# Generalized Mortality Estimator

## Documentation for package ‘GenEst’ version 1.4.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

A B C D E G H I K L M N O P Q R S T U W

## -- A --

aboutContent | GenEst Information
aboutPanel | Create the GenEst User Interface HTML
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 models
aicc.cpmSetSize | Create the AICc tables for a list of sets of searcher efficiency models
aicc.pkm | extract AICc value from pkm object
aicc.pkmSet | Create the AICc tables for a set of searcher efficiency models
aicc.pkmSetSize | Create the AICc tables for a list of sets of searcher efficiency models
aicc.pkmSize | Create the AICc tables for a list of sets of searcher efficiency models
alogit | Compute the logit or anti-logit
analysisPanel | Create the GenEst User Interface HTML
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 display
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, data output
averageSS | Tabulate an average search schedule from a multi-unit SS data table

## -- B --

b | HTML parameters
big | HTML parameters

## -- C --

calcg | Calculate detection probability for given SE and CP parameters and search schedule.
calcRate | Estimate the number of fatalities in each search interval throughout the monitoring period.
calcSplits | Estimate the number of fatalities by up to two splitting covariates
calcTsplit | Estimate the number of fatalities by time interval
cButtonStyle | HTML parameters
center | HTML parameters
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
classText | app utilities for formatting text, tables, figs, etc. for display
clearNotifications | GenEst App Messages
combinePreds | Combine predictors
combinePredsAcrossModels | Combine predictors across models
countCarcs | Count the minimum number of carcasses in the cells
CO_DWP | Associate CO carcasses with appropriate DWP values (by unit and carcass class)
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 persistence model
cpm | Fit cp carcass persistence models
cpm0 | Fit cp carcass persistence models
CPMainPanel | Create the GenEst User Interface HTML
cpmCPCellPlot | Plot cell-specific decay curve for carcass persistence
cpmFail | Check if a CP model is well-fit
cpmSet | Fit cp carcass persistence models
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
cpmSize | Fit cp carcass persistence models
CPPanel | Create the GenEst User Interface HTML
CPSidebar | Create the GenEst User Interface HTML
createvtext | GenEst Information

## -- D --

dataDownloadWidget | Create and manage widgets for data input, function execution, data output
dataInputPanel | Create the GenEst User Interface HTML
dataInputSidebar | Create the GenEst User Interface HTML
dataInputWidget | Create and manage widgets for data input, function execution, data output
dataTabPanel | app panel utility functions
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
disclaimersContent | GenEst Information
disclaimersPanel | Create the GenEst User Interface HTML
disclaimerUSGS | GenEst Information
disclaimerWEST | GenEst Information
dlModTabSE | Create the download version of the Searcher Efficiency model table
downloadCPFig | GenEst app download funtions
downloadCPmod | GenEst app download funtions
downloadgFig | GenEst app download funtions
downloadgres | GenEst app download funtions
downloadMFig | GenEst app download funtions
downloadMres | GenEst app download funtions
downloadSEFig | GenEst app download funtions
downloadSEmod | GenEst app download funtions
downloadsPanel | Create the GenEst User Interface HTML
downloadTable | GenEst app download funtions
DWPCols | Select the DWP-ok columns from a data table
dwpm | Fit density-weighted proportion (DWP) models.

## -- E --

estg | Estimate all carcass-level detection rates and arrival intervals
estgGeneric | Estimate generic g
estgGenericSize | Estimate generic detection probability for multiple carcass classes
estM | Estimate mortality
estText | app utilities for formatting text, tables, figs, etc. for display
eventReaction | The GenEst server definition function
expandModelSetCP | Expand a CP model set for plotting

## -- G --

GeneralInputSidebar | Create the GenEst User Interface HTML
GeneralInputsPanel | Create the GenEst User Interface HTML
GenEst | Generalized estimation of mortality
GenEstAcknowledgements | GenEst Information
GenEstAuthors | GenEst Information
GenEstGUIauthors | GenEst Information
GenEstInlineCSS | HTML parameters
GenEstLicense | GenEst Information
GenEstLogos | GenEst Information
GenEstServer | The GenEst server definition function
GenEstShinyJS | HTML parameters
GenEstUI | Create the GenEst User Interface HTML
gettingStartedContent | GenEst Information
gettingStartedPanel | Create the GenEst User Interface HTML
gMainPanel | Create the GenEst User Interface HTML
gPanel | Create the GenEst User Interface HTML
gSidebar | Create the GenEst User Interface HTML

## -- H --

helpPanel | Create the GenEst User Interface HTML

## -- I --

initialOutput | app utilities for formatting text, tables, figs, etc. for display
initialReactiveValues | app utilities

## -- K --

kFixedWidget | Create and manage widgets for data input, function execution, data output
kFixedWidgetHeader | Create and manage widgets for data input, function execution, data output
kFixedWidgetRow | Create and manage widgets for data input, function execution, data output

## -- L --

li | HTML parameters
loadedDataPanel | Create the GenEst User Interface HTML
logit | Compute the logit or anti-logit
ltranspose | Transpose a list of arrays

## -- M --

matchCells | model utility functions (not exported)
MMainPanel | Create the GenEst User Interface HTML
mock | A mock example data set
modelInputWidget | Create and manage widgets for data input, function execution, data output
modelOutputPanel | app panel utility functions
modelOutputWidget | Create and manage widgets for data input, function execution, data output
modelRunWidget | Create and manage widgets for data input, function execution, data output
modelSelectionWidget | Create and manage widgets for data input, function execution, data output
modelSelectionWidgetHeader | Create and manage widgets for data input, function execution, data output
modelSelectionWidgetRow | Create and manage widgets for data input, function execution, data output
modelSetCells | model utility functions (not exported)
modelSetModelCells | model utility functions (not exported)
modelSetModelPredictors | model utility functions (not exported)
modelSetPredictors | model utility functions (not exported)
model_utility_functions | model utility functions (not exported)
modNamePaste | app utilities
modNameSplit | app utilities
MPanel | Create the GenEst User Interface HTML
msgFracNote | GenEst App Messages
msgList | GenEst App Messages
msgModDone | GenEst App Messages
msgModFail | GenEst App Messages
msgModPartialFail | GenEst App Messages
msgModRun | GenEst App Messages
msgModSENobs | GenEst App Messages
msgModWarning | GenEst App Messages
msgSampleSize | GenEst App Messages
msgSplitFail | GenEst App Messages
msgSSavgFail | GenEst App Messages
msgSSinputFail | GenEst App Messages
MSidebar | Create the GenEst User Interface HTML

## -- N --

navbar | HTML parameters

## -- O --

obsCols_fta | Select the columns from a data table that could be CP First Time Absent observations
obsCols_ltp | Select the columns from a data table that could be CP Last Time Present observations
obsCols_SE | Select the columns from a data table that could be SE observations
ol | HTML parameters

## -- P --

pickSizeclass | app utilities
pkLogLik | Calculate the negative log-likelihood of a searcher efficiency model
pkm | Fit pk searcher efficiency models.
pkm0 | 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
pkmSet | Fit pk searcher efficiency models.
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 specific model with comparison to the cellwise model
pkmSize | Fit pk searcher efficiency models.
pllogis | The CDF of the loglogistic distribution
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
plot.splitFull | Plot summary statistics for splits of mortality estimates
plot.splitSummary | Plot summary statistics for splits of mortality estimates
plotCPCells | Plot the cellwise results of a single model in a set of CP models
plotCPFigure | Plot results of a single CP model in a set
plotCPHeader | The CP plot header
plotNA | app utilities
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 models
plotSEFigure | Plot results of a single SE model in a set
plotSEHeader | The SE plot header
ppersist | Calculate the probability of persistence to detection
predsCols | Select the predictor-ok columns from a data table
prepPredictors | Prepare predictors based on inputs
prepSizeclassText | app utilities
prepSS | Create search schedule data into an prepSS object for convenient splits analyses
preTextMaker | Create and manage widgets for data input, function execution, data output
prettyModTabCP | Create the pretty version of the Carcass Persistence model table
prettyModTabSE | Create the pretty versions of model and summary tables
prettySplitTab | Create the pretty version of the split summary table
print.cpm | Print a 'cpm' model object
print.pkm | Print a 'pkm' model object

## -- Q --

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

## -- R --

rcp | Simulate parameters from a fitted cp model
rdwp | Simulate parameters from a fitted dwp model
reaction | The GenEst server definition function
reactionMessageDone | The GenEst server definition function
reactionMessageRun | The GenEst server definition function
readCSV | Read in csv files in either format
refMod | Return the model with the greatest log-likelihood
removeCols | Remove selected columns from column names
reNULL | app utilities for formatting text, tables, figs, etc. for display
reVal | app utilities
rpk | Simulate parameters from a fitted pk model
runGenEst | Launch the GenEst Application

## -- S --

SEcols | Produce a named vectory with standard SE plot colors
selectData | app utilities
selectedDataPanel | app panel utility functions
SEMainPanel | Create the GenEst User Interface HTML
SEPanel | Create the GenEst User Interface HTML
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
SESidebar | Create the GenEst User Interface HTML
SEsi_left | Calculate conditional probability of observation at a search
SEsi_right | Calculate conditional probability of observation after a series of searches
setFigH | app utilities for formatting text, tables, figs, etc. for display
setFigW | app utilities for formatting text, tables, figs, etc. for display
setkNeed | app utilities
setNotSuspending | app utilities for formatting text, tables, figs, etc. for display
simpleMplot | Plot a total mortality estimation for a simple situation
sizeCols | Select the potential carcass class columns from a data table
small | HTML parameters
solar_powerTower | Power Tower Example Dataset
solar_PV | Photovoltaic Example Dataset
solar_trough | Trough-based solar thermal power simulated example
splitButtonWidget | Create and manage widgets for data input, function execution, data output
style | HTML parameters
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

## -- T --

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

## -- U --

u | HTML parameters
ul | HTML parameters
updateColNames_size | app utilities
updateSizeclasses | app utilities
updatesizeCol | app utilities
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

## -- W --

widgetMaker | Create and manage widgets for data input, function execution, data output
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