analyse_baSAR(): Function to allow the application of Bayesian models (baSAR) on luminescence data
based on the contribution by Combes et al. (2015)
app_RLum(): Wrapper for the function
app_RLum() from the package
RLumShiny by Christoph Burow
bin_RLum.Data: Function for binning in
RLum.Data objects, e.g., binning of
calc_FastRatio(): Function to calculate the fast ratio of CW-OSL
curves after Durcan & Duller (2011)
calc_ThermalLifetime(): Function to calculate thermal lifetimes and their errors of a charge
using the Arrhenius equation
model_LuminescenceSignals(): Wrapper for the function
from the package
RLumModel by Johannes Friedrich, Sebastian Kreutzer and Christoph Schmidt
plot_DetPlot(): Plots the equivalent dose (De) in dependency of the chosen
signal integral (cf. Bailey et al., 2003; #23).
report_RLum(): Function to create a HTML report of RLum objects (or any other), containing
the complete structure and content of the provided object. Requires the packages 'rmarkdown' and 'pander'.
verify_SingleGrainData(): Verify single grain data sets and check for invalid grains, i.e. zero light level grains
set_RLum() gained the new argument
.uid which is by default
presetting the slot with the same name using the internal function
In the previous package version this slot of the RLum-object was filled automatically as well,
but the way it was done was a little bit semitransparent and a different function was used,
the performance of the function was improved significantly.
RLum.Results objects updated, so that
they can handle the new info slot,
RLum.Data.Curve objects new reacts more relaxed for wrong info
object names. Instead of a function error,
NULL is returned. This makes handling
in loops easier,
the function crashed under very rare circumstances if a provided list with RLum-objects
RLum.Analysis objects with zero records; corrected.
The method gained a
... argument for further passing information to the specific
The method for the class
RLum.Analysis gained the new argument
to extent the returned data frame to all info elements. This makes it possible to investigate
RLum.Analysis objects in great detail and subset them efficiently.
.uid from objects of this class has now the prototype
The unique id is only set if the corresponding
set_RLum function is called, which should be,
however, the usual case,
all inherited object classes gained a new slot called
.pid. This slot is reserved
for storing parent ids so that objects can be nested at free will. Corresponding import function
had been adapted in the way the pid will become an inherited uid from the
all inhertied object classes of the class
RLum gained a new slot called
with this a more consistent workflow with the objects should be possible, before only objects
of the class
RLum.Data had such slot.
The function was made an internal function, as this function was used only rarely by users,
but often needed internally. The function and its functionally is still available under its new
name but a lot of integrity checks had been removed from the code, which doubles the
speed when transforming objects, but makes the function failing fast.
Add self call to the function, i.e. as input alternatively now a list of
objects can be provided for a higher efficiency,
the test parameter
intersection_ratio was wrongly calculated; corrected,
correct wrong shift if the option
RF_nat.lim was used,
internal parameter added that allows to show the applied fit, while using
method = "SLIDE",
plot_reduced for a better plot control,
sequence.structure renamed to
support further plot arguments via
method.control = list(trace = TRUE) now shows the control graph as expected for the method
test_parameter renamed to
The function will not stop with an error if no 'OSL' or 'IRSL' record is detected,
NULL and print a warning,
under really rare circumstances, many recycling points and recuperation points the function could crash (fixed).
Fixed a bug in the evaluation of the rejection criteria where the status of the palaedose error criterion was returned as 'OK' even though it was not (Thanks to Annette Kadereit) function could crash (fixed),
add support for testdose error as rejection criteria,
recuperation rate was not shown properely in the rejection criteria plot,
instead of showing failed, the polygon borders are now plotted in red in the rejection criteria plot,
if a list of RLum-objects was provided the rejection criteria could not be change any more fixed (thanks to Andrea Junge),
every rejection criterium now allows the input value
NA, in this case values are calculated,
but not considered as rejection criterium, i.e. the RC.Status will be always
minor graphical adjustments.
silent renamed to
method.Pych.threshold_factor added to have a better control
for the threshold value used for the removal,
MARGIN added to allow the application of the methods along
the wavelength or the time,
set default method to
Fixed a bug in the Monte Carlo Simulation that occured when estimating the number of grains for aliquots with diameters larger than 9.8 mm. The user is, however, now warned that the function assumes common aliquot discs not larger than 9.8 mm when providing larger sample diameters.
Table column headers now have all capital letters,
minor performance improvements,
for very large standard errors uniroot failed, causing a function break; corrected (#270),
if uniroot is not able to solve the equation during the MC runs the function will not stop anymore with an error.
The user is now warned if the final estimate of
mu is larger than
gamma.lower, gamma.upper, sigma.lower, sigma.upper, p0.lower, p0.upper, mu.lower, mu.upper
that can be used to override the default boundary values,
level to allow specifying the required confidence level (defaults to 0.95).
digits introduced to allow direct rounding of the numbers,
sig0 to allow for an extra component of error.
Function now supports the self call mode, i.e. a
objects can be provided as input and the function iterates of this list.
Fix bug that caused a function break if data set contained 0 time values but a
log-scale was wanted; now the
xlim is adjusted and a warning is given.
Support further merge operations:
Fixed a bug where the function failed to get input data from
interactive to produce an interactive plot
notes about consequences of
log.z = TRUE updated,
boxplot option added,
summary keywords homogenised,
if data contain 0 dose values, the values are now positively shifted by 0.01, but only
log.z == TRUE.
If no given dose is provided the horizontal 'ab-lines' (1.0 and +/- 0.1) are no longer plotted,
default value for the argument
given.dose is now
If the input data contain a least one infinite value the function will not crash
any longer, but return
NULL (#263, Norbert Mercier),
check for insufficient values in the data set and return
NULL (before the function crashed),
data frame also exports now error of the D0-values based on the MC runs for the De error,
fit.includingRepeatedRegPoints = FALSE was not respected properly
under all circumstances; corrected,
under rather rare circumstances the function became trapped in an endless mode as the
nls is trapped in such mode if only two points are provided. The minimum
of required data points for
EXP was set to three,
homogenise terminal output.
interactive to produce an interactive plot
Boxplot option added,
Depreciated arguments removed (centrality, dispersion, weights, polygon.col),
Colour specification simplified,
Summary keywords homogenised,
Layout functionality implemented.
... arguments can now be provided as
gain more control of the plot appearance,
abline now works also in combination with
combine = TRUE and
allows to set ablines independently over different plots (#260),
automatic axes labelling improved for
combine = TRUE,
add support for argument
RLum.Data.Curve objects (see
fix minor bug introduced for the acceptence of the argument
Fix seldom bug that causes unexpected function behaviour if
exist as objects on the global environment (#265),
smooth to provide an automatic curve smoothing for plotting based
on a running mean.
matrix as allowed input,
add new argument
limit_counts to further the counts to a maximum value (the value
provided), this might be especially helpful in case of TL spectra,
optical.wavelength.colours was not working in all cases sufficiently; corrected,
minor graphical adjustments,
the 3D plot is now produced using the package
plotly which allows an interactive
visualisation. The new plot type added is called
interactive, the suggestion of the
rgl has been removed with this change.
Fixed a bug where the function failed to get input data from
na.rm got default value
function is now a little bit more robust against odd input values.
Handling of corrupt BIN-files improved, the functions tries to import whatever possible,
n.records was not respected under rare circumstances,
in course of this (corrupt BIN-files, not respected
n.records) the output data frame
was longer than the list of count values; corrected,
in some cases the grain number was not imported correctly; fixed,
minor performance improvements.
Behaviour while using the option
import = TRUE and
fastForward = TRUE
have been improved. If both arguments are combined now only a single data frame with all information
support more arguments in the function self-call mode (argument
file is of type
function gained the new argument
pattern, which can be used to filter imported BIN-files by name,
if the field
FNAME is totally empty in the BIN-file the function files this field with the
name of the BIN-file itself. This can be rather useful in particular cases,
function gained a new argument
zero_data.rm, which is preset to
and removes data with zero data (no count values) errorneously produced during the measurement.
Single grain data had not been converted correctly to
Each grain within a position should represent one
RLum.Analysis object with a set
of curve. This was so far not the case; corrected,
significant performance improvements, especially for big Risoe.BINfileData2RLum.Analysis() objects,
if the argument
grain contains invalid entries the function will
not longer return an error. The invalid values are discarded and the function
tries to import values for valid positions or grains only,
the function gained the new argument
dtype to further limit the converted
data types during the conversion (#269)
version = "06" was a corrupt BINX-file ... fixed.
New internal function
.create_UID() added to create the unique identifier for
RLum-objects. The new function reduces significantly the overhead while producing the objects.
Package 'digits' removed from the dependency list and the functionality (creating a unique identifier for RLum-objects) was implemented using a self-written function.
Package 'rgl' was removed from suggests and replaced by the package 'plotly'.
Package 'RLumModel' added as suggested package.
Package 'RLumShiny' added as suggested package.
Package 'rmarkdown' added as suggested package.
Package 'pander' added as suggested package.
Package 'rstudioapi' added as suggested package.
Package 'rjags' added as suggested package.
New S3 generic
bin implemented, this method dispatches to the S4 method
bin_RLum.Data for the
Add S3 generics to support all combinations for the function
Add S3 generic for method
subset of objects of type
This is a little bit inconsistent, however, still a lot of users are using this object created
by the function
read_BIN2R(..., fastForward = FALSE) and this new method (subset)
tremendously simplifies the work with this object.