Man pages for sustainablefarms/msod
Multispecies Occupancy Detection Models
| apply_to_new_data | Apply function to fitted object after supplanting data with... |
| artificial_runjags | Create a fully artificial fitted object |
| as_list_format | A quick replacement to 'runjags::list.format()' that does... |
| bugsvar2array | Converting Parameter Values in BUGS Name and Format to Arrays... |
| detectednumspec | The number of observed species in a matrix of observation... |
| DunnSmythResiduals | Dunn-Smyth Residuals for Detection and Occupancy for Fitted... |
| DunnSmythResidualsRaw | Dunn-Smyth Residuals for Detection and Occupancy for Given... |
| Edetperspecies.jsodm | Expected number of detections per species per site |
| elpd | Expected log predictive density: the probability density for... |
| elpd_compare | Compare Sitewise Differences in Log Predictive Density;... |
| Enum_compare | Compare Expected Number of Species at ModelSites |
| extend.fit | Extend MCMC chains of fitted model |
| fd_pocc | Functional richness, eveness and diversity from the FD... |
| fitjsodm | Fit detection occupancy models using runjags. |
| get_occ_b | Get Arrays of Draws from Posterior for Each Parameter |
| likelihood.jsodm | Likelihood for Plain JSODM |
| likelihood.jsodm_lv | Likelihood Computation for JSODM_LV Model |
| likelihood.jsodm_lv_sepexp | Likelihood Computation for JSODM_LV Model |
| likelihood_LVvmarg_draw.jsodm_lv | Likelihood Computation for JSODM_LV Model for a Given Draw |
| likelihood_LVvmarg_draw.jsodm_lv_sepexp | Likelihood Computation for JSODM_LV Model for a Given Draw |
| likelihoods.fit | Computing Likelihoods for Occupancy Detection Models |
| mb_stat | Compare observed detection numbers to expected |
| minimise_fit.jsodm_lv | Translate fit object into a smaller object for using in a... |
| modelqualstats | Compute Model Quality Information |
| occspecrich_difference | difference in species richness to reference environmental... |
| paraminits | Initial condition functions |
| parnames | Convert old fit objects to use new parameter naming... |
| pdetection_occupied.ModelSite.theta | Probability of detection and occupation for a single... |
| pdetection_occupied_raw | Probability of Detection Given Occupied |
| pdet_occ_raw.jsodm | Probability of Detection, Given Occupied |
| pdet_occ_raw.jsodm_lv_re | Raw version for random effects in the detection takes a set... |
| poccupancy_margotherspecies.jsodm_lv | Prediction Summaries for jsodm_lv Model for New Sites |
| poccupy | Occupancy Probability Calculations |
| poccupy.jsodm_lv | lvvfromposterior = TRUE draws lv.v from the posterior with... |
| prednumsuccess | Expected Biodiversity |
| predsumspeciesRV | Compute predicted distributions of number species detected |
| prepJAGSdata2 | Prepare JAGS-like Data for JSODM |
| rmanybern | Simulate many independent Bernoulli random variables |
| simulate_detections | Simulate observations from parameters of a fitted object. |
| speciesrichness_mltn | Species richness as number of species more likely than not to... |
| sumRV_margrow | For a list of random variables, return random variable that... |
| supplant_new_data | Supplant data in fitted object with new data for the purposes... |
