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.Rapp.history
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supgma <- read.csv("supgma_example_2.csv", header=TRUE)
ex3 <- lm(dist ~ theta1 + theta2 + theta3 + delta1 + delta2, supgma)
summary(ex3)
mem.limits
memory.limit
plot(c(1,2), c(3,4))
plot(c(1,2), c(3,4), type="l")
plot(c(c(1,2),c(1,1.5)), c(c(3,4),c(2,3.4)), type="l")
library(ape)
plot(tree)
phylogram.plot
plot.phylo
mean_c <- c(3.46E-06,6.41E-06,6.72E-06)
error_c <- mean_c
mean_c <- c(6.90E-05,7.32E-05,6.86E-05)
library(ggplot2)
psi <- c(0,0.5,1.0)
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_cm ymax=mean_c+error_c))
ggplot() + geom_point(x=psi, y=mean_c) + geom_errorbar(aes(x=psi, ymin=mean_c-error_cm ymax=mean_c+error_c))
ggplot() + geom_point(x=psi, y=mean_c) + geom_errorbar(x=psi, ymin=mean_c-error_cm ymax=mean_c+error_c)
ggplot() + geom_point(x=psi, y=mean_c) + geom_errorbar(x=psi, ymin=mean_c-error_cm, ymax=mean_c+error_c)
ggplot() + geom_point(x=psi, y=mean_c) + geom_errorbar(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c)
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c)
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c))
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.1)
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01)
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c))
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(4e-5, 8e-5))
mean_e <- c(5.36E-05,5.40E-05,5.39E-05)
error_e <- c(1.42E-05,1.03E-05,1.36E-05)
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(4e-5, 8e-5)) + theme_bw()
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(4e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e)) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01) + geom_line(aes(x=psi, y=mean_e))
error_e
error_c
mean_e
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(4e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e)) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01) + geom_line(aes(x=psi, y=mean_e))
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e)) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01) + geom_line(aes(x=psi, y=mean_e))
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e)) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01) + geom_line(aes(x=psi, y=mean_e), colour="red")
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e)) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01, colour="red") + geom_line(aes(x=psi, y=mean_e), colour="red")
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e), colour="red") + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01, colour="red") + geom_line(aes(x=psi, y=mean_e), colour="red")
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e), colour="red", size=2) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01, colour="red") + geom_line(aes(x=psi, y=mean_e), colour="red")
ggplot() + geom_point(aes(x=psi, y=mean_c)) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e), colour="red", size=3) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01, colour="red") + geom_line(aes(x=psi, y=mean_e), colour="red")
ggplot() + geom_point(aes(x=psi, y=mean_c), size=3) + geom_errorbar(aes(x=psi, ymin=mean_c-error_c, ymax=mean_c+error_c), width=0.01) + geom_line(aes(x=psi, y=mean_c)) + scale_y_continuous(limit=c(3e-5, 8e-5)) + theme_bw() + geom_point(aes(x=psi, y=mean_e), colour="red", size=3) + geom_errorbar(aes(x=psi, ymin=mean_e-error_e, ymax=mean_e+error_e), width=0.01, colour="red") + geom_line(aes(x=psi, y=mean_e), colour="red")
poisson(2)
rpois(2)
rpois(10, lamda=2)
rpois(10, lambda=2)
rpois(100, lambda=2)
rpois(100, lambda=0.002)
rpois(1000, lambda=0.002)
60*365.25
60*365.25/0.25
sum(rpois(87660, lambda=2))
sum(rpois(87660, lambda=2))/87660
sum(rpois(87660, lambda=0.002))/87660
sum(rpois(87660, lambda=2))/87660
install.packages("phangorn")
library("phangorn")
lubrary("ape")
library("ape")
distmat <- read.csv("test_distmatrix.csv", header=F)
distmat
as.matrix(distmat)
distmat_mat <- as.matrix(distmat)
upgma(distmat_mat)
dist.dna("test_neutral_supgma.fa")
dist.dna("test_neutral_supgma.fa")
dist.dna(as.DNAbin("test_neutral_supgma.fa"))
as.DNAbin("test_neutral_supgma.fa")
read.dna("test_neutral_supgma.fa")
read.dna("test_neutral_supgma.fa", format="fasta")
dna <- read.dna("test_neutral_supgma.fa", format="fasta")
as.DNAbin(dna)
dna <- read.dna("test_neutral_supgma.fa", format="fasta")
dna <- read.FASTA("test_neutral_supgma.fa")
dna
upgma(dna)
dist.dna(dna)
type(dist.dna(dna))
class(dist.dna(dna))
class(dna))
class(dna)
dist.dna(dna)
dist.dna(dna)
dist.dna(dna)
dist.dna(dna)
distmat <- read.csv("test_distmatrix.csv", header=F)
distmat <- read.csv("test_distmatrix.csv", header=T)
as.dist(distmat)
distmat
as.dist(as.matrix(distmat))
distmat <- read.csv("test_distmatrix.csv", header=T)
distmat
upgma
hclust