Package index • hmde

All functions

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
error_ests() `error_ests<-`(): generic error_ests getter
fit_summary() `fit_summary<-`(): generic fit_summary getter
hmde-package 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_Rhat_hist(): Plot histogram of R_hat values for hmde_fit object.
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_run(): Run chosen pre-built model in Stan
hmde_vb_de(): Differential equation for von Bertalanffy growth single and multi- individual models
individual_ests() `individual_ests<-`(): generic individual_ests getter
measurement_ests() `measurement_ests<-`(): generic measurement_ests getter
method() `method<-`(): generic method getter
model_level() `model_level<-`() obs_data() `obs_data<-`(): generic model_level setter
model_name() `model_name<-`(): generic model_name getter
par_names() `par_names<-`(): generic par_names getter
population_ests() `population_ests<-`(): generic population_ests setter
prior_pars() `prior_pars<-`(): generic prior_pars getter
runtime() `runtime<-`(): generic runtime getter