GenEst: Generalized estimation of mortality

Description

This package is designed to analyze searcher efficiency, carcass persistence, search schedule, and carcass observation data for the estimation of bird and bat mortality at wind and solar power facilities.

Arguments

Information

browseVignettes("GenEst") packageDescription("GenEst") disclaimers()

Data sets

mock wind_cleared wind_RP wind_RPbat solar_powerTower solar_PV solar_trough

Main command-line functions

pkm, cpm: estimate searcher efficiency (pk) and carcass persistence (cp) parameters
estM: estimate mortality given pkm, cpm and data
calcSplits: split mortality estimates by subcategories
plot: S3 function for pkm, pkmSet, cpm, cpmSet, estM, splitFull, splitSummary, gGeneric, and gGenericSize objects
transposeSplits: transpose 2-d splits
summary: S3 function for estM, splitFull, gGeneric, gGenericSize objects
aicc: S3 function for extracting models' AICc values from pkm, pkmSet, pkmSize, pkmSetSize, cpm, cpmSet, cpmSize, and cpmSetSize objects
estgGeneric, estgGenericSize: estimate detection probability (g) for given searcher efficiency and carcass persistence model
runGenEst(): start the GUI

Potentially useful calculation functions

rpk, rcp estg, calcg ppersist, SEsi alogit, logit Ecbinom pkLogLik, cpLogLik calcRate, calcTsplit, ltranspose

Potentially useful editing functions

prepSS averageSS trimSetSize combinePreds combinePredsAcrossModels DWPbyCarcass pkmSetSizeFailRemove pkmSetFailRemove cpmSetSizeFailRemove cpmSetFailRemove tidyModelSetCP tidyModelSetSE

Other functions (primarily associated with the GUI)

aboutContent aboutPanel analysisPanel b big cButtonStyle center checkComponents checkDate checkSpecificModelCP checkSpecificModelSE clearNotifications combinePredsAcrossModels countCarcs CPcols CPdistOptions CPMainPanel cpmCPCellPlot cpmFail cpmSetFail cpmSetSpecCPCellPlot CPPanel CPSidebar initialReactiveValues createvtext dataDownloadWidget dataInputPanel dataInputSidebar dataInputWidget dataTabPanel dateCols dateToDay disclaimersContent disclaimersPanel disclaimerUSGS disclaimerWEST dlModTabCP dlModTabSE downloadCPFig downloadData downloadgFig downloadMFig downloadSEFig downloadsPanel downloadTable DWPCols expandModelSetCP GeneralInputSidebar GeneralInputsPanel GenEstAcknowledgements GenEstAuthors GenEstGUIauthors GenEstInlineCSS GenEstLicense GenEstLogos GenEstShinyJS GenEstUI gettingStartedContent gettingStartedPanel gMainPanel gPanel gSidebar helpPanel initialOutput isNeverDecreasing kFixedWidget kFixedWidgetHeader kFixedWidgetRow li loadedDataPanel matchCells MMainPanel modelInputWidget modelOutputPanel modelOutputWidget modelRunWidget modelSelectionWidget modelSelectionWidgetHeader modelSelectionWidgetRow modelSetCells modelSetModelCells modelSetModelPredictors modelSetPredictors modNamePaste modNameSplit MPanel msgFracNote msgList msgModDone msgModFail msgModPartialFail msgModRun msgModSENobs msgModWarning msgSampleSize msgSplitFail msgSSavgFail msgSSinputFail MSidebar navbar obsCols_fta obsCols_ltp obsCols_SE ol pickSizeclass pkmFail pkmParamPlot pkmSECellPlot pkmSet pkmSetAllFail pkmSetFail pkmSetSizeFail pkmSetSpecParamPlot pkmSetSpecSECellPlot plotCPCells plotCPFigure plotCPHeader plotNA plotSEBoxPlots plotSEBoxTemplate plotSECells plotSEFigure plotSEHeader predsCols prepPredictors prepSizeclassText preTextMaker prettyModTabCP prettyModTabSE prettySplitTab readCSV refMod removeCols SEcols selectData selectedDataPanel SEMainPanel SEPanel SEsi_left SEsi_right SEsi0 SESidebar setFigH setFigW setkNeed simpleMplot sizeCols small splitButtonWidget style trimSetSize trueLength u ul update_input update_output update_rv updateColNames_size updateSizeclasses updatesizeCol widgetMaker