Generalised Fatality Estimator

alogit | Compute the anti-logit. |

calcMhat | Calculate Mhat for a given Mtilde and DWP |

checkComponents | Check if all component terms and interactions are included in... |

combinePreds | Create the predictor combination table for a searcher... |

countCarcs | Count the minimum number of carcasses in the cells |

CPdistOptions | Produce the options for the distributions in the CP model |

cpLogLik | Calculate the negative log-likelihood of a carcass... |

cpm | Fit a single carcass persistence model. |

cpmCPCellPlot | Plot cell-specific decay curve for carcass persistence |

cpmSet | Run a set of cpm models based on predictor inputs |

cpmSetAICcTab | Create the AICc tables for a set of carcass persistence... |

cpmSetFail | Check if all of the cpm models fail |

cpmSetFailRemove | Remove failed pkm models |

cpmSetSize | Fit all possible carcass persistence models across all size... |

cpmSetSizeFail | Check if all of the cpm models fail |

cpmSetSizeFailRemove | Remove failed cpm models |

cpmSetSpecCPCellPlot | Plot cell-specific decay curve for carcass persistence |

dateToDay | Convert calendar date to day from reference |

DWPbyCarcass | Expand the density weighted proportion table to a value for... |

Ecbinom | Calculates the expected value of a continuous binomial |

GenEst | Generalized estimation of fatalities |

isNeverDecreasing | Check if a vector is never decreasing |

kFillPropose | Propose a k value if it is not in the model table |

kSuggest | Suggest a value for k based on a weighted mean of the... |

logit | Compute the logit. |

makeMenu | Make a model menu |

matchCells | Match cells between a (potentially) reduced and full model |

mockData | Completely mock example data set |

modNamePaste | Paste the parts of a model's name back together |

modNameSplit | Split model names into their components and remove only a... |

modTabColNamesCP | Creates the names for the Carcass Persistence model table... |

modTabColNamesSE | Creates the names for the Searcher Efficiency model table... |

msgModDoneM | Creates the M finished message |

msgModFail | Creates the error message for when no models are fit... |

msgModPartialFail | Creates the warning message for when only some models are fit... |

msgModRun | Creates a model running message |

msgNobsSE | Creates the SE data size notification |

msgSampleSize | Creates the small sample size warning |

pickSizeclass | Locate the sizeclass selected by the inputs |

pkLogLik | Calculate the negative log-likelihood of a searcher... |

pkm | Fit a single searcher efficiency model. |

pkmParamPlot | Plot parameter box plots for each cell for either p or k |

pkmSECellPlot | Plot cell-specific decay curve for searcher efficiency |

pkmSet | Run a set of pkm models based on predictor inputs |

pkmSetAICcTab | Create the AICc tables for the searcher efficiency models |

pkmSetFail | Check if all of the pkm models fail |

pkmSetFailRemove | Remove failed pkm models |

pkmSetSize | Fit all possible searcher efficiency models across all size... |

pkmSetSizeFail | Check if all of the pkm models fail |

pkmSetSizeFailRemove | Remove failed pkm models |

pkmSetSpecParamPlot | Plot parameter box plots for each cell within a model for... |

pkmSetSpecSECellPlot | Plot cell-specific decay curve for searcher efficiency for a... |

plot.cpm | Plot results of a single cp model |

plot.cpmSet | Plot results of a cp model set |

plot.pkm | Plot results of a single pk model |

plot.pkmSet | Plot results of a pk model set |

ppersist | Calculate the probability of persistence to detection |

ppersist_loglogistic | Calculate the probability of persistence to for a loglogistic |

prepPredictors | Prepares predictors based on inputs |

prepSizeclassText | Prepare text for size classes |

rcp | Simulate parameters from a fitted cp model. |

rghat | Simulate ghat values and arrival intervals for a set of... |

rghatCarcass | Simulate ghat values and arrival intervals for a carcass from... |

rMhat | Draw values for Mhat given a ghat and DWP |

rMtilde | Draw values for Mtilde given a ghat |

rpk | Simulate p and k parameters from a fitted pk model. |

runGenEst | Launch the app |

rXtilde | Draw values for Xtilde given a ghat |

selectData | Select particular columns from a data set |

server | Create the UI |

SEsi | Calculate searcher efficiency after some searches |

SEsi0 | Calculate searcher efficiency after some searches for a... |

setFigH | Set the figure height based on the number of cells |

setFigW | Set the figure width based on the number of cells |

setkFillNeed | Creates the kFillNeed text |

setkFix | Update the fixed k value |

trueLength | Length of non-missing values in a vector |

ui | Create the UI |

updateColNames_all | Updates the string of column names that are in all the needed... |

updateSizeclassCol | Updates the name of the size class column based on available... |

updateSizeclasses | Update the size classes |

whichCleanout | Determine which carcasses were from cleanout searches |

yyyymmdd | Converts the standard Excel date format (m/d/YYYY) to... |

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