NEWS | R Documentation |
calc_CentralDose()
: fixed an error that occurred when
output.plot = FALSE
(#106, reported by Peter Dobak)
analyse_SAR.CWOSL()
: fixed an error that forced a chrash if no
information in the irradiation time was found in the measurement data
plot_GrowthCurve()
:
Fixed an error that forced a chrash when 'par.default' was
not found (for option output.plotExtended = FALSE
),
confusing vector label for De '(intercept)' occurred when using
fit.method = "LIN"
removed (#117, reported by Thomas Kolb),
direct argument xlab
removed, but it can still be used
via the ...
argument,
support ylim
and xlim
for the growth curve via
the ...
argument,
remove some minor output errors (mostly due to negative values),
prevent function chrash for rare cases using fit.method = "LIN"
where the Lx/Tx error become negative (#118, reported by Thomas Kolb).
apply_CosmicRayRemoval()
:
Optional argument method.Pych.histogram.plot
added to provide a graphical feedback of the removal process,
terminal output providing the number of recognised channels effected by cosmic-rays per frame has been added. (#113 requested by Johanna Lomax),
argument silent
added to suppress terminal output.
calc_FiniteMixture()
: fixed a bug when plotting (layout removed, #114)
plot_KDE()
: calculation of median corrected
plot_RadialPlot()
:
Tick positions for +/- 2 option corrected (#109),
option to handle negative values reduced to 'removed'.
plot_AbanicoPlot()
:
Overplotting of plot outline fixed,
tick positions for +/- 2 option corrected (#109),
transparency for 2-sigma-bar added (#108),
option to handle negative values disabled.
readXSYG2R()
: Corrected for NA
values appearing rarely during
TL curve recalculation.
The PDF with the S4-class object structure has not been linked properly. Fixed by using a self generated HTML index file.
plot_AbanicoPlot()
: New function for standard De distribution plots
plot_DRTResults()
: New function to visualise dose recovery test results
calc_Statistics()
: New function to calculate De/Age/Distribution
statistics that are often used by functions in the package
apply_CosmicRayRemoval()
: New function to remove cosmic rays in
RLum.Data.Spectrum
objects (#80)
apply_EfficiencyCorrection()
: New function to allow spectral efficiency corrections
on RLum.Data.Spectrum
objects using a given spectral response data set for the used system
ExampleData.XSYG
: SAR measurement and TL spectrum imported
from a Freiberg Instruments XSYG file.
RLum
classes and methodsget_RLum.Analysis()
: Add argument keep.object
to allow
returing an RLum.Analysis
object instead of single records when using
the method. For the sake of consistency with previous examples the default
option is keep.object = FALSE
get_RLum.Analysis()
: In cases for that the output contains only one
element the element is returned as non-list element (no list is returned)
calc_OSLLxTxRatio()
: Considering the case that the number of backround intergral
channels is smaller than the number for signal integral channels by implementing
suggestions from Rex Galbraith (2014) (#78, reported by Alexandra Rowell).
calc_OSLLxTxRatio()
: Add preset argument background.count.distribution
calc_OSLLxTxRatio()
: Add optional argument sigmab
and extend value
output
plot_RLum.Analysis()
: Pass col
argument to the plot
calc_FiniteMixture()
: The n.components
argument
now accepts vectors in the form of c(min:max)
to calculate the finite mixtures while increasing stepwise the number of
k components to be fitted
calc_FiniteMixture()
: Added plot output when a vector is provided for
n.components
calc_FiniteMixture()
: Evaluation of BIC scores and maximum
log-likelihoods estimates when a vector is provided for n.components
calc_FiniteMixture()
:Tolerance increased when solving the covariance matrix from
$double.eps (~10^-16) to $double.xmin (~10^-308)
calc_FiniteMixture()
: New examples added
analyse_IRSAR.RF()
: Correct an error that occurred when NaN
are produced during De calculation
analyse_IRSAR.RF()
: Implement automatic predefined
curve
removal from the RLum.Analysis
input object for data imported
from XSYG files
analyse_IRSAR.RF()
: Add limitation of points used for
natural signal calculation by using fit.range.min
analyse_IRSAR.RF()
: Correct an error for the case that a fitting
could not be applied
analyse_SAR.CWOSL()
: Add support for palaeodose error
as rejection criteria
Risoe.BINfileData2RLum.Analysis()
: Setting of arguments run
,
set
and ltype
had no effect: Corrected (#87, reported by Thomas Kolb).
plot_Histogram()
: Add summary options and y-limits
plot_Histogram()
: Fix odd plotting (#89)
plot_KDE()
: Fix bug for using multiple datasets. KDE can now
calculated with error-weights; however per default set to FALSE
as
it will be a PD plot otherwise
plot_KDE()
: Add argument values.cumulative
to show
cummulative values individually (#88)
plot_KDE()
, plot_Histogram
, plot_RadialPlot
: flexible
placement of statistical summary and legend added
plot_RLum.Data.Spectrum()
: Add plot type single
to
allow single curve output and optimise code
plot_RLum.Data.Spectrum()
: Add arguments for horizontal
(bin.rows
) and vertical binning (bin.cols
)
plot_RLum.Data.Spectrum()
: Add argument bg.channels
to allow the specification of background channels that are subtracted from
the other channels.
plot_RLum.Data.Spectrum()
: Correct an error that occurred if no xlab or
ylab information are provided
plot_RLum.Data.Spectrum()
: Add new plot option mutiple.lines
,
allowing to draw all frames in one plot
plot_GrowthCurve()
: Correct mtext
behaviour as expected
(#91)
plot_GrowthCurve()
: Now resets global par
parameter
after plotting
plot_RadialPlot()
: Provide note on polygone behaviour (#90)
plot_RadialPlot()
: Correct 2-sigma label plotting (#92)
plot_RadialPlot()
: Some minor graphical adjustments
merge_Risoe.BINfileData()
: New argument added
position.number.append.gap
allowing to account for a specific
position number structure within the data sets (#94, requested by
Thomas Kolb)
merge_Risoe.BINfileData()
: Correct an error that occured
for merging more than two BIN-files (#93, reported by Thomas Kolb)
readXSYG2R()
: Rewritten TL curve recalculation routine;
argument recalculate.TL.curves
set now to TRUE
by default.
(#86)
calc_FuchsLang2001()
: Function now allows RLum.Results
object
as input and returns an RLum.Results
object.
calc_FuchsLang2001()
: Now supports the ...
argument.
The arguments cex.global
, main
, xlab
, sample.mtext
have been therefore removed.
calc_AliquotSize()
: added the option to estimate the
amount of grains on an aliquot by monte carlo simulation; implement RLum.Results
object handling (output)
calc_MaxDose3()
: removed the option to print results to a file
calc_MinDose3()
: removed the option to print results to a file
calc_MinDose4()
: removed the option to print results to a file
calc_CosmicDoseRate()
: Implement RLum.Results
object handling (output)
fit_CWCurve()
: Now uses package colour library and par
settings will
be reset after plotting
fit_LMCurve()
: Now uses package colour library and par
settings will
be reset after plotting
calc_OSLLxTxRatio
: Correct critical error that calculates
the Lx/Tx ratio without background subtraction since version 0.3. This
error had been fixed previously (version 0.2.2), however, it had been accidentally
reintroduced with version 0.3. (#82)
analyse_SAR.TL
: Added option "EXCLUDE"
in the argument sequence.structure
to support exclusion of TL curves
(this fixes #27)
calc_TLLxTxRatio
: Added NULL
object support for background
curves
fit_LMCurve
: Extent component.contribution.matrix
to allow
calculation of absolute contributions to sum signal of each component (#67)
fit_CWCurve
: Extent component.contribution.matrix
to allow
calculation of absolute contributions to sum signal of each component (#67)
CW2pHMi
: Implement a warning message when NA
values are produced
by the function approx
are deteted (#8)
CW2pHMi
: Remove unwanted data output accidentally introduced during
bug fixing
plot_RadialPlot
: added parameters: line, line.col,
line.label, centrality, negatives
plot_RadialPlot
: robust coding of x-axes labels
plot_RadialPlot
: major bug fixed: polygon ends now at
highest data value, not at z-axis
plot_RadialPlot
: z-axis now scales with user-defined x-axis limits
plot_RadialPlot
: axes lengths when user-define
plot_RadialPlot
: some minor tweaks for code and plot polishing
plot_GrowthCurve
: prevent rare error occured during MC simulation for EXP+LIN error estimation
plot_RLum
: fix error for passing RLum.Data.Spectrum
objects
analyse_SAR.CWOSL
: add argument dose.points
calc_CosmicDoseRate
: remove unwanted terminal output
Added S4-class RLum.Data.Spectrum
for TL/OSL spectra.
set_RLum.Data.Spectrum()
: Constructor method for
RLum.Data.Spectrum
objects
merge_RLum.Results()
: Correct an error that results in a false
combination of list elements
get_Risoe.BINfileData()
: get-method has been added formally.
In fact it does not allow a direct access, but is showing
a message.
get_RLum.Analysis()
: Added argument curveType
to method.
get_RLum.Analysis()
: Allow more flexibility using the argument
recordType
to method.
get_RLum.Analysis()
: Added argument RLum.type
to method.
RLum.Results()
: Add generic show method (#68)
RLum.Data.Curve()
: get-method for object class has been added (#57)
plot_RLum.Data.Spectrum()
: Plot function for corresponding
S4-class object
length_RLum.Analyis()
: Return length (i.e. number of records) for
RLum.Analysis
objects
calc_MaxDose3()
: Apply the maximum age model to a given De distribution
(#45, suggestion by Kathryn Fitzsimmons)
calc_MinDose3()
: Graphical output has been changed from
postscript to display device output; output.plot = TRUE
as default
calc_MinDose3()
: Implement RLum.Results
object
handling (input/output)
calc_MinDose4()
: Graphical output has been changed from
postscript to display device output; output.plot = TRUE
as default
calc_MinDose4()
: Implement RLum.Results
object
handling (input/output)
calc_CommonDose()
: Implement RLum.Results
object handling (input/output)
calc_FiniteMixture()
: Implement RLum.Results
object handling (input/output)
calc_HomogenityTest()
: Implement RLum.Results
object handling (input/output)
calc_CentralDose()
: Implement RLum.Results
object handling (input/output)
calc_CentralDose()
: Now working with data sets with no overdispersion (#65)
plot_KDE()
: Option na.exclude
did not work as expected and ended up with an error message; corrected
plot_KDE()
: Add statistic paramter for kurtosis and skewness
for the argument summary
plot_KDE()
: Add argument output
plot_KDE()
: Add output values summary.pos
plot_KDE()
: Now allows keywords for summary.pos
, e.g. 'topleft'
plot_RLum.Analysis()
: log
argument will now be passed to the output plot
plot_GrowthCurve()
: Now an additional Formula
object containing the equation used
for fitting is provided with the output.
analyse_SAR.CWOSL()
: Argument output.plot.single
added to allow for separate plot outputs
plot_RadialPlot
: Function has been completely new written
readXSYG2R
: Add support for TL/OSL spectra has been added by using RLum.Data.Spectrum
objects
plot_RLum
: Add support for RLum.Data.Spectrum
plot_RLum.Analysis
: Add support for RLum.Data.Spectrum
plot_RLum.Data.Curve
: Forward further plot arguments, like lwd
.
pch
, lty
readXSYG2R
: Considerably import performance improvements by using the argument useInternalNodes = TRUE
during XML parsing
readXSYG2R
: Add argument recalculate.TL.curves
to allow temperature
values instead of time values in the x-axis for TL curves; along with this option
the heating rate will be calculated and stored in the info element RATE
plot_RLum.Data.Curve
: Allow for more flexible TL
curve detection
calc_AliquotSize()
: Fix return values (#66)
calc_CosmicDoseRate()
: Fitting procedure for the soft-component optimised (#75)
calc_CosmicDoseRate()
: Erroneous estimation of parameters F, J and H fixed. Non-linear parts now fitted with a 3-degree polynomial (#76)
calc_CosmicDoseRate()
: Conversion from geographic to geomagnetic latitude fixed (#71)
fit_LMCurve()
: Correct for an error in the plotting of the component
to sum contribution
fit_CWCurve()
: Correct for an error in the plotting of the component
to sum contribution
fit_CWCurve()
: Improve convergence stability during fitting by using
a two step fitting approach; add comment that the functions has beta status
fit_CWCurve()
: Correct for an error, for component signal
plotting (#77)
calc_OSLLxTxRatio
: Add error message for the case signal integral > background integral
ExampleData.RLum.Analysis
: data set has been replaced, as the containing curve elements did not fit the changed RLum.Data.Curve
object
Complete conversion to inlinedoc
documentation for the entire
package
Allow more fun during plotting.
The most substantial changes in this package version are introduced by the usage of S4 objects. Inherited classes have been designed to store input and output data for luminescence dating data analysis. Most of the existing functions now allow RLum objects as input data along with generic R objects. The S4-class structure in this package is shown in the additional PDF provided with this package. The following S4 object classes are implemented:
RLum
(virtual class)
RLum.Data
(virtual class)
RLum.Data.Curve
(object containing one measured curve)
RLum.Analysis
(contains RLum.Data (e.g. RLum.Data.Curve) objects for protocol analysis)
RLum.Results
(contains output of package functions)
set_RLum.Data.Curve()
: Constructor method for RLum.Data.Curve
objects
set_RLum.Analysis()
: Constructor method for RLum.Analysis
objects
get_RLum.Analyis()
: Accessor method for RLum.Analysis
objects
set_RLum.Results()
: Constructor method for RLum.Results
objects
get_RLum.Results()
: Accessor method for RLum.Results
objects
merge_RLum.Results()
: Function to merge RLum.Results
objects
get_structure.RLum.Analysis()
: to parse the structure of an RLum.Analysis
object
set_Risoe.BINfileData()
: Constructor method for Risoe.BINfileData
objects
plot_RLum()
: Wrapper function for plotting various RLum
-objects
plot_RLum.Data.Curve()
: Plot function for RLum.Data.Curve
objects. Usually accessed by plot_RLum()
plot_RLum.Analysis()
: Plot function for RLum.Analysis
objects. Usually accessed by plot_RLum()
Risoe.BINfileData2RLum.Analysis()
: Converts parts of an Risoe.BINfileData
object to an RLum.Analysis
object, depending on the chosen position, run/set or record id.
Risoe.BINfileData2RLum.Data.Curve()
: Lossy conversion of an Risoe.BINfileData
object to an RLum.Data.Curve
object
writeR2BIN()
: Function to export Risoe.BINfileData
objects to BIN or BINX files
merge_Risoe.BINfileData()
: Merge BIN/BINX files or Risoe.BINfileData
objects
analyse_SAR.CWOSL()
: Function to analyse SAR CW-OSL measurements, will at some time replace the exisiting function Analyse_SAR.OSLdata
analyse_SAR.TL()
: Function to analyse SAR TL measurements (beta version)
calc_TLLxTxRatio()
: Function to calculate Lx/Tx ratios for TL curves used by analyse_SAR.TL()
(beta version)
analyse_IRSAR.RF()
: Function to analyse IRSAR RF measurements according to Erfurt et al. (2003)
calc_CosmicDoseRate()
: Function to calculate the cosmic dose rate
calc_HomogeneityTest()
: Function to apply the homogenity test after Galbraith (2003)
calc_AliquotSize()
: Function to estimate the amount of grains on an aliquot
readXSYG2R()
: Function to support the Freiberg Instruments XSYG file format
ExampleData.RLum.Analysis
: Luminescence dating measurement dataset as RLum.Analysis
object
BaseDataSet.CosmicDoseRate
: Data set used by the function calc_CosmicDoseRate()
ExampleData.BINfileData
: dataset now contains two objects CWOSL.SAR.Data
and TL.SAR.Data
(depending examples have been modified)
Calc_OSLLxTxRatio()
: Function renamed to calc_OSLLxTxRatio()
Calc_CommonDose()
: Function renamed to calc_CommonDose()
Calc_CentralDose()
: Function renamed to calc_CentralDose()
Calc_FiniteMixture()
: Function renamed to calc_FiniteMixture()
Calc_MinDose3()
: Function renamed to calc_MinDose3()
Calc_MinDose4()
: Function renamed to calc_MinDose4()
Calc_FadingCorr()
: Function renamed to calc_FadingCorr()
Calc_FuchsLang2001()
: Function renamed to calc_FuchsLang2001()
plot_BINfileData()
: Function renamed to plot_Risoe.BINfileData()
for the sake of consistency
calc_OSLLxTxRatio()
: Function now allows for a matrix
as input object
calc_OSLLxTxRatio()
: Function now returns an RLum.Results
object
Analyse_SAR.OSLdata()
: Function modified according to the changes in the function calc_OSLLxTxRatio()
Analyse_SAR.OSLdata()
: Function corrected for an error that occured with more than one recyling point
Analyse_SAR.OSLdata()
: Function corrected for an error that occured when the dose of the first recycling point was used twice
Risoe.BINfileData-class
: An error in the show method has been corrected
plot_GrowthCurve()
: An error occurred if no fitting could be applied. Corrected by setting De to NA
plot_GrowthCurve()
: The function now checks if at least two regeneration points are given
plot_GrowthCurve()
: Function corrected for an infinite loop error occured using only two dose points and the EXP fit option
plot_GrowthCurve()
: The function now provides an extra argument na.exclude
to exclude NA
values
plot_KDE()
: The function now provides an extra argument na.exclude
to exclude NA
values
plot_KDE()
: The function now allows for an RLum.Results
object as input object
plot_KDE()
: The function now allows for plotting multiple data sets
plot_Histogram()
: The function now provides an extra argument na.exclude
to exclude NA
values
plot_Histogram()
: The function now allows for an RLum.Results
object as input object
plot_RadialPlot()
: The function now provides an extra argument na.exclude
to exclude NA
values
CW2pLMi()
: A test has been implemented to check if P=0 (which is not allowed)
CW2pLMi()
: Now an RLum.Data.Curve
object is allowed as input and an object of the same data type as the input will be returned
CW2pHMi()
: Now an RLum.Data.Curve
object is allowed as input and an object of the same data type as the input will be returned
CW2pPMi()
: Now an RLum.Data.Curve
object is allowed as input and an object of the same data type as the input will be returned
CW2pLM()
: Now an RLum.Data.Curve
object is allowed as input and an object of the same data type as the input will be returned
fit_CWCurve()
: The function now returns an RLum.Results
object and as input an RLum.Data.Curve
object is now allowed
fit_CWCure()
: An additional component.contribution.matrix
is now returned to allow
for individual component to sum contribution plots
fit_CWCure()
: A critical error has been corrected in the used fitting equation. Now it has been set to f(t) = I0[i]*lambda[i]*exp(-lambda[i]*t)
fit_LMCurve()
: The function now returns an RLum.Results
object and as input an RLum.Data.Curve
object is now allowed
fit_LMCure()
: An additional component.contribution.matrix
is now returned to allow
for individual component to sum contribution plots
readBIN2R()
: BINX file format support has been added
readBIN2R()
: An argument forced.VersionNumber
has been added to cheat the internal version check routine if needed
Risoe.BINfileData-class
: The *.binx file format support has been added
RLum.Analysis
: Add argument get.index
just to show the index values
We partially started to create package documentation using the R pacakge 'inlinedocs', meaning that the documentation is now be part of the source code itself
A namespace .LuminescenceEnv in zzz.R has been added
A variable col
has been added to the namespace .LuminescenceEnv
in the file zzz.R to define a standard colour palette for graphical output in package
NEWS are now provided as *.Rd file; der corresponding ASCII file is produced using the function Rd2txt
An unicode character for the temperature degree symbol 'deg. C' has been added
The S4-object structure has been added as PDF documentation to the package