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Resources","sub_category":"Soil and Land","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/ncss-tech/soilReports/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/ncss-tech/soilReports/actions/workflows/R-CMD-check.yml)\n\u003c!-- badges: end --\u003e\n\n# soilReports\nReports are a handy way to summarize large volumes of data, particularly with figures and tables. `soilReports` is an R package \"container\" designed to accommodate the maintenance, documentation, and distribution of [R-based reporting tools](http://rmarkdown.rstudio.com/). Inside the package are report templates, setup files, documentation, and example configuration files. \n\nThe `soilReports` package provides a couple important helper functions that do most of the work:\n\n * `listReports()`: print a listing of the available reports, version numbers, and basic metadata\n * `reportSetup(...)`: download any R packages required by the named report, e.g. *\"southwest/mu-comparison\"*\n * `reportInit(...)` | `reportCopy(...)`: copy a named report template into a specific directory\n * `reportUpdate(...)`: update a named report in a specific directory, replacing `report.Rmd` only\n\nEach report contains several files:\n\n * `report.Rmd`: an [R Markdown file](http://rmarkdown.rstudio.com/) that is \"knit\" into a final HTML or DOC report\n * `README.md`: report-specific instructions\n * `custom.R`: report-specific functions\n * `categorical_definitions.R`: report-specific color mapping and metadata for categorical raster data (user-editable)\n * `config.R`: configuration file to set report parameters (user-editable)\n * `changes.txt`: notes on changes and associated version numbers\n\n\n\n\u003c!-- mark for deletion --\u003e\n## R Profile Setup\n\n**NOTE: The following instructions are rarely, if ever, needed with R 4.2+**\n\nOn many of our machines, the `$HOME` directory points to a network share. This can cause all kinds of problems when installing R packages, especially if you connect to the network by VPN. The following code is a one-time solution and will cause R packages to be installed on a local disk by adding an `.Rprofile` file to your `$HOME` directory. This file will instruct R to use `C:/Users/FirstName.LastName/Documents/R/` for installing R packages. Again, you only have to do this **once**.\n\n```r\n# determine your current $HOME directory\npath.expand('~')\n\n# install .Rprofile\nsource('https://raw.githubusercontent.com/ncss-tech/soilReports/master/R/installRprofile.R')\ninstallRprofile(overwrite=TRUE)\n```\n\n\n## soilReports Installation - First time or after R upgrade\nRun this code if you don't yet have the `soilReports` package or after a new version of R has been installed on your machine.\n\n```r\n# need devtools to install packages from GitHub\ninstall.packages('remotes', dep = TRUE)\n\n# get the latest version of the 'soilReports' package\nremotes::install_github(\"ncss-tech/soilReports\", dependencies = FALSE, upgrade_dependencies = FALSE) \n```\n\n## Choose an Available Report\n\n  * Region 2\n     + [Map Unit Comparison/Summary Report](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/southwest/mu-comparison)\n     + [MLRA Comparison/Summary Report](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/southwest/mlra-comparison)\n     + [DMU Difference Report](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/southwest/dmu-diff)\n     + [QA Summary Report](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/southwest/QA-summary)\n     + [Shiny Pedon Summary](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/southwest/shiny-pedon-summary)\n     \n  * Region 11\n     + [Component Summary by Project](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/northcentral/component_summary_by_project)\n     + [MUPOLYGON Summary by Project](https://github.com/ncss-tech/soilReports/tree/master/inst/reports/northcentral/mupolygon_summary_by_project)\n\n\n## Example Output\n\n### Reports for Raster Summary by MU or MLRA\n  \n  * [summary of select CA630 map units](http://ncss-tech.github.io/example-reports/mu-comparison/CA630-mu-comparison.html)\n  * [summary of select MLRA](http://ncss-tech.github.io/example-reports/MLRA-comparison.html)\n  * [summary of mupolygon layer](http://ncss-tech.github.io/example-reports/mupolygon_report.html)\n\n### Reports for DMU QC/QA\n\n  * [DMU differences](http://ncss-tech.github.io/example-reports/dmu-diff-example.html)\n  * [QA Summary](http://ncss-tech.github.io/example-reports/QA-summary-example.html)\n  * [DMU Summary](http://ncss-tech.github.io/example-reports/DMU-summary-example.html)\n  * [summary of soil components](http://ncss-tech.github.io/example-reports/component_report.html)\n  \n\n### Reports for Pedon Data\n\n  * [CA792: mendel](http://ncss-tech.github.io/example-reports/CA792-pedon/mendel.html)\n  * [CA792: canisrocks](http://ncss-tech.github.io/example-reports/CA792-pedon/canisrocks.html)\n  * [CA792: siberian](http://ncss-tech.github.io/example-reports/CA792-pedon/siberian.html)\n  * [CA792: isosceles](http://ncss-tech.github.io/example-reports/CA792-pedon/isosceles.html)\n  * [summary of pedon data](http://ncss-tech.github.io/example-reports/pedon_report.html)\n  * [summary of lab data](http://ncss-tech.github.io/example-reports/lab_report.html)\n  * [NEW: Shiny Pedon Summary - interactive plots and tables for pedon data](https://ncss-tech.github.io/soilReports/docs/shiny-pedon-summary/shiny-pedon_loafercreek-taxadjuncts.PNG)\n\n\n## Run a Report - Example: Map Unit Comparison report\n\n```r\n# load this library\nlibrary(soilReports)\n\n# list reports in the package\nlistReports()\n\n# install required packages for a named report\nreportSetup(reportName='southwest/mu-comparison')\n\n# copy report file 'MU-comparison' to your current working directory\nreportInit(reportName='southwest/mu-comparison', outputDir='MU-comparison')\n```\n\n## Updating Existing Reports - Example: Map Unit Comparison report \nUpdates to report templates, documentation, and custom functions are available *after installing the latest* `soilReports` package from GitHub. Use the following examples to update an existing copy of the \"southwest/mu-comparison\" report. Note that your existing configuration files will not be modified.\n\n```r\n# get latest version of package + report templates\nremotes::install_github(\"ncss-tech/soilReports\", dependencies=FALSE, upgrade_dependencies=FALSE)\n\n# load this library\nlibrary(soilReports)\n\n# get any new packages that may be required by the latest version\nreportSetup(reportName='southwest/mu-comparison')\n\n# overwrite report files in an existing report instance (does NOT overwrite config)\nreportUpdate(reportName='southwest/mu-comparison', outputDir='MU-comparison')\n```\n\n## Suggested Background Material\n\n * [The user is familiar with Rstudio](http://ncss-tech.github.io/stats_for_soil_survey/chapters/1_introduction/1_introduction.html)\n * NASIS selected set is loaded with the necessary tables (e.g. \"Project - legend/mapunit/dmu by sso, pname \u0026 uprojectid\")\n * [ODBC connection to NASIS is setup](http://ncss-tech.github.io/AQP/soilDB/setup_local_nasis.html)\n * [custom .Rprofile exists](https://github.com/ncss-tech/soilReports#pre-installation-nrcs-only-this-is-only-required-once)\n * [necessary R packages are installed](http://ncss-tech.github.io/stats_for_soil_survey/chapters/0_pre-class-assignment/pre-class-assignment.html)\n\n## Troubleshooting\n * If you haven't run R in a while, consider updating all packages with: `update.packages(ask=FALSE, checkBuilt=TRUE)`.\n * Make sure that all raster data sources are [GDAL-compatible formats](http://www.gdal.org/formats_list.html): GeoTiff, ERDAS IMG, ArcGRID, etc. (not ESRI FGDB)\n * Make sure that the map unit polygon data source is an [OGR-compatible format](http://www.gdal.org/ogr_formats.html): ESRI SHP, ESRI FGDB, etc.\n * Make sure that the extent of raster data includes the full extent of map unit polygon data.\n * If there is a problem installing packages with `reportSetup()`, consider adding the `upgrade=TRUE` argument.\n * If you are encountering errors with \"Knit HTML\" in RStudio, try: `update.packages(ask=FALSE, checkBuilt=TRUE)`.\n\n## TODO\nSee [issue tracker](https://github.com/ncss-tech/soilReports/issues) for TODO items.\n\n\n## Related Packages\n * [aqp](https://github.com/ncss-tech/aqp)\n * [soilDB](https://github.com/ncss-tech/soilDB)\n * [sharpshootR](https://github.com/ncss-tech/sharpshootR)\n \n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["digital-soil-mapping","pedology","pedometrics","kssl","soil-data-access","soilweb","eda","ncss","s4ss","spatial-data"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/1018","html_url":"https://ost.ecosyste.ms/projects/1018"}