Generalized Mortality Estimator

aicc | Generic S3 function for summarizing AICc |

aicc.cpm | Extract AIC and AICc for a carcass persistence model |

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

aicc.cpmSetSize | Create the AICc tables for a list of sets of searcher... |

aicc.pkm | extract AICc value from pkm object |

aicc.pkmSet | Create the AICc tables for a set of searcher efficiency... |

aicc.pkmSetSize | Create the AICc tables for a list of sets of searcher... |

aicc.pkmSize | Create the AICc tables for a list of sets of searcher... |

app_content | GenEst Information |

app_download_functions | GenEst app download funtions |

app_msg_functions | GenEst App Messages |

app_output_utilities | app utilities for formatting text, tables, figs, etc. for... |

app_panels | app panel utility functions |

app_server | The GenEst server definition function |

app_ui | Create the GenEst User Interface HTML |

app_ui_utilities | HTML parameters |

app_utilities | app utilities |

app_widgets | Create and manage widgets for data input, function execution,... |

averageSS | Tabulate an average search schedule from a multi-unit SS data... |

calcg | Calculate detection probability for given SE and CP... |

calcRate | Estimate the number of fatalities in each search interval... |

calcSplits | Estimate the number of fatalities by up to two splitting... |

calcTsplit | Estimate the number of fatalities by time interval |

checkComponents | Check for model components |

checkDate | Checks whether a vector of data can be interpreted as dates |

checkSpecificModelCP | Error check a specific model selection for a CP plot |

checkSpecificModelSE | Error check a specific model selection for an SE plot |

CO_DWP | Associate CO carcasses with appropriate DWP values (by unit... |

combinePreds | Combine predictors |

combinePredsAcrossModels | Combine predictors across models |

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

CPcols | Produce a named vector of standard CP plot colors |

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

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

cpm | Fit cp carcass persistence models |

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

cpmFail | Check if a CP model is well-fit |

cpmSetFail | Check if cpm models fail |

cpmSetFailRemove | Remove failed cpm models from a 'cpmSet' object |

cpmSetSizeFail | Check if all of the cpm models fail |

cpmSetSizeFailRemove | Remove failed cpm models from a 'cpmSetSize' object |

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

dateCols | Select the date columns from a data table |

dateToDay | Calculate day of study from calendar date |

defineUnitCol | Auto-parsing to find the name of the unit column ('unitCol')... |

desc | Descriptive statistics for a fitted CP model |

dlModTabSE | Create the download version of the Searcher Efficiency model... |

DWPCols | Select the DWP-ok columns from a data table |

dwpm | Fit density-weighted proportion (DWP) models. |

estg | Estimate all carcass-level detection rates and arrival... |

estgGeneric | Estimate generic g |

estgGenericSize | Estimate generic detection probability for multiple carcass... |

estM | Estimate mortality |

expandModelSetCP | Expand a CP model set for plotting |

GenEst | Generalized estimation of mortality |

logit | Compute the logit or anti-logit |

ltranspose | Transpose a list of arrays |

mock | A mock example data set |

model_utility_functions | model utility functions (not exported) |

obsCols_fta | Select the columns from a data table that could be CP First... |

obsCols_ltp | Select the columns from a data table that could be CP Last... |

obsCols_SE | Select the columns from a data table that could be SE... |

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

pkm | Fit pk searcher efficiency models. |

pkmFail | Check if a pk model is well-fit |

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

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

pkmSetAllFail | Check if all of the pkm models fail within a given set |

pkmSetFail | Check if pkm models fail |

pkmSetFailRemove | Remove failed pkm models from a 'pkmSet' object |

pkmSetSizeFail | Check if all of the pkm models fail |

pkmSetSizeFailRemove | Remove failed pkm models from a 'pkmSetSize' object |

pkmSetSpecParamPlot | p or k box plots for an SE model set |

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

pllogis | The CDF of the loglogistic distribution |

plotCPCells | Plot the cellwise results of a single model in a set of CP... |

plotCPFigure | Plot results of a single CP model in a set |

plotCPHeader | The CP plot header |

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

plot.cpmSet | Plot results of a set of CP models |

plot.estM | Plot total mortality estimation |

plot.gGeneric | Plot results of a single generic ghat estimation |

plot.gGenericSize | Plot results of a set of size-based generic ghat estimations |

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

plot.pkmSet | Plot results of a set of SE models |

plotSEBoxPlots | p and k box plots for an SE model set |

plotSEBoxTemplate | template box plot |

plotSECells | Plot the cellwise results of a single model in a set of SE... |

plotSEFigure | Plot results of a single SE model in a set |

plotSEHeader | The SE plot header |

plot.splitFull | Plot summary statistics for splits of mortality estimates |

plot.splitSummary | Plot summary statistics for splits of mortality estimates |

ppersist | Calculate the probability of persistence to detection |

predsCols | Select the predictor-ok columns from a data table |

prepPredictors | Prepare predictors based on inputs |

prepSS | Create search schedule data into an prepSS object for... |

prettyModTabCP | Create the pretty version of the Carcass Persistence model... |

prettyModTabSE | Create the pretty versions of model and summary tables |

prettySplitTab | Create the pretty version of the split summary table |

print.corpus_frame | Generic S3 function for printing corpus_frame |

print.cpm | Print a 'cpm' model object |

print.pkm | Print a 'pkm' model object |

qpk | Quantiles of marginal distributions of \hat{p} and \hat{k} |

rcp | Simulate parameters from a fitted cp model |

rdwp | Simulate parameters from a fitted dwp model |

readCSV | Read in csv files in either format |

refMod | Return the model with the greatest log-likelihood |

removeCols | Remove selected columns from column names |

rpk | Simulate parameters from a fitted pk model |

runGenEst | Launch the GenEst Application |

SEboxes | Produce boxplots 'p' and/or 'k' for all cells for reference... |

SEcols | Produce a named vectory with standard SE plot colors |

SEfig | Plot results of a single SE model in a set |

SEpanel | Produce a single panel in an SE summary/diagnostic plot |

SEsi | Calculate decayed searcher efficiency |

SEsi0 | Calculate decayed searcher efficiency for a single pk |

SEsi_left | Calculate conditional probability of observation at a search |

SEsi_right | Calculate conditional probability of observation after a... |

simpleMplot | Plot a total mortality estimation for a simple situation |

sizeCols | Select the potential carcass class columns from a data table |

solar_powerTower | Power Tower Example Dataset |

solar_PV | Photovoltaic Example Dataset |

solar_trough | Trough-based solar thermal power simulated example |

summary.estM | Summarize total mortality estimation |

summary.gGeneric | Summarize the gGeneric list to a simple table |

summary.gGenericSize | Summarize the gGenericSize list to a list of simple tables |

summary.splitFull | Summarize results of mortality estimate splits |

tidyModelSetCP | Tidy a CP model set |

tidyModelSetSE | Tidy an SE model set |

transposeSplits | Transpose a 'splitFull' array (preserving attributes) |

trimSetSize | Trim a Model-Set-Size Complex to a Single Model Per Size |

update_input | Update the inputs when an event occurs |

update_output | Update the outputs when an event occurs |

update_rv | Update the reactive value list when an event occurs |

wind_cleared | Wind cleared plot (60m) Search Example |

wind_RP | Wind Road and Pad (120m) Example |

wind_RPbat | Wind Bat-Only Road and Pad (120m) Example |

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