Isotopic Tracer Analysis Using MCMC

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Documentation for package ‘isotracer’ version 1.1.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
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