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Introduction to the R language Mathew Plucinski University of Cambridge / UC Berkeley
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What is it A free version of S+ Statistical programming Used extensively in computational biology, to a lesser extent in applied statistics, financial mathematics Interpretive language
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Outline 1.Introduction to R Console 2.Basic arithmetic, working with vectors, and simple statistics 3.A more serious example – Gillespie Algorithm
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Stochastic, Discrete SIR model SIR λIλIµ
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S t,I t,R t
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Stochastic, Discrete SIR model S t,I t,R t Infection Recovery
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Stochastic, Discrete SIR model S t,I t,R t Infection Recovery
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Stochastic, Discrete SIR model S t,I t,R t S t -1,I t +1,R t Infection
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Stochastic, Discrete SIR model S t,I t,R t S t -1,I t +1,R t Infection Recovery
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Stochastic, Discrete SIR model S t,I t,R t S t -1,I t +1,R t S t,I t -1,R t +1 Infection Recovery
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Stochastic, Discrete SIR model Rate: λS t I t S t,I t,R t S t -1,I t +1,R t S t,I t -1,R t +1 Rate: µI t
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Stochastic, Discrete SIR model p=λS t I t /(λS t I t + µI t ) S t,I t,R t S t -1,I t +1,R t S t,I t -1,R t +1 p= µI t /(λS t I t + µI t )
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