1718.sagews

#Caroline/Reggie

from scipy import *
from pylab import *
from math import *
import numpy as np

#calling file, making lists
file=open("/home/mike/Code/chse.txt").readlines()

for i in xrange(len(file)):
    file[i]=file[i].split()
    
for i in range(len(file)):
    for j in range(len(file[i])):
        file[i][j]=float(file[i][j])
        
x = range(len(file))
mx = [file[F][3] for F in range(len(file))]
lx = [file[p][2] for p in range(len(file))]
sx = [file[p][1] for p in range(len(file))]

#bisect
x = np.array([x])
mx = np.array([mx])
lx = np.array([lx]) 
lm = lx * mx
R0 = np.sum(lm)
G = (np.sum(x*lx*mx))/R0

def Rest(x, lx, mx)
    return (log(R0))/G

r_list=[]

def calc_error(lm, r, x):
    return 1. - np.sum(lm*np.e**(-r*x))

def bisect(lm, mx, x):
    error = calc_error(lm, Rest(x,lx,mx), x)
    if error>=0:
         Rlow = Rest(x,lx,mx) - 1.
         Rhigh = Rest(x,lx,mx)
    else:
         Rhigh = Rest(x,lx,mx) + 1.
         Rlow = Rest(x,lx,mx)
    while np.abs(error) > 0.001:
        Rguess = ((Rhigh + Rlow) / 2.)
        error = calc_error(bl, Rguess, x)
        if error >=0:
            Rhigh = Rguess
        else:
            Rlow = Rguess


#multiplying fecundity array
    
def fecund(mx,f):
    return(bx/bx[15])*f
    
for f in range(60):
    nmx=fecund(mx,f)
    Rest=Rest(x,lx,nmx)
    r_list.append(bisect(lm,nmx,x))

#plotting list
plot_data=[]
for years in range(60):
    plot_data.append([years, r_list[years]])

Traceback (most recent call last): File "", line 1, in <module> File "/tmp/tmpM2tBTc/___code___.py", line 8, in <module> file=open("/home/mike/Code/chse.txt").readlines() IOError: [Errno 2] No such file or directory: '/home/mike/Code/chse.txt'