Publications by Tyler Whitfield
A Bit About Me
Hello, my name is Tyler Whitfield. I am a junior computational biology major at Pitt. I have previously taken classes in Visual Basic and Java, and I am currently taking a class in Python and R too. Java is the language that I have the most experience with (3 semesters). I hope to conduct some form of computational research regarding oral health ...
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R Markdown This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com. When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within t...
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Distance-based phylogenetic trees in R
Overview of Data Used This paragraph will explain how I obtained the data to build the 5x5 matrix and accompanying phylogenetic trees. First, I accessed the chimp sequence alignments and color coded the bases. This made it easy to quickly identify each base in the table. I then selected 10 polymorphic loci to work with. A loci occurs when all 5 t...
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Computational Ecology: Population Viability Analysis 9/15/2020 - 9/17/2020
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. # Index of years of data census <- 1:39 year t The year: 1959 to 1997 (Dennis et al use 1959-1987) #Years of interest from 1957-19...
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9-15 Class Notes
Functions 9-15 Bulleted lists in markdown mean() var() Census # Index of years of data census <- 1:39 Years #Years of intrest from 1957-1997 year.t <- 1959:1997 Population Size #Dummy info representing the population size of females each year females.N <- c(1,2,3) Population growth rate is the change in population over the time. (Usually a...
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Computational Ecology: Population Viability Analysis 9/15/2020
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. # Index of years of data census <- 1:39 year t The year: 1959 to 1997 (Dennis et al use 1959-1987) #Years of interest from 1957-19...
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Replicating Higgs and Attwood’s analysis on the properties of amino acids
Introduction The purpose of this script is to replicate the calculations and analysis that Higgs and Attwood conducted by using cluster analysis, PCA, and other means of searching for statistical relationships.This analysis focused around amino acids, and many of their properties. In analyzing these properties, we can search for relationships bet...
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Tutorial: Building dataframe 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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Function Writing Assignment
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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