{ "_id": "6a10af19acfb0bcc41cc1c37", "Package": "a4adiags", "Title": "Additional Diagnostics for FLa4a stock Assessment Models", "Version": "0.1.6", "Authors@R": "c(\nperson(\"Iago\", \"Mosqueira\", email = \"iago.mosqueira@wur.nl\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3252-0591\")),\nperson(\"Henning\", \"Winker\", email = \"henning.winker@ec.europa.eu\",\nrole = c(\"aut\")),\nperson(\"European Union\", role = c(\"fnd\", \"cph\")))", "Description": "A series of extra diagnostics for the FLa4a model,\nincluding prediction skill through restrospective prediction of\nmodel inputs and runs tests. Contains ggplot-based plot\nfuntions of diagnostics outputs.", "License": "EUPL", "VignetteBuilder": "knitr", "Additional_repositories": "http://flr-project.org/R", "LazyData": "true", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libgsl0-dev libjpeg-dev libpng-dev", "Repository": "https://flr.r-universe.dev", "Date/Publication": "2025-10-20 15:46:00 UTC", "RemoteUrl": "https://github.com/flr/a4adiags", "RemoteRef": "HEAD", "RemoteSha": "2f12dd7107e80a3ffc98b93a80fb48e9a19c4707", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 18:57:13 UTC", "User": "root" }, "Author": "Iago Mosqueira [aut, cre] (ORCID:\n),\nHenning Winker [aut],\nEuropean Union [fnd, cph]", "Maintainer": "Iago Mosqueira ", "MD5sum": "d381b8bcefb08eb5252405b2a3e74c47", "_user": "flr", "_type": "src", "_file": "a4adiags_0.1.6.tar.gz", "_fileid": "8dce39ada289cdc821c2a2049578026d0a3c1896d97b8d2fe28320df45057afb", "_filesize": 1882245, "_sha256": 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"tojson": false } ], "_help": [ { "page": "a4aBioidx", "title": "a4aBioidx Computes observed and expected FLIndexBiomass from a4a fits", "topics": [ "a4aBioidx" ] }, { "page": "a4ahcxval", "title": "Compute a retrospective hindcast cross-validation of a4a stock and indices", "topics": [ "a4ahcxval" ] }, { "page": "mase2", "title": "Adjusted mase function for dealing with NAs", "topics": [ "mase2" ] }, { "page": "plota4aBioidx", "title": "plota4aBioidx Computes observed and expected FLIndexBiomass from a4a fits plota4aBioidx(stock, fit, indices) \\itemstockInput FLStock object. \\itemfitobject a4a fit . \\itemindicesInput FLIndices object. \\itemnyearsNumber if years for retrospective, defaults to 5. \\itemnsqNumber of years for average biology and selectivity, defaults to 3. \\itemfixed.ksIs the number of knots is splines with 'year' constant? ggplot plota4aBioidx Computes observed and expected FLIndexBiomass from a4a fits data(sol274) # models fmod <- ~te(replace(age, age > 8, 8), year, k = c(4, 22)) + s(replace(age, age > 8, 8), k=4) + s(year, k=22, by=as.numeric(age==1)) qmod <- list(~s(age, k=3), ~s(age, k=3)) vmod <- list(~s(age, k=3), ~s(age, k=3), ~s(age, k=3)) srmod <- ~factor(year) # RUN a4a fit <- sca(stock, indices, fmodel=fmod, qmodel=qmod, vmodel=vmod,sr=srmod) idxs = a4aBioidx(stock,fit,indices) plota4aBioidx(stock,fit,indices)", "topics": [ "plota4aBioidx" ] }, { "page": "plotRunstest-a4aFitSA-FLIndices-method", "title": "plotRunstest Plot the runs test result for one or more time series", "topics": [ "plotRunstest,a4aFitSA,FLIndices-method" ] }, { "page": "plotXval2", "title": "Plot of FLIndices cross-validation by retrospective hindcast", "topics": [ "plotXval2" ] }, { "page": "runstest-a4aFitSA-FLIndices-method", "title": "Computes Runs Test p-values", "topics": [ "runstest,a4aFitSA,FLIndices-method" ] }, { "page": "data", "title": "Data from the 2020 ICES stock assessment of North Sea sole (sol.27.4)", "topics": [ "indices", "sol274", "sol274fit", "stock" ] } ], "_pkglogo": "https://github.com/flr/a4adiags/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/flr/a4adiags/raw/HEAD/README.md", "_rundeps": [ "ADGofTest", "boot", "cli", "cluster", "coda", "codetools", "colorspace", "copula", "cowplot", "cpp11", "data.table", "deldir", "farver", "FLa4a", "FLasher", "FLCore", "FLFishery", "foreach", "ggplot2", "ggplotFL", "ggrepel", "glue", "gridExtra", "gsl", "gtable", "interp", "isoband", "iterators", "jpeg", "labeling", "lattice", "latticeExtra", "lifecycle", "MASS", "Matrix", "mgcv", "mvtnorm", "nlme", "numDeriv", "patchwork", "pcaPP", "png", "pspline", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "S7", "scales", "stabledist", "triangle", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "a4adiags.Rmd", "filename": "a4adiags.html", "title": "Model Diagnostics for FLa4a", "author": "Iago MOSQUEIRA (WMR), Henning WINKER (EC JRC)", "engine": "knitr::rmarkdown", "headings": [ "Example model fit", "Prediction skill by hindcasting cross-validation", "Runs test", "More information", "Software Versions", "Author information", "References" ], "created": "2020-12-22 16:33:45", "modified": "2021-01-29 10:01:59", "commits": 8 } ], "_score": 2.6989700043360187, "_indexed": true, "_nocasepkg": "a4adiags", "_universes": [ "flr", "iagomosqueira" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.6", "date": "2026-05-22T19:04:44.000Z", "distro": "noble", "commit": "2f12dd7107e80a3ffc98b93a80fb48e9a19c4707", "fileid": "daf77217b6fba375bd3ebc52b98b18703a8b383ed52eb7e009ca89d94d920a67", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/flr/actions/runs/26279407022" }, { "r": "4.6.0", "os": "linux", "version": "0.1.6", "date": "2026-05-22T19:04:33.000Z", "distro": "noble", "commit": "2f12dd7107e80a3ffc98b93a80fb48e9a19c4707", "fileid": "051f4482f837bb1b46f73ef785670eef6d9f075c123e45423bde694e6c13c6ad", "status": "success", "check": 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