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") disclaimerUSGS() disclaimerWEST()

Data sets

mock wind_cleared wind_RP wind_RPbat solar_powerTower solar_PV solar_trough

Main command-line functions

pkm, cpm, dwpm: estimate searcher efficiency (pk), carcass persistence (cp), and (dwp) 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
desc: Calculate descriptive statistics for a fitted CP model
estgGeneric: estimate detection probability (g) for given searcher efficiency and carcass persistence model
runGenEst(): start the GUI

Potentially useful calculation functions

rpk, qpk, rcp, rdwp estg, calcg ppersist, SEsi alogit, logit pkLogLik, cpLogLik calcRate, calcTsplit, ltranspose refMod countCarcs simpleMplot

Potentially useful editing functions

estgGenericSize prepSS averageSS tidyModelSetCP tidyModelSetSE checkDate dateCols dateToDay defineUnitCol dlModTabSE prettyModTabCP prettyModTabSE prettySplitTab

Other functions

trimSetSize combinePreds combinePredsAcrossModels pkmSetSizeFailRemove pkmSetFailRemove cpmSetSizeFailRemove cpmSetSizeFail cpmSetFailRemove CO_DWP CPcols cpmCPCellPlot cpmFail cpmSetFail cpmSetSpecCPCellPlot DWPCols expandModelSetCP obsCols_SE pkmFail pkmSetAllFail pkmSetFail pkmSetSizeFail plotCPCells plotCPFigure plotCPHeader predsCols SEsi_left SEsi_right SEsi0 sizeCols matchCells checkComponents checkSpecificModelCP checkSpecificModelSE combinePredsAcrossModels CPdistOptions obsCols_fta obsCols_ltp pkmParamPlot pkmSECellPlot pkmSet pkmSetSpecParamPlot pkmSetSpecSECellPlot plotSEBoxPlots plotSEBoxTemplate plotSECells plotSEFigure plotSEHeader prepPredictors readCSV removeCols

Internal functions (not exported)

_GenEst_calcRateC _GenEst_calcTsplitC calcRateC calcTsplitC aboutContent aboutPanel analysisPanel b big cButtonStyle center classText clearNotifications CPMainPanel CPPanel downloadCPFig estText CPSidebar initialReactiveValues createvtext dataDownloadWidget dataInputPanel dataInputSidebar dataInputWidget dataTabPanel disclaimersContent disclaimersPanel downloadCPFig downloadCPMod downloadCPMres downloadSEmod downloadgFig downloadMFig downloadSEFig downloadsPanel downloadTable eventReaction GeneralInputSidebar GeneralInputsPanel GenEstAcknowledgements GenEstAuthors GenEstGUIauthors GenEstInlineCSS GenEstLicense GenEstLogos GenEstShinyJS GenEstUI GenEstServer gettingStartedContent gettingStartedPanel gMainPanel gPanel gSidebar helpPanel initialOutput kFixedWidget kFixedWidgetHeader kFixedWidgetRow li loadedDataPanel 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 ol pickSizeclass plotNA prepSizeclassText preTextMaker reaction reactionMessageDone reactionMessageRun reNULL reVal SEboxes SEcols selectData selectedDataPanel SEMainPanel SEPanel SEpanel SESidebar setkNeed setNotSuspending small splitButtonWidget style trimSetSize u ul update_input update_output update_rv updateColNames_size updateSizeclasses updatesizeCol widgetMaker