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.
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 pacakges required by the named report, e.g. "region2/mu-comparison"
reportCopy(...): copy a named report template into a specific directory
reportUpdate(...): update a named report in a specific directory, replacing
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
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('devtools', dep=TRUE) # get the latest version of the 'soilReports' package remotes::install_github("ncss-tech/soilReports", dependencies=FALSE, upgrade_dependencies=FALSE)
# 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')
reportSetup(), consider adding the
See issue tracker for TODO items.
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