coleoguy

# function creates a stochastic character mapped tree as a modified "phylo" object
# written by Liam Revell 2013, 2014, 2015
# lines 238, 245, 251, and 258 written by Heath Blackmon
make.simmap<-function(tree,x,model="SYM",nsim=1,...){
	if(inherits(tree,"multiPhylo")){
		ff<-function(yy,x,model,nsim,...){
			zz<-make.simmap(yy,x,model,nsim,...)
			if(nsim>1) class(zz)<-NULL
			return(zz)
		}	

coleoguy

SimThresh3 <- function(tree, liabilities=F){
  ## This internal function just determines what the
  ## observed discrete state is
  returnState <- function(x,y){
    state <- vector()
    # angle A is at origin
    # angle B is at 1,0
    # angle C is at x,y
    # so we can calculate the sides like this
    a <- sqrt((x-1)^2 + (y)^2)

coleoguy

library(phytools)
library(evobiR)
tree<-pbtree(n=500, scale=1)
tip.state.full <- SimThresh3(tree, liabilities=T)
ShowTree(tree, tip.state.full[[1]],  
         cols = c("red", "blue", "green"), 
         tip.cex=.5, type="fan")

coleoguy

SimThresh3 <- function(tree, liabilities=F){
  ## This internal function just determines what the
  ## observed discrete state is
  returnState <- function(x,y){
    state <- vector()
    # angle A is at origin
    # angle B is at 1,0
    # angle C is at x,y
    # so we can calculate the sides like this
    a <- sqrt((x-1)^2 + (y)^2)

coleoguy

x <- rnorm(n=100000, mean=1)
mean(x)
x <- sapply(x, StochRound)
mean(x)

coleoguy

StochRound <- function(x){
  ## extract the decimal portion
  q <- abs(x - trunc(x))
  
  ## draw a value 0 or 1 with probability
  ## based on how close we already are
  adj <- sample(0:1, size = 1, prob = c(1 - q, q))
  
  ## make it negative if x is
  if(x < 0) adj <- adj * -1

coleoguy

# this time lets set the axis limits to 1:100
plot(0, 0, col = "white", xaxt = "n", yaxt = "n", xlab = "", ylab = "", xlim=c(0,100), ylim=c(0,100))
# now lets try printing a bunch
x <- sample(1:100, size = 100, replace = T)
y <- sample(1:100, size = 100, replace = T)
fl.col <- viridis::viridis(100)
for(i in 1:100){
  flower(x = x[i], y = y[i], colx = fl.col[i], cex.x = 1, cex.y = 1.5, cex.f = 1)
}

coleoguy

# set up a base plot
plot(0, 0, col = "white", xaxt = "n", yaxt = "n", xlab = "", ylab = "")
flower(x = 0, y = 0, colx = "red", cex.x = .015, cex.y = .035, cex.f = 1)

coleoguy

flower <- function(x, y, colx="red", cex.x=1, cex.y=1, cex.f=1){
  petalsx <- cex.x * c(0, 1,  0, -1)
  petalsy <- cex.y * c(1, 0, -1,  0)
  # this loop prints the petals
  for(i in 1:4){
    points(x + petalsx[i], 
           y + petalsy[i], 
           pch = 16, col = colx, 
           cex = cex.f)
  }

coleoguy

library(shiny)
# Define UI for application
shinyUI(fluidPage(
  # Application title
  titlePanel("Brownian Motion"),
  # Sidebar for user input
  sidebarLayout(
    sidebarPanel(
      # select how many generations to run
      sliderInput("gens",