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 |
---|---|
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 |
timestamp | logical (with default):
|
show_report | logical (with default): If set to |
launch.browser | logical (with default):
|
css.file | character (optional): Path to a CSS file to change the default styling of the HTML document. |
quiet | logical (with default):
|
clean | logical (with default):
|
... | 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'.
0.1.3
Christoph Burow, University of Cologne (Germany),
Sebastian Kreutzer, Geography & Earth Sciences, Aberystwyth University (United Kingdom)
, RLum Developer Team
Burow, C., Kreutzer, S., 2021. report_RLum(): Create a HTML-report for (RLum) objects. Function version 0.1.3. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., 2021. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.11. https://CRAN.R-project.org/package=Luminescence
if (FALSE) { ## 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") }