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
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_Rhat(): Calculate Rhat statistics for a hmde_fit object
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_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_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
plot(<hmde_model_template>): Plot function for hmde_model_template object
print(<hmde_model_template>): Print function for hmde_model_template object
summary(<hmde_model_template>): Summary function for hmde_model_template object