{ "_id": "6ac9f781fe5cc25786e8371c", "Package": "DM", "Type": "Package", "Title": "Dynamic Model", "Version": "1.7.5", "Date": "2017-03-27", "SystemRequirements": "WinBUGS 1.4, jags (>= 3.3.0)", "Author": "Eli Holmes, Martin Liermann, Howard Coleman, NOAA, Seattle, USA", "Maintainer": "Elizabeth Holmes - NOAA Federal ", "Description": "This package uses comma-delimited data exported from the\nA&P Excel files to estimate the SR parameters for a\nuser-specified SR function.", "License": "GPL-2", "BuildVignettes": "yes", "Packaged": { "Date": "2026-10-10 08:10:09 UTC", "User": "root" }, "NeedsCompilation": "no", "RoxygenNote": "6.0.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make jags libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://nmfs-opensci.r-universe.dev", "Date/Publication": "2018-02-05 20:50:49 UTC", "RemoteUrl": "https://github.com/nwfsc-math-bio/DM", "RemoteRef": "HEAD", "RemoteSha": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "_user": "nmfs-opensci", "_type": "src", "_file": "DM_1.7.5.tar.gz", "_fileid": "https://r2.ropensci.org/20767e01521823022b793b265bde670a26af7893e665d15e6f6f9e48692236cf", "_filesize": 196075, "_sha256": "20767e01521823022b793b265bde670a26af7893e665d15e6f6f9e48692236cf", "_expires": "2027-01-18T08:29:51.000Z", "_created": "2026-10-10T08:10:09.000Z", "_published": "2026-10-10T08:29:53.131Z", "_buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827", "_status": "failure", "_host": "GitHub-Actions", "_jobs": [ { "job": 114169316902, "time": 171, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11664328785" }, { "job": 114169316938, "time": 121, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11663864067" }, { "job": 114169316957, "time": 121, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11663628962" }, { "job": 114169316895, "time": 136, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11664670753" }, { "job": 114168375157, "time": 323, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11663803735" }, { "job": 114169316936, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11664232536" }, { "job": 114169316884, "time": 105, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11664328654" }, { "job": 114169316887, "time": 93, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11663869010" }, { "job": 114169316899, "time": 93, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11664558483" } ], "_upstream": "https://github.com/nwfsc-math-bio/DM", "_commit": { "id": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "author": "Eli Holmes ", "committer": "Eli Holmes ", "message": "Set theme jekyll-theme-slate", "time": 1517863849 }, "_maintainer": { "name": "Elizabeth Holmes - NOAA Federal", "email": "eli.holmes@noaa.gov", "login": "eeholmes", "orcid": "0000-0001-9128-8393", "description": "NMFS Open Science lead\nUniv of WA School of Fisheries, Affiliate Faculty", "uuid": 2545978 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.0", "role": "Depends" }, { "package": "R2jags", "role": "Depends" }, { "package": "R2WinBUGS", "role": "Depends" }, { "package": "coda", "role": "Depends" }, { "package": "KernSmooth", "role": "Depends" }, { "package": "GenSA", "role": "Depends" }, { "package": "stringr", "role": "Depends" }, { "package": "tools", "role": "Depends" }, { "package": "knitr", "role": "Depends" }, { "package": "shiny", "role": "Depends" }, { "package": "openxlsx", "role": "Depends" }, { "package": "VRAP", "version": ">= 1.3.6", "role": "Depends" }, { "package": "Gmedian", "role": "Depends" }, { "package": "rmarkdown", "role": "Depends" } ], "_owner": "nwfsc-math-bio", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "bayesian", "protected-species", "salmon", "jags", "cpp" ], "_stars": 0, "_contributors": [ { "user": "eeholmes", "count": 105, "uuid": 2545978 } ], "_userbio": { "uuid": 110112201, "type": "organization", "name": "nmfs-opensci", "followers": 146, "description": "GiHub org for NMFS Open Science" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DM" }, "_devurl": "https://github.com/nwfsc-math-bio/dm", "_searchresults": 523, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DM.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "centerProdCap", "createPriors", "createRAVfile", "findOptimum", "getPostDraws", "plotPriors", "plotResults", "readData", "runModel", "uncenterProdCap", "writeReport", "writeResultsToFile" ], "_help": [ { "page": "calcHarvest", "title": "Calculate harvest rate", "topics": [ "calcHarvest" ] }, { "page": "calcInitVals", "title": "Calculate initial values for MCMC.", "topics": [ "calcInitVals" ] }, { "page": "calculateHarvested", "title": "Calculate harvested recruits and escapement", "topics": [ "calculateHarvested" ] }, { "page": "calculatePEandSmsy", "title": "Calculate process error and SMSY.", "topics": [ "calculatePEandSmsy" ] }, { "page": "centerProdCap", "title": "Center productivty and log capacity parameters", "topics": [ "centerProdCap" ] }, { "page": "conditionalcenterProdCap", "title": "Center productivty and log capacity parameters conditioned on values in input", "topics": [ "conditionalcenterProdCap" ] }, { "page": "createBUGSdata", "title": "Create bugs data for model with or without age data.", "topics": [ "createBUGSdata" ] }, { "page": "createPriors", "title": "Create a priors list.", "topics": [ "createPriors" ] }, { "page": "createRAVfile", "title": "Create rav file.", "topics": [ "createRAVfile" ] }, { "page": "DM", "title": "Shiny app to run DM and VRAP", "topics": [ "DM", "DMVRAP" ] }, { "page": "findOptimum", "title": "Optimization functions.", "topics": [ "findOptimum" ] }, { "page": "getPostDraws", "title": "Get the simulations from a jags output list.", "topics": [ "getPostDraws" ] }, { "page": "info", "title": "Helper file for creating text for the reports.", "topics": [ "info" ] }, { "page": "plotAgeComp", "title": "Create plots of age composition", "topics": [ "plotAgeComp" ] }, { "page": "plotCapacity", "title": "Create plots of capacity posteriors", "topics": [ "plotCapacity" ] }, { "page": "plotCoefs", "title": "Create plots of covariate coefficients", "topics": [ "plotCoefs" ] }, { "page": "plotPriors", "title": "Create plots of priors for productivity and log capacity.", "topics": [ "plotPriors" ] }, { "page": "plotProductivity", "title": "Create plots of productivity posteriors", "topics": [ "plotProductivity" ] }, { "page": "plotResults", "title": "Create plots from DM runs", "topics": [ "plotResults" ] }, { "page": "readData", "title": "This reads in the csv file saved from an A & P file and creates dat and input", "topics": [ "readData" ] }, { "page": "runJAGS", "title": "Call JAGS to get the posterior draws.", "topics": [ "runJAGS" ] }, { "page": "runModel", "title": "Run the DM model", "topics": [ "runModel" ] }, { "page": "selectSR", "title": "Helper function that takes the name of SR function and returns the recruits", "topics": [ "selectSR" ] }, { "page": "simplePlot", "title": "Create posterior credible interval plots from multiple DM runs", "topics": [ "simplePlot" ] }, { "page": "srfunctions", "title": "SR funcitons", "topics": [ "bevertonHolt", "hockeyStick", "ricker", "srfunctions" ] }, { "page": "SSTfuncDM", "title": "Original dynamic model", "topics": [ "SSTfuncDM" ] }, { "page": "summarizeRuns", "title": "Summarize runs", "topics": [ "summarizeRuns" ] }, { "page": "uncenterProdCap", "title": "Uncenter productivty and log capacity parameters", "topics": [ "uncenterProdCap" ] }, { "page": "writeBUGScode", "title": "write the model in BUGS language", "topics": [ "writeBUGScode" ] }, { "page": "writeReport", "title": "Creates a report with plots.", "topics": [ "writeReport" ] }, { "page": "writeResultsToFile", "title": "Save DM output.", "topics": [ "writeResultsToFile" ] } ], "_readme": "https://github.com/nwfsc-math-bio/DM/raw/HEAD/README.md", "_rundeps": [ "abind", "base64enc", "boot", "bslib", "cachem", "cli", "coda", "codetools", "commonmark", "DEoptimR", "digest", "doParallel", "doSNOW", "evaluate", "fastmap", "fontawesome", "foreach", "fs", "GenSA", "glue", "Gmedian", "highr", "htmltools", "httpuv", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "later", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "openxlsx", "otel", "promises", "R2jags", "R2WinBUGS", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "RcppEigen", "rjags", "rlang", "rmarkdown", "robustbase", "RSpectra", "sass", "shiny", "shinyAce", "snow", "sourcetools", "stringi", "stringr", "tinytex", "vctrs", "VRAP", "withr", "xfun", "xtable", "yaml", "zip" ], "_sysdeps": [ { "shlib": "libjags", "package": "jags", "headers": "jags", "source": "jags", "version": "4.3.2-2.2604.0", "name": "jags", "homepage": "https://mcmc-jags.sourceforge.io", "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.417471693203293, "_indexed": false, "_nocasepkg": "dm", "_universes": [ "nmfs-opensci" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.5", "date": "2026-10-10T08:12:54.000Z", "distro": "resolute", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/712b7ef9d0f8a540d69e93e226c8b238137efd23a7d04fc5523073372a912345", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.6.1", "os": "linux", "version": "1.7.5", "date": "2026-10-10T08:12:11.000Z", "distro": "resolute", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/ca003a5e8bdd23d68d43e0cdab48c3995e7599db24e487f2229691c3f4eb61c8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.5.3", "os": "mac", "version": "1.7.5", "date": "2026-10-10T08:29:07.000Z", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/9d7f8923e5c44ae492c07a38d2e13ab57e98fa845f0afcf4d5970e696e9b97e3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.6.1", "os": "mac", "version": "1.7.5", "date": "2026-10-10T08:27:06.000Z", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/b1139dfdc19d2513bda0fc16ddfd7371125e7940391cb65a09d068b8a684edf2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.5", "date": "2026-10-10T08:12:37.000Z", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/4abb8433d04641c93fb4527950e8ea1c9be05205fd71a5d0bd8ff0c7824aebf3", "status": "success", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.7.0", "os": "win", "version": "1.7.5", "date": "2026-10-10T08:11:50.000Z", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/2a64e2e74e531fd0256d8eedbba52f24516f92e96a54a7fecc5750406a9c8f34", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.5.3", "os": "win", "version": "1.7.5", "date": "2026-10-10T08:11:33.000Z", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/595f44780c817eb0aadcecae1367a0349c9f0730c2d35f7e8dc69bb1084f833a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" }, { "r": "4.6.1", "os": "win", "version": "1.7.5", "date": "2026-10-10T08:11:27.000Z", "commit": "b8feb2e17aeb74abe83c83edadd50aa282ab1e66", "fileid": "https://r2.ropensci.org/04e807d72f1ad1e4e7e20d35a6366ef1de8be303387b9095b313de78da040723", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/nmfs-opensci/actions/runs/38036637827" } ] }