├── README.md ├── book_src ├── bib │ ├── ode.bib │ ├── ode.pub │ ├── papers.bib │ ├── papers.pub │ ├── papers.pub.bak │ └── venues.list ├── book │ ├── clean.sh │ ├── clean_all.sh │ ├── make_html.sh │ ├── make_ipynb.sh │ ├── make_pdf.sh │ ├── ode_book.do.txt │ ├── svmonodo.cls │ └── t4do.sty └── chapters │ ├── .gitignore │ ├── adaptive.do.txt │ ├── chapter1.do.txt │ ├── clean.sh │ ├── diffeq.do.txt │ ├── disease_modeling.do.txt │ ├── figs_appA │ ├── comic_root.pdf │ ├── comic_root.png │ ├── diffeq_integral_of_Gaussian.pdf │ ├── diffeq_integral_of_Gaussian.png │ ├── logistic_diffeq.py │ ├── logistic_growth1.pdf │ └── logistic_growth1.png │ ├── figs_ch1 │ ├── FE_n_10_20.pdf │ ├── FE_n_10_20.png │ ├── logistic_func_mpl.pdf │ ├── logistic_func_mpl.png │ ├── pendulum.png │ ├── pendulum_FE.pdf │ ├── pendulum_scipy.pdf │ └── pendulum_sketch.pptx │ ├── figs_ch2 │ └── ch2_simplecompare.pdf │ ├── figs_ch3 │ ├── stab_region_erk.pdf │ ├── stab_region_erk.png │ ├── stab_region_irk0.pdf │ ├── stab_region_radau.pdf │ ├── vanderpol1.pdf │ ├── vanderpol2.pdf │ ├── vanderpol_be.pdf │ └── vanderpol_irk.pdf │ ├── figs_ch4 │ ├── hh_adaptive_tr_bdf2.pdf │ └── hodgkinhuxley_AP.pdf │ ├── figs_ch5 │ ├── SEEIIR.pdf │ ├── SEEIIR.png │ ├── SEIR.pdf │ ├── SEIR.png │ ├── SIR0.pdf │ ├── SIR0.png │ ├── SIR1.pdf │ ├── SIR1.png │ ├── SIR_immunity_loss.pdf │ └── SIR_simple.pdf │ ├── mako │ ├── .dict4spell.txt │ ├── main_mako.do.txt │ ├── make.sh │ ├── make_all.sh │ ├── mako.do.txt │ └── src-mako │ │ └── mako_func.py │ ├── mako_code.txt │ ├── preface_ode.do.txt │ ├── rungekutta1.do.txt │ └── rungekutta2.do.txt └── docs ├── README.md ├── _config.yml ├── figs └── ode_cover.jpg ├── ipynb.zip ├── ipynb ├── ODESolver.py ├── adaptive.ipynb ├── diffeq.ipynb ├── disease_modeling.ipynb ├── ode_intro.ipynb ├── ode_systems.ipynb ├── rungekutta1.ipynb └── rungekutta2.ipynb ├── ode_book.pdf ├── src.zip └── src ├── appendix1 ├── Newton.py ├── fibonacci_diffeq.py ├── fortune_inflation.py ├── interest_v1.py ├── 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