Man pages for RMark
R Code for Mark Analysis
| ABeginnersGuide | A beginners introduction and guide to RMark |
| add.design.data | Add design data |
| adjust.parameter.count | Adjust count of estimated parameters |
| adjust.value | Adjust over-dispersion scale or a result value such as... |
| Blackduck | Black duck known fate data |
| brownie | San Luis Valley mallard data |
| Burnham | Burnham Live-Dead Model |
| cleanup | Removes unused MARK output files |
| coef.mark | MARK model beta parameters |
| collect.model.names | Collect names of MARK model objects from list of R objects... |
| collect.models | Collect MARK models into a list and optionally construct a... |
| compute.design.data | Compute design data for a specific parameter in the MARK... |
| compute.link | Compute estimates of link values |
| compute.links.from.reals | Compute link values from real parameters |
| compute.real | Compute estimates of real parameters |
| convert.inp | Convert MARK input file to RMark dataframe |
| convert.link.to.real | Convert link values to real parameters |
| covariate.predictions | Compute estimates of real parameters for multiple covariate... |
| crdms | Example data for Closed Robust Design Multistrata |
| create.mark.mcmc | Create mcmc object for analysis with coda |
| create.model.list | Creates a dataframe of all combinations of parameter... |
| deer | White-tailed deer double observer spotlight capture-recapture... |
| deltamethod.special | Compute delta method variance for sum, cumsum, prod and... |
| Density | Density Estimation with Telemetry |
| deriv_inverse.link | Derivatives of inverse of link function (internal use) |
| dipper | Dipper capture-recapture data |
| Donovan.7 | Exercise 7 example data |
| Donovan.8 | Exercise 8 example data |
| edwards.eberhardt | Rabbit capture-recapture data |
| example.data | Simulated data from Cormack-Jolly-Seber model |
| export.chdata | Export capture-history data to MARK .inp format |
| export.MARK | Export data and models for import in MARK |
| export.model | Export output files for appending into MARK .dbf/.fpt format |
| extract.indices | Various utility functions |
| extract.mark.output | Extract results from MARK output file (internal use) |
| fill.covariates | Fill covariate entries in MARK design matrix with values |
| find.covariates | Find covariates in MARK design matrix |
| get.link | Compute sets of link values for real parameters |
| get.real | Extract or compute sets of real parameters |
| IELogitNormalMR | Example of Immigration-Emigration LogitNormal Mark-Resight... |
| import.chdata | Import capture-recapture data sets from space or... |
| inverse.link | Inverse link functions (internal use) |
| killdeer | Killdeer nest survival example data |
| larksparrow | Lark Sparrow |
| load.model | Load external model |
| LogitNormalMR | Example of LogitNormal Mark-Resight model |
| make.design.data | Create design dataframes for MARK model specification |
| make.mark.model | Create a MARK model for analysis |
| make.time.factor | Make time-varying dummy variables from time-varying factor... |
| mallard | Mallard nest survival example |
| mark | Interface to MARK for fitting capture-recapture models |
| mark.wrapper | Constructs and runs a set of MARK models from a dataframe of... |
| mark.wrapper.parallel | Constructs and runs in parallel a set of MARK models from a... |
| mata.wald | Model-Averaged Tail Area Wald (MATA-Wald) confidence... |
| merge_design.covariates | Merge time (occasion) and/or group specific covariates into... |
| merge.mark | Merge mark model objects and lists of mark model objects |
| model.average | Compute model averaged estimates |
| model.average.list | Compute model averaged estimates of real parameters from a... |
| model.average.marklist | Compute model averaged estimates of real parameters |
| model.table | Create table of MARK model selection results |
| MS_popan | Convert Multistate data for POPAN-style abundance estimation |
| mstrata | Multistrata example data |
| MStruncate | Truncate capture histories for multi-state models |
| NicholsMSOccupancy | Multi-state occupancy example data |
| NSpeciesOcc | Multiple Species Occupancy |
| Paradise_shelduck | Mulstistate Live-Dead Paradise Shelduck Data |
| PIMS | Display PIM for a parameter |
| PoissonMR | Example of Poisson Mark-Resight model |
| Poisson_twoMR | Example of Poisson Mark-Resight model |
| popan.derived | Computes some derived abundance estimates for POPAN models |
| predict_real | Compute estimates of real parameters with individual and... |
| print.mark | Print MARK objects |
| print.marklist | Print MARK list objects |
| print.summary.mark | Prints summary of MARK model parameters and results |
| process.ch | Process release-recapture history data |
| process.data | Process encounter history dataframe for MARK analysis |
| RDMultScalOcc | Multi-scale dynamic occupancy models in RMark |
| RDOccupancy | Robust Design occupancy example data |
| RDSalamander | Robust design salamander occupancy data |
| readMarkVcv | Reads binary file output from MARK and returns a list of the... |
| release.gof | Runs RELEASE for goodness of fit test |
| remove.mark | Remove mark models from list |
| rerun.mark | Runs a previous MARK model with new starting values |
| robust | Robust design example data |
| run.mark.model | Runs analysis with MARK model using MARK.EXE |
| run.models | Runs a set of MARK models |
| salamander | Salamander occupancy data |
| setup.model | Defines model specific parameters (internal use) |
| setup.parameters | Setup parameter structure specific to model (internal use) |
| skagit | An example of the Multistrata (multi-state) model in which... |
| splitCH | Split/collapse capture histories |
| store | Store models externally or restore to workspace from external... |
| strip.comments | Strip comments |
| summary_ch | Provides a summary for the capture histories |
| summary.mark | Summary of MARK model parameters and results |
| TransitionMatrix | Multi-state Transition Functions |
| valid.parameters | Determine validity of parameters for a model (internal use) |
| var.components | Variance components estimation |
| var.components.reml | Variance components estimation using REML or maximum... |
| weta | Occupancy data for Mahoenui Giant Weta |
| Whatsnew | Summary of changes by version |
| wwdo.popan | White-winged dove Jolly-Seber POPAN Analysis Details |
