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Life and Fishery","monthly_downloads":776,"total_dependent_repos":3,"total_dependent_packages":0,"readme":"---\noutput:\n  md_document:\n    variant: gfm\n---\n\n![Project Status](https://www.repostatus.org/badges/latest/active.svg)\n[![r-universe name](https://ices-tools-prod.r-universe.dev/badges/:name)](https://ices-tools-prod.r-universe.dev)\n[![version number](https://ices-tools-prod.r-universe.dev/badges/icesSAG)](https://ices-tools-prod.r-universe.dev/icesSAG)\n![branch version number](https://img.shields.io/badge/branch_version-`r packageDescription(\"icesSAG\")$Version`-blue)\n[![GitHub release](https://img.shields.io/github/release/ices-tools-prod/icesSAG.svg?maxAge=6000)]()\n[![License](https://img.shields.io/badge/license-GPL%20(%3E%3D%202)-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)\n\nCRAN status:\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/icesSAG)](https://cran.r-project.org/package=icesSAG)\n![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/icesSAG)\n![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/grand-total/icesSAG)\n\n[\u003cimg align=\"right\" alt=\"ICES Logo\" width=\"17%\" height=\"17%\" src=\"http://ices.dk/_layouts/15/1033/images/icesimg/iceslogo.png\"\u003e](http://ices.dk)\n\n### icesSAG\n\nicesSAG provides R functions that access the\n[web services](https://sg.ices.dk/webservices.aspx) of the [ICES](https://www.ices.dk)\n[Stock Assessment Graphs](https://sg.ices.dk) database.\n\nicesSAG is implemented as an [R](https://www.r-project.org) package and\nis currently hosted on [r-universe](https://ices-tools-prod.r-universe.dev)\nand available on [CRAN](https://cran.r-project.org/package=icesSAG).\n\n### Installation\n\n\nThe stable version of icesSAG can be installed from CRAN using the `install.packages` command:\n\n```r\ninstall.packages(\"icesSAG\", repos = \"https://cloud.r-project.org\")\n```\n\nor a potentially more recent, but less stable version installed from r-universe:\n\n```r\ninstall.packages(\"icesSAG\", repos = \"https://ices-tools-prod.r-universe.dev\")\n```\n\n### Usage\n\n\nFor a summary of the package:\n\n```r\nlibrary(icesSAG)\n?icesSAG\n```\n\n### Examples\n\n```{r, echo = FALSE}\noptions(icesSAG.messages = FALSE)\noptions(icesSAG.use_token = FALSE)\nlibrary(icesSAG)\nlibrary(ggplot2)\n```\n\nTo download the summary data for all sandeel stocks published in 2018 use:\n```{r}\nsummary_data \u003c- getSAG(stock = \"sandeel\", year = 2023)\nhead(summary_data)\nggplot(summary_data[complete.cases(summary_data[c(\"Year\", \"recruitment\")]),],\n       aes(x=Year, y=recruitment, group = fishstock, colour = fishstock)) +\n    geom_line()\n```\n\n\n#### verbose web service calls\n\nIf you want to see all the web service calls being made set this option\n\n```{r echo = TRUE}\nsag_messages(TRUE)\n```\n\nThe result will be\n\n```{r}\ncodKeys \u003c- findAssessmentKey(\"cod\", year = 2017)\n```\n\nwhich allows you to investigate the actual web service data if you are interested:\n[https://sag.ices.dk/SAG_API/api/StockList?year=2017](https://sag.ices.dk/SAG_API/api/StockList?year=2017)\n\n\n#### Authorised access via tokens\n\nICES provides public access to the results of published stock assessments.  If you are an ICES stock assessor and wish to access unpublished results, or to upload your results, this can be done using token authentication.\n\nThis is easy to set up, simply run the following line and all future requests to the SAG database will be authenticated.\n\n```r\nsag_use_token(TRUE)\n```\n\n#### uploading data\n\nTo upload the results of a stock assessment to SAG you must provide two pieces of information, Stock information, such as stock code, assessment year and reference points, and yearly results, such as landings and estimated fishing mortality.  There are two helper functions to create the required objects.\n\n```r\nstockInfo()\n```\n\nreturns a `list` (it requires a stock code, assessment year and contact email as a minimum), with the correctly named elements.  And,\n\n```r\nstockFishdata()\n```\n\nreturns a `data.frame` (it requires year as default) with the correctly named columns\n\nA simple (almost) minimal example is:\n\n```{r echo = FALSE}\nsag_messages(FALSE)\n```\n\n```{r, eval=FALSE}\ninfo \u003c-\n  stockInfo(\n    StockCode = \"whg.27.7a\",\n    AssessmentYear = 2021,\n    ContactPerson = \"its_me@somewhere.gov\",\n    StockCategory = 3,\n    Purpose = \"Unofficial\",\n    ModelType = \"A\",\n    ModelName = \"XSA\"\n  )\nfishdata \u003c- stockFishdata(1950:2020)\n\n# simulate some landings for something a bit intesting\nset.seed(1232)\nfishdata$Landings \u003c- 10^6 * exp(cumsum(cumsum(rnorm(nrow(fishdata), 0, 0.1))))\n\n# you can create an XML file to upload yourself\nxml \u003c- createSAGxml(info, fishdata)\n# here we use a temporary file to store the XML, but you can safe this to your output or report folder\ntempfile \u003c- tempfile(fileext = \".xml\")\ncat(xml, file = tempfile)\n\n# this file can then be uploaded using the SAG webservices\nkey \u003c- uploadStock(tempfile, upload = TRUE)\n\n# if you want to just check the file and not upload:\nuploadStock(tempfile, upload = FALSE)\n```\n\nYou can check that the data was uploaded by searching for our stock. Note you will need to make sure the icesSAG.use_token option is set to TRUE\n\n```{r}\nsag_use_token(TRUE)\nfindAssessmentKey('whg.27.7a', 2020, full = TRUE)\n```\n\n### Displaying graphs\n\nWe can also look at the landings graph created from the data that were uploaded, NOTE you may need to modify the settings at sag.ices.dk.\n\n```{r, landings-plot, eval=FALSE}\nplot(getLandingsGraph(key))\n```\n\nor download all four summary graphs and display them in a 2x2 grid.\n\n```{r, summary-plot, eval=FALSE}\ngraphs \u003c- getSAGGraphs(key)\nplot(graphs)\n```\n\n\n### References\n\nICES Stock Assessment Graphs database:\nhttps://sg.ices.dk\n\nICES Stock Assessment Graphs web services:\nhttps://sg.ices.dk/webservices.aspx\n\n### Development\n\nicesSAG is developed openly on\n[GitHub](https://github.com/ices-tools-prod/icesSAG).\n\nFeel free to open an [issue](https://github.com/ices-tools-prod/icesSAG/issues)\nthere if you encounter problems or have suggestions for future versions.\n\nThe current development version can be installed using:\n\n```R\nlibrary(devtools)\ninstall_github(\"ices-tools-prod/icesSAG@development\")\n```\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/299662","html_url":"https://ost.ecosyste.ms/projects/299662"}