Descriptive Morphological Statistics

I had a lot of different sized seed pod measurements I graphed:



Of these, there are 3 different groups to look at. But these are a lot of dots. There are methods to look at averages, but I thought if I added a 0.1 [later I use 5%] area circle around each dot, then combined those circles by group, I would get an area. What percent area overlap would I get from the different groups?

To explain better:



Above a drew some random points that could be graphed on a chart with x,y values. Looking at them, pink and black overlap, but green doesn’t. How much do pink and black overlap?



I then drew a line around the points. I did this by hand so it is not exact, but that is ok for my example.



I then shaded the regions in. Where the pink and black overlapped, I shaded blue.
It could be possible to calculate the area for each shaded region.



Above I made up some random areas based on how they looked, but they weren’t measured exactly.



I then added the x and y axis for discussion. Note the overlap in measurements. I will go on a tangent here: so which is bigger? Well black is closer to zero of both axis, it must be small, although it does overlap a little with pink pods. I want to say pink is larger because it has more of a blob higher than the rest, but we can just say pink is wider than the rest. Green gets close to as long as pink, is never short in length compared to the others, but isn’t as wide as the pink. To get sizes, the length and width would have to be multiplied resulting in a single value. Then using those values you can compare the sizes to the other groups. Woah complicated and I explained it poorly. This isn’t what I am originally asking. I leave the tangent here. If the blob is closer to the 0,0 point of the chart, then it is smaller, but keep in mind something like a 1 width that is 100 long is larger than a 2 width that is 10 long.

Back on course. Let us say I measure a random width and length of a pod. I then plot that length and width on my graph as a red dot.



Based on my chart, there is no question our random red dot sample is of the pink variety. Here we make assumptions that the value we measured was a normal individual, not a mutant or abnormally different individual. Another tangent example, if I measured the height of all the children in a 3rd grade school class room. For visual think of it as green. Then I measured the basketball player Yao Ming who is over 7 feet tall, the red dot. I don’t know the height of 3rd graders, they are all shorter I know that much. Both groups are humans, but you couldn’t compare such to such a chart. That didn’t explain too well, but it was to get you thinking.

Back on course, if we assume we have normal individuals from the group, then we can be confident our sample red dot is a pinky.

Notice pink is a larger area. That means pink can be more different measurements than the other areas, more variation in sizes. Green has less area, so it has less variation of individuals.



Above I have a new measurement, the red dot now falls within the blue area. We can conclude our sample is possibly a black or a pink. I tried to avoid the table, but now we may need it.



Looking at the table, our red dot falls within the 12.5% chance area to be a pink and within the 25% chance area to be a black. But we aren’t going to know or ever find out, again I just reported what you could do with this type of analysis.



Above, now my red dot doesn’t fall in any of the shaded areas. This means it is not a normal black, pink, or green, it has 0% chance to be any of them. It could be something new. Could be another color. Could be a mutant of the other colors that is just abnormally different in size. We don’t know, it is a mystery! I made it up, so it doesn’t matter. We are ok.

I’m sure there are some statistical tests that explain the same stuff number-wise, but the graphics helped me explain it. Now back to my original graph with many points.



I can’t draw a circle perfect enough around all those points. Maybe I can use a program that examines area. I will try with ArcGIS, a mapping program. My points are basically x,y coordinates of a map. For the world, the coordinate system uses its own distance. Instead of trying to add a coordinate system, I just decided to try to add the data. To add the data, copy the data into a new excel document and save it. Then open the ArcGIS (10.3 I think) program and add the data by selecting the excel file and the sheet within it. Then from the table of contents, right click and display the data. A warning will pop-up saying many of the options for the resulting points won’t be functional, which I will fix in a little bit. Here is what it generated.



Not bad at all, seems it worked. I right clicked the resulting points on the table of contents and exported the data to a personal file geodatabase. I then added that exported data to the map, and removed the original from the excel data. This process now restored the functions the program warned me about.

I then changed some symbols and zoom into the area.



Above looks great. If I wanted to draw circles around the colors, I could, but now the program can do such activities for us. Just looking at the points, it seems blue has the largest area, largest possible variation. The green seems to be the smallest. I guess blue can get to be the biggest. Red seems to be able to be the smallest [I accurately determine size later]. All have overlap. My next steps will be to calculate the area and overlap percentages of the points.

After some trial and error, my measurements are small, too small to compare the distance, or to place a buffer. I multiplied my measurements by 100, then I was able to put a 15 meter buffer around the dots.



Why did I chose 15 m?  My average size for all measurements regardless of soil and plant type was 3.05 x 2.38. I then multiplied these numbers by .05 to get 5% of their distance: 0.15 x 0.12. I decided to go with the larger, the length, the 0.15 as a buffer distance of 5% of the average. Since I multiplied all my measurements by 100 for plotting purposes, I would do the same for my buffer distance of 0.15 x 100 = 15 m. I don’t know how statistically strong this is, but I am looking more for descriptive details anyway.



Then removing the dots:



Looking at the buffers, most form a nice connected blob. A speck of buffer are found within the blob indicating we didn’t have complete coverage within that blog. Blobs not connected to the main blog are a sort of outlier, but that is probably due to a lack of measurements to cover the in-between, meaning I would have to measure more pods of the true population of seed pods and it should eventually join those to the main blob. Non-connected blobs and inside specks should be fine for what I am doing.

To calculate the area of the blobs, in the ArcGIS program, to each buffer attributes table, I added a new column. I then added a new field. Then in an edit session, I calculated the geometry, area.



Now I have more accurately determined the exact size of each blob. Now I can confirm what I thought, green is the smallest and blue is the largest. Variation of measurements is comparative to size of blog area. Blue has a larger variation range for sizes than the others and so forth.

Using the Intersect Geoprocessing tool, I can get an area of overlaps for each blob, then calculate that area similar to my previous method.



More tables:



This table tells us the area of overlap between two colors.



Table reduced:




The table just tells us percent the colors overlap.

Now how about for areas where nothing is overlapping? To accomplish this, I used the Geoprocessing clip function twice, then the merge, then the dissolve function. It became complex. Example: I clipped red from the blue to give me the red x blue area. I then clipped green from the blue to give me the green x blue area. I then merged these two clips. I then dissolved the resulting merge. Then I added a new field and calculated the geometry of the area with overlap. I then took the total area of the blue and subtracted the area with overlap to obtain the area with nothing. I repeated this process for the other colors. –Yes it was that complex.

Now how about for areas where all 3 overlap each other? First I merged all three buffers, then dissolved the resulting shape. With this all merge, I then clipped one at a time, each color buffer from the all merge. Each cut reduced the area that overlapped with another buffer to the point where I was only left with the part that had all 3 overlapping.

So what did we accomplish? What was the point of all this? We generated 2 tools: 1. a variation range and 2. an estimate of possibilities.

  

What and how to use the tools?

Example: If I took another measurement of a seed pod, and it was of the green variety, what are the chances I could be confusing it’s size with a blue variety?

Answer: I look at the table. I go to the bottom green section. I find the Green Blue overlap. I read 83%.

Example: What are the chances that I would measure a seed pod and find it was of the Blue variety with no chance to be confused with any other variety?

Answer: I look at the table. I go to the blue section. I find the Blue None overlap. I read 55%.

Example: If I took a measurement of a seed pod, I could then compare using the x and y axis graph by plotting that point. Wherever the point falls, I will be able to explain it could be of a certain variety if it falls within its outline. See the following where I took 4 measurements to compare to the graph; measurements are labeled A, B, C, and D.

 

Well A could be any variety because it is within the buffer of all 3 colors. B has to be blue only. I have no clue what C could be. D could either be red or blue.

The boss told me to get only blue variety seed pods. I look at what we have and they all look the same. From the graph, the x –axis is the length. Seems if I pick only seed pods of length 4 or greater, I will only get blue variety seed pods. Note: I wrote the 4 in place, but I could generate a graph that has tick marks for measurements for the axes.

It is important to remember the assumptions that I am obtaining sample measurements from seed pods that are normal.

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

Seed Collection Notebook

Seed Notebook

This idea was not my own, I viewed a seed notebook at a training I went to. I found it fascinating! Usually plants are displayed and you can see their differences. In some cases different species look very much so alike. Yet, sometimes the seed are so different from adult plants that species can be identified from them! This is and will be discussed in a future post on the difference between Drosera brevifolia and Drosera capillaris. Anyway, the seed notebook:

Supplies needed:
Coin holders – like for coin collections
Coin holder sheets – again usually for coin collections
A stapler – to seal the coin holder
An adventurous spirit to collect seeds!

Quarter size coin holder.

Quarter size coin holder notebook sheet.

All supplies needed to make a seed collection notebook. Folder not included.

A seed collection is useful as an identification tool when the seeds are properly identified. From my experience, I would find the plant, watch it grow, then collect seeds from it. Using field guides, I could accurately identify plants. Thus I have correctly identified seeds. Well to the best of my abilities. Here is a sample of my first completed sheet:

Filled seed collection note sheet.

We see seeds and know they have differences, but to see them side by side is something else!

A sort of slide, I am then able to look at the seeds in the holders under microscopes.

Compound microscope look at a seed collection notebook slide. Flashlight adds extra light.

This is how I get the close up detailed pictures of seeds. Sometimes 400x magnification of some very small seeds!

A look at seeds of a seed collection notebook slide, under a compound microscope.

 

 

Seeds come in many differences sizes, shapes, colors, and textures. Some have protrusions. Some are metallic looking. From examining different seeds, I think I have become a better botanist. I learned a lot about seeds, and a lot more about myself.

Seeds in a coin holder for a seed collection notebook.

Depending on seed size, the coin holder can be folded either way. For the really small seeds, I don’t want any space for the seeds to shift, and I fold the coin holder appropriately. Stapling required some practice, but I got the hang of it. Modifications can be used such as gluing cards together. I used quarter size card holders, but other sizes can be used. I save half dollar holders, but thought that is too big with too few specimens on a single coin holder sheet. Smaller coins seemed too small. But for others, maybe difference sized coin holders would work. It is important to make sure seeds are not allowed to escape from the coin holder. Seeds for this type of display should be for permanent display, without plans of planting. There are ways to sterilize seeds, and this may be a good idea before storing seeds in the coin holders. Do allow seeds to dry before added to a coin holder. Make sure to remove any seed pests. I repeat this because it is important, make sure seeds do not escape the coin holders! Glue may be a good idea. Some seeds may not be practical for such a display, example: a coconut.

I searched the internet for others who posted using this technique, but couldn’t find anything. So hopefully this post may encourage more users to get with the program.

I encourage others to start making seed notebooks with your other botanist friends! Collect and trade seed cards! Be the envy of your peers with the best collection ever!!!! Let me know if you have seeds to trade 😀

Warning: Do not eat seeds. Keep seed collections out of reach of children that may destroy or eat seeds. Do not leave seed collections alone with birds or small mammals which find seeds a primary source of their diet. Seed collecting may become addicting. Non-botanist friends may not share your excitement or enthusiasm collecting seeds, and may not be interesting in looking at your collection. In those cases force your collection upon them to convert them into fellow collectors. Your significant other may distance themselves from you for having a seed collection. In those cases you are probably better off because seed collecting is the bestus!

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

Crusader Kings 2 - Society Modification

Crusader Kings 2 Society Modification
5/13/2017

I thought it might be cool to make my own mod for Crusader Kings 2, a society. Theme Botany. I will try to create a society that can collect a plant or artifact from a county to add to their collection. I guess this could be duplicated for any type of county collecting of whatever item.

To start:
https://www.youtube.com/watch?v=WGwCoFX1nn0
This guide tells you how to make a mod shell so you don't ruin your game. Step 1. Must do. If you follow its instructions, if the game start up screen you should be able to check your mod in the mod categories, even though there is nothing in it. It worked for me!



I named my mod folder:
...Documents\Paradox Interactive\Crusader Kings II\mod\BotanicalSociety_TMCcustom

From this location:
C:\Program Files (x86)\Steam\steamapps\common\Crusader Kings II
I copied the following folders:
localisation
interface
gfx
decisions
events
common
to the following folder:
...Documents\Paradox Interactive\Crusader Kings II\mod\BotanicalSociety_TMCcustom
 This was a lot of files so it took a few moments. This copies everything I think I will need and now I can edit the files in this folder and not ruin my original game.

I went into:
...Documents\Paradox Interactive\Crusader Kings II\mod\BotanicalSociety_TMCcustom\common\societies

I searched for the Hermetic society. I then copied it, pasted it on top of the file, then changed Hermetic with Botanistic.



###BOTANISTIC ORDER###
Botanistic = {
    primary_attribute = learning
    society_ranks_gfx = generic_ranks
    opinion_to_other_members = +10
    opinion_per_rank_above = +5
    sound = hermetic_society_interface
    non_interference = {
        always = yes
    }
   
    active = {
        has_dlc = "Mystics"
    }
    indestructible = yes
   
    can_join_society = {
        hidden_trigger = {
            NAND = {
                ai = yes
                is_society_rank_full = {
                    society = Botanistic
                    rank = 1
                }
            }
            OR = {
                is_landed = yes
                is_patrician = yes
            }
        }
        learning = 10
        OR = {
            religion_group = christian
            religion_group = muslim
            religion_group = jewish_group
            religion_group = zoroastrian_group
            custom_tooltip = {
                text = zunist_hermetic_join_tooltip
                hidden_trigger = {
                    OR = {
                        religion = zun_pagan                   
                        religion = zun_pagan_reformed
                    }
                }
            }
            religion = hellenic_pagan
        }
        NOR = {
            is_nomadic = yes
            is_tribal = yes
        }
        hidden_trigger = { mercenary = no }
        age = 16
        hidden_trigger = {
            NOT = { has_character_flag = society_join_block }
        }
    }

    show_society = {
        OR = {
            religion_group = christian
            religion_group = muslim
            religion_group = jewish_group
            religion_group = zoroastrian_group
            religion = zun_pagan
            religion = zun_pagan_reformed
            religion = hellenic_pagan
        }
    }
   
    potential = {
        NOR = {
            is_nomadic = yes
            is_tribal = yes
        }
        age = 16
        #If something else is added here, it could break apprenticeship. Create an event if they can get kicked out. title_Botanistic_apprentice
    }
   
    society_rank = {
        level = 1
        limit = 200
        startup_limit = 10
        modifier = {
            church_opinion = -10
            #economy_techpoints = 0.05
        }
        decisions = {
            Botanistic_write_theory_paper # Enables you to write a theorem paper that, if approved, gives you society power
        }
    }
   
    society_rank = {
        level = 2
        limit = 100
        startup_limit = 6
        modifier = {
            learning = 1
            church_opinion = -10
        }
        decisions = {
            Botanistic_perform_scrying # Enables you to perform a scrying and gain an omen
            brew_happiness_potion # Enables you to brew a potion
        }
    }
   
    society_rank = {
        level = 3
        limit = 50
        startup_limit = 4
        modifier = {
            learning = 2
            church_opinion = -10
        }
        decisions = {
            Botanistic_make_horoscope # Enables you to "predict" your children's future
        }
    }

    society_rank = {
        level = 4
        limit = 20
        startup_limit = 2
        modifier = {
            learning = 3
            church_opinion = -10
        }
        decisions = {
            choose_hermetic_art # Enables you to pick/change your lifestyle trait
            Botanistic_write_magnum_opus # Write an enciphered book of lore (artifact)
        }
    }
   
    plots = {
    }
   
    monthly_currency_gain = {
        name = currency_name_Botanistic
       
        per_attribute = {
            name = learning
            value = 0.5
        }
        has_trait = {
            value = 2
            trait = diligent
        }
        has_trait = {
            value = 1
            trait = scholar
        }
        has_trait = {
            value = 1
            trait = mystic
        }
        has_trait = {
            value = 1
            trait = erudite
        }
        has_trait = {
            value = 1
            trait = stubborn
        }
        has_trait = {
            value = 1
            trait = patient
        }
        has_trait = {
            value = 1
            trait = genius
        }
        has_trait = {
            value = 1
            trait = quick
        }
        has_trait = {
            value = 1
            trait = shrewd
        }
        has_trait = {
            value = 1
            trait = just
        }
        society_rank = {
            rank = 4
            value = 10
        }
    }

    member_score_per_attribute = 3
    member_score_per_rank = 100

    member_score = {
        value = 10

        modifier = {
            factor = 2
            trait = diligent
        }
        modifier = {
            factor = 1.5
            trait = scholar
        }
        modifier = {
            factor = 1.5
            trait = mystic
        }
        modifier = {
            factor = 1.5
            trait = erudite
        }
        modifier = {
            factor = 1.5
            trait = stubborn
        }
        modifier = {
            factor = 1.5
            trait = patient
        }
        modifier = {
            factor = 1.5
            OR = {
                trait = genius
                trait = quick
                trait = shrewd
            }
        }
        modifier = {
            factor = 1.5
            trait = just
        }
    }
   
    startup_populate = {
        trigger = {
            ai = yes
            controls_religion = no
            age = 16
            is_in_society = no
            is_dumb_trigger = no
            OR = {
                NOT = { is_priest = yes }
                OR = {
                    trait = mystic
                    trait = scholar
                    trait = cynical
                }
            }
            OR = {
                AND = {
                    is_landed = yes
                    OR = {
                        learning = 14
                        trait = scholar
                        trait = faqih
                        trait = erudite
                        trait = genius
                        trait = mystic
                    }
                }
                AND = {
                    learning = 18
                    OR = {
                        trait = scholar
                        trait = faqih
                        trait = erudite
                        trait = genius
                        trait = mystic
                        learning = 20
                    }
                }
            }
            OR = {
                religion_group = christian
                religion_group = muslim
                religion_group = jewish_group
                religion_group = zoroastrian_group
                religion = zun_pagan
                religion = zun_pagan_reformed
                religion = hellenic_pagan
            }
        }
    }
}

Saved it all. Then I checked it out in game. Seems it worked! I saw the society. They even put a lot of priests into it. When I click join society, I can't. This will be a long road to follow.




Note I put the curser to see the rank of the society members. This was my next goal.

I subscribed to the the_great_trade_league by Maal mod from the Steam Workshop. From there I looked at his files.

At this location:
...Documents\Paradox Interactive\Crusader Kings II\mod\BotanicalSociety_TMCcustom\localisation
I copied from the the_great_trade_league by Maal mod left only a few lines of the csv file. Yes now I am using excel rather than just Notepad++.



Rough picture, but good for the speed I made it. Pay attention to the Botanistic_Rank_1_male areas. I did not modify the female versions yet. So I modified the male ranks to Gardener, Farmer, Botanist, Curator. Yes I spelled it wrong in the file.

I pasted this excel csv file into:
...Documents\Paradox Interactive\Crusader Kings II\mod\BotanicalSociety_TMCcustom\localisation

Then I ran the game.



This changed the name of the ranks. I still cant do anything with the society. I just made a shell of The Botanical Society in the game. I then named the ranks of the society. I can't join it. The society copies much of the Hermitic society. This isn't a functional mod, but it did change a few things. Took a few hours, but through looking at the work of others, I figured out what I could.

Do what you can with this, maybe I will do more later.

Have a nice day! Comment if you want!

Mistaken Location of Pilosocereus robinii

The United States Fish & Wildlife Service Mistaken Location of the Endangered Pilosocereus robinii, Key Tree Cactus

Overview

As a young naïve, recently graduated, graduate student, I was excited about going out and working helping to save endangered species. Since then I’ve worked to try to do such a task. During the course of that work I contacted many employees who work in agencies directly responsible for endangered species programs. Some are very nice and they did the best they could to help me. Others are very rude and are verbally abusive. I have had multiple cases of both. Some of my questions still haven’t been answered. This is years later.

First I want to say if you want to help endangered species you are in for a horrible, frustrating road.

Second I suggest you document everything.

For my research I needed data from the United States Fish & Wildlife Service. During my search I found an error by the “Service,” as they call themselves. I’ve found these things before. I’ve ignored them before. So I thought, well let me tell someone so maybe they will fix it. I’ve told people before, and the results varied. From those past times, I learned I need to document stuff.

My research took the state location of where species are found. Through the service website, I obtained this information as is available for any school student with interest in such a topic. Pilosocereus robinii, the Key Tree Cactus, was shown to be in Florida and California. To this day I guess “Key” in the common name comes from the Florida Keys. Anyway, California and Florida are far apart. How is an endangered plant rare yet found on different coasts? I then researched more into this question by reading the available recovery plan and status reviews. The researched did not provide evidence for California. I concluded it as an error, the plant is NOT found in California. Funny the website map for the species didn’t even show Florida, rather it focused on California completely omitting the species range.

I documented the mistake so that I could explain the problem to a service employee. That was my original rational for why I still have the following information. I saved the website view as a PDF, that PDF is pictured below. Take note that the species is believed to occur in California (red circle) and that Florida wasn’t even pictured (part of circle because Florida wasn’t available).

I think, obviously an error. Let me contact someone to confirm, then maybe contact someone to fix the problem. The FWS has a great ask a question spot. It has both helped me and not helped me in the past. In this case they didn’t help me, but it did help me. The response I received and the message I submitted is below (my information blotted out):

I applaud whoever responded. They tried to help me. They looked at what I found out and went with what they saw. They even suggested I contact another office. Well I called that office, they transferred me multiple times, eventually leading to a Mr. Olah. I think I got his answering machine, but in any case the person in charge was not available. I searched the internet and found his contact information and sent him an email. That email is below (I censored my identification information).

It is February 2017 as I type this. Maybe they still have me on the list to return my email.

Well then I had to go away from my quest for answers due to work. While away one night, I thought to look up the website again. To my surprise the site had changed! California was no longer listed. My email showed no reply from anyone, it was late April 2016 when I checked. So within 6 weeks of my email, the website was fixed! No thank you or anything for my email. Now February 2017, I show what the site looks like now: https://ecos.fws.gov/ecp0/profile/speciesProfile?spcode=Q208 also pictured below.

 

No more California. Look I even helped them find Florida!

Thanks to my research, I helped the service determine and remove a federally endangered species from the State of California of the Endangered Species Act. It was unfortunately for all the school children, scientists, and government employees who were misled by the erroneous information, as I had been. Yet for future children, scientists, and government employees this information has been corrected!

Mistakes do happen. This mistake wasn’t that big of a deal. When you think of cactus, you might think of Arizona or New Mexico. Maybe even California. Florida has fewer species. Maybe they mixed cactus with cactus somewhere that originally caused the mistake. So much other information I found does appear to be correct, mistakes are way fewer. Thank you to the Service for making information publicly available. Unlike me thanking the Service, the Service has yet to thank me for helping them. I don’t care so much about credit. What I care about is helping recover endangered plant species.

Helping endangered species is a brutal fight, an uphill climb against the Service. I have asked to help the Service recover species. They tell me no. They tell me no every single time. Well so I need to make them see I can help. By showing them such an example, I hope they will listen.

This was an example I had documented. So many other, more worthy, activities I don’t have documented. Yet the Service has thwarted my efforts. The Service is only hurting itself when they ignore citizens. The current state of the Service produces a lot of bureaucracy without return of species recovery. It will take big changes. The Endangered Species Act is great and has the potential to be great. Unfortunately they have some bad people managing it. They will have to change before endangered and threatened plant species can be expected to recover. They will have to work with private citizens, not ignore and reject them.

Thank you for reading. Comment for discussion if you would like. Have a nice day!