calc_EED_Model()
models incomplete and heterogeneous bleaching of
mobile grains after Guibert et al. (2017). Along with the function,
the new ExampleData.MortarData
data set was added.
fit_DoseResponseCurve()
and plot_DoseResponseCurve()
are two new
functions derived from plot_GrowthCurve()
: the first only performs
the fitting of a dose-response curve, while the second plots it. This
brings greater flexibility and increased speed, as plotting is now
independent of fitting (#141, fixed in #318).
melt_RLum()
: Creates a new flat data.frame
from the objects that
can be used for instance in combination with 'ggplot2'
. Works only
on RLum.Data.Curve-class
and RLum.Analysis-class
objects and lists
of such objects.
merge_RLum.Data.Spectrum()
: This new function allows to merge two or
more RLum.Data.Spectrum
objects in different ways (#368, fixed in
#419).
add_metadata()
, rename_metadata()
, replace_metadata()
: These
function allow to manipulate the metadata of Risoe.BINfileData
,
RLum.Analysis
and RLum.Data
objects (#480, fixed in #514, #524,
#525, #527, #534, #545).
view()
: Provides a shortcut to the utils::View()
spreadsheet-like
data viewer tailored to the objects in the package (#489, fixed in
#490).
We have dropped our dependency on the readxl
package: functions
analyse_baSAR()
and use_DRAC()
now do not accept XLS files anymore
but CSV files instead (#237, fixed in #270). CSV files can be easily
generated from XLS files by Excel or similar applications, or by
reading them with readxl::read_excel()
and saving them with
write.csv()
.
The plot.single
option, which was available for several functions,
sometimes under a slightly different name, has now been renamed to
plot_singlePanels
for overall consistency and clarity. Function
scale_GammaDose()
used that option but gave it the opposite meaning:
now also this function conforms to the rest of the package. The use of
the older names is now deprecated and will produce a warning (#351,
fixed in #408).
The NumberIterations.MC
option of plot_GrowthCurve()
has now been
renamed to n.MC
for consistency with other functions. Potentially
affected are also analyse_Al2O3C_ITC()
, analyse_baSAR()
,
analyse_SAR.CWOSL()
, analyse_SAR.TL()
, calc_Huntley2006()
,
calc_Lamothe2003()
, as they may pass that option
plot_GrowthCurve()
via their ...
argument. The use of the older
name is now deprecated and will produce a warning (#546, fixed in
#547).
Function Analyse_SAR.OSLdata()
is now officially deprecated,
analyse_SAR.CWOSL()
should be used instead (#216, fixed in #264).
Functions CW2pHMi()
, CW2pLM()
, CW2pLMi()
and CW2pPMi()
have
been renamed to convert_CW2pHMi()
, convert_CW2pLM()
,
convert_CW2pLMi()
and convert_CW2pPMi()
, respectively. The use of
the older names is now deprecated and will produce a warning (#499,
fixed in #503).
Function Second2Gray()
has been renamed to convert_Second2Gray()
(#498, fixed in #500).
Function PSL2Risoe.BINfileData()
has been renamed to
convert_PSL2Risoe.BINfileData()
(#555, fixed in #556).
’vdiffr’
as dependency in suggests
. The
package enables us to automatically verify the consistency of plot
outputs generated by package functions against reference figures
captured earlier. Although this new dependency does not have any
user-visible impact, it becomes necessary (means already installed)
when building ’Luminescence’
from source. The primary advantage lies
in the developer’s domain, as it ensures that modifications to
functions do not inadvertently alter plot outputs.analyse_Al2O3C_CrossTalk()
recordType
is specified
and none of the records in the data set is of that type (#487, fixed
in #488).analyse_baSAR()
XLS_file
has been replaced by CSV_file
and, as mentioned
above, the function now only accepts CSV files as input (#237, fixed
in #270).recordType
passed to get_RLum
in the additional
arguments.plot.single
has been renamed to plot_singlePanels
(#351,
fixed in #408).Risoe.BINFileData-class
object was
provided with and the argument irradiation_times
was set; fixed.variable.names
within the method_control
argument (#521, fixed in
#522).analyse_SAR.CWOSL()
NULL
for various
reasons (e.g., unsuitable set of curves). Here the self-call attempted
to extract information from the results that did not exist in the
first place instead of returning NULL
; fixed.RLum.Results
object now also contains a column for the
grain (#553, fixed in #554).analyse_FadingMeasurement()
RLum.Analysis
object given as input, and reports a
message if a version older than 5 was used (#281, fixed in #282).RLum.Analysis
input files
(#283, fixed in #288).plot.single
has been renamed to plot_singlePanels
(#351,
fixed in #408).analyse_IRSAR.RF()
num_slide_windows
setting (part of the method.control
option), thus allowing to find a
balance between computation time and quality of fit (#372, fixed in
#388, #398 and #399).sequence_structure
misspecifications (#393, fixed in #394).method = "VSLIDE"
(#396, fixed in #397).method.control
has been renamed to method_control
for
consistency with all other functions in the package (#411, fixed in
#412).analyse_pIRIRSequence()
plot.single
has been renamed to plot_singlePanels
(#351,
fixed in #408).RLum.Results
object now also contains a column for the
grain (#553, fixed in #554).analyse_SAR.CWOSL()
plot.single
has been renamed to plot_singlePanels
(#351,
fixed in #408).apply_CosmicRayRamoval()
smooth_RLum
that
can be passed as new argument for method
.calc_AverageDose()
calc_CentralDose()
na.rm
is now deprecated: the function will now always
remove missing values, as otherwise the presence of any NA
would
propagate and produce unusable results (all NA
s) or buggy behaviour
(#302, fixed in #304).sigma < 1e-16
, as allowing
sigma
to become zero leads to infinities and buggy behaviour (also
fixed in #304).calc_FastRatio()
calc_gSGC()
calc_Huntley2006()
rprime
vector that is used
in the calculation of the natural dose response and the field
saturation, so that more points are concentrated in the bulk of the
distribution: this previously depended incorrectly on the number of
Monte Carlo iterations requested, so this change brings an additional
speed boost. The default setting can be overridden via the rprime
argument (#258, fixed in #541 and #542).mode = "extrapolation"
, which made it harder to see where it
extrapolated to (#551, fixed in #552; thanks to @SalOehl for
reporting).calc_IEU()
calc_Lamothe2003()
Ln/Tn
error after fading correction, which led to smaller than
expected errors (#96, fixed in #296).convert_RLum2Risoe.BINFileData()
incompatible types (from raw to character)
error under particular
circumstances; fixed.METADATA
are already available,
however, in the wrong format; fixedextract_IrradiationTimes()
startDate
was missing an in the irradiation
curve the function crashed unexpectedly; fixed.fit_CWCurve()
confint()
failed. This has now been fixed, and in cases of
failures we report the error message received from confint()
(#509,
fixed in #510).get_RLum()
get_RLum()
with subset
was used on info objects of an
RLum.Analysis-class
object it would return wrong results if the info
element was not present in all records; fixed.import_Data()
character
vector
of length > 1 as input (e.g., different file names). Further, the
function got tested against a mixture of input formats. Means, you can
provide many different files formats and they function will try to
import them all in one go.plot_AbanicoPlot()
z.log = TRUE
(the default); fixed.tcl
and tck
arguments via ...
, they were
never used internally.plot_DetPlot()
plot_DRTResults()
na.rm
was used alongside the
preheat
option but the data set contained no missing values (#474,
fixed in #475).plot_GrowthCurve()
fit_DoseResponseCurve()
and plot_DoseResponseCurve()
. There should
be no visible user-facing changes (#319, fixed in #322)....
arguments for plotting (implementation in
plot_DoseResponseCurve()
) for legend
(turn on/off legend) and
reg_points_pch
for fine grained control over the point shape.density_polygon
, density_pologyon_col
, density_rug
, box
as
...
arguments to plot and add respective plot optionsNaN
values during log conversions required for estimating the
start parameters. The result was the error object 'b.MC' not found
(#374; fixed)fit.method
("EXP+LIN"
, "EXP+EXP"
,
"GOK"
and "LambertW"
), the function could get stuck in an endless
loop when the number of parameters was larger than or equal to the
number of data points. This is now checked, and in those cases the
method is changed to "LIN"
(#381, fixed in #465).nls()
with minpack.lm::nlsLM()
as it’s more robust and
can find a fit in cases where nls()
would fail. Please keep in mind
that it does not mean that fit results in those cases make any sense,
it just helps to avoid uncontained events in the R session (addresses
#381).output.plotExtended.single
has been renamed to
plot_singlePanels
(#351, fixed in #408).RLum.Results
as output (#405, fixed in #434).fit.method = "QDR"
and mode = "extrapolation"
(#504, fixed
in #505).NumberIterations.MC
has been renamed to n.MC
(#546, fixed
in #547).plot_RLum.Analysis()
plot_RLum.Data.Curve()
norm
is now better validated so that specifying an
incorrect value returns an error instead of silently skipping curve
normalisation (#250, fixed in #263).plot_RLum.Data.Spectrum()
plot.type = "persp"
is now more
consistent and doesn’t produce artefacts in the regions of transition
between colours (#371, fixed in #380).bin.rows
or bin.cols
value was set
too high or if xlim
and ylim
were set too tight (#415, fixed in
#416).read_BIN2R()
n.records
is now better supported for BIN files v3 and v4
and doesn’t lead to a crash when used in conjunction with the
fastForward
option (#343, fixed in #344).zero_data.rm
was not correctly propagated if the input
object was provided as a list (#342, fixed in #345).METADATA
fields that are not actually read from the BINX file in
case of a ROI record are now set to NA
rather than being assigned
the value from the previous record (#336, fixed in #360)..RESERVED
slot is now kept in sync with the rest of the object
when records are dropped from the input BIN/BINX file (#337, fixed in
#348).fastForward = TRUE
(#356, fixed in #360).read_HeliosOSL2R()
read_XSYG2R()
n_records
argument now enables to control the number of
records to import, which can be useful in case the file is faulty.scale_GammaDose()
plot_single
has been renamed to plot_singlePanels
and was
changed so that plot_singlePanels = TRUE
will produce one plot per
panel, as it would happen for other functions (#351, fixed in #408).template_DRAC()
file_input
that enables the
creating of a DRAC template based on an existing DRAC CSV file. This
way, already available DRAC files can be conveniently modified without
having to call use_DRAC()
first.Cresswelletal2018
). Please ensure that the server
supports that option.trim_RLum.Data()
trim_range
argument that could lead to crashes (#460, fixed in
#461).use_DRAC()
...
arguments:
version_ignore
to ignore the DRAC version check, user
and
password
to access password protected websites.verify_SingleGrainData()
cleanup = TRUE
the result was
not consistent and produced a mixture of RLum.Results
and
RLum.Analysis
/Risoe.BINFileData
objects in particular when run
over a list, this was not what stated in the manual. Now the function
indeed cleans up the object, hence if a list of RLum.Analysis
objects is provided, the result is a cleaned list of that object. If
the clean-up means that the everything was removed, the result is
NULL
. * Improve warning messages; it was indeed not very
intelligible.cleanup = TRUE
.use_fft
that will apply an additional
Fast Discrete Fourier Transform (FFT) verification on the data if
wanted.write_R2BIN()
verbose
argument, which can be used to
suppress output to the terminal (#442, fixed in #444).get_DRAC_references()
now works also on a DRAC.list
got updated
references.