Finalizing dinucleotide CpG island counts with sliding window
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.Rhistory
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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g.breaks <- g.hist$breaks[-c(1,2,3)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.breaks[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.breaks[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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#g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.breaks <- g.hist$breaks # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.breaks[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.probs[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean)/kmin)
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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alpha.LM
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.probs[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=5)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.probs[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
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# Degree Distribution
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# Professor: Dr. McKinney, Spring 2022
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# Noah Schrick - 1492657
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=3)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2)
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################# Linear model: Least-Squares Fit #################
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g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.probs[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4)
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# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
|
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# Degree Distribution
|
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# Professor: Dr. McKinney, Spring 2022
|
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# Noah Schrick - 1492657
|
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library(igraph)
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library(igraphdata)
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data(yeast)
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g <- yeast
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g.netname <- "Yeast"
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################# Set up Work #################
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g.vec <- degree(g)
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g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
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" Network"))
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legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
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"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
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"#006CD1", "#E66100", "#D35FB7"))
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g.mean <- mean(g.vec)
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g.seq <- 0:max(g.vec) # x-axis
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################# Guessing Alpha #################
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alpha.guess <- 1.5
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lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=3)
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################# Poisson #################
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g.pois <- dpois(g.seq, g.mean, log=F)
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lines(g.seq, g.pois, col="#006CD1", lty=2, lwd=3)
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################# Linear model: Least-Squares Fit #################
|
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g.breaks <- g.hist$breaks[-c(1)] # remove 0
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g.probs <- g.hist$density[-1] # make lengths match
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# Need to clean up probabilities that are 0
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nz.probs.mask <- g.probs!=0
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g.breaks.clean <- g.breaks[nz.probs.mask]
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g.probs.clean <- g.probs[nz.probs.mask]
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#plot(log(g.breaks.clean), log(g.probs.clean))
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g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
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summary(g.fit)
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alpha.LM <- coef(g.fit)[2]
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lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3, lwd=3)
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################# Max-Log-Likelihood #################
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n <- length(g.breaks.clean)
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kmin <- g.breaks.clean[1]
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alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
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alpha.ML
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lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4, lwd=3)
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plot(yeast)
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hist(yeast)
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hist(g.vec)
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g.pois
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g.mean
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alpha.LM
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alpha.ML
|
||||
degree(g)
|
||||
sort(degree(g))
|
||||
sort(degree(g),decreasing=FALSE)
|
||||
sort(degree(g),decreasing=F)
|
||||
sort(degree(g),decreasing=false)
|
||||
sort(degree(g), decreasing = TRUE)
|
||||
head(sort(degree(g), decreasing = TRUE))
|
||||
stddev(degree(g))
|
||||
sd(degree(g))
|
||||
tail(sort(degree(g), decreasing = TRUE))
|
||||
plot(log(g.breaks.clean), log(g.probs.clean))
|
||||
# Homework 4 for the University of Tulsa' s CS-7863 Network Theory Course
|
||||
# Degree Distribution
|
||||
# Professor: Dr. McKinney, Spring 2022
|
||||
# Noah Schrick - 1492657
|
||||
library(igraph)
|
||||
library(igraphdata)
|
||||
data(yeast)
|
||||
g <- yeast
|
||||
g.netname <- "Yeast"
|
||||
################# Set up Work #################
|
||||
g.vec <- degree(g)
|
||||
g.hist <- hist(g.vec, freq=FALSE, main=paste("Histogram of the", g.netname,
|
||||
" Network"))
|
||||
legend("topright", c("Guess", "Poisson", "Least-Squares Fit",
|
||||
"Max Log-Likelihood"), lty=c(1,2,3,4), col=c("#40B0A6",
|
||||
"#006CD1", "#E66100", "#D35FB7"))
|
||||
g.mean <- mean(g.vec)
|
||||
g.seq <- 0:max(g.vec) # x-axis
|
||||
################# Guessing Alpha #################
|
||||
alpha.guess <- 1.5
|
||||
lines(g.seq, g.seq^(-alpha.guess), col="#40B0A6", lty=1, lwd=3)
|
||||
################# Poisson #################
|
||||
g.pois <- dpois(g.seq, g.mean, log=F)
|
||||
lines(g.seq, g.pois, col="#006CD1", lty=2, lwd=3)
|
||||
################# Linear model: Least-Squares Fit #################
|
||||
g.breaks <- g.hist$breaks[-c(1)] # remove 0
|
||||
g.probs <- g.hist$density[-1] # make lengths match
|
||||
# Need to clean up probabilities that are 0
|
||||
nz.probs.mask <- g.probs!=0
|
||||
g.breaks.clean <- g.breaks[nz.probs.mask]
|
||||
g.probs.clean <- g.probs[nz.probs.mask]
|
||||
plot(log(g.breaks.clean), log(g.probs.clean))
|
||||
g.fit <- lm(log(g.probs.clean)~log(g.breaks.clean))
|
||||
summary(g.fit)
|
||||
alpha.LM <- coef(g.fit)[2]
|
||||
lines(g.seq, g.seq^(-alpha.LM), col="#E66100", lty=3, lwd=3)
|
||||
################# Max-Log-Likelihood #################
|
||||
n <- length(g.breaks.clean)
|
||||
kmin <- g.breaks.clean[1]
|
||||
alpha.ML <- 1 + n/sum(log(g.breaks.clean/kmin))
|
||||
alpha.ML
|
||||
lines(g.seq, g.seq^(-alpha.ML), col="#D35FB7", lty=4, lwd=3)
|
||||
plot(log(g.breaks.clean), log(g.probs.clean))
|
||||
g.breaks.clean <- g.breaks[nz.probs.mask]
|
||||
g.probs.clean <- g.probs[nz.probs.mask]
|
||||
plot(log(g.breaks.clean), log(g.probs.clean))
|
||||
#### Part B: Loop Recursion Warmup
|
||||
m <- 3 # row edges
|
||||
n <- 6 # col edges
|
||||
path_matrix <- matrix(1, nrow=m+1, ncol=n+1)
|
||||
for (i in seq(2,m+1)){
|
||||
for (j in seq(2, n+1)){
|
||||
path_matrix[i,j] <- path_matrix[i-1,j] + path_matrix[i,j-1]
|
||||
}
|
||||
}
|
||||
path_matrix
|
||||
path_matrix[m][n]
|
||||
path_matrix[m]
|
||||
path_matrix[n]
|
||||
path_matrix[m,n]
|
||||
path_matrix[m+1,n+1]
|
||||
calc.num.paths <- function(n,m){
|
||||
path_matrix <- matrix(1, nrow=m+1, ncol=n+1)
|
||||
for (i in seq(2,m+1)){
|
||||
for (j in seq(2, n+1)){
|
||||
path_matrix[i,j] <- path_matrix[i-1,j] + path_matrix[i,j-1]
|
||||
}
|
||||
}
|
||||
path_matrix[m+1,n+1]
|
||||
}
|
||||
#### Part B: Loop Recursion Warmup
|
||||
calc.num.paths <- function(n,m){
|
||||
path_matrix <- matrix(1, nrow=m+1, ncol=n+1)
|
||||
for (i in seq(2,m+1)){
|
||||
for (j in seq(2, n+1)){
|
||||
path_matrix[i,j] <- path_matrix[i-1,j] + path_matrix[i,j-1]
|
||||
}
|
||||
}
|
||||
path_matrix[m+1,n+1]
|
||||
}
|
||||
m <- 5 # row edges
|
||||
n <- 5 # col edges
|
||||
calc.num.paths(n,m)
|
||||
m <- 5 # row edges
|
||||
n <- 6 # col edges
|
||||
calc.num.paths(n,m)
|
||||
m <- 10 # row edges
|
||||
n <- 10 # col edges
|
||||
calc.num.paths(n,m)
|
||||
factorial(n+m)/(factorial(n)*factorial(m))
|
||||
m <- 5 # row edges
|
||||
n <- 5 # col edges
|
||||
calc.num.paths(n,m)
|
||||
factorial(n+m)/(factorial(n)*factorial(m))
|
||||
m <- 5 # row edges
|
||||
n <- 6 # col edges
|
||||
calc.num.paths(n,m)
|
||||
factorial(n+m)/(factorial(n)*factorial(m))
|
||||
m <- 10 # row edges
|
||||
n <- 10 # col edges
|
||||
calc.num.paths(n,m)
|
||||
factorial(n+m)/(factorial(n)*factorial(m))
|
||||
h1n1.Cali
|
||||
h1n1.Cali.dna.vec <- fasta2vec("FJ969540.1.fasta")
|
||||
#### Part A: EMBOSS pairwise alignment server and influenza
|
||||
## Load associated supportive libraries
|
||||
if (!require("seqinr")) install.packages("seqinr")
|
||||
library(seqinr)
|
||||
## Load in the fasta file
|
||||
fasta2vec <- function(fasta.file){
|
||||
if (!require("seqinr")) install.packages("seqinr")
|
||||
library(seqinr)
|
||||
fasta <- read.fasta(file=fasta.file, as.string= TRUE)
|
||||
fasta.string <- fasta[[1]][1]
|
||||
fasta.list <- strsplit(fasta.string,"")
|
||||
fasta.vec <- unlist(fasta.list)
|
||||
}
|
||||
h1n1.Cali.dna.vec <- fasta2vec("FJ969540.1.fasta")
|
||||
## Set Working Directory to file directory - RStudio approach
|
||||
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
|
||||
h1n1.Cali.dna.vec <- fasta2vec("FJ969540.1.fasta")
|
||||
h1n1.Cali.dna.vec[1:5]
|
||||
?count
|
||||
count(h1n1.Cali.dna.vec[1:5],2)
|
||||
count(h1n1.Cali.dna.vec[1:5],2)["aa"]
|
||||
count(h1n1.Cali.dna.vec[1:5],11)
|
||||
count(h1n1.Cali.dna.vec[1:5],1)
|
||||
#### Part C: Dinucleotide Signals
|
||||
calc.sliding.cpg <- function(fastaVec, slideWin){
|
||||
# allocate memory for odds ratio output
|
||||
cg_dinuc_oddsRatio <- double()
|
||||
n<-length(fastaVec)
|
||||
for (i in 1:(n-slideWin)){
|
||||
# array slice the vectpr on sliding window size and obtain dinuc appearances
|
||||
dinucs<-count(fastaVec[i:(i+slideWin)],2)
|
||||
# retrieve number of times "CG" appeared
|
||||
cg_dinuc_count <- dinucs["cg"]
|
||||
# get counts of all nucleotides
|
||||
nucs<-count(fastaVec[i:(i+slideWin)],1)
|
||||
# obtain times dinuc pairing appeared per times the indiv nucs appeared
|
||||
cg_dinuc_oddsRatio[i] <-
|
||||
cg_dinuc_count/(nucs["c"]*nucs["g"])
|
||||
}
|
||||
return(cg_dinuc_oddsRatio) # returns vector
|
||||
}
|
||||
apoe.fasta.vec <- fasta2vec("apoe.fasta")
|
||||
cpg_vec <- calc.sliding.cpg(apoe.fasta.vec,150)
|
||||
plot(cpg_vec,type="l",main="Observed vs Expected CG",xlab="Base Index", ylab="Obs/Exp")
|
||||
cpg_vec
|
||||
@ -75,4 +75,25 @@ n <- 10 # col edges
|
||||
calc.num.paths(n,m)
|
||||
factorial(n+m)/(factorial(n)*factorial(m))
|
||||
|
||||
#### Part C: Dinucleotide Signals
|
||||
calc.sliding.cpg <- function(fastaVec, slideWin){
|
||||
# allocate memory for odds ratio output
|
||||
cg_dinuc_oddsRatio <- double()
|
||||
n<-length(fastaVec)
|
||||
for (i in 1:(n-slideWin)){
|
||||
# array slice the vectpr on sliding window size and obtain dinuc appearances
|
||||
dinucs<-count(fastaVec[i:(i+slideWin)],2)
|
||||
# retrieve number of times "CG" appeared
|
||||
cg_dinuc_count <- dinucs["cg"]
|
||||
# get counts of all nucleotides
|
||||
nucs<-count(fastaVec[i:(i+slideWin)],1)
|
||||
# obtain times dinuc pairing appeared per times the indiv nucs appeared
|
||||
cg_dinuc_oddsRatio[i] <-
|
||||
cg_dinuc_count/(nucs["c"]*nucs["g"])
|
||||
}
|
||||
return(cg_dinuc_oddsRatio) # returns vector
|
||||
}
|
||||
|
||||
apoe.fasta.vec <- fasta2vec("apoe.fasta")
|
||||
cpg_vec <- calc.sliding.cpg(apoe.fasta.vec,150)
|
||||
plot(cpg_vec,type="l",main="Observed vs Expected CG",xlab="Base Index", ylab="Obs/Exp")
|
||||
|
||||
Binary file not shown.
BIN
Schrick-Noah_CS-6643_Lab-8.pdf
Normal file
BIN
Schrick-Noah_CS-6643_Lab-8.pdf
Normal file
Binary file not shown.
54
apoe.fasta
Normal file
54
apoe.fasta
Normal file
@ -0,0 +1,54 @@
|
||||
>NC_000019.10:44905796-44909393 Homo sapiens chromosome 19, GRCh38.p14 Primary Assembly
|
||||
CTACTCAGCCCCAGCGGAGGTGAAGGACGTCCTTCCCCAGGAGCCGGTGAGAAGCGCAGTCGGGGGCACG
|
||||
GGGATGAGCTCAGGGGCCTCTAGAAAGAGCTGGGACCCTGGGAACCCCTGGCCTCCAGGTAGTCTCAGGA
|
||||
GAGCTACTCGGGGTCGGGCTTGGGGAGAGGAGGAGCGGGGGTGAGGCAAGCAGCAGGGGACTGGACCTGG
|
||||
GAAGGGCTGGGCAGCAGAGACGACCCGACCCGCTAGAAGGTGGGGTGGGGAGAGCAGCTGGACTGGGATG
|
||||
TAAGCCATAGCAGGACTCCACGAGTTGTCACTATCATTTATCGAGCACCTACTGGGTGTCCCCAGTGTCC
|
||||
TCAGATCTCCATAACTGGGGAGCCAGGGGCAGCGACACGGTAGCTAGCCGTCGATTGGAGAACTTTAAAA
|
||||
TGAGGACTGAATTAGCTCATAAATGGAACACGGCGCTTAACTGTGAGGTTGGAGCTTAGAATGTGAAGGG
|
||||
AGAATGAGGAATGCGAGACTGGGACTGAGATGGAACCGGCGGTGGGGAGGGGGTGGGGGGATGGAATTTG
|
||||
AACCCCGGGAGAGGAAGATGGAATTTTCTATGGAGGCCGACCTGGGGATGGGGAGATAAGAGAAGACCAG
|
||||
GAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGCTTGGTAAATGTGCTGGGATTAGGCTGTTGCAGATAA
|
||||
TGCAACAAGGCTTGGAAGGCTAACCTGGGGTGAGGCCGGGTTGGGGCCGGGCTGGGGGTGGGAGGAGTCC
|
||||
TCACTGGCGGTTGATTGACAGTTTCTCCTTCCCCAGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCT
|
||||
GTGGGCTGCGTTGCTGGTCACATTCCTGGCAGGTATGGGGGCGGGGCTTGCTCGGTTCCCCCCGCTCCTC
|
||||
CCCCTCTCATCCTCACCTCAACCTCCTGGCCCCATTCAGGCAGACCCTGGGCCCCCTCTTCTGAGGCTTC
|
||||
TGTGCTGCTTCCTGGCTCTGAACAGCGATTTGACGCTCTCTGGGCCTCGGTTTCCCCCATCCTTGAGATA
|
||||
GGAGTTAGAAGTTGTTTTGTTGTTGTTGTTTGTTGTTGTTGTTTTGTTTTTTTGAGATGAAGTCTCGCTC
|
||||
TGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACTGCAAGCTCCGCCTCCCAGGTCCACGCCA
|
||||
TTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCACATGCCACCACACCCGACTAACTTTTTTG
|
||||
TATTTTCAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTGGAACTCCTGACCTCAGGTGATCT
|
||||
GCCCGTTTCGATCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCTGGGAGTTAGAGGT
|
||||
TTCTAATGCATTGCAGGCAGATAGTGAATACCAGACACGGGGCAGCTGTGATCTTTATTCTCCATCACCC
|
||||
CCACACAGCCCTGCCTGGGGCACACAAGGACACTCAATACATGCTTTTCCGCTGGGCGCGGTGGCTCACC
|
||||
CCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGGGAGGATCACTTGAGCCCAGGAGTTCAACACCAGCCT
|
||||
GGGCAACATAGTGAGACCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGCCACACACCTGT
|
||||
GCTCTCAGCTACTCAGGAGGCTGAGGCAGGAGGATCGCTTGAGCCCAGAAGGTCAAGGTTGCAGTGAACC
|
||||
ATGTTCAGGCCGCTGCACTCCAGCCTGGGTGACAGAGCAAGACCCTGTTTATAAATACATAATGCTTTCC
|
||||
AAGTGATTAAACCGACTCCCCCCTCACCCTGCCCACCATGGCTCCAAAGAAGCATTTGTGGAGCACCTTC
|
||||
TGTGTGCCCCTAGGTACTAGATGCCTGGACGGGGTCAGAAGGACCCTGACCCACCTTGAACTTGTTCCAC
|
||||
ACAGGATGCCAGGCCAAGGTGGAGCAAGCGGTGGAGACAGAGCCGGAGCCCGAGCTGCGCCAGCAGACCG
|
||||
AGTGGCAGAGCGGCCAGCGCTGGGAACTGGCACTGGGTCGCTTTTGGGATTACCTGCGCTGGGTGCAGAC
|
||||
ACTGTCTGAGCAGGTGCAGGAGGAGCTGCTCAGCTCCCAGGTCACCCAGGAACTGAGGTGAGTGTCCCCA
|
||||
TCCTGGCCCTTGACCCTCCTGGTGGGCGGCTATACCTCCCCAGGTCCAGGTTTCATTCTGCCCCTGTCGC
|
||||
TAAGTCTTGGGGGGCCTGGGTCTCTGCTGGTTCTAGCTTCCTCTTCCCATTTCTGACTCCTGGCTTTAGC
|
||||
TCTCTGGAATTCTCTCTCTCAGCTTTGTCTCTCTCTCTTCCCTTCTGACTCAGTCTCTCACACTCGTCCT
|
||||
GGCTCTGTCTCTGTCCTTCCCTAGCTCTTTTATATAGAGACAGAGAGATGGGGTCTCACTGTGTTGCCCA
|
||||
GGCTGGTCTTGAACTTCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTAGAGGC
|
||||
ATGAGCCACCTTGCCCGGCCTCCTAGCTCCTTCTTCGTCTCTGCCTCTGCCCTCTGCATCTGCTCTCTGC
|
||||
ATCTGTCTCTGTCTCCTTCTCTCGGCCTCTGCCCCGTTCCTTCTCTCCCTCTTGGGTCTCTCTGGCTCAT
|
||||
CCCCATCTCGCCCGCCCCATCCCAGCCCTTCTCCCCGCCTCCCACTGTGCGACACCCTCCCGCCCTCTCG
|
||||
GCCGCAGGGCGCTGATGGACGAGACCATGAAGGAGTTGAAGGCCTACAAATCGGAACTGGAGGAACAACT
|
||||
GACCCCGGTGGCGGAGGAGACGCGGGCACGGCTGTCCAAGGAGCTGCAGGCGGCGCAGGCCCGGCTGGGC
|
||||
GCGGACATGGAGGACGTGTGCGGCCGCCTGGTGCAGTACCGCGGCGAGGTGCAGGCCATGCTCGGCCAGA
|
||||
GCACCGAGGAGCTGCGGGTGCGCCTCGCCTCCCACCTGCGCAAGCTGCGTAAGCGGCTCCTCCGCGATGC
|
||||
CGATGACCTGCAGAAGCGCCTGGCAGTGTACCAGGCCGGGGCCCGCGAGGGCGCCGAGCGCGGCCTCAGC
|
||||
GCCATCCGCGAGCGCCTGGGGCCCCTGGTGGAACAGGGCCGCGTGCGGGCCGCCACTGTGGGCTCCCTGG
|
||||
CCGGCCAGCCGCTACAGGAGCGGGCCCAGGCCTGGGGCGAGCGGCTGCGCGCGCGGATGGAGGAGATGGG
|
||||
CAGCCGGACCCGCGACCGCCTGGACGAGGTGAAGGAGCAGGTGGCGGAGGTGCGCGCCAAGCTGGAGGAG
|
||||
CAGGCCCAGCAGATACGCCTGCAGGCCGAGGCCTTCCAGGCCCGCCTCAAGAGCTGGTTCGAGCCCCTGG
|
||||
TGGAAGACATGCAGCGCCAGTGGGCCGGGCTGGTGGAGAAGGTGCAGGCTGCCGTGGGCACCAGCGCCGC
|
||||
CCCTGTGCCCAGCGACAATCACTGAACGCCGAAGCCTGCAGCCATGCGACCCCACGCCACCCCGTGCCTC
|
||||
CTGCCTCCGCGCAGCCTGCAGCGGGAGACCCTGTCCCCGCCCCAGCCGTCCTCCTGGGGTGGACCCTAGT
|
||||
TTAATAAAGATTCACCAAGTTTCACGCA
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user