Constant #10
Constant #10
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* Updated notation and function structure in the multi individual constant model file for consistency. Updated rmot_run, rmot_models to reflect the changes. * Removed old constant stan file and cleared out references to it in stanmodels.R, rmot.rmd. * Updated ignore to exclude compiled binaries. * Cleared out .o and .so files. * Added develop branch as a trigger for PR --------- Co-authored-by: Fonti Kar <[email protected]>
…nette. Need to do test files yet.
…gle/y_multi in global environment not being seen within rmot_assign_data function.
…functions, y_single and y_multi are not evaluated globally #1
…functions, y_single and y_multi are not evaluated globally #1
…ecoevo/rmot into constant_single_individual
…y for single and multiple individuals. Tests all complete dynamically and when run in the testing console.
tests/testthat/helper-testing.R
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Will rmot_test_single_individual and rmot_test_multi_individual be used for other models other than the constant?
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Yes, they form the basis of the testing template for the respective datasets.
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| inst/doc | |||
| /doc/ | |||
| /Meta/ | |||
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Good to exclude this stuff. FYI, I have these files as a general exclusion in my global gitignore, i.e. applying to all projects. Saves setting it up for each project. I'll send you a copy.
inst/stan/constant_multi_ind.stan
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| if(i < n_obs){ | ||
| if(ind_id[i+1]==ind_id[i]){ | ||
| //Analytic solution | ||
| y_hat[i+1] = y_hat[i] + Delta_hat[i]*(time[i+1]-time[i]); |
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I understand there's an analytic solution which is exact, but at first glance this looks like a Euler step. I think to would better to write as something like
y_hat[i+1] = step(y_hat[I], time[I], time[i+1], pars);
i.e. similar syntax to what is sued when you have Canham or other functions. Then put the
details of the step in the step function at the not.
inst/stan/constant_single_ind.stan
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| Delta_hat[i] = growth(y_hat[i], ind_beta); | ||
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| if(i < n_obs){ //Analytic solution | ||
| y_hat[i+1] = y_hat[i] + Delta_hat[i]*(time[i+1]-time[i]); |
… the constant model and removed reference to the constant branch from R-CMD-checn.yaml.
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I've made the requested changes and pushed them to the constant branch. |
Constant model is ready to be folded into the main branch, passes all tests.