update on getting started

doc/LectureNotes/.book.copyright

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+{'holder': ['Morten Hjorth-Jensen'], 'year': '1999-2018', 'license': 'Released under CC Attribution-NonCommercial 4.0 license', 'cite doconce': False}

doc/LectureNotes/book.dlog

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+translating doconce text in book.do.txt to ipynb
+*** error: could not open the file src/plot_Hudson.py used in
+@@@CODE src/plot_Hudson.py
+translating doconce text in book.do.txt to ipynb
+copy complete file src/plot_Hudson.py (format: pypro)
+copy complete file src/Hudson_Bay.py (format: pypro)
+*** error: figure file "fig/Hudson_Bay_sim" does not exist!
+translating doconce text in book.do.txt to ipynb
+copy complete file src/plot_Hudson.py (format: pypro)
+copy complete file src/Hudson_Bay.py (format: pypro)
+figure file fig/Hudson_Bay_data:
+    can use fig/Hudson_Bay_data.png for format ipynb
+figure file fig/Hudson_Bay_sim:
+    can use fig/Hudson_Bay_sim.png for format ipynb
+collected all required additional files in ipynb-book-src.tar.gz which must be distributed with the notebook
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+output in book.ipynb
+*** error: file has a mako construction ${\bf \hat{J}'
+    but seemingly no definition in <%...%>'
+    (it is not a command-line given mako variable either).
+    However, if this is a variable in a Makefile or Bash script
+    run with --no_mako - and you cannot use mako and Makefile or Bash variables
+    in the same document!
+
+*** error: file has a mako construction ${\bf \hat{J}'
+    but seemingly no definition in <%...%>'
+    (it is not a command-line given mako variable either).
+    However, if this is a variable in a Makefile or Bash script
+    run with --no_mako - and you cannot use mako and Makefile or Bash variables
+    in the same document!
+
+translating doconce text in book.do.txt to ipynb
+*** error: found multiple labels:
+    eq:def_covariance eq:autocorrelation_time eq:error_estimate_corr_time
+translating doconce text in book.do.txt to ipynb
+copy complete file src/plot_Hudson.py (format: pypro)
+copy complete file src/Hudson_Bay.py (format: pypro)
+figure file fig/Hudson_Bay_data:
+    can use fig/Hudson_Bay_data.png for format ipynb
+figure file fig/Hudson_Bay_sim:
+    can use fig/Hudson_Bay_sim.png for format ipynb
+collected all required additional files in ipynb-book-src.tar.gz which must be distributed with the notebook
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+output in book.ipynb
+translating doconce text in book.do.txt to ipynb
+copy complete file src/plot_Hudson.py (format: pypro)
+copy complete file src/Hudson_Bay.py (format: pypro)
+figure file fig/Hudson_Bay_data:
+    can use fig/Hudson_Bay_data.png for format ipynb
+figure file fig/Hudson_Bay_sim:
+    can use fig/Hudson_Bay_sim.png for format ipynb
+collected all required additional files in ipynb-book-src.tar.gz which must be distributed with the notebook
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+*** warning: latex envir \begin{bmatrix} does not work well in Markdown.
+    Stick to \[ ... \], equation, equation*, align, or align*
+    environments in math environments.
+
+output in book.ipynb

doc/LectureNotes/src/Hudson_Bay.py~

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+import numpy as np
+import matplotlib.pyplot as plt
+
+def solver(m, H0, L0, dt, a, b, c, d, t0):
+    """Solve the difference equations for H and L over m years
+    with time step dt (measured in years."""
+
+    num_intervals = int(m/float(dt))
+    t = np.linspace(t0, t0 + m, num_intervals+1)
+    H = np.zeros(t.size)
+    L = np.zeros(t.size)
+
+    print 'Init:', H0, L0, dt
+    H[0] = H0
+    L[0] = L0
+
+    for n in range(0, len(t)-1):
+        H[n+1] = H[n] + a*dt*H[n] - b*dt*H[n]*L[n]
+        L[n+1] = L[n] + d*dt*H[n]*L[n] - c*dt*L[n]
+    return H, L, t
+
+# Load in data file
+data = np.loadtxt('Hudson_Bay.csv', delimiter=',', skiprows=1)
+# Make arrays containing x-axis and hares and lynx populations
+t_e = data[:,0]
+H_e = data[:,1]
+L_e = data[:,2]
+
+# Simulate using the model
+H, L, t = solver(m=20, H0=34.91, L0=3.857, dt=0.1,
+                 a=0.4807, b=0.02482, c=0.9272, d=0.02756,
+                 t0=1900)
+
+# Visualize simulations and data
+plt.plot(t_e, H_e, 'b-+', t_e, L_e, 'r-o', t, H, 'm--', t, L, 'k--')
+plt.xlabel('Year')
+plt.ylabel('Numbers of hares and lynx')
+plt.axis([1900, 1920, 0, 140])
+plt.title(r'Population of hares and lynx 1900-1920 (x1000)')
+plt.legend(('H_e', 'L_e', 'H', 'L'), loc='upper left')
+plt.savefig('Hudson_Bay_sim.pdf')
+plt.savefig('Hudson_Bay_sim.png')
+plt.show()

doc/LectureNotes/src/plot_Hudson.py~

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+import numpy as np
+from  matplotlib import pyplot as plt
+
+# Load in data file
+data = np.loadtxt('src/Hudson_Bay.dat', delimiter=',', skiprows=1)
+# Make arrays containing x-axis and hares and lynx populations
+year = data[:,0]
+hares = data[:,1]
+lynx = data[:,2]
+
+plt.plot(year, hares ,'b-+', year, lynx, 'r-o')
+plt.axis([1900,1920,0, 100.0])
+plt.xlabel(r'Year')
+plt.ylabel(r'Numbers of hares and lynx ')
+plt.legend(('Hares','Lynx'), loc='upper right')
+plt.title(r'Population of hares and lynx from 1900-1920 (x1000)}')
+plt.savefig('Hudson_Bay_data.pdf')
+plt.savefig('Hudson_Bay_data.png')
+plt.show()