Bring tara-main up to date with mike's 'main' #3
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- Clean up code - render file into pdf
Use as starting point for fits where individual is kept track of. Processed model equations to get number of parameters.
- Defined own nls_multstart_allfits which returns all of the nls fitted - nls_multstart has a poorly designed 'convergence_count' method - only looks at AIC (not parameters) and to meaninglessly high precision
- Normal error doesn't converge - Poisson error does
- Add t1max parameter to deal with suprious log posterior peak near tmax - Add some plotting functions (though can't get 'main' to work) - Not getting errors when
- Null model results match that of glm_poisson, which is reassuring - stan formulation fails to match glm_qpoisson
This was a file from Kacyi that I accidentally made a duplicate of
Adding Empson Code Files
I tried to pull out data from all temperature loggers to get the range and variance for each chamber (in the repeated 40C trials). I accidentally modified the original temperature logger .txt files, removing the first row (the headers).
- was able successfully create a tibble() with each bootstrapped mean and var values - Modified file name and structure.
fixed issues with bootstrapping function
I renamed my previous R marked down files with more descriptive names along with the date in a different format for clarity. I also created a new R mark down file with the working bootstrap function and the resulting graph of mean(var) vs mean(mean).
Code for working bootstrap function, 2 graphs, start of using brm.
This file has (what I currently think is) working bootstrap and working simulated data of motif counts. The simulated data doesn't match the original data very well so this may not be perfect.
Small updates to spacing in code.
Used terminal to restore the original temperature logger output files from the main branch
- using vectors for filtering - Use system() to get git root - remove creation of 'real' df
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Hopefully haven't broken anything of Tara's