Man pages for jmhewitt/dsdive
Discrete Space Models for Dive Trajectories of Animals
| balance_inds | Split a sequence of integers into a partition with roughly... |
| bound.quad | Build a piecewise-quadratic envelope for a given function |
| bs | Backwards sampling algorithm for Hidden Markov Models |
| dive.sim | Simulated three stage dive |
| ds.df | Build a tidy data frame for dive objects |
| dsdive.align.obs | Realign observations of a dive to the time scale of the dive |
| dsdive.extract | Extract a segment of a fully observed dive trajectory between... |
| dsdive.fwdsample.dive | Simulate dive trajectories across discrete depth bins |
| dsdive.fwdsample.fixedstage | Simulate a dive trajectory within a single stage |
| dsdive.generator.matrix.uniformized | Compute infinitesimal generator matrix for a homogeneous,... |
| dsdive.gibbs.obs | Gibbs sampler for parameters of a model for dives across... |
| dsdive.gibbs.obs.cov | Gibbs sampler for parameters of a model for dives across... |
| dsdive.impute | Impute a complete dive trajectory from partial observations |
| dsdive.impute.sample_n | Sample number of transitions between observations for a CTMC |
| dsdive.observe | Simulate observing a fully observed dive trajectory at... |
| dsdive.obsld | Likelihood for collection of partially observed dives |
| dsdive.obsld_approx | Likelihood for collection of partially observed dives |
| dsdive.obsld_approx_shared | Approximate likelihood for collection of partially observed... |
| dsdive.obsld_shared | Likelihood for collection of partially observed dives |
| dsdive.obs.sample.offsets | Sample t0 and tf offsets from full conditional posteriors |
| dsdive.obs.sampleparams | Sample pi and lambda parameters for a single dive stage |
| dsdive.obs.sampleparams_shared | Sample pi and lambda parameters for a single dive stage |
| dsdive.obs.sample.stages | Sample stage transition times from full conditional posterior |
| dsdive.obstxmat.cov | Compute probability transition matrix for partially observed... |
| dsdive.obstx.matrix | Compute probability transition matrix for partially observed... |
| dsdive.obstx.matrix_interpolator | Interpolators for probability transition matrices of... |
| dsdive.tx.matrix.uniformized | Compute probability transition matrix for embedded DTMCs |
| dsdive.tx.params | Compute transition parameters for a given depth bin |
| envelope.approx | Approximate slope and curvature for each polynomial segment... |
| envelope.logquad | Build a piecewise-quadratic envelope given log of a function |
| envelope.quad | Build a piecewise-quadratic envelope for a given function |
| ff | Forward sampling algorithm for Hidden Markov Models |
| ffbs | Forward-filtering backward-sampling algorithm for hidden... |
| fromInd | Converts array indices to (x,y,z) coordinates |
| gaussapprox | Compute a Gaussian approximation to a density |
| gibbs_init_shared | Initialize shared-memory pointers and node storage for Gibbs... |
| mhrw | Metropolis-Hastings random walk proposal and update |
| MhrwAdaptive | Adaptive Random Walk Metropolis-Hastings (A-RWMH) sampler... |
| plot.dsdive | Plotting functions for completely observed dive trajectories |
| plot.dsobs | Plotting functions for observations of dive trajectories |
| polyval | Use Horner's method to efficiently evaluate an n degree... |
| refine.partition | Refine a partition of an interval |
| sample.gumbeltrick | Sample a categorical variable when given log-probabilities |
| stagevec | Convenience function for building a vector for dive stages |
| toInd | Converts (x,y,z) coordinates to an array index |
