Insert a section on the calculation of the equivalent dose for a given set
of input files. Use this function within a code chunk and make sure to set
the chunk option results = 'asis'.
report_DE(files, title = "Equivalent dose estimation",
title.suffix = "", natural = c(1, 2), natural.comment, dose,
meta = NULL, settings = NULL, fit.repeated = FALSE,
sample.weight = NULL, interval, th = 10, model = "EXP",
amplitudes = NULL, spike = NULL, bootstrap = TRUE,
delim = "\\newpage", ...)
Arguments
| files |
character (required):
file path or directory where the spectra files are stored.
|
| title |
character (optional):
Main title of the section (defaults to 'Equivalent dose estimation').
|
| title.suffix |
character (optional):
Optional text to appear in brackets after the title. Useful if the report
contains multiple DE measurements.
|
| natural |
numeric (optional):
Optional vector of integer values specifying which of the spectra are
repeated natural dose measurements (defaults to c(1, 2)).
|
| natural.comment |
character (optional):
An optional comment on the natural dose. Defaults to the statement that
repeated natural dose measurements were done first and last in the
measurement series.
|
| dose |
character or numeric (required):
Either a file path to a text file containing the irradiation doses or a numeric
vector.
|
| meta |
list (required): A named list with
information on the following elements given in .meta.
Consider using .meta as a constructor.
|
| settings |
list (required): A named list with
information on the following elements given in .settings.
Consider using .settings as a constructor.
|
| fit.repeated |
logical (optional):
Whether a repeated zero-dose measurement should be considered
for fitting or not. If `TRUE` all repeated zero-dose measurements (indicated by
argument `natural`) are removed from the data set before fitting.
|
| sample.weight |
character or numeric (optional):
Either a file path to a text file containing the sample weights or a numeric
vector.
|
| interval |
numeric (required):
A vector of length two specifying the range of x-values where peaks are searched
|
| th |
numeric (optional):
An integer specifying the number of neighbouring values to compare each x-value to.
|
| model |
character (required):
Currently implemented models: single-saturating exponential ("EXP"), linear ("LIN").
|
| amplitudes |
numeric (optional):
A numeric vector of signal amplitudes. If provided, automatic peak finding and
amplitude calculation is skipped.
|
| spike |
character (optional):
Path to a single file of a spike ESR spectrum. The amplitude of the spike
signal will be subtracted from all other amplitudes (default TRUE).
|
| bootstrap |
logical (optional):
Include calculation of the equivalent dose using a bootstrap approach.
|
| delim |
character (required): Keyword specifying
the delimiter insterted before the section. Usually "<br>" or "<hr>"
for HTML and "\\newpage" for PDF reports.
|
| ... |
further arguments passed to fit_DRC,
calc_DePlateau and read_Spectrum. |
Value
Text output via cat.
A [list] with all intermediate and final results useful for debugging.
Examples
# not available yet