{ "_id": "6a1f0ce0b401979e7341cef2", "Package": "stockassessment", "Title": "State-Space Assessment Model", "Version": "0.12.0", "Date": "2025-01-20", "Authors@R": "c(person(\"Anders\",\"Nielsen\",role=c(\"aut\",\"cre\"), email=\"an@aqua.dtu.dk\"),\nperson(\"Casper\",\"Berg\",role=\"aut\"),\nperson(c(\"Christoffer\",\"Moesgaard\"), \"Albertsen\", role=\"aut\"),\nperson(\"Kasper\",\"Kristensen\",role=\"aut\"),\nperson(\"Mollie\", \"Brooks\", role=\"aut\"),\nperson(\"Vanessa\", \"Trijoulet\", role=\"aut\"),\nperson(c(\"Olav\",\"Nikolai\"), \"Breivik\", role=\"aut\"))", "Author": "Anders Nielsen [aut, cre], Casper Berg [aut], Christoffer\nMoesgaard Albertsen [aut], Kasper Kristensen [aut], Mollie\nBrooks [aut], Vanessa Trijoulet [aut], Olav Nikolai Breivik\n[aut]", "Maintainer": "Anders Nielsen ", "Description": "Fitting SAM...", "License": "GPL-2", "Encoding": "UTF-8", "URL": "https://github.com/fishfollower/SAM", "LazyData": "TRUE", "BugReports": 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fishing plot", "topics": [ "b0plot", "b0plot.default", "b0plot.hcr", "b0plot.samforecast" ] }, { "page": "b0table", "title": "B0 biomass table", "topics": [ "b0table", "b0table.default" ] }, { "page": "bc", "title": "Spline basis for use with formula interface", "topics": [ "bc" ] }, { "page": "c.sam", "title": "Collect sam objects", "topics": [ "c.sam" ] }, { "page": "catchbyfleetplot", "title": "SAM catchbyfleet plot", "topics": [ "catchbyfleetplot" ] }, { "page": "catchbyfleettable", "title": "CatchByFleet table", "topics": [ "catchbyfleettable" ] }, { "page": "catchplot", "title": "SAM catch plot", "topics": [ "catchplot", "catchplot.hcr", "catchplot.sam", "catchplot.samforecast", "catchplot.samset" ] }, { "page": "catchtable", "title": "Catch table", "topics": [ "catchtable", "catchtable.sam" ] }, { "page": "caytable", "title": "Catch-at-age in numbers table", "topics": [ "caytable" ] }, { "page": "clean.void.catches", "title": "remove void catches", "topics": [ 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deterministic model of a SAM fit", "topics": [ "deterministicReferencepoints" ] }, { "page": "deterministicReferencepoints.sam", "title": "Function to calculate reference points for the embedded deterministic model of a SAM fit", "topics": [ "deterministicReferencepoints.sam" ] }, { "page": "empirobscorrplot", "title": "Plots the residual between-age correlation matrices by fleet.", "topics": [ "empirobscorrplot", "empirobscorrplot.samres" ] }, { "page": "equilibriumbiomassplot", "title": "SAM equilibrium biomass plot", "topics": [ "equilibriumbiomassplot", "equilibriumbiomassplot.default", "equilibriumbiomassplot.hcr", "equilibriumbiomassplot.samforecast" ] }, { "page": "equilibriumbiomasstable", "title": "equilibrium biomass table", "topics": [ "equilibriumbiomasstable", "equilibriumbiomasstable.default" ] }, { "page": "faytable", "title": "F-at-age table", "topics": [ "faytable", "faytable.sam" ] }, { "page": "fbarplot", "title": "SAM Fbar plot", "topics": [ "fbarplot", 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"iibc", "title": "Double integrated spline basis for use with formula interface", "topics": [ "iibc" ] }, { "page": "is.whole.positive.number", "title": "Function to test if x is ...", "topics": [ "is.whole.positive.number" ] }, { "page": "jacobian", "title": "Calculate jacobian of a function", "topics": [ "jacobian" ] }, { "page": "jit", "title": "Jitter runs", "topics": [ "jit" ] }, { "page": "leaveout", "title": "leaveout run", "topics": [ "leaveout" ] }, { "page": "lifeexpectancyplot", "title": "SAM life expectancy plot", "topics": [ "lifeexpectancyplot", "lifeexpectancyplot.default", "lifeexpectancyplot.hcr", "lifeexpectancyplot.samforecast" ] }, { "page": "lifeexpectancytable", "title": "Life expectancy table", "topics": [ "lifeexpectancytable", "lifeexpectancytable.default" ] }, { "page": "loadConf", "title": "Loads a model configuration from a file", "topics": [ "loadConf" ] }, { "page": "logLik.sam", "title": "Log likelihood of sam object", "topics": [ "logLik.sam" ] }, { "page": "modelDescription", "title": "Description of model", "topics": [ "modelDescription" ] }, { "page": "modelforecast", "title": "Model based forecast function", "topics": [ "modelforecast", "modelforecast.sam" ] }, { "page": "modeltable", "title": "model table", "topics": [ "modeltable", "modeltable.sam", "modeltable.samset" ] }, { "page": "modelVersionInfo", "title": "Description of model", "topics": [ "modelVersionInfo" ] }, { "page": "mohn", "title": "Mohn's rho calculation", "topics": [ "mohn", "mohn.samset" ] }, { "page": "nobs.sam", "title": "Extract number of observations from sam object", "topics": [ "nobs.sam" ] }, { "page": "nscodConf", "title": "nscodConf", "topics": [ "nscodConf" ] }, { "page": "nscodData", "title": "nscodData", "topics": [ "nscodData" ] }, { "page": "nscodParameters", "title": "nscodParameters", "topics": [ "nscodParameters" ] }, { "page": "ntable", "title": "N table", "topics": [ "ntable", "ntable.sam" ] }, { "page": "obscorrplot", "title": "Plots the estimated correlation matrices by fleet.", "topics": [ "obscorrplot", "obscorrplot.sam" ] }, { "page": "obscov", "title": "Extract observation covariance matrices from a SAM fit", "topics": [ "obscov", "obscov.sam", "obscov.samset" ] }, { "page": "parplot", "title": "SAM parameter plot", "topics": [ "parplot", "parplot.sam", "parplot.samset" ] }, { "page": "partable", "title": "parameter table", "topics": [ "partable", "partable.sam" ] }, { "page": "plot.hcr", "title": "Plot hcr object", "topics": [ "plot.hcr" ] }, { "page": "plot.sam", "title": "Plot sam object", "topics": [ "plot.sam" ] }, { "page": "plot.samforecast", "title": "Plot samforecast object", "topics": [ "plot.samforecast" ] }, { "page": "plot.samres", "title": "Plot sam residuals", "topics": [ "plot.samres" ] }, { "page": "plot.samset", "title": "Plot sam object", "topics": [ "plot.samset" ] }, { "page": "plot.samypr", "title": "Plot sam object", "topics": [ "plot.samypr" ] }, { "page": "plotby", "title": "Plot by one or two", "topics": [ "plotby" ] }, { "page": "plotit", "title": "Plot helper", "topics": [ "plotit", "plotit.hcr", "plotit.sam", "plotit.samforecast", "plotit.samset" ] }, { "page": "predstdplot", "title": "Prediction-standard deviation plot", "topics": [ "predstdplot" ] }, { "page": "print.hcr", "title": "Print hcr object", "topics": [ "print.hcr" ] }, { "page": "print.sam", "title": "Print sam object", "topics": [ "print.sam" ] }, { "page": "print.sam_referencepoints", "title": "Print referencepoint object", "topics": [ "print.sam_referencepoints" ] }, { "page": "print.samcoef", "title": "Print samcoef object", "topics": [ "print.samcoef" ] }, { "page": "print.samforecast", "title": "Print samforecast object", "topics": [ "print.samforecast" ] }, { "page": "print.samres", "title": "Print samres object", "topics": [ "print.samres" ] }, { "page": "print.samset", "title": "Print samset object", "topics": [ "print.samset" ] }, { "page": "print.samypr", "title": "Print samypr object", "topics": [ "print.samypr" ] }, { "page": "procres", "title": "Compute process residuals (single joint sample)", "topics": [ "procres" ] }, { "page": "qtable", "title": "table of survey catchabilities", "topics": [ "qtable" ] }, { "page": "qtable.sam", "title": "table of survey catchabilities", "topics": [ "qtable.sam" ] }, { "page": "qtableplot", "title": "plot survey catchabilities", "topics": [ "qtableplot", "qtableplot.samqtable" ] }, { "page": "read.data.files", "title": "Read all standard data SAM files and return a list as created by 'setup.sam.data'", "topics": [ "read.data.files" ] }, { "page": "read.ices", "title": "Function to read ICES/CEFAS data files and validate if input makes sense", "topics": [ "read.ices" ] }, { "page": "read.surveys", "title": "Function to read ices survey format", "topics": [ "read.surveys" ] }, { "page": "read.table.nowarn", "title": "Function to supress incomplete final line warning", "topics": [ "read.table.nowarn" ] }, { "page": "recplot", "title": "SAM Recruits plot", "topics": [ "recplot", "recplot.hcr", "recplot.sam", "recplot.samforecast", "recplot.samset" ] }, { "page": "rectable", "title": "Recruit table", "topics": [ "rectable", "rectable.default" ] }, { "page": "reduce", "title": "reduce helper function to reduce data", "topics": [ "reduce" ] }, { "page": "referencepoints", "title": "Estimate reference points", "topics": [ "referencepoints", "referencepoints.sam" ] }, { "page": "refit", "title": "Re-fit a model from stockassessment.org", "topics": [ "refit" ] }, { "page": "residplot", "title": "Compute and plot residual diagnostic tests for a SAM model fit", "topics": [ "residplot" ] }, { "page": "residuals.sam", "title": "Extract residuals from sam object", "topics": [ "residuals.sam" ] }, { "page": "retro", "title": "retro run", "topics": [ "retro", "retro.sam" ] }, { "page": "rmaxplot", "title": "SAM rmax plot", "topics": [ "rmaxplot", "rmaxplot.default", "rmaxplot.hcr", "rmaxplot.samforecast" ] }, { "page": "rmaxtable", "title": "rmax table", "topics": [ "rmaxtable", "rmaxtable.default" ] }, { "page": "rmvnorm", "title": "rmvnorm helper function to draw multivariate normal samples", "topics": [ "rmvnorm" ] }, { "page": "runwithout", "title": "runwithout helper function", "topics": [ "runwithout", "runwithout.sam" ] }, { "page": "sam.fit", "title": "Fit SAM model", "topics": [ "sam.fit" ] }, { "page": "saveConf", "title": "Saves a model configuration list to a file", "topics": [ "saveConf" ] }, { "page": "sdplot", "title": "Plots the sd of the log observations as estimated in SAM in increasing order", "topics": [ "sdplot", "sdplot.sam" ] }, { "page": "setS", "title": "small helper function", "topics": [ "setS" ] }, { "page": "setSeq", "title": "small helper function", "topics": [ "setSeq" ] }, { "page": "setup.sam.data", "title": "Combine the data sources to SAM readable object", "topics": [ "setup.sam.data" ] }, { "page": "simstudy", "title": "Simulate data from fitted model and re-estimate from each run", "topics": [ "simstudy" ] }, { "page": "simulate.sam", "title": "Simulate from a sam object", "topics": [ "simulate.sam" ] }, { "page": "sprplot", "title": "SAM SPR plot", "topics": [ "sprplot", "sprplot.default", "sprplot.hcr", "sprplot.samforecast" ] }, { "page": "sprtable", "title": "SPR table", "topics": [ "sprtable", "sprtable.default" ] }, { "page": "srplot", "title": "Plots the stock recruitment", "topics": [ "srplot", "srplot.sam" ] }, { "page": "ssbplot", "title": "SAM SSB plot", "topics": [ "ssbplot", "ssbplot.default", "ssbplot.hcr", "ssbplot.samforecast" ] }, { "page": "ssbtable", "title": "SSB table", "topics": [ "ssbtable", "ssbtable.default" ] }, { "page": "stochasticReferencepoints", "title": "Estimate stochastic reference points", "topics": [ "stochasticReferencepoints", "stochasticReferencepoints.sam" ] }, { "page": "stockassessment-deprecated", "title": "Deprecated and defunct functions", "topics": [ "stockassessment-deprecated" ] }, { 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