Package index • sefra

All functions

adult_survival() `adult_survival<-`(): Access or assign distribution parameters for \(S^{opt}_s\)

age_breeding() `age_breeding<-`(): Access or assign distribution parameters for \(A^{curr}_s\)

captures(): Access capture data

capture_codes() `capture_codes<-`() species_names(<sefraData>): Access or assign capture codes

capture_resolutions(): Access captures per capture resolution

codes: Capture codes

code_names: Code names

code_resolution: Taxonomic resolution per capture code

cryptic_capture() `cryptic_capture<-`(): Access or assign distribution for cryptic capture parameter \(\kappa\)

data_prep(): Prepare data for model run

distributions: Probability distributions.

.check_dimensions(): Check number of dimensions

.data_for_model(): Strip names from sefraData object

.distribution_init(): Distribution initial value

.distribution_type(): Distribution type

.Z1(): Create linear matrix maps

fishery_groups() `fishery_groups<-`(): Access or assign fishery groups

get_draws(): Get draws from `CmdStanMCMC` or `sefraModel` object.

get_num_retained(): Get number of retained samples from sefraModel object

get_rhat() plot_rhat() get_neff() plot_neff(): Diagnostic functions

get_traces(): Get draws from CmdStanMCMC or sefraModel object.

initial_values(): Retrieve list of initial values

model_def(): Model definition

months: Months

n_breeding_pairs() `n_breeding_pairs<-`(): Access or assign distribution parameters for \(N^{BP}_s\)

overlap(): Access overlap data

phi() `phi<-`(): Access or assign phi parameter

plot_prior_update(): Plot prior updates from sefraModel model run

print_code_to_code(): Print linear matrix maps

p_breeding() `p_breeding<-`(): Access or assign distribution parameters for \(P^{B}_s\)

p_nest() `p_nest<-`(): Access or assign distribution parameters for \(P^{nest}_{s,m}\)

p_southern() `p_southern<-`(): Access or assign distribution parameters for \(P^{SH}_{s,m}\)

sampler(): Sample from posterior distribution

sefraData(): Class containing input data for model run

sefraModel(): Class containing a compiled SEFRA model

sefraOutputs(): Class containing outputs from model run

species: Species codes

species_groups() `species_groups<-`(): Access or assign species groups

species_names(): Access species_names in sefraData object

summary(<sefraOutputs>): Summarise model outputs

to_integer(): Coerce to integer

trace_plot(): Plot MCMC sample traces

versionUpdate(): Version update

waic(): Calculate ELPD and WAIC