Hierarchical Methods for Differential Equations

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Documentation for package ‘hmde’ version 1.2.1

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hmde-package The 'hmde' package.
hmde The 'hmde' package.
hmde_affine_de Differential equation for affine growth single individual model
hmde_assign_data Assign data to template for chosen model
hmde_canham_de Differential equation for Canham growth single and multi- individual models
hmde_const_de Differential equation for constant growth single and multi- individual models
hmde_extract_estimates Extract samples and return measurement, individual, and population-level estimates
hmde_model Select data configuration template for hmde supported model
hmde_model_des Function to select DE given model name
hmde_model_names Returns names of available models.
hmde_model_pars Show parameter list for hmde supported model
hmde_plot_de_pieces Plot pieces of chosen differential equation model for each individual. Structured to take the individual data tibble that is built by the hmde_extract_estimates function using the ind_par_name_mean estimates. Function piece will go from the first fitted size to the last. Accepted ggplot arguments will change the axis labels, title, line colour, alpha
hmde_plot_obs_est_inds Plot estimated and observed values over time for a chosen number of individuals based on posterior estimates. Structured to take in the measurement_data tibble constructed by the hmde_extract_estimates function.
hmde_run Run chosen pre-built model in Stan
hmde_vb_de Differential equation for von Bertalanffy growth single and multi- individual models
Lizard_Size_Data Skink size data - Lampropholis delicata
Tree_Size_Data Garcinia recondita - Barro Colorado Island data
Tree_Size_Ests Garcinia recondita model estimates - Barro Colorado Island data
Trout_Size_Data SUSTAIN Salmo trutta data