| aerial.survey | Simulated bowhead whale aerial survey dataset. |
| AIC.hmltm | Summarise AIC and related for hmltm object(s). |
| beaked.hmm.pars | Alboran sea beaked whale availability HMM parameters. |
| beaked.ship | Beaked whale shipboard survey dataset from Alboran sea. |
| bootstrap.p.with.Et | Detection probability bootstrap with availability process... |
| bootstrap.p.with.hmm | Detection probability bootstrap with availability HMM. |
| bootsum | Summarise bootstrap results. |
| bootsum.p | Summarise detection probability bootstrap results. |
| bowhead.adat | Greenland bowhead whale availability data time series. |
| bowhead.depths | Greenland bowhead whale depth data time series. |
| bowhead.hmm.pars | Greenland bowhead whale availability HMM parameters. |
| bowhead.hmm.pars.bs | Bootstrapped Greenland bowhead whale availability HMM... |
| bsample | Clone of 'sample' without weird behaviour for length(x)==1. |
| bs.hmltm | Bootstrap for hmltm model. |
| calc.derived | Calculates a bunch of derived statistics from model. |
| cdfy.u | Calculate CDF of forward distance. |
| chisq.gof.y | Chi-squared goodness-of-fit in forward dimension. |
| cv | Caclulates coefficient of variation. |
| cv.avail | Calculate CV of mean time available. |
| est.hmltm | Line transect estimation with a hidden Markov availability... |
| fit.hmltm | Fit detection hazard with a Markov or hidden Markov... |
| fitted.esw | Calculates esw from model. |
| fitted.esw1 | Calculates esw from model. |
| fitted.invesw | Calculates 1/esw from model. |
| fitted.invp | Calculates E[1/p(x)] from model. |
| fitted.invp1 | Calculates E[1/p(x)] from model. |
| fitted.p | Calculates E[p(x)] from model. |
| fitted.px | Calculates fitted values for p(x) from model. |
| fit.xy | Maximises hidden Markov line transect model likelihood. |
| f.plot | Detection hazard plotting. |
| fxfit.plot | Detection function fit plotting. |
| fyfit.plot | Plotting pdf of forward detection distances. |
| getruns | Calculate lengths of all runs in availability. |
| gety.obs | Return all (discrete) forward distances in veiw. |
| histline | Draws histogram. |
| hmltm.esw | Calculates esw from model. |
| hmltm.esw1 | Calculates esw from model. |
| hmltm.invp | Calculates 1/esw from model. |
| hmltm.p | Calculates E[p(x)] from model. |
| hmltm-package | Hidden State Line Transect Models |
| hmltm.px | Calculates perp dist detection probability p(x). |
| hmltm.stat | Calculates various statistics from model. |
| hmmlt.gof.x | Goodness-of-fit in perpendicular dimension. |
| hmmlt.gof.y | Goodness-of-fit in forward dimension. |
| hmmpars.boot | Bootstrap availability HMM. |
| hmmpars.paramtetric.boot | Parameteric bootstrap availability HMM. |
| instant.a | Instantaneous availability correction factor calculation for... |
| invHessvar | Calculates asymptotic variance using Hessian. |
| inv.logit | Inverse logit function. |
| invtfm | Parameter inverse transformation function for all models. |
| is.nullmodel | Decides if model is a null model. |
| jeffa | Laake's availability correction factor calculation for a... |
| laake.a | Laake's availability correction factor calculation for... |
| lnci.nmin | Lognormal confidence interval with lower bound |
| logit | Logit function. |
| make.covb | Constructs linear predictor. |
| makeE | Returns expected time in state for 2-state Markov transition... |
| make.hmm.pars.from.Et | Makes 2-state hidden Markov model list suitable for passing... |
| make.onesit | Reduces MRDS data frame to CDS data frame. |
| makePi | Makes Markov transition matrices from mean times available... |
| make.survey.pars | Makes survey parameter list ('survey.pars') suitable for... |
| mclaren.a | McLaren's availability correction factor calculation for... |
| NDest | Estimates density and abundance. |
| negllik.x | HMM line transect model likelihood with only perpendicular... |
| negllik.xandy | HMM line transect model likelihood with perpendicular and... |
| negllik.xy | HMM line transect model likelihood with at least some forward... |
| nm2m | Converts nm to metres. |
| Npars.from.lNpars | Normal from logNormal parameters. |
| numericfy | Converts factor or character column of data frame to integer. |
| parametric.resample.hmmpars | Parameric resample availability HMM. |
| p.kolomogarov | Kolmogarov-Smirnov goodness-of-fit p-value. |
| poiss.equiv | Constructs a HMM equivalent to a Poisson process. |
| porpoise.hmm.pars | Harbour porpoise availability HMM parameters. |
| p.xy | Calculates probability of first observing animal at (x,y). |
| p.xy1 | Calculate probability of detection at (x,y). |
| resample.hmmpars | Resample availability HMM. |
| richard.a | Richard's availability correction factor calculation for... |
| simest | Simulation test hmltm performance |
| simhmltm | Tabulate point and interval estimates. |
| simhmltm.w | Simulate line transect survey data using availability time... |
| simplea | Simple availability correction factor calculation for single... |
| simple.a | Simple availability correction factor calculation. |
| sintegral | Integration using Simpson's method. |
| strat.estable | Tabulate bootstrap results. |
| sumsim | Summarise simulation results. |
| tfm | Parameter transformation function for all models. |
| truncdat | Data truncation. |
| unvectorize.hmmpars | Reformat vector as hmm.pars object. |
| vectorize.hmmpars | Reformat hmm.pars object as a vector. |
