Added a function to plot sizes over time in parallel with the DE plot… #48
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… function. Changed wording in README to be more accessible.
dfalster
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Dec 5, 2024
Tess-LaCoil
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Dec 10, 2024
* Removed ind_y_0 prior as to include it double-counted the first observation in the likelihood. Also removed y_0_obs data from the required data structures as it is no longer used. The first observation is now fit by setting y_hat = ind_y_0, and then the likelihood that compares y_hat and y_obs does the comparison of the first observed size to the estimated value. * Standardised prior fixed input values, (0,1) for population-level, individual-level, (0,2) for global_error_sigma. Removed Delta_hat from generated quantities. * Corrected testing to account for removing the y_0_obs data. * Changed name of hmde_model_name function to be hmde_model_names as consistent with the file name. * Updated vignette to have better CI printing code. * Added a function to plot sizes over time in parallel with the DE plot… (#48) (#49) * Added a function to plot sizes over time in parallel with the DE plot function. Changed wording in README to be more accessible. * Updated namespace, documentation. * Removed unused args from hmde_plot_obs_est_ind function doc. * Updated vB vignette to be better presented. * Tidied up code in vignettes, re-ran Canham model with RK45 for sure this time and swapped out the saved estimates. * Wrapped up Canham vignette for paper results. * Wrangled some well-organised plots for the paper, added cowplot package to suggests. * Added estimation of distance between the erroneous cluster and true parameters. * Last few things tidied up. * Corrected code problems in vignettes. * Swapped to 1 core for check passing purposes.
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… function. Changed wording in README to be more accessible.