| Generic S3 function for summarizing AICc | aicc |
| Extract AIC and AICc for a carcass persistence model | aicc.cpm |
| Create the AICc tables for a set of carcass persistence models | aicc.cpmSet |
| Create the AICc tables for a list of sets of searcher efficiency models | aicc.cpmSetSize |
| extract AICc value from pkm object | aicc.pkm |
| Create the AICc tables for a set of searcher efficiency models | aicc.pkmSet |
| Create the AICc tables for a list of sets of searcher efficiency models | aicc.pkmSetSize |
| Create the AICc tables for a list of sets of searcher efficiency models | aicc.pkmSize |
| GenEst Information | aboutContent app_content createvtext disclaimersContent disclaimerUSGS disclaimerWEST GenEstAcknowledgements GenEstAuthors GenEstGUIauthors GenEstLicense GenEstLogos gettingStartedContent |
| GenEst app download funtions | app_download_functions downloadCPFig downloadCPmod downloadgFig downloadgres downloadMFig downloadMres downloadSEFig downloadSEmod downloadTable |
| GenEst App Messages | app_msg_functions clearNotifications msgFracNote msgList msgModDone msgModFail msgModPartialFail msgModRun msgModSENobs msgModWarning msgSampleSize msgSplitFail msgSSavgFail msgSSinputFail |
| app utilities for formatting text, tables, figs, etc. for display | app_output_utilities classText estText initialOutput reNULL setFigH setFigW setNotSuspending |
| app panel utility functions | app_panels dataTabPanel modelOutputPanel selectedDataPanel |
| The GenEst server definition function | app_server eventReaction GenEstServer reaction reactionMessageDone reactionMessageRun |
| Create the GenEst User Interface HTML | aboutPanel analysisPanel app_ui CPMainPanel CPPanel CPSidebar dataInputPanel dataInputSidebar disclaimersPanel downloadsPanel GeneralInputSidebar GeneralInputsPanel GenEstUI gettingStartedPanel gMainPanel gPanel gSidebar helpPanel loadedDataPanel MMainPanel MPanel MSidebar SEMainPanel SEPanel SESidebar |
| HTML parameters | app_ui_utilities b big cButtonStyle center GenEstInlineCSS GenEstShinyJS li navbar ol small style u ul |
| app utilities | app_utilities initialReactiveValues modNamePaste modNameSplit pickSizeclass plotNA prepSizeclassText reVal selectData setkNeed updateColNames_size updateSizeclasses updatesizeCol |
| Create and manage widgets for data input, function execution, data output | app_widgets dataDownloadWidget dataInputWidget kFixedWidget kFixedWidgetHeader kFixedWidgetRow modelInputWidget modelOutputWidget modelRunWidget modelSelectionWidget modelSelectionWidgetHeader modelSelectionWidgetRow preTextMaker splitButtonWidget widgetMaker |
| Tabulate an average search schedule from a multi-unit SS data table | averageSS |
| Calculate detection probability for given SE and CP parameters and search schedule. | calcg |
| Estimate the number of fatalities in each search interval throughout the monitoring period. | calcRate |
| Estimate the number of fatalities by up to two splitting covariates | calcSplits |
| Estimate the number of fatalities by time interval | calcTsplit |
| Check for model components | checkComponents |
| Checks whether a vector of data can be interpreted as dates | checkDate |
| Error check a specific model selection for a CP plot | checkSpecificModelCP |
| Error check a specific model selection for an SE plot | checkSpecificModelSE |
| Associate CO carcasses with appropriate DWP values (by unit and carcass class) | CO_DWP |
| Combine predictors | combinePreds |
| Combine predictors across models | combinePredsAcrossModels |
| Count the minimum number of carcasses in the cells | countCarcs |
| Produce a named vector of standard CP plot colors | CPcols |
| Produce the options for the distributions in the CP model | CPdistOptions |
| Calculate the negative log-likelihood of a carcass persistence model | cpLogLik |
| Fit cp carcass persistence models | cpm cpm0 cpmSet cpmSize |
| Plot cell-specific decay curve for carcass persistence | cpmCPCellPlot |
| Check if a CP model is well-fit | cpmFail |
| Check if cpm models fail | cpmSetFail |
| Remove failed cpm models from a 'cpmSet' object | cpmSetFailRemove |
| Check if all of the cpm models fail | cpmSetSizeFail |
| Remove failed cpm models from a 'cpmSetSize' object | cpmSetSizeFailRemove |
| Plot cell-specific decay curve for carcass persistence | cpmSetSpecCPCellPlot |
| Select the date columns from a data table | dateCols |
| Calculate day of study from calendar date | dateToDay |
| Auto-parsing to find the name of the unit column ('unitCol') | defineUnitCol |
| Descriptive statistics for a fitted CP model | desc |
| Create the download version of the Searcher Efficiency model table | dlModTabSE |
| Select the DWP-ok columns from a data table | DWPCols |
| Fit density-weighted proportion (DWP) models. | dwpm |
| Estimate all carcass-level detection rates and arrival intervals | estg |
| Estimate generic g | estgGeneric |
| Estimate generic detection probability for multiple carcass classes | estgGenericSize |
| Estimate mortality | estM |
| Expand a CP model set for plotting | expandModelSetCP |
| Generalized estimation of mortality | GenEst |
| Compute the logit or anti-logit | alogit logit |
| Transpose a list of arrays | ltranspose |
| A mock example data set | mock |
| model utility functions (not exported) | matchCells modelSetCells modelSetModelCells modelSetModelPredictors modelSetPredictors model_utility_functions |
| Select the columns from a data table that could be CP First Time Absent observations | obsCols_fta |
| Select the columns from a data table that could be CP Last Time Present observations | obsCols_ltp |
| Select the columns from a data table that could be SE observations | obsCols_SE |
| Calculate the negative log-likelihood of a searcher efficiency model | pkLogLik |
| Fit pk searcher efficiency models. | pkm pkm0 pkmSet pkmSize |
| Check if a pk model is well-fit | pkmFail |
| Plot parameter box plots for each cell for either p or k | pkmParamPlot |
| Plot cell-specific decay curve for searcher efficiency | pkmSECellPlot |
| Check if all of the pkm models fail within a given set | pkmSetAllFail |
| Check if pkm models fail | pkmSetFail |
| Remove failed pkm models from a 'pkmSet' object | pkmSetFailRemove |
| Check if all of the pkm models fail | pkmSetSizeFail |
| Remove failed pkm models from a 'pkmSetSize' object | pkmSetSizeFailRemove |
| p or k box plots for an SE model set | pkmSetSpecParamPlot |
| Plot cell-specific decay curve for searcher efficiency for a specific model with comparison to the cellwise model | pkmSetSpecSECellPlot |
| The CDF of the loglogistic distribution | pllogis |
| Plot results of a single CP model | plot.cpm |
| Plot results of a set of CP models | plot.cpmSet |
| Plot total mortality estimation | plot.estM |
| Plot results of a single generic ghat estimation | plot.gGeneric |
| Plot results of a set of size-based generic ghat estimations | plot.gGenericSize |
| Plot results of a single pk model | plot.pkm |
| Plot results of a set of SE models | plot.pkmSet |
| Plot summary statistics for splits of mortality estimates | plot.splitFull |
| Plot summary statistics for splits of mortality estimates | plot.splitSummary |
| Plot the cellwise results of a single model in a set of CP models | plotCPCells |
| Plot results of a single CP model in a set | plotCPFigure |
| The CP plot header | plotCPHeader |
| p and k box plots for an SE model set | plotSEBoxPlots |
| template box plot | plotSEBoxTemplate |
| Plot the cellwise results of a single model in a set of SE models | plotSECells |
| Plot results of a single SE model in a set | plotSEFigure |
| The SE plot header | plotSEHeader |
| Calculate the probability of persistence to detection | ppersist |
| Select the predictor-ok columns from a data table | predsCols |
| Prepare predictors based on inputs | prepPredictors |
| Create search schedule data into an prepSS object for convenient splits analyses | prepSS |
| Create the pretty version of the Carcass Persistence model table | prettyModTabCP |
| Create the pretty versions of model and summary tables | prettyModTabSE |
| Create the pretty version of the split summary table | prettySplitTab |
| Print a 'cpm' model object | print.cpm |
| Print a 'pkm' model object | print.pkm |
| Quantiles of marginal distributions of \hat{p} and \hat{k} | qpk |
| Simulate parameters from a fitted cp model | rcp |
| Simulate parameters from a fitted dwp model | rdwp |
| Read in csv files in either format | readCSV |
| Return the model with the greatest log-likelihood | refMod |
| Remove selected columns from column names | removeCols |
| Simulate parameters from a fitted pk model | rpk |
| Launch the GenEst Application | runGenEst |
| Produce a named vectory with standard SE plot colors | SEcols |
| Produce a single panel in an SE summary/diagnostic plot | SEpanel |
| Calculate decayed searcher efficiency | SEsi |
| Calculate conditional probability of observation at a search | SEsi_left |
| Calculate conditional probability of observation after a series of searches | SEsi_right |
| Calculate decayed searcher efficiency for a single pk | SEsi0 |
| Plot a total mortality estimation for a simple situation | simpleMplot |
| Select the potential carcass class columns from a data table | sizeCols |
| Power Tower Example Dataset | solar_powerTower |
| Photovoltaic Example Dataset | solar_PV |
| Trough-based solar thermal power simulated example | solar_trough |
| Summarize total mortality estimation | summary.estM |
| Summarize the gGeneric list to a simple table | summary.gGeneric |
| Summarize the gGenericSize list to a list of simple tables | summary.gGenericSize |
| Summarize results of mortality estimate splits | summary.splitFull |
| Tidy a CP model set | tidyModelSetCP |
| Tidy an SE model set | tidyModelSetSE |
| Transpose a 'splitFull' array (preserving attributes) | transposeSplits |
| Trim a Model-Set-Size Complex to a Single Model Per Size | trimSetSize |
| Update the inputs when an event occurs | update_input |
| Update the outputs when an event occurs | update_output |
| Update the reactive value list when an event occurs | update_rv |
| Wind cleared plot (60m) Search Example | wind_cleared |
| Wind Road and Pad (120m) Example | wind_RP |
| Wind Bat-Only Road and Pad (120m) Example | wind_RPbat |
