My final project

Introduction

We can cite papers by attributing things to publications directly like Felsenstein (1985b) or making declarative statements supported by a publication (Felsenstein 1981), or more than one publication (Felsenstein 1981, 1985a). These citations are in bibtex format in an accompanying file, citations.bibtex. The formatted citations were copied and pasted from the cite button in google scholar for each reference.

It’s easy to include images.

Figure 1: A painting of a mummichog, Fundulus heteroclitus

We can reference Figure 1.

Methods

If you need to explain some code without running it, you can show it like this, denoting the language for syntax highlighting.

head myfile.txt | cut -f 3 | sort | uniq -c

Results

Results subsection 1

I’m going to make a plot of some simulated data.

x <- rnorm(500, mean=5, sd=2)
y <- x + rnorm(500)
plot(x, y)

Figure 2: Totally bogus data.

Results subsection 2

Let’s print this table.

df <- data.frame(x=x,y=y)
df 

Table 1: Random correlated data

Results subsection 3

We can also hide the code and just print the results.

Figure 3: Histogram of random x.

Discussion

You can see from Figure 2 the data are correlated. You can see from Table 1 that rendering the whole table is superfluous. You should not be able to see the histogram code for Figure 3 in the rendered document.

Conclusions

References

Felsenstein, Joseph. 1981. “Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach.” Journal of Molecular Evolution 17: 368–76.

———. 1985a. “Confidence Limits on Phylogenies: An Approach Using the Bootstrap.” Evolution 39 (4): 783–91.

———. 1985b. “Phylogenies and the Comparative Method.” The American Naturalist 125 (1): 1–15.