This is because many, many different combinations of R0 and t0 had to be tried to get a good number of points in the plots, and a reasonable idea of what R0, t0 values will provide the best fit. Note that when you try this code out it will run slowly. In the file fit_iteration.R I provide the code that (eventually, after running a while) produces the above plots. In blue I show the value of (R0,t0) that minimizes the Least Squares statistic, and then in the lower plot I overlay the best fit curve on the data. Rather than changing R0 and t0, and re-running the fit_example.R script many different times, it is much easier to write an R script to do a loop where it randomly samples many different hypotheses for R0 and t0 and calculates the least-squares statistic, keeping track of how the least squares statistic depends on R0 and t0. The values of R0 and t0 that I used in that script are clearly not ideal! In reality, those initial conditions are also unknown model parameters that need to be estimated or the assumptions clearly stated.
In this example we assume that there is just one infected person at time t0, and that the population was fully immune. I assume that the infectious period for flu is 1/gamma=3 days. The script assumes that t0 is week 44 of the year, and that the R0 of the epidemic is 1.35. In the fit_example.R script I get the estimated incidence from an SIR model, with population size equal to the population of the Midwest, and assuming that one infected person is introduced into a completely susceptible population at time t0 (is this a good assumption?). The comma delimited data file I prepared that contains CDC influenza data from the Midwest for the 2007-2008 season, is in midwest_influenza_2007_to_2008.dat Refresher: the old R script for doing the fit with parameter sweeps In that module, we used a Least Squares goodness-of-fit estimator. I'm mainly wanting to know how to make the makefile generator for Dev-C++ rename the exe file and compile folders (similar to the compiling the example folders in allegro).In a past module, we examined how we could use methods in the R deSolve to fit the parameters of an SIR model to confirmed cases of influenza B in the Midwest region during the 2007-2008 flu season (the data were obtained from the CDC). What I'm wanting is to know what other type of options are there I've searched the help file and found nothing. Then I get a makefile box with a selection of 'gcc', 'g++', 'cc', and 'bcc' then there is a section that says: 'Extra Parameters that must given to the compiler :'. I open a project and click the "Generate Makefile" bolt (icon). I know how to bring up the Makefile Dialog Box, but that is where I run into the problem. Īctually, you can create makefiles using Dev-C++.despite the fact that it doesn't use them That's the whole point of an IDEĬhris that's not what I was asking about. That wouldn't shock me DE Dev-C++ doesn't run on makefiles.
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