# R Code for Mark Analysis

## Documentation for package ‘RMark’ version 3.0.8

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N P R S T V W

## -- A --

ABeginnersGuide | A beginners introduction and guide to RMark
add.design.data | Add design data
adjust.chat | Adjust over-dispersion scale or a result value such as effective sample size
adjust.parameter.count | Adjust count of estimated parameters
adjust.value | Adjust over-dispersion scale or a result value such as effective sample size

## -- B --

Blackduck | Black duck known fate data
brownie | San Luis Valley mallard data
Burnham | Burnham Live-Dead Model

## -- C --

cleanup | Removes unused MARK output files
coef.mark | MARK model beta parameters
collapseCH | Split/collapse capture histories
collect.model.names | Collect names of MARK model objects from list of R objects (internal function)
collect.models | Collect MARK models into a list and optionally construct a table of model results
compute.design.data | Compute design data for a specific parameter in the MARK model (internal use)
compute.link | Compute estimates of link values
compute.links.from.reals | Compute link values from real parameters
compute.real | Compute estimates of real parameters
compute.Sn | Various utility functions
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 values
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 specifications

## -- D --

deer | White-tailed deer double observer spotlight capture-recapture analysis
deltamethod.special | Compute delta method variance for sum, cumsum, prod and cumprod functions
Density | Density Estimation with Telemetry
deriv.inverse.link | Derivatives of inverse of link function (internal use)
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

## -- E --

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)

## -- F --

fill.covariates | Fill covariate entries in MARK design matrix with values
find.covariates | Find covariates in MARK design matrix
find.possible.transitions | Multi-state Transition Functions

## -- G --

get.link | Compute sets of link values for real parameters
get.real | Extract or compute sets of real parameters

## -- H --

HidMarkov | Hidden Markov Model

## -- I --

IELogitNormalMR | Example of Immigration-Emigration LogitNormal Mark-Resight model
import.chdata | Import capture-recapture data sets from space or tab-delimited files
inverse.link | Inverse link functions (internal use)

## -- K --

killdeer | Killdeer nest survival example data

## -- L --

larksparrow | Lark Sparrow
LASP | Lark Sparrow
load.model | Load external model
logitCI | Various utility functions
LogitNormalMR | Example of LogitNormal Mark-Resight model

## -- M --

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 variable
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 parameter specifications
mark.wrapper.parallel | Constructs and runs in parallel a set of MARK models from a dataframe of parameter specifications
mata.wald | Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
merge.design.covariates | Merge time (occasion) and/or group specific covariates into design data
merge.mark | Merge mark model objects and lists of mark model objects
merge_design.covariates | Merge time (occasion) and/or group specific covariates into design data
model.average | Compute model averaged estimates
model.average.default | Compute model averaged estimates
model.average.list | Compute model averaged estimates of real parameters from a list structure for estimates
model.average.marklist | Compute model averaged estimates of real parameters
model.table | Create table of MARK model selection results
MSJollySeber | Multistate Jolly Seber
mstrata | Multistrata example data
MStruncate | Truncate capture histories for multi-state models
MS_popan | Convert Multistate data for POPAN-style abundance estimation

## -- N --

nat.surv | Various utility functions
NicholsMSOccupancy | Multi-state occupancy example data
NSpeciesOcc | Multiple Species Occupancy

## -- P --

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
pop.est | Various utility functions
popan.derived | Computes some derived abundance estimates for POPAN models
popan.NGross | Computes some derived abundance estimates for POPAN models
popan.Nt | Computes some derived abundance estimates for POPAN models
predict_real | Compute estimates of real parameters with individual and design covariates
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
ps | Mulstistate Live-Dead Paradise Shelduck Data

## -- R --

RDMultScalOcc | Multi-scale dynamic occupancy models in RMark
RDOccupancy | Robust Design occupancy example data
RDSalamander | Robust design salamander occupancy data
read.mark.binary | Reads binary file output from MARK and returns a list of the results
readMarkVcv | Reads binary file output from MARK and returns a list of the results
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
restore | Store models externally or restore to workspace from external storage
robust | Robust design example data
run.mark.model | Runs analysis with MARK model using MARK.EXE
run.models | Runs a set of MARK models

## -- S --

salamander | Salamander occupancy data
search.output.files | Various utility functions
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 states are routes taken by migrating fish.
splitCH | Split/collapse capture histories
store | Store models externally or restore to workspace from external storage
strip.comments | Strip comments
summary.ch | Provides a summary for the capture histories
summary.mark | Summary of MARK model parameters and results
summary_ch | Provides a summary for the capture histories

## -- T --

tailarea.t | Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
tailarea.z | Model-Averaged Tail Area Wald (MATA-Wald) confidence intervals
transition.pairs | Multi-state Transition Functions
TransitionMatrix | Multi-state Transition Functions

## -- V --

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 likelihood

## -- W --

weta | Occupancy data for Mahoenui Giant Weta
Whatsnew | Summary of changes by version
wwdo.09 | White-winged dove Jolly-Seber POPAN Analysis Details
wwdo.10 | White-winged dove Jolly-Seber POPAN Analysis Details
wwdo.popan | White-winged dove Jolly-Seber POPAN Analysis Details