadowview Biological Research Station on March 19, 2016) with a Sarracenia flava var atropurpurea variety Waccamaw (purchased from Meizzwang on February 15, 2017). I bought the Waccamaw plant as a flowering size plant, and for the cost, it came with a flower. Since my Rugelii had flowers, why not? Lets see what happens. From the Waccamaw flower, the pod was recently transplanted and may not have been 100% giving me just 36 seeds. From the Rugelii flower, it grew well under the conditions of a grow-light, inside an apartment, and I obtained 263 seeds. Note this was in the middle of the Appalachian Mountains of Pennsylvania. Light is poor and temperatures get cold. Haha, being so high on the mountain you might think well I was closer to the sun it should be warmer and sunnier, hahaha I joke because it doesn't work that way.

2017 Partial Plant Collection Grown Inside an Apartment. R = Rugelii. W = Waccamaw. Flowers are circled. Cross pollinated sweet plant love~

Fast forward to the 2018 planting (Planted February 25, 2018), I planted all the seeds from the cross. From the Waccamaw flower (Waccamaw the mother, Rugelii the father), 1 of 36 (3%) seeds germinated. That 1 seedling later died. From the Rugelii flower (Rugelii the mother, Waccamaw the father), 127 of 260 (49%) seeds planted germinated. Of the 127, 86 survived (68%)  to the end of Week 13.

Back to the question of light intensity, since I had so many seeds and planted so many cups, and the cups not shuffled or randomly placed to avoid the affect of positioning, I can then analyze cup positioning related to light.

Cup positioning. Numbers represent plants. The yellow rectangle represents the positioning of the light apparatus.

I counted the plants, the numbers of pitchers on the plants, and decided my own light intensity categorization on the plants. The light intensity categorization ranged from 1 to 4. 4 being directly under the lights. 3 getting some direct and some neglect. 2 on the edge of the shelf away from the light. 1 being on the corner... I felt like it.

Light intensity under grow lights base on cup positioning on the shelf keeping in mind the edge, edge of darkness.

Then I made a table. "Number" is the cup number, a label rather than a measurement. "Plants" are the number of plants in the cup. "Pitchers" are the total count of pitchers on the plants in the cup. "Pitcher/Plant" is the number of pitcher divided by the number of plants in a cup. "Light Intensity" is a light assignment number I chose based on positioning of cups to the shelf in reference to the light and the edge of the shelf, 1 is the least light, 4 is the most light.

Then I do what I do for most of my analyses:

Data Analysis

Light category represents the light intensity. The numbers in the light blue represent the samples. Count is the number of samples for the light intensity. Average is the average of the samples for each light intensity. StDev is the standard deviation and StdError is the standard error for each of the light intensity categories. StdDev is calculated using the =stdev function in Excel. StdError is calculated by dividing the StDev by the square root of the count, example: =StDev/(SQRT(count)). Note the blue text is not part of the function, rather the cell selection.

This now reduced table is all I need to make a graph. The category is there, the average for the bar, the StdError for the standard error bars.

The graph on the x-axis represents the light categories from 1 to 4. The y-axis indicates the average number of pitchers per plant. The number inside the bar are the number of samples used for the bar average. The error bars are 1 standard error of the samples for each category. Note the error bar for light intensity 1 is 0 because both samples were 2, no error... variation/noise to say. The graph reveals the potential for more light intensity may cause the seedlings to grow more pitchers. The bigger bar of light category 4 has no overlap in error bars with the other light intensity categories. It averages nearly half a pitcher more than the other category nearest category. I need to run a statistical test to confirm what I see in the graph, but I am too lazy today and might do it later. When I do, I will lists the instructions on how to do it. The graph was easier to see than reading the positioning chart:

Are more pitchers a good thing? Is more light a good thing? I like the more pitchers because I think it is the plant struggling for nutrients from insects.

Thanks for reading!
Questions or comments let me know!
 Have a Great Holiday Weekend!

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!