Our Objectives | Trophic Position Model | Vignette structure | Load packages | Assess data | Consumer data | Baseline data | Organizing data | Joining isotope data | Bayesian Analysis | Priors | Model convergence | Estimating trophic position | Model | Model output | Trace plots | Predictive posterior check | Posterior draws | Extract posterior draws | Extracting credible intervals | Plotting posterior distributions – single species or group | Density plot | Point interval

List available files | User credentials | Back to the regularly-scheduled programming | Download project or data extraction files | Search and download tag detections | Upload files to MATOS

Our Objectives | Bring in trophic niche data | Estimate posterior distribution with Normal-Inverse-Wishart (NIW) priors. | Extract μ values | Extract Σ values | Plot posterior distrubtion of μ and Σ | Estimate niche ellipse | Plot ellipses, densities of each istope, and isotope biplot | Use {patchwork} to make ellipse, density, and biplots into a paneled figure. | Determine the 95% niche similarties for each species | Estimate overall niche size | Plot niche size

Our Objectives | Bring in trophic data | Convert to {SIBER} object | Bayesian Ellipse Analysis | Extract posterior distributions for μ and Σ | Extract Niche Size | Niche Similarties | Bayesian Estimates of Layman's Community Metrics

Using review() | Including previous data | Applying drift

map() | Map an SSM fit to data, using default settings | Control track components | Change projection

Disclaimer | Models | Data | Argos Least-Squares (LS) location data | Argos Kalman Filter (KF) location data | GPS location data | Light-level geolocation data | Projected location data | A mixture of location data types | Fitting a model | Custom data formats | Access results | Visualising a model fit | References

Processing data | Fit an SSM | emf: specifying error multiplication factors | map: fixing model parameters | control: controlling the optimization | References

References

sim() | Simulate tracks from each of the 3 process models | Plot simulated tracks | Fit SSM to simulated lon,lat locations (with Argos error) | sim_fit() | Simulate tracks from an SSM fit and plot: | Simulate tracks with a potential function to help avoid land: | Simulate central place foraging tracks | sim_filter() | route_path() | Simulate tracks from the posterior of SSM fit(s) - sim_post() | References

Our Objectives | Example 1: Making a soap-film smoother for a Simple boundary - Ramsay's horseshoe | Step 1: Load packages | Step 2: Check if we can make a soap-film for Ramsey's horseshoe | Step 3: Check if the data and the evenly spaced knots fall within the boundary | Step 4: Check the data | Step 5: Run the model | Example 2: Making a soap-film smoother for a more complex boundary. | Step 1: Convert CRS | Step 2: Convert to boundary list | Step 3: Check if the boundary list works | Step 4: Make knots for a more complex boundary using | Step 5: Sissabagama example dataset | Step 6: Run the model | Step 7: Plot our predicted results

Parallel | Listing | Downloading | Summarizing

ACT members

Specifying drift stations | Applying drift | drift() function

morts() function | Duration of residence events | 1. last | 2. any | Cumulative residence events | Notes on selecting a method | Output | infrequent() function | 1. recent | 2. defined | Options | Exclude single detections | Previously identified mortalities | Look backwards | Drift and season

mort format | Other formats | actel | glatos | VTrack | Other packages? | Manual formatting

Basic plotting of residence events | Customizing | Interactive plots | Options | Add flagged mortalities | Seasonality | Facetting | Exclude single detections | Source code

Applying seasonality | overlap argument | season() function

stationchange() function | resmax() function | resmaxcml() function

Example | route_path() | re-route Weddell seal SSM-predicted locations

Data preparation | Model fitting | Model visualisation | State process inference | Covariates | Model checking | Custom plots | Other features | predict functions | knownStates | fit = FALSE | References

Alaska Harbor Seal Example | Essential Packages | Pre-processing Track Data and Land Polygon Data | Re-Route Raw Argos Observations | Limit Barrier Polygon to Region of Interest | Create Visibility Graph | Determine Re-routed Track via Shortest Path | Update Geometry With Re-routed Coordinates | Re-Routing a Movement Model Prediction | Fit Movement Model and Predict Locations | Identify Predicted Locations on Land | Re-route Model Prediction via Shortest Path | Update Predicted Path | Multiple Imputation | Create Multiple Imputations from {crawl} Model | Space Use Analysis

The Test Environment | Re-route the path | Did it work?