Publications by Nathan Brouwer
Higgs Chart Replication
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, 114,1...
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What Was Done: To produce the trees in this assignment the msa of the five different organisms had to be analyzed in excel. 10 random loci were selected from the entire sequence. These 10 loci were then lined up to be scored based on differences in alleles. To do so, two organisms are compared at a time to derive their percent identity. If the al...
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PVA Portfolio
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 <- 1:39 year t The year: 1959 to 1997 (Dennis et al use 1959-1987) year.t <- 1959:1997 Population size Population size is...
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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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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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Intro This script takes data from the amino acids and analyzes it. It includes numerous characteristics about each f the amino acids and plots them based on correlations. PCA and UPGMA are also completed to further enhance the data. The relationships between the data are eventually plotted in a dendrogram based on similarities. Ggplot2 is a packa...
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