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Reports 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 ofR-based reporting tools. Inside the package are report templates, setup files, documentation, and example configuration files.

ThesoilReports package provides a couple important helper functions that do most of the work:

• listReports(): print a listing of the available reports, version numbers, and basic metadata
• reportSetup(...): download any R packages required by the named report, e.g."southwest/mu-comparison"
• reportInit(...) |reportCopy(...): copy a named report template into a specific directory
• reportUpdate(...): update a named report in a specific directory, replacingreport.Rmd only

Each report contains several files:

• report.Rmd: anR Markdown file that is "knit" into a final HTML or DOC report
• README.md: report-specific instructions
• custom.R: report-specific functions
• categorical_definitions.R: report-specific color mapping and metadata for categorical raster data (user-editable)
• config.R: configuration file to set report parameters (user-editable)
• changes.txt: notes on changes and associated version numbers

NOTE: The following instructions are rarely, if ever, needed with R 4.2+

On 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 useC:/Users/FirstName.LastName/Documents/R/ for installing R packages. Again, you only have to do thisonce.

# determine your current $HOME directorypath.expand('~')# install .Rprofilesource('https://raw.githubusercontent.com/ncss-tech/soilReports/master/R/installRprofile.R')installRprofile(overwrite=TRUE)

Run this code if you don't yet have thesoilReports package or after a new version of R has been installed on your machine.

# need devtools to install packages from GitHubinstall.packages('remotes',dep=TRUE)# get the latest version of the 'soilReports' packageremotes::install_github("ncss-tech/soilReports",dependencies=FALSE,upgrade_dependencies=FALSE)

• Region 2

  • Map Unit Comparison/Summary Report
  • MLRA Comparison/Summary Report
  • DMU Difference Report
  • QA Summary Report
  • Shiny Pedon Summary

• Region 11

  • Component Summary by Project
  • MUPOLYGON Summary by Project

• summary of select CA630 map units
• summary of select MLRA
• summary of mupolygon layer

• DMU differences
• QA Summary
• DMU Summary
• summary of soil components

• CA792: mendel
• CA792: canisrocks
• CA792: siberian
• CA792: isosceles
• summary of pedon data
• summary of lab data
• NEW: Shiny Pedon Summary - interactive plots and tables for pedon data

# load this librarylibrary(soilReports)# list reports in the packagelistReports()# install required packages for a named reportreportSetup(reportName='southwest/mu-comparison')# copy report file 'MU-comparison' to your current working directoryreportInit(reportName='southwest/mu-comparison',outputDir='MU-comparison')

Updates to report templates, documentation, and custom functions are availableafter installing the latestsoilReports 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.

# get latest version of package + report templatesremotes::install_github("ncss-tech/soilReports",dependencies=FALSE,upgrade_dependencies=FALSE)# load this librarylibrary(soilReports)# get any new packages that may be required by the latest versionreportSetup(reportName='southwest/mu-comparison')# overwrite report files in an existing report instance (does NOT overwrite config)reportUpdate(reportName='southwest/mu-comparison',outputDir='MU-comparison')

• The user is familiar with Rstudio
• NASIS selected set is loaded with the necessary tables (e.g. "Project - legend/mapunit/dmu by sso, pname & uprojectid")
• ODBC connection to NASIS is setup
• custom .Rprofile exists
• necessary R packages are installed

• If you haven't run R in a while, consider updating all packages with:update.packages(ask=FALSE, checkBuilt=TRUE).
• Make sure that all raster data sources areGDAL-compatible formats: GeoTiff, ERDAS IMG, ArcGRID, etc. (not ESRI FGDB)
• Make sure that the map unit polygon data source is anOGR-compatible format: ESRI SHP, ESRI FGDB, etc.
• Make sure that the extent of raster data includes the full extent of map unit polygon data.
• If there is a problem installing packages withreportSetup(), consider adding theupgrade=TRUE argument.
• If you are encountering errors with "Knit HTML" in RStudio, try:update.packages(ask=FALSE, checkBuilt=TRUE).

Seeissue tracker for TODO items.

• aqp
• soilDB
• sharpshootR