Ok, so I should be sound asleep by now, but instead I've been sitting here plugging away at Verzani and trying to make heads or tails of my homework problems. Here's a summary of the conversation I was having with "R":
me > do this
R: NO! Error could not find function
me> ok, try this instead?
R: NO! Syntax Error
me> Ummmmm... let's be reasonable. How about this?
R: NO! Warning message
me> Puhleeeeeaaaaaasssssee do this? I'll be your friend.
R: ABSOLUTELY NOT! ERROR! ERROR! ERROR!
I have pages like this...
Anyway, I was getting the numbers associated with the Normal(x,y) distribution abbreviation mixed up with max and min. Just before I was about to throw in the towel (resolving to deprive myself of more sleep and work on this early in the morning), I realized that the numbers in the brackets are actually the mean and standard deviation (how did I miss that!?!). After having this epiphany, I was able to finish my homework problems in 10-15 minutes!
It's so weird how I'll sit and stare at the same scribbles on the same pages for hours and miss some of the most important points!
Ok, time for me to hit the hay! See you all in the morning...
Wednesday, February 28, 2007
Tuesday, February 27, 2007
Coley et al 2006
Yesterday for Journal Club we read a paper by Coley et al (2006) for Journal Club titled "The effects of plant quality on caterpillar growth and defense against natural enemies". Although I think we all enjoyed the read, most of our discussion revolved around aspects of the paper that we found problematic. Among the problems we discussed, was one that made me think of what we are and will be learning in Biostats and Experimental Design.
The researchers had opportunistically captured 85 species of caterpillars on 40 different species of plants. The researchers also noted weather the leaf they found the caterpillar on was young or old. The caterpillars were then reared on the same species of plant and the same age of leaf that they had been found on for the remainder of the experiment in order to assess growth rates.
One problem that was brought to my attention by a faculty member, who had reviewed the paper before it went for publication, was that the researchers used an ANOVA to evaluate the caterpillar growth rate data. She explained that an ANOVA was inappropriate because the caterpillars were never randomly assigned treatments. Instead, they were reared only on the plant and leaf age they were found upon, without ever testing to find out how the various species would develop on other, random plant assignments.
I look forward to learning more about how to apply ANOVAs and to the day when I might actually understand how to apply them to my own studies. It is a bit intimidating to know that even very experienced researchers sometimes aren't sure which statistical analyses are best fit for their data!
References:
P. D. Coley, M. L. Bateman, T. A. Kursar (2006) The effects of plant quality on caterpillar growth and defense against natural enemies Oikos 115 (2), 219–228.
The researchers had opportunistically captured 85 species of caterpillars on 40 different species of plants. The researchers also noted weather the leaf they found the caterpillar on was young or old. The caterpillars were then reared on the same species of plant and the same age of leaf that they had been found on for the remainder of the experiment in order to assess growth rates.
One problem that was brought to my attention by a faculty member, who had reviewed the paper before it went for publication, was that the researchers used an ANOVA to evaluate the caterpillar growth rate data. She explained that an ANOVA was inappropriate because the caterpillars were never randomly assigned treatments. Instead, they were reared only on the plant and leaf age they were found upon, without ever testing to find out how the various species would develop on other, random plant assignments.
I look forward to learning more about how to apply ANOVAs and to the day when I might actually understand how to apply them to my own studies. It is a bit intimidating to know that even very experienced researchers sometimes aren't sure which statistical analyses are best fit for their data!
References:
P. D. Coley, M. L. Bateman, T. A. Kursar (2006) The effects of plant quality on caterpillar growth and defense against natural enemies Oikos 115 (2), 219–228.
Thursday, February 15, 2007
New Bling...
I just thought I'd explain the new pictures I've posted. I was very excited when I figured out that I could display pictures, so I dug up a few.
The graph is the result of the problem I tackled from Verzani chapter 3. It is a scatterplot of the correlation between carat size and price (in Singapore dollars) of 48 diamond rings. As you would guess, the correlation is extremely high. I think it was close to 1 when I asked "R" to calculate it for me. When I get a chance, I will try and post my cool new histogram and barplots from Verzani ch 4.
The funny little kid in the hood and great big glasses is my nephew at 8 or 9 years old. He's wearing a pair of glasses I bought for him that are supposed to give you insect vision! If you haven't tried them, the lenses are made up of several prisms, so that when you put them on your view becomes hundreds of tiny pictures instead of one large frame. This is supposed to mimic the multi-faceted compound eye of some insects, such as flies. However, I've recently read that this is a misconception because the animal's brain is able to integrate the many views into one single image. I'll have to tell my nephew before he spreads false information to any more 5th graders.
The last two images relate to the data set that I am planning to use for my independent project. My data set was compiled from pitfall trap collections taken in a grassland in South-Central Texas before and after a prescribed burn. Collections were also taken at a near by control field. The pictures show the manipulated field before and after the burn event. You can see that approximately 85-90% of the living herbaceous matter has been removed by the fire or replaced with standing dead biomass. It will be interesting to see the effects this will have on the resident insect communities. In particular, I would like to focus on the dominant native and invasive ant populations in the field. Some key points are driving my curiosity here:
1) Invasive species are generally positively affected by habitat disturbance.
2) Although native and invasive ants in this field nest below ground, the invasive ants nest much deeper than the natives. Therefore, the invasive species would have an increased ability to retreat away from fatally high temperatures possibly produced by the fire.
3) One of the native ant species is strictly granivorous. The other dominant native ant species is omnivorous, while the invasive species is a highly aggressive, omnivorous scavenger. The variability in diet demands of the dominant ant species in the field make me wonder how the abrupt loss of vegetation (and supposedly a significant portion of the seed bank, according to the grassland specialists from the Lady Bird Johnson Wildflower Center) will immediately affect these populations.
The graph is the result of the problem I tackled from Verzani chapter 3. It is a scatterplot of the correlation between carat size and price (in Singapore dollars) of 48 diamond rings. As you would guess, the correlation is extremely high. I think it was close to 1 when I asked "R" to calculate it for me. When I get a chance, I will try and post my cool new histogram and barplots from Verzani ch 4.
The funny little kid in the hood and great big glasses is my nephew at 8 or 9 years old. He's wearing a pair of glasses I bought for him that are supposed to give you insect vision! If you haven't tried them, the lenses are made up of several prisms, so that when you put them on your view becomes hundreds of tiny pictures instead of one large frame. This is supposed to mimic the multi-faceted compound eye of some insects, such as flies. However, I've recently read that this is a misconception because the animal's brain is able to integrate the many views into one single image. I'll have to tell my nephew before he spreads false information to any more 5th graders.
The last two images relate to the data set that I am planning to use for my independent project. My data set was compiled from pitfall trap collections taken in a grassland in South-Central Texas before and after a prescribed burn. Collections were also taken at a near by control field. The pictures show the manipulated field before and after the burn event. You can see that approximately 85-90% of the living herbaceous matter has been removed by the fire or replaced with standing dead biomass. It will be interesting to see the effects this will have on the resident insect communities. In particular, I would like to focus on the dominant native and invasive ant populations in the field. Some key points are driving my curiosity here:
1) Invasive species are generally positively affected by habitat disturbance.
2) Although native and invasive ants in this field nest below ground, the invasive ants nest much deeper than the natives. Therefore, the invasive species would have an increased ability to retreat away from fatally high temperatures possibly produced by the fire.
3) One of the native ant species is strictly granivorous. The other dominant native ant species is omnivorous, while the invasive species is a highly aggressive, omnivorous scavenger. The variability in diet demands of the dominant ant species in the field make me wonder how the abrupt loss of vegetation (and supposedly a significant portion of the seed bank, according to the grassland specialists from the Lady Bird Johnson Wildflower Center) will immediately affect these populations.
Thursday, February 1, 2007
Vascular and Photosynthetic Plant Structure Diagrams
Stem and Leaf plots were giving me a headache today in class. I'm still not quite sure how the plot for the "island" problem works, but here's an explaination I found online that helped me grasp the concept a little better.
What Are They Used For?They are usually used when there are large amounts of numbers to analyze. Series of scores on sports teams, series of temperatures or rainfall over a period of time, series of classroom test scores are examples of when Stem and Leaf Plots could be used.
What Does a Stem and Leaf Look Like?Example:
Test Scores Out Of 100
Stem Leaf
9 2 2 6 8
8 3 5
7 2 4 6 8 8 9
6 1 4 4 7 8
5 0 0 2 8 8
What does this Stem and Leaf Plot Show?The Stem shows the 'tens' and the leaf. At a glance, one can see that 4 students got a mark in the 90's on their test out of 100. Two students received the same mark of 92. No marks were received below 50. No mark of 100 was received. When you count the total amount of leaves, you know how many students took the test. The information is nicely organized when a Stem and Leaf Plot is used. Stem and Leaf Plots provide an 'at a glance' tool for specific information in large sets of data, otherwise one would have a long list of marks to sift through and analyze.
I also posted this on the notes for JV Ch 2, but I thought that more people might benefit from it if I posted it here as well.
Rebecca
What Are They Used For?They are usually used when there are large amounts of numbers to analyze. Series of scores on sports teams, series of temperatures or rainfall over a period of time, series of classroom test scores are examples of when Stem and Leaf Plots could be used.
What Does a Stem and Leaf Look Like?Example:
Test Scores Out Of 100
Stem Leaf
9 2 2 6 8
8 3 5
7 2 4 6 8 8 9
6 1 4 4 7 8
5 0 0 2 8 8
What does this Stem and Leaf Plot Show?The Stem shows the 'tens' and the leaf. At a glance, one can see that 4 students got a mark in the 90's on their test out of 100. Two students received the same mark of 92. No marks were received below 50. No mark of 100 was received. When you count the total amount of leaves, you know how many students took the test. The information is nicely organized when a Stem and Leaf Plot is used. Stem and Leaf Plots provide an 'at a glance' tool for specific information in large sets of data, otherwise one would have a long list of marks to sift through and analyze.
I also posted this on the notes for JV Ch 2, but I thought that more people might benefit from it if I posted it here as well.
Rebecca
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