Hierarchical Methods for Differential Equations

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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