| AHMbook-package | Functions and data for the Book "Applied Hierarchical... |
| bigCrossCorr | Cross correlations for MCMC output |
| ch2marray | Converts capture-histories to an m-array |
| color_ramps | Color Ramps |
| data_BerneseOberland | Landscape data for the Bernese Oberland around Interlaken, in... |
| data_crestedTit | Count data from the Swiss Breeding Bird Survey MHB for... |
| data_crossbillAHM | Data from the Swiss Breeding Bird Survey MHB for European... |
| data_cswa | Point count and spot-mapping data for Chestnut-sided Warbler |
| data_dragonflies | Fictional data for dragonflies |
| data_duskySalamanders | Age-classified counts of dusky salamanders from two... |
| data_EurasianLynx | Data for Eurasian lynx from Switzerland and Italy (only... |
| data_Finnmark | Data from surveys of birds in Finnmark in NE Norway |
| data_FrenchPeregrines | Data for observations of peregrines from the French Jura... |
| data_greenWoodpecker | Count data from the Swiss Breeding Bird Survey for Green... |
| data_HubbardBrook | Warbler point count data from the Hubbard Brook Experimental... |
| data_MesoCarnivores | Camera trap data for Bobcat, Coyote and Red Fox |
| data_MHB2014 | Data from the Swiss Breeding Bird Survey MHB 2014 |
| data_simDynoccSpatialData | Simulated data from 'simDynoccSpatial' for AHM2 section... |
| data_spottedWoodpecker | Data for observations of Middle Spotted Woodpecker in... |
| data_SwissAtlasHa | Data for 1ha quadrats from the Swiss Breeding Bird Atlas |
| data_SwissEagleOwls | Territory-level, multi-state detection/nondetection data for... |
| data_SwissMarbledWhite | Data for Swiss Marbled White butterflies |
| data_SwissSquirrels | Data for Red Squirrels in Switzerland from the Swiss breeding... |
| data_SwissTits | Data from the Swiss Breeding Bird Survey for 6 species of... |
| data_treeSparrow | American Tree Sparrow data from Alaska |
| data_ttdPeregrine | Time-to-detection data for peregrines from the French Jura... |
| data_UKmarbledWhite | Data for UK Marbled White butterflies |
| data_wagtail | Data for Dutch wagtails |
| data_waterVoles | Data for the Mighty Water Voles of Scotland, UK. |
| data_wigglyLine | Coordinates for a wiggly line transect |
| data_willowWarbler | Constant effort site (CES) data for British Willow Warblers |
| e2dist | Calculates the pair-wise distances between two sets of points |
| fitstats | Functions to return fit statistics |
| getLVcorrMat | Compute results of a Joint Species Distribution Model (JSDM) |
| graphSSM | Plot the results for a Gaussian state-space model |
| image_scale | Helper function to draw scale for image |
| map.Nmix.resi | Mapping of residuals |
| modSelFP | Model selection results from a list of 'unmarkedFitOccuFP'... |
| piFuns | Compute multinomial cell probabilities |
| playRN | Function to play Royle-Nichols (RN) model |
| plot_Nmix_resi | Produce some residual plots |
| ppc.plot | Plot results from posterior predictive check |
| sim3Occ | Simulate detection/nondetection data for static 3-level... |
| simCJS | Simulate individual capture-histories under a... |
| simComm | Simulate community occupancy or community abundance data |
| simDataDK | Simulate data for an integrated species distribution model... |
| simData.fn | Simulate count data under a binomial N-mixture model |
| simDCM | Simulate detection/nondetection data under a general dynamic... |
| simDemoDynocc | Simulate data under a demographic dynamic occupancy model |
| simDM_simDM0 | Simulate count data under the dynamic N-mixture model of... |
| simDSM | Simulate line transect data for density surface modeling |
| simDynocc | Simulate detection/nondetection data under a wide variety of... |
| simDynoccSpatial | Simulate data under a dynamic occupancy model with spatial... |
| simExpCorrRF | Create a Gaussian random field with negative exponential... |
| simFn | Simulate a Poisson point process |
| simFrogDisease | Simulate detection data for diseased frogs |
| simHDS | Simulate data under hierarchical distance sampling protocol... |
| simHDSg | Simulate data under HDS protocol with groups |
| simHDSopen | Simulate open hierarchical distance sampling data |
| simHDSpoint | Simulate data under hierarchical distance sampling point... |
| simHDStr | Simulate HDS time-removal or double-observer data |
| simIDS | Simulate data for an integrated distance sampling, point... |
| simIssj.sim | Simulate open distance sampling data for the Island Scrub... |
| simLdata | Simulation of distance sampling data. |
| simMultMix | Simulate the multinomial-mixture model |
| simNmix | Simulate data for binomial and multinomial mixture models |
| simNmixSpatial | Simulate replicated counts under a spatial, static binomial... |
| simNpC | Generate counts from a single population observed over T... |
| simOcc | Simulate data for static occupancy models under wide range of... |
| simOccSpatial | Simulate replicated detection/nondetection data under a... |
| simOccttd | Simulate time-to-detection occupancy data (single visits) |
| simPdata | Simulate non-hierarchical point transect (= point count) data |
| simPH | Generate counts under a variant of a 'phenomenological model' |
| simpleNmix | Simulate N-mixture data under a time-for-space substitution... |
| simPOP | Simulate data for a demographic state-space model |
| simPPe | Simulate a spatial point pattern in a heterogeneous landscape |
| simSpatialDS | Simulates data for a basic spatial distance sampling model |
| simSpatialDSline | Simulate data for a standardized line transect |
| simSpatialDSte | Simulate data for replicate line transect surveys with... |
| simSpatialHDS | Simulates data for a hierarchical spatial distance sampling... |
| simWigglyOcc | Simulate static occupancy data |
| spline.prep | Prepare input for BUGS model when fitting a spline for a... |
| standardize | Scaling and centering of vectors, matrices and arrays |
| valid_data | Validates simulated observational data against... |
| zinit | Starting values for survival analysis in JAGS/BUGS |
