Man pages for ddalthorp/GenEst
Generalized Mortality Estimator

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...
app_contentGenEst Information
app_download_functionsGenEst app download funtions
app_msg_functionsGenEst App Messages
app_output_utilitiesapp utilities for formatting text, tables, figs, etc. for...
app_panelsapp panel utility functions
app_serverThe GenEst server definition function
app_uiCreate the GenEst User Interface HTML
app_ui_utilitiesHTML parameters
app_utilitiesapp utilities
app_widgetsCreate and manage widgets for data input, function execution,...
averageSSTabulate an average search schedule from a multi-unit SS data...
calcgCalculate detection probability for given SE and CP...
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
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
CO_DWPAssociate CO carcasses with appropriate DWP values (by unit...
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
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')...
descDescriptive statistics for a fitted CP model
dlModTabSECreate the download version of the Searcher Efficiency model...
DWPColsSelect the DWP-ok columns from a data table
dwpmFit density-weighted proportion (DWP) models.
estgEstimate all carcass-level detection rates and arrival...
estgGenericEstimate generic g
estgGenericSizeEstimate generic detection probability for multiple carcass...
estMEstimate mortality
expandModelSetCPExpand a CP model set for plotting
GenEstGeneralized estimation of mortality
logitCompute the logit or anti-logit
ltransposeTranspose a list of arrays
mockA mock example data set
model_utility_functionsmodel utility functions (not exported)
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...
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...
pllogisThe CDF of the loglogistic distribution
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
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
prepSSCreate search schedule data into an prepSS object for...
prettyModTabCPCreate the pretty version of the Carcass Persistence model...
prettyModTabSECreate the pretty versions of model and summary tables
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
qpkQuantiles of marginal distributions of \hat{p} and \hat{k}
rcpSimulate parameters from a fitted cp model
rdwpSimulate parameters from a fitted dwp model
readCSVRead in csv files in either format
refModReturn the model with the greatest log-likelihood
removeColsRemove selected columns from column names
rpkSimulate parameters from a fitted pk model
runGenEstLaunch the GenEst Application
SEboxesProduce boxplots 'p' and/or 'k' for all cells for reference...
SEcolsProduce a named vectory with standard SE plot colors
SEfigPlot results of a single SE model in a set
SEpanelProduce a single panel in an SE summary/diagnostic plot
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...
simpleMplotPlot a total mortality estimation for a simple situation
sizeColsSelect the potential carcass class columns from a data table
solar_powerTowerPower Tower Example Dataset
solar_PVPhotovoltaic Example Dataset
solar_troughTrough-based solar thermal power simulated example
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
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
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 May 23, 2020, 1:20 p.m.