mrbin: Noise handling default paramters are no less exclusive so
true signals are more likely to be retained
mrbin: Solvent removal default paramters for water are more narrow
so true signals aren’t removed
mrbin: Bruker spectrum folders without a file named “title” were
previosuly not displayed, this is now fixed
mrbin: Result files are now compressed to save space. For better
reproducibility, they now again contain the individual estimated noise
levels per bin for each sample
mrbin: Small bug fixes and improvements
checkmrbin: Bugfix: Adding a new variable through editmrbin may have
caused an error message, this is fixed now
annotatemrbin: Major quality improvements. Bugfix: Annotating
reloaded mrbin files failed, this is fixed now
Version 1.9.4
mrbin: Small bug fixes and improvements
mrbin: New colors for boxes in plots for improved visibility
mrplot: Improved placing of labels on plots
mrbin: Spectra can now be loaded in an internal mrbin format to
reduce the package’s space requirements for example data
Version 1.9.3
mrbin: Improved plots
mrbin: Small bug fixes
annotatemrbin: Fixed a bug that stopped the function from working in
some cases
annotatemrbin: New parameter uniqueBins
vignette: Package vignette improved
Version 1.9.2
mrplot: Bug fixed that prevented mrplot to be started in some
cases
mrbin: Time is now also saved as part of file name
mrbin: If no file names is chosen, a standard file name is
generated
mrbin, plotPCA: Sample and bin labels are now no longer clipped but
extend into the figure margin
mrbin: Preview plots now again include PCA loadings plots
mrbin: Small bugfixes
mrbin: When loading a previously saved data set, the variable will
now be named “results” instead of “mrbinResults2”
Version 1.9.1
mrbin: Small bugfixes
mrbin: Better error handling in parallel mode
mrbin: Noise levels per peak and sample are no longer saved in the
output files to save storage and make viewing the files easier
mrbin: An additional output file will be written, containing R code
to regenerate the data set
Version 1.9.0
mrbin: Nicer and speedier plots
mrbin: Improved bin annotation system
mrplot: A vector of mrbin bin names can now be provided to mrplot
and the bin positions will be highlighted
mrplot: Small bugfixes
mrbin: Small bugfixes
mrbin: Clarifications of prompts and reply options
mrbin: Clarifications in the vignette
mrheatmap: New function for heatmaps
examples: A new data set was included for better example
results
Version 1.8.0
mrbin: Speed improvements
mrbin: Pop-up windows for list selection can now be turned off using
graphics=FALSE
plotNMR: Improvements for quicker plot display - For full spectra,
only a subset of the data points is plotted
mrplot: Improved plot manipulation, e.g. zooming in/out, moving
left/right
mrplot: Added options for adjusting the plot, e.g. setting a
background color
mrplot: Small bug fixes
mrbin: Small bug fixes and clarifications of prompts and reply
options
Version 1.7.5
mrbin: Bug fixes especially for plots in (Mac) RStudio
mrbin: The number of bins left after trimming zero-value bins was
displayed incorrectly during an mrbin run, this is now fixed
mrbin: All function examples now use parallel computing by default
for consistency
mrbin: Small bug fixes and clarifications of prompts and reply
options
mrbin: Bin data is now additionally saved as a csv file to disk
(again)
Version 1.7.4
mrbin: Bugfixes especially for plots in (Mac) RStudio
Version 1.7.3
mrbin: Warnings are now displayed during binning
mrbin: New warnings if spectra differ in field strength, pulse
program, solvent, or number of scans. This could cause inconsistent
data
mrbin: Some acquisition parameters such as p1 pulse length are now
saved in parameters$AcquPars
mrbin: Small potential bugs fixed in spectrum selection step
mrbin: Bugfix: In rare cases the preview of features after noise
removal was incorrect, this is now fixed
fia: Predictions now show less output (using verbose=0 within the
predict function)
fia: Memory usage improvements. If using package keras, consider
using kerasClearMemory=2 for massive memory and speed improvements
fia: Parameter innerLoop is now default at 300 (was 100) to increase
quality of results. This increases calculation times.
Version 1.7.2
In setNoiseLevels() there is now a preview of the number of bins
left for noise thresholds between 0.05 and 1
Renaming of duplicated spectrum names was improved, this also fixed
a rare bug that could cause mrbin to get stuck while binning
Previews of all spectra can now be reviewed while running mrbin() to
identify quality issues
Speed improvements in 2D plots by reducing the number of displayed
data points
plotResults() will now show a preview of spectral region evens if no
spectral data has been loaded before. This is useful when using mrbin
objects that have been previously created
Small improvements to documentations and vignette
Version 1.7.1
Bug fix: annotatemrbin() sometimes added extra commas in metabolite
annotations, this has been fixed
Bug fix: checkmrbin(), in rare cases, erroneously flagged unstated
changes to an unchanged mrbin object. This was caused by numeric
instabilities and has now been fixed
Bug fix: mrbin() did not properly add metadata to the result object,
if added at the command line. This is now fixed
New functions setDilutionFactors() and dilutionCorrection() for
individual dilution correction
Variable metaboliteIdentities in metadata was changed to matrix (was
data.frame)
printParameters() now omits empty (NULL, ““, nrow==0) variables, but
prints non-empty metadata now
New function unitVarianceScaling()
Version 1.7.0
mrbin: results are now returned as an object of the new class
“mrbin”, containing bin data, metadata, and change logs. These objects
should only be changed using functions from this package. Individual
edits can be performed using editmrbin()
mrbin: Noise levels are now visually shown for a few spectra to help
pick reasonable signal-to-noise levels
mrbin: Warnings during binning now cause a pop-up message to give
users the chance to review and fix data issues such as phase, reference,
and baseline errors
mrbin: PCA plots do no longer show group memberships during the data
processing phase. To display color-coded groups, add metadata using
mrbinResults<-metadatamrbin(mrbinResults) and then use
plotPCA(mrbinResults)
mrbin: Changes to mrbin objects are now logged in $changeLog to
ensure workflow reproducibility. Undocumented changes can be identified
using checkmrbin(mrbinResults)
mrbin: New functionality to annotate mrbin data with molecule
identities was added
mrbin: Improvements in memory usage to better handle large data
sets. If more than 5000 bins are created, these will not be plotted in
the output plot.
mrbin: The variable noise_level was moved to parameters list in
mrbin environment
mrbin: Bug fix: Excluding the sugar area during PQN could not be
turned off within mrbin, this is now fixed
mrbin: Users will no longer be asked whether to use parallel,
previews and hints, these will be always used now unless turned off by
manually setting the respective parameters
mrbin: Time estimates are now being displayed before and during
binning
Version 1.6.5
New output of fia function: scoresIndividual shows fia score for
each tested sample
Speed improvements in the fia function
Version 1.6.4
Minor changes in calculations in the fia function. Features of
lowest impact now are assigned a (large) FIA score instead of an NA
value
Version 1.6.3
Small bug fixes in the fia function
Small bug fixes in the mrplot function
Version 1.6.2
New function fia for analyzing predictive metabolomics models
Small bug fixes in the mrplot function
Version 1.6.1
Small bug fixes in the mrplot function
Version 1.6.0
Bin intensities are now pseudo-integrals (mean of data points times
range (1D), or times area (2D)). So far, intensities were the mean of
data points in the bin range. For simple rectangular bins, results are
identical apart from a scaling factor, so most data analysis methods
will give identical results. To enforce the old behavior, use
mrbin(parameters=list(useMeanIntensityForBins=TRUE))
Multiple spectra are now shown in previews to visualize
sample-to-sample variability
PCA plots: When using more groups than available symbols (from pch),
letter are now used to mark the groups. This also removes the warning
messages generated in these cases.
Reading spectra without title does no longer create an error in
readBruker(), however, such spectra are still not shown in the spectrum
browser as they are usually not of interest
Before binning, folder list is checked to find missing folders. This
is to avoid long calculation that end with a “could not open file”
error. This uses the new readBruker() parameter checkFiles.
Speed improvements for displaying and saving the final results
plot
New plotting function mrplot()
RStudio plotting issue solved: Plots are now refreshed so the
current plot is displayed timely
Version 1.5.2
Speed improvements for 1D spectra
New quality check function checkBaseline: For severe baseline
distortions in noise region, a warning is displayed
New quality check in function binMultiNMR2: For severe baseline
distortions in the reference region, the reference peak integral might
be negative. In this case,a warning is displayed and the absolute value
is used instead
New quality check function binMultiNMR2: If reference scaling is
used and the reference signal intensity is unexpectedly low, a warning
is displayed
If quality check warnings are generated during a run, the warnings
are saved in the parameter text file for later viewing
Version 1.5.1
Small improvement in spectrum browsing. Experiments with no title
file are no longer displayed during browsing, as these are usually
uninformative pulse calibration data
Added a message recommending installing xquartz on Apple
computers
Citation information was added
Version 1.5.0
An error in reference scaling was fixed, this prevented reference
scaling in some cases
PQN scaling is now performed after fixing negative values by atnv()
(previously: before atnv). This might slightly change PQN scaling
results in rare cases
Speed improvements by adding optional support for parallel computing
using the parallel package
Version 1.4.4
Function PQNScaling now works with externally provided data
Minor improvements for user friendliness
Version 1.4.3
Noise levels per bin are no longer saved in the .txt file to keep
this file clear and tidy. Instead, raw noise levels and median noise
levels (adjusted for bin size) are now saved in the output .txt
file
Version 1.4.2
Summed bins are now calculated with the exact defined borders.
Surrounding bins are truncated
Noise levels are now calculated separately for each bin in each
spectrum, correcting for differences in data points per bin
PCA plot labels now show percentage of variance instead of
percentage of standard deviation
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability, especially
when analyzing single samples and/or single bins
Version 1.4.1
Vignette was expanded
Bin borders are now rounded to avoid floating point
inconsistencies
PQN normalization now also ignores glucose signals in 1D spectra.
This behavior can be turned off now as well.
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability, especially
when analyzing single samples and/or single bins
Version 1.4.0
Solvent region change: Only bins that are completely within the
solvent region are removed
Excluded regions: No NMR data from excluded regions or solvent
regions is now used to calculate bins, even if the bin overlaps with the
excluded region
New trimming function to remove bins that have mostly values of
zero; These are created at the edges of the spectrum and at edges of
removed regions
A vignette was added
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability
Version 1.3.0
Noise is now estimated from raw data points (not bin values) and
mean number of data points per bin
New noise calculations tend to be lower than the previous estimates.
SNR levels may need to be increased by a factor of 2.5. Default SNR
levels have been raised to reflect this.
Solvent region change: Any bins that contain any part of these
regions are removed (previously only if mean of bin was within
region)
Added new way of creating sample names from EXPNO and folder
name
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability
Speed improvements
Version 1.2.0
Default 1D noise range was changed to 10 - 9.5 ppm (was 10-9.4).
Default 1D binning area changed to 10-0.5 (was 9.5-0.5)
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability
Version 1.1.0
All parameters can now be conveniently set from the command line by
passing a list of parameters to mrbin()
Special bin regions can now be defined instead of rectangular bins,
e.g. for lipid analysis
mrbin() now returns the group factors as an additional element
“factors” in the returned list
New function setCurrentSpectrum() to set current spectrum, e.g. for
plotting
Reloading a parameter set from a file now checks whether all
required parameters have been set and adds missing ones
Results plots are nicer now. A new plot shows which regions were
left after all processing steps.
Some minor and major fixes to increase user friendliness
Some minor and major bug fixes to increase stability