isobar-reports {isobar} | R Documentation |
Generation of LaTeX and XLS reports is helped with
functions which facilitate the gathering of relevant information and
creation of tikz plots. create.reports
parses properties (by
calling load.properties
) and initialize environments and
computations (by calling initialize.env
) required by the
reports, calls Sweave and pdflatex.
create.reports(properties.file = "properties.R", global.properties.file = system.file("report","properties.R", package = "isobar"), args = NULL, ..., recreate.properties.env = TRUE, recreate.report.env = TRUE) load.properties(properties.file = "properties.R", global.properties.file = system.file("report","properties.R",package="isobar"), args = NULL, ...) initialize.env(env, properties.env)
properties.file |
File which holds the parameters for data
analysis and report generation. It is parsed as R code after the
global report configuration file |
global.properties.file |
|
args |
Additional (command line) arguments which overrids those
in |
... |
Additional properties. |
recreate.properties.env |
Whether a properties.env existing in the global environment should be used, or it should be recreated. |
recreate.report.env |
Whether a report.env existing in the global environment should be used, or it should be recreated. |
env |
Item to be initialized. |
properties.env |
Environment into which properties are read. |
The directory inst
in the isobar installation directory
system.file("inst",package="isobar")
contains R, Sweave, and LaTeX
files as examples of how to create XLS and PDF reports using isobar
.
Call with Rscript. It is the main file which
parses command line options. --compile
and
--zip
are parsed directly and given as arguments to
create.reports
. Other arguments are given
load.properties
.
calls a perl script to generate a XLS report
generates a LaTeX quality control and analysis report
for the XLS report the script pl/tab2xls.pl is used, which concetenates CSV files to a XLS. See Perl requirements. Sweave is called on report/isobar-qc.Rnw and report/isobar-analysis.Rnw. All files are written the working directory.
Quality control Sweave file.
Data analysis Sweave file.
Default configuration for data analysis.
LaTeX functions for plotting tikz graphics, etc.
Florian P Breitwieser
IBSpectra, isobar-preprocessing isobar-analysis