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plot_RLum.Data.Spectrum()
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+ ad support for light arguments
+ fx cause of index warning
+ ad NEWS
+ up docu
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@RLumSK
RLumSK committed Sep 14, 2024
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142 changes: 3 additions & 139 deletions NEWS.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -13,147 +13,11 @@ header-includes:

## Bugfixes


## Internals



# Changes in version 0.9.25 (2024-09-12)

**This package version requires R >= 4.3**

## New functions
* `read_HeliosOSL2R()`: New import function to support the new zero rad Helios luminescence reader
and its `.osl` file format. The output is an `RLum.Analysis-class` object.

## Bugfixes

### `analyse_baSAR()`
* Fix #183 addressing an edge-case crash when the function was called on
an object containing no records of the appropriate type (#184, @mcol).

### `analyse_FadingMeasurements()`
* Add `...` support to disable the blue trend line via `plot.trend = FALSE`
* Fix #175 to deal gracefully with the case when the size of Lx and Tx
doesn't match (#192, @mcol).

### `analyse_portableOSL()`
* Function did not respect argument `main`; fixed.

### `convert_Wavelength2Energy()`
* Fix #133 addressing cases where R throws an uncontained error when R drops
the object structure in very rare cases (#134; thanks @mcol)

### `calc_Huntley2006()`
* Improve success rate of GOK fitting of the unfaded data using a two step approach: first
an exponential fit is applied then this values are used as start parameters.

### `calc_Statistics()`
* The skewness and kurtosis depended on number of MC samples (#122); fixed with #123 (thanks to @mcol)

### `calc_TLLxTxRatio()`
* Function crashed for `Tx.data.background = NULL` (#129); fixed with #130 thanks to @mcol

### `calc_WodaFuchs2008()`
* The function now officially supports numeric vectors and single-column
data frames as input (#200).
* The function computed the number of breaks for the histogram incorrectly
(#197, fixed with #198).
* The function now supports more types of `RLum.Results` objects without
crashing, although if the object contains only one data point it will stop
immediately to avoid problems with `nls()` (#199, fixed in #219).

### `extract_IrradiationTimes()`
* If a BIN/BINX-file is provided, the function will now check that it contains the
same amount of data as the corresponding XSYG file a bit earlier than before,
thus avoiding a possible crash (#228, fixed in #229).

### `fit_CWCurve()`
* Argument `output.path` has been removed, and a warning is raised when
attempting to use it (#207, fixed in #209).

### `fit_EmissionSpectra()`
* Parameter `input_scale` was not correctly propagated when the function would
self-call (#160, @mcol).

### `fit_OSLLifeTimes()`
* The validation of the minimum dataset size didn't account for the use of
the `signal.range` argument (#182, fixed by #195, @mcol).

### `fit_SurfaceExposure()`
* Fix #162 to remove a dimension mismatch if the input data contained `NA`s,
which would generate unexpected warnings (#163, @mcol).
* The function doesn't stop anymore with an error if called on an
`RLum.Results` object (#165, @mcol).

### `plot_AbanicoPlot()`
* Argument `plot.ratio` will now throw an error on non-positive numerical
values (#221, fixed in #222).
* The function doesn't crash anymore when setting `interactive = TRUE` (#220,
fixed in #233).

### `plot_DetPlot()`
* Argument `signal.integral.max` is now enforced to be greater than
`signal.integral.min`, as otherwise the computation of the number of channels
would produce `Inf` (#203, fixed in #206).
* Fix a crash when using option `analyse_function = "analyse_pIRIRSequence"`
(#210, fixed in #211).

### `plot_GrowthCurve()`
* The function now calculates the relative saturation (`n/N`) using the ratio
of the two integrates. The value is part of the output table.
* Argument `na.rm` has been removed: as of version 0.9.23, it was defunct
and only accepted `TRUE` as valid value and produced an error otherwise,
so there is no effective change in behaviour (#137, fixed in #214).

### `plot_Histogram()`
* The function doesn't crash anymore when setting `interactive = TRUE` (#186,
fixed in #231).

### `plot_KDE()`
* It now officially supports numeric vectors and single-column data frames,
for which it assumes that the De error at each measurement is 10^-9 (#189,
fixed in #194, @mcol).

### `plot_NRt()`
* The function reports an helpful message rather than crashing when applied
to an object of unexpected type or when there is a mismatch in time values
(#177, fixed with #179 by @mcol).

### `plot_RadialPlot()`
* The function doesn't crash anymore when a single-column data frame is
provided (#191, fixed in #212).

### `plot_RLum.Data.Analysis()`
* The function now supports all arguments from `plot_RLum.Data.Spectrum()`; before it
had only basic functionality for `RLum.Data.Spectrum-class` data.

### `plot_RLum.Data.Spectrum()`
* The plot function can now handle non-increasing column values for plotting (with a warning).
* Add support for `lphi` and `ltheta` light direction arguments for `plot.type = "persp"`.
* Fix the reason for the unclear warning `In col.unique == col : longer object length is not a multiple of shorter object length`

### `read_BIN2R()`
* `ignore.RECTYPE` now supports numeric values, e.g., 128. Records for this type
will be ignored during import.
* BINX-files with `RECTYPE = 128` will not crash anymore, thanks for asking Anna-Maartje Boer and replying Karsten Bracht.
* The function now stops graciously when attempting to read an empty file
(#225, fixed in #226).

### `read_PSL2R()`
* The function is out of the beta status, hence the flag was removed.
* The `RLum.Analysis-class` object returned by the function gained a new element `Sequence`, which is a data frame.
with the measured sequence. This way, if the original sequence was lost, it can still be extracted from the `.psl` data.
* If no `.psl` file was found the function got trapped in an infinite loop (#127); fixed with #128 (thanks to @mcol)

### `read_XSYG2R()`
* Fix spectrometer data import for basically broken files.
## Internals

### `read_Daybreak2R()`
* Fix #135 to improve detection of non-ASCII files (#140, @mcol).

### `Risoe.BINfileData2RLum.Analysis()`
* Fix a crash when reading an empty Risoe.BINfileData input (#215, fixed in
#224).

## Internals
* New internal function + tests added `.get_named_list_element()`. It just does what
the names says.
187 changes: 5 additions & 182 deletions NEWS.md
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Expand Up @@ -5,194 +5,17 @@

<!-- NEWS.md was auto-generated by NEWS.Rmd. Please DO NOT edit by hand!-->

# Changes in version 0.9.25.9000 (2024-09-13)
# Changes in version 0.9.25.9000 (2024-09-14)

## New functions

## Bugfixes

## Internals

# Changes in version 0.9.25 (2024-09-12)

**This package version requires R \>= 4.3**

## New functions

- `read_HeliosOSL2R()`: New import function to support the new zero rad
Helios luminescence reader and its `.osl` file format. The output is
an `RLum.Analysis-class` object.

## Bugfixes

### `analyse_baSAR()`

- Fix \#183 addressing an edge-case crash when the function was called
on an object containing no records of the appropriate type (#184,
@mcol).

### `analyse_FadingMeasurements()`

- Add `...` support to disable the blue trend line via
`plot.trend = FALSE`
- Fix \#175 to deal gracefully with the case when the size of Lx and Tx
doesn’t match (#192, @mcol).

### `analyse_portableOSL()`

- Function did not respect argument `main`; fixed.

### `convert_Wavelength2Energy()`

- Fix \#133 addressing cases where R throws an uncontained error when R
drops the object structure in very rare cases (#134; thanks @mcol)

### `calc_Huntley2006()`

- Improve success rate of GOK fitting of the unfaded data using a two
step approach: first an exponential fit is applied then this values
are used as start parameters.

### `calc_Statistics()`

- The skewness and kurtosis depended on number of MC samples (#122);
fixed with \#123 (thanks to @mcol)

### `calc_TLLxTxRatio()`

- Function crashed for `Tx.data.background = NULL` (#129); fixed with
\#130 thanks to @mcol

### `calc_WodaFuchs2008()`

- The function now officially supports numeric vectors and single-column
data frames as input (#200).
- The function computed the number of breaks for the histogram
incorrectly (#197, fixed with \#198).
- The function now supports more types of `RLum.Results` objects without
crashing, although if the object contains only one data point it will
stop immediately to avoid problems with `nls()` (#199, fixed in
\#219).

### `extract_IrradiationTimes()`

- If a BIN/BINX-file is provided, the function will now check that it
contains the same amount of data as the corresponding XSYG file a bit
earlier than before, thus avoiding a possible crash (#228, fixed in
\#229).

### `fit_CWCurve()`

- Argument `output.path` has been removed, and a warning is raised when
attempting to use it (#207, fixed in \#209).

### `fit_EmissionSpectra()`

- Parameter `input_scale` was not correctly propagated when the function
would self-call (#160, @mcol).

### `fit_OSLLifeTimes()`

- The validation of the minimum dataset size didn’t account for the use
of the `signal.range` argument (#182, fixed by \#195, @mcol).

### `fit_SurfaceExposure()`

- Fix \#162 to remove a dimension mismatch if the input data contained
`NA`s, which would generate unexpected warnings (#163, @mcol).
- The function doesn’t stop anymore with an error if called on an
`RLum.Results` object (#165, @mcol).

### `plot_AbanicoPlot()`

- Argument `plot.ratio` will now throw an error on non-positive
numerical values (#221, fixed in \#222).
- The function doesn’t crash anymore when setting `interactive = TRUE`
(#220, fixed in \#233).

### `plot_DetPlot()`

- Argument `signal.integral.max` is now enforced to be greater than
`signal.integral.min`, as otherwise the computation of the number of
channels would produce `Inf` (#203, fixed in \#206).
- Fix a crash when using option
`analyse_function = "analyse_pIRIRSequence"` (#210, fixed in \#211).

### `plot_GrowthCurve()`

- The function now calculates the relative saturation (`n/N`) using the
ratio of the two integrates. The value is part of the output table.
- Argument `na.rm` has been removed: as of version 0.9.23, it was
defunct and only accepted `TRUE` as valid value and produced an error
otherwise, so there is no effective change in behaviour (#137, fixed
in \#214).

### `plot_Histogram()`

- The function doesn’t crash anymore when setting `interactive = TRUE`
(#186, fixed in \#231).

### `plot_KDE()`

- It now officially supports numeric vectors and single-column data
frames, for which it assumes that the De error at each measurement is
10^-9 (#189, fixed in \#194, @mcol).

### `plot_NRt()`

- The function reports an helpful message rather than crashing when
applied to an object of unexpected type or when there is a mismatch in
time values (#177, fixed with \#179 by @mcol).

### `plot_RadialPlot()`

- The function doesn’t crash anymore when a single-column data frame is
provided (#191, fixed in \#212).

### `plot_RLum.Data.Analysis()`

- The function now supports all arguments from
`plot_RLum.Data.Spectrum()`; before it had only basic functionality
for `RLum.Data.Spectrum-class` data.

### `plot_RLum.Data.Spectrum()`

- The plot function can now handle non-increasing column values for
plotting (with a warning).

### `read_BIN2R()`

- `ignore.RECTYPE` now supports numeric values, e.g., 128. Records for
this type will be ignored during import.
- BINX-files with `RECTYPE = 128` will not crash anymore, thanks for
asking Anna-Maartje Boer and replying Karsten Bracht.
- The function now stops graciously when attempting to read an empty
file (#225, fixed in \#226).

### `read_PSL2R()`

- The function is out of the beta status, hence the flag was removed.
- The `RLum.Analysis-class` object returned by the function gained a new
element `Sequence`, which is a data frame. with the measured sequence.
This way, if the original sequence was lost, it can still be extracted
from the `.psl` data.
- If no `.psl` file was found the function got trapped in an infinite
loop (#127); fixed with \#128 (thanks to @mcol)

### `read_XSYG2R()`

- Fix spectrometer data import for basically broken files.

### `read_Daybreak2R()`

- Fix \#135 to improve detection of non-ASCII files (#140, @mcol).

### `Risoe.BINfileData2RLum.Analysis()`

- Fix a crash when reading an empty Risoe.BINfileData input (#215, fixed
in \#224).
- Add support for `lphi` and `ltheta` light direction arguments for
`plot.type = "persp"`.
- Fix the reason for the unclear warning
`In col.unique == col : longer object length is not a multiple of shorter object length`

## Internals

- New internal function + tests added `.get_named_list_element()`. It
just does what the names says.
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