Randomized block experiments with multiple replicates
Unlike many experimental situations, with computer modelling the problem
tends to be an embarrassment of riches. There is no problem with amount of
data. You can gather scads and scads of data. So much so that it can be
hard to find statistical tests that deal with what you’ve got. Right now,
I have data that can be set up and analysed as a randomized block (or
repeated measures) experiment.
Here is an excellent description of randomized block ANOVA and how it
works. The problem is, I not only have randomized blocks, I have multiple
replicates within each block. Psychologists should be so lucky, right? But
no one seems to cover this case, because usually people are lucky to get
enough subjects to do a randomized block experiment with a single value in
each treatment of each block. So, what to do now? I could take the average
of the values and test those, or I could randomly pick one of my
replicates to compare. Both seem plausible. But what is the ‘officially
right’ thing to do? That’s my dilemma.
posted at: 11:34 |
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Randomized Block Anovas with SPSS
Here’s
a pdf that lays it all out.
posted at: 16:14 |
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Testing Matched Data
My modelling setup leads to a need to test paired data, probably using a t-test
for paired observations. Here’s a page on how that
works.
Cheers!
Jen
posted at: 16:05 |
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ANOVA with matched samples
And here’s a
page on an ANOVA with matched samples, or in this case, repeated measures.
posted at: 10:25 |
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Linear Regression
A simple summary of
linear regression.
posted at: 17:07 |
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Nice discussion of 2 way anova
Here’s a nice
discussion of the various results you can get with a 2 way ANOVA and how
to interpret them.
posted at: 14:29 |
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Chi square challenges
Here’s
a discussion of what to do if your contingency chart has columns with
zeros in it.
posted at: 16:24 |
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Points on a sphere
I’ve been avoiding working this out for a while, but I need a way to
generate points on a sphere of a certain radius. That’s because my agents
are composed of spheres, and I need to set their perceptual fields at
points on the outside of the spheres.
It’s easy enough to figure out the general formula for points on a sphere- it’s all points that are the radius away from the center of the sphere. The problem I’m having is getting actual points out of that equation. Picking x and y points randomly is likely to lead to a situation where there is no z value that fits on the sphere. I’m sure there’s some easy way to do this but, as usual, my complete lack of education in 3d geometry is not helping me out here.
I found this
sphere FAQ which might provide some helpful info. I also found this discussion about
how to convert spherical coordinates into cartesian coordinates. And,
doing a bit more searching, I think
this will probably do the trick.
posted at: 11:30 |
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Fish Database
And also, a fish
database that I came across a while a go but forgot to add to my blog.
It has a page on zebrafish, with know information gained from research.
It’s interesting what sort of information has not been published on the
zebrafish. For instance, there appears to be no information available
about how fast zebrafish move, or how they move through the water. This is
data that I have, so I may be able to publish it, and contribute.
posted at: 15:23 |
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Zebra fish anatomy
I’ve spent some time trying to find out about the physical characteristics of
zebra fish, but I’ve never had much luck. This seemed really strange to me,
because everyone is all about the zebra fish these days. Suddenly, today, the
phrase ‘zebra fish anatomy’ popped into my head. Jackpot. My first hit- the Zebrafish anatomy project. Sweeeet.
Also exciting- a zebra fish anatomy
poster.
posted at: 15:20 |
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Zebra Fish Slides
Fishnet is “is a
three dimensional database of zebrafish development from the early embryo
to adult. Models of zebrafish development may be virtually sectioned,
viewed as 3D renderings, or downloaded for your own manipulations.” Is
that insane or what?
posted at: 14:54 |
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Danio Rerio Facts
A fact
sheet on Danio Rerio
posted at: 23:50 |
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Oh those swarming bees
I’ve been looking for some swarming bee pictures to spruce up my IEC
presentation. Lots of pictures of bees not moving, not so many of bees in
the air. But Here’s
one.
posted at: 15:28 |
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Geometric Tools: Source Code for Computer Graphics, Image Analysis and
Numerical Methods
This looks like it might have
lots of interesting code.
posted at: 16:21 |
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3D object intersection
Here’s a nice chart
of links to object intersection code for various objects (triangle, cone,
etc.).
posted at: 12:46 |
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Statistics Glossary
The more statistics words, the merrier. Here’s
a nice list of correlation and regression concepts.
posted at: 14:59 |
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Inverse of coordinate transform matrix is transpose
According to this
posted at: 10:01 |
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Changing from one coordinate system to another
Here’s how
to do it.
posted at: 09:34 |
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JavaView- 3d geometry library
It’s been ages since I’ve posted an links ot my blog- I just haven’t been
doing much research that required saving links, for some reason. But
here’s a thesis research link: JavaView
posted at: 12:12 |
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Zebra Fish
I keep running into model organisms. The water flea, daphnia, is one. The
zebra fish, it turns out, is
another
model organism.
posted at: 11:38 |
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Calculating Rotation Matrix
In a last ditch attempt to figure out how to get my agents doing the right
thing, I typed ‘calculating rotation matrix’ into google. The first hit I
got back was this one.
As it says, “The purpose here is to describe how to obtain a proper matrix
given a location and a target (or a vector), and an amount of roll.” I
also found someone trying to deal with the the same
problem.
posted at: 15:36 |
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Euler Angles
3D geometry is interesting because there’s a direct analogy between this
type of math and 3 dimensional physical space. This means that to work
certain things out about 3 dimensional space, you need to understand 3D
geometery. In the other direction, it also means that to understand 3D
geometry, you can just build 3D models (which in my case translates to
“cardboard boxes and knitting needles”) and see how parts of the models
actually move through space. Handy.
Anyway, I’ve realized that I’ve never really given much in depth thought to 3D space or 3D geometry until now. As it turns out, I’m really quite ignorant with respect to how objects move in three dimensions, and also with respect to how to model and describe this movement mathematical. That’s all starting to change now, however.
One of the new mathematical concepts I’m grappling with
is Euler
Angles.
posted at: 11:15 |
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Common dimensions of fish tanks
Here’s a page that
lists common dimensions of fish tanks.
posted at: 12:34 |
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Some leads on mail order Daphnia
I’m not clear on whether or not animals like Daphnia can be shipped from
the US into Canada. But L.F.S.
Cultures carries them. Ward’s Natural
Science also has them.
posted at: 16:02 |
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Getting Daphnia
Now that I’ve learned about Daphnia, I actually have to get some. It looks
like mail-order might be my only option at the moment.
Here’s
a page with quite detailed information about Daphnia raising, with some
information on how to transition them from arrival to happily living in
their new home, including some useful info about water preparation,
temperature and light. I also found a site with some short
videos. However, I’m having a hard time finding a place to order
Daphnia.
posted at: 15:47 |
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Colouring Daphnia
One aspect of Daphnia that gave me pause, on the video front, is their
see-through nature. Apparently, however, it is possible to colour the
Daphnia by feeding them coloured food (makes sense, since they’re
see-through). I found this tantalizing snippet on google: “Eating the
stained yeast will color the Daphnia red. For changing other Daphnia to
different colors, prepare the yeast solutions with different stains or
…” but unfortunately I don’t have access to the actual page because it’s
through a subscription site. I found another
question and answer
page that talks about feeding them paprika.
Here’s
an article that suggests basically dipping them in a dilute dye solution.
And
here’s
a page that does specifically mention dyeing the yeast with a red food
dye.
Here’s
someone asking about using something to permanently stain their carapace,
which might be a good plan, since I suspect the food moves in and out
fairly
quickly.
posted at: 14:51 |
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Videos of Daphnia
Here’s a website
that has some videos of Daphnia. This is reassuring, since one of my
outstanding questions at the moment is: “Will I be able to trace Daphnia
movement using digital video and my processing programs?”
posted at: 14:32 |
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Daphnia- the water canary
As an interesting aside, daphnia are being used to
detect toxic water levels in industrial waste water before the water
is released into the environment.
posted at: 14:25 |
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More on Daphnia and Green water
I’ve been reading more about raising daphnia and also using daphnia to
control algae blooms in tanks.
Here’s
a series of questions and answers on green water, some of which deal with
clearing green algae with daphnia.Here’s
a site on raising daphnia by feeding them on green water, bacteria and
yeast. And here’s an
extensive article called “Daphnia: An aquarist’s guide.
posted at: 14:10 |
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More on aquarium plants
This entry probably shouldn’t be under ‘school’, but I can pretend, can’t
I? Here’s another article on
aquarium plants.
posted at: 13:19 |
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Exciting Aquaria
I’m feeling very excited about aquaria at the moment, because I’m getting
into setting up the aquarium for my animal aggregate experiment. I’ve also
been thinking about getting my own aquarium at home, because the more I
learn about this stuff, the more I think I would enjoy having my own
personal fish school in my house, that I can stare at and think
about while I’m trying to inspire myself to write my thesis. But now,
things are getting even more exciting. It all started because it looks
like I may be doing some work with water fleas, which are
actually a species (Daphnia) of very small crustaceans (up to 5mm in
size). They also swarm, and it’s easier to look after them and house them
and get ethical approval to shine lights at them than it is to do the same
for fish.
“So what?”, you might ask. The ‘so what’ is that I’ve started doing some research on water fleas, because I need to know how to raise them and take care of them and now I’m getting excited. Daphnia can usually be bought in pet stores, because they are food for fish. In the process of searching for information about this, I came across this page on how to raise daphnia to feed your fish by also raising a tank with algea in it, which you feed to the Daphnia, which you then feed to your fish. And what sort of fish? In a very happy making turn of events, it turns out that Giant Danios- the schooling fish I was planning to study- happen to eat daphnia.
At which point, upon learning this, my head happily exploded. Can you say
ECOSYSTEM! So now I’m
reading about aquatic
plants. Joy! I can’t wait!
posted at: 13:17 |
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Rotating a point
Here’s
a page with an algorithm for rotating a point through space. I may need to
implement this algorithm in my breve model. And
here’s the
Wolfram math page on how to calculate direction cosines. I’ll need to do
that to get the angles for the rotation algorithm.
posted at: 15:17 |
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Camcorders Galore
I’m looking into camcorders, because I’m going to need one for my third
thesis project. As with most consumer electronic equipment, there’s lots
to learn.
Here’s
a PC world video camera buying guide, and
here’s
a beginner’s buying guide from camcorderinfo.com. Of course, I also need
to know what to do with the video once I’ve shot it. Ultimatel, that will
involve a lengthy process of data processing, but first I need to get it onto my
computer.
posted at: 14:40 |
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Random Expression Generator
As part of my second project, evolving models of evolution, I need to
randomly generate mathematical expressions. As usual, I would rather not
reinvent the wheel.
Here’s a function in matlab that will randomly generate functions.
Here’s a
paper that presents an automatic tool to do the same. And
here’s a
somewhat tangential link that discusses creating a random expression
generator that can be be used to automatically create calculus quizzes.
posted at: 13:49 |
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Another fish sensory perception researcher
Here’s
another researcher of fish perceptions, Jacob Engelmann.
posted at: 18:06 |
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John G. New- Large Mouth Bass researcher
It’s always surprising how a slightly new angle will turn up new
researchers on a topic. It turns out that
John G New is
studying vision and lateral line perceptions in the large mouth bass.
posted at: 18:05 |
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Large mouth bass
I’ve just come back from a very interesting conversation with a Carleton
fish researcher who has a ton of data on Large mouth bass. Cool! But how
much do I know about large mouth bass? Very little, other than that I have
always found their name kind of amusing, for some reason (perhaps the
bassomatic has something to do with this). In any case, if I could find
out about their perceptual abilities, that would be really excellent.
Here’s
a bit of a blurb on them. It doesn’t say too much about their percpetual
abilities, but does provide a reference to an interesting looking book on
fish perceptual abilities.
posted at: 14:03 |
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Intersection of plane and ray- you can do it!
Okay, I am settling on the intersection of plane and ray plan.
Here are some instructions on how to do that.
posted at: 15:31 |
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Convex Hull Algorithms- understandable too!
I also need to know if a point is inside or outside a convex hull.
Here,
finally, is a page that is not too hard to understand. Thank you 3D game
designers.
posted at: 12:15 |
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Point to a plane
It looks like there will be some cases when I can just use point to plane
math. Here’s a
nice summary of that.
posted at: 12:15 |
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All material copyrighted by Jen Schellinck. All rights reserved.