{ "_id": "6a1bee741d7bb097a0a20cc4", "Package": "GenEst", "Title": "Generalized Mortality Estimator", "Version": "1.4.9", "Date": "2023-05-25", "Authors@R": "c(\nperson(\"Daniel\", \"Dalthorp\", , \"ddalthorp@protonmail.com\", c(\"aut\", \"cre\")),\nperson(\"Juniper\", \"Simonis\", , \"simonis@dapperstats.com\", \"aut\"),\nperson(\"Lisa\", \"Madsen\", , \"madsenl@oregonstate.edu\", \"aut\"),\nperson(\"Manuela\", \"Huso\", , \"mhuso@usgs.gov\", \"aut\"),\nperson(\"Paul\", \"Rabie\", , \"prabie@west-inc.com\", \"aut\"),\nperson(\"Jeffrey\", \"Mintz\", , \"mintzj@oregonstate.edu\", \"aut\"),\nperson(\"Robert\", \"Wolpert\", , \"wolpert@stat.duke.edu\", \"aut\"),\nperson(\"Jared\", \"Studyvin\", , \"jstudyvin@west-inc.com\", \"aut\"),\nperson(\"Franzi\", \"Korner-Nievergelt\", , \"fraenzi.korner@oikostat.ch\", \"aut\"))", "Description": "Command-line and 'shiny' GUI implementation of the GenEst\nmodels for estimating bird and bat mortality at wind and solar\npower facilities, following Dalthorp, et al. 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"class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "aicc", "title": "Generic S3 function for summarizing AICc", "topics": [ "aicc" ] }, { "page": "aicc.cpm", "title": "Extract AIC and AICc for a carcass persistence model", "topics": [ "aicc.cpm" ] }, { "page": "aicc.cpmSet", "title": "Create the AICc tables for a set of carcass persistence models", "topics": [ "aicc.cpmSet" ] }, { "page": "aicc.cpmSetSize", "title": "Create the AICc tables for a list of sets of searcher efficiency models", "topics": [ "aicc.cpmSetSize" ] }, { "page": "aicc.pkm", "title": "extract AICc value from pkm object", "topics": [ "aicc.pkm" ] }, { "page": "aicc.pkmSet", "title": "Create the AICc tables for a set of searcher efficiency models", "topics": [ "aicc.pkmSet" ] }, { "page": "aicc.pkmSetSize", "title": "Create the AICc tables for a list of sets of searcher efficiency models", "topics": [ "aicc.pkmSetSize" ] }, { "page": "aicc.pkmSize", "title": "Create the AICc tables for a list of sets of searcher efficiency models", "topics": [ "aicc.pkmSize" ] }, { "page": "app_content", "title": "GenEst Information", "topics": [ "aboutContent", "app_content", "createvtext", "disclaimersContent", "disclaimerUSGS", "disclaimerWEST", "GenEstAcknowledgements", "GenEstAuthors", "GenEstGUIauthors", "GenEstLicense", "GenEstLogos", "gettingStartedContent" ] }, { "page": "app_download_functions", "title": "GenEst app download funtions", "topics": [ "app_download_functions", "downloadCPFig", "downloadCPmod", "downloadgFig", "downloadgres", "downloadMFig", "downloadMres", "downloadSEFig", "downloadSEmod", "downloadTable" ] }, { "page": "app_msg_functions", "title": "GenEst App Messages", "topics": [ "app_msg_functions", "clearNotifications", "msgFracNote", "msgList", "msgModDone", "msgModFail", "msgModPartialFail", "msgModRun", "msgModSENobs", "msgModWarning", "msgSampleSize", "msgSplitFail", "msgSSavgFail", "msgSSinputFail" ] }, { "page": "app_output_utilities", "title": "app utilities for formatting text, tables, figs, etc. for display", "topics": [ "app_output_utilities", "classText", "estText", "initialOutput", "reNULL", "setFigH", "setFigW", "setNotSuspending" ] }, { "page": "app_panels", "title": "app panel utility functions", "topics": [ "app_panels", "dataTabPanel", "modelOutputPanel", "selectedDataPanel" ] }, { "page": "app_server", "title": "The GenEst server definition function", "topics": [ "app_server", "eventReaction", "GenEstServer", "reaction", "reactionMessageDone", "reactionMessageRun" ] }, { "page": "app_ui", "title": "Create the GenEst User Interface HTML", "topics": [ "aboutPanel", "analysisPanel", "app_ui", "CPMainPanel", "CPPanel", "CPSidebar", "dataInputPanel", "dataInputSidebar", "disclaimersPanel", "downloadsPanel", "GeneralInputSidebar", "GeneralInputsPanel", "GenEstUI", "gettingStartedPanel", "gMainPanel", "gPanel", "gSidebar", "helpPanel", "loadedDataPanel", "MMainPanel", "MPanel", "MSidebar", "SEMainPanel", "SEPanel", "SESidebar" ] }, { "page": "app_ui_utilities", "title": "HTML parameters", "topics": [ "app_ui_utilities", "b", "big", "cButtonStyle", "center", "GenEstInlineCSS", "GenEstShinyJS", "li", "navbar", "ol", "small", "style", "u", "ul" ] }, { "page": "app_utilities", "title": "app utilities", "topics": [ "app_utilities", "initialReactiveValues", "modNamePaste", "modNameSplit", "pickSizeclass", "plotNA", "prepSizeclassText", "reVal", "selectData", "setkNeed", "updateColNames_size", "updateSizeclasses", "updatesizeCol" ] }, { "page": "app_widgets", "title": "Create and manage widgets for data input, function execution, data output", "topics": [ "app_widgets", "dataDownloadWidget", "dataInputWidget", "kFixedWidget", "kFixedWidgetHeader", "kFixedWidgetRow", "modelInputWidget", "modelOutputWidget", "modelRunWidget", "modelSelectionWidget", "modelSelectionWidgetHeader", "modelSelectionWidgetRow", "preTextMaker", "splitButtonWidget", "widgetMaker" ] }, { "page": "averageSS", "title": 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"checkSpecificModelCP" ] }, { "page": "checkSpecificModelSE", "title": "Error check a specific model selection for an SE plot", "topics": [ "checkSpecificModelSE" ] }, { "page": "CO_DWP", "title": "Associate CO carcasses with appropriate DWP values (by unit and carcass class)", "topics": [ "CO_DWP" ] }, { "page": "combinePreds", "title": "Combine predictors", "topics": [ "combinePreds" ] }, { "page": "combinePredsAcrossModels", "title": "Combine predictors across models", "topics": [ "combinePredsAcrossModels" ] }, { "page": "countCarcs", "title": "Count the minimum number of carcasses in the cells", "topics": [ "countCarcs" ] }, { "page": "CPcols", "title": "Produce a named vector of standard CP plot colors", "topics": [ "CPcols" ] }, { "page": "CPdistOptions", "title": "Produce the options for the distributions in the CP model", "topics": [ "CPdistOptions" ] }, { "page": "cpLogLik", "title": "Calculate the negative log-likelihood of a carcass persistence model", "topics": [ "cpLogLik" ] }, { "page": "cpm", "title": "Fit cp carcass persistence models", "topics": [ "cpm", "cpm0", "cpmSet", "cpmSize" ] }, { "page": "cpmCPCellPlot", "title": "Plot cell-specific decay curve for carcass persistence", "topics": [ "cpmCPCellPlot" ] }, { "page": "cpmFail", "title": "Check if a CP model is well-fit", "topics": [ "cpmFail" ] }, { "page": "cpmSetFail", "title": "Check if cpm models fail", "topics": [ "cpmSetFail" ] }, { "page": "cpmSetFailRemove", "title": "Remove failed cpm models from a 'cpmSet' object", "topics": [ "cpmSetFailRemove" ] }, { "page": "cpmSetSizeFail", "title": "Check if all of the cpm models fail", "topics": [ "cpmSetSizeFail" ] }, { "page": "cpmSetSizeFailRemove", "title": "Remove failed cpm models from a 'cpmSetSize' object", "topics": [ "cpmSetSizeFailRemove" ] }, { "page": "cpmSetSpecCPCellPlot", "title": "Plot cell-specific decay curve for carcass persistence", "topics": [ "cpmSetSpecCPCellPlot" ] }, { "page": "dateCols", "title": "Select the date columns from a data table", "topics": [ "dateCols" ] }, { "page": "dateToDay", "title": "Calculate day of study from calendar date", "topics": [ "dateToDay" ] }, { "page": "defineUnitCol", "title": "Auto-parsing to find the name of the unit column ('unitCol')", "topics": [ "defineUnitCol" ] }, { "page": "desc", "title": "Descriptive statistics for a fitted CP model", "topics": [ "desc" ] }, { "page": "dlModTabSE", "title": "Create the download version of the Searcher Efficiency model table", "topics": [ "dlModTabSE" ] }, { "page": "DWPCols", "title": "Select the DWP-ok columns from a data table", "topics": [ "DWPCols" ] }, { "page": "dwpm", "title": "Fit density-weighted proportion (DWP) models.", "topics": [ "dwpm" ] }, { "page": "estg", "title": "Estimate all carcass-level detection rates and arrival intervals", "topics": [ "estg" ] }, { "page": "estgGeneric", "title": "Estimate generic g", "topics": [ "estgGeneric" ] }, { "page": "estgGenericSize", "title": "Estimate generic detection probability for multiple carcass classes", "topics": [ "estgGenericSize" ] }, { "page": "estM", "title": "Estimate mortality", "topics": [ "estM" ] }, { "page": "expandModelSetCP", "title": "Expand a CP model set for plotting", "topics": [ "expandModelSetCP" ] }, { "page": "GenEst", "title": "Generalized estimation of mortality", "topics": [ "GenEst" ] }, { "page": "logit", "title": "Compute the logit or anti-logit", "topics": [ "alogit", "logit" ] }, { "page": "ltranspose", "title": "Transpose a list of arrays", "topics": [ "ltranspose" ] }, { "page": "mock", "title": "A mock example data set", "topics": [ "mock" ] }, { "page": "model_utility_functions", "title": "model utility functions (not exported)", "topics": [ "matchCells", "modelSetCells", "modelSetModelCells", "modelSetModelPredictors", "modelSetPredictors", "model_utility_functions" ] }, { "page": "obsCols_fta", "title": "Select the columns from a data table that could be CP First Time Absent observations", "topics": [ "obsCols_fta" ] }, { "page": "obsCols_ltp", "title": "Select the columns from a data table that could be CP Last Time Present observations", "topics": [ "obsCols_ltp" ] }, { "page": "obsCols_SE", "title": "Select the columns from a data table that could be SE observations", "topics": [ "obsCols_SE" ] }, { "page": "pkLogLik", "title": "Calculate the negative log-likelihood of a searcher efficiency model", "topics": [ "pkLogLik" ] }, { "page": "pkm", "title": "Fit pk searcher efficiency models.", "topics": [ "pkm", "pkm0", "pkmSet", "pkmSize" ] }, { "page": "pkmFail", "title": "Check if a pk model is well-fit", "topics": [ "pkmFail" ] }, { "page": "pkmParamPlot", "title": "Plot parameter box plots for each cell for either p or k", "topics": [ "pkmParamPlot" ] }, { "page": "pkmSECellPlot", "title": "Plot cell-specific decay curve for searcher efficiency", "topics": [ "pkmSECellPlot" ] }, { "page": "pkmSetAllFail", "title": "Check if all of the pkm models fail within a given 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