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Wrap 3rd example in \dontrun{} in calc_Huntley2006() and rebuild for …
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@RLumSK
RLumSK committed Mar 9, 2018
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Expand Up @@ -4,7 +4,7 @@ Changes in version 0.8.1 (March 9th, 2018):

New functions:

• 'calc_Huntley2006()'
• ‘calc_Huntley2006()’

• A function to calculate the expected sample specific
fraction of saturation based on the model of Huntley
Expand All @@ -19,15 +19,15 @@ Changes in version 0.8.1 (March 9th, 2018):

Bugfixes and changes:

• 'calc_Kars2008()'
• ‘calc_Kars2008()’

• This function is now deprecated and will eventually be
removed in an upcoming version of the 'Luminescence'
package. Older scripts using this function will still
work, but it is highly recommended to use the newly
introduced function 'calc_Huntley2006()'.

• 'calc_MinDose()'
• ‘calc_MinDose()’

• Previously, the function globally disabled warning
messages via 'options(warn = -1)' due to the overly
Expand All @@ -42,32 +42,32 @@ Changes in version 0.8.1 (March 9th, 2018):
log of infinite (Inf, -Inf) values, which produced 'NaN'
warnings.

• 'get_RLum()'
• ‘get_RLum()’

• The argument 'subset' was broken and not working
anymore, similar to the S3-method 'subset' dispatching
to 'get_RLum' for 'RLum.Analysis'-objects. Both issues
• The argument ‘subset’ was broken and not working
anymore, similar to the S3-method ‘subset’ dispatching
to ‘get_RLum’ for ‘RLum.Analysis’-objects. Both issues
have been fixed.

• 'plot_DRTResults()'
• ‘plot_DRTResults()’

• If 'boxplot = TRUE' and 'give.dose = NULL' the plot
• If ‘boxplot = TRUE’ and ‘give.dose = NULL’ the plot
still showed the abline at 1 including the +/- 10 %
error range. Now, the abline is only showed if a numeric
value is provided for 'give.dose', 'NULL' plots no
value is provided for ‘give.dose’, ‘NULL’ plots no
abline.

• 'plot_GrowthCurve()'
• ‘plot_GrowthCurve()’

• Now allows fitting of the general-order kinetics
function after Guralnik et al. (2015). Use '"GOK"' as
input for argument 'fit.method'.
function after Guralnik et al. (2015). Use ‘"GOK"’ as
input for argument ‘fit.method’.

• 'template_DRAC()'
• ‘template_DRAC()’

• New argument 'preset' to allow the selection of
• New argument ‘preset’ to allow the selection of
pre-defined templates for various configurations (e.g.,
''quartz_coarse'') for quartz coarse grain data. The
‘'quartz_coarse'’) for quartz coarse grain data. The
templates bring pre-filled values to speed up the
workflow, however, they do not free the researcher from
cross-checking these values.
Expand All @@ -86,78 +86,78 @@ Changes in version 0.8.0 (Feburary 9th, 2018):

New functions:

• 'analyse_Al2O3C_ITC()': Function to analyse data determined
• ‘analyse_Al2O3C_ITC()’: Function to analyse data determined
to correct irradiation times as suggested by Kreutzer et
al., 2018

• 'analyse_Al2O3C_CrossTalk()': Function to analyse data to
• ‘analyse_Al2O3C_CrossTalk()’: Function to analyse data to
analyse crosstalk measurements as shown in Kreutzer et al.,
2018

• 'analyse_Al2O3C_Measurement()': Function to analyse Al2O3:C
• ‘analyse_Al2O3C_Measurement()’: Function to analyse Al2O3:C
data as shown by Kreutzer et al., 2018

• 'convert_Activity2Concentration()': converts nuclide
• ‘convert_Activity2Concentration()’: converts nuclide
activity data (Bq/kg) to concentrations (ppm or %) and vice
versa

• 'convert_RLum2Risoe.BINfileData()': Function to convert
'RLum.Analysis' and 'RLum.Data.Curve' objects to
'Risoe.BINfileData', which can be exported to BIN/BINX-files
using the function 'write_R2BIN()'.
• ‘convert_RLum2Risoe.BINfileData()’: Function to convert
‘RLum.Analysis’ and ‘RLum.Data.Curve’ objects to
‘Risoe.BINfileData’, which can be exported to BIN/BINX-files
using the function ‘write_R2BIN()’.

• 'calc_WodaFuchs2008()': Function to obtain the equivalent
• ‘calc_WodaFuchs2008()’: Function to obtain the equivalent
dose using the approach proposed by Woda and Fuchs, 2008.

• 'fit_SurfaceExposure()': Function to fit eq. 1 in Sohbati et
• ‘fit_SurfaceExposure()’: Function to fit eq. 1 in Sohbati et
al. (2012a) to OSL surface exposure data and derive
estimates of its parameters (i.a., the age). Alternatively,
eq. 12 in Sohbati et al. (2012b) can be fitted, which also
considers the dose rate.

• 'calc_Lamothe2003()': Function to support the fading
• ‘calc_Lamothe2003()’: Function to support the fading
correction suggested by Lamothe et al., 2003. As input the
function accepts 'data.frame' output from the functions
'analyse_SAR.CWOSL()' and 'analyse_pIRIRSequence)'.
function accepts ‘data.frame’ output from the functions
‘analyse_SAR.CWOSL()’ and ‘analyse_pIRIRSequence)’.

New example data:

• 'ExampleData.SurfaceExposure': A set of synthetic OSL
• ‘ExampleData.SurfaceExposure’: A set of synthetic OSL
surface exposure dating data to demonstrate the
fit_SurfaceExposure() functionality. See
?ExampleData.SurfaceExposure for details.

• 'ExampleData.Al2O3C': Al2O3:C chips measurement data to
• ‘ExampleData.Al2O3C’: Al2O3:C chips measurement data to
supplement the newly implemented functions to analyse
Al2O3:C data.

S4-classes and methods:

• The 'RLum.Analysis' show method failed for
'RLum.Data.Spectrum' objects; fixed.
• The ‘RLum.Analysis’ show method failed for
‘RLum.Data.Spectrum’ objects; fixed.

• Method for 'get_RLum' with signature 'NULL' added. Now it
returns 'NULL'.
• Method for ‘get_RLum’ with signature ‘NULL’ added. Now it
returns ‘NULL’.

• The coercion from 'list' to 'RLum.Results' using 'as()' did
• The coercion from ‘list’ to ‘RLum.Results’ using ‘as()’ did
not work; fixed.

• Method 'get_RLum' for 'RLum.Analysis' returned a confusing
• Method ‘get_RLum’ for ‘RLum.Analysis’ returned a confusing
error if what was provided via 'subset' was not a logical
expression; fixed.

• 'structure_RLum()' and 'names_RLum()' each got a method to
deal with a list of 'RLum' objects.
• ‘structure_RLum()’ and ‘names_RLum()’ each got a method to
deal with a list of ‘RLum’ objects.

Bugfixes and changes:

• 'analyse_SAR.CWOSL()'
• ‘analyse_SAR.CWOSL()’

• The function gained a new argument ''onlyLxTxTable''. If
set to 'TRUE' only the Lx/Tx table is returned
• The function gained a new argument ‘'onlyLxTxTable'’. If
set to ‘TRUE’ only the Lx/Tx table is returned
(including regeneration point sorting).

• 'analyse_IRSAR.RF()'
• ‘analyse_IRSAR.RF()’

• Multicore processing now also supports Windows (#47)

Expand All @@ -172,23 +172,23 @@ Changes in version 0.8.0 (Feburary 9th, 2018):
• the function will not break anymore uncontrolled of both
RF curves are of similar extension on the x-axis.

• 'analyse_pIRIRSequence()'
• ‘analyse_pIRIRSequence()’

• If the number of records did not match the sequence
structure the function crashed with a confusing error
message. Now it shows an error and returns 'NULL',
message. Now it shows an error and returns ‘NULL’,

• make the argument 'main' more powerful if the input is a
• make the argument ‘main’ more powerful if the input is a
list,

• add missing items to the manual.

• 'calc_HomogeneityTest()'
• ‘calc_HomogeneityTest()’

• The calculation was wrong for the option 'log = TRUE'
• The calculation was wrong for the option ‘log = TRUE’
(the default); fixed (#63).

• 'calc_Kars2008()'
• ‘calc_Kars2008()’

• In some cases the calculated LxTx values of the
simulated natural dose-response curve were slightly
Expand All @@ -203,65 +203,65 @@ Changes in version 0.8.0 (Feburary 9th, 2018):
• The number of digits for the numeric output in the plot
was slightly adjusted.

• 'plot_FilterCombinations()'
• ‘plot_FilterCombinations()’

• Add interactive mode ('interactive = TRUE'),
• Add interactive mode (‘interactive = TRUE’),

• correct wrong visualisation of transmission windows for
long or short pass filters,

• fix legend error if only one filter was provided (due to
a recent matrix behaviour change).

• 'plot_GrowthCurve()'
• ‘plot_GrowthCurve()’

• The function now turns 'Inf' into 'NA',
• The function now turns ‘Inf’ into ‘NA’,

• the argument 'na.rm' is defunct and should not be used
• the argument ‘na.rm’ is defunct and should not be used
anymore,

• minor code modifications to handle special cases such as
input values with a 'data.frame' with no error column,
input values with a ‘data.frame’ with no error column,

• extent examples by for test data set by Berger & Huntley
(1989),

• remove one more confusion warning if the fit did not
work.

• 'plot_Historgram()'
• ‘plot_Historgram()’

• The forwarded argument 'breaks' was not treated
• The forwarded argument ‘breaks’ was not treated
correctly (#54); fixed.

• 'plot_RLum()'
• ‘plot_RLum()’

• The function now supports plotting even of highly nested
lists of `RLum-objects`.

• 'plot_RLum.Analysis()'
• ‘plot_RLum.Analysis()’

• The option `col` was not working as expected if `black`
was provided; fixed,

• setting 'ylim' caused a function break (#65); fixed.
• setting ‘ylim’ caused a function break (#65); fixed.

• 'read_BIN2R()'
• ‘read_BIN2R()’

• The function unexpectedly dropped are warning for an
unused connection; fixed,

• if a file link was provided and the argument 'pattern'
• if a file link was provided and the argument ‘pattern’
was set and error was shown; fixed.

• 'read_Daybreak2R()'
• ‘read_Daybreak2R()’

• The functions did not work anymore on ASCII files;
fixed!

• 'read_XSYG2R()'
• ‘read_XSYG2R()’

• Argument 'verbose' added for more consistency with other
• Argument ‘verbose’ added for more consistency with other
functions,

• the functions now supports the import form files via the
Expand All @@ -275,19 +275,19 @@ Changes in version 0.8.0 (Feburary 9th, 2018):
• set option `XML_PARSE_HUGE` to allow parsing of larger
nodes within the XSYG-file,

• the metadata entries 'curveType' and 'parentID' appeared
• the metadata entries ‘curveType’ and ‘parentID’ appeared
duplicated, fixed.

• 'read_SPE2R()'
• ‘read_SPE2R()’

• Add support for internet connections,

• fix unclear file extension recognition.

• 'write_R2BIN()'
• ‘write_R2BIN()’

• The BIN-file export to version 04 failed in very rare
cases for 'NA' values in the byte position 'SEQUENCE';
cases for ‘NA’ values in the byte position ‘SEQUENCE’;
fixed,

• the compatibility mode was extended, now limiting the
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