isotracer-package |
The 'isotracer' package |
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 |
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) |
li2017_counts |
Protein degradation in Arabidopsis plants (Li et al. 2017) |
li2017_prots |
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 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 |
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 |
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_priors |
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 |
[.networkModelStanfit |
Subset method for 'networkModelStanfit' objects |