Publications by Nathan Brouwer
Amino Acid Chemistry Data
Build the dataframe This code makes all of the columns and makes a dataframe aa <-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y') MW.da <-c(89,121,133,146,165,75,155,131,146,131,149,132,115,147,174,105,119,117,204,181) volume <-c(67,86,91,109,135,48,118,124,135,124,124,96,90, 114,148,...
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Bear Population Simulation
TUESDAY’s CODE Data: Figure 5 (plus 10 years) Make data vectors, calculate lambda, and put together dataframe with all necessary data. census The census period; an index from 1 to 39 of how many years of data have been collected. census <- c(1:39) year t The year: 1959 to 1997 (Dennis et al use 1959-1987) year.t <- c(1959:1997) Population s...
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Test
Test R Markdown Testing random sample generation in R (from lecture 5) telos.dist <- rnorm(n = 10000, #dreamy sample size mean = 10000, #odin mode sd = 30) summary(telos.dist) ## Min. 1st Qu. Median Mean 3rd Qu. Max. ## 9888 9979 9999 9999 10019 10114 Testing graph generation in ...
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Distance-based phylogenetic trees in R
Obtaining Matrices To obtain the matrix for constructing phylogenetic trees, we randomly selected 10 loci in the Excel sheet for sequences of all five species (Mahale East, Gombe, Bodongo, Tai West and Mali West) and aligned them. We then summed up the similarities and differences pairwise by writing logical functions and determined the ratio of ...
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Replicating Higgs and Attwood's analysis on the properties of amino acids
Introduction We attempt to replicate Higgs and Attwood’s analysis on various properties of amino acids on a different set of data (Higgs 2009). We build data frames based on the data, and from there visualize our data in different ways in order to find patterns and relationships. We start with making a correlation matrix which allows us to see ...
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Assignment: Function writing
Assignment: unrooted trees We often don’t root phylogenetic trees. This reduces the number of possible trees and is described by the equation: Text: (2n-5)!/[2n-3*(n-3)!] Rendered: \(\frac{(2*n-5)!}{2^{n-3} * (n-3)!}\) Assignment part 1 Modify the function used in the “number of phylogenetic trees” tutorial to work for unrooted trees. Comp...
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Building dataframe in R by hand
Introduction This exercise is meant to challenge you to build a dataframe by hand in R. It is based off of the Table 1 in Drake (1991) “A constant rate of spontaneous mutation in DNA-base microbes” (PNAS August 15, 1991 88 (16) 7160-7164; https://doi.org/10.1073/pnas.88.16.7160) There are two parts to this tutorial. This versions will guide y...
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