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,
...
)(required):
The object to be reported on, preferably of any RLum-class.
character (with default): A character string naming the output file. If no filename is provided a temporary file is created.
character (with default): A character string specifying the title of the document.
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.
logical (with default):
TRUE to add a timestamp to the filename (suffix).
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.
logical (with default):
TRUE to open the HTML file in the system's default web browser after
it has been rendered.
character (optional): Path to a CSS file to change the default styling of the HTML document.
logical (with default):
TRUE to suppress printing of the pandoc command line.
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'.
0.1.4
Burow, C., Kreutzer, S., 2023. report_RLum(): Create a HTML-report for (RLum) objects. Function version 0.1.4. 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., 2023. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.23. 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")
}