Man pages for isotracer
Isotopic Tracer Analysis Using MCMC
| add_covariates | Add fixed effects of one or several covariates to some... |
| add_pulse_event | Register a pulse event on one of the compartment of a... |
| aquarium_mod | A simple aquarium network model, ready to run |
| aquarium_run | An MCMC run from a simple aquarium network model |
| as.mcmc.list.tidy_flows | Convert a 'tidy_flows' object to an 'mcmc.list' |
| as.mcmc.list.tidy_steady_states | Convert a 'tidy_steady_states' object to an 'mcmc.list' |
| as_tbl_graph | Generic for as_tbl_graph() |
| as_tbl_graph.topology | Convert a network topology to a tbl_graph |
| available_priors | List the available priors for model parameters |
| calculate_steady_state | Calculate steady-state compartment sizes for a network |
| c.mcmc.list | Combine mcmc.list objects |
| comps | Return the compartments of a network model |
| constant_p | Define a fixed-value prior |
| delta2prop | Convert delta notation to proportion of heavy isotope |
| dic | Calculate DIC from a model output |
| eelgrass | Eelgrass phosphate incorporation data (McRoy & Barsdate 1970) |
| exponential_p | Define an exponential prior |
| filter | Filter (alias for filter function from dplyr) |
| filter_by_group | Filter a tibble based on the "group" column |
| filter.ppcNetworkModel | Filter method for output of tidy_data_and_posterior_predict() |
| format.prior | Pretty formatting of a 'prior' object |
| format.prior_tibble | Pretty formatting of a 'prior_tibble' object |
| gamma_p | Define a gamma prior |
| ggflows | A quick-and-dirty way of visualizing relative flows in a... |
| ggtopo | Plot a topology |
| ggtopo.networkModel | Plot a network topology |
| ggtopo.topology | Plot a topology |
| groups.networkModel | Get the grouping for a 'networkModel' object |
| hcauchy_p | Define a half-Cauchy prior (on [0;+Inf]) |
| isotracer-package | The 'isotracer' package |
| lalaja | Dataset for nitrogren fluxes in a Trinidadian mountain stream... |
| li2017 | Protein degradation in Arabidopsis plants (Li et al. 2017) |
| Math.mcmc.list | Math generics for mcmc.list objects |
| mcmc_heatmap | Draw a heatmap based on the correlations between parameters |
| missing_priors | Get a table with parameters which are missing priors |
| new_networkModel | Create an empty network model |
| normal_p | Define a truncated normal prior (on [0;+Inf]) |
| obj_sum.prior | Function used for displaying 'prior' object in tibbles |
| Ops.mcmc.list | Ops generics for 'mcmc.list' objects |
| Ops.prior | Implementation of the '==' operator for priors |
| Ops.topology | Ops generics for 'topology' objects |
| params | Return the parameters of a network model |
| pillar_shaft.prior | Function used for displaying 'prior' object in tibbles |
| plot.networkModel | Plot observations/trajectories/predictions from a network... |
| plot.ready_for_unit_plot | Plot output from 'split_to_unit_plot' |
| posterior_predict | Draw from the posterior predictive distribution of the model... |
| posterior_predict.networkModelStanfit | Draw from the posterior predictive distribution of the model... |
| predict.networkModel | Add a column with predictions from a fit |
| print.networkModel | Print method for 'networkModel' objects |
| print.prior | Pretty printing of a 'prior' object |
| print.prior_tibble | Pretty printing of a 'prior_tibble' object |
| print.topology | Pretty printing of a 'topology' object |
| priors | Return the tibble containing the priors of a networkModel |
| project | Calculate the trajectories of a network model |
| prop2delta | Convert isotopic proportions to delta values |
| prop_family | Return the distribution family for observed proportions |
| quick_sankey | Draw a Sankey plot with basic defaults |
| reexports | Objects exported from other packages |
| run_mcmc | Run a MCMC sampler on a network model using Stan |
| sample_from | Generate samples from a network model |
| sample_from_prior | Sample from a prior object |
| sample_params | Sample parameter values from priors |
| sankey | Draw a Sankey plot for a network and estimated flows |
| scaled_beta_p | Define a beta prior (on [0;scale]) |
| select.mcmc.list | Select parameters based on their names |
| set_half_life | Set the half-life for radioactive tracers |
| set_init | Set initial conditions in a network model |
| set_obs | Set observations in a network model |
| set_params | Set the parameters in a network model |
| set_prior | Set prior(s) for a network model |
| set_prop_family | Set the distribution family for observed proportions |
| set_size_family | Set the distribution family for observed sizes |
| set_split | Flag some network compartments as being split compartments |
| set_steady | Flag some network compartments as being in a steady state |
| set_topo | Set the topology in a network model. |
| size_family | Return the distribution family for observed sizes |
| stanfit_to_named_mcmclist | Convert a Stanfit object to a nicely named mcmc.list object |
| sub-.networkModelStanfit | Subset method for 'networkModelStanfit' objects |
| tidy_data | Extract data from a networkModel object into a tidy tibble. |
| tidy_dpp | Prepare tidy data and posterior predictions |
| tidy_flows | Build a tidy table with the flows for each iteration |
| tidy_mcmc | Extract a tidy output from an mcmc.list |
| tidy_posterior_predict | Draw from the posterior predictive distribution of the model... |
| tidy_steady_states | Build a tidy table with the calculated steady states for each... |
| tidy_trajectories | Build a tidy table with the trajectories for each iteration |
| topo | Return the list of topologies, or a unique topology if all... |
| traceplot | Plot mcmc.list objects |
| trini_mod | Network model for nitrogen fluxes in Trinidadian streams... |
| type_sum.prior | Function used for displaying 'prior' object in tibbles |
| uniform_p | Define a uniform prior |
