# Generalized Mortality Estimator

## Documentation for package ‘GenEst’ version 1.4.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

GenEst-package | Generalized estimation of mortality

## -- 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') If a unit column is not explicitly defined by user in the arg list to 'estM' or 'estg', then 'defineUnitCol' parses the CO, DWP, and SS files to extract the unit column if possible. Criteria that a column must meet to be a unit column are that it is found in both 'data_CO' and 'data_DWP', all units in 'data_CO' must also be included among units in 'data_DWP', all units in both 'data_CO' and 'data_DWP' must be included among the column names in 'data_SS'. If 'data_DWP = NULL', then the unit column must be included in 'data_CO' and all its units must be included among the column names of 'data_SS'.

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
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.corpus_frame | Generic S3 function for printing corpus_frame
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