Create a HTML-report for (RLum) objects
report_RLum( object, file = tempfile(), title = "RLum.Report", compact = TRUE, timestamp = TRUE, show_report = TRUE, launch.browser = FALSE, css.file = NULL, quiet = TRUE, clean = TRUE, ... )
object: (required ): The object to be reported on, preferably of any RLum-class.
file: character (with default): A character string naming the output file. If no filename is provided a temporary file is created.
title: character (with default): A character string specifying the title of the document.
compact: logical (with default): When TRUE the following report components are hidden: @.pid, @.uid, 'Object structure', 'Session Info'
and only the first and last 5 rows of long matrices and data frames are shown. See details.
timestamp: logical (with default): TRUE to add a timestamp to the filename (suffix).
show_report: logical (with default): If set to TRUE the function tries to display the report output in the local viewer, e.g., within RStudio after rendering.
launch.browser: logical (with default): TRUE to open the HTML file in the system's default web browser after it has been rendered.
css.file: character (optional): Path to a CSS file to change the default styling of the HTML document.
quiet: logical (with default): TRUE to suppress printing of the pandoc command line.
clean: logical (with default): TRUE to clean intermediate files created during rendering.
...: further arguments passed to or from other methods and to control the document's structure (see details).
Writes a HTML and .Rds file.
This function creates a HTML-report for a given object, listing its complete structure and content. The object itself is saved as a serialised .Rds file. The report file serves both as a convenient way of browsing through objects with complex data structures as well as a mean of properly documenting and saving objects.
The HTML report is created with rmarkdown::render and has the following structure:
| Section | Description |
Header | A summary of general characteristics of the object |
Object content | A comprehensive list of the complete structure and content of the provided object. |
Object structure | Summary of the objects structure given as a table |
File | Information on the saved RDS file |
Session Info | Captured output from sessionInfo() |
Plots | ( optional ) For RLum-class objects a variable number of plots |
The structure of the report can be controlled individually by providing one or more of the following arguments (all logical):
| Argument | Description |
header | Hide or show general information on the object |
main | Hide or show the object's content |
structure | Hide or show object's structure |
rds | Hide or show information on the saved RDS file |
session | Hide or show the session info |
plot | Hide or show the plots (depending on object) |
Note that these arguments have higher precedence than compact.
Further options that can be provided via the ... argument:
| Argument | Description |
short_table | If TRUE only show the first and last 5 rows of long tables. |
theme | Specifies the Bootstrap theme to use for the report. Valid themes include "default" , "cerulean" , "journal" , "flatly" , "readable" , "spacelab" , "united" , "cosmo" , "lumen" , "paper" , "sandstone" , "simplex" , and "yeti" . |
highlight | Specifies the syntax highlighting style. Supported styles include "default" , "tango" , "pygments" , "kate" , "monochrome" , "espresso" , "zenburn" , "haddock" , and "textmate" . |
css | TRUE or FALSE to enable/disable custom CSS styling |
The following arguments can be used to customise the report via CSS (Cascading Style Sheets):
| Argument | Description |
font_family | Define the font family of the HTML document (default: "arial" ) |
headings_size | Size of the <h1> to <h6> tags used to define HTML headings (default: 166%). |
content_color | Colour of the object's content (default: #a72925). |
Note that these arguments must all be of class character and follow standard CSS syntax.
For exhaustive CSS styling you can provide a custom CSS file for argument css.file.
CSS styling can be turned of using css = FALSE.
This function requires the R packages 'rmarkdown', 'pander' and 'rstudioapi'.
0.1.5
## Not run: ## Example: RLum.Results ---- # load example data data("ExampleData.DeValues") # apply the MAM-3 age model and save results mam <- calc_MinDose(ExampleData.DeValues$CA1, sigmab = 0.2) # create the HTML report report_RLum(object = mam, file = "~/CA1_MAM.Rmd", timestamp = FALSE, title = "MAM-3 for sample CA1") # when creating a report the input file is automatically saved to a # .Rds file (see saveRDS()). mam_report <- readRDS("~/CA1_MAM.Rds") all.equal(mam, mam_report) ## Example: Temporary file & Viewer/Browser ---- # (a) # Specifying a filename is not necessarily required. If no filename is provided, # the report is rendered in a temporary file. If you use the RStudio IDE, the # temporary report is shown in the interactive Viewer pane. report_RLum(object = mam) # (b) # Additionally, you can view the HTML report in your system's default web browser. report_RLum(object = mam, launch.browser = TRUE) ## Example: RLum.Analysis ---- data("ExampleData.RLum.Analysis") # create the HTML report (note that specifying a file # extension is not necessary) report_RLum(object = IRSAR.RF.Data, file = "~/IRSAR_RF") ## Example: RLum.Data.Curve ---- data.curve <- get_RLum(IRSAR.RF.Data)[[1]] # create the HTML report report_RLum(object = data.curve, file = "~/Data_Curve") ## Example: Any other object ---- x <- list(x = 1:10, y = runif(10, -5, 5), z = data.frame(a = LETTERS[1:20], b = dnorm(0:9)), NA) report_RLum(object = x, file = "~/arbitray_list") ## End(Not run)
rmarkdown::render , pander::pander_return , pander::openFileInOS , rstudioapi::viewer , browseURL
Christoph Burow, University of Cologne (Germany), Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
, RLum Developer Team
Burow, C., Kreutzer, S., 2025. report_RLum(): Create a HTML-report for (RLum) objects. Function version 0.1.5. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., Colombo, M., Steinbuch, L., Boer, A.d., 2025. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 1.0.1. https://r-lum.github.io/Luminescence/