Man pages for ddalthorp/GenEst
Generalized Mortality Estimator

aboutContentCreate the Content for the About Pabel
aiccGeneric S3 function for summarizing AICc
aicc.cpmExtract AIC and AICc for a carcass persistence model
aicc.cpmSetCreate the AICc tables for a set of carcass persistence...
aicc.cpmSetSizeCreate the AICc tables for a list of sets of searcher...
aicc.pkmextract AICc value from pkm object
aicc.pkmSetCreate the AICc tables for a set of searcher efficiency...
aicc.pkmSetSizeCreate the AICc tables for a list of sets of searcher...
aicc.pkmSizeCreate the AICc tables for a list of sets of searcher...
averageSSTabulate an average search schedule from a multi-unit SS data...
calcgCalculate cell-level generic detection probability
calcRateEstimate the number of fatalities in each search interval...
calcSplitsEstimate the number of fatalities by up to two splitting...
calcTsplitEstimate the number of fatalities by time interval
cButtonStyleDefine Clear Button Style
checkComponentsCheck for model components
checkDateChecks whether a vector of data can be interpreted as dates
checkSpecificModelCPError check a specific model selection for a CP plot
checkSpecificModelSEError check a specific model selection for an SE plot
classTextPrepare class text header
clearNotificationsClear all notifications
combinePredsCombine predictors
combinePredsAcrossModelsCombine predictors across models
countCarcsCount the minimum number of carcasses in the cells
CPcolsProduce a named vector of standard CP plot colors
CPdistOptionsProduce the options for the distributions in the CP model
cpLogLikCalculate the negative log-likelihood of a carcass...
cpmFit cp carcass persistence models
cpmCPCellPlotPlot cell-specific decay curve for carcass persistence
cpmFailCheck if a CP model is well-fit
cpmSetFailCheck if cpm models fail
cpmSetFailRemoveRemove failed cpm models from a 'cpmSet' object
cpmSetSizeFailCheck if all of the cpm models fail
cpmSetSizeFailRemoveRemove failed cpm models from a 'cpmSetSize' object
cpmSetSpecCPCellPlotPlot cell-specific decay curve for carcass persistence
createvtextCreate the version text for GenEst
dataDownloadWidgetCreate a Data Download Widget for the GenEst User Interface...
dataInputWidgetCreate a Data Input Widget for the GenEst User Interface HTML
dataTabPanelCreate a Data Tab Panel for the GenEst User Interface HTML
dateColsSelect the date columns from a data table
dateToDayCalculate day of study from calendar date
defineUnitColAuto-parsing to find the name of the unit column ('unitCol')...
disclaimersContentCreate the Content for the Disclaimers Pabel
dlModTabCPCreate the download version of the Carcass Persistence model...
dlModTabSECreate the download version of the Searcher Efficiency model...
downloadCPFigDownload the CP figure
downloadDataDownload a zipped data set
downloadgFigDownload the g figure
downloadMFigDownload the M figure
downloadSEFigDownload the SE figure
downloadTableDownload a table
DWPbyCarcassAssign DWP value to each carcass
DWPColsSelect the DWP-ok columns from a data table
EcbinomExpected value of a continuous binomial with size = 1/g
estgEstimate all carcass-level detection rates and arrival...
estgGenericEstimate generic g
estgGenericSizeEstimate generic detection probability for multiple size...
estMEstimate mortality
estTextPrepare the text for the estimation table
expandModelSetCPExpand a CP model set for plotting
GenEstGeneralized estimation of mortality
GenEstInlineCSSGenerate the Inline CSS Definition
GenEstServerThe GenEst server definition function
GenEstShinyJSShiny Java Script (via shinyjs) Enabler
GenEstUICreate the GenEst User Interface HTML
gettingStartedContentCreate the Content for the Getting Started Pabel
initialOutputUpdate the output list upon initiation of the app
initialReactiveValuesCreate the main reactive value list for GenEst
isNeverDecreasingIs a vector never decreasing?
kFixedWidgetMake a kFixed Widget
logitCompute the logit or anti-logit
ltransposeTranspose a list of arrays
matchCellsMatch cells between models.
mockA mock example data set
modelInputWidgetCreate a Model Input Widget for the GenEst User Interface...
modelOutputPanelCreate a Model Output Tab Panel for the GenEst User Interface...
modelOutputWidgetCreate a Model Output Widget for the GenEst User Interface...
modelRunWidgetCreate a Model Run Widget for the GenEst User Interface HTML
modelSelectionWidgetMake a Model Selection Widget
modelSetCellsDetermine the cell table for a full model set
modelSetModelCellsDetermine the cells from each model in a model set
modelSetModelPredictorsDetermine the predictors from each model in a model set
modelSetPredictorsDetermine the predictors for a whole model set
modNamePastePaste the parts of a model's name back together
modNameSplitSplit model names into their components and remove only a...
msgFracNoteCreate the message for when an incorrect FFS is input
msgListProduce the message list
msgModDoneCreate a model done message
msgModFailCreate the error message for when no models are fit...
msgModPartialFailCreate the warning message text for when only some models are...
msgModRunCreate a model running message
msgModSENobsCreate the SE data size notification
msgModWarningCreate the warning message for a model run (if needed)
msgSampleSizeCreate the warning message text for small sample sizes
msgSplitFailCreate the fail message for when splits aren't done correctly
msgSSavgFailCreate the warning message for when the SS average doesn't...
msgSSinputFailCreate the warning message for when the SS based on inputs...
navbarCreate the HTML for the navigation bar UI element
obsCols_ftaSelect the columns from a data table that could be CP First...
obsCols_ltpSelect the columns from a data table that could be CP Last...
obsCols_SESelect the columns from a data table that could be SE...
pickSizeclassLocate the sizeclass selected by the inputs
pkLogLikCalculate the negative log-likelihood of a searcher...
pkmFit pk searcher efficiency models.
pkmFailCheck if a pk model is well-fit
pkmParamPlotPlot parameter box plots for each cell for either p or k
pkmSECellPlotPlot cell-specific decay curve for searcher efficiency
pkmSetAllFailCheck if all of the pkm models fail within a given set
pkmSetFailCheck if pkm models fail
pkmSetFailRemoveRemove failed pkm models from a 'pkmSet' object
pkmSetSizeFailCheck if all of the pkm models fail
pkmSetSizeFailRemoveRemove failed pkm models from a 'pkmSetSize' object
pkmSetSpecParamPlotp or k box plots for an SE model set
pkmSetSpecSECellPlotPlot cell-specific decay curve for searcher efficiency for a...
plotCPCellsPlot the cellwise results of a single model in a set of CP...
plotCPFigurePlot results of a single CP model in a set
plotCPHeaderThe CP plot header
plot.cpmPlot results of a single CP model
plot.cpmSetPlot results of a set of CP models
plot.estMPlot total mortality estimation
plot.gGenericPlot results of a single generic ghat estimation
plot.gGenericSizePlot results of a set of size-based generic ghat estimations
plotNAProduce a blank plot for unsucessful fits
plot.pkmPlot results of a single pk model
plot.pkmSetPlot results of a set of SE models
plotSEBoxPlotsp and k box plots for an SE model set
plotSEBoxTemplatetemplate box plot
plotSECellsPlot the cellwise results of a single model in a set of SE...
plotSEFigurePlot results of a single SE model in a set
plotSEHeaderThe SE plot header
plot.splitFullPlot summary statistics for splits of mortality estimates
plot.splitSummaryPlot summary statistics for splits of mortality estimates
ppersistCalculate the probability of persistence to detection
predsColsSelect the predictor-ok columns from a data table
prepPredictorsPrepare predictors based on inputs
prepSizeclassTextPrepare text for size classes
prepSSCreate search schedule data into an prepSS object for...
prettyModTabCPCreate the pretty version of the Carcass Persistence model...
prettyModTabSECreate the pretty version of the Searcher Efficiency model...
prettySplitTabCreate the pretty version of the split summary table
print.corpus_frameGeneric S3 function for printing corpus_frame
print.cpmPrint a 'cpm' model object
print.pkmPrint a 'pkm' model object
rcpSimulate parameters from a fitted cp model
readCSVRead in csv files in either format
refModReturn the model with the greatest log-likelihood
removeColsRemove selected columns from column names
renderDTnsRender a data table without server-side processing
reNULLReset values of a list to NULL
reValReset values of a reactive values list
rpkSimulate parameters from a fitted pk model
runGenEstLaunch the GenEst Application
SEcolsProduce a named vectory with standard SE plot colors
selectDataSelect particular columns from a data set
selectedDataPanelCreate a Selected Data Tab Panel for the GenEst User...
SEsiCalculate decayed searcher efficiency
SEsi0Calculate decayed searcher efficiency for a single pk
SEsi_leftCalculate conditional probability of observation at a search
SEsi_rightCalculate conditional probability of observation after a...
setFigWSet Figure width and height based on the number of cells
setkNeedCreate the kNeed text
setNotSuspending(Re)set outputOptions to not suspending for given elements
simpleMplotPlot a total mortality estimation for a simple situation
sizeColsSelect the potential size class columns from a data table
solar_powerTowerPower Tower Example Dataset
solar_PVPhotovoltaic Example Dataset
solar_troughTrough-based solar thermal power simulated example
styleHTML tag functions
summary.estMSummarize total mortality estimation
summary.gGenericSummarize the gGeneric list to a simple table
summary.gGenericSizeSummarize the gGenericSize list to a list of simple tables
summary.splitFullSummarize results of mortality estimate splits
tidyModelSetCPTidy a CP model set
tidyModelSetSETidy an SE model set
transposeSplitsTranspose a 'splitFull' array (preserving attributes)
trimSetSizeTrim a Model-Set-Size Complex to a Single Model Per Size
trueLengthGet the length of real (non-NA) things
updateColNames_sizeUpdate the string of column names that are in all the needed...
update_inputUpdate the inputs when an event occurs
update_outputUpdate the outputs when an event occurs
update_rvUpdate the reactive value list when an event occurs
updateSizeclassesUpdate the size classes
updatesizeColUpdate the name of the size class column based on available...
widgetMakerInput Widget Maker
wind_clearedWind cleared plot (60m) Search Example
wind_RPWind Road and Pad (120m) Example
wind_RPbatWind Bat-Only Road and Pad (120m) Example
ddalthorp/GenEst documentation built on Dec. 8, 2018, 5:21 p.m.