Math.mcmc.list          Math generics for mcmc.list objects
Ops.mcmc.list           Ops generics for 'mcmc.list' objects
Ops.prior               Implementation of the '==' operator for priors
Ops.topology            Ops generics for 'topology' objects
[.networkModelStanfit   Subset method for 'networkModelStanfit' objects
add_covariates          Add fixed effects of one or several covariates
                        to some parameters.
add_pulse_event         Register a pulse event on one of the
                        compartment of a topology
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
c.mcmc.list             Combine mcmc.list objects
calculate_steady_state
                        Calculate steady-state compartment sizes for a
                        network
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.ppcNetworkModel
                        Filter method for output of
                        tidy_data_and_posterior_predict()
filter_by_group         Filter a tibble based on the "group" column
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 network
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 (Collins 2016)
li2017                  Protein degradation in Arabidopsis plants (Li
                        et al. 2017)
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
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 model
plot.ready_for_unit_plot
                        Plot output from 'split_to_unit_plot'
posterior_predict       Draw from the posterior predictive distribution
                        of the model outcome
posterior_predict.networkModelStanfit
                        Draw from the posterior predictive distribution
                        of the model outcome
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
prop_family             Return the distribution family for observed
                        proportions
quick_sankey            Draw a Sankey plot with basic defaults
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
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 outcome
tidy_steady_states      Build a tidy table with the calculated steady
                        states for each iteration
tidy_trajectories       Build a tidy table with the trajectories for
                        each iteration
topo                    Return the list of topologies, or a unique
                        topology if all identical
traceplot               Plot mcmc.list objects
trini_mod               Network model for nitrogen fluxes in
                        Trinidadian streams (Collins et al. 2016)
type_sum.prior          Function used for displaying 'prior' object in
                        tibbles
uniform_p               Define a uniform prior
