In jaishimuku/WrightLab_FBD: Expanded Functions for Use with FossilSim

Reads logfile

foss_data <- read.table("mukunda_foss.log", sep = '\t',  head = TRUE)
head(foss_data)
View(foss_data) ## for view

Sampling

library(FossilSim)
foss_data <- read.table("mukunda_foss.log", sep = '\t',  head = TRUE)

foss_function <- function(data_frame, arg_1, arg_2) ## data_frame: my dataset(.log file), arg : which row
{
  ## for arg1
  m1 <- data_frame$mu[arg_1]  ## mu value stored in m1
  l1 <- data_frame$lambda[arg_1] ## lamda value stored in m1
  p1 <- data_frame$psi.1.[arg_1]  ## psi value stored in p1

  ## for arg2
  m2 <- data_frame$mu[arg_1]  
  l2 <- data_frame$lambda[arg_1] 
  p2 <- data_frame$psi.2.[arg_1]



  ## store mu, lamda and psi in vector
  mu_value <- c(m1,m2)
  lambda_value <- c(l1,l2)
  psi_value <- c(p1,p2)

  all_values <- c(mu_value,lambda_value,psi_value)

  ## n = 666 (given)
  ## numbsim =  1
  ## from LONI times = (29,70) 
  tree <- sim.fbd.rateshift.taxa(666,1,lambda = lambda_value, mu=mu_value, psi=psi_value, times=c(29,70), complete = FALSE )
  {
    return(rangeplot.asymmetric(tree[[1]])) ## draws a sim.fbd.rateshift.taxa tree
  }

return(all_values) # returns all the values
}
foss_function(foss_data,120,20)

library(FossilSim)
foss_data <- read.table("mukunda_foss.log", sep = '\t',  head = TRUE)

foss_function <- function(n_extant, n_trees, data_frame,  mu, lambda, psi, rows, times) {

  mi <- c(foss_data [rows, mu])
  li <- c(foss_data [rows, lambda])
  pi <- c(foss_data [rows, psi]) 

 tree <- sim.fbd.rateshift.taxa(n_extant, n_trees, li, mi, pi, times, complete = TRUE)
 {
   return(rangeplot.asymmetric(tree[[1]]))
 } 
  # return(foss_model)
}
foss_function(666,1, foss_data, mu = "mu", lambda = "lambda", psi = "psi.1.", c(10,12) ,times = c(29,70) )

jaishimuku/WrightLab_FBD documentation built on July 17, 2020, 12:05 a.m.