Generalized Mortality Estimator

Documentation for package ‘GenEst’ version 1.4.9

Help Pages

-- 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