MDS(Multi-Dimensional Scaling)
Like PCA, MDS is trying to understand the structure of observations.
Use R data "gardenflowers" in the package “HSAUR2". The dissimilarity matrix of
18 species of garden flowers is shown. Use some form of multidimensional scaling to investigate which species share common properties.
#Interpretation:
Now for the fun part, let’s guess how these are graded and why they cluster into four groups:
First Attempt: Taxonomy
In biology class we learned how to classify all creatures using Taxonomy:
Kingdom - Phylum - Class - Order - Family - Genus - Species
And how we can understand a plant by reading it’s Binomial Nomenclature. This is a good start:
? Conclusion of First Attempt:
It’s safe to say, the researcher who defines the similarity doesn’t take into consideration the Taxonomy since flowers who belongs to the same “Phylum” are quite far away and lives in different clusters.
Notes: Actually I was extremely confident that this is how those flowers are categorized and spend hours after hours self-re-educating this classification rule; because it is a well-established and popular method to attributed plants to different classes. And it is also something that imprinted in my mind how we should properly classify any living creatures ever since Biology class.
I was really anxious that this doesn’t work until I found in the book (listed as reference) how these distances are originally defined and calculated. Well, now I’m curious how these classification rules differ.
Second Attempt: Fragrance
I saw my rose-fragranced hand cream and realized that it’s almost obligatory for a flower to have fragrant.
But how could I know if a flower has fragrance of not besides common sense?
Wiki fails to provide this information.
I consulted friends studying Biochemistry and learned that the only two causal effect of the fragrance of flowers are: Eleocyte Evaporation or Glycoside Decomposed by Enzyme. But it seems that there’s no website listing whether or not a flower contains either one or both of the chemicals.
So, dead-end again.
But, whatever has fragrance should probably been made into perfumes. This is one way to figure out if a flower has fragrance. I went on Amazon and check which flowers are made into perfumes. Here is the result:
? Conclusion of Second Attempt:
That’s a good start: Those live in south of MDS-plot (i.e. class 3) have one thing in common: Fragrance-Free!
Let’s dig deeper (next page)
Third Attempt: Temperature
In China we have loads of poems regarding to Chimonanthus, a flower that blooms only in the extreme coldness of the winter; let me check if “ability to survive coldness” could be one criteria:
Conclusion of Third Attempt:
- Now we have a line from SouthWest corner to NorthEast corner (the red line):
- Every flower below this line can live in cold weather;
- Almost Every flower above this line cannot survive the cold;
Forget-me-not is an exception: From the plot it seems to be closer to Class “1”; But it can survive cold weather.
Should I adjust my line so Forget-me-not could reunite with her cold-enduring friend?
Fourth Attempt: Colours
Flowers are supposed to be colourful, let me check if colours could be a criterion:
Conclusion of Fourth Attempt:
Probably NOT a criterion. Maybe it’s not a great idea. Look at the second class, “Yellow, Pink and White”. This doesn’t really make sense.
In fact, I even Googled pictures of all these flowers and load it into PS to check RGB index and Googled the frequency of these colors to see if there’s something worth noticing.
Still Nothing.
Keep trying.
Fifth Attempt: Sunlight Exposure
We’ve checked the endurance of coldness of a flower, so let’s see if whether a flower can survive constant exposure to sunlight or not could be a criterion.
Conclusion of Fifth Attempt:
1. Now we have a line from SouthEast corner to NorthWest corner (the blue line): 2. Every flower below this line can survive constant direct sunlight;
3. Almost Every flower below this line cannot survive constant direct sunlight;
4. Pink Carnation is an exception:
a) From the plot it seems to be closer to Class “1”;
b) But it can survive constant direct sunlight.
SUMMARY:
- Red Line: Endurance of cold temperature ()
- Every flower below the red line can live in cold weather;
- Almost Every flower above the red line cannot survive the cold;
2. Blue Line:
- Every flower below this line can survive constant direct sunlight;
- Almost Every flower above this line cannot survive constant direct sunlight;
3. Class 3 is the only class that is Fragrance-Free
