# Hierarchical Methods for Differential Equations

## Documentation for package ‘hmde’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

hmde-package | The 'hmde' package.
error_ests | generic error_ests getter
error_ests<- | generic error_ests getter
fit_summary | generic fit_summary getter
fit_summary<- | generic fit_summary getter
hmde | The 'hmde' package.
hmde_affine_de | Differential equation for affine growth single individual 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_Rhat | Calculate Rhat statistics for a hmde_fit object
hmde_model | helper function for hmde_data_template that provides data structure for model, Also used to guide the user on the required structure for the model they want.
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_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_plot_Rhat_hist | Plot histogram of R_hat values for hmde_fit object.
hmde_run | Run chosen pre-built model in Stan
hmde_vb_de | Differential equation for von Bertalanffy growth single and multi- individual models
individual_ests | generic individual_ests getter
individual_ests<- | generic individual_ests getter
Lizard_Size_Data | Skink size data - Lampropholis delicata
measurement_ests | generic measurement_ests getter
measurement_ests<- | generic measurement_ests getter
method | generic method getter
method<- | generic method getter
model_level | generic model_level setter
model_level<- | generic model_level setter
model_name | generic model_name getter
model_name<- | generic model_name getter
obs_data | generic model_level setter
obs_data<- | generic model_level setter
par_names | generic par_names getter
par_names<- | generic par_names getter
population_ests | generic population_ests setter
population_ests<- | generic population_ests setter
prior_pars | generic prior_pars getter
prior_pars<- | generic prior_pars getter
runtime | generic runtime getter
runtime<- | generic runtime getter
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