GenEst: Generalized estimation of mortality

In ddalthorp/GenEst: Generalized Mortality Estimator

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.

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

ddalthorp/GenEst documentation built on June 4, 2023, 1 a.m.