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

The soilReports 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. "region2/mu-comparison"
• reportInit(...) | reportCopy(...): copy a named report template into a specific directory
• reportUpdate(...): update a named report in a specific directory, replacing report.Rmd only

Each report contains several files:

• report.Rmd: an R 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 use C:/Users/FirstName.LastName/Documents/R/ for installing R packages. Again, you only have to do this once.

# determine your current $HOME directory
path.expand('~')

# install .Rprofile
source('https://raw.githubusercontent.com/ncss-tech/soilReports/master/R/installRprofile.R')
installRprofile(overwrite=TRUE)

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

# need devtools to install packages from GitHub
install.packages('remotes', dep = TRUE)

# get the latest version of the 'soilReports' package
remotes::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 library
library(soilReports)

# list reports in the package
listReports()

# install required packages for a named report
reportSetup(reportName='region2/mu-comparison')

# copy report file 'MU-comparison' to your current working directory
reportInit(reportName='region2/mu-comparison', outputDir='MU-comparison')

Updates 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 "region2/mu-comparison" report. Note that your existing configuration files will not be modified.

# get latest version of package + report templates
remotes::install_github("ncss-tech/soilReports", dependencies=FALSE, upgrade_dependencies=FALSE)

# load this library
library(soilReports)

# get any new packages that may be required by the latest version
reportSetup(reportName='region2/mu-comparison')

# overwrite report files in an existing report instance (does NOT overwrite config)
reportUpdate(reportName='region2/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 are GDAL-compatible formats: GeoTiff, ERDAS IMG, ArcGRID, etc. (not ESRI FGDB)
• Make sure that the map unit polygon data source is an OGR-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 with reportSetup(), consider adding the upgrade=TRUE argument.
• If you are encountering errors with "Knit HTML" in RStudio, try: update.packages(ask=FALSE, checkBuilt=TRUE).

See issue tracker for TODO items.

• aqp
• soilDB
• sharpshootR